diff --git a/BioModelsRAG/2data/BIOMD0000000001.txt b/BioModelsRAG/2data/BIOMD0000000001.txt
deleted file mode 100644
index a372fc16aae623ce4435e2d867fd11e3de0ceef6..0000000000000000000000000000000000000000
--- a/BioModelsRAG/2data/BIOMD0000000001.txt
+++ /dev/null
@@ -1,224 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000001()
-
-  // Compartments and Species:
-  compartment comp1;
-  species BLL in comp1, IL in comp1, AL in comp1, A in comp1, BL in comp1;
-  species B in comp1, DLL in comp1, D in comp1, ILL in comp1, DL in comp1;
-  species I in comp1, ALL in comp1;
-
-  // Reactions:
-  React0: B -> BL; comp1*(kf_0*B - kr_0*BL);
-  React1: BL -> BLL; comp1*(kf_1*BL - kr_1*BLL);
-  React2: BLL -> ALL; comp1*(kf_2*BLL - kr_2*ALL);
-  React3: A -> AL; comp1*(kf_3*A - kr_3*AL);
-  React4: AL -> ALL; comp1*(kf_4*AL - kr_4*ALL);
-  React5: B -> A; comp1*(kf_5*B - kr_5*A);
-  React6: BL -> AL; comp1*(kf_6*BL - kr_6*AL);
-  React7: I -> IL; comp1*(kf_7*I - kr_7*IL);
-  React8: IL -> ILL; comp1*(kf_8*IL - kr_8*ILL);
-  React9: A -> I; comp1*(kf_9*A - kr_9*I);
-  React10: AL -> IL; comp1*(kf_10*AL - kr_10*IL);
-  React11: ALL -> ILL; comp1*(kf_11*ALL - kr_11*ILL);
-  React12: D -> DL; comp1*(kf_12*D - kr_12*DL);
-  React13: DL -> DLL; comp1*(kf_13*DL - kr_13*DLL);
-  React14: I -> D; comp1*(kf_14*I - kr_14*D);
-  React15: IL -> DL; comp1*(kf_15*IL - kr_15*DL);
-  React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL);
-
-  // Events:
-  RemovalACh: at time > t2: kf_13 = 0, kf_8 = 0, kf_4 = 0, kf_1 = 0, kf_12 = 0, kf_7 = 0, kf_3 = 0, kf_0 = 0;
-
-  // Species initializations:
-  BLL = 0;
-  IL = 0;
-  AL = 0;
-  A = 0;
-  BL = 0;
-  B = 1.66057788110262e-21/comp1;
-  DLL = 0;
-  D = 0;
-  ILL = 0;
-  DL = 0;
-  I = 0;
-  ALL = 0;
-
-  // Compartment initializations:
-  comp1 = 1e-16;
-
-  // Variable initializations:
-  t2 = 20;
-  kf_0 = 3000;
-  kf_3 = 3000;
-  kf_7 = 3000;
-  kf_12 = 3000;
-  kf_1 = 1500;
-  kf_4 = 1500;
-  kf_8 = 1500;
-  kf_13 = 1500;
-  kr_0 = 8000;
-  kr_1 = 16000;
-  kf_2 = 30000;
-  kr_2 = 700;
-  kr_3 = 8.64;
-  kr_4 = 17.28;
-  kf_5 = 0.54;
-  kr_5 = 10800;
-  kf_6 = 130;
-  kr_6 = 2740;
-  kr_7 = 4;
-  kr_8 = 8;
-  kf_9 = 19.7;
-  kr_9 = 3.74;
-  kf_10 = 19.85;
-  kr_10 = 1.74;
-  kf_11 = 20;
-  kr_11 = 0.81;
-  kr_12 = 4;
-  kr_13 = 8;
-  kf_14 = 0.05;
-  kr_14 = 0.0012;
-  kf_15 = 0.05;
-  kr_15 = 0.0012;
-  kf_16 = 0.05;
-  kr_16 = 0.0012;
-
-  // Other declarations:
-  var kf_0, kf_3, kf_7, kf_12, kf_1, kf_4, kf_8, kf_13;
-  const comp1, t2, kr_0, kr_1, kf_2, kr_2, kr_3, kr_4, kf_5, kr_5, kf_6, kr_6;
-  const kr_7, kr_8, kf_9, kr_9, kf_10, kr_10, kf_11, kr_11, kr_12, kr_13;
-  const kf_14, kr_14, kf_15, kr_15, kf_16, kr_16;
-
-  // Display Names:
-  comp1 is "compartment1";
-  BLL is "BasalACh2";
-  IL is "IntermediateACh";
-  AL is "ActiveACh";
-  A is "Active";
-  BL is "BasalACh";
-  B is "Basal";
-  DLL is "DesensitisedACh2";
-  D is "Desensitised";
-  ILL is "IntermediateACh2";
-  DL is "DesensitisedACh";
-  I is "Intermediate";
-  ALL is "ActiveACh2";
-  RemovalACh is "removal of ACh";
-
-  // SBO terms:
-  comp1.sboTerm = 290
-  BLL.sboTerm = 297
-  IL.sboTerm = 297
-  AL.sboTerm = 297
-  A.sboTerm = 420
-  BL.sboTerm = 297
-  B.sboTerm = 420
-  DLL.sboTerm = 297
-  D.sboTerm = 420
-  ILL.sboTerm = 297
-  DL.sboTerm = 297
-  I.sboTerm = 420
-  ALL.sboTerm = 297
-  kf_0.sboTerm = 35
-  kf_3.sboTerm = 35
-  kf_7.sboTerm = 35
-  kf_12.sboTerm = 35
-  kf_1.sboTerm = 35
-  kf_4.sboTerm = 35
-  kf_8.sboTerm = 35
-  kf_13.sboTerm = 35
-  kr_0.sboTerm = 38
-  kr_1.sboTerm = 38
-  kf_2.sboTerm = 35
-  kr_2.sboTerm = 38
-  kr_3.sboTerm = 38
-  kr_4.sboTerm = 38
-  kf_5.sboTerm = 35
-  kr_5.sboTerm = 38
-  kf_6.sboTerm = 35
-  kr_6.sboTerm = 38
-  kr_7.sboTerm = 38
-  kr_8.sboTerm = 38
-  kf_9.sboTerm = 35
-  kr_9.sboTerm = 38
-  kf_10.sboTerm = 35
-  kr_10.sboTerm = 38
-  kf_11.sboTerm = 35
-  kr_11.sboTerm = 38
-  kr_12.sboTerm = 38
-  kr_13.sboTerm = 38
-  kf_14.sboTerm = 35
-  kr_14.sboTerm = 38
-  kf_15.sboTerm = 35
-  kr_15.sboTerm = 38
-  kf_16.sboTerm = 35
-  kr_16.sboTerm = 38
-  React0.sboTerm = 177
-  React1.sboTerm = 177
-  React2.sboTerm = 181
-  React3.sboTerm = 177
-  React4.sboTerm = 177
-  React5.sboTerm = 181
-  React6.sboTerm = 181
-  React7.sboTerm = 177
-  React8.sboTerm = 177
-  React9.sboTerm = 181
-  React10.sboTerm = 181
-  React11.sboTerm = 181
-  React12.sboTerm = 177
-  React13.sboTerm = 177
-  React14.sboTerm = 181
-  React15.sboTerm = 181
-  React16.sboTerm = 181
-
-  // CV terms:
-  comp1 identity "http://identifiers.org/go/GO:0031594"
-  BLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  IL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  AL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  A hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  BL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  B hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  DLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  D hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ILL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  DL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  I hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ALL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  React0 identity "http://identifiers.org/go/GO:0042166"
-  React1 identity "http://identifiers.org/go/GO:0042166"
-  React2 identity "http://identifiers.org/go/GO:0004889"
-  React3 identity "http://identifiers.org/go/GO:0042166"
-  React4 identity "http://identifiers.org/go/GO:0042166"
-  React5 identity "http://identifiers.org/go/GO:0004889"
-  React6 identity "http://identifiers.org/go/GO:0004889"
-  React7 identity "http://identifiers.org/go/GO:0042166"
-  React8 identity "http://identifiers.org/go/GO:0042166"
-  React9 identity "http://identifiers.org/go/GO:0004889"
-  React10 identity "http://identifiers.org/go/GO:0004889"
-  React11 identity "http://identifiers.org/go/GO:0004889"
-  React12 identity "http://identifiers.org/go/GO:0042166"
-  React13 identity "http://identifiers.org/go/GO:0042166"
-end
-
-BIOMD0000000001 is "Edelstein1996 - EPSP ACh event"
-
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6613849442"
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000001"
-BIOMD0000000001 description "http://identifiers.org/pubmed/8983160"
-BIOMD0000000001 hypernym "http://identifiers.org/go/GO:0007274",
-                         "http://identifiers.org/go/GO:0007166",
-                         "http://identifiers.org/go/GO:0019226"
-BIOMD0000000001 taxon "http://identifiers.org/taxonomy/7787"
diff --git a/BioModelsRAG/__init__.py b/BioModelsRAG/__init__.py
deleted file mode 100644
index 74ca525c2c72610f83ecffde4008ccd00b4f84f8..0000000000000000000000000000000000000000
--- a/BioModelsRAG/__init__.py
+++ /dev/null
@@ -1,19 +0,0 @@
-__version__ = "0.1.0"
-__author__ = "Bhavyahshree Navaneetha Krishnan"
-
-from langchain_text_splitters import CharacterTextSplitter
-import os
-import chromadb
-from chromadb.utils import embedding_functions
-import ollama
-
-import splitBioModels
-import createVectorDB
-import createDocuments
-# Import functions from other modules
-from splitBioModels import splitBioModels
-from createVectorDB import createVectorDB
-from createDocuments import createDocuments
-
-# Define __all__ to specify which names are publicly accessible
-__all__ = ['splitBioModels', 'createVectorDB', 'createDocuments']
diff --git a/BioModelsRAG/__pycache__/__init__.cpython-311.pyc b/BioModelsRAG/__pycache__/__init__.cpython-311.pyc
deleted file mode 100644
index 510b1f11d02cbeeeb0361863633ef98990ab7b63..0000000000000000000000000000000000000000
Binary files a/BioModelsRAG/__pycache__/__init__.cpython-311.pyc and /dev/null differ
diff --git a/BioModelsRAG/data/BIOMD0000000001.txt b/BioModelsRAG/data/BIOMD0000000001.txt
deleted file mode 100644
index a372fc16aae623ce4435e2d867fd11e3de0ceef6..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000001.txt
+++ /dev/null
@@ -1,224 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000001()
-
-  // Compartments and Species:
-  compartment comp1;
-  species BLL in comp1, IL in comp1, AL in comp1, A in comp1, BL in comp1;
-  species B in comp1, DLL in comp1, D in comp1, ILL in comp1, DL in comp1;
-  species I in comp1, ALL in comp1;
-
-  // Reactions:
-  React0: B -> BL; comp1*(kf_0*B - kr_0*BL);
-  React1: BL -> BLL; comp1*(kf_1*BL - kr_1*BLL);
-  React2: BLL -> ALL; comp1*(kf_2*BLL - kr_2*ALL);
-  React3: A -> AL; comp1*(kf_3*A - kr_3*AL);
-  React4: AL -> ALL; comp1*(kf_4*AL - kr_4*ALL);
-  React5: B -> A; comp1*(kf_5*B - kr_5*A);
-  React6: BL -> AL; comp1*(kf_6*BL - kr_6*AL);
-  React7: I -> IL; comp1*(kf_7*I - kr_7*IL);
-  React8: IL -> ILL; comp1*(kf_8*IL - kr_8*ILL);
-  React9: A -> I; comp1*(kf_9*A - kr_9*I);
-  React10: AL -> IL; comp1*(kf_10*AL - kr_10*IL);
-  React11: ALL -> ILL; comp1*(kf_11*ALL - kr_11*ILL);
-  React12: D -> DL; comp1*(kf_12*D - kr_12*DL);
-  React13: DL -> DLL; comp1*(kf_13*DL - kr_13*DLL);
-  React14: I -> D; comp1*(kf_14*I - kr_14*D);
-  React15: IL -> DL; comp1*(kf_15*IL - kr_15*DL);
-  React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL);
-
-  // Events:
-  RemovalACh: at time > t2: kf_13 = 0, kf_8 = 0, kf_4 = 0, kf_1 = 0, kf_12 = 0, kf_7 = 0, kf_3 = 0, kf_0 = 0;
-
-  // Species initializations:
-  BLL = 0;
-  IL = 0;
-  AL = 0;
-  A = 0;
-  BL = 0;
-  B = 1.66057788110262e-21/comp1;
-  DLL = 0;
-  D = 0;
-  ILL = 0;
-  DL = 0;
-  I = 0;
-  ALL = 0;
-
-  // Compartment initializations:
-  comp1 = 1e-16;
-
-  // Variable initializations:
-  t2 = 20;
-  kf_0 = 3000;
-  kf_3 = 3000;
-  kf_7 = 3000;
-  kf_12 = 3000;
-  kf_1 = 1500;
-  kf_4 = 1500;
-  kf_8 = 1500;
-  kf_13 = 1500;
-  kr_0 = 8000;
-  kr_1 = 16000;
-  kf_2 = 30000;
-  kr_2 = 700;
-  kr_3 = 8.64;
-  kr_4 = 17.28;
-  kf_5 = 0.54;
-  kr_5 = 10800;
-  kf_6 = 130;
-  kr_6 = 2740;
-  kr_7 = 4;
-  kr_8 = 8;
-  kf_9 = 19.7;
-  kr_9 = 3.74;
-  kf_10 = 19.85;
-  kr_10 = 1.74;
-  kf_11 = 20;
-  kr_11 = 0.81;
-  kr_12 = 4;
-  kr_13 = 8;
-  kf_14 = 0.05;
-  kr_14 = 0.0012;
-  kf_15 = 0.05;
-  kr_15 = 0.0012;
-  kf_16 = 0.05;
-  kr_16 = 0.0012;
-
-  // Other declarations:
-  var kf_0, kf_3, kf_7, kf_12, kf_1, kf_4, kf_8, kf_13;
-  const comp1, t2, kr_0, kr_1, kf_2, kr_2, kr_3, kr_4, kf_5, kr_5, kf_6, kr_6;
-  const kr_7, kr_8, kf_9, kr_9, kf_10, kr_10, kf_11, kr_11, kr_12, kr_13;
-  const kf_14, kr_14, kf_15, kr_15, kf_16, kr_16;
-
-  // Display Names:
-  comp1 is "compartment1";
-  BLL is "BasalACh2";
-  IL is "IntermediateACh";
-  AL is "ActiveACh";
-  A is "Active";
-  BL is "BasalACh";
-  B is "Basal";
-  DLL is "DesensitisedACh2";
-  D is "Desensitised";
-  ILL is "IntermediateACh2";
-  DL is "DesensitisedACh";
-  I is "Intermediate";
-  ALL is "ActiveACh2";
-  RemovalACh is "removal of ACh";
-
-  // SBO terms:
-  comp1.sboTerm = 290
-  BLL.sboTerm = 297
-  IL.sboTerm = 297
-  AL.sboTerm = 297
-  A.sboTerm = 420
-  BL.sboTerm = 297
-  B.sboTerm = 420
-  DLL.sboTerm = 297
-  D.sboTerm = 420
-  ILL.sboTerm = 297
-  DL.sboTerm = 297
-  I.sboTerm = 420
-  ALL.sboTerm = 297
-  kf_0.sboTerm = 35
-  kf_3.sboTerm = 35
-  kf_7.sboTerm = 35
-  kf_12.sboTerm = 35
-  kf_1.sboTerm = 35
-  kf_4.sboTerm = 35
-  kf_8.sboTerm = 35
-  kf_13.sboTerm = 35
-  kr_0.sboTerm = 38
-  kr_1.sboTerm = 38
-  kf_2.sboTerm = 35
-  kr_2.sboTerm = 38
-  kr_3.sboTerm = 38
-  kr_4.sboTerm = 38
-  kf_5.sboTerm = 35
-  kr_5.sboTerm = 38
-  kf_6.sboTerm = 35
-  kr_6.sboTerm = 38
-  kr_7.sboTerm = 38
-  kr_8.sboTerm = 38
-  kf_9.sboTerm = 35
-  kr_9.sboTerm = 38
-  kf_10.sboTerm = 35
-  kr_10.sboTerm = 38
-  kf_11.sboTerm = 35
-  kr_11.sboTerm = 38
-  kr_12.sboTerm = 38
-  kr_13.sboTerm = 38
-  kf_14.sboTerm = 35
-  kr_14.sboTerm = 38
-  kf_15.sboTerm = 35
-  kr_15.sboTerm = 38
-  kf_16.sboTerm = 35
-  kr_16.sboTerm = 38
-  React0.sboTerm = 177
-  React1.sboTerm = 177
-  React2.sboTerm = 181
-  React3.sboTerm = 177
-  React4.sboTerm = 177
-  React5.sboTerm = 181
-  React6.sboTerm = 181
-  React7.sboTerm = 177
-  React8.sboTerm = 177
-  React9.sboTerm = 181
-  React10.sboTerm = 181
-  React11.sboTerm = 181
-  React12.sboTerm = 177
-  React13.sboTerm = 177
-  React14.sboTerm = 181
-  React15.sboTerm = 181
-  React16.sboTerm = 181
-
-  // CV terms:
-  comp1 identity "http://identifiers.org/go/GO:0031594"
-  BLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  IL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  AL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  A hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  BL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  B hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  DLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  D hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ILL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  DL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  I hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ALL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  React0 identity "http://identifiers.org/go/GO:0042166"
-  React1 identity "http://identifiers.org/go/GO:0042166"
-  React2 identity "http://identifiers.org/go/GO:0004889"
-  React3 identity "http://identifiers.org/go/GO:0042166"
-  React4 identity "http://identifiers.org/go/GO:0042166"
-  React5 identity "http://identifiers.org/go/GO:0004889"
-  React6 identity "http://identifiers.org/go/GO:0004889"
-  React7 identity "http://identifiers.org/go/GO:0042166"
-  React8 identity "http://identifiers.org/go/GO:0042166"
-  React9 identity "http://identifiers.org/go/GO:0004889"
-  React10 identity "http://identifiers.org/go/GO:0004889"
-  React11 identity "http://identifiers.org/go/GO:0004889"
-  React12 identity "http://identifiers.org/go/GO:0042166"
-  React13 identity "http://identifiers.org/go/GO:0042166"
-end
-
-BIOMD0000000001 is "Edelstein1996 - EPSP ACh event"
-
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6613849442"
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000001"
-BIOMD0000000001 description "http://identifiers.org/pubmed/8983160"
-BIOMD0000000001 hypernym "http://identifiers.org/go/GO:0007274",
-                         "http://identifiers.org/go/GO:0007166",
-                         "http://identifiers.org/go/GO:0019226"
-BIOMD0000000001 taxon "http://identifiers.org/taxonomy/7787"
diff --git a/BioModelsRAG/data/BIOMD0000000002.txt b/BioModelsRAG/data/BIOMD0000000002.txt
deleted file mode 100644
index 809ba11be2fab031cc9eb60920ae91b22b9399d3..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000002.txt
+++ /dev/null
@@ -1,155 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000002()
-
-  // Compartments and Species:
-  compartment comp1;
-  species BLL in comp1, IL in comp1, AL in comp1, A in comp1, BL in comp1;
-  species B in comp1, DLL in comp1, D in comp1, ILL in comp1, DL in comp1;
-  species I in comp1, ALL in comp1, L in comp1;
-
-  // Reactions:
-  React0: B + L -> BL; comp1*(kf_0*B*L - kr_0*BL);
-  React1: BL + L -> BLL; comp1*(kf_1*BL*L - kr_1*BLL);
-  React2: BLL -> ALL; comp1*(kf_2*BLL - kr_2*ALL);
-  React3: A + L -> AL; comp1*(kf_3*A*L - kr_3*AL);
-  React4: AL + L -> ALL; comp1*(kf_4*AL*L - kr_4*ALL);
-  React5: B -> A; comp1*(kf_5*B - kr_5*A);
-  React6: BL -> AL; comp1*(kf_6*BL - kr_6*AL);
-  React7: I + L -> IL; comp1*(kf_7*I*L - kr_7*IL);
-  React8: IL + L -> ILL; comp1*(kf_8*IL*L - kr_8*ILL);
-  React9: A -> I; comp1*(kf_9*A - kr_9*I);
-  React10: AL -> IL; comp1*(kf_10*AL - kr_10*IL);
-  React11: ALL -> ILL; comp1*(kf_11*ALL - kr_11*ILL);
-  React12: D + L -> DL; comp1*(kf_12*D*L - kr_12*DL);
-  React13: DL + L -> DLL; comp1*(kf_13*DL*L - kr_13*DLL);
-  React14: I -> D; comp1*(kf_14*I - kr_14*D);
-  React15: IL -> DL; comp1*(kf_15*IL - kr_15*DL);
-  React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL);
-
-  // Species initializations:
-  BLL = 0;
-  IL = 0;
-  AL = 0;
-  A = 0;
-  BL = 0;
-  B = 1e-22/comp1;
-  DLL = 0;
-  D = 0;
-  ILL = 0;
-  DL = 0;
-  I = 0;
-  ALL = 0;
-  L = 1e-21/comp1;
-
-  // Compartment initializations:
-  comp1 = 1e-16;
-
-  // Variable initializations:
-  kf_0 = 300000000;
-  kr_0 = 8000;
-  kf_1 = 150000000;
-  kr_1 = 16000;
-  kf_2 = 30000;
-  kr_2 = 700;
-  kf_3 = 300000000;
-  kr_3 = 8.64;
-  kf_4 = 150000000;
-  kr_4 = 17.28;
-  kf_5 = 0.54;
-  kr_5 = 10800;
-  kf_6 = 130;
-  kr_6 = 2740;
-  kf_7 = 300000000;
-  kr_7 = 4;
-  kf_8 = 150000000;
-  kr_8 = 8;
-  kf_9 = 19.7;
-  kr_9 = 3.74;
-  kf_10 = 19.85;
-  kr_10 = 1.74;
-  kf_11 = 20;
-  kr_11 = 0.81;
-  kf_12 = 300000000;
-  kr_12 = 4;
-  kf_13 = 150000000;
-  kr_13 = 8;
-  kf_14 = 0.05;
-  kr_14 = 0.0012;
-  kf_15 = 0.05;
-  kr_15 = 0.0012;
-  kf_16 = 0.05;
-  kr_16 = 0.0012;
-
-  // Other declarations:
-  const comp1, kf_0, kr_0, kf_1, kr_1, kf_2, kr_2, kf_3, kr_3, kf_4, kr_4;
-  const kf_5, kr_5, kf_6, kr_6, kf_7, kr_7, kf_8, kr_8, kf_9, kr_9, kf_10;
-  const kr_10, kf_11, kr_11, kf_12, kr_12, kf_13, kr_13, kf_14, kr_14, kf_15;
-  const kr_15, kf_16, kr_16;
-
-  // Display Names:
-  comp1 is "compartment1";
-  BLL is "BasalACh2";
-  IL is "IntermediateACh";
-  AL is "ActiveACh";
-  A is "Active";
-  BL is "BasalACh";
-  B is "Basal";
-  DLL is "DesensitisedACh2";
-  D is "Desensitised";
-  ILL is "IntermediateACh2";
-  DL is "DesensitisedACh";
-  I is "Intermediate";
-  ALL is "ActiveACh2";
-  L is "ACh";
-
-  // CV terms:
-  comp1 identity "http://identifiers.org/go/GO:0031594"
-  BLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  IL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  AL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  A hypernym "http://identifiers.org/go/GO:0005892"
-  BL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  B hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  DLL hypernym "http://identifiers.org/go/GO:0005892"
-  D hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ILL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  DL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  I hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ALL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  L identity "http://identifiers.org/chebi/CHEBI:15355",
-             "http://identifiers.org/kegg.compound/C01996"
-  React0 identity "http://identifiers.org/go/GO:0042166"
-  React1 identity "http://identifiers.org/go/GO:0042166"
-  React2 identity "http://identifiers.org/go/GO:0004889"
-  React3 identity "http://identifiers.org/go/GO:0042166"
-  React4 identity "http://identifiers.org/go/GO:0042166"
-  React5 identity "http://identifiers.org/go/GO:0004889"
-  React6 identity "http://identifiers.org/go/GO:0004889"
-  React7 identity "http://identifiers.org/go/GO:0042166"
-  React8 identity "http://identifiers.org/go/GO:0042166"
-  React9 identity "http://identifiers.org/go/GO:0004889"
-  React10 identity "http://identifiers.org/go/GO:0004889"
-  React11 identity "http://identifiers.org/go/GO:0004889"
-  React12 identity "http://identifiers.org/go/GO:0042166"
-  React13 identity "http://identifiers.org/go/GO:0042166"
-end
-
-BIOMD0000000002 is "Edelstein1996 - EPSP ACh species"
-
-BIOMD0000000002 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614086398"
-BIOMD0000000002 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000002"
-BIOMD0000000002 description "http://identifiers.org/pubmed/8983160"
-BIOMD0000000002 taxon "http://identifiers.org/taxonomy/7787"
-BIOMD0000000002 hypernym "http://identifiers.org/go/GO:0007166",
-                         "http://identifiers.org/go/GO:0007274",
-                         "http://identifiers.org/go/GO:0019226"
diff --git a/BioModelsRAG/data/BIOMD0000000003.txt b/BioModelsRAG/data/BIOMD0000000003.txt
deleted file mode 100644
index c2a1caa4dba162fb4c168d3db7350b320ad7adc2..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000003.txt
+++ /dev/null
@@ -1,124 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000003()
-
-  // Compartments and Species:
-  compartment cell;
-  species C in cell, M in cell, X in cell;
-
-  // Assignment Rules:
-  V1 := C*VM1*(C + Kc)^-1;
-  V3 := M*VM3;
-
-  // Reactions:
-  reaction1:  => C; cell*reaction1_vi;
-  reaction2: C => ; C*cell*reaction2_kd;
-  reaction3: C => ; C*cell*reaction3_vd*X*(C + reaction3_Kd)^-1;
-  reaction4:  => M; cell*(1 + -1*M)*V1*(reaction4_K1 + -1*M + 1)^-1;
-  reaction5: M => ; cell*M*reaction5_V2*(reaction5_K2 + M)^-1;
-  reaction6:  => X; cell*V3*(1 + -1*X)*(reaction6_K3 + -1*X + 1)^-1;
-  reaction7: X => ; cell*reaction7_V4*X*(reaction7_K4 + X)^-1;
-
-  // Species initializations:
-  C = 0.01;
-  C has substance_per_volume;
-  M = 0.01;
-  M has substance_per_volume;
-  X = 0.01;
-  X has substance_per_volume;
-
-  // Compartment initializations:
-  cell = 1;
-  cell has volume;
-
-  // Variable initializations:
-  VM1 = 3;
-  Kc = 0.5;
-  VM3 = 1;
-  reaction1_vi = 0.025;
-  reaction2_kd = 0.01;
-  reaction3_vd = 0.25;
-  reaction3_Kd = 0.02;
-  reaction4_K1 = 0.005;
-  reaction5_V2 = 1.5;
-  reaction5_K2 = 0.005;
-  reaction6_K3 = 0.005;
-  reaction7_K4 = 0.005;
-  reaction7_V4 = 0.5;
-
-  // Other declarations:
-  var V1, V3;
-  const cell, VM1, Kc, VM3;
-
-  // Unit definitions:
-  unit volume = litre;
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  C is "Cyclin";
-  M is "CDC-2 Kinase";
-  X is "Cyclin Protease";
-  reaction1 is "creation of cyclin";
-  reaction2 is "default degradation of cyclin";
-  reaction3 is "cdc2 kinase triggered degration of cyclin";
-  reaction4 is "activation of cdc2 kinase";
-  reaction5 is "deactivation of cdc2 kinase";
-  reaction6 is "activation of cyclin protease";
-  reaction7 is "deactivation of cyclin protease";
-
-  // SBO terms:
-  cell.sboTerm = 290
-  C.sboTerm = 252
-  M.sboTerm = 252
-  X.sboTerm = 297
-  V1.sboTerm = 186
-  VM1.sboTerm = 25
-  Kc.sboTerm = 27
-  V3.sboTerm = 186
-  VM3.sboTerm = 186
-  reaction1.sboTerm = 393
-  reaction1_vi.sboTerm = 48
-  reaction2.sboTerm = 179
-  reaction2_kd.sboTerm = 22
-  reaction3.sboTerm = 179
-  reaction3_vd.sboTerm = 186
-  reaction3_Kd.sboTerm = 27
-  reaction4.sboTerm = 330
-  reaction4_K1.sboTerm = 27
-  reaction5.sboTerm = 216
-  reaction5_V2.sboTerm = 186
-  reaction5_K2.sboTerm = 27
-  reaction6.sboTerm = 216
-  reaction6_K3.sboTerm = 27
-  reaction7.sboTerm = 330
-  reaction7_K4.sboTerm = 27
-  reaction7_V4.sboTerm = 186
-
-  // CV terms:
-  cell identity "http://identifiers.org/go/GO:0005623"
-  C hypernym "http://identifiers.org/uniprot/Q4KLA0",
-             "http://identifiers.org/interpro/IPR006670"
-  M version "http://identifiers.org/uniprot/P24033",
-            "http://identifiers.org/uniprot/P35567"
-  X hypernym "http://identifiers.org/go/GO:0005680"
-  X version "http://identifiers.org/reactome/REACT_7165.1"
-  reaction1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction2 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction3 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/go/GO:0045737",
-                     "http://identifiers.org/go/GO:0006470"
-  reaction5 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                     "http://identifiers.org/go/GO:0045736",
-                     "http://identifiers.org/go/GO:0006468"
-end
-
-BIOMD0000000003 is "Goldbeter1991 - Min Mit Oscil"
-
-BIOMD0000000003 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614271263"
-BIOMD0000000003 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000003"
-BIOMD0000000003 description "http://identifiers.org/pubmed/1833774"
-BIOMD0000000003 homolog "http://identifiers.org/reactome/REACT_152"
-BIOMD0000000003 hypernym "http://identifiers.org/kegg.pathway/hsa04110",
-                         "http://identifiers.org/go/GO:0000278"
-BIOMD0000000003 taxon "http://identifiers.org/taxonomy/8292"
diff --git a/BioModelsRAG/data/BIOMD0000000004.txt b/BioModelsRAG/data/BIOMD0000000004.txt
deleted file mode 100644
index 37c23d2a08c2593df3e83659070f3122ccf30277..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000004.txt
+++ /dev/null
@@ -1,102 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000004()
-
-  // Compartments and Species:
-  compartment cell;
-  species C in cell, M in cell, X in cell, MI in cell, XI in cell;
-
-  // Assignment Rules:
-  V1 := C*VM1*(C + Kc)^-1;
-  V3 := M*VM3;
-
-  // Reactions:
-  reaction1:  => C; cell*reaction1_vi;
-  reaction2: C => ; C*cell*reaction2_kd;
-  reaction3: C => ; C*cell*reaction3_vd*X*(C + reaction3_Kd)^-1;
-  reaction4: MI => M; cell*MI*V1*(reaction4_K1 + MI)^-1;
-  reaction5: M => MI; cell*M*reaction5_V2*(reaction5_K2 + M)^-1;
-  reaction6: XI => X; cell*V3*XI*(reaction6_K3 + XI)^-1;
-  reaction7: X => XI; cell*reaction7_V4*X*(reaction7_K4 + X)^-1;
-
-  // Species initializations:
-  C = 0.01;
-  C has substance_per_volume;
-  M = 0.01;
-  M has substance_per_volume;
-  X = 0.01;
-  X has substance_per_volume;
-  MI = 0.99;
-  MI has substance_per_volume;
-  XI = 0.99;
-  XI has substance_per_volume;
-
-  // Compartment initializations:
-  cell = 1;
-  cell has volume;
-
-  // Variable initializations:
-  VM1 = 3;
-  Kc = 0.5;
-  VM3 = 1;
-  reaction1_vi = 0.025;
-  reaction2_kd = 0.01;
-  reaction3_vd = 0.25;
-  reaction3_Kd = 0.02;
-  reaction4_K1 = 0.005;
-  reaction5_V2 = 1.5;
-  reaction5_K2 = 0.005;
-  reaction6_K3 = 0.005;
-  reaction7_K4 = 0.005;
-  reaction7_V4 = 0.5;
-
-  // Other declarations:
-  var V1, V3;
-  const cell, VM1, Kc, VM3;
-
-  // Unit definitions:
-  unit volume = litre;
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  C is "Cyclin";
-  M is "Active CDC-2 Kinase";
-  X is "Active Cyclin Protease";
-  MI is "Inactive CDC-2 Kinase";
-  XI is "Inactive Cyclin Protease";
-  reaction1 is "creation of cyclin";
-  reaction2 is "default degradation of cyclin";
-  reaction3 is "cdc2 kinase triggered degration of cyclin";
-  reaction4 is "activation of cdc2 kinase";
-  reaction5 is "deactivation of cdc2 kinase";
-  reaction6 is "activation of cyclin protease";
-  reaction7 is "deactivation of cyclin protease";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  C hypernym "http://identifiers.org/interpro/IPR006670"
-  M version "http://identifiers.org/uniprot/P24033",
-            "http://identifiers.org/uniprot/P35567"
-  MI version "http://identifiers.org/uniprot/P24033",
-             "http://identifiers.org/uniprot/P35567"
-  reaction1 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  reaction2 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  reaction3 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  reaction4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0045737",
-                     "http://identifiers.org/obo.go/GO:0006470"
-  reaction5 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                     "http://identifiers.org/obo.go/GO:0045736",
-                     "http://identifiers.org/obo.go/GO:0006468"
-end
-
-BIOMD0000000004 is "Goldbeter1991 - Min Mit Oscil, Expl Inact"
-
-BIOMD0000000004 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614389071"
-BIOMD0000000004 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000004"
-BIOMD0000000004 description "http://identifiers.org/pubmed/1833774"
-BIOMD0000000004 origin "http://identifiers.org/biomodels.db/BIOMD0000000003"
-BIOMD0000000004 hypernym "http://identifiers.org/kegg.pathway/hsa04110",
-                         "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000004 homolog "http://identifiers.org/reactome/REACT_152"
-BIOMD0000000004 taxon "http://identifiers.org/taxonomy/8292"
diff --git a/BioModelsRAG/data/BIOMD0000000005.txt b/BioModelsRAG/data/BIOMD0000000005.txt
deleted file mode 100644
index aa5f21eb247e58aa3e0949fb1264b07461f8c069..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000005.txt
+++ /dev/null
@@ -1,114 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000005()
-
-  // Compartments and Species:
-  compartment cell;
-  species $EmptySet in cell, C2 in cell, CP in cell, M in cell, pM in cell;
-  species Y in cell, YP in cell, $YT in cell, $CT in cell;
-
-  // Assignment Rules:
-  YT := Y + YP + M + pM;
-  CT := C2 + CP + M + pM;
-
-  // Reactions:
-  Reaction1: M => C2 + YP; cell*Reaction1_k6*M;
-  Reaction2: C2 => CP; cell*C2*Reaction2_k8notP;
-  Reaction3: CP => C2; cell*CP*Reaction3_k9;
-  Reaction4: CP + Y => pM; cell*CP*Reaction4_k3*Y;
-  Reaction5: M => pM; cell*Reaction5_k5notP*M;
-  Reaction6: $EmptySet => Y; cell*Reaction6_k1aa;
-  Reaction7: Y => $EmptySet; cell*Reaction7_k2*Y;
-  Reaction8: YP => $EmptySet; cell*Reaction8_k7*YP;
-  Reaction9: pM => M; cell*pM*(Reaction9_k4prime + Reaction9_k4*(M/CT)^2);
-
-  // Species initializations:
-  EmptySet = 0;
-  C2 = 0;
-  CP = 0.75/cell;
-  M = 0;
-  pM = 0.25/cell;
-  Y = 0;
-  YP = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  Reaction1_k6 = 1;
-  Reaction2_k8notP = 1000000;
-  Reaction3_k9 = 1000;
-  Reaction4_k3 = 200;
-  Reaction5_k5notP = 0;
-  Reaction6_k1aa = 0.015;
-  Reaction7_k2 = 0;
-  Reaction8_k7 = 0.6;
-  Reaction9_k4 = 180;
-  Reaction9_k4prime = 0.018;
-
-  // Other declarations:
-  const cell;
-
-  // Display Names:
-  C2 is "cdc2k";
-  CP is "cdc2k-P";
-  M is "p-cyclin_cdc2";
-  pM is "p-cyclin_cdc2-p";
-  Y is "cyclin";
-  YP is "p-cyclin";
-  YT is "total_cyclin";
-  CT is "total_cdc2";
-  Reaction1 is "cyclin_cdc2k dissociation";
-  Reaction2 is "cdc2k phosphorylation";
-  Reaction3 is "cdc2k dephosphorylation";
-  Reaction4 is "cyclin cdc2k-p association";
-  Reaction5 is "deactivation of cdc2 kinase";
-  Reaction6 is "cyclin biosynthesis";
-  Reaction7 is "default degradation of cyclin";
-  Reaction8 is "cdc2 kinase triggered degration of cyclin";
-  Reaction9 is "activation of cdc2 kinase";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  C2 hypernym "http://identifiers.org/uniprot/P04551"
-  CP hypernym "http://identifiers.org/uniprot/P04551"
-  M part "http://identifiers.org/uniprot/P04551",
-         "http://identifiers.org/interpro/IPR006670"
-  pM part "http://identifiers.org/uniprot/P04551",
-          "http://identifiers.org/interpro/IPR006670"
-  Y hypernym "http://identifiers.org/interpro/IPR006670"
-  YP hypernym "http://identifiers.org/interpro/IPR006670"
-  YT hypernym "http://identifiers.org/interpro/IPR006670"
-  CT hypernym "http://identifiers.org/uniprot/P04551"
-  Reaction1 version "http://identifiers.org/reactome/REACT_6308"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0000079"
-  Reaction2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                     "http://identifiers.org/obo.go/GO:0006468"
-  Reaction3 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0006470"
-  Reaction4 version "http://identifiers.org/reactome/REACT_6216",
-                    "http://identifiers.org/reactome/REACT_6308"
-  Reaction5 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                     "http://identifiers.org/obo.go/GO:0006468",
-                     "http://identifiers.org/obo.go/GO:0045736"
-  Reaction5 version "http://identifiers.org/reactome/REACT_3178",
-                    "http://identifiers.org/reactome/REACT_6327"
-  Reaction6 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  Reaction9 version "http://identifiers.org/reactome/REACT_6257",
-                    "http://identifiers.org/reactome/REACT_6175",
-                    "http://identifiers.org/reactome/REACT_6294"
-  Reaction9 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0006470",
-                     "http://identifiers.org/obo.go/GO:0045737"
-end
-
-BIOMD0000000005 is "Tyson1991 - Cell Cycle 6 var"
-
-BIOMD0000000005 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614644188"
-BIOMD0000000005 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000005"
-BIOMD0000000005 description "http://identifiers.org/pubmed/1831270"
-BIOMD0000000005 taxon "http://identifiers.org/taxonomy/33154"
-BIOMD0000000005 hypernym "http://identifiers.org/kegg.pathway/sce04111",
-                         "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000005 version "http://identifiers.org/reactome/REACT_152"
diff --git a/BioModelsRAG/data/BIOMD0000000006.txt b/BioModelsRAG/data/BIOMD0000000006.txt
deleted file mode 100644
index 830a1c7ecd9646eb55fea96c460b0806ec3b6b71..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000006.txt
+++ /dev/null
@@ -1,66 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000006()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species $EmptySet in cell, $u in cell, $v in cell, $z in cell;
-
-  // Assignment Rules:
-  alpha := k4prime/k4;
-  z := v - u;
-
-  // Rate Rules:
-  u' = k4*(v - u)*(alpha + u^2) - k6*u;
-  v' = kappa - k6*u;
-
-  // Reactions:
-  Reaction1: $EmptySet => $z; kappa;
-  Reaction2: $u => $EmptySet; k6*u;
-  Reaction3: $z => $u; k4*z*(k4prime/k4 + u^2);
-
-  // Species initializations:
-  EmptySet = 1/cell;
-  u = 0;
-  v = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  k4 = 180;
-  k6 = 1;
-  kappa = 0.015;
-  k4prime = 0.018;
-
-  // Other declarations:
-  var alpha;
-  const cell, k4, k6, kappa, k4prime;
-
-  // SBO terms:
-  EmptySet.sboTerm = 291
-  u.sboTerm = 297
-  v.sboTerm = 297
-  z.sboTerm = 297
-  Reaction1.sboTerm = 205
-  Reaction2.sboTerm = 179
-  Reaction3.sboTerm = 176
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  u property "http://identifiers.org/obo.go/GO:0004693"
-  u hypernym "http://identifiers.org/obo.go/GO:0031387"
-  v version "http://identifiers.org/uniprot/P04551"
-  v version "http://identifiers.org/obo.go/GO:0031387"
-  v property "http://identifiers.org/obo.go/GO:0004693"
-  z version "http://identifiers.org/uniprot/P04551"
-end
-
-BIOMD0000000006 is "Tyson1991 - Cell Cycle 2 var"
-
-BIOMD0000000006 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614715255"
-BIOMD0000000006 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000006"
-BIOMD0000000006 description "http://identifiers.org/pubmed/1831270"
-BIOMD0000000006 taxon "http://identifiers.org/taxonomy/33154"
-BIOMD0000000006 identity "http://identifiers.org/kegg.pathway/sce04111"
-BIOMD0000000006 hypernym "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000006 version "http://identifiers.org/reactome/REACT_152"
diff --git a/BioModelsRAG/data/BIOMD0000000007.txt b/BioModelsRAG/data/BIOMD0000000007.txt
deleted file mode 100644
index d22e00febb2aff7e36fcca72f726f7a1309b7398..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000007.txt
+++ /dev/null
@@ -1,266 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000007()
-
-  // Compartments and Species:
-  compartment Cell;
-  substanceOnly species UbE in Cell, UbE2 in Cell, Wee1 in Cell, Cdc25 in Cell;
-  substanceOnly species G2K in Cell, R in Cell, G1K in Cell, IE in Cell, PG2 in Cell;
-  substanceOnly species G1R in Cell, G2R in Cell, PG2R in Cell, $SPF in Cell;
-  substanceOnly species $MPF in Cell, $IEB in Cell, $UbEB in Cell, $UbE2B in Cell;
-  substanceOnly species $Wee1B in Cell, $Cdc25B in Cell, $Rum1Total in Cell;
-  substanceOnly species $Cdc13Total in Cell, $Cig2Total in Cell;
-
-  // Assignment Rules:
-  SPF := Cig1 + alpha*G1K + MPF;
-  MPF := G2K + beta*PG2;
-  IEB := 1 - IE;
-  UbEB := 1 - UbE;
-  UbE2B := 1 - UbE2;
-  Wee1B := 1 - Wee1;
-  Cdc25B := 1 - Cdc25;
-  Rum1Total := G1R + G2R + PG2R + R;
-  Cdc13Total := G2K + G2R + PG2 + PG2R;
-  Cig2Total := G1K + G1R;
-  k2 := UbE*V2 + (1 - UbE)*V2prime;
-  k6 := UbE2*V6 + (1 - UbE2)*V6prime;
-  kwee := Vwprime*(1 - Wee1) + Vw*Wee1;
-  k25 := Cdc25*V25 + (1 - Cdc25)*V25prime;
-
-  // Rate Rules:
-  Mass' = Mass*mu;
-
-  // Reactions:
-  G2K_Creation:  => G2K; k1;
-  G1K_Creation:  => G1K; k5;
-  Cdc2Phos: G2K -> PG2; G2K*kwee - k25*PG2;
-  G2R_Creation: G2K + R -> G2R; G2K*k7*R - G2R*k7r;
-  PG2R_Creation: PG2 + R -> PG2R; k7*PG2*R - k7r*PG2R;
-  Rum1DegInG2R: G2R => G2K; G2R*k4;
-  Rum1Deg: R => ; k4*R;
-  Rum1DegInPG2R: PG2R => PG2; k4*PG2R;
-  RumDegInG1R: G1R => G1K; G1R*k4;
-  G2K_dissoc: G2K => ; G2K*k2;
-  PG2_dissoc: PG2 => ; k2*PG2;
-  G1K_Dissociation: G1K => ; G1K*k6;
-  PG2R_Dissociation: PG2R => R; k2prime*PG2R;
-  G2R_Dissociation: G2R => R; G2R*k2prime;
-  G1R_Dissociation: G1R => R; G1R*k6prime;
-  G1R_Binding: G1K + R -> G1R; G1K*k8*R - G1R*k8r;
-  G2R_Dissociation_UbE: G2R => R; G2R*k2;
-  PG2R_Dissociation_UbE: PG2R => R; k2*PG2R;
-  Rum1_Production:  => R; k3;
-  Rum1_Deg_SPF: R => ; kp*Mass*R*SPF/(Kmp + R);
-  IE_Reaction: $IEB -> IE; IEB*ki*MPF/(IEB + Kmi) - IE*kir/(IE + Kmir);
-  UbE_Reaction: $UbEB -> UbE; IE*ku*UbEB/(Kmu + UbEB) - kur*UbE/(Kmur + UbE);
-  UbE2_Reaction: $UbE2B -> UbE2; ku2*MPF*UbE2B/(Kmu2 + UbE2B) - kur2*UbE2/(Kmur2 + UbE2);
-  Wee1_Reaction: $Wee1B -> Wee1; kwr*Wee1B/(Kmwr + Wee1B) - kw*MPF*Wee1/(Kmw + Wee1);
-  Cdc25_Reaction: $Cdc25B -> Cdc25; Cdc25B*kc*MPF/(Cdc25B + Kmc) - Cdc25*kcr/(Cdc25 + Kmcr);
-
-  // Events:
-  Start: at 60 after SPF >= 0.1: kp = kp/2;
-  Division: at UbE <= 0.1: Mass = Mass/2, kp = 2*kp;
-
-  // Species initializations:
-  UbE = 0.11/Cell;
-  UbE2 = 0;
-  Wee1 = 0;
-  Cdc25 = 0;
-  G2K = 0;
-  R = 0.4/Cell;
-  G1K = 0;
-  IE = 0;
-  PG2 = 0;
-  G1R = 0;
-  G2R = 0;
-  PG2R = 0;
-
-  // Compartment initializations:
-  Cell = 1;
-  Cell has volume;
-
-  // Variable initializations:
-  Cig1 = 0;
-  alpha = 0.25;
-  beta = 0.05;
-  kp = 3.25;
-  Mass = 0.49;
-  mu = 0.00495;
-  k1 = 0.015;
-  k2prime = 0.05;
-  k3 = 0.09375;
-  k4 = 0.1875;
-  k5 = 0.00175;
-  k6prime = 0;
-  k7 = 100;
-  k7r = 0.1;
-  k8 = 10;
-  k8r = 0.1;
-  kc = 1;
-  kcr = 0.25;
-  ki = 0.4;
-  kir = 0.1;
-  ku = 0.2;
-  kur = 0.1;
-  ku2 = 1;
-  kur2 = 0.3;
-  kw = 1;
-  kwr = 0.25;
-  V2 = 0.25;
-  V2prime = 0.0075;
-  V6 = 7.5;
-  V6prime = 0.0375;
-  V25 = 0.5;
-  V25prime = 0.025;
-  Vw = 0.35;
-  Vwprime = 0.035;
-  Kmc = 0.1;
-  Kmcr = 0.1;
-  Kmi = 0.01;
-  Kmir = 0.01;
-  Kmp = 0.001;
-  Kmu = 0.01;
-  Kmur = 0.01;
-  Kmu2 = 0.05;
-  Kmur2 = 0.05;
-  Kmw = 0.1;
-  Kmwr = 0.1;
-
-  // Other declarations:
-  var kp, Mass, k2, k6, kwee, k25;
-  const Cell, Cig1, alpha, beta, mu, k1, k2prime, k3, k4, k5, k6prime, k7;
-  const k7r, k8, k8r, kc, kcr, ki, kir, ku, kur, ku2, kur2, kw, kwr, V2, V2prime;
-  const V6, V6prime, V25, V25prime, Vw, Vwprime, Kmc, Kmcr, Kmi, Kmir, Kmp;
-  const Kmu, Kmur, Kmu2, Kmur2, Kmw, Kmwr;
-
-  // Unit definitions:
-  unit time_unit = 60 second;
-  unit volume = litre;
-
-  // Display Names:
-  time_unit is "minutes";
-  UbE is "ubiquitinProtease1";
-  UbE2 is "ubiquitinProtease2";
-  G2K is "Cdc13_Cdc2";
-  R is "FreeRum1";
-  G1K is "Cig2_Cdc2";
-  IE is "IntermediaryEnzyme";
-  PG2 is "Cdc13_P-Cdc2";
-  G1R is "Cig2_Cdc2_Rum1";
-  G2R is "Cdc13_Cdc2_Rum1";
-  PG2R is "Cdc13_P-Cdc2_Rum1";
-  SPF is "S-phasePromotingFactor";
-  MPF is "M-phasePromotingFactor";
-  IEB is "BoundIntermediaryEnzyme";
-  UbEB is "BoundUbiquitinProtease1";
-  UbE2B is "BoundUbiquitinProtease2";
-  Wee1B is "BoundWee1";
-  Cdc25B is "BoundCdc25";
-  Rum1Total is "TotalRum1";
-  Cdc13Total is "TotalCdc13";
-  Cig2Total is "TotalCig2";
-  Start is "S-Phase Start";
-  Division is "Cell Division";
-  k2prime is "k2'";
-  k6prime is "k6'";
-  V2prime is "V2'";
-  V6prime is "V6'";
-  V25prime is "V25'";
-  Vwprime is "Vw'";
-  G2K_Creation is "Cdc13_Cdc2 creation";
-  G1K_Creation is "Cig2_Cdc2 creation";
-  Cdc2Phos is "Cdc2 phosphorylation";
-  G2R_Creation is "binding of Rum1 with Cdc13_Cdc2";
-  PG2R_Creation is "binding of Rum1 with Cdc13_P-Cdc2";
-  Rum1DegInG2R is "Rum1 degradation in Rum1_Cdc13_Cdc2";
-  Rum1Deg is "Rum1 degradation in solution";
-  Rum1DegInPG2R is "Rum1 degradation in Rum1_Cdc13_P-Cdc2";
-  RumDegInG1R is "Rum1 degradation in Rum1_Cig2_Cdc2";
-  G2K_dissoc is "Cdc13 degradation in Cdc13_Cdc2";
-  PG2_dissoc is "Cdc13 degradation in Cdc13_P-Cdc2";
-  G1K_Dissociation is "Cig2 degradation in Cig2_Cdc2";
-  PG2R_Dissociation is "Cdc13 degradation in Rum1_Cdc13_P-Cdc2";
-  G2R_Dissociation is "Cdc13 degradation in Rum1_Cdc13_Cdc2";
-  G1R_Dissociation is "Cig2 degradation in Rum1_Cig2_Cdc2";
-  G1R_Binding is "Binding of Rum1 to Cig2_Cdc2";
-  G2R_Dissociation_UbE is "UbE mediated degradation of Cdc13_Cdc2 in Rum1_Cdc13_Cdc2";
-  PG2R_Dissociation_UbE is "UbE mediated degradation of Cdc13_Cdc2 in Rum1_Cdc13_P-Cdc2";
-  Rum1_Production is "Rum1 creation";
-  Rum1_Deg_SPF is "Rum1 degradation by SPF";
-  IE_Reaction is "IE production & degradation";
-  UbE_Reaction is "UbE production & degradation";
-  UbE2_Reaction is "UbE2 production & degradation";
-  Wee1_Reaction is "Wee1 production & degradation";
-  Cdc25_Reaction is "Cdc25 production & degradation";
-
-  // CV terms:
-  Cell identity "http://identifiers.org/go/GO:0005623"
-  UbE hypernym "http://identifiers.org/go/GO:0000502"
-  UbE2 hypernym "http://identifiers.org/go/GO:0000502"
-  Wee1 version "http://identifiers.org/uniprot/P30290",
-               "http://identifiers.org/uniprot/P07527"
-  Cdc25 identity "http://identifiers.org/uniprot/P06652"
-  G2K part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P10815"
-  R hypernym "http://identifiers.org/uniprot/P40380"
-  G1K part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P36630"
-  PG2 part "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P04551"
-  G1R part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P36630",
-           "http://identifiers.org/uniprot/P40380"
-  G2R part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P40380"
-  PG2R part "http://identifiers.org/uniprot/P10815",
-            "http://identifiers.org/uniprot/P04551",
-            "http://identifiers.org/uniprot/P40380"
-  SPF part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P36630"
-  MPF part "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P04551"
-  UbEB hypernym "http://identifiers.org/go/GO:0000502"
-  UbE2B hypernym "http://identifiers.org/go/GO:0000502"
-  Wee1B version "http://identifiers.org/uniprot/P07527",
-                "http://identifiers.org/uniprot/P30290"
-  Cdc25B hypernym "http://identifiers.org/uniprot/P06652"
-  Rum1Total identity "http://identifiers.org/uniprot/P40380"
-  Cdc13Total identity "http://identifiers.org/uniprot/P10815"
-  Cig2Total identity "http://identifiers.org/uniprot/P36630"
-  Cdc2Phos part "http://identifiers.org/reactome/REACT_6294",
-                "http://identifiers.org/reactome/REACT_6327"
-  Cdc2Phos part "http://identifiers.org/reactome/REACT_6257",
-                "http://identifiers.org/reactome/REACT_6178"
-  Cdc2Phos hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                    "http://identifiers.org/go/GO:0006468"
-  G2R_Creation hypernym "http://identifiers.org/go/GO:0006461"
-  PG2R_Creation hypernym "http://identifiers.org/go/GO:0006461"
-  Rum1DegInG2R hypernym "http://identifiers.org/go/GO:0030163"
-  Rum1Deg hypernym "http://identifiers.org/go/GO:0030163"
-  Rum1DegInPG2R hypernym "http://identifiers.org/go/GO:0030163"
-  RumDegInG1R hypernym "http://identifiers.org/go/GO:0030163"
-  G2K_dissoc hypernym "http://identifiers.org/go/GO:0008054"
-  PG2_dissoc hypernym "http://identifiers.org/go/GO:0008054"
-  G1K_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  PG2R_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  G2R_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  G1R_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  G1R_Binding hypernym "http://identifiers.org/go/GO:0006461"
-  G2R_Dissociation_UbE hypernym "http://identifiers.org/kegg.pathway/spo04120",
-                                "http://identifiers.org/go/GO:0030163"
-  PG2R_Dissociation_UbE hypernym "http://identifiers.org/kegg.pathway/spo04120",
-                                 "http://identifiers.org/go/GO:0030163"
-  Rum1_Deg_SPF hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-BIOMD0000000007 is "Novak1997 - Cell Cycle"
-
-BIOMD0000000007 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614787694"
-BIOMD0000000007 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000007"
-BIOMD0000000007 description "http://identifiers.org/pubmed/9256450"
-BIOMD0000000007 origin "http://identifiers.org/pubmed/10395816"
-BIOMD0000000007 taxon "http://identifiers.org/taxonomy/4896"
-BIOMD0000000007 hypernym "http://identifiers.org/kegg.pathway/ko04110",
-                         "http://identifiers.org/go/GO:0000278"
-BIOMD0000000007 homolog "http://identifiers.org/reactome/REACT_152"
diff --git a/BioModelsRAG/data/BIOMD0000000008.txt b/BioModelsRAG/data/BIOMD0000000008.txt
deleted file mode 100644
index b8f93c665b31f708fcccf06658aced8f106aaa23..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000008.txt
+++ /dev/null
@@ -1,121 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000008()
-
-  // Compartments and Species:
-  compartment Cell;
-  species C in Cell, X in Cell, M in Cell, Y in Cell, Z in Cell;
-
-  // Assignment Rules:
-  V1 := C*V1p*(C + K6)^-1;
-  V3 := M*V3p;
-
-  // Reactions:
-  reaction1:  => C; reaction1_vi;
-  reaction2: C => ; C*reaction2_k1*X*(C + reaction2_K5)^-1;
-  reaction3: C => ; C*reaction3_kd;
-  reaction4:  => M; (1 + -1*M)*V1*(reaction4_K1 + -1*M + 1)^-1;
-  reaction5: M => ; M*reaction5_V2*(reaction5_K2 + M)^-1;
-  reaction6:  => X; V3*(1 + -1*X)*(reaction6_K3 + -1*X + 1)^-1;
-  reaction7: X => ; reaction7_V4*X*(reaction7_K4 + X)^-1;
-  reaction8: C + Y => Z; reaction8_a1*C*Y;
-  reaction9: Z => C + Y; reaction9_a2*Z;
-  reaction10: Z => C; reaction10_alpha*reaction10_d1*Z;
-  reaction11: Z => Y; reaction11_alpha*reaction11_kd*Z;
-  reaction12:  => Y; reaction12_vs;
-  reaction13: Y => ; reaction13_d1*Y;
-
-  // Species initializations:
-  C = 0;
-  C has substance_per_volume;
-  X = 0;
-  X has substance_per_volume;
-  M = 0;
-  M has substance_per_volume;
-  Y = 1/Cell;
-  Y has substance_per_volume;
-  Z = 1/Cell;
-  Z has substance_per_volume;
-
-  // Compartment initializations:
-  Cell = 1;
-  Cell has volume;
-
-  // Variable initializations:
-  V1p = 0.75;
-  K6 = 0.3;
-  V3p = 0.3;
-  reaction1_vi = 0.1;
-  reaction2_k1 = 0.5;
-  reaction2_K5 = 0.02;
-  reaction3_kd = 0.02;
-  reaction4_K1 = 0.1;
-  reaction5_V2 = 0.25;
-  reaction5_K2 = 0.1;
-  reaction6_K3 = 0.2;
-  reaction7_K4 = 0.1;
-  reaction7_V4 = 0.1;
-  reaction8_a1 = 0.05;
-  reaction9_a2 = 0.05;
-  reaction10_alpha = 0.1;
-  reaction10_d1 = 0.05;
-  reaction11_kd = 0.02;
-  reaction11_alpha = 0.1;
-  reaction12_vs = 0.2;
-  reaction13_d1 = 0.05;
-
-  // Other declarations:
-  var V1, V3;
-  const Cell, V1p, K6, V3p;
-
-  // Unit definitions:
-  unit volume = litre;
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  C is "cyclin";
-  X is "protease";
-  M is "cdc2k";
-  Y is "cyclin inhibitor";
-  Z is "complex inhibitor-cyclin";
-  reaction1 is "creation of cyclin";
-  reaction2 is "cdc2 kinase triggered degration of cyclin";
-  reaction3 is "default degradation of cyclin";
-  reaction4 is "activation of cdc2 kinase";
-  reaction5 is "deactivation of cdc2 kinase";
-  reaction6 is "activation of cyclin protease";
-  reaction7 is "deactivation of cyclin protease";
-  reaction10 is "desinhibition of cyclin";
-  reaction11 is "degradation of inhibited cyclin";
-  reaction12 is "creation of cyclin inhibitor";
-  reaction13 is "degradation of cyclin inhibitor";
-
-  // CV terms:
-  Cell identity "http://identifiers.org/go/GO:0005737"
-  C identity "http://identifiers.org/interpro/IPR006670"
-  X property "http://identifiers.org/go/GO:0008233"
-  M version "http://identifiers.org/uniprot/P35567",
-            "http://identifiers.org/uniprot/P24033"
-  Z part "http://identifiers.org/interpro/IPR006670"
-  reaction1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction2 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction3 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction4 hypernym "http://identifiers.org/go/GO:0045737"
-  reaction5 hypernym "http://identifiers.org/go/GO:0045736"
-  reaction9 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction10 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction11 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction12 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction13 hypernym "http://identifiers.org/go/GO:0044257"
-end
-
-BIOMD0000000008 is "Gardner1998 - Cell Cycle Goldbeter"
-
-BIOMD0000000008 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614879888"
-BIOMD0000000008 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000008"
-BIOMD0000000008 description "http://identifiers.org/pubmed/9826676"
-BIOMD0000000008 origin "http://identifiers.org/biomodels.db/BIOMD0000000003",
-                       "http://identifiers.org/biomodels.db/BIOMD0000000004"
-BIOMD0000000008 hypernym "http://identifiers.org/go/GO:0000278"
-BIOMD0000000008 taxon "http://identifiers.org/taxonomy/8292"
-BIOMD0000000008 homolog "http://identifiers.org/reactome/REACT_152"
diff --git a/BioModelsRAG/data/BIOMD0000000009.txt b/BioModelsRAG/data/BIOMD0000000009.txt
deleted file mode 100644
index f4960d986770bba9a9967a579c6af419173e7a4b..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000009.txt
+++ /dev/null
@@ -1,250 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000009()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species E1 in compartment_, E2 in compartment_, KKK in compartment_, P_KKK in compartment_;
-  species KK in compartment_, P_KK in compartment_, PP_KK in compartment_;
-  species K in compartment_, P_K in compartment_, PP_K in compartment_, KPase in compartment_;
-  species KKPase in compartment_, E1_KKK in compartment_, E2_P_KKK in compartment_;
-  species P_KKK_KK in compartment_, P_KKK_P_KK in compartment_, PP_KK_K in compartment_;
-  species PP_KK_P_K in compartment_, KKPase_PP_KK in compartment_, KKPase_P_KK in compartment_;
-  species KPase_PP_K in compartment_, KPase_P_K in compartment_, $K_PP_norm in compartment_;
-  species $KK_PP_norm in compartment_, $KKK_P_norm in compartment_, $rel_K_PP_max in compartment_;
-
-  // Assignment Rules:
-  K_PP_norm := (PP_K + KPase_PP_K)/(PP_K + P_K + K + PP_KK_K + PP_KK_P_K + KPase_PP_K + KPase_P_K);
-  KK_PP_norm := (PP_KK + PP_KK_K + PP_KK_P_K + KKPase_PP_KK)/(PP_KK + P_KK + KK + PP_KK_K + PP_KK_P_K + P_KKK_KK + P_KKK_P_KK + KKPase_PP_KK + KKPase_P_KK);
-  KKK_P_norm := (P_KKK + P_KKK_KK + P_KKK_P_KK)/(KKK + P_KKK + P_KKK_KK + P_KKK_P_KK);
-  rel_K_PP_max := K_PP_norm/K_PP_norm_max;
-
-  // Reactions:
-  r1a: KKK + E1 -> E1_KKK; compartment_*(r1a_a1*E1*KKK - r1a_d1*E1_KKK);
-  r1b: E1_KKK => E1 + P_KKK; compartment_*r1b_k2*E1_KKK;
-  r2a: P_KKK + E2 -> E2_P_KKK; compartment_*(r2a_a2*E2*P_KKK - r2a_d2*E2_P_KKK);
-  r2b: E2_P_KKK => E2 + KKK; compartment_*r2b_k2*E2_P_KKK;
-  r3a: KK + P_KKK -> P_KKK_KK; compartment_*(r3a_a3*KK*P_KKK - r3a_d3*P_KKK_KK);
-  r3b: P_KKK_KK => P_KK + P_KKK; compartment_*r3b_k3*P_KKK_KK;
-  r4a: P_KK + KKPase -> KKPase_P_KK; compartment_*(r4a_a4*P_KK*KKPase - r4a_d4*KKPase_P_KK);
-  r4b: KKPase_P_KK => KK + KKPase; compartment_*r4b_k4*KKPase_P_KK;
-  r5a: P_KK + P_KKK -> P_KKK_P_KK; compartment_*(r5a_a5*P_KK*P_KKK - r5a_d5*P_KKK_P_KK);
-  r5b: P_KKK_P_KK => PP_KK + P_KKK; compartment_*r5b_k5*P_KKK_P_KK;
-  r6a: PP_KK + KKPase -> KKPase_PP_KK; compartment_*(r6a_a6*PP_KK*KKPase - r6a_d6*KKPase_PP_KK);
-  r6b: KKPase_PP_KK => P_KK + KKPase; compartment_*r6b_k6*KKPase_PP_KK;
-  r7a: K + PP_KK -> PP_KK_K; compartment_*(r7a_a7*K*PP_KK - r7a_d7*PP_KK_K);
-  r7b: PP_KK_K => P_K + PP_KK; compartment_*r7b_k7*PP_KK_K;
-  r8a: P_K + KPase -> KPase_P_K; compartment_*(r8a_a8*P_K*KPase - r8a_d8*KPase_P_K);
-  r8b: KPase_P_K => K + KPase; compartment_*r8b_k8*KPase_P_K;
-  r9a: P_K + PP_KK -> PP_KK_P_K; compartment_*(r9a_a9*P_K*PP_KK - r9a_d9*PP_KK_P_K);
-  r9b: PP_KK_P_K => PP_KK + PP_K; compartment_*r9b_k9*PP_KK_P_K;
-  r10a: PP_K + KPase -> KPase_PP_K; compartment_*(r10a_a10*PP_K*KPase - r10a_d10*KPase_PP_K);
-  r10b: KPase_PP_K => P_K + KPase; compartment_*r10b_k10*KPase_PP_K;
-
-  // Species initializations:
-  E1 = 3e-05;
-  E2 = 0.0003;
-  KKK = 0.003;
-  P_KKK = 0;
-  KK = 1.2;
-  P_KK = 0;
-  PP_KK = 0;
-  K = 1.2;
-  P_K = 0;
-  PP_K = 0;
-  KPase = 0.12;
-  KKPase = 0.0003;
-  E1_KKK = 0;
-  E2_P_KKK = 0;
-  P_KKK_KK = 0;
-  P_KKK_P_KK = 0;
-  PP_KK_K = 0;
-  PP_KK_P_K = 0;
-  KKPase_PP_KK = 0;
-  KKPase_P_KK = 0;
-  KPase_PP_K = 0;
-  KPase_P_K = 0;
-
-  // Compartment initializations:
-  compartment_ = 4e-12;
-
-  // Variable initializations:
-  K_PP_norm_max = 0.900049;
-  r1a_a1 = 1000;
-  r1a_d1 = 150;
-  r1b_k2 = 150;
-  r2a_a2 = 1000;
-  r2a_d2 = 150;
-  r2b_k2 = 150;
-  r3a_a3 = 1000;
-  r3a_d3 = 150;
-  r3b_k3 = 150;
-  r4a_a4 = 1000;
-  r4a_d4 = 150;
-  r4b_k4 = 150;
-  r5a_a5 = 1000;
-  r5a_d5 = 150;
-  r5b_k5 = 150;
-  r6a_a6 = 1000;
-  r6a_d6 = 150;
-  r6b_k6 = 150;
-  r7a_a7 = 1000;
-  r7a_d7 = 150;
-  r7b_k7 = 150;
-  r8a_a8 = 1000;
-  r8a_d8 = 150;
-  r8b_k8 = 150;
-  r9a_a9 = 1000;
-  r9a_d9 = 150;
-  r9b_k9 = 150;
-  r10a_a10 = 1000;
-  r10a_d10 = 150;
-  r10b_k10 = 150;
-
-  // Other declarations:
-  const compartment_, K_PP_norm_max;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  E1 is "MAPKKK activator (Ras)";
-  E2 is "MAPKKK inactivator";
-  KKK is "Mos";
-  P_KKK is "Mos-P";
-  KK is "Mek1";
-  P_KK is "Mek1-P";
-  PP_KK is "Mek1-PP";
-  K is "Erk2";
-  P_K is "Erk2-P";
-  PP_K is "Erk2-PP";
-  KPase is "MAPK-Pase";
-  KKPase is "MAPKK-Pase";
-  E1_KKK is "E1_Mos";
-  E2_P_KKK is "E2_Mos-P";
-  P_KKK_KK is "P-Mos_Mek1";
-  P_KKK_P_KK is "P-Mos_P-Mek1";
-  PP_KK_K is "PP-Mek1_Erk2";
-  PP_KK_P_K is "PP-Mek1_P-Erk2";
-  KKPase_PP_KK is "MAPKK-Pase_PP-Mek1";
-  KKPase_P_KK is "MAPKK-Pase_P-Mek1";
-  KPase_PP_K is "MAPK-Pase_PP-Erk2";
-  KPase_P_K is "MAPK-Pase_P-Erk2";
-  rel_K_PP_max is "relative maximal K_PP";
-  r1a is "binding of MAPKKK activator";
-  r1b is "MAPKKK activation";
-  r2a is "binding of MAPKKK inactivator";
-  r2b is "MAPKKK inactivation";
-  r3a is "binding P-MAPKKK and MAPKK";
-  r3b is "phosphorylation of MAPKK";
-  r4a is "binding MAPKK-Pase and P-MAPKK";
-  r4b is "dephosphorylation of P-MAPKK";
-  r5a is "binding P-MAPKKK and P-MAPKK";
-  r5b is "phosphorylation of P-MAPKK";
-  r6a is "binding MAPKK-Pase and PP-MAPKK";
-  r6b is "dephosphorylation of PP-MAPKK";
-  r7a is "binding MAPK and PP-MAPKK";
-  r7b is "phosphorylation of MAPK";
-  r8a is "binding MAPK-Pase and P-MAPK";
-  r8b is "dephosphorylation of P-MAPK";
-  r9a is "binding PP-MAPKK and P-MAPK";
-  r9b is "phosphorylation of P-MAPK";
-  r10a is "binding MAPK-Pase and PP-MAPK";
-  r10b is "dephosphorylation of PP-MAPK";
-
-  // CV terms:
-  E1 hypernym "http://identifiers.org/interpro/IPR003577"
-  KKK hypernym "http://identifiers.org/uniprot/P12965"
-  P_KKK hypernym "http://identifiers.org/uniprot/P12965"
-  KK hypernym "http://identifiers.org/uniprot/Q05116"
-  P_KK hypernym "http://identifiers.org/uniprot/Q05116"
-  PP_KK hypernym "http://identifiers.org/uniprot/Q05116"
-  K hypernym "http://identifiers.org/uniprot/P26696"
-  P_K hypernym "http://identifiers.org/uniprot/P26696"
-  PP_K hypernym "http://identifiers.org/uniprot/P26696"
-  KPase identity "http://identifiers.org/uniprot/Q90W58"
-  E1_KKK part "http://identifiers.org/uniprot/P12965",
-              "http://identifiers.org/interpro/IPR003577"
-  E2_P_KKK part "http://identifiers.org/uniprot/P12965"
-  P_KKK_KK part "http://identifiers.org/uniprot/P12965",
-                "http://identifiers.org/uniprot/Q05116"
-  P_KKK_P_KK part "http://identifiers.org/uniprot/P12965",
-                  "http://identifiers.org/uniprot/Q05116"
-  PP_KK_K part "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  PP_KK_P_K part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  KKPase_PP_KK part "http://identifiers.org/uniprot/Q05116"
-  KKPase_P_KK part "http://identifiers.org/uniprot/Q05116"
-  KPase_PP_K part "http://identifiers.org/uniprot/Q90W58",
-                  "http://identifiers.org/uniprot/P26696"
-  KPase_P_K part "http://identifiers.org/uniprot/P26696",
-                 "http://identifiers.org/uniprot/Q90W58"
-  r1a homolog "http://identifiers.org/reactome/REACT_996"
-  r1a hypernym "http://identifiers.org/go/GO:0031435"
-  r1b homolog "http://identifiers.org/reactome/REACT_525"
-  r1b hypernym "http://identifiers.org/ec-code/2.7.11.1",
-               "http://identifiers.org/go/GO:0008349",
-               "http://identifiers.org/go/GO:0000185"
-  r2a hypernym "http://identifiers.org/go/GO:0031435"
-  r2b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0051390",
-               "http://identifiers.org/go/GO:0006470"
-  r3a homolog "http://identifiers.org/reactome/REACT_143"
-  r3a hypernym "http://identifiers.org/go/GO:0031434",
-               "http://identifiers.org/go/GO:0031435"
-  r3b homolog "http://identifiers.org/reactome/REACT_614"
-  r3b hypernym "http://identifiers.org/ec-code/2.7.11.25",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004709"
-  r4a hypernym "http://identifiers.org/go/GO:0031434"
-  r4b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  r5a homolog "http://identifiers.org/reactome/REACT_143"
-  r5a hypernym "http://identifiers.org/go/GO:0031435",
-               "http://identifiers.org/go/GO:0031434"
-  r5b homolog "http://identifiers.org/reactome/REACT_614"
-  r5b hypernym "http://identifiers.org/ec-code/2.7.11.25",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004709",
-               "http://identifiers.org/go/GO:0000186"
-  r6a hypernym "http://identifiers.org/go/GO:0031434"
-  r6b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470",
-               "http://identifiers.org/go/GO:0051389"
-  r7a version "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  r7a hypernym "http://identifiers.org/go/GO:0031434",
-               "http://identifiers.org/go/GO:0051019"
-  r7b version "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  r7b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004708"
-  r8a hypernym "http://identifiers.org/go/GO:0051019"
-  r8b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  r9a version "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  r9a hypernym "http://identifiers.org/go/GO:0051019",
-               "http://identifiers.org/go/GO:0031434"
-  r9b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004708",
-               "http://identifiers.org/go/GO:0000187"
-  r9b version "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  r10a hypernym "http://identifiers.org/go/GO:0051019"
-  r10b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470",
-                "http://identifiers.org/go/GO:0000188"
-end
-
-BIOMD0000000009 is "Huang1996 - Ultrasensitivity in MAPK cascade"
-
-BIOMD0000000009 model_entity_is "http://identifiers.org/biomodels.db/MODEL6615048798"
-BIOMD0000000009 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000009"
-BIOMD0000000009 description "http://identifiers.org/pubmed/8816754"
-BIOMD0000000009 homolog "http://identifiers.org/reactome/REACT_634"
-BIOMD0000000009 hypernym "http://identifiers.org/go/GO:0000165"
-BIOMD0000000009 taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000010.txt b/BioModelsRAG/data/BIOMD0000000010.txt
deleted file mode 100644
index f0f5bc9197738de17664c6570d17e07feed098fd..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000010.txt
+++ /dev/null
@@ -1,140 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000010()
-
-  // Compartments and Species:
-  compartment uVol;
-  species MKKK in uVol, MKKK_P in uVol, MKK in uVol, MKK_P in uVol, MKK_PP in uVol;
-  species MAPK in uVol, MAPK_P in uVol, MAPK_PP in uVol;
-
-  // Reactions:
-  J0: MKKK => MKKK_P; uVol*J0_V1*MKKK/((1 + (MAPK_PP/J0_Ki)^J0_n)*(J0_K1 + MKKK));
-  J1: MKKK_P => MKKK; uVol*J1_V2*MKKK_P/(J1_KK2 + MKKK_P);
-  J2: MKK => MKK_P; uVol*J2_k3*MKKK_P*MKK/(J2_KK3 + MKK);
-  J3: MKK_P => MKK_PP; uVol*J3_k4*MKKK_P*MKK_P/(J3_KK4 + MKK_P);
-  J4: MKK_PP => MKK_P; uVol*J4_V5*MKK_PP/(J4_KK5 + MKK_PP);
-  J5: MKK_P => MKK; uVol*J5_V6*MKK_P/(J5_KK6 + MKK_P);
-  J6: MAPK => MAPK_P; uVol*J6_k7*MKK_PP*MAPK/(J6_KK7 + MAPK);
-  J7: MAPK_P => MAPK_PP; uVol*J7_k8*MKK_PP*MAPK_P/(J7_KK8 + MAPK_P);
-  J8: MAPK_PP => MAPK_P; uVol*J8_V9*MAPK_PP/(J8_KK9 + MAPK_PP);
-  J9: MAPK_P => MAPK; uVol*J9_V10*MAPK_P/(J9_KK10 + MAPK_P);
-
-  // Species initializations:
-  MKKK = 90;
-  MKKK_P = 10;
-  MKK = 280;
-  MKK_P = 10;
-  MKK_PP = 10;
-  MAPK = 280;
-  MAPK_P = 10;
-  MAPK_PP = 10;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  J0_V1 = 2.5;
-  J0_Ki = 9;
-  J0_n = 1;
-  J0_K1 = 10;
-  J1_V2 = 0.25;
-  J1_KK2 = 8;
-  J2_k3 = 0.025;
-  J2_KK3 = 15;
-  J3_k4 = 0.025;
-  J3_KK4 = 15;
-  J4_V5 = 0.75;
-  J4_KK5 = 15;
-  J5_V6 = 0.75;
-  J5_KK6 = 15;
-  J6_k7 = 0.025;
-  J6_KK7 = 15;
-  J7_k8 = 0.025;
-  J7_KK8 = 15;
-  J8_V9 = 0.5;
-  J8_KK9 = 15;
-  J9_V10 = 0.5;
-  J9_KK10 = 15;
-
-  // Other declarations:
-  const uVol;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole";
-  MKKK is "Mos";
-  MKKK_P is "Mos-P";
-  MKK is "Mek1";
-  MKK_P is "Mek1-P";
-  MKK_PP is "Mek1-PP";
-  MAPK is "Erk2";
-  MAPK_P is "Erk2-P";
-  MAPK_PP is "Erk2-PP";
-  J0 is "MAPKKK activation";
-  J1 is "MAPKKK inactivation";
-  J2 is "phosphorylation of MAPKK";
-  J3 is "phosphorylation of MAPKK-P";
-  J4 is "dephosphorylation of MAPKK-PP";
-  J5 is "dephosphorylation of MAPKK-P";
-  J6 is "phosphorylation of MAPK";
-  J7 is "phosphorylation of MAPK-P";
-  J8 is "dephosphorylation of MAPK-PP";
-  J9 is "dephosphorylation of MAPK-P";
-
-  // CV terms:
-  MKKK hypernym "http://identifiers.org/uniprot/P09560"
-  MKKK_P hypernym "http://identifiers.org/uniprot/P09560"
-  MKK hypernym "http://identifiers.org/uniprot/Q05116"
-  MKK_P hypernym "http://identifiers.org/uniprot/Q05116"
-  MKK_PP hypernym "http://identifiers.org/uniprot/Q05116"
-  MAPK hypernym "http://identifiers.org/uniprot/P26696"
-  MAPK_P hypernym "http://identifiers.org/uniprot/P26696"
-  MAPK_PP hypernym "http://identifiers.org/uniprot/P26696"
-  J0 homolog "http://identifiers.org/reactome/REACT_525"
-  J0 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-              "http://identifiers.org/go/GO:0000185",
-              "http://identifiers.org/go/GO:0008349"
-  J1 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0051390",
-              "http://identifiers.org/go/GO:0006470"
-  J2 homolog "http://identifiers.org/reactome/REACT_614"
-  J2 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-              "http://identifiers.org/go/GO:0004709",
-              "http://identifiers.org/go/GO:0006468"
-  J3 homolog "http://identifiers.org/reactome/REACT_614"
-  J3 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-              "http://identifiers.org/go/GO:0000186",
-              "http://identifiers.org/go/GO:0006468",
-              "http://identifiers.org/go/GO:0004709"
-  J4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470",
-              "http://identifiers.org/go/GO:0051389"
-  J5 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-  J6 version "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  J6 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0006468"
-  J7 version "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  J7 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0006468",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0000187"
-  J8 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0000188",
-              "http://identifiers.org/go/GO:0006470"
-  J9 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-end
-
-BIOMD0000000010 is "Kholodenko2000 - Ultrasensitivity and negative feedback bring oscillations in MAPK cascade"
-
-BIOMD0000000010 model_entity_is "http://identifiers.org/biomodels.db/MODEL6615119181"
-BIOMD0000000010 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000010"
-BIOMD0000000010 description "http://identifiers.org/pubmed/10712587"
-BIOMD0000000010 hypernym "http://identifiers.org/go/GO:0000165"
-BIOMD0000000010 homolog "http://identifiers.org/reactome/REACT_634"
-BIOMD0000000010 taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000011.txt b/BioModelsRAG/data/BIOMD0000000011.txt
deleted file mode 100644
index b11b2a260f9b44c2dce717b1ecffd22f2601b090..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000011.txt
+++ /dev/null
@@ -1,272 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MAPK_in_Solution()
-
-  // Compartments and Species:
-  compartment Cytoplasm;
-  substanceOnly species MAPK in Cytoplasm, MAPKMEKpp in Cytoplasm, MAPKp in Cytoplasm;
-  substanceOnly species MAPKPH in Cytoplasm, MAPKpMAPKPH in Cytoplasm, MAPKpMEKpp in Cytoplasm;
-  substanceOnly species MAPKpp in Cytoplasm, MAPKppMAPKPH in Cytoplasm, MEK in Cytoplasm;
-  substanceOnly species MEKp in Cytoplasm, MEKPH in Cytoplasm, MEKpMEKPH in Cytoplasm;
-  substanceOnly species MEKpp in Cytoplasm, MEKppMEKPH in Cytoplasm, MEKpRAFp in Cytoplasm;
-  substanceOnly species MEKRAFp in Cytoplasm, RAF in Cytoplasm, RAFK in Cytoplasm;
-  substanceOnly species RAFp in Cytoplasm, RAFPH in Cytoplasm, RAFpRAFPH in Cytoplasm;
-  substanceOnly species RAFRAFK in Cytoplasm;
-
-  // Reactions:
-  Reaction1: RAF + RAFK => RAFRAFK; Reaction1_a1*RAF*RAFK;
-  Reaction2: RAFRAFK => RAF + RAFK; Reaction2_d1*RAFRAFK;
-  Reaction3: RAFRAFK => RAFK + RAFp; Reaction3_k1*RAFRAFK;
-  Reaction4: RAFp + RAFPH => RAFpRAFPH; Reaction4_a2*RAFp*RAFPH;
-  Reaction5: RAFpRAFPH => RAFp + RAFPH; Reaction5_d2*RAFpRAFPH;
-  Reaction6: RAFpRAFPH => RAF + RAFPH; Reaction6_k2*RAFpRAFPH;
-  Reaction7: MEK + RAFp => MEKRAFp; Reaction7_a3*MEK*RAFp;
-  Reaction8: MEKRAFp => MEK + RAFp; Reaction8_d3*MEKRAFp;
-  Reaction9: MEKRAFp => MEKp + RAFp; Reaction9_k3*MEKRAFp;
-  Reaction10: MEKp + MEKPH => MEKpMEKPH; Reaction10_a4*MEKp*MEKPH;
-  Reaction11: MEKpMEKPH => MEKp + MEKPH; Reaction11_d4*MEKpMEKPH;
-  Reaction12: MEKpMEKPH => MEK + MEKPH; Reaction12_k4*MEKpMEKPH;
-  Reaction13: MEKp + RAFp => MEKpRAFp; Reaction13_a5*MEKp*RAFp;
-  Reaction14: MEKpRAFp => MEKp + RAFp; Reaction14_d5*MEKpRAFp;
-  Reaction15: MEKpRAFp => MEKpp + RAFp; Reaction15_k5*MEKpRAFp;
-  Reaction16: MEKPH + MEKpp => MEKppMEKPH; Reaction16_a6*MEKPH*MEKpp;
-  Reaction17: MEKppMEKPH => MEKPH + MEKpp; Reaction17_d6*MEKppMEKPH;
-  Reaction18: MEKppMEKPH => MEKp + MEKPH; Reaction18_k6*MEKppMEKPH;
-  Reaction19: MAPK + MEKpp => MAPKMEKpp; Reaction19_a7*MAPK*MEKpp;
-  Reaction20: MAPKMEKpp => MAPK + MEKpp; Reaction20_d7*MAPKMEKpp;
-  Reaction21: MAPKMEKpp => MAPKp + MEKpp; Reaction21_k7*MAPKMEKpp;
-  Reaction22: MAPKp + MAPKPH => MAPKpMAPKPH; Reaction22_a8*MAPKp*MAPKPH;
-  Reaction23: MAPKpMAPKPH => MAPKp + MAPKPH; Reaction23_d8*MAPKpMAPKPH;
-  Reaction24: MAPKpMAPKPH => MAPK + MAPKPH; Reaction24_k8*MAPKpMAPKPH;
-  Reaction25: MAPKp + MEKpp => MAPKpMEKpp; Reaction25_a9*MAPKp*MEKpp;
-  Reaction26: MAPKpMEKpp => MAPKp + MEKpp; Reaction26_d9*MAPKpMEKpp;
-  Reaction27: MAPKpMEKpp => MAPKpp + MEKpp; Reaction27_k9*MAPKpMEKpp;
-  Reaction28: MAPKPH + MAPKpp => MAPKppMAPKPH; Reaction28_a10*MAPKPH*MAPKpp;
-  Reaction29: MAPKppMAPKPH => MAPKPH + MAPKpp; Reaction29_d10*MAPKppMAPKPH;
-  Reaction30: MAPKppMAPKPH => MAPKp + MAPKPH; Reaction30_k10*MAPKppMAPKPH;
-
-  // Species initializations:
-  MAPK = 0.4/Cytoplasm;
-  MAPKMEKpp = 0;
-  MAPKp = 0;
-  MAPKPH = 0.3/Cytoplasm;
-  MAPKpMAPKPH = 0;
-  MAPKpMEKpp = 0;
-  MAPKpp = 0;
-  MAPKppMAPKPH = 0;
-  MEK = 0.2/Cytoplasm;
-  MEKp = 0;
-  MEKPH = 0.2/Cytoplasm;
-  MEKpMEKPH = 0;
-  MEKpp = 0;
-  MEKppMEKPH = 0;
-  MEKpRAFp = 0;
-  MEKRAFp = 0;
-  RAF = 0.3/Cytoplasm;
-  RAFK = 0.2/Cytoplasm;
-  RAFp = 0;
-  RAFPH = 0.3/Cytoplasm;
-  RAFpRAFPH = 0;
-  RAFRAFK = 0;
-
-  // Compartment initializations:
-  Cytoplasm = 1;
-
-  // Variable initializations:
-  Reaction1_a1 = 1;
-  Reaction2_d1 = 0.4;
-  Reaction3_k1 = 0.1;
-  Reaction4_a2 = 0.5;
-  Reaction5_d2 = 0.5;
-  Reaction6_k2 = 0.1;
-  Reaction7_a3 = 3.3;
-  Reaction8_d3 = 0.42;
-  Reaction9_k3 = 0.1;
-  Reaction10_a4 = 10;
-  Reaction11_d4 = 0.8;
-  Reaction12_k4 = 0.1;
-  Reaction13_a5 = 3.3;
-  Reaction14_d5 = 0.4;
-  Reaction15_k5 = 0.1;
-  Reaction16_a6 = 10;
-  Reaction17_d6 = 0.8;
-  Reaction18_k6 = 0.1;
-  Reaction19_a7 = 20;
-  Reaction20_d7 = 0.6;
-  Reaction21_k7 = 0.1;
-  Reaction22_a8 = 5;
-  Reaction23_d8 = 0.4;
-  Reaction24_k8 = 0.1;
-  Reaction25_a9 = 20;
-  Reaction26_d9 = 0.6;
-  Reaction27_k9 = 0.1;
-  Reaction28_a10 = 5;
-  Reaction29_d10 = 0.4;
-  Reaction30_k10 = 0.1;
-
-  // Other declarations:
-  const Cytoplasm;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  MAPKMEKpp is "MAPK_MEK-PP";
-  MAPKp is "MAPK-P";
-  MAPKPH is "MAPK phosphatase";
-  MAPKpMAPKPH is "MAPK-P_MAPKPase";
-  MAPKpMEKpp is "MAPK-P_MEK-PP";
-  MAPKpp is "MAPK-PP";
-  MAPKppMAPKPH is "MAPK-PP_MAPKPase";
-  MEKp is "MEK-P";
-  MEKPH is "MEK phosphatase";
-  MEKpMEKPH is "MEK-P_MEKPase";
-  MEKpp is "MEK-PP";
-  MEKppMEKPH is "MEK-PP_MEKPase";
-  MEKpRAFp is "MEK-P_RAF-P";
-  MEKRAFp is "MEK_RAF-P";
-  RAFp is "RAF-P";
-  RAFPH is "RAF phosphatase";
-  RAFpRAFPH is "RAF-P_RAFPase";
-  RAFRAFK is "RAF_RAFK";
-  Reaction1 is "binding of RAF and RAFK";
-  Reaction2 is "dissociation of RAF_RAFK";
-  Reaction3 is "phosphorylation of RAF";
-  Reaction4 is "binding of RAF-P and RAF phosphatase";
-  Reaction5 is "dissociation of RAF-P_RAFPase";
-  Reaction6 is "dephosphorylation of RAF-P";
-  Reaction7 is "binding of MEK and RAF-P";
-  Reaction8 is "dissociation of MEK_RAF-P";
-  Reaction9 is "phosphorylation of MEK";
-  Reaction10 is "binding of MEK-P and MEK phosphatase";
-  Reaction11 is "dissociation of MEK-P_MEKPase";
-  Reaction12 is "dephosphorylation of MEK-P";
-  Reaction13 is "binding of MEK-P and RAF-P";
-  Reaction14 is "dissociation of MEK-P_RAF-P";
-  Reaction15 is "phosphorylation of MEK-P";
-  Reaction16 is "binding of MEK-PP and MEK phosphatase";
-  Reaction17 is "dissociation of MEK-PP_MEKPase";
-  Reaction18 is "dephosphorylation of MEK-PP";
-  Reaction19 is "binding of MAPK and MEK-PP";
-  Reaction20 is "dissociation of MAPK_MEK-PP";
-  Reaction21 is "phosphorylation of MAPK";
-  Reaction22 is "binding of MAPK-P and MAPK phosphatase";
-  Reaction23 is "dissociation of MAPK-P_MAPKPase";
-  Reaction24 is "dephosphorylation of MAPK-P";
-  Reaction25 is "binding of MAPK-P and MEK-PP";
-  Reaction26 is "dissociation of MAPK-P_MEK-PP";
-  Reaction27 is "phosphorylation of MAPK-P";
-  Reaction28 is "binding of MAPK-PP and MAPK phosphatase";
-  Reaction29 is "dissociation of MAPK-PP_MAPKPase";
-  Reaction30 is "dephosphorylation of MAPK-PP";
-
-  // CV terms:
-  Cytoplasm identity "http://identifiers.org/obo.go/GO:0005737"
-  MAPK hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKMEKpp part "http://identifiers.org/uniprot/P26696",
-                 "http://identifiers.org/uniprot/Q05116"
-  MAPKp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKPH identity "http://identifiers.org/uniprot/Q90W58"
-  MAPKpMAPKPH part "http://identifiers.org/uniprot/P26696",
-                   "http://identifiers.org/uniprot/Q90W58"
-  MAPKpMEKpp part "http://identifiers.org/uniprot/Q05116",
-                  "http://identifiers.org/uniprot/P26696"
-  MAPKpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKppMAPKPH part "http://identifiers.org/uniprot/P26696",
-                    "http://identifiers.org/uniprot/Q90W58"
-  MEK hypernym "http://identifiers.org/uniprot/Q05116"
-  MEKp hypernym "http://identifiers.org/uniprot/Q05116"
-  MEKpMEKPH part "http://identifiers.org/uniprot/Q05116"
-  MEKpp hypernym "http://identifiers.org/uniprot/Q05116"
-  MEKppMEKPH part "http://identifiers.org/uniprot/Q05116"
-  MEKpRAFp part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  MEKRAFp part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116"
-  RAF hypernym "http://identifiers.org/uniprot/P09560"
-  RAFK hypernym "http://identifiers.org/interpro/IPR003577"
-  RAFp hypernym "http://identifiers.org/uniprot/P09560"
-  RAFpRAFPH part "http://identifiers.org/uniprot/P09560"
-  RAFRAFK part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/interpro/IPR003577"
-  Reaction1 homolog "http://identifiers.org/reactome/REACT_996"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0031435"
-  Reaction2 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction3 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                     "http://identifiers.org/obo.go/GO:0008349",
-                     "http://identifiers.org/obo.go/GO:0000185",
-                     "http://identifiers.org/obo.go/GO:0006468"
-  Reaction4 hypernym "http://identifiers.org/obo.go/GO:0031435"
-  Reaction5 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction6 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0051390",
-                     "http://identifiers.org/obo.go/GO:0006470"
-  Reaction7 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                     "http://identifiers.org/obo.go/GO:0031435"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction9 homolog "http://identifiers.org/reactome/REACT_614"
-  Reaction9 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-                     "http://identifiers.org/obo.go/GO:0004709",
-                     "http://identifiers.org/obo.go/GO:0006468"
-  Reaction10 hypernym "http://identifiers.org/obo.go/GO:0031434"
-  Reaction11 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction12 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0006470"
-  Reaction13 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction13 hypernym "http://identifiers.org/obo.go/GO:0031435",
-                      "http://identifiers.org/obo.go/GO:0031434"
-  Reaction14 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction15 homolog "http://identifiers.org/reactome/REACT_614"
-  Reaction15 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-                      "http://identifiers.org/obo.go/GO:0006468",
-                      "http://identifiers.org/obo.go/GO:0004709",
-                      "http://identifiers.org/obo.go/GO:0000186"
-  Reaction16 hypernym "http://identifiers.org/obo.go/GO:0031434"
-  Reaction17 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction18 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0051389",
-                      "http://identifiers.org/obo.go/GO:0006470"
-  Reaction19 homolog "http://identifiers.org/reactome/REACT_495",
-                     "http://identifiers.org/reactome/REACT_1780"
-  Reaction19 identity "http://identifiers.org/obo.go/GO:0051019",
-                      "http://identifiers.org/obo.go/GO:0031434"
-  Reaction20 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction21 homolog "http://identifiers.org/reactome/REACT_2247",
-                     "http://identifiers.org/reactome/REACT_136"
-  Reaction21 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                      "http://identifiers.org/obo.go/GO:0006468",
-                      "http://identifiers.org/obo.go/GO:0004708"
-  Reaction22 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  Reaction23 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction24 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0006470"
-  Reaction25 homolog "http://identifiers.org/reactome/REACT_495",
-                     "http://identifiers.org/reactome/REACT_1780"
-  Reaction25 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                      "http://identifiers.org/obo.go/GO:0031434"
-  Reaction26 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction27 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                      "http://identifiers.org/obo.go/GO:0000187",
-                      "http://identifiers.org/obo.go/GO:0006468",
-                      "http://identifiers.org/obo.go/GO:0004708"
-  Reaction27 homolog "http://identifiers.org/reactome/REACT_136",
-                     "http://identifiers.org/reactome/REACT_2247"
-  Reaction28 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  Reaction29 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction30 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0006470",
-                      "http://identifiers.org/obo.go/GO:0000188"
-end
-
-MAPK_in_Solution is "Levchenko2000_MAPK_noScaffold"
-
-MAPK_in_Solution model_entity_is "http://identifiers.org/biomodels.db/MODEL6615234250"
-MAPK_in_Solution model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000011"
-MAPK_in_Solution description "http://identifiers.org/pubmed/10823939"
-MAPK_in_Solution origin "http://identifiers.org/biomodels.db/BIOMD0000000009",
-                        "http://identifiers.org/pubmed/6501300",
-                        "http://identifiers.org/pubmed/6947258"
-MAPK_in_Solution homolog "http://identifiers.org/reactome/REACT_634"
-MAPK_in_Solution hypernym "http://identifiers.org/obo.go/GO:0000165"
-MAPK_in_Solution taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000012.txt b/BioModelsRAG/data/BIOMD0000000012.txt
deleted file mode 100644
index 985a9d8b9c8d0c7b5514d47422df2bc5b3f8e634..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000012.txt
+++ /dev/null
@@ -1,161 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000012()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species PX in cell, PY in cell, PZ in cell, X in cell, Y in cell;
-  substanceOnly species Z in cell;
-
-  // Assignment Rules:
-  beta := tau_mRNA/tau_prot;
-  alpha0 := a0_tr*eff*tau_prot/(ln(2)*KM);
-  a0_tr := ps_0*60;
-  alpha := a_tr*eff*tau_prot/(ln(2)*KM);
-  a_tr := (ps_a - ps_0)*60;
-  t_ave := tau_mRNA/ln(2);
-  kd_mRNA := ln(2)/tau_mRNA;
-  kd_prot := ln(2)/tau_prot;
-  k_tl := eff/t_ave;
-
-  // Reactions:
-  Reaction1: X => ; kd_mRNA*X;
-  Reaction2: Y => ; kd_mRNA*Y;
-  Reaction3: Z => ; kd_mRNA*Z;
-  Reaction4:  => PX; k_tl*X;
-  Reaction5:  => PY; k_tl*Y;
-  Reaction6:  => PZ; k_tl*Z;
-  Reaction7: PX => ; kd_prot*PX;
-  Reaction8: PY => ; kd_prot*PY;
-  Reaction9: PZ => ; kd_prot*PZ;
-  Reaction10:  => X; a0_tr + a_tr*KM^n/(KM^n + PZ^n);
-  Reaction11:  => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n);
-  Reaction12:  => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n);
-
-  // Species initializations:
-  PX = 0;
-  PY = 0;
-  PZ = 0;
-  X = 0;
-  Y = 20/cell;
-  Z = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  tau_mRNA = 2;
-  tau_prot = 10;
-  eff = 20;
-  KM = 40;
-  n = 2;
-  ps_a = 0.5;
-  ps_0 = 0.0005;
-
-  // Other declarations:
-  var beta, alpha0, a0_tr, alpha, a_tr, t_ave, kd_mRNA, kd_prot, k_tl;
-  const cell, tau_mRNA, tau_prot, eff, KM, n, ps_a, ps_0;
-
-  // Unit definitions:
-  unit volume = 1e-15 litre;
-  unit substance = item;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  volume is "cubic microns";
-  substance is "item";
-  time_unit is "minute";
-  PX is "LacI protein";
-  PY is "TetR protein";
-  PZ is "cI protein";
-  X is "LacI mRNA";
-  Y is "TetR mRNA";
-  Z is "cI mRNA";
-  tau_mRNA is "mRNA half life";
-  tau_prot is "protein half life";
-  eff is "translation efficiency";
-  t_ave is "average mRNA life time";
-  ps_a is "tps_active";
-  ps_0 is "tps_repr";
-  Reaction1 is "degradation of LacI transcripts";
-  Reaction2 is "degradation of TetR transcripts";
-  Reaction3 is "degradation of CI transcripts";
-  Reaction4 is "translation of LacI";
-  Reaction5 is "translation of TetR";
-  Reaction6 is "translation of CI";
-  Reaction7 is "degradation of LacI";
-  Reaction8 is "degradation of TetR";
-  Reaction9 is "degradation of CI";
-  Reaction10 is "transcription of LacI";
-  Reaction11 is "transcription of TetR";
-  Reaction12 is "transcription of CI";
-
-  // SBO terms:
-  cell.sboTerm = 290
-  PX.sboTerm = 252
-  PY.sboTerm = 252
-  PZ.sboTerm = 252
-  X.sboTerm = 250
-  Y.sboTerm = 250
-  Z.sboTerm = 250
-  tau_mRNA.sboTerm = 332
-  tau_prot.sboTerm = 332
-  alpha0.sboTerm = 485
-  a0_tr.sboTerm = 485
-  KM.sboTerm = 288
-  alpha.sboTerm = 186
-  a_tr.sboTerm = 186
-  n.sboTerm = 190
-  t_ave.sboTerm = 348
-  kd_mRNA.sboTerm = 356
-  kd_prot.sboTerm = 356
-  k_tl.sboTerm = 16
-  ps_a.sboTerm = 186
-  ps_0.sboTerm = 485
-  Reaction1.sboTerm = 179
-  Reaction2.sboTerm = 179
-  Reaction3.sboTerm = 179
-  Reaction4.sboTerm = 184
-  Reaction5.sboTerm = 184
-  Reaction6.sboTerm = 184
-  Reaction7.sboTerm = 179
-  Reaction8.sboTerm = 179
-  Reaction9.sboTerm = 179
-  Reaction10.sboTerm = 183
-  Reaction11.sboTerm = 183
-  Reaction12.sboTerm = 183
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  PX identity "http://identifiers.org/uniprot/P03023"
-  PY identity "http://identifiers.org/uniprot/P04483"
-  PZ identity "http://identifiers.org/uniprot/P03034"
-  X hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  X encodement "http://identifiers.org/uniprot/P03023"
-  Y hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  Y encodement "http://identifiers.org/uniprot/P04483"
-  Z hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  Z encodement "http://identifiers.org/uniprot/P03034"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction2 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction3 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction4 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction5 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction6 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction9 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction10 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction11 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction12 hypernym "http://identifiers.org/obo.go/GO:0006351"
-end
-
-BIOMD0000000012 is "Elowitz2000 - Repressilator"
-
-BIOMD0000000012 model_entity_is "http://identifiers.org/biomodels.db/MODEL6615351360"
-BIOMD0000000012 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000012"
-BIOMD0000000012 description "http://identifiers.org/pubmed/10659856"
-BIOMD0000000012 taxon "http://identifiers.org/taxonomy/562"
-BIOMD0000000012 hypernym "http://identifiers.org/obo.go/GO:0040029"
diff --git a/BioModelsRAG/data/BIOMD0000000013.txt b/BioModelsRAG/data/BIOMD0000000013.txt
deleted file mode 100644
index aa0b5329c530fd283e752a287e406d949769143a..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000013.txt
+++ /dev/null
@@ -1,264 +0,0 @@
-// Created by libAntimony v2.13.0
-model *untitled()
-
-  // Compartments and Species:
-  compartment chloroplast, cytosol;
-  species $x_CO2 in chloroplast, RuBP_ch in chloroplast, PGA_ch in chloroplast;
-  species ATP_ch in chloroplast, BPGA_ch in chloroplast, $x_NADPH_ch in chloroplast;
-  species GAP_ch in chloroplast, Pi_ch in chloroplast, DHAP_ch in chloroplast;
-  species FBP_ch in chloroplast, F6P_ch in chloroplast, E4P_ch in chloroplast;
-  species X5P_ch in chloroplast, SBP_ch in chloroplast, S7P_ch in chloroplast;
-  species R5P_ch in chloroplast, Ru5P_ch in chloroplast, $x_Pi_cyt in cytosol;
-  species $x_GAP_cyt in cytosol, G6P_ch in chloroplast, $x_NADP_ch in chloroplast;
-  species $x_PGA_cyt in cytosol, ADP_ch in chloroplast, $x_DHAP_cyt in cytosol;
-  species $x_Proton_ch in chloroplast, G1P_ch in chloroplast, $x_Starch_ch in chloroplast;
-
-  // Reactions:
-  E1: RuBP_ch + $x_CO2 => 2 PGA_ch; Light_on*E1_Rbco_vm*RuBP_ch*chloroplast/(RuBP_ch + E1_Rbco_km*(1 + PGA_ch/E1_Rbco_KiPGA + FBP_ch/E1_Rbco_KiFBP + SBP_ch/E1_Rbco_KiSBP + Pi_ch/E1_Rbco_KiPi + x_NADPH_ch/E1_Rbco_KiNADPH));
-  E2: PGA_ch + ATP_ch => BPGA_ch + ADP_ch; Light_on*E2_PGK_v*chloroplast*(PGA_ch*ATP_ch - BPGA_ch*ADP_ch/E2_q2);
-  E3: $x_NADPH_ch + BPGA_ch + $x_Proton_ch => $x_NADP_ch + GAP_ch + Pi_ch; Light_on*E3_G3Pdh_v*chloroplast*(BPGA_ch*x_NADPH_ch*x_Proton_ch - x_NADP_ch*GAP_ch*Pi_ch/E3_q3);
-  E4: GAP_ch -> DHAP_ch; chloroplast*E4_TPI_v*(GAP_ch - DHAP_ch/E4_q4);
-  E5: GAP_ch + DHAP_ch -> FBP_ch; E5_F_Aldo_v*chloroplast*(DHAP_ch*GAP_ch - FBP_ch/E5_q5);
-  E6: FBP_ch => F6P_ch + Pi_ch; Light_on*E6_FBPase_ch_vm*FBP_ch*chloroplast/(FBP_ch + E6_FBPase_ch_km*(1 + F6P_ch/E6_FBPase_ch_KiF6P + Pi_ch/E6_FBPase_ch_KiPi));
-  E7: GAP_ch + F6P_ch -> X5P_ch + E4P_ch; chloroplast*E7_F_TKL_v*(F6P_ch*GAP_ch - E4P_ch*X5P_ch/E7_q7);
-  E8: DHAP_ch + E4P_ch -> SBP_ch; chloroplast*E8_E_Aldo_v*(E4P_ch*DHAP_ch - SBP_ch/E8_q8);
-  E9: SBP_ch => Pi_ch + S7P_ch; Light_on*E9_SBPase_ch_vm*SBP_ch*chloroplast/(SBP_ch + E9_SBPase_ch_km*(1 + Pi_ch/E9_SBPase_ch_KiPi));
-  E10: S7P_ch + GAP_ch -> R5P_ch + X5P_ch; chloroplast*E10_G_TKL_v*(GAP_ch*S7P_ch - X5P_ch*R5P_ch/E10_q10);
-  E11: R5P_ch -> Ru5P_ch; E11_R5Piso_v*chloroplast*(R5P_ch - Ru5P_ch/E11_q11);
-  E12: X5P_ch -> Ru5P_ch; chloroplast*E12_X5Pepi_v*(X5P_ch - Ru5P_ch/E12_q12);
-  E13: Ru5P_ch + ATP_ch => RuBP_ch + ADP_ch; Light_on*E13_Ru5Pk_ch_vm*Ru5P_ch*chloroplast*ATP_ch/((Ru5P_ch + E13_Ru5Pk_ch_km1*(1 + PGA_ch/E13_Ru5Pk_ch_KiPGA + RuBP_ch/E13_Ru5Pk_ch_KiRuBP + Pi_ch/E13_Ru5Pk_ch_KiPi))*(ATP_ch*(1 + ADP_ch/E13_Ru5Pk_ch_KiADP1) + E13_Ru5Pk_ch_km2*(1 + ADP_ch/E13_Ru5Pk_ch_KiADP2)));
-  E14: F6P_ch -> G6P_ch; E14_PGI_v*chloroplast*(F6P_ch - G6P_ch/E14_q14);
-  E15: G6P_ch -> G1P_ch; E15_PGM_v*chloroplast*(G6P_ch - G1P_ch/E15_q15);
-  light_reaction: Pi_ch + ADP_ch => ATP_ch; Light_on*light_reaction_LR_vm*ADP_ch*Pi_ch*chloroplast/((ADP_ch + light_reaction_LR_kmADP)*(Pi_ch + light_reaction_LR_kmPi));
-  E16: ATP_ch + G1P_ch => $x_Starch_ch + ADP_ch + 2 Pi_ch; E16_StSyn_vm*G1P_ch*ATP_ch*chloroplast/((G1P_ch + E16_stsyn_ch_km1)*(1 + ADP_ch/E16_stsyn_ch_Ki)*(ATP_ch + E16_stsyn_ch_km2) + E16_stsyn_ch_km2*Pi_ch/(E16_stsyn_ch_ka1*PGA_ch) + E16_stsyn_ch_ka2*F6P_ch + E16_stsyn_ch_ka3*FBP_ch);
-  E17: $x_Starch_ch + Pi_ch => G1P_ch; E17_StPase_Vm*Pi_ch*chloroplast/(Pi_ch + E17_StPase_km*(1 + G1P_ch/E17_StPase_kiG1P));
-  E18_DHAP: $x_Pi_cyt + DHAP_ch => $x_DHAP_cyt + Pi_ch; E18_DHAP_TP_Piap_vm*DHAP_ch*chloroplast/(E18_DHAP_TP_Piap_kDHAP_ch*(1 + (1 + E18_DHAP_TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/E18_DHAP_TP_Piap_kPi_ch + PGA_ch/E18_DHAP_TP_Piap_kPGA_ch + DHAP_ch/E18_DHAP_TP_Piap_kDHAP_ch + GAP_ch/E18_DHAP_TP_Piap_kGAP_ch)));
-  E18_PGA: $x_Pi_cyt + PGA_ch => $x_PGA_cyt + Pi_ch; E18_PGA_PGA_xpMult*E18_PGA_TP_Piap_vm*PGA_ch*chloroplast/(E18_PGA_TP_Piap_kPGA_ch*(1 + (1 + E18_PGA_TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/E18_PGA_TP_Piap_kPi_ch + PGA_ch/E18_PGA_TP_Piap_kPGA_ch + DHAP_ch/E18_PGA_TP_Piap_kDHAP_ch + GAP_ch/E18_PGA_TP_Piap_kGAP_ch)));
-  E18_GAP: $x_Pi_cyt + GAP_ch => $x_GAP_cyt + Pi_ch; E18_GAP_TP_Piap_vm*GAP_ch*chloroplast/(E18_GAP_TP_Piap_kGAP_ch*(1 + (1 + E18_GAP_TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/E18_GAP_TP_Piap_kPi_ch + PGA_ch/E18_GAP_TP_Piap_kPGA_ch + DHAP_ch/E18_GAP_TP_Piap_kDHAP_ch + GAP_ch/E18_GAP_TP_Piap_kGAP_ch)));
-
-  // Species initializations:
-  x_CO2 = 1;
-  RuBP_ch = 0.33644;
-  PGA_ch = 3.35479;
-  ATP_ch = 0.49806;
-  BPGA_ch = 0.14825;
-  x_NADPH_ch = 0.21;
-  GAP_ch = 0.01334;
-  Pi_ch = 1.5662;
-  DHAP_ch = 0.29345;
-  FBP_ch = 0.02776;
-  F6P_ch = 1.36481;
-  E4P_ch = 0.41021;
-  X5P_ch = 0.00363;
-  SBP_ch = 1.56486;
-  S7P_ch = 0.00541;
-  R5P_ch = 0.00599;
-  Ru5P_ch = 0.00235;
-  x_Pi_cyt = 0.5;
-  x_GAP_cyt = 1;
-  G6P_ch = 3.1396;
-  x_NADP_ch = 0.29;
-  x_PGA_cyt = 1;
-  ADP_ch = 0.00149;
-  x_DHAP_cyt = 1;
-  x_Proton_ch = 2.512e-05;
-  G1P_ch = 0.18206;
-  x_Starch_ch = 1;
-
-  // Compartment initializations:
-  chloroplast = 1;
-  cytosol = 1;
-
-  // Variable initializations:
-  Light_on = 1;
-  E1_Rbco_vm = 340;
-  E1_Rbco_km = 0.02;
-  E1_Rbco_KiPGA = 0.84;
-  E1_Rbco_KiFBP = 0.04;
-  E1_Rbco_KiSBP = 0.075;
-  E1_Rbco_KiPi = 0.9;
-  E1_Rbco_KiNADPH = 0.07;
-  E2_PGK_v = 500000000;
-  E2_q2 = 0.00031;
-  E3_G3Pdh_v = 500000000;
-  E3_q3 = 16000000;
-  E4_TPI_v = 500000000;
-  E4_q4 = 22;
-  E5_F_Aldo_v = 500000000;
-  E5_q5 = 7.1;
-  E6_FBPase_ch_vm = 200;
-  E6_FBPase_ch_km = 0.03;
-  E6_FBPase_ch_KiF6P = 0.7;
-  E6_FBPase_ch_KiPi = 12;
-  E7_F_TKL_v = 500000000;
-  E7_q7 = 0.084;
-  E8_E_Aldo_v = 500000000;
-  E8_q8 = 13;
-  E9_SBPase_ch_vm = 40;
-  E9_SBPase_ch_km = 0.013;
-  E9_SBPase_ch_KiPi = 12;
-  E10_G_TKL_v = 500000000;
-  E10_q10 = 0.85;
-  E11_R5Piso_v = 500000000;
-  E11_q11 = 0.4;
-  E12_X5Pepi_v = 500000000;
-  E12_q12 = 0.67;
-  E13_Ru5Pk_ch_vm = 10000;
-  E13_Ru5Pk_ch_km1 = 0.05;
-  E13_Ru5Pk_ch_KiPGA = 2;
-  E13_Ru5Pk_ch_KiRuBP = 0.7;
-  E13_Ru5Pk_ch_KiPi = 4;
-  E13_Ru5Pk_ch_KiADP1 = 2.5;
-  E13_Ru5Pk_ch_km2 = 0.05;
-  E13_Ru5Pk_ch_KiADP2 = 0.4;
-  E14_PGI_v = 500000000;
-  E14_q14 = 2.3;
-  E15_PGM_v = 500000000;
-  E15_q15 = 0.058;
-  light_reaction_LR_vm = 3500;
-  light_reaction_LR_kmADP = 0.014;
-  light_reaction_LR_kmPi = 0.3;
-  E16_StSyn_vm = 40;
-  E16_stsyn_ch_km1 = 0.08;
-  E16_stsyn_ch_Ki = 10;
-  E16_stsyn_ch_km2 = 0.08;
-  E16_stsyn_ch_ka1 = 0.1;
-  E16_stsyn_ch_ka2 = 0.02;
-  E16_stsyn_ch_ka3 = 0.02;
-  E17_StPase_Vm = 40;
-  E17_StPase_km = 0.1;
-  E17_StPase_kiG1P = 0.05;
-  E18_DHAP_TP_Piap_vm = 250;
-  E18_DHAP_TP_Piap_kDHAP_ch = 0.077;
-  E18_DHAP_TP_Piap_kPi_cyt = 0.74;
-  E18_DHAP_TP_Piap_kPi_ch = 0.63;
-  E18_DHAP_TP_Piap_kPGA_ch = 0.25;
-  E18_DHAP_TP_Piap_kGAP_ch = 0.075;
-  E18_PGA_PGA_xpMult = 0.75;
-  E18_PGA_TP_Piap_vm = 250;
-  E18_PGA_TP_Piap_kPGA_ch = 0.25;
-  E18_PGA_TP_Piap_kPi_cyt = 0.74;
-  E18_PGA_TP_Piap_kPi_ch = 0.63;
-  E18_PGA_TP_Piap_kDHAP_ch = 0.077;
-  E18_PGA_TP_Piap_kGAP_ch = 0.075;
-  E18_GAP_TP_Piap_vm = 250;
-  E18_GAP_TP_Piap_kGAP_ch = 0.075;
-  E18_GAP_TP_Piap_kPi_cyt = 0.74;
-  E18_GAP_TP_Piap_kPi_ch = 0.63;
-  E18_GAP_TP_Piap_kPGA_ch = 0.25;
-  E18_GAP_TP_Piap_kDHAP_ch = 0.077;
-
-  // Other declarations:
-  const chloroplast, cytosol, Light_on;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-
-  // Display Names:
-  substance is "mM";
-
-  // CV terms:
-  chloroplast identity "http://identifiers.org/go/GO:0009570"
-  cytosol identity "http://identifiers.org/go/GO:0005829"
-  x_CO2 identity "http://identifiers.org/chebi/CHEBI:16526",
-                 "http://identifiers.org/kegg.compound/C00011"
-  RuBP_ch identity "http://identifiers.org/kegg.compound/C01182"
-  PGA_ch identity "http://identifiers.org/kegg.compound/C00197"
-  ATP_ch identity "http://identifiers.org/chebi/CHEBI:15422",
-                  "http://identifiers.org/kegg.compound/C00002"
-  BPGA_ch identity "http://identifiers.org/kegg.compound/C00236"
-  x_NADPH_ch identity "http://identifiers.org/chebi/CHEBI:16474",
-                      "http://identifiers.org/kegg.compound/C00005"
-  GAP_ch identity "http://identifiers.org/chebi/CHEBI:17138",
-                  "http://identifiers.org/kegg.compound/C00118"
-  Pi_ch identity "http://identifiers.org/chebi/CHEBI:18367",
-                 "http://identifiers.org/kegg.compound/C00009"
-  DHAP_ch identity "http://identifiers.org/chebi/CHEBI:16108",
-                   "http://identifiers.org/kegg.compound/C00111"
-  FBP_ch identity "http://identifiers.org/chebi/CHEBI:28013",
-                  "http://identifiers.org/kegg.compound/C05378"
-  F6P_ch hypernym "http://identifiers.org/chebi/CHEBI:57634"
-  E4P_ch identity "http://identifiers.org/chebi/CHEBI:48153",
-                  "http://identifiers.org/kegg.compound/C00279"
-  X5P_ch identity "http://identifiers.org/chebi/CHEBI:16332",
-                  "http://identifiers.org/kegg.compound/C00231"
-  SBP_ch identity "http://identifiers.org/chebi/CHEBI:17969",
-                  "http://identifiers.org/kegg.compound/C00447"
-  S7P_ch identity "http://identifiers.org/chebi/CHEBI:15721",
-                  "http://identifiers.org/kegg.compound/C05382"
-  R5P_ch identity "http://identifiers.org/chebi/CHEBI:17797",
-                  "http://identifiers.org/kegg.compound/C00117"
-  Ru5P_ch identity "http://identifiers.org/chebi/CHEBI:17363",
-                   "http://identifiers.org/kegg.compound/C00199"
-  x_Pi_cyt identity "http://identifiers.org/chebi/CHEBI:18367",
-                    "http://identifiers.org/kegg.compound/C00009"
-  x_GAP_cyt identity "http://identifiers.org/chebi/CHEBI:17138",
-                     "http://identifiers.org/kegg.compound/C00661"
-  G6P_ch identity "http://identifiers.org/chebi/CHEBI:14314",
-                  "http://identifiers.org/kegg.compound/C00668"
-  x_NADP_ch identity "http://identifiers.org/chebi/CHEBI:18009",
-                     "http://identifiers.org/kegg.compound/C00006"
-  x_PGA_cyt identity "http://identifiers.org/kegg.compound/C00197"
-  ADP_ch identity "http://identifiers.org/chebi/CHEBI:16761",
-                  "http://identifiers.org/kegg.compound/C00008"
-  x_DHAP_cyt identity "http://identifiers.org/chebi/CHEBI:16108",
-                      "http://identifiers.org/kegg.compound/C00111"
-  x_Proton_ch identity "http://identifiers.org/chebi/CHEBI:24636"
-  G1P_ch identity "http://identifiers.org/chebi/CHEBI:58601",
-                  "http://identifiers.org/kegg.compound/C00103"
-  x_Starch_ch identity "http://identifiers.org/kegg.compound/C00369"
-  E1 hypernym "http://identifiers.org/ec-code/4.1.1.39"
-  E1 identity "http://identifiers.org/kegg.reaction/R00024"
-  E2 hypernym "http://identifiers.org/ec-code/2.7.2.3"
-  E2 identity "http://identifiers.org/kegg.reaction/R01512",
-              "http://identifiers.org/reactome/REACT_1186"
-  E3 hypernym "http://identifiers.org/ec-code/1.2.1.13"
-  E3 identity "http://identifiers.org/kegg.reaction/R01063"
-  E4 hypernym "http://identifiers.org/ec-code/5.3.1.1"
-  E4 identity "http://identifiers.org/kegg.reaction/R01015",
-              "http://identifiers.org/reactome/REACT_775"
-  E5 hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  E5 identity "http://identifiers.org/kegg.reaction/R01070",
-              "http://identifiers.org/reactome/REACT_1602"
-  E6 hypernym "http://identifiers.org/ec-code/3.1.3.11"
-  E6 identity "http://identifiers.org/kegg.reaction/R04780"
-  E7 hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  E7 identity "http://identifiers.org/kegg.reaction/R01830",
-              "http://identifiers.org/reactome/REACT_1811"
-  E8 hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  E8 identity "http://identifiers.org/kegg.reaction/R01829"
-  E9 hypernym "http://identifiers.org/ec-code/3.1.3.37"
-  E9 identity "http://identifiers.org/kegg.reaction/R01845"
-  E10 hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  E10 identity "http://identifiers.org/kegg.reaction/R01641",
-               "http://identifiers.org/reactome/REACT_1629"
-  E11 hypernym "http://identifiers.org/ec-code/5.3.1.6"
-  E11 identity "http://identifiers.org/kegg.reaction/R01056",
-               "http://identifiers.org/reactome/REACT_2033"
-  E12 hypernym "http://identifiers.org/ec-code/5.1.3.1"
-  E12 identity "http://identifiers.org/kegg.reaction/R01429",
-               "http://identifiers.org/reactome/REACT_1522"
-  E13 hypernym "http://identifiers.org/ec-code/2.7.1.19"
-  E13 identity "http://identifiers.org/kegg.reaction/R01423"
-  E14 hypernym "http://identifiers.org/ec-code/5.3.1.9"
-  E14 identity "http://identifiers.org/kegg.reaction/R00771",
-               "http://identifiers.org/reactome/REACT_1164"
-  E15 identity "http://identifiers.org/kegg.reaction/R00959"
-  E15 hypernym "http://identifiers.org/ec-code/5.4.2.2"
-  light_reaction hypernym "http://identifiers.org/go/GO:0006176"
-  E16 identity "http://identifiers.org/kegg.reaction/R02111"
-  E16 hypernym "http://identifiers.org/ec-code/2.4.1.1"
-  E17 identity "http://identifiers.org/kegg.reaction/R02111"
-  E17 hypernym "http://identifiers.org/ec-code/2.4.1.1"
-  E18_DHAP hypernym "http://identifiers.org/go/GO:0051407"
-  E18_PGA hypernym "http://identifiers.org/go/GO:0051408"
-  E18_GAP hypernym "http://identifiers.org/go/GO:0051408"
-end
-
-untitled is "Poolman2004_CalvinCycle"
-
-untitled model_entity_is "http://identifiers.org/biomodels.db/MODEL6615594069"
-untitled model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000013"
-untitled description "http://identifiers.org/pubmed/15073223"
-untitled taxon "http://identifiers.org/taxonomy/4097"
-untitled hypernym "http://identifiers.org/go/GO:0019253"
diff --git a/BioModelsRAG/data/BIOMD0000000014.txt b/BioModelsRAG/data/BIOMD0000000014.txt
deleted file mode 100644
index 271ba48bdd7b4ce3cf3b726f2bb4c7eed9ab4bf7..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000014.txt
+++ /dev/null
@@ -1,1635 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MAPK_in_Scaffold()
-
-  // Compartments and Species:
-  compartment Cytoplasm;
-  substanceOnly species MAPKP in Cytoplasm, MEKP in Cytoplasm, RAFK in Cytoplasm;
-  substanceOnly species RAFP in Cytoplasm, K_1_0 in Cytoplasm, K_1_1 in Cytoplasm;
-  substanceOnly species K_1_2 in Cytoplasm, K_2_0 in Cytoplasm, K_2_1 in Cytoplasm;
-  substanceOnly species K_2_2 in Cytoplasm, K_3_0 in Cytoplasm, K_3_1 in Cytoplasm;
-  substanceOnly species K_K_1_0_2_2 in Cytoplasm, K_K_1_1_2_2 in Cytoplasm;
-  substanceOnly species K_K_2_0_3_1 in Cytoplasm, K_K_2_1_3_1 in Cytoplasm;
-  substanceOnly species K_MAPKP_1_1 in Cytoplasm, K_MAPKP_1_2 in Cytoplasm;
-  substanceOnly species K_MEKP_2_1 in Cytoplasm, K_MEKP_2_2 in Cytoplasm;
-  substanceOnly species K_RAFK_3_0 in Cytoplasm, K_RAFP_3_1 in Cytoplasm;
-  substanceOnly species S_m1_m1_m1 in Cytoplasm, S_m1_m1_0 in Cytoplasm, S_m1_m1_1 in Cytoplasm;
-  substanceOnly species S_m1_0_m1 in Cytoplasm, S_m1_0_0 in Cytoplasm, S_m1_0_1 in Cytoplasm;
-  substanceOnly species S_m1_1_m1 in Cytoplasm, S_m1_1_0 in Cytoplasm, S_m1_1_1 in Cytoplasm;
-  substanceOnly species S_m1_2_m1 in Cytoplasm, S_m1_2_0 in Cytoplasm, S_m1_2_1 in Cytoplasm;
-  substanceOnly species S_0_m1_m1 in Cytoplasm, S_0_m1_0 in Cytoplasm, S_0_m1_1 in Cytoplasm;
-  substanceOnly species S_0_0_m1 in Cytoplasm, S_0_0_0 in Cytoplasm, S_0_0_1 in Cytoplasm;
-  substanceOnly species S_0_1_m1 in Cytoplasm, S_0_1_0 in Cytoplasm, S_0_1_1 in Cytoplasm;
-  substanceOnly species S_0_2_m1 in Cytoplasm, S_0_2_0 in Cytoplasm, S_0_2_1 in Cytoplasm;
-  substanceOnly species S_1_m1_m1 in Cytoplasm, S_1_m1_0 in Cytoplasm, S_1_m1_1 in Cytoplasm;
-  substanceOnly species S_1_0_m1 in Cytoplasm, S_1_0_0 in Cytoplasm, S_1_0_1 in Cytoplasm;
-  substanceOnly species S_1_1_m1 in Cytoplasm, S_1_1_0 in Cytoplasm, S_1_1_1 in Cytoplasm;
-  substanceOnly species S_1_2_m1 in Cytoplasm, S_1_2_0 in Cytoplasm, S_1_2_1 in Cytoplasm;
-  substanceOnly species S_2_m1_m1 in Cytoplasm, S_2_m1_0 in Cytoplasm, S_2_m1_1 in Cytoplasm;
-  substanceOnly species S_2_0_m1 in Cytoplasm, S_2_0_0 in Cytoplasm, S_2_0_1 in Cytoplasm;
-  substanceOnly species S_2_1_m1 in Cytoplasm, S_2_1_0 in Cytoplasm, S_2_1_1 in Cytoplasm;
-  substanceOnly species S_2_2_m1 in Cytoplasm, S_2_2_0 in Cytoplasm, S_2_2_1 in Cytoplasm;
-  substanceOnly species S_RAFK_m1_m1_0 in Cytoplasm, S_RAFK_m1_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_m1_1_0 in Cytoplasm, S_RAFK_m1_2_0 in Cytoplasm;
-  substanceOnly species S_RAFK_0_m1_0 in Cytoplasm, S_RAFK_0_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_0_1_0 in Cytoplasm, S_RAFK_0_2_0 in Cytoplasm;
-  substanceOnly species S_RAFK_1_m1_0 in Cytoplasm, S_RAFK_1_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_1_1_0 in Cytoplasm, S_RAFK_1_2_0 in Cytoplasm;
-  substanceOnly species S_RAFK_2_m1_0 in Cytoplasm, S_RAFK_2_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_2_1_0 in Cytoplasm, S_RAFK_2_2_0 in Cytoplasm;
-
-  // Reactions:
-  Reaction1: RAFK + K_3_0 => K_RAFK_3_0; Reaction1_a1*RAFK*K_3_0;
-  Reaction2: K_RAFK_3_0 => RAFK + K_3_0; Reaction2_d1*K_RAFK_3_0;
-  Reaction3: K_RAFK_3_0 => RAFK + K_3_1; Reaction3_k1*K_RAFK_3_0;
-  Reaction4: RAFP + K_3_1 => K_RAFP_3_1; Reaction4_a2*RAFP*K_3_1;
-  Reaction5: K_RAFP_3_1 => RAFP + K_3_1; Reaction5_d2*K_RAFP_3_1;
-  Reaction6: K_RAFP_3_1 => RAFP + K_3_0; Reaction6_k2*K_RAFP_3_1;
-  Reaction7: K_2_0 + K_3_1 => K_K_2_0_3_1; Reaction7_a3*K_2_0*K_3_1;
-  Reaction8: K_K_2_0_3_1 => K_2_0 + K_3_1; Reaction8_d3*K_K_2_0_3_1;
-  Reaction9: K_K_2_0_3_1 => K_2_1 + K_3_1; Reaction9_k3*K_K_2_0_3_1;
-  Reaction10: MEKP + K_2_1 => K_MEKP_2_1; Reaction10_a4*MEKP*K_2_1;
-  Reaction11: K_MEKP_2_1 => MEKP + K_2_1; Reaction11_d4*K_MEKP_2_1;
-  Reaction12: K_MEKP_2_1 => MEKP + K_2_0; Reaction12_k4*K_MEKP_2_1;
-  Reaction13: K_2_1 + K_3_1 => K_K_2_1_3_1; Reaction13_a5*K_2_1*K_3_1;
-  Reaction14: K_K_2_1_3_1 => K_2_1 + K_3_1; Reaction14_d5*K_K_2_1_3_1;
-  Reaction15: K_K_2_1_3_1 => K_2_2 + K_3_1; Reaction15_k5*K_K_2_1_3_1;
-  Reaction16: MEKP + K_2_2 => K_MEKP_2_2; Reaction16_a6*MEKP*K_2_2;
-  Reaction17: K_MEKP_2_2 => MEKP + K_2_2; Reaction17_d6*K_MEKP_2_2;
-  Reaction18: K_MEKP_2_2 => MEKP + K_2_1; Reaction18_k6*K_MEKP_2_2;
-  Reaction19: K_1_0 + K_2_2 => K_K_1_0_2_2; Reaction19_a7*K_1_0*K_2_2;
-  Reaction20: K_K_1_0_2_2 => K_1_0 + K_2_2; Reaction20_d7*K_K_1_0_2_2;
-  Reaction21: K_K_1_0_2_2 => K_1_1 + K_2_2; Reaction21_k7*K_K_1_0_2_2;
-  Reaction22: MAPKP + K_1_1 => K_MAPKP_1_1; Reaction22_a8*MAPKP*K_1_1;
-  Reaction23: K_MAPKP_1_1 => MAPKP + K_1_1; Reaction23_d8*K_MAPKP_1_1;
-  Reaction24: K_MAPKP_1_1 => MAPKP + K_1_0; Reaction24_k8*K_MAPKP_1_1;
-  Reaction25: K_1_1 + K_2_2 => K_K_1_1_2_2; Reaction25_a9*K_1_1*K_2_2;
-  Reaction26: K_K_1_1_2_2 => K_1_1 + K_2_2; Reaction26_d9*K_K_1_1_2_2;
-  Reaction27: K_K_1_1_2_2 => K_1_2 + K_2_2; Reaction27_k9*K_K_1_1_2_2;
-  Reaction28: MAPKP + K_1_2 => K_MAPKP_1_2; Reaction28_a10*MAPKP*K_1_2;
-  Reaction29: K_MAPKP_1_2 => MAPKP + K_1_2; Reaction29_d10*K_MAPKP_1_2;
-  Reaction30: K_MAPKP_1_2 => MAPKP + K_1_1; Reaction30_k10*K_MAPKP_1_2;
-  Reaction31: K_1_0 + S_m1_m1_m1 => S_0_m1_m1; Reaction31_kon*K_1_0*S_m1_m1_m1;
-  Reaction32: S_0_m1_m1 => K_1_0 + S_m1_m1_m1; Reaction32_koff*S_0_m1_m1;
-  Reaction33: K_1_0 + S_m1_m1_0 => S_0_m1_0; Reaction33_kon*K_1_0*S_m1_m1_0;
-  Reaction34: S_0_m1_0 => K_1_0 + S_m1_m1_0; Reaction34_koff*S_0_m1_0;
-  Reaction35: K_1_0 + S_m1_m1_1 => S_0_m1_1; Reaction35_kon*K_1_0*S_m1_m1_1;
-  Reaction36: S_0_m1_1 => K_1_0 + S_m1_m1_1; Reaction36_koff*S_0_m1_1;
-  Reaction37: K_1_0 + S_m1_0_m1 => S_0_0_m1; Reaction37_kon*K_1_0*S_m1_0_m1;
-  Reaction38: S_0_0_m1 => K_1_0 + S_m1_0_m1; Reaction38_koff*S_0_0_m1;
-  Reaction39: K_1_0 + S_m1_0_0 => S_0_0_0; Reaction39_kon*K_1_0*S_m1_0_0;
-  Reaction40: S_0_0_0 => K_1_0 + S_m1_0_0; Reaction40_koff*S_0_0_0;
-  Reaction41: K_1_0 + S_m1_0_1 => S_0_0_1; Reaction41_kon*K_1_0*S_m1_0_1;
-  Reaction42: S_0_0_1 => K_1_0 + S_m1_0_1; Reaction42_koff*S_0_0_1;
-  Reaction43: K_1_0 + S_m1_1_m1 => S_0_1_m1; Reaction43_kon*K_1_0*S_m1_1_m1;
-  Reaction44: S_0_1_m1 => K_1_0 + S_m1_1_m1; Reaction44_koff*S_0_1_m1;
-  Reaction45: K_1_0 + S_m1_1_0 => S_0_1_0; Reaction45_kon*K_1_0*S_m1_1_0;
-  Reaction46: S_0_1_0 => K_1_0 + S_m1_1_0; Reaction46_koff*S_0_1_0;
-  Reaction47: K_1_0 + S_m1_1_1 => S_0_1_1; Reaction47_kon*K_1_0*S_m1_1_1;
-  Reaction48: S_0_1_1 => K_1_0 + S_m1_1_1; Reaction48_koff*S_0_1_1;
-  Reaction49: K_1_0 + S_m1_2_m1 => S_0_2_m1; Reaction49_kon*K_1_0*S_m1_2_m1;
-  Reaction50: S_0_2_m1 => K_1_0 + S_m1_2_m1; Reaction50_koff*S_0_2_m1;
-  Reaction51: K_1_0 + S_m1_2_0 => S_0_2_0; Reaction51_kon*K_1_0*S_m1_2_0;
-  Reaction52: S_0_2_0 => K_1_0 + S_m1_2_0; Reaction52_koff*S_0_2_0;
-  Reaction53: K_1_0 + S_m1_2_1 => S_0_2_1; Reaction53_kon*K_1_0*S_m1_2_1;
-  Reaction54: S_0_2_1 => K_1_0 + S_m1_2_1; Reaction54_koff*S_0_2_1;
-  Reaction55: K_1_1 + S_m1_m1_m1 => S_1_m1_m1; Reaction55_kpon*K_1_1*S_m1_m1_m1;
-  Reaction56: S_1_m1_m1 => K_1_1 + S_m1_m1_m1; Reaction56_kpoff*S_1_m1_m1;
-  Reaction57: K_1_1 + S_m1_m1_0 => S_1_m1_0; Reaction57_kpon*K_1_1*S_m1_m1_0;
-  Reaction58: S_1_m1_0 => K_1_1 + S_m1_m1_0; Reaction58_kpoff*S_1_m1_0;
-  Reaction59: K_1_1 + S_m1_m1_1 => S_1_m1_1; Reaction59_kpon*K_1_1*S_m1_m1_1;
-  Reaction60: S_1_m1_1 => K_1_1 + S_m1_m1_1; Reaction60_kpoff*S_1_m1_1;
-  Reaction61: K_1_1 + S_m1_0_m1 => S_1_0_m1; Reaction61_kpon*K_1_1*S_m1_0_m1;
-  Reaction62: S_1_0_m1 => K_1_1 + S_m1_0_m1; Reaction62_kpoff*S_1_0_m1;
-  Reaction63: K_1_1 + S_m1_0_0 => S_1_0_0; Reaction63_kpon*K_1_1*S_m1_0_0;
-  Reaction64: S_1_0_0 => K_1_1 + S_m1_0_0; Reaction64_kpoff*S_1_0_0;
-  Reaction65: K_1_1 + S_m1_0_1 => S_1_0_1; Reaction65_kpon*K_1_1*S_m1_0_1;
-  Reaction66: S_1_0_1 => K_1_1 + S_m1_0_1; Reaction66_kpoff*S_1_0_1;
-  Reaction67: K_1_1 + S_m1_1_m1 => S_1_1_m1; Reaction67_kpon*K_1_1*S_m1_1_m1;
-  Reaction68: S_1_1_m1 => K_1_1 + S_m1_1_m1; Reaction68_kpoff*S_1_1_m1;
-  Reaction69: K_1_1 + S_m1_1_0 => S_1_1_0; Reaction69_kpon*K_1_1*S_m1_1_0;
-  Reaction70: S_1_1_0 => K_1_1 + S_m1_1_0; Reaction70_kpoff*S_1_1_0;
-  Reaction71: K_1_1 + S_m1_1_1 => S_1_1_1; Reaction71_kpon*K_1_1*S_m1_1_1;
-  Reaction72: S_1_1_1 => K_1_1 + S_m1_1_1; Reaction72_kpoff*S_1_1_1;
-  Reaction73: K_1_1 + S_m1_2_m1 => S_1_2_m1; Reaction73_kpon*K_1_1*S_m1_2_m1;
-  Reaction74: S_1_2_m1 => K_1_1 + S_m1_2_m1; Reaction74_kpoff*S_1_2_m1;
-  Reaction75: K_1_1 + S_m1_2_0 => S_1_2_0; Reaction75_kpon*K_1_1*S_m1_2_0;
-  Reaction76: S_1_2_0 => K_1_1 + S_m1_2_0; Reaction76_kpoff*S_1_2_0;
-  Reaction77: K_1_1 + S_m1_2_1 => S_1_2_1; Reaction77_kpon*K_1_1*S_m1_2_1;
-  Reaction78: S_1_2_1 => K_1_1 + S_m1_2_1; Reaction78_kpoff*S_1_2_1;
-  Reaction79: K_1_2 + S_m1_m1_m1 => S_2_m1_m1; Reaction79_kpon*K_1_2*S_m1_m1_m1;
-  Reaction80: S_2_m1_m1 => K_1_2 + S_m1_m1_m1; Reaction80_kpoff*S_2_m1_m1;
-  Reaction81: K_1_2 + S_m1_m1_0 => S_2_m1_0; Reaction81_kpon*K_1_2*S_m1_m1_0;
-  Reaction82: S_2_m1_0 => K_1_2 + S_m1_m1_0; Reaction82_kpoff*S_2_m1_0;
-  Reaction83: K_1_2 + S_m1_m1_1 => S_2_m1_1; Reaction83_kpon*K_1_2*S_m1_m1_1;
-  Reaction84: S_2_m1_1 => K_1_2 + S_m1_m1_1; Reaction84_kpoff*S_2_m1_1;
-  Reaction85: K_1_2 + S_m1_0_m1 => S_2_0_m1; Reaction85_kpon*K_1_2*S_m1_0_m1;
-  Reaction86: S_2_0_m1 => K_1_2 + S_m1_0_m1; Reaction86_kpoff*S_2_0_m1;
-  Reaction87: K_1_2 + S_m1_0_0 => S_2_0_0; Reaction87_kpon*K_1_2*S_m1_0_0;
-  Reaction88: S_2_0_0 => K_1_2 + S_m1_0_0; Reaction88_kpoff*S_2_0_0;
-  Reaction89: K_1_2 + S_m1_0_1 => S_2_0_1; Reaction89_kpon*K_1_2*S_m1_0_1;
-  Reaction90: S_2_0_1 => K_1_2 + S_m1_0_1; Reaction90_kpoff*S_2_0_1;
-  Reaction91: K_1_2 + S_m1_1_m1 => S_2_1_m1; Reaction91_kpon*K_1_2*S_m1_1_m1;
-  Reaction92: S_2_1_m1 => K_1_2 + S_m1_1_m1; Reaction92_kpoff*S_2_1_m1;
-  Reaction93: K_1_2 + S_m1_1_0 => S_2_1_0; Reaction93_kpon*K_1_2*S_m1_1_0;
-  Reaction94: S_2_1_0 => K_1_2 + S_m1_1_0; Reaction94_kpoff*S_2_1_0;
-  Reaction95: K_1_2 + S_m1_1_1 => S_2_1_1; Reaction95_kpon*K_1_2*S_m1_1_1;
-  Reaction96: S_2_1_1 => K_1_2 + S_m1_1_1; Reaction96_kpoff*S_2_1_1;
-  Reaction97: K_1_2 + S_m1_2_m1 => S_2_2_m1; Reaction97_kpon*K_1_2*S_m1_2_m1;
-  Reaction98: S_2_2_m1 => K_1_2 + S_m1_2_m1; Reaction98_kpoff*S_2_2_m1;
-  Reaction99: K_1_2 + S_m1_2_0 => S_2_2_0; Reaction99_kpon*K_1_2*S_m1_2_0;
-  Reaction100: S_2_2_0 => K_1_2 + S_m1_2_0; Reaction100_kpoff*S_2_2_0;
-  Reaction101: K_1_2 + S_m1_2_1 => S_2_2_1; Reaction101_kpon*K_1_2*S_m1_2_1;
-  Reaction102: S_2_2_1 => K_1_2 + S_m1_2_1; Reaction102_kpoff*S_2_2_1;
-  Reaction103: K_2_0 + S_m1_m1_m1 => S_m1_0_m1; Reaction103_kon*K_2_0*S_m1_m1_m1;
-  Reaction104: S_m1_0_m1 => K_2_0 + S_m1_m1_m1; Reaction104_koff*S_m1_0_m1;
-  Reaction105: K_2_0 + S_m1_m1_0 => S_m1_0_0; Reaction105_kon*K_2_0*S_m1_m1_0;
-  Reaction106: S_m1_0_0 => K_2_0 + S_m1_m1_0; Reaction106_koff*S_m1_0_0;
-  Reaction107: K_2_0 + S_m1_m1_1 => S_m1_0_1; Reaction107_kon*K_2_0*S_m1_m1_1;
-  Reaction108: S_m1_0_1 => K_2_0 + S_m1_m1_1; Reaction108_koff*S_m1_0_1;
-  Reaction109: K_2_1 + S_m1_m1_m1 => S_m1_1_m1; Reaction109_kpon*K_2_1*S_m1_m1_m1;
-  Reaction110: S_m1_1_m1 => K_2_1 + S_m1_m1_m1; Reaction110_kpoff*S_m1_1_m1;
-  Reaction111: K_2_1 + S_m1_m1_0 => S_m1_1_0; Reaction111_kpon*K_2_1*S_m1_m1_0;
-  Reaction112: S_m1_1_0 => K_2_1 + S_m1_m1_0; Reaction112_kpoff*S_m1_1_0;
-  Reaction113: K_2_1 + S_m1_m1_1 => S_m1_1_1; Reaction113_kpon*K_2_1*S_m1_m1_1;
-  Reaction114: S_m1_1_1 => K_2_1 + S_m1_m1_1; Reaction114_kpoff*S_m1_1_1;
-  Reaction115: K_2_2 + S_m1_m1_m1 => S_m1_2_m1; Reaction115_kpon*K_2_2*S_m1_m1_m1;
-  Reaction116: S_m1_2_m1 => K_2_2 + S_m1_m1_m1; Reaction116_kpoff*S_m1_2_m1;
-  Reaction117: K_2_2 + S_m1_m1_0 => S_m1_2_0; Reaction117_kpon*K_2_2*S_m1_m1_0;
-  Reaction118: S_m1_2_0 => K_2_2 + S_m1_m1_0; Reaction118_kpoff*S_m1_2_0;
-  Reaction119: K_2_2 + S_m1_m1_1 => S_m1_2_1; Reaction119_kpon*K_2_2*S_m1_m1_1;
-  Reaction120: S_m1_2_1 => K_2_2 + S_m1_m1_1; Reaction120_kpoff*S_m1_2_1;
-  Reaction121: K_2_0 + S_0_m1_m1 => S_0_0_m1; Reaction121_kon*K_2_0*S_0_m1_m1;
-  Reaction122: S_0_0_m1 => K_2_0 + S_0_m1_m1; Reaction122_koff*S_0_0_m1;
-  Reaction123: K_2_0 + S_0_m1_0 => S_0_0_0; Reaction123_kon*K_2_0*S_0_m1_0;
-  Reaction124: S_0_0_0 => K_2_0 + S_0_m1_0; Reaction124_koff*S_0_0_0;
-  Reaction125: K_2_0 + S_0_m1_1 => S_0_0_1; Reaction125_kon*K_2_0*S_0_m1_1;
-  Reaction126: S_0_0_1 => K_2_0 + S_0_m1_1; Reaction126_koff*S_0_0_1;
-  Reaction127: K_2_1 + S_0_m1_m1 => S_0_1_m1; Reaction127_kpon*K_2_1*S_0_m1_m1;
-  Reaction128: S_0_1_m1 => K_2_1 + S_0_m1_m1; Reaction128_kpoff*S_0_1_m1;
-  Reaction129: K_2_1 + S_0_m1_0 => S_0_1_0; Reaction129_kpon*K_2_1*S_0_m1_0;
-  Reaction130: S_0_1_0 => K_2_1 + S_0_m1_0; Reaction130_kpoff*S_0_1_0;
-  Reaction131: K_2_1 + S_0_m1_1 => S_0_1_1; Reaction131_kpon*K_2_1*S_0_m1_1;
-  Reaction132: S_0_1_1 => K_2_1 + S_0_m1_1; Reaction132_kpoff*S_0_1_1;
-  Reaction133: K_2_2 + S_0_m1_m1 => S_0_2_m1; Reaction133_kpon*K_2_2*S_0_m1_m1;
-  Reaction134: S_0_2_m1 => K_2_2 + S_0_m1_m1; Reaction134_kpoff*S_0_2_m1;
-  Reaction135: K_2_2 + S_0_m1_0 => S_0_2_0; Reaction135_kpon*K_2_2*S_0_m1_0;
-  Reaction136: S_0_2_0 => K_2_2 + S_0_m1_0; Reaction136_kpoff*S_0_2_0;
-  Reaction137: K_2_2 + S_0_m1_1 => S_0_2_1; Reaction137_kpon*K_2_2*S_0_m1_1;
-  Reaction138: S_0_2_1 => K_2_2 + S_0_m1_1; Reaction138_kpoff*S_0_2_1;
-  Reaction139: K_2_0 + S_1_m1_m1 => S_1_0_m1; Reaction139_kon*K_2_0*S_1_m1_m1;
-  Reaction140: S_1_0_m1 => K_2_0 + S_1_m1_m1; Reaction140_koff*S_1_0_m1;
-  Reaction141: K_2_0 + S_1_m1_0 => S_1_0_0; Reaction141_kon*K_2_0*S_1_m1_0;
-  Reaction142: S_1_0_0 => K_2_0 + S_1_m1_0; Reaction142_koff*S_1_0_0;
-  Reaction143: K_2_0 + S_1_m1_1 => S_1_0_1; Reaction143_kon*K_2_0*S_1_m1_1;
-  Reaction144: S_1_0_1 => K_2_0 + S_1_m1_1; Reaction144_koff*S_1_0_1;
-  Reaction145: K_2_1 + S_1_m1_m1 => S_1_1_m1; Reaction145_kpon*K_2_1*S_1_m1_m1;
-  Reaction146: S_1_1_m1 => K_2_1 + S_1_m1_m1; Reaction146_kpoff*S_1_1_m1;
-  Reaction147: K_2_1 + S_1_m1_0 => S_1_1_0; Reaction147_kpon*K_2_1*S_1_m1_0;
-  Reaction148: S_1_1_0 => K_2_1 + S_1_m1_0; Reaction148_kpoff*S_1_1_0;
-  Reaction149: K_2_1 + S_1_m1_1 => S_1_1_1; Reaction149_kpon*K_2_1*S_1_m1_1;
-  Reaction150: S_1_1_1 => K_2_1 + S_1_m1_1; Reaction150_kpoff*S_1_1_1;
-  Reaction151: K_2_2 + S_1_m1_m1 => S_1_2_m1; Reaction151_kpon*K_2_2*S_1_m1_m1;
-  Reaction152: S_1_2_m1 => K_2_2 + S_1_m1_m1; Reaction152_kpoff*S_1_2_m1;
-  Reaction153: K_2_2 + S_1_m1_0 => S_1_2_0; Reaction153_kpon*K_2_2*S_1_m1_0;
-  Reaction154: S_1_2_0 => K_2_2 + S_1_m1_0; Reaction154_kpoff*S_1_2_0;
-  Reaction155: K_2_2 + S_1_m1_1 => S_1_2_1; Reaction155_kpon*K_2_2*S_1_m1_1;
-  Reaction156: S_1_2_1 => K_2_2 + S_1_m1_1; Reaction156_kpoff*S_1_2_1;
-  Reaction157: K_2_0 + S_2_m1_m1 => S_2_0_m1; Reaction157_kon*K_2_0*S_2_m1_m1;
-  Reaction158: S_2_0_m1 => K_2_0 + S_2_m1_m1; Reaction158_koff*S_2_0_m1;
-  Reaction159: K_2_0 + S_2_m1_0 => S_2_0_0; Reaction159_kon*K_2_0*S_2_m1_0;
-  Reaction160: S_2_0_0 => K_2_0 + S_2_m1_0; Reaction160_koff*S_2_0_0;
-  Reaction161: K_2_0 + S_2_m1_1 => S_2_0_1; Reaction161_kon*K_2_0*S_2_m1_1;
-  Reaction162: S_2_0_1 => K_2_0 + S_2_m1_1; Reaction162_koff*S_2_0_1;
-  Reaction163: K_2_1 + S_2_m1_m1 => S_2_1_m1; Reaction163_kpon*K_2_1*S_2_m1_m1;
-  Reaction164: S_2_1_m1 => K_2_1 + S_2_m1_m1; Reaction164_kpoff*S_2_1_m1;
-  Reaction165: K_2_1 + S_2_m1_0 => S_2_1_0; Reaction165_kpon*K_2_1*S_2_m1_0;
-  Reaction166: S_2_1_0 => K_2_1 + S_2_m1_0; Reaction166_kpoff*S_2_1_0;
-  Reaction167: K_2_1 + S_2_m1_1 => S_2_1_1; Reaction167_kpon*K_2_1*S_2_m1_1;
-  Reaction168: S_2_1_1 => K_2_1 + S_2_m1_1; Reaction168_kpoff*S_2_1_1;
-  Reaction169: K_2_2 + S_2_m1_m1 => S_2_2_m1; Reaction169_kpon*K_2_2*S_2_m1_m1;
-  Reaction170: S_2_2_m1 => K_2_2 + S_2_m1_m1; Reaction170_kpoff*S_2_2_m1;
-  Reaction171: K_2_2 + S_2_m1_0 => S_2_2_0; Reaction171_kpon*K_2_2*S_2_m1_0;
-  Reaction172: S_2_2_0 => K_2_2 + S_2_m1_0; Reaction172_kpoff*S_2_2_0;
-  Reaction173: K_2_2 + S_2_m1_1 => S_2_2_1; Reaction173_kpon*K_2_2*S_2_m1_1;
-  Reaction174: S_2_2_1 => K_2_2 + S_2_m1_1; Reaction174_kpoff*S_2_2_1;
-  Reaction175: K_3_0 + S_m1_m1_m1 => S_m1_m1_0; Reaction175_kon*K_3_0*S_m1_m1_m1;
-  Reaction176: S_m1_m1_0 => K_3_0 + S_m1_m1_m1; Reaction176_koff*S_m1_m1_0;
-  Reaction177: K_3_1 + S_m1_m1_m1 => S_m1_m1_1; Reaction177_kpon*K_3_1*S_m1_m1_m1;
-  Reaction178: S_m1_m1_1 => K_3_1 + S_m1_m1_m1; Reaction178_kpoff*S_m1_m1_1;
-  Reaction179: K_3_0 + S_m1_0_m1 => S_m1_0_0; Reaction179_kon*K_3_0*S_m1_0_m1;
-  Reaction180: S_m1_0_0 => K_3_0 + S_m1_0_m1; Reaction180_koff*S_m1_0_0;
-  Reaction181: K_3_1 + S_m1_0_m1 => S_m1_0_1; Reaction181_kpon*K_3_1*S_m1_0_m1;
-  Reaction182: S_m1_0_1 => K_3_1 + S_m1_0_m1; Reaction182_kpoff*S_m1_0_1;
-  Reaction183: K_3_0 + S_m1_1_m1 => S_m1_1_0; Reaction183_kon*K_3_0*S_m1_1_m1;
-  Reaction184: S_m1_1_0 => K_3_0 + S_m1_1_m1; Reaction184_koff*S_m1_1_0;
-  Reaction185: K_3_1 + S_m1_1_m1 => S_m1_1_1; Reaction185_kpon*K_3_1*S_m1_1_m1;
-  Reaction186: S_m1_1_1 => K_3_1 + S_m1_1_m1; Reaction186_kpoff*S_m1_1_1;
-  Reaction187: K_3_0 + S_m1_2_m1 => S_m1_2_0; Reaction187_kon*K_3_0*S_m1_2_m1;
-  Reaction188: S_m1_2_0 => K_3_0 + S_m1_2_m1; Reaction188_koff*S_m1_2_0;
-  Reaction189: K_3_1 + S_m1_2_m1 => S_m1_2_1; Reaction189_kpon*K_3_1*S_m1_2_m1;
-  Reaction190: S_m1_2_1 => K_3_1 + S_m1_2_m1; Reaction190_kpoff*S_m1_2_1;
-  Reaction191: K_3_0 + S_0_m1_m1 => S_0_m1_0; Reaction191_kon*K_3_0*S_0_m1_m1;
-  Reaction192: S_0_m1_0 => K_3_0 + S_0_m1_m1; Reaction192_koff*S_0_m1_0;
-  Reaction193: K_3_1 + S_0_m1_m1 => S_0_m1_1; Reaction193_kpon*K_3_1*S_0_m1_m1;
-  Reaction194: S_0_m1_1 => K_3_1 + S_0_m1_m1; Reaction194_kpoff*S_0_m1_1;
-  Reaction195: K_3_0 + S_0_0_m1 => S_0_0_0; Reaction195_kon*K_3_0*S_0_0_m1;
-  Reaction196: S_0_0_0 => K_3_0 + S_0_0_m1; Reaction196_koff*S_0_0_0;
-  Reaction197: K_3_1 + S_0_0_m1 => S_0_0_1; Reaction197_kpon*K_3_1*S_0_0_m1;
-  Reaction198: S_0_0_1 => K_3_1 + S_0_0_m1; Reaction198_kpoff*S_0_0_1;
-  Reaction199: K_3_0 + S_0_1_m1 => S_0_1_0; Reaction199_kon*K_3_0*S_0_1_m1;
-  Reaction200: S_0_1_0 => K_3_0 + S_0_1_m1; Reaction200_koff*S_0_1_0;
-  Reaction201: K_3_1 + S_0_1_m1 => S_0_1_1; Reaction201_kpon*K_3_1*S_0_1_m1;
-  Reaction202: S_0_1_1 => K_3_1 + S_0_1_m1; Reaction202_kpoff*S_0_1_1;
-  Reaction203: K_3_0 + S_0_2_m1 => S_0_2_0; Reaction203_kon*K_3_0*S_0_2_m1;
-  Reaction204: S_0_2_0 => K_3_0 + S_0_2_m1; Reaction204_koff*S_0_2_0;
-  Reaction205: K_3_1 + S_0_2_m1 => S_0_2_1; Reaction205_kpon*K_3_1*S_0_2_m1;
-  Reaction206: S_0_2_1 => K_3_1 + S_0_2_m1; Reaction206_kpoff*S_0_2_1;
-  Reaction207: K_3_0 + S_1_m1_m1 => S_1_m1_0; Reaction207_kon*K_3_0*S_1_m1_m1;
-  Reaction208: S_1_m1_0 => K_3_0 + S_1_m1_m1; Reaction208_koff*S_1_m1_0;
-  Reaction209: K_3_1 + S_1_m1_m1 => S_1_m1_1; Reaction209_kpon*K_3_1*S_1_m1_m1;
-  Reaction210: S_1_m1_1 => K_3_1 + S_1_m1_m1; Reaction210_kpoff*S_1_m1_1;
-  Reaction211: K_3_0 + S_1_0_m1 => S_1_0_0; Reaction211_kon*K_3_0*S_1_0_m1;
-  Reaction212: S_1_0_0 => K_3_0 + S_1_0_m1; Reaction212_koff*S_1_0_0;
-  Reaction213: K_3_1 + S_1_0_m1 => S_1_0_1; Reaction213_kpon*K_3_1*S_1_0_m1;
-  Reaction214: S_1_0_1 => K_3_1 + S_1_0_m1; Reaction214_kpoff*S_1_0_1;
-  Reaction215: K_3_0 + S_1_1_m1 => S_1_1_0; Reaction215_kon*K_3_0*S_1_1_m1;
-  Reaction216: S_1_1_0 => K_3_0 + S_1_1_m1; Reaction216_koff*S_1_1_0;
-  Reaction217: K_3_1 + S_1_1_m1 => S_1_1_1; Reaction217_kpon*K_3_1*S_1_1_m1;
-  Reaction218: S_1_1_1 => K_3_1 + S_1_1_m1; Reaction218_kpoff*S_1_1_1;
-  Reaction219: K_3_0 + S_1_2_m1 => S_1_2_0; Reaction219_kon*K_3_0*S_1_2_m1;
-  Reaction220: S_1_2_0 => K_3_0 + S_1_2_m1; Reaction220_koff*S_1_2_0;
-  Reaction221: K_3_1 + S_1_2_m1 => S_1_2_1; Reaction221_kpon*K_3_1*S_1_2_m1;
-  Reaction222: S_1_2_1 => K_3_1 + S_1_2_m1; Reaction222_kpoff*S_1_2_1;
-  Reaction223: K_3_0 + S_2_m1_m1 => S_2_m1_0; Reaction223_kon*K_3_0*S_2_m1_m1;
-  Reaction224: S_2_m1_0 => K_3_0 + S_2_m1_m1; Reaction224_koff*S_2_m1_0;
-  Reaction225: K_3_1 + S_2_m1_m1 => S_2_m1_1; Reaction225_kpon*K_3_1*S_2_m1_m1;
-  Reaction226: S_2_m1_1 => K_3_1 + S_2_m1_m1; Reaction226_kpoff*S_2_m1_1;
-  Reaction227: K_3_0 + S_2_0_m1 => S_2_0_0; Reaction227_kon*K_3_0*S_2_0_m1;
-  Reaction228: S_2_0_0 => K_3_0 + S_2_0_m1; Reaction228_koff*S_2_0_0;
-  Reaction229: K_3_1 + S_2_0_m1 => S_2_0_1; Reaction229_kpon*K_3_1*S_2_0_m1;
-  Reaction230: S_2_0_1 => K_3_1 + S_2_0_m1; Reaction230_kpoff*S_2_0_1;
-  Reaction231: K_3_0 + S_2_1_m1 => S_2_1_0; Reaction231_kon*K_3_0*S_2_1_m1;
-  Reaction232: S_2_1_0 => K_3_0 + S_2_1_m1; Reaction232_koff*S_2_1_0;
-  Reaction233: K_3_1 + S_2_1_m1 => S_2_1_1; Reaction233_kpon*K_3_1*S_2_1_m1;
-  Reaction234: S_2_1_1 => K_3_1 + S_2_1_m1; Reaction234_kpoff*S_2_1_1;
-  Reaction235: K_3_0 + S_2_2_m1 => S_2_2_0; Reaction235_kon*K_3_0*S_2_2_m1;
-  Reaction236: S_2_2_0 => K_3_0 + S_2_2_m1; Reaction236_koff*S_2_2_0;
-  Reaction237: K_3_1 + S_2_2_m1 => S_2_2_1; Reaction237_kpon*K_3_1*S_2_2_m1;
-  Reaction238: S_2_2_1 => K_3_1 + S_2_2_m1; Reaction238_kpoff*S_2_2_1;
-  Reaction239: S_0_2_m1 => S_1_2_m1; Reaction239_k7*S_0_2_m1;
-  Reaction240: S_0_2_0 => S_1_2_0; Reaction240_k7*S_0_2_0;
-  Reaction241: S_0_2_1 => S_1_2_1; Reaction241_k7*S_0_2_1;
-  Reaction242: S_1_2_m1 => S_2_2_m1; Reaction242_k9a*S_1_2_m1;
-  Reaction243: S_1_2_0 => S_2_2_0; Reaction243_k9a*S_1_2_0;
-  Reaction244: S_1_2_1 => S_2_2_1; Reaction244_k9a*S_1_2_1;
-  Reaction245: S_m1_0_1 => S_m1_1_1; Reaction245_k3*S_m1_0_1;
-  Reaction246: S_m1_1_1 => S_m1_2_1; Reaction246_k5a*S_m1_1_1;
-  Reaction247: S_0_0_1 => S_0_1_1; Reaction247_k3*S_0_0_1;
-  Reaction248: S_0_1_1 => S_0_2_1; Reaction248_k5a*S_0_1_1;
-  Reaction249: S_1_0_1 => S_1_1_1; Reaction249_k3*S_1_0_1;
-  Reaction250: S_1_1_1 => S_1_2_1; Reaction250_k5a*S_1_1_1;
-  Reaction251: S_2_0_1 => S_2_1_1; Reaction251_k3*S_2_0_1;
-  Reaction252: S_2_1_1 => S_2_2_1; Reaction252_k5a*S_2_1_1;
-  Reaction253: RAFK + S_m1_m1_0 => S_RAFK_m1_m1_0; Reaction253_k1a*RAFK*S_m1_m1_0;
-  Reaction254: S_RAFK_m1_m1_0 => RAFK + S_m1_m1_0; Reaction254_d1a*S_RAFK_m1_m1_0;
-  Reaction255: S_RAFK_m1_m1_0 => RAFK + S_m1_m1_1; Reaction255_k1*S_RAFK_m1_m1_0;
-  Reaction256: RAFK + S_m1_0_0 => S_RAFK_m1_0_0; Reaction256_k1a*RAFK*S_m1_0_0;
-  Reaction257: S_RAFK_m1_0_0 => RAFK + S_m1_0_0; Reaction257_d1a*S_RAFK_m1_0_0;
-  Reaction258: S_RAFK_m1_0_0 => RAFK + S_m1_0_1; Reaction258_k1*S_RAFK_m1_0_0;
-  Reaction259: RAFK + S_m1_1_0 => S_RAFK_m1_1_0; Reaction259_k1a*RAFK*S_m1_1_0;
-  Reaction260: S_RAFK_m1_1_0 => RAFK + S_m1_1_0; Reaction260_d1a*S_RAFK_m1_1_0;
-  Reaction261: S_RAFK_m1_1_0 => RAFK + S_m1_1_1; Reaction261_k1*S_RAFK_m1_1_0;
-  Reaction262: RAFK + S_m1_2_0 => S_RAFK_m1_2_0; Reaction262_k1a*RAFK*S_m1_2_0;
-  Reaction263: S_RAFK_m1_2_0 => RAFK + S_m1_2_0; Reaction263_d1a*S_RAFK_m1_2_0;
-  Reaction264: S_RAFK_m1_2_0 => RAFK + S_m1_2_1; Reaction264_k1*S_RAFK_m1_2_0;
-  Reaction265: RAFK + S_0_m1_0 => S_RAFK_0_m1_0; Reaction265_k1a*RAFK*S_0_m1_0;
-  Reaction266: S_RAFK_0_m1_0 => RAFK + S_0_m1_0; Reaction266_d1a*S_RAFK_0_m1_0;
-  Reaction267: S_RAFK_0_m1_0 => RAFK + S_0_m1_1; Reaction267_k1*S_RAFK_0_m1_0;
-  Reaction268: RAFK + S_0_0_0 => S_RAFK_0_0_0; Reaction268_k1a*RAFK*S_0_0_0;
-  Reaction269: S_RAFK_0_0_0 => RAFK + S_0_0_0; Reaction269_d1a*S_RAFK_0_0_0;
-  Reaction270: S_RAFK_0_0_0 => RAFK + S_0_0_1; Reaction270_k1*S_RAFK_0_0_0;
-  Reaction271: RAFK + S_0_1_0 => S_RAFK_0_1_0; Reaction271_k1a*RAFK*S_0_1_0;
-  Reaction272: S_RAFK_0_1_0 => RAFK + S_0_1_0; Reaction272_d1a*S_RAFK_0_1_0;
-  Reaction273: S_RAFK_0_1_0 => RAFK + S_0_1_1; Reaction273_k1*S_RAFK_0_1_0;
-  Reaction274: RAFK + S_0_2_0 => S_RAFK_0_2_0; Reaction274_k1a*RAFK*S_0_2_0;
-  Reaction275: S_RAFK_0_2_0 => RAFK + S_0_2_0; Reaction275_d1a*S_RAFK_0_2_0;
-  Reaction276: S_RAFK_0_2_0 => RAFK + S_0_2_1; Reaction276_k1*S_RAFK_0_2_0;
-  Reaction277: RAFK + S_1_m1_0 => S_RAFK_1_m1_0; Reaction277_k1a*RAFK*S_1_m1_0;
-  Reaction278: S_RAFK_1_m1_0 => RAFK + S_1_m1_0; Reaction278_d1a*S_RAFK_1_m1_0;
-  Reaction279: S_RAFK_1_m1_0 => RAFK + S_1_m1_1; Reaction279_k1*S_RAFK_1_m1_0;
-  Reaction280: RAFK + S_1_0_0 => S_RAFK_1_0_0; Reaction280_k1a*RAFK*S_1_0_0;
-  Reaction281: S_RAFK_1_0_0 => RAFK + S_1_0_0; Reaction281_d1a*S_RAFK_1_0_0;
-  Reaction282: S_RAFK_1_0_0 => RAFK + S_1_0_1; Reaction282_k1*S_RAFK_1_0_0;
-  Reaction283: RAFK + S_1_1_0 => S_RAFK_1_1_0; Reaction283_k1a*RAFK*S_1_1_0;
-  Reaction284: S_RAFK_1_1_0 => RAFK + S_1_1_0; Reaction284_d1a*S_RAFK_1_1_0;
-  Reaction285: S_RAFK_1_1_0 => RAFK + S_1_1_1; Reaction285_k1*S_RAFK_1_1_0;
-  Reaction286: RAFK + S_1_2_0 => S_RAFK_1_2_0; Reaction286_k1a*RAFK*S_1_2_0;
-  Reaction287: S_RAFK_1_2_0 => RAFK + S_1_2_0; Reaction287_d1a*S_RAFK_1_2_0;
-  Reaction288: S_RAFK_1_2_0 => RAFK + S_1_2_1; Reaction288_k1*S_RAFK_1_2_0;
-  Reaction289: RAFK + S_2_m1_0 => S_RAFK_2_m1_0; Reaction289_k1a*RAFK*S_2_m1_0;
-  Reaction290: S_RAFK_2_m1_0 => RAFK + S_2_m1_0; Reaction290_d1a*S_RAFK_2_m1_0;
-  Reaction291: S_RAFK_2_m1_0 => RAFK + S_2_m1_1; Reaction291_k1*S_RAFK_2_m1_0;
-  Reaction292: RAFK + S_2_0_0 => S_RAFK_2_0_0; Reaction292_k1a*RAFK*S_2_0_0;
-  Reaction293: S_RAFK_2_0_0 => RAFK + S_2_0_0; Reaction293_d1a*S_RAFK_2_0_0;
-  Reaction294: S_RAFK_2_0_0 => RAFK + S_2_0_1; Reaction294_k1*S_RAFK_2_0_0;
-  Reaction295: RAFK + S_2_1_0 => S_RAFK_2_1_0; Reaction295_k1a*RAFK*S_2_1_0;
-  Reaction296: S_RAFK_2_1_0 => RAFK + S_2_1_0; Reaction296_d1a*S_RAFK_2_1_0;
-  Reaction297: S_RAFK_2_1_0 => RAFK + S_2_1_1; Reaction297_k1*S_RAFK_2_1_0;
-  Reaction298: RAFK + S_2_2_0 => S_RAFK_2_2_0; Reaction298_k1a*RAFK*S_2_2_0;
-  Reaction299: S_RAFK_2_2_0 => RAFK + S_2_2_0; Reaction299_d1a*S_RAFK_2_2_0;
-  Reaction300: S_RAFK_2_2_0 => RAFK + S_2_2_1; Reaction300_k1*S_RAFK_2_2_0;
-
-  // Species initializations:
-  MAPKP = 0.3/Cytoplasm;
-  MEKP = 0.2/Cytoplasm;
-  RAFK = 0.1/Cytoplasm;
-  RAFP = 0.3/Cytoplasm;
-  K_1_0 = 0.4/Cytoplasm;
-  K_1_1 = 0;
-  K_1_2 = 0;
-  K_2_0 = 0.2/Cytoplasm;
-  K_2_1 = 0;
-  K_2_2 = 0;
-  K_3_0 = 0.3/Cytoplasm;
-  K_3_1 = 0;
-  K_K_1_0_2_2 = 0;
-  K_K_1_1_2_2 = 0;
-  K_K_2_0_3_1 = 0;
-  K_K_2_1_3_1 = 0;
-  K_MAPKP_1_1 = 0;
-  K_MAPKP_1_2 = 0;
-  K_MEKP_2_1 = 0;
-  K_MEKP_2_2 = 0;
-  K_RAFK_3_0 = 0;
-  K_RAFP_3_1 = 0;
-  S_m1_m1_m1 = 0.1/Cytoplasm;
-  S_m1_m1_0 = 0;
-  S_m1_m1_1 = 0;
-  S_m1_0_m1 = 0;
-  S_m1_0_0 = 0;
-  S_m1_0_1 = 0;
-  S_m1_1_m1 = 0;
-  S_m1_1_0 = 0;
-  S_m1_1_1 = 0;
-  S_m1_2_m1 = 0;
-  S_m1_2_0 = 0;
-  S_m1_2_1 = 0;
-  S_0_m1_m1 = 0;
-  S_0_m1_0 = 0;
-  S_0_m1_1 = 0;
-  S_0_0_m1 = 0;
-  S_0_0_0 = 0;
-  S_0_0_1 = 0;
-  S_0_1_m1 = 0;
-  S_0_1_0 = 0;
-  S_0_1_1 = 0;
-  S_0_2_m1 = 0;
-  S_0_2_0 = 0;
-  S_0_2_1 = 0;
-  S_1_m1_m1 = 0;
-  S_1_m1_0 = 0;
-  S_1_m1_1 = 0;
-  S_1_0_m1 = 0;
-  S_1_0_0 = 0;
-  S_1_0_1 = 0;
-  S_1_1_m1 = 0;
-  S_1_1_0 = 0;
-  S_1_1_1 = 0;
-  S_1_2_m1 = 0;
-  S_1_2_0 = 0;
-  S_1_2_1 = 0;
-  S_2_m1_m1 = 0;
-  S_2_m1_0 = 0;
-  S_2_m1_1 = 0;
-  S_2_0_m1 = 0;
-  S_2_0_0 = 0;
-  S_2_0_1 = 0;
-  S_2_1_m1 = 0;
-  S_2_1_0 = 0;
-  S_2_1_1 = 0;
-  S_2_2_m1 = 0;
-  S_2_2_0 = 0;
-  S_2_2_1 = 0;
-  S_RAFK_m1_m1_0 = 0;
-  S_RAFK_m1_0_0 = 0;
-  S_RAFK_m1_1_0 = 0;
-  S_RAFK_m1_2_0 = 0;
-  S_RAFK_0_m1_0 = 0;
-  S_RAFK_0_0_0 = 0;
-  S_RAFK_0_1_0 = 0;
-  S_RAFK_0_2_0 = 0;
-  S_RAFK_1_m1_0 = 0;
-  S_RAFK_1_0_0 = 0;
-  S_RAFK_1_1_0 = 0;
-  S_RAFK_1_2_0 = 0;
-  S_RAFK_2_m1_0 = 0;
-  S_RAFK_2_0_0 = 0;
-  S_RAFK_2_1_0 = 0;
-  S_RAFK_2_2_0 = 0;
-
-  // Compartment initializations:
-  Cytoplasm = 1;
-
-  // Variable initializations:
-  Reaction1_a1 = 1;
-  Reaction2_d1 = 0.4;
-  Reaction3_k1 = 0.1;
-  Reaction4_a2 = 0.5;
-  Reaction5_d2 = 0.5;
-  Reaction6_k2 = 0.1;
-  Reaction7_a3 = 3.3;
-  Reaction8_d3 = 0.42;
-  Reaction9_k3 = 0.1;
-  Reaction10_a4 = 10;
-  Reaction11_d4 = 0.8;
-  Reaction12_k4 = 0.1;
-  Reaction13_a5 = 3.3;
-  Reaction14_d5 = 0.4;
-  Reaction15_k5 = 0.1;
-  Reaction16_a6 = 10;
-  Reaction17_d6 = 0.8;
-  Reaction18_k6 = 0.1;
-  Reaction19_a7 = 20;
-  Reaction20_d7 = 0.6;
-  Reaction21_k7 = 0.1;
-  Reaction22_a8 = 5;
-  Reaction23_d8 = 0.4;
-  Reaction24_k8 = 0.1;
-  Reaction25_a9 = 20;
-  Reaction26_d9 = 0.6;
-  Reaction27_k9 = 0.1;
-  Reaction28_a10 = 5;
-  Reaction29_d10 = 0.4;
-  Reaction30_k10 = 0.1;
-  Reaction31_kon = 10;
-  Reaction32_koff = 0.5;
-  Reaction33_kon = 10;
-  Reaction34_koff = 0.5;
-  Reaction35_kon = 10;
-  Reaction36_koff = 0.5;
-  Reaction37_kon = 10;
-  Reaction38_koff = 0.5;
-  Reaction39_kon = 10;
-  Reaction40_koff = 0.5;
-  Reaction41_kon = 10;
-  Reaction42_koff = 0.5;
-  Reaction43_kon = 10;
-  Reaction44_koff = 0.5;
-  Reaction45_kon = 10;
-  Reaction46_koff = 0.5;
-  Reaction47_kon = 10;
-  Reaction48_koff = 0.5;
-  Reaction49_kon = 10;
-  Reaction50_koff = 0.5;
-  Reaction51_kon = 10;
-  Reaction52_koff = 0.5;
-  Reaction53_kon = 10;
-  Reaction54_koff = 0.5;
-  Reaction55_kpon = 0;
-  Reaction56_kpoff = 0.05;
-  Reaction57_kpon = 0;
-  Reaction58_kpoff = 0.05;
-  Reaction59_kpon = 0;
-  Reaction60_kpoff = 0.05;
-  Reaction61_kpon = 0;
-  Reaction62_kpoff = 0.05;
-  Reaction63_kpon = 0;
-  Reaction64_kpoff = 0.05;
-  Reaction65_kpon = 0;
-  Reaction66_kpoff = 0.05;
-  Reaction67_kpon = 0;
-  Reaction68_kpoff = 0.05;
-  Reaction69_kpon = 0;
-  Reaction70_kpoff = 0.05;
-  Reaction71_kpon = 0;
-  Reaction72_kpoff = 0.05;
-  Reaction73_kpon = 0;
-  Reaction74_kpoff = 0.05;
-  Reaction75_kpon = 0;
-  Reaction76_kpoff = 0.05;
-  Reaction77_kpon = 0;
-  Reaction78_kpoff = 0.05;
-  Reaction79_kpon = 0;
-  Reaction80_kpoff = 0.05;
-  Reaction81_kpon = 0;
-  Reaction82_kpoff = 0.05;
-  Reaction83_kpon = 0;
-  Reaction84_kpoff = 0.05;
-  Reaction85_kpon = 0;
-  Reaction86_kpoff = 0.05;
-  Reaction87_kpon = 0;
-  Reaction88_kpoff = 0.05;
-  Reaction89_kpon = 0;
-  Reaction90_kpoff = 0.05;
-  Reaction91_kpon = 0;
-  Reaction92_kpoff = 0.05;
-  Reaction93_kpon = 0;
-  Reaction94_kpoff = 0.05;
-  Reaction95_kpon = 0;
-  Reaction96_kpoff = 0.05;
-  Reaction97_kpon = 0;
-  Reaction98_kpoff = 0.05;
-  Reaction99_kpon = 0;
-  Reaction100_kpoff = 0.05;
-  Reaction101_kpon = 0;
-  Reaction102_kpoff = 0.05;
-  Reaction103_kon = 10;
-  Reaction104_koff = 0.5;
-  Reaction105_kon = 10;
-  Reaction106_koff = 0.5;
-  Reaction107_kon = 10;
-  Reaction108_koff = 0.5;
-  Reaction109_kpon = 0;
-  Reaction110_kpoff = 0.05;
-  Reaction111_kpon = 0;
-  Reaction112_kpoff = 0.05;
-  Reaction113_kpon = 0;
-  Reaction114_kpoff = 0.05;
-  Reaction115_kpon = 0;
-  Reaction116_kpoff = 0.05;
-  Reaction117_kpon = 0;
-  Reaction118_kpoff = 0.05;
-  Reaction119_kpon = 0;
-  Reaction120_kpoff = 0.05;
-  Reaction121_kon = 10;
-  Reaction122_koff = 0.5;
-  Reaction123_kon = 10;
-  Reaction124_koff = 0.5;
-  Reaction125_kon = 10;
-  Reaction126_koff = 0.5;
-  Reaction127_kpon = 0;
-  Reaction128_kpoff = 0.05;
-  Reaction129_kpon = 0;
-  Reaction130_kpoff = 0.05;
-  Reaction131_kpon = 0;
-  Reaction132_kpoff = 0.05;
-  Reaction133_kpon = 0;
-  Reaction134_kpoff = 0.05;
-  Reaction135_kpon = 0;
-  Reaction136_kpoff = 0.05;
-  Reaction137_kpon = 0;
-  Reaction138_kpoff = 0.05;
-  Reaction139_kon = 10;
-  Reaction140_koff = 0.5;
-  Reaction141_kon = 10;
-  Reaction142_koff = 0.5;
-  Reaction143_kon = 10;
-  Reaction144_koff = 0.5;
-  Reaction145_kpon = 0;
-  Reaction146_kpoff = 0.05;
-  Reaction147_kpon = 0;
-  Reaction148_kpoff = 0.05;
-  Reaction149_kpon = 0;
-  Reaction150_kpoff = 0.05;
-  Reaction151_kpon = 0;
-  Reaction152_kpoff = 0.05;
-  Reaction153_kpon = 0;
-  Reaction154_kpoff = 0.05;
-  Reaction155_kpon = 0;
-  Reaction156_kpoff = 0.05;
-  Reaction157_kon = 10;
-  Reaction158_koff = 0.5;
-  Reaction159_kon = 10;
-  Reaction160_koff = 0.5;
-  Reaction161_kon = 10;
-  Reaction162_koff = 0.5;
-  Reaction163_kpon = 0;
-  Reaction164_kpoff = 0.05;
-  Reaction165_kpon = 0;
-  Reaction166_kpoff = 0.05;
-  Reaction167_kpon = 0;
-  Reaction168_kpoff = 0.05;
-  Reaction169_kpon = 0;
-  Reaction170_kpoff = 0.05;
-  Reaction171_kpon = 0;
-  Reaction172_kpoff = 0.05;
-  Reaction173_kpon = 0;
-  Reaction174_kpoff = 0.05;
-  Reaction175_kon = 10;
-  Reaction176_koff = 0.5;
-  Reaction177_kpon = 0;
-  Reaction178_kpoff = 0.05;
-  Reaction179_kon = 10;
-  Reaction180_koff = 0.5;
-  Reaction181_kpon = 0;
-  Reaction182_kpoff = 0.05;
-  Reaction183_kon = 10;
-  Reaction184_koff = 0.5;
-  Reaction185_kpon = 0;
-  Reaction186_kpoff = 0.05;
-  Reaction187_kon = 10;
-  Reaction188_koff = 0.5;
-  Reaction189_kpon = 0;
-  Reaction190_kpoff = 0.05;
-  Reaction191_kon = 10;
-  Reaction192_koff = 0.5;
-  Reaction193_kpon = 0;
-  Reaction194_kpoff = 0.05;
-  Reaction195_kon = 10;
-  Reaction196_koff = 0.5;
-  Reaction197_kpon = 0;
-  Reaction198_kpoff = 0.05;
-  Reaction199_kon = 10;
-  Reaction200_koff = 0.5;
-  Reaction201_kpon = 0;
-  Reaction202_kpoff = 0.05;
-  Reaction203_kon = 10;
-  Reaction204_koff = 0.5;
-  Reaction205_kpon = 0;
-  Reaction206_kpoff = 0.05;
-  Reaction207_kon = 10;
-  Reaction208_koff = 0.5;
-  Reaction209_kpon = 0;
-  Reaction210_kpoff = 0.05;
-  Reaction211_kon = 10;
-  Reaction212_koff = 0.5;
-  Reaction213_kpon = 0;
-  Reaction214_kpoff = 0.05;
-  Reaction215_kon = 10;
-  Reaction216_koff = 0.5;
-  Reaction217_kpon = 0;
-  Reaction218_kpoff = 0.05;
-  Reaction219_kon = 10;
-  Reaction220_koff = 0.5;
-  Reaction221_kpon = 0;
-  Reaction222_kpoff = 0.05;
-  Reaction223_kon = 10;
-  Reaction224_koff = 0.5;
-  Reaction225_kpon = 0;
-  Reaction226_kpoff = 0.05;
-  Reaction227_kon = 10;
-  Reaction228_koff = 0.5;
-  Reaction229_kpon = 0;
-  Reaction230_kpoff = 0.05;
-  Reaction231_kon = 10;
-  Reaction232_koff = 0.5;
-  Reaction233_kpon = 0;
-  Reaction234_kpoff = 0.05;
-  Reaction235_kon = 10;
-  Reaction236_koff = 0.5;
-  Reaction237_kpon = 0;
-  Reaction238_kpoff = 0.05;
-  Reaction239_k7 = 0.1;
-  Reaction240_k7 = 0.1;
-  Reaction241_k7 = 0.1;
-  Reaction242_k9a = 0.1;
-  Reaction243_k9a = 0.1;
-  Reaction244_k9a = 0.1;
-  Reaction245_k3 = 0.1;
-  Reaction246_k5a = 0.1;
-  Reaction247_k3 = 0.1;
-  Reaction248_k5a = 0.1;
-  Reaction249_k3 = 0.1;
-  Reaction250_k5a = 0.1;
-  Reaction251_k3 = 0.1;
-  Reaction252_k5a = 0.1;
-  Reaction253_k1a = 100;
-  Reaction254_d1a = 0;
-  Reaction255_k1 = 0.1;
-  Reaction256_k1a = 100;
-  Reaction257_d1a = 0;
-  Reaction258_k1 = 0.1;
-  Reaction259_k1a = 100;
-  Reaction260_d1a = 0;
-  Reaction261_k1 = 0.1;
-  Reaction262_k1a = 100;
-  Reaction263_d1a = 0;
-  Reaction264_k1 = 0.1;
-  Reaction265_k1a = 100;
-  Reaction266_d1a = 0;
-  Reaction267_k1 = 0.1;
-  Reaction268_k1a = 100;
-  Reaction269_d1a = 0;
-  Reaction270_k1 = 0.1;
-  Reaction271_k1a = 100;
-  Reaction272_d1a = 0;
-  Reaction273_k1 = 0.1;
-  Reaction274_k1a = 100;
-  Reaction275_d1a = 0;
-  Reaction276_k1 = 0.1;
-  Reaction277_k1a = 100;
-  Reaction278_d1a = 0;
-  Reaction279_k1 = 0.1;
-  Reaction280_k1a = 100;
-  Reaction281_d1a = 0;
-  Reaction282_k1 = 0.1;
-  Reaction283_k1a = 100;
-  Reaction284_d1a = 0;
-  Reaction285_k1 = 0.1;
-  Reaction286_k1a = 100;
-  Reaction287_d1a = 0;
-  Reaction288_k1 = 0.1;
-  Reaction289_k1a = 100;
-  Reaction290_d1a = 0;
-  Reaction291_k1 = 0.1;
-  Reaction292_k1a = 100;
-  Reaction293_d1a = 0;
-  Reaction294_k1 = 0.1;
-  Reaction295_k1a = 100;
-  Reaction296_d1a = 0;
-  Reaction297_k1 = 0.1;
-  Reaction298_k1a = 100;
-  Reaction299_d1a = 0;
-  Reaction300_k1 = 0.1;
-
-  // Other declarations:
-  const Cytoplasm;
-
-  // Display Names:
-  MAPKP is "MAPK phosphatase";
-  MEKP is "MEK phosphatase";
-  RAFK is "RAF kinase";
-  RAFP is "RAF phosphatase";
-  K_1_0 is "MAPK";
-  K_1_1 is "MAPK-P";
-  K_1_2 is "MAPK-PP";
-  K_2_0 is "MEK";
-  K_2_1 is "MEK-P";
-  K_2_2 is "MEK-PP";
-  K_3_0 is "RAF";
-  K_3_1 is "RAF-P";
-  K_K_1_0_2_2 is "MAPK_MEK-PP";
-  K_K_1_1_2_2 is "MAPK-P_MEK-PP";
-  K_K_2_0_3_1 is "MEK_RAF-P";
-  K_K_2_1_3_1 is "MEK-P_RAF-P";
-  K_MAPKP_1_1 is "MAPK-P_MAPKPase";
-  K_MAPKP_1_2 is "MAPK-PP_MAPKPase";
-  K_MEKP_2_1 is "MEK-P_MEKPase";
-  K_MEKP_2_2 is "MEK-PP_MEKPase";
-  K_RAFK_3_0 is "RAF_RAFK";
-  K_RAFP_3_1 is "RAF-P_RAFPase";
-  S_m1_m1_m1 is "Scaffold";
-  S_m1_m1_0 is "Scaffold_RAF";
-  S_m1_m1_1 is "Scaffold_RAF-P";
-  S_m1_0_m1 is "Scaffold_MEK";
-  S_m1_0_0 is "Scaffold_MEK_RAF";
-  S_m1_0_1 is "Scaffold_MEK_RAF-P";
-  S_m1_1_m1 is "Scaffold_MEK-P";
-  S_m1_1_0 is "Scaffold_MEK-P_RAF";
-  S_m1_1_1 is "Scaffold_MEK-P_RAF-P";
-  S_m1_2_m1 is "Scaffold_MEK-PP";
-  S_m1_2_0 is "Scaffold_MEK-PP_RAF";
-  S_m1_2_1 is "Scaffold_MEK-PP_RAF-P";
-  S_0_m1_m1 is "Scaffold_MAPK";
-  S_0_m1_0 is "Scaffold_MAPK_RAF";
-  S_0_m1_1 is "Scaffold_MAPK_RAF-P";
-  S_0_0_m1 is "Scaffold_MAPK_MEK";
-  S_0_0_0 is "Scaffold_MAPK_MEK_RAF";
-  S_0_0_1 is "Scaffold_MAPK_MEK_RAF-P";
-  S_0_1_m1 is "Scaffold_MAPK_MEK-P";
-  S_0_1_0 is "Scaffold_MAPK_MEK-P_RAF";
-  S_0_1_1 is "Scaffold_MAPK_MEK-P_RAF-P";
-  S_0_2_m1 is "Scaffold_MAPK_MEK-PP";
-  S_0_2_0 is "Scaffold_MAPK_MEK-PP_RAF";
-  S_0_2_1 is "Scaffold_MAPK_MEK-PP_RAF-P";
-  S_1_m1_m1 is "Scaffold_MAPK-P";
-  S_1_m1_0 is "Scaffold_MAPK-P_RAF";
-  S_1_m1_1 is "Scaffold_MAPK-P_RAF-P";
-  S_1_0_m1 is "Scaffold_MAPK-P_MEK";
-  S_1_0_0 is "Scaffold_MAPK-P_MEK_RAF";
-  S_1_0_1 is "Scaffold_MAPK-P_MEK_RAF-P";
-  S_1_1_m1 is "Scaffold_MAPK-P_MEK-P";
-  S_1_1_0 is "Scaffold_MAPK-P_MEK-P_RAF";
-  S_1_1_1 is "Scaffold_MAPK-P_MEK-P_RAF-P";
-  S_1_2_m1 is "Scaffold_MAPK-P_MEK-PP";
-  S_1_2_0 is "Scaffold_MAPK-P_MEK-PP_RAF";
-  S_1_2_1 is "Scaffold_MAPK-P_MEK-PP_RAF-P";
-  S_2_m1_m1 is "Scaffold_MAPK-PP";
-  S_2_m1_0 is "Scaffold_MAPK-PP_RAF";
-  S_2_m1_1 is "Scaffold_MAPK-PP_RAF-P";
-  S_2_0_m1 is "Scaffold_MAPK-PP_MEK";
-  S_2_0_0 is "Scaffold_MAPK-PP_MEK_RAF";
-  S_2_0_1 is "Scaffold_MAPK-PP_MEK_RAF-P";
-  S_2_1_m1 is "Scaffold_MAPK-PP_MEK-P";
-  S_2_1_0 is "Scaffold_MAPK-PP_MEK-P_RAF";
-  S_2_1_1 is "Scaffold_MAPK-PP_MEK-P_RAF-P";
-  S_2_2_m1 is "Scaffold_MAPK-PP_MEK-PP";
-  S_2_2_0 is "Scaffold_MAPK-PP_MEK-PP_RAF";
-  S_2_2_1 is "Scaffold_MAPK-PP_MEK-PP_RAF-P";
-  S_RAFK_m1_m1_0 is "Scaffold_RAF";
-  S_RAFK_m1_0_0 is "Scaffold_MEK_RAF";
-  S_RAFK_m1_1_0 is "Scaffold_MEK-P_RAF";
-  S_RAFK_m1_2_0 is "Scaffold_MEK-PP_RAF";
-  S_RAFK_0_m1_0 is "Scaffold_MAPK_RAF";
-  S_RAFK_0_0_0 is "Scaffold_MAPK_MEK_RAF";
-  S_RAFK_0_1_0 is "Scaffold_MAPK_MEK-P_RAF";
-  S_RAFK_0_2_0 is "Scaffold_MAPK_MEK-PP_RAF";
-  S_RAFK_1_m1_0 is "Scaffold_MAPK-P_RAF";
-  S_RAFK_1_0_0 is "Scaffold_MAPK-P_MEK_RAF";
-  S_RAFK_1_1_0 is "Scaffold_MAPK-P_MEK-P_RAF";
-  S_RAFK_1_2_0 is "Scaffold_MAPK-P_MEK-PP_RAF";
-  S_RAFK_2_m1_0 is "Scaffold_MAPK-PP_RAF";
-  S_RAFK_2_0_0 is "Scaffold_MAPK-PP_MEK_RAF";
-  S_RAFK_2_1_0 is "Scaffold_MAPK-PP_MEK-P_RAF";
-  S_RAFK_2_2_0 is "Scaffold_MAPK-PP_MEK-PP_RAF";
-  Reaction1 is "binding of RAF and RAFK";
-  Reaction2 is "dissociation of RAF_RAFK";
-  Reaction3 is "phosphorylation of RAF";
-  Reaction4 is "binding of RAF-P and RAF phosphatase";
-  Reaction5 is "dissociation of RAF-P_RAFPase";
-  Reaction6 is "dephosphorylation of RAF-P";
-  Reaction7 is "binding of MEK and RAF-P";
-  Reaction8 is "dissociation of MEK_RAF-P";
-  Reaction9 is "phosphorylation of MEK";
-  Reaction10 is "binding of MEK-P and MEK phosphatase";
-  Reaction11 is "dissociation of MEK-P_MEKPase";
-  Reaction12 is "dephosphorylation of MEK-P";
-  Reaction13 is "binding of MEK-P and RAF-P";
-  Reaction14 is "dissociation of MEK-P_RAF-P";
-  Reaction15 is "phosphorylation of MEK-P";
-  Reaction16 is "binding of MEK-PP and MEK phosphatase";
-  Reaction17 is "dissociation of MEK-PP_MEKPase";
-  Reaction18 is "dephosphorylation of MEK-PP";
-  Reaction19 is "binding of MAPK and MEK-PP";
-  Reaction20 is "dissociation of MAPK_MEK-PP";
-  Reaction21 is "phosphorylation of MAPK";
-  Reaction22 is "binding of MAPK-P and MAPK phosphatase";
-  Reaction23 is "dissociation of MAPK-P_MAPKPase";
-  Reaction24 is "dephosphorylation of MAPK-P";
-  Reaction25 is "binding of MAPK-P and MEK-PP";
-  Reaction26 is "dissociation of MAPK-P_MEK-PP";
-  Reaction27 is "phosphorylation of MAPK-P";
-  Reaction28 is "binding of MAPK-PP and MAPK phosphatase";
-  Reaction29 is "dissociation of MAPK-PP_MAPKPase";
-  Reaction30 is "dephosphorylation of MAPK-PP";
-  Reaction31 is "binding of MAPK on scaffold";
-  Reaction32 is "dissociation of MAPK from scaffold";
-  Reaction33 is "binding of MAPK on scaffold";
-  Reaction34 is "dissociation of MAPK from scaffold";
-  Reaction35 is "binding of MAPK on scaffold";
-  Reaction36 is "dissociation of MAPK from scaffold";
-  Reaction37 is "binding of MAPK on scaffold";
-  Reaction38 is "dissociation of MAPK from scaffold";
-  Reaction39 is "binding of MAPK on scaffold";
-  Reaction40 is "dissociation of MAPK from scaffold";
-  Reaction41 is "binding of MAPK on scaffold";
-  Reaction42 is "dissociation of MAPK from scaffold";
-  Reaction43 is "binding of MAPK on scaffold";
-  Reaction44 is "dissociation of MAPK from scaffold";
-  Reaction45 is "binding of MAPK on scaffold";
-  Reaction46 is "dissociation of MAPK from scaffold";
-  Reaction47 is "binding of MAPK on scaffold";
-  Reaction48 is "dissociation of MAPK from scaffold";
-  Reaction49 is "binding of MAPK on scaffold";
-  Reaction50 is "dissociation of MAPK from scaffold";
-  Reaction51 is "binding of MAPK on scaffold";
-  Reaction52 is "dissociation of MAPK from scaffold";
-  Reaction53 is "binding of MAPK on scaffold";
-  Reaction54 is "dissociation of MAPK from scaffold";
-  Reaction55 is "binding of MAPK-P on scaffold";
-  Reaction56 is "dissociation of MAPK-P from scaffold";
-  Reaction57 is "binding of MAPK-P on scaffold";
-  Reaction58 is "dissociation of MAPK-P from scaffold";
-  Reaction59 is "binding of MAPK-P on scaffold";
-  Reaction60 is "dissociation of MAPK-P from scaffold";
-  Reaction61 is "binding of MAPK-P on scaffold";
-  Reaction62 is "dissociation of MAPK-P from scaffold";
-  Reaction63 is "binding of MAPK-P on scaffold";
-  Reaction64 is "dissociation of MAPK-P from scaffold";
-  Reaction65 is "binding of MAPK-P on scaffold";
-  Reaction66 is "dissociation of MAPK-P from scaffold";
-  Reaction67 is "binding of MAPK-P on scaffold";
-  Reaction68 is "dissociation of MAPK-P from scaffold";
-  Reaction69 is "binding of MAPK-P on scaffold";
-  Reaction70 is "dissociation of MAPK-P from scaffold";
-  Reaction71 is "binding of MAPK-P on scaffold";
-  Reaction72 is "dissociation of MAPK-P from scaffold";
-  Reaction73 is "binding of MAPK-P on scaffold";
-  Reaction74 is "dissociation of MAPK-P from scaffold";
-  Reaction75 is "binding of MAPK-P on scaffold";
-  Reaction76 is "dissociation of MAPK-P from scaffold";
-  Reaction77 is "binding of MAPK-P on scaffold";
-  Reaction78 is "dissociation of MAPK-P from scaffold";
-  Reaction79 is "binding of MAPK-PP on scaffold";
-  Reaction80 is "dissociation of MAPK-PP from scaffold";
-  Reaction81 is "binding of MAPK-PP on scaffold";
-  Reaction82 is "dissociation of MAPK-PP from scaffold";
-  Reaction83 is "binding of MAPK-PP on scaffold";
-  Reaction84 is "dissociation of MAPK-PP from scaffold";
-  Reaction85 is "binding of MAPK-PP on scaffold";
-  Reaction86 is "dissociation of MAPK-PP from scaffold";
-  Reaction87 is "binding of MAPK-PP on scaffold";
-  Reaction88 is "dissociation of MAPK-PP from scaffold";
-  Reaction89 is "binding of MAPK-PP on scaffold";
-  Reaction90 is "dissociation of MAPK-PP from scaffold";
-  Reaction91 is "binding of MAPK-PP on scaffold";
-  Reaction92 is "dissociation of MAPK-PP from scaffold";
-  Reaction93 is "binding of MAPK-PP on scaffold";
-  Reaction94 is "dissociation of MAPK-PP from scaffold";
-  Reaction95 is "binding of MAPK-PP on scaffold";
-  Reaction96 is "dissociation of MAPK-PP from scaffold";
-  Reaction97 is "binding of MAPK-PP on scaffold";
-  Reaction98 is "dissociation of MAPK-PP from scaffold";
-  Reaction99 is "binding of MAPK-PP on scaffold";
-  Reaction100 is "dissociation of MAPK-PP from scaffold";
-  Reaction101 is "binding of MAPK-PP on scaffold";
-  Reaction102 is "dissociation of MAPK-PP from scaffold";
-  Reaction103 is "binding of MEK on scaffold";
-  Reaction104 is "dissociation of MEK from scaffold";
-  Reaction105 is "binding of MEK on scaffold";
-  Reaction106 is "dissociation of MEK from scaffold";
-  Reaction107 is "binding of MEK on scaffold";
-  Reaction108 is "dissociation of MEK from scaffold";
-  Reaction109 is "binding of MEK-P on scaffold";
-  Reaction110 is "dissociation of MEK-P from scaffold";
-  Reaction111 is "binding of MEK-P on scaffold";
-  Reaction112 is "dissociation of MEK-P from scaffold";
-  Reaction113 is "binding of MEK-P on scaffold";
-  Reaction114 is "dissociation of MEK-P from scaffold";
-  Reaction115 is "binding of MEK-PP on scaffold";
-  Reaction116 is "dissociation of MEK-PP from scaffold";
-  Reaction117 is "binding of MEK-PP on scaffold";
-  Reaction118 is "dissociation of MEK-PP from scaffold";
-  Reaction119 is "binding of MEK-PP on scaffold";
-  Reaction120 is "dissociation of MEK-PP from scaffold";
-  Reaction121 is "binding of MEK on scaffold";
-  Reaction122 is "dissociation of MEK from scaffold";
-  Reaction123 is "binding of MEK on scaffold";
-  Reaction124 is "dissociation of MEK from scaffold";
-  Reaction125 is "binding of MEK on scaffold";
-  Reaction126 is "dissociation of MEK from scaffold";
-  Reaction127 is "binding of MEK-P on scaffold";
-  Reaction128 is "dissociation of MEK-P from scaffold";
-  Reaction129 is "binding of MEK-P on scaffold";
-  Reaction130 is "dissociation of MEK-P from scaffold";
-  Reaction131 is "binding of MEK-P on scaffold";
-  Reaction132 is "dissociation of MEK-P from scaffold";
-  Reaction133 is "binding of MEK-PP on scaffold";
-  Reaction134 is "dissociation of MEK-PP from scaffold";
-  Reaction135 is "binding of MEK-PP on scaffold";
-  Reaction136 is "dissociation of MEK-PP from scaffold";
-  Reaction137 is "binding of MEK-PP on scaffold";
-  Reaction138 is "dissociation of MEK-PP from scaffold";
-  Reaction139 is "binding of MEK on scaffold";
-  Reaction140 is "dissociation of MEK from scaffold";
-  Reaction141 is "binding of MEK on scaffold";
-  Reaction142 is "dissociation of MEK from scaffold";
-  Reaction143 is "binding of MEK on scaffold";
-  Reaction144 is "dissociation of MEK from scaffold";
-  Reaction145 is "binding of MEK-P on scaffold";
-  Reaction146 is "dissociation of MEK-P from scaffold";
-  Reaction147 is "binding of MEK-P on scaffold";
-  Reaction148 is "dissociation of MEK-P from scaffold";
-  Reaction149 is "binding of MEK-P on scaffold";
-  Reaction150 is "dissociation of MEK-P from scaffold";
-  Reaction151 is "binding of MEK-PP on scaffold";
-  Reaction152 is "dissociation of MEK-PP from scaffold";
-  Reaction153 is "binding of MEK-PP on scaffold";
-  Reaction154 is "dissociation of MEK-PP from scaffold";
-  Reaction155 is "binding of MEK-PP on scaffold";
-  Reaction156 is "dissociation of MEK-PP from scaffold";
-  Reaction157 is "binding of MEK on scaffold";
-  Reaction158 is "dissociation of MEK from scaffold";
-  Reaction159 is "binding of MEK on scaffold";
-  Reaction160 is "dissociation of MEK from scaffold";
-  Reaction161 is "binding of MEK on scaffold";
-  Reaction162 is "dissociation of MEK from scaffold";
-  Reaction163 is "binding of MEK-P on scaffold";
-  Reaction164 is "dissociation of MEK-P from scaffold";
-  Reaction165 is "binding of MEK-P on scaffold";
-  Reaction166 is "dissociation of MEK-P from scaffold";
-  Reaction167 is "binding of MEK-P on scaffold";
-  Reaction168 is "dissociation of MEK-P from scaffold";
-  Reaction169 is "binding of MEK-PP on scaffold";
-  Reaction170 is "dissociation of MEK-PP from scaffold";
-  Reaction171 is "binding of MEK-PP on scaffold";
-  Reaction172 is "dissociation of MEK-PP from scaffold";
-  Reaction173 is "binding of MEK-PP on scaffold";
-  Reaction174 is "dissociation of MEK-PP from scaffold";
-  Reaction175 is "binding of RAF on scaffold";
-  Reaction176 is "dissociation of RAF from scaffold";
-  Reaction177 is "binding of RAF-P on scaffold";
-  Reaction178 is "dissociation of RAF-P from scaffold";
-  Reaction179 is "binding of RAF on scaffold";
-  Reaction180 is "dissociation of RAF from scaffold";
-  Reaction181 is "binding of RAF-P on scaffold";
-  Reaction182 is "dissociation of RAF-P from scaffold";
-  Reaction183 is "binding of RAF on scaffold";
-  Reaction184 is "dissociation of RAF from scaffold";
-  Reaction185 is "binding of RAF-P on scaffold";
-  Reaction186 is "dissociation of RAF-P from scaffold";
-  Reaction187 is "binding of RAF on scaffold";
-  Reaction188 is "dissociation of RAF from scaffold";
-  Reaction189 is "binding of RAF-P on scaffold";
-  Reaction190 is "dissociation of RAF-P from scaffold";
-  Reaction191 is "binding of RAF on scaffold";
-  Reaction192 is "dissociation of RAF from scaffold";
-  Reaction193 is "binding of RAF-P on scaffold";
-  Reaction194 is "dissociation of RAF-P from scaffold";
-  Reaction195 is "binding of RAF on scaffold";
-  Reaction196 is "dissociation of RAF from scaffold";
-  Reaction197 is "binding of RAF-P on scaffold";
-  Reaction198 is "dissociation of RAF from scaffold";
-  Reaction199 is "binding of RAF on scaffold";
-  Reaction200 is "dissociation of RAF from scaffold";
-  Reaction201 is "binding of RAF-P on scaffold";
-  Reaction202 is "dissociation of RAF-P from scaffold";
-  Reaction203 is "binding of RAF on scaffold";
-  Reaction204 is "dissociation of RAF from scaffold";
-  Reaction205 is "binding of RAF-P on scaffold";
-  Reaction206 is "dissociation of RAF-P from scaffold";
-  Reaction207 is "binding of RAF on scaffold";
-  Reaction208 is "dissociation of RAF from scaffold";
-  Reaction209 is "binding of RAF-P on scaffold";
-  Reaction210 is "dissociation of RAF-P from scaffold";
-  Reaction211 is "binding of RAF on scaffold";
-  Reaction212 is "dissociation of RAF from scaffold";
-  Reaction213 is "binding of RAF-P on scaffold";
-  Reaction214 is "dissociation of RAF-P from scaffold";
-  Reaction215 is "binding of RAF on scaffold";
-  Reaction216 is "dissociation of RAF from scaffold";
-  Reaction217 is "binding of RAF-P on scaffold";
-  Reaction218 is "dissociation of RAF-P from scaffold";
-  Reaction219 is "binding of RAF on scaffold";
-  Reaction220 is "dissociation of RAF from scaffold";
-  Reaction221 is "binding of RAF-P on scaffold";
-  Reaction222 is "dissociation of RAF-P from scaffold";
-  Reaction223 is "binding of RAF on scaffold";
-  Reaction224 is "dissociation of RAF from scaffold";
-  Reaction225 is "binding of RAF-P on scaffold";
-  Reaction226 is "dissociation of RAF-P from scaffold";
-  Reaction227 is "binding of RAF on scaffold";
-  Reaction228 is "dissociation of RAF from scaffold";
-  Reaction229 is "binding of RAF-P on scaffold";
-  Reaction230 is "dissociation of RAF-P from scaffold";
-  Reaction231 is "binding of RAF on scaffold";
-  Reaction232 is "dissociation of RAF from scaffold";
-  Reaction233 is "binding of RAF-P on scaffold";
-  Reaction234 is "dissociation of RAF-P from scaffold";
-  Reaction235 is "binding of RAF on scaffold";
-  Reaction236 is "dissociation of RAF from scaffold";
-  Reaction237 is "binding of RAF-P on scaffold";
-  Reaction238 is "dissociation of RAF-P from scaffold";
-  Reaction239 is "phosphorylation of MAPK on scaffold";
-  Reaction240 is "phosphorylation of MAPK on scaffold";
-  Reaction241 is "phosphorylation of MAPK on scaffold";
-  Reaction242 is "phosphorylation of MAPK-P on scaffold";
-  Reaction243 is "phosphorylation of MAPK-P on scaffold";
-  Reaction244 is "phosphorylation of MAPK-P on scaffold";
-  Reaction245 is "phosphorylation of MEK on scaffold";
-  Reaction246 is "phosphorylation of MEK-P on scaffold";
-  Reaction247 is "phosphorylation of MEK on scaffold";
-  Reaction248 is "phosphorylation of MEK-P on scaffold";
-  Reaction249 is "phosphorylation of MEK on scaffold";
-  Reaction250 is "phosphorylation of MEK-P on scaffold";
-  Reaction251 is "phosphorylation of MEK on scaffold";
-  Reaction252 is "phosphorylation of MEK-P on scaffold";
-  Reaction253 is "binding of RAF and RAFK";
-  Reaction254 is "dissociation of RAF_RAFK";
-  Reaction255 is "phosphorylation of RAF on scaffold";
-  Reaction256 is "binding of RAF and RAFK";
-  Reaction257 is "dissociation of RAF_RAFK";
-  Reaction258 is "phosphorylation of RAF on scaffold";
-  Reaction259 is "binding of RAF and RAFK";
-  Reaction260 is "dissociation of RAF_RAFK";
-  Reaction261 is "phosphorylation of RAF on scaffold";
-  Reaction262 is "binding of RAF and RAFK";
-  Reaction263 is "dissociation of RAF_RAFK";
-  Reaction264 is "phosphorylation of RAF on scaffold";
-  Reaction265 is "binding of RAF and RAFK";
-  Reaction266 is "dissociation of RAF_RAFK";
-  Reaction267 is "phosphorylation of RAF on scaffold";
-  Reaction268 is "binding of RAF and RAFK";
-  Reaction269 is "dissociation of RAF_RAFK";
-  Reaction270 is "phosphorylation of RAF on scaffold";
-  Reaction271 is "binding of RAF and RAFK";
-  Reaction272 is "dissociation of RAF_RAFK";
-  Reaction273 is "phosphorylation of RAF on scaffold";
-  Reaction274 is "binding of RAF and RAFK";
-  Reaction275 is "dissociation of RAF_RAFK";
-  Reaction276 is "phosphorylation of RAF on scaffold";
-  Reaction277 is "binding of RAF and RAFK";
-  Reaction278 is "dissociation of RAF_RAFK";
-  Reaction279 is "phosphorylation of RAF on scaffold";
-  Reaction280 is "binding of RAF and RAFK";
-  Reaction281 is "dissociation of RAF_RAFK";
-  Reaction282 is "phosphorylation of RAF on scaffold";
-  Reaction283 is "binding of RAF and RAFK";
-  Reaction284 is "dissociation of RAF_RAFK";
-  Reaction285 is "phosphorylation of RAF on scaffold";
-  Reaction286 is "binding of RAF and RAFK";
-  Reaction287 is "dissociation of RAF_RAFK";
-  Reaction288 is "phosphorylation of RAF on scaffold";
-  Reaction289 is "binding of RAF and RAFK";
-  Reaction290 is "dissociation of RAF_RAFK";
-  Reaction291 is "phosphorylation of RAF on scaffold";
-  Reaction292 is "binding of RAF and RAFK";
-  Reaction293 is "dissociation of RAF_RAFK";
-  Reaction294 is "phosphorylation of RAF on scaffold";
-  Reaction295 is "binding of RAF and RAFK";
-  Reaction296 is "dissociation of RAF_RAFK";
-  Reaction297 is "phosphorylation of RAF on scaffold";
-  Reaction298 is "binding of RAF and RAFK";
-  Reaction299 is "dissociation of RAF_RAFK";
-  Reaction300 is "phosphorylation of RAF on scaffold";
-
-  // CV terms:
-  Cytoplasm hypernym "http://identifiers.org/go/GO:0005737"
-  MAPKP identity "http://identifiers.org/uniprot/Q90W58"
-  RAFK hypernym "http://identifiers.org/interpro/IPR003577"
-  K_1_0 hypernym "http://identifiers.org/uniprot/P26696"
-  K_1_1 hypernym "http://identifiers.org/uniprot/P26696"
-  K_1_2 hypernym "http://identifiers.org/uniprot/P26696"
-  K_2_0 hypernym "http://identifiers.org/uniprot/Q05116"
-  K_2_1 hypernym "http://identifiers.org/uniprot/Q05116"
-  K_2_2 identity "http://identifiers.org/uniprot/Q05116"
-  K_3_0 hypernym "http://identifiers.org/uniprot/P09560"
-  K_3_1 hypernym "http://identifiers.org/uniprot/P09560"
-  K_K_1_0_2_2 part "http://identifiers.org/uniprot/Q05116",
-                   "http://identifiers.org/uniprot/P26696"
-  K_K_1_1_2_2 part "http://identifiers.org/uniprot/Q05116",
-                   "http://identifiers.org/uniprot/P26696"
-  K_K_2_0_3_1 part "http://identifiers.org/uniprot/P09560",
-                   "http://identifiers.org/uniprot/Q05116"
-  K_K_2_1_3_1 part "http://identifiers.org/uniprot/P09560",
-                   "http://identifiers.org/uniprot/Q05116"
-  K_MAPKP_1_1 part "http://identifiers.org/uniprot/P26696",
-                   "http://identifiers.org/uniprot/Q90W58"
-  K_MAPKP_1_2 part "http://identifiers.org/uniprot/P26696",
-                   "http://identifiers.org/uniprot/Q90W58"
-  K_MEKP_2_1 part "http://identifiers.org/uniprot/Q05116"
-  K_MEKP_2_2 part "http://identifiers.org/uniprot/Q05116"
-  K_RAFK_3_0 part "http://identifiers.org/uniprot/P09560"
-  K_RAFP_3_1 part "http://identifiers.org/uniprot/P09560"
-  S_m1_m1_0 part "http://identifiers.org/uniprot/P09560"
-  S_m1_m1_1 part "http://identifiers.org/uniprot/P09560"
-  S_m1_0_m1 part "http://identifiers.org/uniprot/Q05116"
-  S_m1_0_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_0_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_1_m1 part "http://identifiers.org/uniprot/Q05116"
-  S_m1_1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_2_m1 part "http://identifiers.org/uniprot/Q05116"
-  S_m1_2_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_2_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_0_m1_m1 part "http://identifiers.org/uniprot/P26696"
-  S_0_m1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_m1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_0_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_0_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_0_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_1_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_1_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_1_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_2_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_2_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_2_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_m1_m1 part "http://identifiers.org/uniprot/P26696"
-  S_1_m1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_m1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_0_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_0_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_0_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_1_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_1_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_1_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_2_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_2_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_2_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_m1_m1 part "http://identifiers.org/uniprot/P26696"
-  S_2_m1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_m1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_0_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_0_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_0_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_1_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_1_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_1_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_2_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_2_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_2_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_RAFK_m1_m1_0 part "http://identifiers.org/uniprot/P09560"
-  S_RAFK_m1_0_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/Q05116"
-  S_RAFK_m1_1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/Q05116"
-  S_RAFK_m1_2_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/Q05116"
-  S_RAFK_0_m1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/P26696"
-  S_RAFK_0_0_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_0_1_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_0_2_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_m1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_0_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_1_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_2_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_m1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_0_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_1_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_2_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  Reaction1 homolog "http://identifiers.org/reactome/REACT_996"
-  Reaction1 hypernym "http://identifiers.org/go/GO:0031435",
-                     "http://identifiers.org/go/GO:0006461"
-  Reaction2 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction3 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                     "http://identifiers.org/go/GO:0008349",
-                     "http://identifiers.org/go/GO:0000185"
-  Reaction4 hypernym "http://identifiers.org/go/GO:0031435"
-  Reaction5 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction6 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/go/GO:0006470"
-  Reaction7 hypernym "http://identifiers.org/go/GO:0031434",
-                     "http://identifiers.org/go/GO:0031435"
-  Reaction7 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction8 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction9 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-                     "http://identifiers.org/go/GO:0004709",
-                     "http://identifiers.org/go/GO:0006468"
-  Reaction10 hypernym "http://identifiers.org/go/GO:0031435"
-  Reaction11 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction12 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/go/GO:0006470"
-  Reaction13 hypernym "http://identifiers.org/go/GO:0031434",
-                      "http://identifiers.org/go/GO:0031435"
-  Reaction13 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction14 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction15 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                      "http://identifiers.org/go/GO:0000186",
-                      "http://identifiers.org/go/GO:0004709",
-                      "http://identifiers.org/go/GO:0006468"
-  Reaction15 homolog "http://identifiers.org/reactome/REACT_614"
-  Reaction16 hypernym "http://identifiers.org/go/GO:0031434"
-  Reaction17 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction18 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/go/GO:0006470"
-  Reaction19 hypernym "http://identifiers.org/go/GO:0051019",
-                      "http://identifiers.org/go/GO:0031434"
-  Reaction19 homolog "http://identifiers.org/reactome/REACT_1780",
-                     "http://identifiers.org/reactome/REACT_495"
-  Reaction20 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction21 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                      "http://identifiers.org/go/GO:0004708",
-                      "http://identifiers.org/go/GO:0006468"
-  Reaction21 homolog "http://identifiers.org/reactome/REACT_136",
-                     "http://identifiers.org/reactome/REACT_2247"
-  Reaction22 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction23 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction24 hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  Reaction25 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction26 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction27 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                      "http://identifiers.org/go/GO:0000187",
-                      "http://identifiers.org/go/GO:0004708"
-  Reaction28 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction29 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction30 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/go/GO:0000188"
-  Reaction31 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction32 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction33 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction34 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction35 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction36 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction37 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction38 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction39 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction40 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction41 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction42 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction43 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction44 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction45 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction46 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction47 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction48 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction49 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction50 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction51 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction52 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction53 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction54 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction55 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction56 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction57 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction58 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction59 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction60 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction61 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction62 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction63 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction64 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction65 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction66 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction67 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction68 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction69 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction70 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction71 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction72 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction73 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction74 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction75 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction76 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction77 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction78 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction79 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction80 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction81 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction82 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction83 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction84 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction85 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction86 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction87 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction88 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction89 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction90 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction91 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction92 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction93 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction94 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction95 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction96 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction97 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction98 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction99 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction101 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction102 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction104 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction106 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction108 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction110 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction112 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction114 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction116 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction118 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction120 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction122 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction124 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction126 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction128 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction130 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction132 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction134 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction136 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction138 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction140 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction142 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction144 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction146 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction148 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction150 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction152 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction154 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction156 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction158 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction160 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction162 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction164 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction166 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction168 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction170 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction172 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction174 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction176 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction178 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction180 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction182 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction184 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction186 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction188 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction190 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction192 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction194 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction196 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction198 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction200 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction202 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction204 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction206 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction208 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction210 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction212 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction214 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction216 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction218 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction220 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction222 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction224 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction226 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction228 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction230 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction232 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction234 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction236 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction238 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction239 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction240 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction241 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction242 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000187",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction243 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000187",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction244 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000187",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction245 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction246 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction247 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction248 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction249 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction250 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction251 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction252 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction253 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction254 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction255 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction256 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction257 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction258 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction259 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction260 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction261 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction262 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction263 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction264 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction265 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction266 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction267 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction268 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction269 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction270 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction271 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction272 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction273 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction274 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction275 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction276 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction277 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction278 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction279 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction280 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction281 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction282 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction283 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction284 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction285 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction286 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction287 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction288 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction289 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction290 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction291 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction292 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction293 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction294 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction295 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction296 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction297 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction298 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction299 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction300 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-end
-
-MAPK_in_Scaffold is "Levchenko2000_MAPK_Scaffold"
-
-MAPK_in_Scaffold model_entity_is "http://identifiers.org/biomodels.db/MODEL6616691524"
-MAPK_in_Scaffold model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000014"
-MAPK_in_Scaffold description "http://identifiers.org/pubmed/10823939"
-MAPK_in_Scaffold origin "http://identifiers.org/biomodels.db/BIOMD0000000011"
-MAPK_in_Scaffold hypernym "http://identifiers.org/go/GO:0005078",
-                          "http://identifiers.org/go/GO:0000165"
-MAPK_in_Scaffold homolog "http://identifiers.org/reactome/REACT_634"
-MAPK_in_Scaffold taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000015.txt b/BioModelsRAG/data/BIOMD0000000015.txt
deleted file mode 100644
index 94e954d0c1f4b7cf796ce124a010e1a73e42a462..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000015.txt
+++ /dev/null
@@ -1,411 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000015()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species PRPP in cell, IMP in cell, SAMP in cell, ATP in cell;
-  substanceOnly species SAM in cell, Ade in cell, XMP in cell, GTP in cell;
-  substanceOnly species dATP in cell, dGTP in cell, RNA in cell, DNA_ in cell;
-  substanceOnly species HX in cell, Xa in cell, Gua in cell, UA in cell, $R5P in cell;
-  substanceOnly species $Pi in cell;
-
-  // Reactions:
-  ada: ATP => HX; ada_aada*ATP^ada_fada4;
-  ade: Ade => ; ade_aade*Ade^ade_fade6;
-  adna: dATP => DNA_; adna_aadna*dATP^adna_fdnap9*dGTP^adna_fdnap10;
-  adrnr: ATP => dATP; adrnr_aadrnr*ATP^adrnr_fadrnr4*dATP^adrnr_fadrnr9*dGTP^adrnr_fadrnr10;
-  ampd: ATP => IMP; ampd_aampd*ATP^ampd_fampd4*GTP^ampd_fampd8*Pi^ampd_fampd18;
-  aprt: PRPP + Ade => ATP; aprt_aaprt*PRPP^aprt_faprt1*ATP^aprt_faprt4*Ade^aprt_faprt6;
-  arna: ATP => RNA; arna_aarna*ATP^arna_frnap4*GTP^arna_frnap8;
-  asuc: IMP => SAMP; asuc_aasuc*IMP^asuc_fasuc2*ATP^asuc_fasuc4*GTP^asuc_fasuc8*Pi^asuc_fasuc18;
-  asli: SAMP => ATP; asli_aasli*SAMP^asli_fasli3*ATP^asli_fasli4;
-  dada: dATP => HX; dada_adada*dATP^dada_fdada9;
-  den: PRPP => IMP; den_aden*PRPP^den_fden1*IMP^den_fden2*ATP^den_fden4*GTP^den_fden8*Pi^den_fden18;
-  dgnuc: dGTP => Gua; dgnuc_adgnuc*dGTP^dgnuc_fdgnuc10;
-  dnaa: DNA_ => dATP; dnaa_adnaa*DNA_^dnaa_fdnan12;
-  dnag: DNA_ => dGTP; dnag_adnag*DNA_^dnag_fdnan12;
-  gdna: dGTP => DNA_; gdna_agdna*dATP^gdna_fdnap9*dGTP^gdna_fdnap10;
-  gdrnr: GTP => dGTP; gdrnr_agdrnr*GTP^gdrnr_fgdrnr8*dATP^gdrnr_fgdrnr9*dGTP^gdrnr_fgdrnr10;
-  gmpr: GTP => IMP; gmpr_agmpr*IMP^gmpr_fgmpr2*ATP^gmpr_fgmpr4*XMP^gmpr_fgmpr7*GTP^gmpr_fgmpr8;
-  gmps: XMP => GTP; gmps_agmps*ATP^gmps_fgmps4*XMP^gmps_fgmps7;
-  gnuc: GTP => Gua; gnuc_agnuc*GTP^gnuc_fgnuc8*Pi^gnuc_fgnuc18;
-  gprt: Gua + PRPP => GTP; gprt_agprt*PRPP^gprt_fgprt1*GTP^gprt_fgprt8*Gua^gprt_fgprt15;
-  grna: GTP => RNA; grna_agrna*ATP^grna_frnap4*GTP^grna_frnap8;
-  gua: Gua => Xa; gua_agua*Gua^gua_fgua15;
-  hprt: HX + PRPP => IMP; hprt_ahprt*PRPP^hprt_fhprt1*IMP^hprt_fhprt2*HX^hprt_fhprt13;
-  hx: HX => ; hx_ahx*HX^hx_fhx13;
-  hxd: HX => Xa; hxd_ahxd*HX^hxd_fhxd13;
-  impd: IMP => XMP; impd_aimpd*IMP^impd_fimpd2*XMP^impd_fimpd7*GTP^impd_fimpd8;
-  inuc: IMP => HX; inuc_ainuc*IMP^inuc_finuc2*Pi^inuc_finuc18;
-  mat: ATP => SAM; mat_amat*ATP^mat_fmat4*SAM^mat_fmat5;
-  polyam: SAM => Ade; polyam_apolyam*SAM^polyam_fpolyam5;
-  prpps: $R5P => PRPP; prpps_aprpps*PRPP^prpps_fprpps1*ATP^prpps_fprpps4*GTP^prpps_fprpps8*R5P^prpps_fprpps17*Pi^prpps_fprpps18;
-  pyr: PRPP => ; pyr_apyr*PRPP^pyr_fpyr1;
-  rnaa: RNA => ATP; rnaa_arnaa*RNA^rnaa_frnan11;
-  rnag: RNA => GTP; rnag_arnag*RNA^rnag_frnan11;
-  trans: SAM => ATP; trans_atrans*SAM^trans_ftrans5;
-  ua: UA => ; ua_aua*UA^ua_fua16;
-  x: Xa => ; x_ax*Xa^x_fx14;
-  xd: Xa => UA; xd_axd*Xa^xd_fxd14;
-
-  // Species initializations:
-  PRPP = 5.01742/cell;
-  IMP = 98.2634/cell;
-  SAMP = 0.198189/cell;
-  ATP = 2475.35/cell;
-  SAM = 3.99187/cell;
-  Ade = 0.98473/cell;
-  XMP = 24.793/cell;
-  GTP = 410.223/cell;
-  dATP = 6.01413/cell;
-  dGTP = 3.02581/cell;
-  RNA = 28680.5/cell;
-  DNA_ = 5179.34/cell;
-  HX = 9.51785/cell;
-  Xa = 5.05941/cell;
-  Gua = 5.50638/cell;
-  UA = 100.293/cell;
-  R5P = 18/cell;
-  Pi = 1400/cell;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  ada_aada = 0.001062;
-  ada_fada4 = 0.97;
-  ade_aade = 0.01;
-  ade_fade6 = 0.55;
-  adna_aadna = 3.2789;
-  adna_fdnap9 = 0.42;
-  adna_fdnap10 = 0.33;
-  adrnr_aadrnr = 0.0602;
-  adrnr_fadrnr4 = 0.1;
-  adrnr_fadrnr9 = -0.3;
-  adrnr_fadrnr10 = 0.87;
-  ampd_aampd = 0.02688;
-  ampd_fampd4 = 0.8;
-  ampd_fampd8 = -0.03;
-  ampd_fampd18 = -0.1;
-  aprt_aaprt = 233.8;
-  aprt_faprt1 = 0.5;
-  aprt_faprt4 = -0.8;
-  aprt_faprt6 = 0.75;
-  arna_aarna = 614.5;
-  arna_frnap4 = 0.05;
-  arna_frnap8 = 0.13;
-  asuc_aasuc = 3.5932;
-  asuc_fasuc2 = 0.4;
-  asuc_fasuc4 = -0.24;
-  asuc_fasuc8 = 0.2;
-  asuc_fasuc18 = -0.05;
-  asli_aasli = 66544;
-  asli_fasli3 = 0.99;
-  asli_fasli4 = -0.95;
-  dada_adada = 0.03333;
-  dada_fdada9 = 1;
-  den_aden = 5.2728;
-  den_fden1 = 2;
-  den_fden2 = -0.06;
-  den_fden4 = -0.25;
-  den_fden8 = -0.2;
-  den_fden18 = -0.08;
-  dgnuc_adgnuc = 0.03333;
-  dgnuc_fdgnuc10 = 1;
-  dnaa_adnaa = 0.001938;
-  dnaa_fdnan12 = 1;
-  dnag_adnag = 0.001318;
-  dnag_fdnan12 = 1;
-  gdna_agdna = 2.2296;
-  gdna_fdnap9 = 0.42;
-  gdna_fdnap10 = 0.33;
-  gdrnr_agdrnr = 0.1199;
-  gdrnr_fgdrnr8 = 0.4;
-  gdrnr_fgdrnr9 = -1.2;
-  gdrnr_fgdrnr10 = -0.39;
-  gmpr_agmpr = 0.3005;
-  gmpr_fgmpr2 = -0.15;
-  gmpr_fgmpr4 = -0.07;
-  gmpr_fgmpr7 = -0.76;
-  gmpr_fgmpr8 = 0.7;
-  gmps_agmps = 0.3738;
-  gmps_fgmps4 = 0.12;
-  gmps_fgmps7 = 0.16;
-  gnuc_agnuc = 0.2511;
-  gnuc_fgnuc8 = 0.9;
-  gnuc_fgnuc18 = -0.34;
-  gprt_agprt = 361.69;
-  gprt_fgprt1 = 1.2;
-  gprt_fgprt8 = -1.2;
-  gprt_fgprt15 = 0.42;
-  grna_agrna = 409.6;
-  grna_frnap4 = 0.05;
-  grna_frnap8 = 0.13;
-  gua_agua = 0.4919;
-  gua_fgua15 = 0.5;
-  hprt_ahprt = 12.569;
-  hprt_fhprt1 = 1.1;
-  hprt_fhprt2 = -0.89;
-  hprt_fhprt13 = 0.48;
-  hx_ahx = 0.003793;
-  hx_fhx13 = 1.12;
-  hxd_ahxd = 0.2754;
-  hxd_fhxd13 = 0.65;
-  impd_aimpd = 1.2823;
-  impd_fimpd2 = 0.15;
-  impd_fimpd7 = -0.09;
-  impd_fimpd8 = -0.03;
-  inuc_ainuc = 0.9135;
-  inuc_finuc2 = 0.8;
-  inuc_finuc18 = -0.36;
-  mat_amat = 7.2067;
-  mat_fmat4 = 0.2;
-  mat_fmat5 = -0.6;
-  polyam_apolyam = 0.29;
-  polyam_fpolyam5 = 0.9;
-  prpps_aprpps = 0.9;
-  prpps_fprpps1 = -0.03;
-  prpps_fprpps4 = -0.45;
-  prpps_fprpps8 = -0.04;
-  prpps_fprpps17 = 0.65;
-  prpps_fprpps18 = 0.7;
-  pyr_apyr = 1.2951;
-  pyr_fpyr1 = 1.27;
-  rnaa_arnaa = 0.06923;
-  rnaa_frnan11 = 1;
-  rnag_arnag = 0.04615;
-  rnag_frnan11 = 1;
-  trans_atrans = 8.8539;
-  trans_ftrans5 = 0.33;
-  ua_aua = 8.744e-05;
-  ua_fua16 = 2.21;
-  x_ax = 0.0012;
-  x_fx14 = 2;
-  xd_axd = 0.949;
-  xd_fxd14 = 0.55;
-
-  // Other declarations:
-  const cell;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-  PRPP is "phosphoribosylpyrophosphate";
-  IMP is "inosine monophosphate";
-  SAMP is "adenylosuccinate";
-  ATP is "ATP_ADP_AMP_Ado";
-  SAM is "s-adenosyl-L-methionine";
-  Ade is "adenine";
-  XMP is "xanthosine monophosphate";
-  GTP is "GTP_GDP_GMP";
-  dATP is "dATP_dADP_dAMP_dAdo";
-  dGTP is "dGTP_dGDP_dGMP";
-  HX is "dIno_Ino_HX";
-  Xa is "xanthine";
-  Gua is "guanine";
-  UA is "uric acid";
-  R5P is "ribose-5-phosphate";
-  Pi is "phosphate";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005623"
-  PRPP identity "http://identifiers.org/chebi/CHEBI:17111",
-                "http://identifiers.org/kegg.compound/C00119"
-  IMP identity "http://identifiers.org/chebi/CHEBI:17202",
-               "http://identifiers.org/kegg.compound/C00130"
-  SAMP identity "http://identifiers.org/chebi/CHEBI:15919",
-                "http://identifiers.org/kegg.compound/C03794"
-  ATP part "http://identifiers.org/chebi/CHEBI:15422",
-           "http://identifiers.org/chebi/CHEBI:16335",
-           "http://identifiers.org/chebi/CHEBI:16027",
-           "http://identifiers.org/chebi/CHEBI:16761"
-  ATP part "http://identifiers.org/kegg.compound/C00008",
-           "http://identifiers.org/kegg.compound/C00212",
-           "http://identifiers.org/kegg.compound/C00020",
-           "http://identifiers.org/kegg.compound/C00002",
-           "http://identifiers.org/chebi/CHEBI:16761"
-  SAM identity "http://identifiers.org/chebi/CHEBI:15414",
-               "http://identifiers.org/kegg.compound/C00019"
-  Ade identity "http://identifiers.org/chebi/CHEBI:16708",
-               "http://identifiers.org/kegg.compound/C00147"
-  XMP identity "http://identifiers.org/chebi/CHEBI:15652",
-               "http://identifiers.org/kegg.compound/C00655"
-  GTP part "http://identifiers.org/kegg.compound/C00035",
-           "http://identifiers.org/kegg.compound/C00144",
-           "http://identifiers.org/kegg.compound/C00044",
-           "http://identifiers.org/chebi/CHEBI:17552"
-  GTP part "http://identifiers.org/chebi/CHEBI:17345",
-           "http://identifiers.org/chebi/CHEBI:17552",
-           "http://identifiers.org/chebi/CHEBI:15996"
-  dATP part "http://identifiers.org/kegg.compound/C00131",
-            "http://identifiers.org/kegg.compound/C00206",
-            "http://identifiers.org/kegg.compound/C00360",
-            "http://identifiers.org/kegg.compound/C00559",
-            "http://identifiers.org/chebi/CHEBI:16284"
-  dATP part "http://identifiers.org/chebi/CHEBI:16284",
-            "http://identifiers.org/chebi/CHEBI:16174",
-            "http://identifiers.org/chebi/CHEBI:17256",
-            "http://identifiers.org/chebi/CHEBI:17713"
-  dGTP part "http://identifiers.org/kegg.compound/C00286",
-            "http://identifiers.org/kegg.compound/C00362",
-            "http://identifiers.org/kegg.compound/C00361",
-            "http://identifiers.org/chebi/CHEBI:16497"
-  dGTP part "http://identifiers.org/chebi/CHEBI:28862",
-            "http://identifiers.org/chebi/CHEBI:16192",
-            "http://identifiers.org/chebi/CHEBI:16497"
-  RNA identity "http://identifiers.org/kegg.compound/C00046"
-  DNA_ identity "http://identifiers.org/kegg.compound/C00039",
-                "http://identifiers.org/chebi/CHEBI:16991"
-  HX part "http://identifiers.org/kegg.compound/C00262",
-          "http://identifiers.org/kegg.compound/C05512",
-          "http://identifiers.org/kegg.compound/C00294"
-  HX part "http://identifiers.org/chebi/CHEBI:17596",
-          "http://identifiers.org/chebi/CHEBI:17368",
-          "http://identifiers.org/chebi/CHEBI:28997"
-  Xa identity "http://identifiers.org/chebi/CHEBI:17712",
-              "http://identifiers.org/kegg.compound/C00385"
-  Gua part "http://identifiers.org/kegg.compound/C00242",
-           "http://identifiers.org/kegg.compound/C00330",
-           "http://identifiers.org/kegg.compound/C00387"
-  Gua part "http://identifiers.org/chebi/CHEBI:16450",
-           "http://identifiers.org/chebi/CHEBI:16235",
-           "http://identifiers.org/chebi/CHEBI:17172"
-  UA identity "http://identifiers.org/chebi/CHEBI:17775",
-              "http://identifiers.org/kegg.compound/C00366"
-  R5P identity "http://identifiers.org/chebi/CHEBI:17797",
-               "http://identifiers.org/kegg.compound/C00117"
-  Pi identity "http://identifiers.org/chebi/CHEBI:18367",
-              "http://identifiers.org/kegg.compound/C00009"
-  ada hypernym "http://identifiers.org/ec-code/3.5.4.4"
-  ada version "http://identifiers.org/kegg.reaction/R01560",
-              "http://identifiers.org/reactome/REACT_1687"
-  ade hypernym "http://identifiers.org/go/GO:0006146"
-  adna hypernym "http://identifiers.org/ec-code/2.7.7.7"
-  adna identity "http://identifiers.org/kegg.reaction/R00375"
-  adrnr version "http://identifiers.org/ec-code/1.17.4.2",
-                "http://identifiers.org/ec-code/1.17.4.1",
-                "http://identifiers.org/kegg.reaction/R02017",
-                "http://identifiers.org/kegg.reaction/R02014",
-                "http://identifiers.org/reactome/REACT_2136"
-  ampd identity "http://identifiers.org/kegg.reaction/R00181"
-  ampd hypernym "http://identifiers.org/ec-code/3.5.4.6"
-  aprt hypernym "http://identifiers.org/ec-code/2.4.2.7"
-  aprt identity "http://identifiers.org/kegg.reaction/R00190"
-  arna hypernym "http://identifiers.org/ec-code/2.7.7.6"
-  arna identity "http://identifiers.org/kegg.reaction/R00435"
-  asuc hypernym "http://identifiers.org/ec-code/6.3.4.4"
-  asuc identity "http://identifiers.org/kegg.reaction/R01135",
-                "http://identifiers.org/reactome/REACT_42"
-  asli hypernym "http://identifiers.org/ec-code/4.3.2.2"
-  asli identity "http://identifiers.org/kegg.reaction/R01083",
-                "http://identifiers.org/reactome/REACT_1042"
-  dada hypernym "http://identifiers.org/ec-code/3.5.4.4"
-  dada identity "http://identifiers.org/kegg.reaction/R02556",
-                "http://identifiers.org/reactome/REACT_2135"
-  den part "http://identifiers.org/reactome/REACT_108",
-           "http://identifiers.org/reactome/REACT_812",
-           "http://identifiers.org/reactome/REACT_1463",
-           "http://identifiers.org/reactome/REACT_589",
-           "http://identifiers.org/reactome/REACT_1917",
-           "http://identifiers.org/reactome/REACT_1509",
-           "http://identifiers.org/reactome/REACT_740",
-           "http://identifiers.org/reactome/REACT_285",
-           "http://identifiers.org/reactome/REACT_1427",
-           "http://identifiers.org/reactome/REACT_263"
-  den part "http://identifiers.org/ec-code/2.4.2.14",
-           "http://identifiers.org/ec-code/6.3.4.13",
-           "http://identifiers.org/ec-code/2.1.2.2",
-           "http://identifiers.org/ec-code/6.3.5.3",
-           "http://identifiers.org/ec-code/6.3.3.1",
-           "http://identifiers.org/ec-code/4.1.1.21",
-           "http://identifiers.org/ec-code/6.3.2.6",
-           "http://identifiers.org/ec-code/4.3.2.2",
-           "http://identifiers.org/ec-code/2.1.2.3",
-           "http://identifiers.org/ec-code/3.5.4.10"
-  den part "http://identifiers.org/kegg.reaction/R04144",
-           "http://identifiers.org/kegg.reaction/R04325",
-           "http://identifiers.org/kegg.reaction/R04463",
-           "http://identifiers.org/kegg.reaction/R04208",
-           "http://identifiers.org/kegg.reaction/R04209",
-           "http://identifiers.org/kegg.reaction/R04559",
-           "http://identifiers.org/kegg.reaction/R04560",
-           "http://identifiers.org/kegg.reaction/R04591",
-           "http://identifiers.org/kegg.reaction/R01127",
-           "http://identifiers.org/kegg.reaction/R01072"
-  dgnuc hypernym "http://identifiers.org/ec-code/3.1.3.5"
-  dgnuc identity "http://identifiers.org/kegg.reaction/R01968",
-                 "http://identifiers.org/reactome/REACT_1209"
-  dnaa hypernym "http://identifiers.org/go/GO:0006308"
-  dnag hypernym "http://identifiers.org/go/GO:0006308"
-  gdna identity "http://identifiers.org/kegg.reaction/R00376"
-  gdna hypernym "http://identifiers.org/ec-code/2.7.7.7"
-  gdrnr version "http://identifiers.org/ec-code/1.17.4.2",
-                "http://identifiers.org/ec-code/1.17.4.1",
-                "http://identifiers.org/kegg.reaction/R02019",
-                "http://identifiers.org/kegg.reaction/R02020",
-                "http://identifiers.org/reactome/REACT_906"
-  gmpr hypernym "http://identifiers.org/ec-code/1.7.1.7"
-  gmpr identity "http://identifiers.org/kegg.reaction/R01134"
-  gmps hypernym "http://identifiers.org/ec-code/6.3.5.2"
-  gmps identity "http://identifiers.org/kegg.reaction/R01231",
-                "http://identifiers.org/reactome/REACT_628"
-  gnuc hypernym "http://identifiers.org/ec-code/3.1.3.5"
-  gnuc identity "http://identifiers.org/kegg.reaction/R01227",
-                "http://identifiers.org/reactome/REACT_1774"
-  gprt hypernym "http://identifiers.org/ec-code/2.4.2.7"
-  gprt identity "http://identifiers.org/kegg.reaction/R01229"
-  grna hypernym "http://identifiers.org/ec-code/2.7.7.6"
-  grna identity "http://identifiers.org/kegg.reaction/R00441"
-  gua hypernym "http://identifiers.org/ec-code/3.5.4.3"
-  gua identity "http://identifiers.org/kegg.reaction/R01676",
-               "http://identifiers.org/reactome/REACT_1442"
-  hprt hypernym "http://identifiers.org/ec-code/2.4.2.8"
-  hprt identity "http://identifiers.org/kegg.reaction/R01132"
-  hx hypernym "http://identifiers.org/go/GO:0009114"
-  hxd hypernym "http://identifiers.org/ec-code/1.17.3.2"
-  hxd identity "http://identifiers.org/kegg.reaction/R01769",
-               "http://identifiers.org/reactome/REACT_401"
-  impd hypernym "http://identifiers.org/ec-code/1.1.1.205"
-  impd identity "http://identifiers.org/kegg.reaction/R01130",
-                "http://identifiers.org/reactome/REACT_1488"
-  inuc identity "http://identifiers.org/kegg.reaction/R01126",
-                "http://identifiers.org/reactome/REACT_430"
-  inuc hypernym "http://identifiers.org/ec-code/3.1.3.5"
-  mat identity "http://identifiers.org/kegg.reaction/R00177"
-  mat hypernym "http://identifiers.org/ec-code/2.5.1.6"
-  polyam part "http://identifiers.org/kegg.reaction/R02869",
-              "http://identifiers.org/kegg.reaction/R00178",
-              "http://identifiers.org/kegg.reaction/R01401"
-  polyam part "http://identifiers.org/ec-code/3.2.2.16",
-              "http://identifiers.org/ec-code/2.5.1.22",
-              "http://identifiers.org/ec-code/4.1.1.50"
-  polyam parthood "http://identifiers.org/kegg.pathway/map00330"
-  prpps identity "http://identifiers.org/kegg.reaction/R01049"
-  prpps hypernym "http://identifiers.org/ec-code/2.7.6.1"
-  pyr identity "http://identifiers.org/kegg.reaction/R01870",
-               "http://identifiers.org/reactome/REACT_33"
-  pyr parthood "http://identifiers.org/kegg.pathway/map00240"
-  pyr hypernym "http://identifiers.org/ec-code/2.4.2.10"
-  rnaa hypernym "http://identifiers.org/go/GO:0006401"
-  rnag hypernym "http://identifiers.org/go/GO:0006401"
-  trans identity "http://identifiers.org/go/GO:0008757"
-  ua hypernym "http://identifiers.org/go/GO:0007588"
-  x hypernym "http://identifiers.org/go/GO:0009115"
-  xd identity "http://identifiers.org/kegg.reaction/R02107",
-              "http://identifiers.org/reactome/REACT_624"
-  xd hypernym "http://identifiers.org/ec-code/1.17.3.2"
-end
-
-BIOMD0000000015 is "Curto1998 - purine metabolism"
-
-BIOMD0000000015 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617035399"
-BIOMD0000000015 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000015"
-BIOMD0000000015 description "http://identifiers.org/pubmed/9664759"
-BIOMD0000000015 taxon "http://identifiers.org/taxonomy/9606"
-BIOMD0000000015 identity "http://identifiers.org/kegg.pathway/hsa00230",
-                         "http://identifiers.org/reactome/REACT_522"
-BIOMD0000000015 hypernym "http://identifiers.org/go/GO:0006144"
diff --git a/BioModelsRAG/data/BIOMD0000000016.txt b/BioModelsRAG/data/BIOMD0000000016.txt
deleted file mode 100644
index 28c3c4881dcfb4cfe6b37684ef2ed8976b4b95d8..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000016.txt
+++ /dev/null
@@ -1,119 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter1995()
-
-  // Compartments and Species:
-  compartment default, CYTOPLASM, compartment_0000004;
-  species $EmptySet in default, M in CYTOPLASM, P0 in CYTOPLASM, P1 in CYTOPLASM;
-  species P2 in CYTOPLASM, Pn in compartment_0000004, $Pt in CYTOPLASM;
-
-  // Assignment Rules:
-  Pt := P0 + P1 + P2 + Pn;
-
-  // Reactions:
-  rM: $EmptySet => M; default*rM_Vs*rM_KI^rM_n/(rM_KI^rM_n + Pn^rM_n);
-  rTL: $EmptySet => P0; rTL_ks*M*default;
-  rP01: P0 => P1; CYTOPLASM*rP01_V1*P0/(rP01_K1 + P0);
-  rP10: P1 => P0; CYTOPLASM*rP10_V2*P1/(rP10_K2 + P1);
-  rP12: P1 => P2; CYTOPLASM*rP12_V3*P1/(rP12_K3 + P1);
-  rP21: P2 => P1; CYTOPLASM*rP21_V4*P2/(rP21_K4 + P2);
-  rP2n: P2 => Pn; rP2n_k1*P2*CYTOPLASM;
-  rPn2: Pn => P2; rPn2_k2*Pn*compartment_0000004;
-  rmRNAd: M => $EmptySet; rmRNAd_Vm*M*CYTOPLASM/(rmRNAd_Km + M);
-  rVd: P2 => $EmptySet; CYTOPLASM*rVd_Vd*P2/(rVd_Kd + P2);
-
-  // Species initializations:
-  EmptySet = 0;
-  M = 0.1;
-  P0 = 0.25;
-  P1 = 0.25;
-  P2 = 0.25;
-  Pn = 0.25;
-
-  // Compartment initializations:
-  default = 1e-15;
-  CYTOPLASM = 1e-15;
-  compartment_0000004 = 1e-15;
-
-  // Variable initializations:
-  rM_Vs = 0.76;
-  rM_KI = 1;
-  rM_n = 4;
-  rTL_ks = 0.38;
-  rP01_V1 = 3.2;
-  rP01_K1 = 2;
-  rP10_V2 = 1.58;
-  rP10_K2 = 2;
-  rP12_V3 = 5;
-  rP12_K3 = 2;
-  rP21_V4 = 2.5;
-  rP21_K4 = 2;
-  rP2n_k1 = 1.9;
-  rPn2_k2 = 1.3;
-  rmRNAd_Km = 0.5;
-  rmRNAd_Vm = 0.65;
-  rVd_Vd = 0.95;
-  rVd_Kd = 0.2;
-
-  // Other declarations:
-  const default, CYTOPLASM, compartment_0000004;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "heure (default)";
-  compartment_0000004 is "NUCLEUS";
-  M is "PER mRNA";
-  P0 is "unphosphorylated PER";
-  P1 is "monophosphorylated PER";
-  P2 is "biphosphorylated PER";
-  Pn is "nuclear PER";
-  Pt is "total PER";
-  rM is "transcription of PER";
-  rTL is "translation of PER";
-  rP01 is "first phosphorylation of PER";
-  rP10 is "removal of the first PER phosphate";
-  rP12 is "second phosphorylation of PER";
-  rP21 is "removal of the second PER phosphate";
-  rP2n is "translocation of PER to the nucleus";
-  rPn2 is "translocation of PER to the cytoplasm";
-  rmRNAd is "degradation of PER mRNA";
-  rVd is "degradation of PER";
-
-  // CV terms:
-  CYTOPLASM identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000004 identity "http://identifiers.org/go/GO:0005634"
-  M hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  P0 hypernym "http://identifiers.org/uniprot/P07663"
-  P1 hypernym "http://identifiers.org/uniprot/P07663"
-  P2 hypernym "http://identifiers.org/uniprot/P07663"
-  Pn identity "http://identifiers.org/uniprot/P07663"
-  Pt identity "http://identifiers.org/uniprot/P07663"
-  rM hypernym "http://identifiers.org/go/GO:0006355",
-              "http://identifiers.org/go/GO:0009299"
-  rTL hypernym "http://identifiers.org/go/GO:0006412"
-  rP01 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                "http://identifiers.org/go/GO:0006468"
-  rP10 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470"
-  rP12 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                "http://identifiers.org/go/GO:0006468"
-  rP21 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470"
-  rP2n hypernym "http://identifiers.org/go/GO:0006606"
-  rPn2 hypernym "http://identifiers.org/go/GO:0006611"
-  rmRNAd hypernym "http://identifiers.org/go/GO:0006402"
-  rVd hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-Goldbeter1995 is "Goldbeter1995_CircClock"
-
-Goldbeter1995 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617161845"
-Goldbeter1995 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000016"
-Goldbeter1995 description "http://identifiers.org/pubmed/8587874"
-Goldbeter1995 identity "http://identifiers.org/kegg.pathway/dme04710"
-Goldbeter1995 taxon "http://identifiers.org/taxonomy/7227"
-Goldbeter1995 hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000017.txt b/BioModelsRAG/data/BIOMD0000000017.txt
deleted file mode 100644
index ac421146043a333f3259eed0ad754b68398f0b8c..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000017.txt
+++ /dev/null
@@ -1,218 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Hoefnagel2002_PyruvateBranches()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species $PO4 in compartment_;
-  substanceOnly species ADP in compartment_, NAD in compartment_, ATP in compartment_;
-  substanceOnly species NADH in compartment_, pyruvate in compartment_, $lactate in compartment_;
-  substanceOnly species CoA in compartment_, $halfglucose in compartment_;
-  substanceOnly species AcCoA in compartment_, AcP in compartment_, $Ac in compartment_;
-  substanceOnly species AcO in compartment_, $EtOH in compartment_, AcLac in compartment_;
-  substanceOnly species AcetoinIn in compartment_, $AcetoinOut in compartment_;
-  substanceOnly species $Butanediol in compartment_, $O2 in compartment_;
-
-  // Reactions:
-  R1: ADP + NAD + $halfglucose => ATP + NADH + pyruvate; 2*R1_V_1*(halfglucose/(2*R1_Kglc_1))*(NAD/R1_Knad_1)*(ADP/R1_Kadp_1)/((1 + halfglucose/(2*R1_Kglc_1) + pyruvate/R1_Kpyr_1)*(1 + NAD/R1_Knad_1 + NADH/R1_Knadh_1)*(1 + ADP/R1_Kadp_1 + ATP/R1_Katp_1));
-  R2: NADH + pyruvate => NAD + $lactate; R2_V_2*((pyruvate*NADH - lactate*NAD/R2_Keq_2)/(R2_Kpyr_2*R2_Knadh_2))/((1 + pyruvate/R2_Kpyr_2 + lactate/R2_Klac_2)*(1 + NADH/R2_Knadh_2 + NAD/R2_Knad_2));
-  R3: NAD + pyruvate + CoA => NADH + AcCoA; R3_V_3*(pyruvate/R3_Kpyr_3)*(NAD/R3_Knad_3)*(CoA/R3_Kcoa_3)*(NAD/(NAD + R3_Ki_3*NADH))/((1 + pyruvate/R3_Kpyr_3)*(1 + NAD/R3_Knad_3 + NADH/R3_Knadh_3)*(1 + CoA/R3_Kcoa_3 + AcCoA/R3_Kaccoa_3));
-  R4: AcCoA + $PO4 => CoA + AcP; R4_V_4*((AcCoA*PO4 - AcP*CoA/R4_Keq_4)/(R4_Kiaccoa_4*R4_Kpi_4))/(1 + AcCoA/R4_Kiaccoa_4 + PO4/R4_Kipi_4 + AcP/R4_Kiacp_4 + CoA/R4_Kicoa_4 + AcCoA*PO4/(R4_Kiaccoa_4*R4_Kpi_4) + AcP*CoA/(R4_Kacp_4*R4_Kicoa_4));
-  R5: ADP + AcP => ATP + $Ac; R5_V_5*((AcP*ADP - Ac*ATP/R5_Keq_5)/(R5_Kadp_5*R5_Kacp_5))/((1 + AcP/R5_Kacp_5 + Ac/R5_Kac_5)*(1 + ADP/R5_Kadp_5 + ATP/R5_Katp_5));
-  R6: NADH + AcCoA => NAD + CoA + AcO; R6_V_6*((AcCoA*NADH - CoA*NAD*AcO/R6_Keq_6)/(R6_Kaccoa_6*R6_Knadh_6))/((1 + NAD/R6_Knad_6 + NADH/R6_Knadh_6)*(1 + AcCoA/R6_Kaccoa_6 + CoA/R6_Kcoa_6)*(1 + AcO/R6_Kaco_6));
-  R7: NADH + AcO => NAD + $EtOH; R7_V_7*((AcO*NADH - EtOH*NAD/R7_Keq_7)/(R7_Kaco_7*R7_Knadh_7))/((1 + NAD/R7_Knad_7 + NADH/R7_Knadh_7)*(1 + AcO/R7_Kaco_7 + EtOH/R7_Ketoh_7));
-  R8: 2 pyruvate => AcLac; R8_V_8*(pyruvate/R8_Kpyr_8)*(1 - AcLac/(pyruvate*R8_Keq_8))*(pyruvate/R8_Kpyr_8 + AcLac/R8_Kaclac_8)^(R8_n_8 - 1)/(1 + (pyruvate/R8_Kpyr_8 + AcLac/R8_Kaclac_8)^R8_n_8);
-  R9: AcLac => AcetoinIn; R9_V_9*(AcLac/R9_Kaclac_9)/(1 + AcLac/R9_Kaclac_9 + AcetoinIn/R9_Kacet_9);
-  R10: AcetoinIn => $AcetoinOut; R10_V_10*(AcetoinIn/R10_Kacet_10)/(1 + AcetoinIn/R10_Kacet_10);
-  R11: NADH + AcetoinIn => NAD + $Butanediol; R11_V_11*((AcetoinIn*NADH - Butanediol*NAD/R11_Keq_11)/(R11_Kacet_11*R11_Knadh_11))/((1 + AcetoinIn/R11_Kacet_11 + Butanediol/R11_Kbut_11)*(1 + NADH/R11_Knadh_11 + NAD/R11_Knad_11));
-  R12: ATP => ADP; R12_V_12*(ATP/(ADP*R12_Katp_12))^R12_n_12/(1 + (ATP/(ADP*R12_Katp_12))^R12_n_12);
-  R13: NADH + $O2 => NAD; R13_V_13*(NADH*O2/(R13_Knadh_13*R13_Ko_13))/((1 + NADH/R13_Knadh_13 + NAD/R13_Knad_13)*(1 + O2/R13_Ko_13));
-  R14: AcLac => AcetoinIn; R14_k_14*AcLac;
-
-  // Species initializations:
-  ADP = 4.9/compartment_;
-  NAD = 6.33/compartment_;
-  ATP = 0.1/compartment_;
-  NADH = 3.67/compartment_;
-  pyruvate = 1/compartment_;
-  lactate = 0.1/compartment_;
-  CoA = 1/compartment_;
-  halfglucose = 30/compartment_;
-  AcCoA = 0;
-  AcP = 0;
-  Ac = 1/compartment_;
-  AcO = 0;
-  EtOH = 1/compartment_;
-  AcLac = 0;
-  AcetoinIn = 0;
-  AcetoinOut = 0;
-  Butanediol = 0.01/compartment_;
-  O2 = 0.2/compartment_;
-  PO4 = 10/compartment_;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  R1_V_1 = 2397;
-  R1_Kglc_1 = 0.1;
-  R1_Knad_1 = 0.1412;
-  R1_Kadp_1 = 0.04699;
-  R1_Kpyr_1 = 2.5;
-  R1_Knadh_1 = 0.08999;
-  R1_Katp_1 = 0.01867;
-  R2_V_2 = 5118;
-  R2_Keq_2 = 21120.69;
-  R2_Kpyr_2 = 1.5;
-  R2_Knadh_2 = 0.08;
-  R2_Klac_2 = 100;
-  R2_Knad_2 = 2.4;
-  R3_V_3 = 259;
-  R3_Kpyr_3 = 1;
-  R3_Knad_3 = 0.4;
-  R3_Kcoa_3 = 0.014;
-  R3_Ki_3 = 46.4159;
-  R3_Knadh_3 = 0.1;
-  R3_Kaccoa_3 = 0.008;
-  R4_V_4 = 42;
-  R4_Keq_4 = 0.0065;
-  R4_Kiaccoa_4 = 0.2;
-  R4_Kpi_4 = 2.6;
-  R4_Kipi_4 = 2.6;
-  R4_Kiacp_4 = 0.2;
-  R4_Kicoa_4 = 0.029;
-  R4_Kacp_4 = 0.7;
-  R5_V_5 = 2700;
-  R5_Keq_5 = 174.217;
-  R5_Kadp_5 = 0.5;
-  R5_Kacp_5 = 0.16;
-  R5_Kac_5 = 7;
-  R5_Katp_5 = 0.07;
-  R6_V_6 = 97;
-  R6_Keq_6 = 1;
-  R6_Kaccoa_6 = 0.007;
-  R6_Knadh_6 = 0.025;
-  R6_Knad_6 = 0.08;
-  R6_Kcoa_6 = 0.008;
-  R6_Kaco_6 = 10;
-  R7_V_7 = 162;
-  R7_Keq_7 = 12354.9;
-  R7_Kaco_7 = 0.03;
-  R7_Knadh_7 = 0.05;
-  R7_Knad_7 = 0.08;
-  R7_Ketoh_7 = 1;
-  R8_V_8 = 600;
-  R8_Kpyr_8 = 50;
-  R8_Keq_8 = 9000000000000;
-  R8_Kaclac_8 = 100;
-  R8_n_8 = 2.4;
-  R9_V_9 = 106;
-  R9_Kaclac_9 = 10;
-  R9_Kacet_9 = 100;
-  R10_V_10 = 200;
-  R10_Kacet_10 = 5;
-  R11_V_11 = 105;
-  R11_Keq_11 = 1400;
-  R11_Kacet_11 = 0.06;
-  R11_Knadh_11 = 0.02;
-  R11_Kbut_11 = 2.6;
-  R11_Knad_11 = 0.16;
-  R12_V_12 = 900;
-  R12_Katp_12 = 6.196;
-  R12_n_12 = 2.58;
-  R13_V_13 = 118;
-  R13_Knadh_13 = 0.041;
-  R13_Ko_13 = 0.2;
-  R13_Knad_13 = 1;
-  R14_k_14 = 0.0003;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  pyruvate identity "http://identifiers.org/chebi/CHEBI:15361",
-                    "http://identifiers.org/kegg.compound/C00022"
-  lactate identity "http://identifiers.org/chebi/CHEBI:24996",
-                   "http://identifiers.org/kegg.compound/C00186"
-  CoA identity "http://identifiers.org/chebi/CHEBI:15346",
-               "http://identifiers.org/kegg.compound/C00010"
-  AcCoA identity "http://identifiers.org/chebi/CHEBI:15351",
-                 "http://identifiers.org/kegg.compound/C00024"
-  AcP identity "http://identifiers.org/chebi/CHEBI:15350",
-               "http://identifiers.org/kegg.compound/C00227"
-  Ac identity "http://identifiers.org/chebi/CHEBI:30089",
-              "http://identifiers.org/kegg.compound/C00033"
-  AcO identity "http://identifiers.org/chebi/CHEBI:15343",
-               "http://identifiers.org/kegg.compound/C00084"
-  EtOH identity "http://identifiers.org/chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  AcLac identity "http://identifiers.org/chebi/CHEBI:16444",
-                 "http://identifiers.org/kegg.compound/C00900"
-  AcetoinIn identity "http://identifiers.org/chebi/CHEBI:15688",
-                     "http://identifiers.org/kegg.compound/C00466"
-  AcetoinOut identity "http://identifiers.org/chebi/CHEBI:15688",
-                      "http://identifiers.org/kegg.compound/C00466"
-  Butanediol version "http://identifiers.org/chebi/CHEBI:16812",
-                     "http://identifiers.org/chebi/CHEBI:16982",
-                     "http://identifiers.org/kegg.compound/C03046",
-                     "http://identifiers.org/kegg.compound/C03044"
-  O2 identity "http://identifiers.org/chebi/CHEBI:15379",
-              "http://identifiers.org/kegg.compound/C00007"
-  PO4 identity "http://identifiers.org/chebi/CHEBI:18367",
-               "http://identifiers.org/kegg.compound/C00009"
-  R1 parthood "http://identifiers.org/kegg.pathway/map00010"
-  R2 version "http://identifiers.org/ec-code/1.1.1.27",
-             "http://identifiers.org/ec-code/1.1.1.28",
-             "http://identifiers.org/kegg.reaction/R00703",
-             "http://identifiers.org/kegg.reaction/R00704",
-             "http://identifiers.org/reactome/REACT_178"
-  R3 hypernym "http://identifiers.org/ec-code/1.2.1.51"
-  R3 identity "http://identifiers.org/kegg.reaction/R00209"
-  R4 hypernym "http://identifiers.org/ec-code/2.3.1.8"
-  R4 identity "http://identifiers.org/kegg.reaction/R00230"
-  R5 hypernym "http://identifiers.org/ec-code/2.7.2.1"
-  R5 identity "http://identifiers.org/kegg.reaction/R00315"
-  R6 hypernym "http://identifiers.org/ec-code/1.2.1.10"
-  R6 identity "http://identifiers.org/kegg.reaction/R00228"
-  R7 hypernym "http://identifiers.org/ec-code/1.1.1.1"
-  R7 identity "http://identifiers.org/kegg.reaction/R00754",
-              "http://identifiers.org/reactome/REACT_799"
-  R8 hypernym "http://identifiers.org/ec-code/2.2.1.6"
-  R8 identity "http://identifiers.org/kegg.reaction/R00006"
-  R9 identity "http://identifiers.org/kegg.reaction/R02947"
-  R9 hypernym "http://identifiers.org/ec-code/4.1.1.5"
-  R10 hypernym "http://identifiers.org/go/GO:0015562"
-  R11 version "http://identifiers.org/ec-code/1.1.1.4",
-              "http://identifiers.org/ec-code/1.1.1.76",
-              "http://identifiers.org/kegg.reaction/R02344",
-              "http://identifiers.org/kegg.reaction/R02946"
-  R12 hypernym "http://identifiers.org/go/GO:0016887"
-  R13 hypernym "http://identifiers.org/go/GO:0006116"
-end
-
-Hoefnagel2002_PyruvateBranches is "Hoefnagel2002_PyruvateBranches"
-
-Hoefnagel2002_PyruvateBranches model_entity_is "http://identifiers.org/biomodels.db/MODEL6617235316"
-Hoefnagel2002_PyruvateBranches model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000017"
-Hoefnagel2002_PyruvateBranches description "http://identifiers.org/pubmed/11932446"
-Hoefnagel2002_PyruvateBranches hypernym "http://identifiers.org/go/GO:0006090",
-                                        "http://identifiers.org/go/GO:0006089"
-Hoefnagel2002_PyruvateBranches parthood "http://identifiers.org/kegg.pathway/map00620",
-                                        "http://identifiers.org/kegg.pathway/map00650"
-Hoefnagel2002_PyruvateBranches taxon "http://identifiers.org/taxonomy/1358"
-Hoefnagel2002_PyruvateBranches property "http://identifiers.org/mamo/MAMO_0000046"
diff --git a/BioModelsRAG/data/BIOMD0000000018.txt b/BioModelsRAG/data/BIOMD0000000018.txt
deleted file mode 100644
index 89c91df43f414cb8bc50b1a205de067855020bb6..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000018.txt
+++ /dev/null
@@ -1,341 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MorrisonAllegra()
-
-  // Compartments and Species:
-  compartment ext_, cell;
-  species FH2f in cell, $FH2b in cell, DHFRf in cell, $DHFRtot in cell, MTX1b in cell;
-  species MTX2b in cell, MTX3b in cell, MTX4b in cell, MTX5b in cell, FH4 in cell;
-  species CH2FH4 in cell, CH3FH4 in cell, CHOFH4 in cell, FFH2 in cell, HCHO in cell;
-  species FGAR in cell, AICAR in cell, MTX1 in cell, MTX2 in cell, MTX3 in cell;
-  species MTX4 in cell, MTX5 in cell, $EMTX in ext_, $dUMP in cell, $GAR in cell;
-  species $serine in cell, $formate in cell, $ATP in cell, $glutamine in cell;
-  species $glycine in cell, $NADP in cell, $NADPH in cell, $homocysteine in cell;
-
-  // Assignment Rules:
-  FH2b := FH2f*DHFRf/Keq;
-  DHFRtot := FH2b + DHFRf + MTX1b + MTX2b + MTX3b + MTX4b + MTX5b;
-
-  // Reactions:
-  SHMT: FH4 + $serine => CH2FH4; cell*(SHMT_Vm*(serine/SHMT_Km2/(1 + serine/SHMT_Km2))*(FH4/SHMT_Km1)/(1 + FH4/SHMT_Km1));
-  SHMTr: CH2FH4 => FH4; cell*(SHMTr_Vm*(glycine/SHMTr_Km2/(1 + glycine/SHMTr_Km2))*(CH2FH4/SHMTr_Km1)/(1 + CH2FH4/SHMTr_Km1));
-  HCHOtoCH2FH4: FH4 + HCHO => CH2FH4; cell*HCHOtoCH2FH4_hp*FH4*HCHO;
-  CH2FH4toHCHO: CH2FH4 => FH4 + HCHO; cell*CH2FH4toHCHO_hl*CH2FH4;
-  MTHFR: CH2FH4 + $NADPH => CH3FH4; cell*(MTHFR_Vm*CH2FH4*NADPH/(NADPH*CH2FH4 + CH2FH4*MTHFR_Km2 + (NADPH + MTHFR_Km2)*MTHFR_Km1*(1 + MTX1/MTHFR_Ki21 + MTX2/MTHFR_Ki22 + MTX3/MTHFR_Ki23 + MTX4/MTHFR_Ki24 + MTX5/MTHFR_Ki25 + FH2f/MTHFR_Ki1)));
-  MTR: CH3FH4 + $homocysteine => FH4; cell*(MTR_Vm*(homocysteine/MTR_Km2/(1 + homocysteine/MTR_Km2))*(CH3FH4/MTR_Km1)/(1 + CH3FH4/MTR_Km1));
-  HCOOHtoCHOFH4: FH4 + $formate + $ATP => CHOFH4; cell*(HCOOHtoCHOFH4_Vm/((1 + HCOOHtoCHOFH4_Km1/FH4)*(1 + HCOOHtoCHOFH4_Km2/ATP)*(1 + HCOOHtoCHOFH4_Km3/formate)));
-  GARFT: CHOFH4 + $GAR => FGAR + FH4; cell*(GARFT_Vm*CHOFH4*GAR/(GAR*CHOFH4 + CHOFH4*GARFT_Km2 + (GAR + GARFT_Km2)*GARFT_Km1*(1 + MTX1/GARFT_Ki21 + MTX2/GARFT_Ki22 + MTX3/GARFT_Ki23 + MTX4/GARFT_Ki24 + MTX5/GARFT_Ki25 + FH2f/GARFT_Ki1 + FFH2/GARFT_Ki1f)));
-  ATIC7: CHOFH4 + AICAR => FH4; cell*(ATIC7_Vm*CHOFH4*AICAR/(AICAR*CHOFH4 + CHOFH4*ATIC7_Km2 + (AICAR + ATIC7_Km2)*ATIC7_Km1*(1 + MTX1/ATIC7_Ki21 + MTX2/ATIC7_Ki22 + MTX3/ATIC7_Ki23 + MTX4/ATIC7_Ki24 + MTX5/ATIC7_Ki25 + FH2f/ATIC7_Ki1 + FFH2/ATIC7_Ki1f)));
-  MTHFD: CH2FH4 + $NADP => CHOFH4; cell*MTHFD_Vm*(CH2FH4/MTHFD_Km1/(1 + CH2FH4/MTHFD_Km1))*(NADP/MTHFD_Km2/(1 + NADP/MTHFD_Km2));
-  TYMS: CH2FH4 + $dUMP => FH2f; cell*(TYMS_Vm*CH2FH4*dUMP/(dUMP*CH2FH4*(1 + MTX1/TYMS_Ki21 + MTX2/TYMS_Ki22 + MTX3/TYMS_Ki23 + MTX4/TYMS_Ki24 + MTX5/TYMS_Ki25 + FH2f/TYMS_Ki1) + TYMS_Km1*dUMP*((FFH2/TYMS_Ki1f)*(MTX1/TYMS_Ki21) + (1 + FFH2/TYMS_Ki1f)*(1 + MTX2/TYMS_Ki22 + MTX3/TYMS_Ki23 + MTX4/TYMS_Ki24 + MTX5/TYMS_Ki25 + FH2f/TYMS_Ki1)) + TYMS_Km1*TYMS_Km2*(1 + MTX2/TYMS_Ki22 + MTX3/TYMS_Ki23 + MTX4/TYMS_Ki24 + MTX5/TYMS_Ki25 + FH2f/TYMS_Ki1)));
-  DHFReductase: FH2f => FH4; cell*DHFReductase_kter*FH2b;
-  FFH2syn: FH2f => FFH2; cell*FFH2syn_Vm*FH2f;
-  ATIC12: FFH2 + AICAR => FH2f; cell*(ATIC12_Vm*FFH2*AICAR/(AICAR*FFH2 + FFH2*ATIC12_Km2 + (AICAR + ATIC12_Km2)*ATIC12_Km1*(1 + MTX1/ATIC12_Ki21 + MTX2/ATIC12_Ki22 + MTX3/ATIC12_Ki23 + MTX4/ATIC12_Ki24 + MTX5/ATIC12_Ki25 + FH2f/ATIC12_Ki1 + FFH2/ATIC12_Ki1f)));
-  AICARsyn: FGAR => AICAR; cell*AICARsyn_Vm*(glutamine/AICARsyn_Km1/(1 + glutamine/AICARsyn_Km1))*(FGAR/AICARsyn_Km2/(1 + FGAR/AICARsyn_Km2));
-  FPGS12: MTX1 => MTX2; cell*FPGS12_Vm*MTX1;
-  FPGS23: MTX2 => MTX3; cell*FPGS23_Vm*MTX2;
-  FPGS34: MTX3 => MTX4; cell*FPGS34_Vm*MTX3;
-  FPGS45: MTX4 => MTX5; cell*FPGS45_Vm*MTX4;
-  GGH21: MTX2 => MTX1; cell*GGH21_Vm*MTX2;
-  GGH32: MTX3 => MTX2; cell*GGH32_Vm*MTX3;
-  GGH43: MTX4 => MTX3; cell*GGH43_Vm*MTX4;
-  GGH54: MTX5 => MTX4; cell*GGH54_Vm*MTX5;
-  RFC: $EMTX => MTX1; ext_*(RFC_Vm*EMTX/(RFC_Km + EMTX));
-  MTX1export: MTX1 => ; cell*MTX1export_Vm*MTX1;
-  MTX2export: MTX2 => ; cell*MTX2export_Vm*MTX2;
-  MTX3export: MTX3 => ; cell*MTX3export_Vm*MTX3;
-  MTX4export: MTX4 => ; cell*MTX4export_Vm*MTX4;
-  MTX5export: MTX5 => ; cell*MTX5export_Vm*MTX5;
-  MTX1on: MTX1 + DHFRf => MTX1b; cell*MTX1on_Vm*DHFRf*MTX1;
-  MTX2on: MTX2 + DHFRf => MTX2b; cell*MTX2on_Vm*DHFRf*MTX2;
-  MTX3on: MTX3 + DHFRf => MTX3b; cell*MTX3on_Vm*DHFRf*MTX3;
-  MTX4on: MTX4 + DHFRf => MTX4b; cell*MTX4on_Vm*DHFRf*MTX4;
-  MTX5on: MTX5 + DHFRf => MTX5b; cell*MTX5on_Vm*DHFRf*MTX5;
-  MTX1off: MTX1b => MTX1 + DHFRf; cell*MTX1off_Vm*MTX1b;
-  MTX2off: MTX2b => MTX2 + DHFRf; cell*MTX2off_Vm*MTX2b;
-  MTX3off: MTX3b => MTX3 + DHFRf; cell*MTX3off_Vm*MTX3b;
-  MTX4off: MTX4b => MTX4 + DHFRf; cell*MTX4off_Vm*MTX4b;
-  MTX5off: MTX5b => MTX5 + DHFRf; cell*MTX5off_Vm*MTX5b;
-  DHFRfsyn:  => DHFRf; cell*(DHFRfsyn_k0 + DHFRfsyn_k1*EMTX);
-  DHFRdeg: DHFRf => ; DHFRdeg_Vm*cell*(DHFRf + FH2b);
-  FH2bdeg:  => FH2f; cell*FH2bdeg_Vm*FH2b;
-  MTX1deg: MTX1b => MTX1; cell*MTX1deg_Vm*MTX1b;
-  MTX2deg: MTX2b => MTX2; cell*MTX2deg_Vm*MTX2b;
-  MTX3deg: MTX3b => MTX3; cell*MTX3deg_Vm*MTX3b;
-  MTX4deg: MTX4b => MTX4; cell*MTX4deg_Vm*MTX4b;
-  MTX5deg: MTX5b => MTX5; cell*MTX5deg_Vm*MTX5b;
-
-  // Species initializations:
-  FH2f = 0.0012;
-  DHFRf = 0.64;
-  MTX1b = 0;
-  MTX2b = 0;
-  MTX3b = 0;
-  MTX4b = 0;
-  MTX5b = 0;
-  FH4 = 0.46;
-  CH2FH4 = 0.26;
-  CH3FH4 = 1.63;
-  CHOFH4 = 1;
-  FFH2 = 0.000332;
-  HCHO = 0.0074;
-  FGAR = 16.49;
-  AICAR = 3.695;
-  MTX1 = 0;
-  MTX2 = 0;
-  MTX3 = 0;
-  MTX4 = 0;
-  MTX5 = 0;
-  EMTX = 0;
-  dUMP = 20.76;
-  GAR = 689.6;
-  serine = 123.3;
-  formate = 500;
-  ATP = 2980;
-  glutamine = 7170;
-  glycine = 1600;
-  NADP = 6.73;
-  NADPH = 294;
-  homocysteine = 10;
-
-  // Compartment initializations:
-  ext_ = 1;
-  cell = 1;
-
-  // Variable initializations:
-  Keq = 0.32;
-  SHMT_Vm = 18330;
-  SHMT_Km1 = 1.7;
-  SHMT_Km2 = 210;
-  SHMTr_Vm = 12200000;
-  SHMTr_Km1 = 3200;
-  SHMTr_Km2 = 10000;
-  HCHOtoCH2FH4_hp = 23.2;
-  CH2FH4toHCHO_hl = 0.3;
-  MTHFR_Vm = 224.8;
-  MTHFR_Km1 = 50;
-  MTHFR_Km2 = 50;
-  MTHFR_Ki1 = 0.4;
-  MTHFR_Ki21 = 59;
-  MTHFR_Ki22 = 21.3;
-  MTHFR_Ki23 = 7.68;
-  MTHFR_Ki24 = 2.77;
-  MTHFR_Ki25 = 1;
-  MTR_Vm = 22600;
-  MTR_Km1 = 125;
-  MTR_Km2 = 2900;
-  HCOOHtoCHOFH4_Vm = 3600;
-  HCOOHtoCHOFH4_Km1 = 230;
-  HCOOHtoCHOFH4_Km2 = 56;
-  HCOOHtoCHOFH4_Km3 = 1600;
-  GARFT_Vm = 4126;
-  GARFT_Km1 = 4.9;
-  GARFT_Km2 = 52;
-  GARFT_Ki1 = 5;
-  GARFT_Ki1f = 1;
-  GARFT_Ki21 = 84;
-  GARFT_Ki22 = 60;
-  GARFT_Ki23 = 43;
-  GARFT_Ki24 = 31;
-  GARFT_Ki25 = 22;
-  ATIC7_Vm = 31675;
-  ATIC7_Km1 = 5.5;
-  ATIC7_Km2 = 24;
-  ATIC7_Ki1 = 2.89;
-  ATIC7_Ki1f = 5.3;
-  ATIC7_Ki21 = 40;
-  ATIC7_Ki22 = 31.5;
-  ATIC7_Ki23 = 2.33;
-  ATIC7_Ki24 = 3.61;
-  ATIC7_Ki25 = 5.89;
-  MTHFD_Vm = 68500;
-  MTHFD_Km1 = 3;
-  MTHFD_Km2 = 21.8;
-  TYMS_Vm = 58;
-  TYMS_Km1 = 2.5;
-  TYMS_Km2 = 1.8;
-  TYMS_Ki1 = 3;
-  TYMS_Ki1f = 1.6;
-  TYMS_Ki21 = 13;
-  TYMS_Ki22 = 0.08;
-  TYMS_Ki23 = 0.07;
-  TYMS_Ki24 = 0.065;
-  TYMS_Ki25 = 0.047;
-  DHFReductase_kter = 2109.4;
-  FFH2syn_Vm = 65;
-  ATIC12_Vm = 9503;
-  ATIC12_Km1 = 5.3;
-  ATIC12_Km2 = 24;
-  ATIC12_Ki1 = 2.89;
-  ATIC12_Ki1f = 5.5;
-  ATIC12_Ki21 = 40;
-  ATIC12_Ki22 = 31.5;
-  ATIC12_Ki23 = 2.33;
-  ATIC12_Ki24 = 3.61;
-  ATIC12_Ki25 = 5.89;
-  AICARsyn_Vm = 4656;
-  AICARsyn_Km1 = 100;
-  AICARsyn_Km2 = 100;
-  FPGS12_Vm = 0.129;
-  FPGS23_Vm = 0.369;
-  FPGS34_Vm = 0.118;
-  FPGS45_Vm = 0.185;
-  GGH21_Vm = 0.195;
-  GGH32_Vm = 0.025;
-  GGH43_Vm = 0.031;
-  GGH54_Vm = 0.191;
-  RFC_Vm = 82.2;
-  RFC_Km = 8.2;
-  MTX1export_Vm = 4.65;
-  MTX2export_Vm = 0;
-  MTX3export_Vm = 0.063;
-  MTX4export_Vm = 0.063;
-  MTX5export_Vm = 0.063;
-  MTX1on_Vm = 23100;
-  MTX2on_Vm = 44300;
-  MTX3on_Vm = 85100;
-  MTX4on_Vm = 163000;
-  MTX5on_Vm = 314000;
-  MTX1off_Vm = 0.42;
-  MTX2off_Vm = 0.42;
-  MTX3off_Vm = 0.42;
-  MTX4off_Vm = 0.42;
-  MTX5off_Vm = 0.42;
-  DHFRfsyn_k0 = 0.0192;
-  DHFRfsyn_k1 = 0.04416;
-  DHFRdeg_Vm = 0.03;
-  FH2bdeg_Vm = 0.03;
-  MTX1deg_Vm = 0.03;
-  MTX2deg_Vm = 0.03;
-  MTX3deg_Vm = 0.03;
-  MTX4deg_Vm = 0.03;
-  MTX5deg_Vm = 0.03;
-
-  // Other declarations:
-  const ext_, cell, Keq;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "micromole (new default)";
-  time_unit is "heure (new default)";
-  FH2f is "dihydrofolate free";
-  FH2b is "dihydrofolate bound";
-  DHFRf is "dihydrofolate reductase free";
-  DHFRtot is "dihydrofolate reductase total";
-  FH4 is "tetrahydrofolate";
-  CH2FH4 is "5,10-methylene-tetrahydrofolate";
-  CH3FH4 is "5-methyl-tetrahydrofolate";
-  CHOFH4 is "10-formyl-tetrahydrofolate";
-  FFH2 is "10-formyl-dihydrofolate";
-
-  // CV terms:
-  ext_ identity "http://identifiers.org/go/GO:0005615"
-  cell identity "http://identifiers.org/go/GO:0005623"
-  FH2f hypernym "http://identifiers.org/chebi/CHEBI:15633",
-                "http://identifiers.org/kegg.compound/C00415"
-  FH2b hypernym "http://identifiers.org/chebi/CHEBI:15633",
-                "http://identifiers.org/kegg.compound/C00415"
-  DHFRf identity "http://identifiers.org/uniprot/P00374"
-  DHFRtot identity "http://identifiers.org/uniprot/P00374"
-  MTX1b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX2b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX3b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX4b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX5b identity "http://identifiers.org/kegg.compound/C01937"
-  FH4 identity "http://identifiers.org/chebi/CHEBI:20506",
-               "http://identifiers.org/kegg.compound/C00101"
-  CH2FH4 identity "http://identifiers.org/chebi/CHEBI:15636",
-                  "http://identifiers.org/kegg.compound/C00143"
-  CH3FH4 identity "http://identifiers.org/chebi/CHEBI:15641",
-                  "http://identifiers.org/kegg.compound/C00440"
-  CHOFH4 identity "http://identifiers.org/chebi/CHEBI:15637",
-                  "http://identifiers.org/kegg.compound/C00234"
-  FFH2 identity "http://identifiers.org/chebi/CHEBI:15634",
-                "http://identifiers.org/kegg.compound/C03204"
-  HCHO identity "http://identifiers.org/chebi/CHEBI:16842",
-                "http://identifiers.org/kegg.compound/C00067"
-  FGAR identity "http://identifiers.org/kegg.compound/C04376"
-  AICAR identity "http://identifiers.org/chebi/CHEBI:18406",
-                 "http://identifiers.org/kegg.compound/C04677"
-  MTX1 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX2 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX3 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX4 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX5 identity "http://identifiers.org/kegg.compound/C01937"
-  EMTX identity "http://identifiers.org/kegg.compound/C01937"
-  dUMP identity "http://identifiers.org/chebi/CHEBI:17622",
-                "http://identifiers.org/kegg.compound/C00365"
-  GAR identity "http://identifiers.org/kegg.compound/C03838"
-  serine identity "http://identifiers.org/chebi/CHEBI:17115",
-                  "http://identifiers.org/kegg.compound/C00065"
-  formate identity "http://identifiers.org/chebi/CHEBI:15740",
-                   "http://identifiers.org/kegg.compound/C00058"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  glutamine identity "http://identifiers.org/chebi/CHEBI:18050",
-                     "http://identifiers.org/kegg.compound/C00064"
-  glycine identity "http://identifiers.org/chebi/CHEBI:15428",
-                   "http://identifiers.org/kegg.compound/C00037"
-  NADP identity "http://identifiers.org/chebi/CHEBI:18009",
-                "http://identifiers.org/kegg.compound/C00006"
-  NADPH identity "http://identifiers.org/chebi/CHEBI:16474",
-                 "http://identifiers.org/kegg.compound/C00005"
-  homocysteine identity "http://identifiers.org/chebi/CHEBI:17230",
-                        "http://identifiers.org/kegg.compound/C05330"
-  SHMT identity "http://identifiers.org/kegg.reaction/R00945"
-  SHMT hypernym "http://identifiers.org/ec-code/2.1.2.1"
-  SHMTr identity "http://identifiers.org/kegg.reaction/R00945"
-  SHMTr hypernym "http://identifiers.org/ec-code/2.1.2.1"
-  MTHFR identity "http://identifiers.org/kegg.reaction/R01224"
-  MTHFR hypernym "http://identifiers.org/ec-code/1.5.1.20"
-  MTR identity "http://identifiers.org/kegg.reaction/R00946"
-  MTR hypernym "http://identifiers.org/ec-code/2.1.1.13"
-  HCOOHtoCHOFH4 identity "http://identifiers.org/kegg.reaction/R00943"
-  HCOOHtoCHOFH4 hypernym "http://identifiers.org/ec-code/6.3.4.3"
-  GARFT identity "http://identifiers.org/kegg.reaction/R04325",
-                 "http://identifiers.org/reactome/REACT_1509"
-  GARFT hypernym "http://identifiers.org/ec-code/2.1.2.2"
-  ATIC7 identity "http://identifiers.org/kegg.reaction/R04560",
-                 "http://identifiers.org/reactome/REACT_812"
-  ATIC7 hypernym "http://identifiers.org/ec-code/2.1.2.3"
-  MTHFD part "http://identifiers.org/ec-code/1.5.1.5",
-             "http://identifiers.org/ec-code/6.3.4.3",
-             "http://identifiers.org/kegg.reaction/R01220",
-             "http://identifiers.org/kegg.reaction/R01655"
-  TYMS identity "http://identifiers.org/kegg.reaction/R02101"
-  TYMS hypernym "http://identifiers.org/ec-code/2.1.1.45"
-  DHFReductase identity "http://identifiers.org/kegg.reaction/R00939"
-  DHFReductase hypernym "http://identifiers.org/ec-code/1.5.1.3"
-  FFH2syn identity "http://identifiers.org/kegg.reaction/R02238"
-  FFH2syn hypernym "http://identifiers.org/ec-code/6.3.4.17"
-  ATIC12 hypernym "http://identifiers.org/ec-code/2.1.2.3"
-  ATIC12 identity "http://identifiers.org/kegg.reaction/R04560"
-  AICARsyn hypernym "http://identifiers.org/ec-code/6.3.5.3"
-  FPGS12 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  FPGS23 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  FPGS34 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  FPGS45 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  GGH21 hypernym "http://identifiers.org/ec-code/3.4.19.9"
-  GGH32 hypernym "http://identifiers.org/ec-code/3.4.19.9"
-  GGH43 identity "http://identifiers.org/ec-code/3.4.19.9"
-  GGH54 identity "http://identifiers.org/ec-code/3.4.19.9"
-  RFC identity "http://identifiers.org/go/GO:0008517"
-  MTX1export identity "http://identifiers.org/go/GO:0008517"
-  MTX2export identity "http://identifiers.org/go/GO:0008517"
-  MTX3export identity "http://identifiers.org/go/GO:0008517"
-  MTX4export hypernym "http://identifiers.org/go/GO:0008517"
-  MTX5export hypernym "http://identifiers.org/go/GO:0008517"
-end
-
-MorrisonAllegra is "Morrison1989 - Folate Cycle"
-
-MorrisonAllegra model_entity_is "http://identifiers.org/biomodels.db/MODEL6617317313"
-MorrisonAllegra model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000018"
-MorrisonAllegra description "http://identifiers.org/pubmed/2732237"
-MorrisonAllegra taxon "http://identifiers.org/taxonomy/9606"
-MorrisonAllegra part "http://identifiers.org/kegg.pathway/map00670",
-                     "http://identifiers.org/kegg.pathway/map00790"
-MorrisonAllegra hypernym "http://identifiers.org/go/GO:0046655"
-MorrisonAllegra property "http://identifiers.org/doid/DOID:1612"
diff --git a/BioModelsRAG/data/BIOMD0000000019.txt b/BioModelsRAG/data/BIOMD0000000019.txt
deleted file mode 100644
index f53a7be43ac759da86a50cffba44bf63bfeeea59..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000019.txt
+++ /dev/null
@@ -1,652 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000019()
-
-  // Compartments and Species:
-  compartment c1, c2, c3;
-  substanceOnly species $x1 in c1, x2 in c1, x3 in c2, x4 in c2, x5 in c2;
-  substanceOnly species x6 in c2, x7 in c2, x8 in c2, x9 in c2, x10 in c2;
-  substanceOnly species x11 in c2, x12 in c2, x13 in c3, x14 in c2, x15 in c3;
-  substanceOnly species x16 in c2, x17 in c2, x18 in c2, x19 in c2, x20 in c2;
-  substanceOnly species x21 in c2, x22 in c2, x23 in c2, x24 in c2, x25 in c2;
-  substanceOnly species x26 in c2, x27 in c2, x28 in c2, x29 in c2, x30 in c2;
-  substanceOnly species x31 in c2, x32 in c2, x33 in c2, x34 in c2, x35 in c2;
-  substanceOnly species x36 in c2, x37 in c2, x38 in c2, x39 in c2, x40 in c2;
-  substanceOnly species x41 in c2, x42 in c2, x43 in c2, x44 in c2, x45 in c2;
-  substanceOnly species x46 in c2, x47 in c2, x48 in c2, x49 in c2, x50 in c2;
-  substanceOnly species x51 in c2, x52 in c2, x53 in c2, x54 in c2, x55 in c2;
-  substanceOnly species x56 in c2, x57 in c2, x58 in c2, x59 in c2, x60 in c2;
-  substanceOnly species x61 in c2, x62 in c2, x63 in c2, x64 in c2, x65 in c2;
-  substanceOnly species x66 in c2, x67 in c2, x68 in c2, x69 in c2, x70 in c2;
-  substanceOnly species x71 in c2, x72 in c2, x73 in c2, x74 in c2, x75 in c2;
-  substanceOnly species x76 in c2, x77 in c2, x78 in c2, x79 in c2, x80 in c2;
-  substanceOnly species x81 in c2, x82 in c2, x83 in c2, x84 in c2, x85 in c2;
-  substanceOnly species x86 in c2, x87 in c2, x88 in c2, x89 in c2, x90 in c2;
-  substanceOnly species x91 in c2, x92 in c2, x93 in c2, x94 in c2, $Raf_act in c2;
-  substanceOnly species $Ras_GTP in c2, $MEK_PP in c2, $ERK_PP in c2, $SHC_P_t in c2;
-  substanceOnly species $EGF_EGFR_act in c2;
-
-  // Assignment Rules:
-  Raf_act := x45 + x46 + x48 + x50 + x72 + x73 + x74 + x76;
-  Ras_GTP := x42 + x28 + x70 + x69;
-  MEK_PP := x51 + x77;
-  ERK_PP := x59 + x83;
-  SHC_P_t := x33 + x34 + x35 + x36 + x37 + x38 + x39 + x40 + x91 + x92 + x93 + x94 + x64 + x65 + x66 + x67 + x68;
-  EGF_EGFR_act := x5 + x7 + x15 + x23 + x25 + x27 + x29 + x32 + x33 + x34 + x35 + x36 + x37 + x88 + x89 + x90 + x91 + x92 + x93 + x94 + x8 + x11 + x17 + x18 + x19 + x20 + x21 + x63 + x64 + x65 + x66 + x67 + x68;
-  k5 := piecewise(1.55, C < 3100, 0.2, C > 100000, C*-1.35e-5 + 1.55);
-  C := RT/(kr1/(k1*x1) + 1);
-
-  // Reactions:
-  v1: $x1 + x2 -> x3; k1*x1*x2 - kr1*x3;
-  v2: 2 x3 -> x4; k2*x3*x3 - kr2*x4;
-  v3: x4 -> x5; k3*x4 - kr3*x5;
-  v4: x23 + x12 -> x7; k4*x23*x12 - kr4*x7;
-  v5: x7 -> x18 + x9; k5*x7;
-  v6: x2 -> x6; k6*x2 - kr6*x6;
-  v7: x5 => x8; k7*x5;
-  v8: x5 + x14 -> x15; k8*x5*x14 - kr8*x15;
-  v9: x23 => x18; k7*x23;
-  v10: x6 + x16 -> x10; k10*x6*x16 - kr10*x10;
-  v11: 2 x10 -> x11; k2*x10*x10 - kr2*x11;
-  v12: x11 -> x8; k3*x11 - kr3*x8;
-  v13:  => x2; k13;
-  v14: x8 + x14 -> x17; k14*x8*x14 - kr14*x17;
-  v15: x9 => x12; k15*x9;
-  v16: x22 + x15 -> x23; k16*x22*x15 - kr16*x23;
-  v17: x24 + x23 -> x25; k17*x24*x23 - kr17*x25;
-  v18: x26 + x25 -> x27; k18*x26*x25 - kr18*x27;
-  v19: x27 -> x28 + x25; k19*x27 - kr19*x28*x25;
-  v20: x25 + x43 -> x29; k20*x25*x43 - kr20*x29;
-  v21: x29 -> x25 + x26; k21*x29 - kr21*x25*x26;
-  v22: x31 + x15 -> x32; k22*x31*x15 - kr22*x32;
-  v23: x32 -> x33; k23*x32 - kr23*x33;
-  v24: x22 + x33 -> x34; k24*x22*x33 - kr24*x34;
-  v25: x24 + x34 -> x35; k25*x24*x34 - kr25*x35;
-  v26: x26 + x35 -> x36; k18*x26*x35 - kr18*x36;
-  v27: x36 -> x35 + x28; k19*x36 - kr19*x35*x28;
-  v28: x28 + x41 -> x42; k28*x28*x41 - kr28*x42;
-  v29: x42 -> x43 + x45; k29*x42 - kr29*x43*x45;
-  v30: x35 + x43 -> x37; k20*x35*x43 - kr20*x37;
-  v31: x37 -> x35 + x26; k21*x37 - kr21*x35*x26;
-  v32: x35 -> x15 + x38; k32*x35 - kr32*x15*x38;
-  v33: x38 -> x40 + x30; k33*x38 - kr33*x40*x30;
-  v34: x25 -> x15 + x30; k34*x25 - kr34*x15*x30;
-  v35: x30 -> x24 + x22; k35*x30 - kr35*x24*x22;
-  v36: x40 => x31; Vm36*x40/(Km36 + x40);
-  v37: x33 -> x15 + x40; k37*x33 - kr37*x15*x40;
-  v38: x22 + x40 -> x39; k24*x22*x40 - kr24*x39;
-  v39: x34 -> x15 + x39; k37*x34 - kr37*x15*x39;
-  v40: x24 + x39 -> x38; k40*x24*x39 - kr40*x38;
-  v41: x30 + x33 -> x35; k41*x30*x33 - kr41*x35;
-  v42: x44 + x45 -> x46; k42*x44*x45 - kr42*x46;
-  v43: x46 -> x41 + x44; k43*x46;
-  v44: x47 + x45 -> x48; k44*x47*x45 - kr44*x48;
-  v45: x48 -> x49 + x45; k45*x48;
-  v46: x49 + x45 -> x50; k44*x49*x45 - kr44*x50;
-  v47: x50 -> x51 + x45; k47*x50;
-  v48: x51 + x53 -> x52; k48*x51*x53 - kr48*x52;
-  v49: x52 -> x49 + x53; k49*x52;
-  v50: x53 + x49 -> x54; k50*x53*x49 - kr50*x54;
-  v51: x54 -> x47 + x53; k49*x54;
-  v52: x55 + x51 -> x56; k52*x55*x51 - kr52*x56;
-  v53: x56 -> x51 + x57; k53*x56;
-  v54: x51 + x57 -> x58; k52*x51*x57 - kr52*x58;
-  v55: x58 -> x59 + x51; k55*x58;
-  v56: x59 + x60 -> x61; k56*x59*x60 - kr56*x61;
-  v57: x61 -> x57 + x60; k57*x61;
-  v58: x60 + x57 -> x62; k58*x60*x57 - kr58*x62;
-  v59: x62 -> x55 + x60; k59*x62;
-  v60: x6 => x86; k60*x6;
-  v61: x16 => x13; k61*x16;
-  v62: x8 => x87; k60*x8;
-  v63: x17 + x22 -> x18; k16*x17*x22 - kr16*x18;
-  v64: x24 + x18 -> x19; k17*x24*x18 - kr17*x19;
-  v65: x26 + x19 -> x20; k18*x26*x19 - kr18*x20;
-  v66: x20 -> x69 + x19; k19*x20 - kr19*x69*x19;
-  v67: x71 + x19 -> x21; k20*x71*x19 - kr20*x21;
-  v68: x21 -> x19 + x26; k21*x21 - kr21*x19*x26;
-  v69: x31 + x17 -> x63; k22*x31*x17 - kr22*x63;
-  v70: x63 -> x64; k23*x63 - kr23*x64;
-  v71: x22 + x64 -> x65; k24*x22*x64 - kr24*x65;
-  v72: x24 + x65 -> x66; k25*x24*x65 - kr25*x66;
-  v73: x26 + x66 -> x67; k18*x26*x66 - kr18*x67;
-  v74: x67 -> x66 + x69; k19*x67 - kr19*x66*x69;
-  v75: x69 + x41 -> x70; k28*x69*x41 - kr28*x70;
-  v76: x70 -> x71 + x72; k29*x70 - kr29*x71*x72;
-  v77: x71 + x66 -> x68; k20*x71*x66 - kr20*x68;
-  v78: x68 -> x66 + x26; k21*x68 - kr21*x66*x26;
-  v79: x66 -> x17 + x38; k32*x66 - kr32*x17*x38;
-  v80: x19 -> x17 + x30; k34*x19 - kr34*x17*x30;
-  v81: x64 -> x17 + x40; k37*x64 - kr37*x17*x40;
-  v82: x65 -> x17 + x39; k37*x65 - kr37*x17*x39;
-  v83: x30 + x64 -> x66; k41*x30*x64 - kr41*x66;
-  v84: x44 + x72 -> x73; k42*x44*x72 - kr42*x73;
-  v85: x73 -> x41 + x44; k43*x73;
-  v86: x47 + x72 -> x74; k44*x47*x72 - kr44*x74;
-  v87: x74 -> x75 + x72; k45*x74;
-  v88: x72 + x75 -> x76; k44*x72*x75 - kr44*x76;
-  v89: x76 -> x72 + x77; k47*x76;
-  v90: x77 + x53 -> x78; k48*x77*x53 - kr48*x78;
-  v91: x78 -> x75 + x53; k49*x78;
-  v92: x53 + x75 -> x79; k50*x53*x75 - kr50*x79;
-  v93: x79 -> x47 + x53; k49*x79;
-  v94: x55 + x77 -> x80; k52*x55*x77 - kr52*x80;
-  v95: x80 -> x81 + x77; k53*x80;
-  v96: x77 + x81 -> x82; k52*x77*x81 - kr52*x82;
-  v97: x82 -> x83 + x77; k55*x82;
-  v98: x83 + x60 -> x84; k56*x83*x60 - kr56*x84;
-  v99: x84 -> x81 + x60; k57*x84;
-  v100: x60 + x81 -> x85; k58*x60*x81 - kr58*x85;
-  v101: x85 -> x55 + x60; k59*x85;
-  v102: x15 -> x17; k6*x15 - kr6*x17;
-  v103: x32 -> x63; k6*x32 - kr6*x63;
-  v104: x33 -> x64; k6*x33 - kr6*x64;
-  v105: x25 -> x19; k6*x25 - kr6*x19;
-  v106: x25 + x12 -> x88; k4*x25*x12 - kr4*x88;
-  v107: x88 -> x9 + x19; k5*x88;
-  v108: x27 -> x20; k6*x27 - kr6*x20;
-  v109: x27 + x12 -> x89; k4*x27*x12 - kr4*x89;
-  v110: x89 -> x9 + x20; k5*x89;
-  v111: x29 -> x21; k6*x29 - kr6*x21;
-  v112: x29 + x12 -> x90; k4*x29*x12 - kr4*x90;
-  v113: x90 -> x9 + x21; k5*x90;
-  v114: x34 -> x65; k6*x34 - kr6*x65;
-  v115: x34 + x12 -> x91; k4*x34*x12 - kr4*x91;
-  v116: x91 -> x9 + x65; k5*x91;
-  v117: x35 -> x66; k6*x35 - kr6*x66;
-  v118: x35 + x12 -> x92; k4*x35*x12 - kr4*x92;
-  v119: x92 -> x9 + x66; k5*x92;
-  v120: x36 -> x67; k6*x36 - kr6*x67;
-  v121: x36 + x12 -> x93; k4*x36*x12 - kr4*x93;
-  v122: x93 -> x9 + x67; k5*x93;
-  v123: x37 -> x68; k6*x37 - kr6*x68;
-  v124: x37 + x12 -> x94; k4*x37*x12 - kr4*x94;
-  v125: x94 -> x68 + x9; k5*x94;
-
-  // Species initializations:
-  x1 = 4962/c1;
-  x2 = 50000/c1;
-  x3 = 0;
-  x4 = 0;
-  x5 = 0;
-  x6 = 0;
-  x7 = 0;
-  x8 = 0;
-  x9 = 0;
-  x10 = 0;
-  x11 = 0;
-  x12 = 81000/c2;
-  x13 = 0;
-  x14 = 12000/c2;
-  x15 = 0;
-  x16 = 0;
-  x17 = 0;
-  x18 = 0;
-  x19 = 0;
-  x20 = 0;
-  x21 = 0;
-  x22 = 11000/c2;
-  x23 = 0;
-  x24 = 26300/c2;
-  x25 = 0;
-  x26 = 72000/c2;
-  x27 = 0;
-  x28 = 0;
-  x29 = 0;
-  x30 = 40000/c2;
-  x31 = 101000/c2;
-  x32 = 0;
-  x33 = 0;
-  x34 = 0;
-  x35 = 0;
-  x36 = 0;
-  x37 = 0;
-  x38 = 0;
-  x39 = 0;
-  x40 = 0;
-  x41 = 40000/c2;
-  x42 = 0;
-  x43 = 0;
-  x44 = 40000/c2;
-  x45 = 0;
-  x46 = 0;
-  x47 = 22000000/c2;
-  x48 = 0;
-  x49 = 0;
-  x50 = 0;
-  x51 = 0;
-  x52 = 0;
-  x53 = 40000/c2;
-  x54 = 0;
-  x55 = 21000000/c2;
-  x56 = 0;
-  x57 = 0;
-  x58 = 0;
-  x59 = 0;
-  x60 = 10000000/c2;
-  x61 = 0;
-  x62 = 0;
-  x63 = 0;
-  x64 = 0;
-  x65 = 0;
-  x66 = 0;
-  x67 = 0;
-  x68 = 0;
-  x69 = 0;
-  x70 = 0;
-  x71 = 0;
-  x72 = 0;
-  x73 = 0;
-  x74 = 0;
-  x75 = 0;
-  x76 = 0;
-  x77 = 0;
-  x78 = 0;
-  x79 = 0;
-  x80 = 0;
-  x81 = 0;
-  x82 = 0;
-  x83 = 0;
-  x84 = 0;
-  x85 = 0;
-  x86 = 0;
-  x87 = 0;
-  x88 = 0;
-  x89 = 0;
-  x90 = 0;
-  x91 = 0;
-  x92 = 0;
-  x93 = 0;
-  x94 = 0;
-
-  // Compartment initializations:
-  c1 = 1;
-  c2 = 1;
-  c3 = 4.3e-06;
-
-  // Variable initializations:
-  k1 = 0.003;
-  k1 has pipmin;
-  kr1 = 0.228;
-  kr1 has pmin;
-  kr2 = 6;
-  kr2 has pmin;
-  k2 = 0.001;
-  k2 has pipmin;
-  k3 = 60;
-  k3 has pmin;
-  kr3 = 0.6;
-  kr3 has pmin;
-  k4 = 1.038e-05;
-  k4 has pipmin;
-  kr4 = 0.0996;
-  kr4 has pmin;
-  k5 has pmin;
-  k6 = 0.003;
-  k6 has pmin;
-  kr6 = 0.3;
-  kr6 has pmin;
-  k7 = 0.003;
-  k7 has pmin;
-  k8 = 0.0001;
-  k8 has pipmin;
-  kr8 = 12;
-  kr8 has pmin;
-  k10 = 3.25581;
-  k10 has pipmin;
-  kr10 = 0.66;
-  kr10 has pmin;
-  kr11 = 6;
-  kr11 has pmin;
-  k11 = 0.001;
-  k11 has pipmin;
-  kr12 = 0.6;
-  kr12 has pmin;
-  k12 = 60;
-  k12 has pmin;
-  k13 = 130.2;
-  k13 has ipmin;
-  k14 = 0.0001;
-  k14 has pipmin;
-  kr14 = 12;
-  kr14 has pmin;
-  k15 = 600000;
-  k15 has pmin;
-  kr16 = 16.5;
-  kr16 has pmin;
-  k16 = 0.001;
-  k16 has pipmin;
-  kr17 = 3.6;
-  kr17 has pmin;
-  k17 = 0.001;
-  k17 has pipmin;
-  kr18 = 78;
-  kr18 has pmin;
-  k18 = 0.0015;
-  k18 has pipmin;
-  kr19 = 1e-05;
-  kr19 has pipmin;
-  k19 = 30;
-  k19 has pmin;
-  kr20 = 24;
-  kr20 has pmin;
-  k20 = 0.00021;
-  k20 has pipmin;
-  k21 = 1.38;
-  k21 has pmin;
-  kr21 = 2.2e-05;
-  kr21 has pipmin;
-  k22 = 0.0021;
-  k22 has pipmin;
-  kr22 = 6;
-  kr22 has pmin;
-  k23 = 360;
-  k23 has pmin;
-  kr23 = 36;
-  kr23 has pmin;
-  k24 = 0.001;
-  k24 has pipmin;
-  kr24 = 33;
-  kr24 has pmin;
-  kr25 = 1.284;
-  kr25 has pmin;
-  k25 = 0.001;
-  k25 has pipmin;
-  k28 = 0.0001;
-  k28 has pipmin;
-  kr28 = 0.318;
-  kr28 has pmin;
-  k29 = 60;
-  k29 has pmin;
-  kr29 = 7e-05;
-  kr29 has pipmin;
-  kr32 = 2.4e-05;
-  kr32 has pipmin;
-  k32 = 6;
-  k32 has pmin;
-  k33 = 12;
-  k33 has pmin;
-  kr33 = 0.0021;
-  kr33 has pipmin;
-  k34 = 1.8;
-  k34 has pmin;
-  kr34 = 0.00045;
-  kr34 has pipmin;
-  k35 = 0.09;
-  k35 has pmin;
-  kr35 = 0.00045;
-  kr35 has pipmin;
-  Vm36 = 61200;
-  Vm36 has ipmin;
-  Km36 = 200000000000000;
-  Km36 has substance;
-  k37 = 18;
-  k37 has pmin;
-  kr37 = 9e-05;
-  kr37 has pipmin;
-  k40 = 0.003;
-  k40 has pipmin;
-  kr40 = 3.84;
-  kr40 has pmin;
-  kr41 = 2.574;
-  kr41 has pmin;
-  k41 = 0.003;
-  k41 has pipmin;
-  k42 = 0.0071;
-  k42 has pipmin;
-  kr42 = 12;
-  kr42 has pmin;
-  k43 = 60;
-  k43 has pmin;
-  kr44 = 1.0998;
-  kr44 has pmin;
-  k44 = 0.00111;
-  k44 has pipmin;
-  k45 = 210;
-  k45 has pmin;
-  k47 = 174;
-  k47 has pmin;
-  kr48 = 48;
-  kr48 has pmin;
-  k48 = 0.00143;
-  k48 has pipmin;
-  k49 = 3.48;
-  k49 has pmin;
-  kr50 = 30;
-  kr50 has pmin;
-  k50 = 2.5e-05;
-  k50 has pipmin;
-  k52 = 0.00534;
-  k52 has pipmin;
-  kr52 = 1.98;
-  kr52 has pmin;
-  k53 = 960;
-  k53 has pmin;
-  k55 = 342;
-  k55 has pmin;
-  kr56 = 36;
-  kr56 has pmin;
-  k56 = 0.00145;
-  k56 has pipmin;
-  k57 = 16.2;
-  k57 has pmin;
-  kr58 = 30;
-  kr58 has pmin;
-  k58 = 0.0005;
-  k58 has pipmin;
-  k59 = 18;
-  k59 has pmin;
-  k60 = 0.04002;
-  k60 has pmin;
-  k61 = 0.01002;
-  k61 has pmin;
-  RT = 50000;
-  RT has substance;
-
-  // Other declarations:
-  var k5, C;
-  const c1, c2, c3, k1, kr1, kr2, k2, k3, kr3, k4, kr4, k6, kr6, k7, k8, kr8;
-  const k10, kr10, kr11, k11, kr12, k12, k13, k14, kr14, k15, kr16, k16, kr17;
-  const k17, kr18, k18, kr19, k19, kr20, k20, k21, kr21, k22, kr22, k23, kr23;
-  const k24, kr24, kr25, k25, k28, kr28, k29, kr29, kr32, k32, k33, kr33;
-  const k34, kr34, k35, kr35, Vm36, Km36, k37, kr37, k40, kr40, kr41, k41;
-  const k42, kr42, k43, kr44, k44, k45, k47, kr48, k48, k49, kr50, k50, k52;
-  const kr52, k53, k55, kr56, k56, k57, kr58, k58, k59, k60, k61, RT;
-
-  // Unit definitions:
-  unit substance = item;
-  unit time_unit = 60 second;
-  unit volume = 1e-12 litre;
-  unit pmin = 1 / 60 second;
-  unit ipmin = item / 60 second;
-  unit pipmin = 1 / (60 second * item);
-  unit piplpmin = 1e-12 litre / (item * 60 second);
-
-  // Display Names:
-  substance is "items";
-  time_unit is "min";
-  volume is "pl";
-  pmin is "permin";
-  ipmin is "itemspermin";
-  pipmin is "peritempermin";
-  piplpmin is "plperitempermin";
-  c1 is "extracellular volume";
-  c2 is "cytoplasm";
-  c3 is "endosomal volume";
-  x1 is "EGF";
-  x2 is "EGFR";
-  x3 is "EGF-EGFR";
-  x4 is "EGF-EGFR^2";
-  x5 is "EGF-EGFR*^2";
-  x6 is "EGFRi";
-  x7 is "EGF-EGFR*^2-GAP-Grb2-Prot";
-  x8 is "EGF-EGFRi*^2";
-  x9 is "Proti";
-  x10 is "EGF-EGFRi";
-  x11 is "EGF-EGFRi^2";
-  x12 is "Prot";
-  x13 is "EGFideg";
-  x14 is "GAP";
-  x15 is "EGF-EGFR*^2-GAP";
-  x16 is "EGFi";
-  x17 is "EGF-EGFRi*^2-GAP";
-  x18 is "EGF-EGFRi*^2-GAP-Grb2";
-  x19 is "EGF-EGFRi*^2-GAP-Grb2-Sos";
-  x20 is "EGF-EGFRi*^2-GAP-Grb2-Sos-Ras-GDP";
-  x21 is "EGF-EGFRi*^2-GAP-Grb2-Sos-Ras-GTP";
-  x22 is "Grb2";
-  x23 is "EGF-EGFR*^2-GAP-Grb2";
-  x24 is "Sos";
-  x25 is "EGF-EGFR*^2-GAP-Grb2-Sos";
-  x26 is "Ras-GDP";
-  x27 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GDP";
-  x28 is "Ras-GTP";
-  x29 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GTP";
-  x30 is "Grb2-Sos";
-  x31 is "Shc";
-  x32 is "EGF-EGFR*^2-GAP-Shc";
-  x33 is "EGF-EGFR*^2-GAP-Shc*";
-  x34 is "EGF-EGFR*^2-GAP-Shc*-Grb2";
-  x35 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos";
-  x36 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GDP";
-  x37 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GTP";
-  x38 is "Shc*-Grb2-Sos";
-  x39 is "Shc*-Grb2";
-  x40 is "Shc*";
-  x41 is "Raf";
-  x42 is "Raf-Ras-GTP";
-  x43 is "Ras-GTP*";
-  x44 is "Phosphotase1";
-  x45 is "Raf*";
-  x46 is "Raf*-P'ase";
-  x47 is "MEK";
-  x48 is "MEK-Raf*";
-  x49 is "MEK-P";
-  x50 is "MEK-P-Raf*";
-  x51 is "MEK-PP";
-  x52 is "MEK-PP-P'ase2";
-  x53 is "Phosphatase2";
-  x54 is "MEK-P-P'ase2";
-  x55 is "ERK";
-  x56 is "ERK-MEK-PP";
-  x57 is "ERK-P";
-  x58 is "ERK-P-MEK-PP";
-  x59 is "ERK-PP";
-  x60 is "Phosphotase3";
-  x61 is "ERK-PP-P'ase3";
-  x62 is "ERK-P-P'ase3";
-  x63 is "EGF-EGFRi*^2-GAP-Shc";
-  x64 is "EGF-EGFRi*^2-GAP-Shc*";
-  x65 is "EGF-EGFRi*^2-GAP-Shc*-Grb2";
-  x66 is "EGF-EGFRi*^2-GAP-Shc*-Grb2-Sos";
-  x67 is "EGF-EGFRi*^2-GAP-Shc*-Grb2-Sos-Ras-GDP";
-  x68 is "EGF-EGFRi*^2-GAP-Shc*-Grb2-Sos-Ras-GTP";
-  x69 is "Rasi-GTP";
-  x70 is "Rafi-Rasi-GTP";
-  x71 is "Rasi-GTP*";
-  x72 is "Rafi*";
-  x73 is "Rafi*-P'ase";
-  x74 is "MEKi-Rafi*";
-  x75 is "MEKi-P";
-  x76 is "MEKi-P-Rafi*";
-  x77 is "MEKi-PP";
-  x78 is "MEKi-PP-P'ase2i";
-  x79 is "MEKi-P-P'ase2i";
-  x80 is "ERKi-MEKi-PP";
-  x81 is "ERKi-P";
-  x82 is "ERKi-P-MEKi-PP";
-  x83 is "ERKi-PP";
-  x84 is "ERKi-PP-P'ase3i";
-  x85 is "ERKi-P-P'ase3i";
-  x86 is "EGFRideg";
-  x87 is "EGF-EGFRi*^2deg";
-  x88 is "EGF-EGFR*^2-GAP-Grb2-Sos-Prot";
-  x89 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GDP-Prot";
-  x90 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GTP-Prot";
-  x91 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Prot";
-  x92 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Prot";
-  x93 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GDP-Prot";
-  x94 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GTP-Prot";
-  Raf_act is "t_Raf*";
-  Ras_GTP is "t_Ras_GTP";
-  MEK_PP is "t_MEK_PP";
-  ERK_PP is "t_ERK_PP";
-  SHC_P_t is "t_SHC_P_t";
-  EGF_EGFR_act is "t_EGF_EGFR*";
-  C is "C_internalization";
-  RT is "total_Receptors";
-
-  // CV terms:
-  c1 identity "http://identifiers.org/go/GO:0005615"
-  c2 identity "http://identifiers.org/go/GO:0005737"
-  c3 identity "http://identifiers.org/go/GO:0005768"
-  x3 hypernym "http://identifiers.org/reactome/REACT_9893"
-  x3 version "http://identifiers.org/uniprot/P01133",
-             "http://identifiers.org/uniprot/P00533"
-  x4 hypernym "http://identifiers.org/reactome/REACT_9820"
-  x4 version "http://identifiers.org/uniprot/P01133",
-             "http://identifiers.org/uniprot/P00533"
-  x5 hypernym "http://identifiers.org/kegg.compound/C00562"
-  x5 version "http://identifiers.org/uniprot/P00533",
-             "http://identifiers.org/uniprot/P01133"
-  x6 hypernym "http://identifiers.org/uniprot/P00533"
-  x7 version "http://identifiers.org/uniprot/P20936",
-             "http://identifiers.org/uniprot/P62993",
-             "http://identifiers.org/uniprot/P00533",
-             "http://identifiers.org/uniprot/P01133",
-             "http://identifiers.org/go/GO:0030119"
-  x8 version "http://identifiers.org/uniprot/P00533",
-             "http://identifiers.org/uniprot/P01133"
-  x9 hypernym "http://identifiers.org/go/GO:0030119"
-  x10 version "http://identifiers.org/uniprot/P01133",
-              "http://identifiers.org/uniprot/P00533"
-  x14 hypernym "http://identifiers.org/interpro/IPR001936"
-  x14 hypernym "http://identifiers.org/uniprot/P20936"
-  x14 description "http://identifiers.org/omim/139150"
-  x22 hypernym "http://identifiers.org/uniprot/P62993"
-  x22 description "http://identifiers.org/omim/108355"
-  x24 hypernym "http://identifiers.org/uniprot/Q07889"
-  x24 description "http://identifiers.org/omim/182530"
-  x26 part "http://identifiers.org/chebi/CHEBI:17552",
-           "http://identifiers.org/uniprot/P01112"
-  x28 part "http://identifiers.org/chebi/CHEBI:15996",
-           "http://identifiers.org/uniprot/P01112"
-  x31 hypernym "http://identifiers.org/uniprot/P98077"
-  x31 description "http://identifiers.org/omim/605217"
-  x41 hypernym "http://identifiers.org/uniprot/P04049"
-  x41 description "http://identifiers.org/omim/164760"
-  x47 hypernym "http://identifiers.org/uniprot/Q02750",
-               "http://identifiers.org/uniprot/A4QPA9"
-  x47 description "http://identifiers.org/omim/176872"
-  x49 hypernym "http://identifiers.org/uniprot/Q02750",
-               "http://identifiers.org/uniprot/A4QPA9",
-               "http://identifiers.org/kegg.compound/C00562"
-  x49 description "http://identifiers.org/omim/176872"
-  x55 hypernym "http://identifiers.org/uniprot/P28482"
-  x55 description "http://identifiers.org/omim/176948"
-  v1 hypernym "http://identifiers.org/go/GO:0005154",
-              "http://identifiers.org/go/GO:0048408"
-  v1 hypernym "http://identifiers.org/reactome/REACT_9481"
-  v2 hypernym "http://identifiers.org/go/GO:0007171",
-              "http://identifiers.org/go/GO:0046983"
-  v2 hypernym "http://identifiers.org/reactome/REACT_9397"
-  v3 hypernym "http://identifiers.org/go/GO:0007171",
-              "http://identifiers.org/go/GO:0046777",
-              "http://identifiers.org/go/GO:0004713"
-  v3 hypernym "http://identifiers.org/reactome/REACT_9388"
-  v6 hypernym "http://identifiers.org/go/GO:0031623"
-  v7 hypernym "http://identifiers.org/go/GO:0031623"
-  v10 hypernym "http://identifiers.org/go/GO:0031623"
-  v100 description "http://identifiers.org/omim/164760"
-  v101 description "http://identifiers.org/omim/164760"
-end
-
-BIOMD0000000019 is "Schoeberl2002 - EGF MAPK"
-
-BIOMD0000000019 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617455076"
-BIOMD0000000019 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000019"
-BIOMD0000000019 description "http://identifiers.org/pubmed/11923843"
-BIOMD0000000019 taxon "http://identifiers.org/taxonomy/9606"
-BIOMD0000000019 hypernym "http://identifiers.org/reactome/REACT_9417.3",
-                         "http://identifiers.org/go/GO:0007173"
-BIOMD0000000019 version "http://identifiers.org/go/GO:0007265",
-                        "http://identifiers.org/go/GO:0000165"
diff --git a/BioModelsRAG/data/BIOMD0000000020.txt b/BioModelsRAG/data/BIOMD0000000020.txt
deleted file mode 100644
index 37187972eb4970fc81a6d1e85ace4bc22a2abf0a..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000020.txt
+++ /dev/null
@@ -1,101 +0,0 @@
-// Created by libAntimony v2.13.0
-model *hhsa_1952()
-
-  // Compartments and Species:
-  compartment unit_compartment;
-
-  // Assignment Rules:
-  i_Na := g_Na*m^3*h*(V - V_Na);
-  i_K := g_K*n^4*(V - V_K);
-  i_L := g_L*(V - V_L);
-  V_neg := -V;
-  E := V + E_R;
-  V_Na := E_Na - E_R;
-  V_K := E_K - E_R;
-  V_L := E_L - E_R;
-  alpha_m := 0.1*(V + 25)/(exp((V + 25)/10) - 1);
-  beta_m := 4*exp(V/18);
-  alpha_h := 0.07*exp(V/20);
-  beta_h := 1/(exp((V + 30)/10) + 1);
-  alpha_n := 0.01*(V + 10)/(exp((V + 10)/10) - 1);
-  beta_n := 0.125*exp(V/80);
-
-  // Rate Rules:
-  V' = (I - (i_Na + i_K + i_L))/Cm;
-  m' = alpha_m*(1 - m) - beta_m*m;
-  h' = alpha_h*(1 - h) - beta_h*h;
-  n' = alpha_n*(1 - n) - beta_n*n;
-
-  // Compartment initializations:
-  unit_compartment = 1;
-
-  // Variable initializations:
-  V = 0;
-  V has mV;
-  I = 0;
-  Cm = 1;
-  V_neg has mV;
-  E has mV;
-  E_R = -75;
-  E_R has mV;
-  g_Na = 120;
-  m = 0.052932;
-  h = 0.59612;
-  V_Na has mV;
-  g_K = 36;
-  n = 0.31768;
-  V_K has mV;
-  g_L = 0.3;
-  V_L has mV;
-  E_Na = -190;
-  E_Na has mV;
-  E_K = -63;
-  E_K has mV;
-  E_L = -85.613;
-  E_L has mV;
-
-  // Other declarations:
-  var V, i_Na, i_K, i_L, V_neg, E, m, h, V_Na, n, V_K, V_L, alpha_m, beta_m;
-  var alpha_h, beta_h, alpha_n, beta_n;
-  const unit_compartment, I, Cm, E_R, g_Na, g_K, g_L, E_Na, E_K, E_L;
-
-  // Unit definitions:
-  unit time_unit = 1e-3 second;
-  unit mV = 1e-3 volt;
-
-  // Display Names:
-  time_unit is "millisecond";
-  alpha_h is "auxiliary alpha_h";
-
-  // SBO terms:
-  V.sboTerm = 259
-  Cm.sboTerm = 258
-  V_neg.sboTerm = 259
-  E.sboTerm = 259
-  E_R.sboTerm = 259
-  g_Na.sboTerm = 257
-  V_Na.sboTerm = 259
-  g_K.sboTerm = 257
-  V_K.sboTerm = 259
-  g_L.sboTerm = 257
-  V_L.sboTerm = 259
-  E_Na.sboTerm = 259
-  E_K.sboTerm = 259
-  E_L.sboTerm = 259
-
-  // CV terms:
-  i_Na hypernym "http://identifiers.org/obo.go/GO:0005248"
-  i_K hypernym "http://identifiers.org/obo.go/GO:0008076"
-  i_L hypernym "http://identifiers.org/obo.go/GO:0022840"
-end
-
-hhsa_1952 is "hodgkin-huxley squid-axon 1952"
-
-hhsa_1952 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617668482"
-hhsa_1952 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000020"
-hhsa_1952 description "http://identifiers.org/pubmed/12991237"
-hhsa_1952 hypernym "http://identifiers.org/obo.go/GO:0019227",
-                   "http://identifiers.org/obo.go/GO:0005248",
-                   "http://identifiers.org/obo.go/GO:0005249"
-hhsa_1952 taxon "http://identifiers.org/taxonomy/6618",
-                "http://identifiers.org/obo.go/GO:0042757"
diff --git a/BioModelsRAG/data/BIOMD0000000021.txt b/BioModelsRAG/data/BIOMD0000000021.txt
deleted file mode 100644
index 0c51ff8c820da6e8e25ee7d2e5bee68b7367f264..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000021.txt
+++ /dev/null
@@ -1,214 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Leloup1999_CircClock_periodic()
-
-  // Compartments and Species:
-  compartment Cell, compartment_0000002;
-  species P0 in Cell, T0 in Cell, P1 in Cell, T1 in Cell, P2 in Cell, T2 in Cell;
-  species CC in Cell, Cn in compartment_0000002, Mp in Cell, Mt in Cell;
-
-  // Assignment Rules:
-  Pt := CC + Cn + P0 + P1 + P2;
-  Tt := CC + Cn + T0 + T1 + T2;
-
-  // Reactions:
-  P0_to_P1: P0 => P1; Cell*P0_to_P1_V_1P*P0/(P0_to_P1_K1_P + P0);
-  T0_to_T1: T0 => T1; Cell*T0_to_T1_V_1T*T0/(T0_to_T1_K_1T + T0);
-  P1_to_P0: P1 => P0; Cell*P1_to_P0_V_2P*P1/(P1_to_P0_K_2P + P1);
-  T1_to_T0: T1 => T0; Cell*T1_to_T0_V_2T*T1/(T1_to_T0_K_2T + T1);
-  P1_to_P2: P1 => P2; Cell*P1_to_P2_V_3P*P1/(P1_to_P2_K_3P + P1);
-  T1_to_T2: T1 => T2; Cell*T1_to_T2_V_3T*T1/(T1_to_T2_K_3T + T1);
-  P2_to_P1: P2 => P1; Cell*P2_to_P1_V_4P*P2/(P2_to_P1_K_4P + P2);
-  T2_to_T1: T2 => T1; Cell*T2_to_T1_V_4T*T2/(T2_to_T1_K_4T + T2);
-  P0_degradation: P0 => ; Cell*P0_degradation_k_d*P0;
-  T0_degradation: T0 => ; Cell*T0_degradation_k_d*T0;
-  P1_degradation: P1 => ; Cell*P1_degradation_k_d*P1;
-  T1_degradation: T1 => ; Cell*T1_degradation_k_d*T1;
-  P2_degradation: P2 => ; Cell*P2_degradation_k_d*P2 + Cell*P2_degradation_V_dP*P2/(P2_degradation_K_dP + P2);
-  T2_degradation: T2 => ; Cell*T2_degradation_k_d*T2 + Cell*V_dT*T2/(T2_degradation_K_dT + T2);
-  PT_complex_formation: P2 + T2 -> CC; Cell*PT_complex_formation_k3*P2*T2 - Cell*PT_complex_formation_k4*CC;
-  PT_complex_nucleation: CC -> Cn; Cell*PT_complex_nucleation_k1*CC - compartment_0000002*PT_complex_nucleation_k2*Cn;
-  PT_complex_degradation: CC => ; Cell*PT_complex_degradation_k_dC*CC;
-  PTnucl_complex_degradation: Cn => ; compartment_0000002*PTnucl_complex_degradation_k_dN*Cn;
-  Mp_production:  => Mp; Cell*Mp_production_v_sP*Mp_production_K_IP^Mp_production_n/(Mp_production_K_IP^Mp_production_n + Cn^Mp_production_n);
-  Mt_production:  => Mt; Cell*Mt_production_V_sT*Mt_production_K_IT^Mt_production_n/(Mt_production_K_IT^Mt_production_n + Cn^Mt_production_n);
-  P0_production:  => P0; Cell*P0_production_k_sP*Mp;
-  T0_production:  => T0; Cell*T0_production_k_sT*Mt;
-  Mp_degradation: Mp => ; Cell*Mp_degradation_k_d*Mp + Cell*Mp_degradation_V_mP*Mp/(Mp_degradation_K_mP + Mp);
-  Mt_degradation: Mt => ; Cell*Mt_degradation_k_d*Mt + Cell*V_mT*Mt/(Mt_degradation_K_mT + Mt);
-
-  // Species initializations:
-  P0 = 0;
-  T0 = 0;
-  P1 = 0;
-  T1 = 0;
-  P2 = 0;
-  T2 = 0;
-  CC = 0;
-  Cn = 0;
-  Mp = 0;
-  Mt = 0;
-
-  // Compartment initializations:
-  Cell = 1;
-  compartment_0000002 = 1;
-
-  // Variable initializations:
-  V_mT = 0.7;
-  V_dT = 2;
-  P0_to_P1_K1_P = 2;
-  P0_to_P1_V_1P = 8;
-  T0_to_T1_K_1T = 2;
-  T0_to_T1_V_1T = 8;
-  P1_to_P0_K_2P = 2;
-  P1_to_P0_V_2P = 1;
-  T1_to_T0_K_2T = 2;
-  T1_to_T0_V_2T = 1;
-  P1_to_P2_K_3P = 2;
-  P1_to_P2_V_3P = 8;
-  T1_to_T2_K_3T = 2;
-  T1_to_T2_V_3T = 8;
-  P2_to_P1_K_4P = 2;
-  P2_to_P1_V_4P = 1;
-  T2_to_T1_K_4T = 2;
-  T2_to_T1_V_4T = 1;
-  P0_degradation_k_d = 0.01;
-  T0_degradation_k_d = 0.01;
-  P1_degradation_k_d = 0.01;
-  T1_degradation_k_d = 0.01;
-  P2_degradation_k_d = 0.01;
-  P2_degradation_V_dP = 2;
-  P2_degradation_K_dP = 0.2;
-  T2_degradation_k_d = 0.01;
-  T2_degradation_K_dT = 0.2;
-  PT_complex_formation_k3 = 1.2;
-  PT_complex_formation_k4 = 0.6;
-  PT_complex_nucleation_k1 = 0.6;
-  PT_complex_nucleation_k2 = 0.2;
-  PT_complex_degradation_k_dC = 0.01;
-  PTnucl_complex_degradation_k_dN = 0.01;
-  Mp_production_v_sP = 1;
-  Mp_production_K_IP = 1;
-  Mp_production_n = 4;
-  Mt_production_V_sT = 1;
-  Mt_production_K_IT = 1;
-  Mt_production_n = 4;
-  P0_production_k_sP = 0.9;
-  T0_production_k_sT = 0.9;
-  Mp_degradation_k_d = 0.01;
-  Mp_degradation_V_mP = 0.7;
-  Mp_degradation_K_mP = 0.2;
-  Mt_degradation_k_d = 0.01;
-  Mt_degradation_K_mT = 0.2;
-
-  // Other declarations:
-  var Pt, Tt;
-  const Cell, compartment_0000002, V_mT, V_dT;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  time_unit is "hour (default)";
-  Cell is "cytoplasm";
-  compartment_0000002 is "nucleus";
-  P0 is "PER Protein (unphosphorylated)";
-  T0 is "TIM Protein (unphosphorylated)";
-  P1 is "PER Protein (mono-phosphorylated)";
-  T1 is "TIM Protein (mono-phosphorylated)";
-  P2 is "PER Protein (bi-phosphorylated)";
-  T2 is "TIM Protein (bi-phosphorylated)";
-  CC is "Cytosolic PER-TIM Complex";
-  Cn is "Nuclear PER-TIM Complex";
-  Mp is "PER mRNA";
-  Mt is "TIM mRNA";
-  Pt is "Total Per";
-  Tt is "Total Tim";
-  P0_to_P1 is "First Phosphorylation of PER";
-  T0_to_T1 is "First Phosphorylation of TIM";
-  P1_to_P0 is "Dephosphorylation of PER (1st P)";
-  T1_to_T0 is "Dephosphorylation of TIM (1st P)";
-  P1_to_P2 is "Second Phosphorylation of PER";
-  T1_to_T2 is "Second Phosphorylation of TIM";
-  P2_to_P1 is "Dephosphorylation of PER (2nd P)";
-  T2_to_T1 is "Dephosphorylation of TIM (2nd P)";
-  P0_degradation is "PER degradation";
-  T0_degradation is "TIM degradation";
-  P1_degradation is "PER-1 degradation";
-  T1_degradation is "TIM-1 degradation";
-  P2_degradation is "PER-2 degradation";
-  T2_degradation is "TIM-2 degradation";
-  PT_complex_formation is "PER-TIM complex formation";
-  PT_complex_nucleation is "PER-TIM complex nucleation";
-  PT_complex_degradation is "PER-TIM complex degradation (cytosol)";
-  PTnucl_complex_degradation is "PER-TIM complex degradation (nuclear)";
-  Mp_production is "PER mRNA production";
-  Mt_production is "TIM mRNA production";
-  P0_production is "PER production";
-  T0_production is "TIM production";
-  Mp_degradation is "PER mRNA degradation";
-  Mt_degradation is "TIM mRNA degradation";
-
-  // CV terms:
-  Cell identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000002 identity "http://identifiers.org/go/GO:0005634"
-  P0 hypernym "http://identifiers.org/uniprot/P07663"
-  T0 hypernym "http://identifiers.org/uniprot/P49021"
-  P1 hypernym "http://identifiers.org/uniprot/P07663"
-  T1 hypernym "http://identifiers.org/uniprot/P49021"
-  P2 hypernym "http://identifiers.org/uniprot/P07663"
-  T2 hypernym "http://identifiers.org/uniprot/P49021"
-  CC part "http://identifiers.org/uniprot/P49021",
-          "http://identifiers.org/uniprot/P07663"
-  Cn part "http://identifiers.org/uniprot/P49021",
-          "http://identifiers.org/uniprot/P07663"
-  Mp hypernym "http://identifiers.org/chebi/CHEBI:33699",
-              "http://identifiers.org/kegg.compound/C00046"
-  Mt hypernym "http://identifiers.org/chebi/CHEBI:33699",
-              "http://identifiers.org/kegg.compound/C00046"
-  P0_to_P1 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  T0_to_T1 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  P1_to_P0 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  T1_to_T0 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  P1_to_P2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  T1_to_T2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  P2_to_P1 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  T2_to_T1 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  P0_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  T0_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  P1_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  T1_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  P2_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  T2_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  PT_complex_formation hypernym "http://identifiers.org/go/GO:0006461"
-  PT_complex_nucleation hypernym "http://identifiers.org/go/GO:0006606"
-  PT_complex_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  PTnucl_complex_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  Mp_production hypernym "http://identifiers.org/go/GO:0009299",
-                         "http://identifiers.org/go/GO:0006355"
-  Mt_production hypernym "http://identifiers.org/go/GO:0009299",
-                         "http://identifiers.org/go/GO:0006355"
-  P0_production hypernym "http://identifiers.org/go/GO:0006412"
-  T0_production hypernym "http://identifiers.org/go/GO:0006412"
-  Mp_degradation hypernym "http://identifiers.org/go/GO:0006402"
-  Mt_degradation hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-Leloup1999_CircClock_periodic is "Leloup1999_CircClock"
-
-Leloup1999_CircClock_periodic model_entity_is "http://identifiers.org/biomodels.db/MODEL6617834203"
-Leloup1999_CircClock_periodic model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000021"
-Leloup1999_CircClock_periodic description "http://identifiers.org/pubmed/10366496"
-Leloup1999_CircClock_periodic origin "http://identifiers.org/biomodels.db/BIOMD0000000171"
-Leloup1999_CircClock_periodic taxon "http://identifiers.org/taxonomy/7227"
-Leloup1999_CircClock_periodic identity "http://identifiers.org/kegg.pathway/dme04710"
-Leloup1999_CircClock_periodic hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000022.txt b/BioModelsRAG/data/BIOMD0000000022.txt
deleted file mode 100644
index 1668b0861844e56953eb512308ec2b3a655391c1..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000022.txt
+++ /dev/null
@@ -1,257 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Ueda2001_CircClock()
-
-  // Compartments and Species:
-  compartment Drosophilia, compartment_0000003, compartment_0000002;
-  species $EmptySet in Drosophilia, CCc in compartment_0000003, CCn in compartment_0000002;
-  species Clkc in compartment_0000003, Clkm in compartment_0000003, Perc in compartment_0000003;
-  species Perm in compartment_0000003, PTc in compartment_0000003, PTn in compartment_0000002;
-  species Timc in compartment_0000003, Timm in compartment_0000003, $species_0000012 in compartment_0000003;
-  species $species_0000013 in compartment_0000003;
-
-  // Reactions:
-  Reaction1: $EmptySet => Perm; compartment_0000003*(Reaction1_c1 + (Reaction1_B1 + (CCn/Reaction1_A1)^Reaction1_a)*Reaction1_s1/(1 + Reaction1_B1 + (CCn/Reaction1_A1)^Reaction1_a + (PTn/Reaction1_r1)^Reaction1_r));
-  Reaction2: Perm => $EmptySet; compartment_0000003*Reaction2_D0*Perm;
-  Reaction3: $EmptySet => Timm; compartment_0000003*(Reaction3_c2 + (Reaction3_B2 + (CCn/Reaction3_A2)^Reaction3_a)*Reaction3_s3/(1 + Reaction3_B2 + (CCn/Reaction3_A2)^Reaction3_a + (PTn/Reaction3_r2)^Reaction3_r));
-  Reaction4: Timm => $EmptySet; Drosophilia*Reaction4_D0*Timm;
-  Reaction5: $EmptySet => Clkm; compartment_0000003*(Reaction5_c3 + (Reaction5_B3 + (PTn/Reaction5_A3)^Reaction5_a)*Reaction5_s5/(1 + Reaction5_B3 + (PTn/Reaction5_A3)^Reaction5_a + (CCn/Reaction5_r3)^Reaction5_r));
-  Reaction6: Clkm => $EmptySet; Drosophilia*Clkm*Reaction6_D0;
-  Reaction7: CCc => CCn; compartment_0000003*(CCc*Reaction7_T3/(Reaction7_k3 + CCc));
-  Reaction8: CCn => CCc; compartment_0000002*(CCn*Reaction8_T4/(Reaction8_k4 + CCn));
-  Reaction9: PTn => PTc; compartment_0000002*(PTn*Reaction9_T2/(Reaction9_k2 + PTn));
-  Reaction10: PTc => PTn; compartment_0000003*(PTc*Reaction10_T1/(Reaction10_k1 + PTc));
-  Reaction11: $species_0000012 + Clkc -> CCc; compartment_0000003*(Clkc*Reaction11_v3*species_0000012 - Reaction11_parameter_0000073*CCc);
-  Reaction12: Perc + Timc -> PTc; compartment_0000003*(Perc*Timc*Reaction12_v1 - Reaction12_parameter_0000072*PTc);
-  Reaction16: $EmptySet => Timc; compartment_0000003*Reaction16_s4*Timm;
-  Reaction18: $EmptySet => Clkc; compartment_0000003*Clkm*Reaction18_s6;
-  Reaction19: $EmptySet => Perc; compartment_0000003*Reaction19_s2*Perm;
-  Reaction20: Perc => $EmptySet; Drosophilia*Reaction20_D0*Perc;
-  Reaction21: PTc => $EmptySet; compartment_0000003*Reaction21_D0*PTc;
-  Reaction23: PTn => $EmptySet; compartment_0000002*Reaction23_D0*PTn;
-  Reaction24: CCc => $EmptySet; compartment_0000003*CCc*Reaction24_D0;
-  Reaction25: Clkc => $EmptySet; compartment_0000003*Clkc*Reaction25_D0;
-  Reaction26: CCn => $EmptySet; compartment_0000002*CCn*Reaction26_D0;
-  Reaction27: Timc => $EmptySet; compartment_0000003*Reaction27_D0*Timc;
-  Reaction28: Perm => $EmptySet; compartment_0000003*(Reaction28_D1*Perm/(Reaction28_L1 + Perm));
-  Reaction29: Perc => $EmptySet; compartment_0000003*(Reaction29_D2*species_0000013*Perc/(Reaction29_L2 + Perc));
-  Reaction30: Timm => $EmptySet; compartment_0000003*(Reaction30_D3*Timm/(Reaction30_L3 + Timm));
-  Reaction31: Timc => $EmptySet; compartment_0000003*(Reaction31_D4*Timc/(Reaction31_L4 + Timc));
-  Reaction32: PTc => $EmptySet; compartment_0000003*(Reaction32_D5*PTc/(Reaction32_L5 + PTc));
-  Reaction33: PTn => $EmptySet; compartment_0000002*(Reaction33_D6*PTn/(Reaction33_L6 + PTn));
-  Reaction34: Clkm => $EmptySet; compartment_0000003*(Clkm*Reaction34_D7/(Clkm + Reaction34_L7));
-  Reaction35: Clkc => $EmptySet; compartment_0000003*(Clkc*Reaction35_D8/(Clkc + Reaction35_L8));
-  Reaction36: CCc => $EmptySet; compartment_0000003*(CCc*Reaction36_D9/(CCc + Reaction36_L9));
-  Reaction37: CCn => $EmptySet; compartment_0000002*(CCn*Reaction37_D10/(CCn + Reaction37_L10));
-
-  // Species initializations:
-  EmptySet = 0;
-  CCc = 0.3/compartment_0000003;
-  CCn = 0.4/compartment_0000002;
-  Clkc = 0.2/compartment_0000003;
-  Clkm = 0.1/compartment_0000003;
-  Perc = 0.6/compartment_0000003;
-  Perm = 0.5/compartment_0000003;
-  PTc = 0.9/compartment_0000003;
-  PTn = 1/compartment_0000002;
-  Timc = 0.8/compartment_0000003;
-  Timm = 0.7/compartment_0000003;
-  species_0000012 = 1/compartment_0000003;
-  species_0000013 = 1/compartment_0000003;
-
-  // Compartment initializations:
-  Drosophilia = 1;
-  compartment_0000003 = 1;
-  compartment_0000002 = 1;
-
-  // Variable initializations:
-  Reaction1_a = 1;
-  Reaction1_A1 = 0.45;
-  Reaction1_B1 = 0;
-  Reaction1_c1 = 0;
-  Reaction1_r1 = 1.02;
-  Reaction1_s1 = 1.45;
-  Reaction1_r = 4;
-  Reaction2_D0 = 0.012;
-  Reaction3_a = 1;
-  Reaction3_A2 = 0.45;
-  Reaction3_B2 = 0;
-  Reaction3_c2 = 0;
-  Reaction3_r2 = 1.02;
-  Reaction3_s3 = 1.45;
-  Reaction3_r = 4;
-  Reaction4_D0 = 0.012;
-  Reaction5_a = 1;
-  Reaction5_A3 = 0.8;
-  Reaction5_B3 = 0.6;
-  Reaction5_c3 = 0;
-  Reaction5_r3 = 0.89;
-  Reaction5_s5 = 1.63;
-  Reaction5_r = 4;
-  Reaction6_D0 = 0.012;
-  Reaction7_k3 = 2;
-  Reaction7_T3 = 1.63;
-  Reaction8_k4 = 2;
-  Reaction8_T4 = 0.52;
-  Reaction9_k2 = 2;
-  Reaction9_T2 = 0.72;
-  Reaction10_k1 = 2;
-  Reaction10_T1 = 1.73;
-  Reaction11_v3 = 1.63;
-  Reaction11_parameter_0000073 = 1.63;
-  Reaction12_v1 = 1.45;
-  Reaction12_parameter_0000072 = 1.45;
-  Reaction16_s4 = 0.48;
-  Reaction18_s6 = 0.47;
-  Reaction19_s2 = 0.48;
-  Reaction20_D0 = 0.012;
-  Reaction21_D0 = 0.012;
-  Reaction23_D0 = 0.012;
-  Reaction24_D0 = 0.012;
-  Reaction25_D0 = 0.012;
-  Reaction26_D0 = 0.012;
-  Reaction27_D0 = 0.012;
-  Reaction28_D1 = 0.94;
-  Reaction28_L1 = 0.3;
-  Reaction29_D2 = 0.44;
-  Reaction29_L2 = 0.2;
-  Reaction30_D3 = 0.94;
-  Reaction30_L3 = 0.3;
-  Reaction31_D4 = 0.44;
-  Reaction31_L4 = 0.2;
-  Reaction32_D5 = 0.44;
-  Reaction32_L5 = 0.2;
-  Reaction33_D6 = 0.29;
-  Reaction33_L6 = 0.2;
-  Reaction34_D7 = 0.54;
-  Reaction34_L7 = 0.13;
-  Reaction35_D8 = 0.6;
-  Reaction35_L8 = 0.2;
-  Reaction36_D9 = 0.6;
-  Reaction36_L9 = 0.2;
-  Reaction37_D10 = 0.3;
-  Reaction37_L10 = 0.2;
-
-  // Other declarations:
-  const Drosophilia, compartment_0000003, compartment_0000002;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  time_unit is "hour (default)";
-  compartment_0000003 is "cytoplasm";
-  compartment_0000002 is "nucleus";
-  CCc is "Clk-Cyc_cyt";
-  CCn is "Clk-Cyc_nuc";
-  Clkc is "Clk_cyt";
-  Clkm is "Clk_mRNA";
-  Perc is "Per_cyt";
-  Perm is "Per_mRNA";
-  PTc is "Per-Tim_cyt";
-  PTn is "Per-Tim_nuc";
-  Timc is "Tim_cyt";
-  Timm is "Tim_mRNA";
-  species_0000012 is "Cyc_cyt";
-  species_0000013 is "Dbt_cyt";
-  Reaction1 is "Per transcription";
-  Reaction2 is "non-specific Per mRNA degradation";
-  Reaction3 is "Tim transcription";
-  Reaction4 is "non-specific Tim mRNA degradation";
-  Reaction5 is "Clk transcription";
-  Reaction6 is "non-specific Clk mRNA degradation";
-  Reaction7 is "Clk-Cyc nuclear import";
-  Reaction8 is "Clk-Cyc nuclear export";
-  Reaction9 is "Per-Tim nuclear export";
-  Reaction10 is "Per-Tim nuclear import";
-  Reaction11 is "Clk Cyc equilibrium";
-  Reaction12 is "Per Tim equilibrium";
-  Reaction16 is "Tim translation";
-  Reaction18 is "Clk translation";
-  Reaction19 is "Per translation";
-  Reaction20 is "non-specific Per_cyt degradation";
-  Reaction21 is "non-specific Per-Tim_cyt degradation";
-  Reaction23 is "non-specific Per-Tim_nuc degradation";
-  Reaction24 is "non-specific Clk-Cyc_cyt degradation";
-  Reaction25 is "non-specific Clk_cyt degradation";
-  Reaction26 is "non-specific Clk-Cyc_nuc degradation";
-  Reaction27 is "non-specific Tim_cyt degradation";
-  Reaction28 is "Per mRNA degradation";
-  Reaction29 is "Dbt regulated Per_cyt degradation";
-  Reaction30 is "Tim mRNA degradation";
-  Reaction31 is "Tim_cyt degradation";
-  Reaction32 is "Per-Tim_cyt degradation";
-  Reaction33 is "Per-Tim_nuc degradation";
-  Reaction34 is "Clk mRNA degradation";
-  Reaction35 is "Clk_cyt degradation";
-  Reaction36 is "Clk-Cyc_cyt degradation";
-
-  // CV terms:
-  compartment_0000003 identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000002 identity "http://identifiers.org/go/GO:0005634"
-  CCc part "http://identifiers.org/uniprot/O61735",
-           "http://identifiers.org/uniprot/O61734"
-  CCn part "http://identifiers.org/uniprot/O61734",
-           "http://identifiers.org/uniprot/O61735"
-  Clkc identity "http://identifiers.org/uniprot/O61735"
-  Clkm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  Perc identity "http://identifiers.org/uniprot/P07663"
-  Perm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  PTc part "http://identifiers.org/uniprot/P07663",
-           "http://identifiers.org/uniprot/P49021"
-  PTn part "http://identifiers.org/uniprot/P07663",
-           "http://identifiers.org/uniprot/P49021"
-  Timc identity "http://identifiers.org/uniprot/P49021"
-  Timm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  species_0000012 identity "http://identifiers.org/uniprot/O61734"
-  species_0000013 identity "http://identifiers.org/uniprot/O76324"
-  Reaction1 hypernym "http://identifiers.org/go/GO:0006355",
-                     "http://identifiers.org/go/GO:0009299"
-  Reaction2 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction3 hypernym "http://identifiers.org/go/GO:0009299",
-                     "http://identifiers.org/go/GO:0006355"
-  Reaction4 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction5 hypernym "http://identifiers.org/go/GO:0009299",
-                     "http://identifiers.org/go/GO:0006355"
-  Reaction6 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction7 hypernym "http://identifiers.org/go/GO:0006606"
-  Reaction8 hypernym "http://identifiers.org/go/GO:0006611"
-  Reaction9 hypernym "http://identifiers.org/go/GO:0006611"
-  Reaction10 hypernym "http://identifiers.org/go/GO:0006606"
-  Reaction11 hypernym "http://identifiers.org/go/GO:0006461"
-  Reaction12 hypernym "http://identifiers.org/go/GO:0006461"
-  Reaction16 hypernym "http://identifiers.org/go/GO:0006412"
-  Reaction18 hypernym "http://identifiers.org/go/GO:0006412"
-  Reaction19 hypernym "http://identifiers.org/go/GO:0006412"
-  Reaction20 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction21 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction23 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction24 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction25 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction26 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction27 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction28 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction29 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction30 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction31 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction32 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction33 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction34 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction35 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction36 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction37 hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-Ueda2001_CircClock is "Ueda2001_CircClock"
-
-Ueda2001_CircClock model_entity_is "http://identifiers.org/biomodels.db/MODEL6617909980"
-Ueda2001_CircClock model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000022"
-Ueda2001_CircClock description "http://identifiers.org/pubmed/11403560"
-Ueda2001_CircClock origin "http://identifiers.org/pubmed/10531060"
-Ueda2001_CircClock hypernym "http://identifiers.org/kegg.pathway/dme04710"
-Ueda2001_CircClock taxon "http://identifiers.org/taxonomy/7227"
-Ueda2001_CircClock hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000023.txt b/BioModelsRAG/data/BIOMD0000000023.txt
deleted file mode 100644
index 6e6226959a5bbe96576779a23f7c303427301bc2..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000023.txt
+++ /dev/null
@@ -1,175 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Rohwer2001_Sucrose()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Fru in compartment_, Glc in compartment_, HexP in compartment_;
-  species Suc6P in compartment_, Suc in compartment_, $Sucvac in compartment_;
-  species $glycolysis in compartment_, $phos in compartment_, $UDP in compartment_;
-  species $ADP in compartment_, $ATP in compartment_, $Glcex in compartment_;
-  species $Fruex in compartment_;
-
-  // Reactions:
-  v1: $Fruex -> Fru; compartment_*(v1_Vmax1*Fruex/(v1_Km1Fruex*(1 + Fru/v1_Ki1Fru) + Fruex));
-  v2: $Glcex -> Glc; compartment_*(v2_Vmax2*Glcex/(v2_Km2Glcex*(1 + Glc/v2_Ki2Glc) + Glcex));
-  v3: $ATP + Glc -> HexP + $ADP; compartment_*(v3_Vmax3*(Glc/v3_Km3Glc)*(ATP/v3_Km3ATP)/((1 + ATP/v3_Km3ATP)*(1 + Glc/v3_Km3Glc + Fru/v3_Km4Fru + 0.113*HexP/v3_Ki3G6P + 0.0575*HexP/v3_Ki4F6P)));
-  v4: Fru + $ATP -> HexP + $ADP; compartment_*(v4_Vmax4*(Fru/v4_Km4Fru)*(ATP/v4_Km4ATP)/((1 + ATP/v4_Km4ATP)*(1 + Glc/v4_Km3Glc + Fru/v4_Km4Fru + 0.113*HexP/v4_Ki3G6P + 0.0575*HexP/v4_Ki4F6P)));
-  v5: Fru + $ATP -> HexP + $ADP; compartment_*((v5_Vmax5/(1 + Fru/v5_Ki5Fru))*(Fru/v5_Km5Fru)*(ATP/v5_Km5ATP)/(1 + Fru/v5_Km5Fru + ATP/v5_Km5ATP + Fru*ATP/(v5_Km5Fru*v5_Km5ATP) + ADP/v5_Ki5ADP));
-  v6: 2 HexP -> $UDP + Suc6P; compartment_*(v6_Vmax6f*(0.0575*HexP*0.8231*HexP - Suc6P*UDP/v6_Keq6)/(0.0575*HexP*0.8231*HexP*(1 + Suc6P/v6_Ki6Suc6P) + v6_Km6F6P*(1 + phos/v6_Ki6Pi)*(0.8231*HexP + v6_Ki6UDPGlc) + v6_Km6UDPGlc*0.0575*HexP + (v6_Vmax6f/(v6_Vmax6r*v6_Keq6))*(v6_Km6UDP*Suc6P*(1 + 0.8231*HexP/v6_Ki6UDPGlc) + UDP*(v6_Km6Suc6P*(1 + v6_Km6UDPGlc*0.0575*HexP/(v6_Ki6UDPGlc*v6_Km6F6P*(1 + phos/v6_Ki6Pi))) + Suc6P*(1 + 0.0575*HexP/v6_Ki6F6P)))));
-  v7: Suc6P -> Suc + $phos; compartment_*(v7_Vmax7*Suc6P/(v7_Km7Suc6P + Suc6P));
-  v8: HexP + Fru -> Suc + $UDP; compartment_*(-v8_Vmax8f*(Suc*UDP - Fru*0.8231*HexP/v8_Keq8)/(Suc*UDP*(1 + Fru/v8_Ki8Fru) + v8_Km8Suc*(UDP + v8_Ki8UDP) + v8_Km8UDP*Suc + (v8_Vmax8f/(v8_Vmax8r*v8_Keq8))*(v8_Km8UDPGlc*Fru*(1 + UDP/v8_Ki8UDP) + 0.8231*HexP*(v8_Km8Fru*(1 + v8_Km8UDP*Suc/(v8_Ki8UDP*v8_Km8Suc)) + Fru*(1 + Suc/v8_Ki8Suc)))));
-  v9: Suc -> Fru + Glc; compartment_*((v9_Vmax9/(1 + Glc/v9_Ki9Glc))*Suc/(v9_Km9Suc*(1 + Fru/v9_Ki9Fru) + Suc));
-  v10: HexP -> $glycolysis; compartment_*(v10_Vmax10*0.0575*HexP/(v10_Km10F6P + 0.0575*HexP));
-  v11: Suc -> $Sucvac; compartment_*(v11_Vmax11*Suc/(v11_Km11Suc + Suc));
-
-  // Species initializations:
-  Fru = 1;
-  Glc = 1;
-  HexP = 1;
-  Suc6P = 1;
-  Suc = 1;
-  Sucvac = 0;
-  glycolysis = 0;
-  phos = 5.1;
-  UDP = 0.2;
-  ADP = 0.2;
-  ATP = 1;
-  Glcex = 5;
-  Fruex = 5;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_Vmax1 = 0.286;
-  v1_Km1Fruex = 0.2;
-  v1_Ki1Fru = 1;
-  v2_Vmax2 = 0.286;
-  v2_Km2Glcex = 0.2;
-  v2_Ki2Glc = 1;
-  v3_Vmax3 = 0.197;
-  v3_Km3Glc = 0.07;
-  v3_Km3ATP = 0.25;
-  v3_Km4Fru = 10;
-  v3_Ki3G6P = 0.1;
-  v3_Ki4F6P = 10;
-  v4_Vmax4 = 0.197;
-  v4_Km4Fru = 10;
-  v4_Km4ATP = 0.25;
-  v4_Km3Glc = 0.07;
-  v4_Ki3G6P = 0.1;
-  v4_Ki4F6P = 10;
-  v5_Vmax5 = 0.164;
-  v5_Ki5Fru = 12;
-  v5_Km5Fru = 0.1;
-  v5_Km5ATP = 0.085;
-  v5_Ki5ADP = 2;
-  v6_Vmax6f = 0.379;
-  v6_Keq6 = 10;
-  v6_Ki6Suc6P = 0.07;
-  v6_Km6F6P = 0.6;
-  v6_Ki6Pi = 3;
-  v6_Ki6UDPGlc = 1.4;
-  v6_Km6UDPGlc = 1.8;
-  v6_Vmax6r = 0.2;
-  v6_Km6UDP = 0.3;
-  v6_Km6Suc6P = 0.1;
-  v6_Ki6F6P = 0.4;
-  v7_Vmax7 = 0.5;
-  v7_Km7Suc6P = 0.1;
-  v8_Vmax8f = 0.677;
-  v8_Keq8 = 5;
-  v8_Ki8Fru = 4;
-  v8_Km8Suc = 50;
-  v8_Ki8UDP = 0.3;
-  v8_Km8UDP = 0.3;
-  v8_Vmax8r = 0.3;
-  v8_Km8UDPGlc = 0.3;
-  v8_Km8Fru = 4;
-  v8_Ki8Suc = 40;
-  v9_Vmax9 = 0.372;
-  v9_Ki9Glc = 15;
-  v9_Km9Suc = 10;
-  v9_Ki9Fru = 15;
-  v10_Vmax10 = 0.1;
-  v10_Km10F6P = 0.2;
-  v11_Vmax11 = 1;
-  v11_Km11Suc = 100;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole (default)";
-  time_unit is "minute (default)";
-  compartment_ is "cell";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005623"
-  Fru identity "http://identifiers.org/obo.chebi/CHEBI:15824",
-               "http://identifiers.org/kegg.compound/C00095"
-  Glc identity "http://identifiers.org/obo.chebi/CHEBI:17634",
-               "http://identifiers.org/kegg.compound/C00031"
-  HexP version "http://identifiers.org/obo.chebi/CHEBI:16218",
-               "http://identifiers.org/obo.chebi/CHEBI:15946",
-               "http://identifiers.org/obo.chebi/CHEBI:14314"
-  HexP version "http://identifiers.org/kegg.compound/C00029",
-               "http://identifiers.org/kegg.compound/C00668",
-               "http://identifiers.org/kegg.compound/C00085",
-               "http://identifiers.org/kegg.compound/C00103",
-               "http://identifiers.org/chebi/CHEBI:18066"
-  Suc6P identity "http://identifiers.org/obo.chebi/CHEBI:16308",
-                 "http://identifiers.org/kegg.compound/C02591"
-  Suc identity "http://identifiers.org/obo.chebi/CHEBI:17992",
-               "http://identifiers.org/kegg.compound/C00089"
-  Sucvac identity "http://identifiers.org/obo.chebi/CHEBI:17992",
-                  "http://identifiers.org/kegg.compound/C00089"
-  glycolysis identity "http://identifiers.org/kegg.compound/C05378",
-                      "http://identifiers.org/chebi/CHEBI:28013"
-  phos identity "http://identifiers.org/obo.chebi/CHEBI:18367",
-                "http://identifiers.org/kegg.compound/C00009"
-  UDP identity "http://identifiers.org/obo.chebi/CHEBI:17659",
-               "http://identifiers.org/kegg.compound/C00015"
-  ADP identity "http://identifiers.org/obo.chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  ATP identity "http://identifiers.org/obo.chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  Glcex identity "http://identifiers.org/obo.chebi/CHEBI:17634",
-                 "http://identifiers.org/kegg.compound/C00031"
-  Fruex identity "http://identifiers.org/obo.chebi/CHEBI:15824",
-                 "http://identifiers.org/kegg.compound/C00095"
-  v1 hypernym "http://identifiers.org/obo.go/GO:0015755"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0015758"
-  v3 hypernym "http://identifiers.org/ec-code/2.7.1.2"
-  v3 identity "http://identifiers.org/kegg.reaction/R00299"
-  v4 hypernym "http://identifiers.org/ec-code/2.7.1.4"
-  v4 identity "http://identifiers.org/kegg.reaction/R03920",
-              "http://identifiers.org/kegg.reaction/R00760"
-  v5 hypernym "http://identifiers.org/ec-code/2.7.1.4"
-  v5 identity "http://identifiers.org/kegg.reaction/R00760"
-  v6 hypernym "http://identifiers.org/ec-code/2.4.1.14"
-  v6 identity "http://identifiers.org/kegg.reaction/R00766"
-  v7 hypernym "http://identifiers.org/ec-code/3.1.3.24"
-  v7 identity "http://identifiers.org/kegg.reaction/R00805"
-  v8 hypernym "http://identifiers.org/ec-code/2.4.1.13"
-  v8 identity "http://identifiers.org/kegg.reaction/R00806"
-  v9 hypernym "http://identifiers.org/ec-code/3.2.1.26",
-              "http://identifiers.org/ec-code/3.2.1.48",
-              "http://identifiers.org/ec-code/3.2.1.20"
-  v9 identity "http://identifiers.org/kegg.reaction/R00802"
-  v10 hypernym "http://identifiers.org/obo.go/GO:0006096"
-  v11 hypernym "http://identifiers.org/obo.go/GO:0015770"
-end
-
-Rohwer2001_Sucrose is "Rohwer2001_Sucrose"
-
-Rohwer2001_Sucrose model_entity_is "http://identifiers.org/biomodels.db/MODEL6618063111"
-Rohwer2001_Sucrose model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000023"
-Rohwer2001_Sucrose description "http://identifiers.org/pubmed/11513743"
-Rohwer2001_Sucrose taxon "http://identifiers.org/taxonomy/4547"
-Rohwer2001_Sucrose hypernym "http://identifiers.org/obo.go/GO:0005986"
-Rohwer2001_Sucrose identity "http://identifiers.org/kegg.pathway/map00500"
diff --git a/BioModelsRAG/data/BIOMD0000000024.txt b/BioModelsRAG/data/BIOMD0000000024.txt
deleted file mode 100644
index 49fe4559947c21a4f811e2f5ba4cb38c7a120c09..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000024.txt
+++ /dev/null
@@ -1,67 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Scheper1999()
-
-  // Compartments and Species:
-  compartment compartment_0000004;
-  species $EmptySet in compartment_0000004, M in compartment_0000004, P in compartment_0000004;
-
-  // Reactions:
-  TC: $EmptySet => M; compartment_0000004*(TC_rM/(1 + (P/TC_k)^TC_n));
-  TL: $EmptySet => P; compartment_0000004*TL_rP*delay(M, TL_parameter_0000009)^TL_m;
-  Md: M => $EmptySet; compartment_0000004*Md_qM*M;
-  Pd: P => $EmptySet; compartment_0000004*Pd_qP*P;
-
-  // Species initializations:
-  EmptySet = 0;
-  M = 1e-15/compartment_0000004;
-  P = 1e-15/compartment_0000004;
-
-  // Compartment initializations:
-  compartment_0000004 = 1e-15;
-
-  // Variable initializations:
-  TC_rM = 1;
-  TC_k = 1;
-  TC_n = 2;
-  TL_rP = 1;
-  TL_m = 3;
-  TL_parameter_0000009 = 4;
-  Md_qM = 0.21;
-  Pd_qP = 0.21;
-
-  // Other declarations:
-  const compartment_0000004;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  compartment_0000004 is "cytoplasm";
-  M is "mRNA";
-  P is "protein";
-  TC is "mRNA production";
-  TL is "protein production";
-  Md is "messenger degradation";
-  Pd is "protein degradation";
-
-  // CV terms:
-  compartment_0000004 identity "http://identifiers.org/go/GO:0005737"
-  M hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  P identity "http://identifiers.org/kegg.compound/C00017",
-             "http://identifiers.org/chebi/CHEBI:16541"
-  TC hypernym "http://identifiers.org/go/GO:0009299"
-  TL hypernym "http://identifiers.org/go/GO:0006412"
-  Md hypernym "http://identifiers.org/go/GO:0006402"
-  Pd hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-Scheper1999 is "Scheper1999_CircClock"
-
-Scheper1999 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618241436"
-Scheper1999 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000024"
-Scheper1999 description "http://identifiers.org/pubmed/9870936"
-Scheper1999 taxon "http://identifiers.org/taxonomy/10036",
-                  "http://identifiers.org/taxonomy/7227"
-Scheper1999 identity "http://identifiers.org/kegg.pathway/dme04711"
-Scheper1999 hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000025.txt b/BioModelsRAG/data/BIOMD0000000025.txt
deleted file mode 100644
index c171b0b3c461b4771546ff6398e25bd084d6393b..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000025.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Smolen2002()
-
-  // Compartments and Species:
-  compartment CELL;
-  species $EmptySet in CELL, Per in CELL, dClk in CELL, $dClkF in CELL;
-
-  // Assignment Rules:
-  dClkF := piecewise(0, (dClk - Per) < 0, dClk - Per);
-  dClkF_tau1 := piecewise(0, (delay(dClk, tau1) - delay(Per, tau1)) < 0, delay(dClk, tau1) - delay(Per, tau1));
-  dClkF_tau2 := piecewise(0, (delay(dClk, tau2) - delay(Per, tau2)) < 0, delay(dClk, tau2) - delay(Per, tau2));
-
-  // Reactions:
-  rPer: $EmptySet => Per; Vsp*(dClkF_tau1/(K1 + dClkF_tau1))*CELL;
-  rdClk: $EmptySet => dClk; CELL*Vsc*(K2/(K2 + dClkF_tau2));
-  rPerD: Per => $EmptySet; kdc*Per*CELL;
-  rdClkD: dClk => $EmptySet; kdp*dClk*CELL;
-
-  // Species initializations:
-  EmptySet = 0;
-  Per = 5e-16;
-  dClk = 1e-16;
-
-  // Compartment initializations:
-  CELL = 1e-15;
-  dClkF_tau1 has nM;
-
-  // Variable initializations:
-  tau1 = 10;
-  tau1 has time_unit;
-  dClkF_tau2 has nM;
-  tau2 = 10;
-  tau2 has time_unit;
-  Vsp = 0.5;
-  Vsp has nM_per_hr;
-  K1 = 0.3;
-  K1 has nM;
-  Vsc = 0.25;
-  Vsc has nM_per_hr;
-  K2 = 0.1;
-  K2 has nM;
-  kdc = 0.5;
-  kdc has per_hr;
-  kdp = 0.5;
-  kdp has per_hr;
-
-  // Other declarations:
-  var dClkF_tau1, dClkF_tau2;
-  const CELL, tau1, tau2, Vsp, K1, Vsc, K2, kdc, kdp;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-  unit nM = 1e-9 mole / litre;
-  unit nM_per_hr = 1e-9 mole / (litre * 3600 second);
-  unit per_hr = 1 / 3600 second;
-
-  // Display Names:
-  time_unit is "hour (new default)";
-  substance is "nanomole (new default)";
-  dClkF is "free dClk";
-  rPer is "Per production";
-  rdClk is "dClk production";
-  rPerD is "Per degradation";
-  rdClkD is "dClk degradation";
-
-  // CV terms:
-  CELL identity "http://identifiers.org/go/GO:0005623"
-  Per identity "http://identifiers.org/uniprot/P07663"
-  dClk part "http://identifiers.org/uniprot/P07663",
-            "http://identifiers.org/uniprot/O61735"
-  dClkF identity "http://identifiers.org/uniprot/O61735"
-  rPer hypernym "http://identifiers.org/go/GO:0006412"
-  rdClk hypernym "http://identifiers.org/go/GO:0006412"
-  rPerD hypernym "http://identifiers.org/go/GO:0030163"
-  rdClkD hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-Smolen2002 is "Smolen2002_CircClock"
-
-Smolen2002 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618294363"
-Smolen2002 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000025"
-Smolen2002 description "http://identifiers.org/pubmed/12414672"
-Smolen2002 origin "http://identifiers.org/pubmed/11517254"
-Smolen2002 taxon "http://identifiers.org/taxonomy/7227"
-Smolen2002 identity "http://identifiers.org/kegg.pathway/dme04710"
-Smolen2002 hypernym "http://identifiers.org/go/GO:0032922"
diff --git a/BioModelsRAG/data/BIOMD0000000026.txt b/BioModelsRAG/data/BIOMD0000000026.txt
deleted file mode 100644
index 5bda92c6f7f4178f847255bebb767a0de7a25abb..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000026.txt
+++ /dev/null
@@ -1,135 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Markevich2004_MAPK_orderedelementary()
-
-  // Compartments and Species:
-  compartment uVol;
-  species M in uVol, Mp in uVol, Mpp in uVol, MAPKK in uVol, MKP3 in uVol;
-  species M_MAPKK in uVol, Mp_MAPKK in uVol, Mpp_MKP3 in uVol, Mp_MKP3_dep in uVol;
-  species Mp_MKP3 in uVol, M_MKP3 in uVol;
-
-  // Reactions:
-  v1a: M + MAPKK -> M_MAPKK; uVol*(k1*M*MAPKK - k_1*M_MAPKK);
-  v1b: M_MAPKK => Mp + MAPKK; uVol*k2*M_MAPKK;
-  v2a: Mp + MAPKK -> Mp_MAPKK; uVol*(k3*Mp*MAPKK - k_3*Mp_MAPKK);
-  v2b: Mp_MAPKK => Mpp + MAPKK; uVol*k4*Mp_MAPKK;
-  v3a: Mpp + MKP3 -> Mpp_MKP3; uVol*(h1*Mpp*MKP3 - h_1*Mpp_MKP3);
-  v3b: Mpp_MKP3 => Mp_MKP3_dep; uVol*h2*Mpp_MKP3;
-  v3c: Mp_MKP3_dep -> Mp + MKP3; h3*Mp_MKP3_dep - h_3*Mp*MKP3;
-  v4a: Mp + MKP3 -> Mp_MKP3; uVol*(h4*Mp*MKP3 - h_4*Mp_MKP3);
-  v4b: Mp_MKP3 => M_MKP3; uVol*h5*Mp_MKP3;
-  v4c: M_MKP3 -> M + MKP3; uVol*(h6*M_MKP3 - h_6*M*MKP3);
-
-  // Species initializations:
-  M = 500/uVol;
-  Mp = 0;
-  Mpp = 0;
-  MAPKK = 50/uVol;
-  MKP3 = 100/uVol;
-  M_MAPKK = 0;
-  Mp_MAPKK = 0;
-  Mpp_MKP3 = 0;
-  Mp_MKP3_dep = 0;
-  Mp_MKP3 = 0;
-  M_MKP3 = 0;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  k1 = 0.02;
-  k_1 = 1;
-  k2 = 0.01;
-  k3 = 0.032;
-  k_3 = 1;
-  k4 = 15;
-  h1 = 0.045;
-  h_1 = 1;
-  h2 = 0.092;
-  h3 = 1;
-  h_3 = 0.01;
-  h4 = 0.01;
-  h_4 = 1;
-  h5 = 0.5;
-  h6 = 0.086;
-  h_6 = 0.0011;
-
-  // Other declarations:
-  const uVol, k1, k_1, k2, k3, k_3, k4, h1, h_1, h2, h3, h_3, h4, h_4, h5;
-  const h6, h_6;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  MKP3 is "MKP";
-  Mpp_MKP3 is "Mpp_MKP";
-  Mp_MKP3_dep is "Mp_MKP";
-  Mp_MKP3 is "Mp_MKP*";
-  M_MKP3 is "M_MKP";
-  v1a is "binding MAPK and PP-MAPKK";
-  v1b is "phosphorylation of MAPK";
-  v2a is "binding PP-MAPKK and P-MAPK";
-  v2b is "phosphorylation of P-MAPK";
-  v3a is "binding MKP and PP-MAPK";
-  v3b is "dephosphorylation of PP-MAPK";
-  v3c is "dissociation of MKP from P-MAPK";
-  v4a is "binding MKP and P-MAPK";
-  v4b is "dephosphorylation of P-MAPK";
-  v4c is "dissociation of MKP from MAPK";
-
-  // CV terms:
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  Mp hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  M_MAPKK part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  Mp_MAPKK part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  Mpp_MKP3 part "http://identifiers.org/uniprot/Q90W58",
-                "http://identifiers.org/uniprot/P26696"
-  Mp_MKP3_dep part "http://identifiers.org/uniprot/Q90W58",
-                   "http://identifiers.org/uniprot/P26696"
-  Mp_MKP3 part "http://identifiers.org/uniprot/Q90W58",
-               "http://identifiers.org/uniprot/P26696"
-  M_MKP3 part "http://identifiers.org/uniprot/Q90W58",
-              "http://identifiers.org/uniprot/P26696"
-  v1a hypernym "http://identifiers.org/obo.go/GO:0031434",
-               "http://identifiers.org/obo.go/GO:0051019"
-  v1a homolog "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  v1b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/obo.go/GO:0006468",
-               "http://identifiers.org/obo.go/GO:0004708"
-  v1b homolog "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  v2a hypernym "http://identifiers.org/obo.go/GO:0031434",
-               "http://identifiers.org/obo.go/GO:0051019"
-  v2a homolog "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  v2b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/obo.go/GO:0000187",
-               "http://identifiers.org/obo.go/GO:0006468",
-               "http://identifiers.org/obo.go/GO:0004708"
-  v2b homolog "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  v3a hypernym "http://identifiers.org/obo.go/GO:0031434",
-               "http://identifiers.org/obo.go/GO:0051019"
-  v3b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/obo.go/GO:0000188",
-               "http://identifiers.org/obo.go/GO:0006470"
-  v3c hypernym "http://identifiers.org/obo.go/GO:0043241"
-  v4a hypernym "http://identifiers.org/obo.go/GO:0051019"
-  v4b hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  v4c hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-Markevich2004_MAPK_orderedelementary is "Markevich2004_MAPK_orderedElementary"
-
-Markevich2004_MAPK_orderedelementary model_entity_is "http://identifiers.org/biomodels.db/MODEL6618379269"
-Markevich2004_MAPK_orderedelementary model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000026"
-Markevich2004_MAPK_orderedelementary description "http://identifiers.org/pubmed/14744999"
-Markevich2004_MAPK_orderedelementary taxon "http://identifiers.org/taxonomy/8355"
-Markevich2004_MAPK_orderedelementary hypernym "http://identifiers.org/obo.go/GO:0000165"
diff --git a/BioModelsRAG/data/BIOMD0000000027.txt b/BioModelsRAG/data/BIOMD0000000027.txt
deleted file mode 100644
index 9612e64794de2e48342af42dd590704be8d4cfb4..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000027.txt
+++ /dev/null
@@ -1,78 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Markevich2004_MAPK_orderedMM()
-
-  // Compartments and Species:
-  compartment uVol;
-  species M in uVol, Mp in uVol, Mpp in uVol, $MAPKK in uVol, $MKP3 in uVol;
-
-  // Reactions:
-  v1: M => Mp; uVol*(k1cat*MAPKK*M/Km1/(1 + M/Km1 + Mp/Km2));
-  v2: Mp => Mpp; uVol*(k2cat*MAPKK*Mp/Km2/(1 + M/Km1 + Mp/Km2));
-  v3: Mpp => Mp; uVol*(k3cat*MKP3*Mpp/Km3/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-  v4: Mp => M; uVol*(k4cat*MKP3*Mp/Km4/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-
-  // Species initializations:
-  M = 500/uVol;
-  Mp = 0;
-  Mpp = 0;
-  MAPKK = 50/uVol;
-  MKP3 = 100/uVol;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  k1cat = 0.01;
-  Km1 = 50;
-  k2cat = 15;
-  Km2 = 500;
-  k3cat = 0.084;
-  Km3 = 22;
-  k4cat = 0.06;
-  Km4 = 18;
-  Km5 = 78;
-
-  // Other declarations:
-  const uVol, k1cat, Km1, k2cat, Km2, k3cat, Km3, k4cat, Km4, Km5;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  v1 is "phosphorylation of MAPK";
-  v2 is "phosphorylation of P-MAPK";
-  v3 is "dephosphorylation of PP-MAPK";
-  v4 is "dephosphorylation of P-MAPK";
-
-  // CV terms:
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  Mp hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  v1 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0006468"
-  v2 homolog "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0000187",
-              "http://identifiers.org/go/GO:0006468"
-  v3 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0000188",
-              "http://identifiers.org/go/GO:0006470"
-  v4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-end
-
-Markevich2004_MAPK_orderedMM is "Markevich2004 - MAPK double phosphorylation,  ordered Michaelis-Menton"
-
-Markevich2004_MAPK_orderedMM model_entity_is "http://identifiers.org/biomodels.db/MODEL6618496308"
-Markevich2004_MAPK_orderedMM model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000027"
-Markevich2004_MAPK_orderedMM description "http://identifiers.org/pubmed/14744999"
-Markevich2004_MAPK_orderedMM hypernym "http://identifiers.org/go/GO:0000165"
-Markevich2004_MAPK_orderedMM taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000028.txt b/BioModelsRAG/data/BIOMD0000000028.txt
deleted file mode 100644
index 6582c32fcd822279d26f31f4407eaf9791884ab6..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000028.txt
+++ /dev/null
@@ -1,208 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, MpY in cell, MpT in cell, Mpp in cell, MEK in cell, MKP3 in cell;
-  species MpY_MEK in cell, MpT_MEK in cell, M_MEK_Y in cell, M_MEK_T in cell;
-  species Mpp_MKP3 in cell, MpY_MKP3 in cell, MpT_MKP3_Y in cell, MpT_MKP3_T in cell;
-  species M_MKP3_T in cell, M_MKP3_Y in cell;
-
-  // Reactions:
-  reaction_0000001: M + MEK -> M_MEK_Y; cell*(k1*M*MEK - k_1*M_MEK_Y);
-  reaction_0000002: M_MEK_Y => MpY + MEK; cell*k2*M_MEK_Y;
-  reaction_0000003: MpY + MEK -> MpY_MEK; cell*(k3*MpY*MEK - k_3*MpY_MEK);
-  reaction_0000004: MpY_MEK => Mpp + MEK; cell*k4*MpY_MEK;
-  reaction_0000005: M + MEK -> M_MEK_T; cell*(k5*M*MEK - k_5*M_MEK_T);
-  reaction_0000006: M_MEK_T => MpT + MEK; cell*k6*M_MEK_T;
-  reaction_0000007: MpT + MEK -> MpT_MEK; cell*(k7*MpT*MEK - k_7*MpT_MEK);
-  reaction_0000008: MpT_MEK => Mpp + MEK; cell*k8*MpT_MEK;
-  reaction_0000009: Mpp + MKP3 -> Mpp_MKP3; cell*(h1*Mpp*MKP3 - h_1*Mpp_MKP3);
-  reaction_0000010: Mpp_MKP3 => MpT_MKP3_Y; cell*h2*Mpp_MKP3;
-  reaction_0000011: MpT_MKP3_Y -> MpT + MKP3; cell*(h3*MpT_MKP3_Y - h_3*MpT*MKP3);
-  reaction_0000012: MpT_MKP3_T => M_MKP3_T; cell*h5*MpT_MKP3_T;
-  reaction_0000013: MpT + MKP3 -> MpT_MKP3_T; cell*(h4*MpT*MKP3 - h_4*MpT_MKP3_T);
-  reaction_0000014: MpY_MKP3 => M_MKP3_Y; cell*h8*MpY_MKP3;
-  reaction_0000015: M_MKP3_T -> M + MKP3; cell*(h6*M_MKP3_T - h_6*M*MKP3);
-  reaction_0000017: MpY + MKP3 -> MpY_MKP3; cell*(h7*MpY*MKP3 - h_7*MpY_MKP3);
-  reaction_0000019: M_MKP3_Y -> M + MKP3; cell*(h9*M_MKP3_Y - h_9*M*MKP3);
-
-  // Species initializations:
-  M = 800;
-  MpY = 0;
-  MpT = 0;
-  Mpp = 0;
-  MEK = 180;
-  MKP3 = 100;
-  MpY_MEK = 0;
-  MpT_MEK = 0;
-  M_MEK_Y = 0;
-  M_MEK_T = 0;
-  Mpp_MKP3 = 0;
-  MpY_MKP3 = 0;
-  MpT_MKP3_Y = 0;
-  MpT_MKP3_T = 0;
-  M_MKP3_T = 0;
-  M_MKP3_Y = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  k1 = 0.005;
-  k_1 = 1;
-  k2 = 1.08;
-  k3 = 0.025;
-  k_3 = 1;
-  k4 = 0.007;
-  k5 = 0.05;
-  k_5 = 1;
-  k6 = 0.008;
-  k7 = 0.005;
-  k_7 = 1;
-  k8 = 0.45;
-  h1 = 0.045;
-  h_1 = 1;
-  h2 = 0.092;
-  h3 = 1;
-  h_3 = 0.01;
-  h4 = 0.01;
-  h_4 = 1;
-  h5 = 0.5;
-  h6 = 0.086;
-  h_6 = 0.0011;
-  h7 = 0.01;
-  h_7 = 1;
-  h8 = 0.47;
-  h9 = 0.14;
-  h_9 = 0.0018;
-
-  // Other declarations:
-  const cell, k1, k_1, k2, k3, k_3, k4, k5, k_5, k6, k7, k_7, k8, h1, h_1;
-  const h2, h3, h_3, h4, h_4, h5, h6, h_6, h7, h_7, h8, h9, h_9;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  M is "ERK";
-  MpY is "ERK-PY";
-  MpT is "ERK-PT";
-  Mpp is "ERK-PP";
-  MpY_MEK is "ERK-PY_MEK";
-  MpT_MEK is "ERK-PT_MEK";
-  M_MEK_Y is "ERK_MEK_Y";
-  M_MEK_T is "ERK_MEK_T";
-  Mpp_MKP3 is "ERK-PP_MKP3";
-  MpY_MKP3 is "ERK-PY_MKP3";
-  MpT_MKP3_Y is "ERK-PT_MKP3_Y";
-  MpT_MKP3_T is "ERK-PT_MKP3_T";
-  M_MKP3_T is "ERK_MKP3_T";
-  M_MKP3_Y is "ERK_MKP3_Y";
-  reaction_0000001 is "binding ERK and MEK";
-  reaction_0000002 is "tyr phosphorylation of ERK";
-  reaction_0000003 is "binding ERK-PY and MEK";
-  reaction_0000004 is "thr phosphorylation of ERK";
-  reaction_0000005 is "binding ERK and MEK";
-  reaction_0000006 is "thr phosphorylation of ERK";
-  reaction_0000007 is "binding ERK-PT and MEK";
-  reaction_0000008 is "tyr phosphorylation of ERK";
-  reaction_0000009 is "binding ERK-PP and MKP3";
-  reaction_0000010 is "dephosphorylation of tyr on ERK-PP";
-  reaction_0000011 is "dissociation ERK-PT and MKP3";
-  reaction_0000012 is "dephosphorylation of ERK-PT";
-  reaction_0000013 is "binding ERK-PT and MKP3";
-  reaction_0000014 is "dephosphorylation of ERK-PY";
-  reaction_0000015 is "dissociation ERK and MKP3";
-  reaction_0000017 is "binding ERK-PY and MKP3";
-  reaction_0000019 is "Dissociation ERK and MKP3";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  MpY hypernym "http://identifiers.org/uniprot/P26696"
-  MpT hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MEK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  MpY_MEK part "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  MpT_MEK part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  M_MEK_Y part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  M_MEK_T part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  Mpp_MKP3 part "http://identifiers.org/uniprot/P26696",
-                "http://identifiers.org/uniprot/Q90W58"
-  MpY_MKP3 part "http://identifiers.org/uniprot/P26696",
-                "http://identifiers.org/uniprot/Q90W58"
-  MpT_MKP3_Y part "http://identifiers.org/uniprot/P26696",
-                  "http://identifiers.org/uniprot/Q90W58"
-  MpT_MKP3_T part "http://identifiers.org/uniprot/P26696",
-                  "http://identifiers.org/uniprot/Q90W58"
-  M_MKP3_T part "http://identifiers.org/uniprot/P26696",
-                "http://identifiers.org/uniprot/Q90W58"
-  M_MKP3_Y part "http://identifiers.org/uniprot/Q90W58",
-                "http://identifiers.org/uniprot/P26696"
-  reaction_0000001 homolog "http://identifiers.org/reactome/REACT_495",
-                           "http://identifiers.org/reactome/REACT_1780"
-  reaction_0000001 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000002 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000002 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0018108",
-                            "http://identifiers.org/obo.go/GO:0004708"
-  reaction_0000003 homolog "http://identifiers.org/reactome/REACT_495",
-                           "http://identifiers.org/reactome/REACT_1780"
-  reaction_0000003 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000004 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000004 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018107",
-                            "http://identifiers.org/obo.go/GO:0000187"
-  reaction_0000005 homolog "http://identifiers.org/reactome/REACT_495",
-                           "http://identifiers.org/reactome/REACT_1780"
-  reaction_0000005 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000006 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000006 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0018107",
-                            "http://identifiers.org/obo.go/GO:0004708"
-  reaction_0000007 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000007 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000008 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000008 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0000187",
-                            "http://identifiers.org/obo.go/GO:0018108",
-                            "http://identifiers.org/obo.go/GO:0004708"
-  reaction_0000009 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000010 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470",
-                            "http://identifiers.org/obo.go/GO:0000188"
-  reaction_0000011 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000012 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000013 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000014 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000015 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000017 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000019 hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-model_0000001 is "Markevich2004_MAPK_phosphoRandomElementary"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618552953"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000028"
-model_0000001 description "http://identifiers.org/pubmed/14744999"
-model_0000001 hypernym "http://identifiers.org/obo.go/GO:0000165"
-model_0000001 taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000029.txt b/BioModelsRAG/data/BIOMD0000000029.txt
deleted file mode 100644
index 552a07b398318971b864f2e56438462436f2b7a3..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000029.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, MpY in cell, MpT in cell, Mpp in cell, $MEK in cell;
-  species $MKP3 in cell;
-
-  // Reactions:
-  v1: M => MpY; cell*(kcat1*MEK*M/Km1/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v2: MpY => Mpp; cell*(kcat2*MEK*MpY/Km2/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v3: M => MpT; cell*(kcat3*MEK*M/Km3/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v4: MpT => Mpp; cell*(kcat4*MEK*MpT/Km4/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v5: Mpp => MpT; cell*(kcat5*MKP3*Mpp/Km5/(1 + Mpp/Km5 + MpT/Km6 + MpY/Km7 + M/Km8));
-  v6: MpT => M; cell*(kcat6*MKP3*MpT/Km6/(1 + Mpp/Km5 + MpT/Km6 + MpY/Km7 + M/Km8));
-  v7: MpY => M; cell*(kcat7*MKP3*MpY/Km7/(1 + Mpp/Km5 + MpT/Km6 + MpY/Km7 + M/Km8));
-
-  // Species initializations:
-  M = 800;
-  MpY = 0;
-  MpT = 0;
-  Mpp = 0;
-  MEK = 180;
-  MKP3 = 100;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  Km1 = 410;
-  kcat1 = 1.08;
-  Km2 = 40;
-  kcat2 = 0.007;
-  Km3 = 20;
-  kcat3 = 0.008;
-  Km4 = 300;
-  kcat4 = 0.45;
-  Km5 = 22;
-  kcat5 = 0.084;
-  Km6 = 18;
-  kcat6 = 0.06;
-  Km7 = 34;
-  kcat7 = 0.108;
-  Km8 = 40;
-
-  // Other declarations:
-  const cell, Km1, kcat1, Km2, kcat2, Km3, kcat3, Km4, kcat4, Km5, kcat5;
-  const Km6, kcat6, Km7, kcat7, Km8;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  M is "ERK";
-  MpY is "ERK-PY";
-  MpT is "ERK-PT";
-  Mpp is "ERK-PP";
-  v1 is "phosphorylation of ERK on Tyr";
-  v2 is "phosphorylation of ERK-PY on Thr";
-  v3 is "phosphorylation of ERK on Thr";
-  v4 is "phosphorylation of ERK-PT on Tyr";
-  v5 is "dephosphorylation of ERK-PP on Tyr";
-  v6 is "dephosphorylation of ERK-PT";
-  v7 is "dephosphorylation of ERK-PY";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  MpY hypernym "http://identifiers.org/uniprot/P26696"
-  MpT hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MEK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0018108",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v1 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v2 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0018107",
-              "http://identifiers.org/obo.go/GO:0000187",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v3 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0018107",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v3 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v4 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v4 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0004708",
-              "http://identifiers.org/obo.go/GO:0000187",
-              "http://identifiers.org/obo.go/GO:0018108"
-  v5 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0000188",
-              "http://identifiers.org/obo.go/GO:0006470"
-  v6 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0006470"
-  v7 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0006470"
-end
-
-model_0000001 is "Markevich2004_MAPK_phosphoRandomMM"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618620128"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000029"
-model_0000001 description "http://identifiers.org/pubmed/14744999"
-model_0000001 hypernym "http://identifiers.org/obo.go/GO:0000165"
-model_0000001 taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000030.txt b/BioModelsRAG/data/BIOMD0000000030.txt
deleted file mode 100644
index 8f46aee8dd8080bff5cc71c52c35429b2e914ab7..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000030.txt
+++ /dev/null
@@ -1,233 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, MpY in cell, MpT in cell, Mpp in cell, MAPKK in cell;
-  species MKP in cell, MpY_MAPKK in cell, MpT_MAPKK in cell, M_MAPKK_Y in cell;
-  species M_MAPKK_T in cell, Mpp_MKP_Y in cell, Mpp_MKP_T in cell, MpY_MKP_Y in cell;
-  species MpY_MKP_T in cell, MpT_MKP_Y in cell, MpT_MKP_T in cell, M_MKP_T in cell;
-  species M_MKP_Y in cell;
-
-  // Reactions:
-  reaction_0000001: M + MAPKK -> M_MAPKK_Y; cell*(k1*M*MAPKK - k_1*M_MAPKK_Y);
-  reaction_0000002: M_MAPKK_Y => MpY + MAPKK; cell*k2*M_MAPKK_Y;
-  reaction_0000003: MpY + MAPKK -> MpY_MAPKK; cell*(k3*MpY*MAPKK - k_3*MpY_MAPKK);
-  reaction_0000004: MpY_MAPKK => Mpp + MAPKK; cell*k4*MpY_MAPKK;
-  reaction_0000005: M + MAPKK -> M_MAPKK_T; cell*(k5*M*MAPKK - k_5*M_MAPKK_T);
-  reaction_0000006: M_MAPKK_T => MpT + MAPKK; cell*k6*M_MAPKK_T;
-  reaction_0000007: MpT + MAPKK -> MpT_MAPKK; cell*(k7*MpT*MAPKK - k_7*MpT_MAPKK);
-  reaction_0000008: MpT_MAPKK => Mpp + MAPKK; cell*k8*MpT_MAPKK;
-  reaction_0000009: Mpp + MKP -> Mpp_MKP_Y; cell*(h1*Mpp*MKP - h_1*Mpp_MKP_Y);
-  reaction_0000010: Mpp_MKP_Y => MpT_MKP_Y; cell*h2*Mpp_MKP_Y;
-  reaction_0000011: MpT_MKP_Y -> MpT + MKP; cell*(h3*MpT_MKP_Y - h_3*MpT*MKP);
-  reaction_0000013: MpT + MKP -> MpT_MKP_T; cell*(h4*MpT*MKP - h_4*MpT_MKP_T);
-  reaction_0000012: MpT_MKP_T => M_MKP_T; cell*h5*MpT_MKP_T;
-  reaction_0000015: M_MKP_T -> M + MKP; cell*(h6*M_MKP_T - h_6*M*MKP);
-  reaction_0000017: MpY + MKP -> MpY_MKP_Y; cell*(h7*MpY*MKP - h_7*MpY_MKP_Y);
-  reaction_0000014: MpY_MKP_Y => M_MKP_Y; cell*h8*MpY_MKP_Y;
-  reaction_0000019: M_MKP_Y -> M + MKP; cell*(h9*M_MKP_Y - h_9*M*MKP);
-  reaction_0000020: Mpp + MKP -> Mpp_MKP_T; cell*(h10*Mpp*MKP - h_10*Mpp_MKP_T);
-  reaction_0000021: Mpp_MKP_T => MpY_MKP_T; cell*h11*Mpp_MKP_T;
-  reaction_0000022: MpY_MKP_T -> MpY + MKP; cell*(h12*MpY_MKP_T - h_12*MpY*MKP);
-
-  // Species initializations:
-  M = 800;
-  MpY = 0;
-  MpT = 0;
-  Mpp = 0;
-  MAPKK = 180;
-  MKP = 100;
-  MpY_MAPKK = 0;
-  MpT_MAPKK = 0;
-  M_MAPKK_Y = 0;
-  M_MAPKK_T = 0;
-  Mpp_MKP_Y = 0;
-  Mpp_MKP_T = 0;
-  MpY_MKP_Y = 0;
-  MpY_MKP_T = 0;
-  MpT_MKP_Y = 0;
-  MpT_MKP_T = 0;
-  M_MKP_T = 0;
-  M_MKP_Y = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  k1 = 0.02;
-  k_1 = 1;
-  k2 = 0.01;
-  k3 = 0.032;
-  k_3 = 1;
-  k4 = 15;
-  k5 = 0.02;
-  k_5 = 1;
-  k6 = 0.01;
-  k7 = 0.032;
-  k_7 = 1;
-  k8 = 15;
-  h1 = 0.045;
-  h_1 = 1;
-  h2 = 0.092;
-  h3 = 1;
-  h_3 = 0.01;
-  h4 = 0.01;
-  h_4 = 1;
-  h5 = 0.5;
-  h6 = 0.086;
-  h_6 = 0.0011;
-  h7 = 0.01;
-  h_7 = 1;
-  h8 = 0.47;
-  h9 = 0.14;
-  h_9 = 0.0018;
-  h10 = 0.045;
-  h_10 = 1;
-  h11 = 0.092;
-  h12 = 1;
-  h_12 = 0.01;
-
-  // Other declarations:
-  const cell, k1, k_1, k2, k3, k_3, k4, k5, k_5, k6, k7, k_7, k8, h1, h_1;
-  const h2, h3, h_3, h4, h_4, h5, h6, h_6, h7, h_7, h8, h9, h_9, h10, h_10;
-  const h11, h12, h_12;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  M is "MAPK";
-  MpY is "MAPK-PY";
-  MpT is "MAPK-PT";
-  Mpp is "MAPK-PP";
-  MpY_MAPKK is "MAPK-PY_MAPKK";
-  MpT_MAPKK is "MAPK-PT_MAPKK";
-  M_MAPKK_Y is "MAPK_MAPKK_Y";
-  M_MAPKK_T is "MAPK_MAPKK_T";
-  Mpp_MKP_Y is "MAPK-PP_MKP_T";
-  Mpp_MKP_T is "MAPK-PP_MKP_Y";
-  MpY_MKP_Y is "MAPK-PY_MKP_Y";
-  MpY_MKP_T is "MAPK-PY_MKP_T";
-  MpT_MKP_Y is "MAPK-PT_MKP_Y";
-  MpT_MKP_T is "MAPK-PT_MKP_T";
-  M_MKP_T is "MAPK_MKP_T";
-  M_MKP_Y is "MAPK_MKP_Y";
-  reaction_0000001 is "binding MAPKK on Tyr site of MAPK";
-  reaction_0000002 is "tyr phosphorylation of MAPK";
-  reaction_0000003 is "binding of MAPKK on MAPK-PY";
-  reaction_0000004 is "thr phosphorylation of MAPK";
-  reaction_0000005 is "binding of MAPKK on Thr site of MAPK";
-  reaction_0000006 is "thr phosphorylation of MAPK";
-  reaction_0000007 is "binding MAPK-PT and MAPKK";
-  reaction_0000008 is "tyr phosphorylation of MAPK";
-  reaction_0000009 is "binding of MKP on Tyr site of MAPK-PP";
-  reaction_0000010 is "dephosphorylation of Tyr on MAPKK-PP";
-  reaction_0000011 is "dissociation MAPK-PT and MKP";
-  reaction_0000013 is "binding of MKP on Thr site of MAPK-PT";
-  reaction_0000012 is "dephosphorylation of MAPK-PT";
-  reaction_0000015 is "dissociation MAPK and MKP";
-  reaction_0000017 is "binding of MKP on the Tyr site of MAPK-PY";
-  reaction_0000014 is "dephosphorylation of MAPK-PY";
-  reaction_0000019 is "Dissociation MAPK and MKP";
-  reaction_0000020 is "binding of MKP on Thr site of MAPK-PP";
-  reaction_0000021 is "dephosphorylation of Thr on MAPKK-PP";
-  reaction_0000022 is "dissociation MAPK-PY and MKP";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  MpY hypernym "http://identifiers.org/uniprot/P26696"
-  MpT hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK identity "http://identifiers.org/uniprot/Q05116"
-  MKP identity "http://identifiers.org/uniprot/Q90W58"
-  MpY_MAPKK part "http://identifiers.org/uniprot/P26696",
-                 "http://identifiers.org/uniprot/Q05116"
-  MpT_MAPKK part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  M_MAPKK_Y part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  M_MAPKK_T part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  Mpp_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  Mpp_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpY_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpY_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpT_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpT_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  M_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-               "http://identifiers.org/uniprot/P26696"
-  M_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-               "http://identifiers.org/uniprot/P26696"
-  reaction_0000001 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000001 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                            "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000002 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000002 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018108"
-  reaction_0000003 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000003 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                            "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000004 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000004 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018107",
-                            "http://identifiers.org/obo.go/GO:0000187"
-  reaction_0000005 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000005 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                            "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000006 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000006 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018107"
-  reaction_0000007 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000007 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000008 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000008 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018108",
-                            "http://identifiers.org/obo.go/GO:0000187"
-  reaction_0000009 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000010 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0000188",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000011 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000013 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000012 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000015 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000017 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000014 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000019 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000020 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000021 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0000188",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000022 hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-model_0000001 is "Markevich2004_MAPK_AllRandomElementary"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618676537"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000030"
-model_0000001 description "http://identifiers.org/pubmed/14744999"
-model_0000001 hypernym "http://identifiers.org/obo.go/GO:0000165"
-model_0000001 taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000031.txt b/BioModelsRAG/data/BIOMD0000000031.txt
deleted file mode 100644
index e63907a1b2de689eb72a6b5b875c68c12bec99ad..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000031.txt
+++ /dev/null
@@ -1,80 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Markevich2004_MAPK_orderedMM2kinases()
-
-  // Compartments and Species:
-  compartment uVol;
-  species M in uVol, Mp in uVol, Mpp in uVol, $MAPKK1 in uVol, $MAPKK2 in uVol;
-  species $MKP3 in uVol;
-
-  // Reactions:
-  v1: M => Mp; uVol*(k1cat*MAPKK1*M/Km1/(1 + M/Km1));
-  v2: Mp => Mpp; uVol*(k2cat*MAPKK2*Mp/Km2/(1 + Mp/Km2));
-  v3: Mpp => Mp; uVol*(k3cat*MKP3*Mpp/Km3/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-  v4: Mp => M; uVol*(k4cat*MKP3*Mp/Km4/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-
-  // Species initializations:
-  M = 500/uVol;
-  Mp = 0;
-  Mpp = 0;
-  MAPKK1 = 100/uVol;
-  MAPKK2 = 1/uVol;
-  MKP3 = 100/uVol;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  k1cat = 0.01;
-  Km1 = 50;
-  k2cat = 15;
-  Km2 = 500;
-  k3cat = 0.084;
-  Km3 = 5;
-  k4cat = 0.06;
-  Km4 = 18;
-  Km5 = 78;
-
-  // Other declarations:
-  const uVol, k1cat, Km1, k2cat, Km2, k3cat, Km3, k4cat, Km4, Km5;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  v1 is "phosphorylation of MAPK";
-  v2 is "phosphorylation of P-MAPK";
-  v3 is "dephosphorylation of PP-MAPK";
-  v4 is "dephosphorylation of P-MAPK";
-
-  // CV terms:
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  Mp hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK1 identity "http://identifiers.org/uniprot/Q05116"
-  MAPKK2 identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  v1 homolog "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0006468",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v2 homolog "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0004708",
-              "http://identifiers.org/obo.go/GO:0000187"
-  v3 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0000188",
-              "http://identifiers.org/obo.go/GO:0006470"
-  v4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0006470"
-end
-
-Markevich2004_MAPK_orderedMM2kinases is "Markevich2004_MAPK_orderedMM2kinases"
-
-Markevich2004_MAPK_orderedMM2kinases model_entity_is "http://identifiers.org/biomodels.db/MODEL6618738800"
-Markevich2004_MAPK_orderedMM2kinases model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000031"
-Markevich2004_MAPK_orderedMM2kinases description "http://identifiers.org/pubmed/14744999"
-Markevich2004_MAPK_orderedMM2kinases hypernym "http://identifiers.org/obo.go/GO:0000165"
-Markevich2004_MAPK_orderedMM2kinases taxon "http://identifiers.org/taxonomy/8355"
diff --git a/BioModelsRAG/data/BIOMD0000000032.txt b/BioModelsRAG/data/BIOMD0000000032.txt
deleted file mode 100644
index d996ed31fc558a75779bf895fd88b3957367f8f8..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000032.txt
+++ /dev/null
@@ -1,423 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Kofahl2004_PheromonePathway()
-
-  // Compartments and Species:
-  compartment Extracellular, compartment_;
-  species alpha in Extracellular, Ste2 in compartment_, Ste2a in compartment_;
-  species Gabc in compartment_, GaGTP in compartment_, Gbc in compartment_;
-  species GaGDP in compartment_, complexC in compartment_, complexD in compartment_;
-  species Ste5 in compartment_, Ste11 in compartment_, complexA in compartment_;
-  species Ste7 in compartment_, Fus3 in compartment_, complexB in compartment_;
-  species Ste20 in compartment_, complexE in compartment_, complexF in compartment_;
-  species complexG in compartment_, complexH in compartment_, complexI in compartment_;
-  species complexL in compartment_, Fus3PP in compartment_, complexK in compartment_;
-  species Ste12 in compartment_, Ste12a in compartment_, Bar1 in compartment_;
-  species Bar1a in compartment_, Bar1aex in Extracellular, Far1 in compartment_;
-  species Far1PP in compartment_, Far1U in compartment_, complexM in compartment_;
-  species complexN in compartment_, Cdc28 in compartment_, Sst2 in compartment_;
-  species $p in compartment_;
-
-  // Reactions:
-  v1: alpha -> ; Extracellular*alpha*Bar1aex*v1_k1;
-  v2: Ste2 -> Ste2a; compartment_*Ste2*alpha*v2_k2;
-  v3: Ste2a -> Ste2; compartment_*Ste2a*v3_k3;
-  v4: Ste2a -> $p; compartment_*Ste2a*v4_k4;
-  v5: Ste2 -> ; compartment_*Ste2*v5_k5;
-  v6: Gabc -> GaGTP + Gbc; compartment_*Ste2a*Gabc*v6_k6;
-  v7: GaGTP -> GaGDP; compartment_*GaGTP*v7_k7;
-  v8: GaGTP -> GaGDP; compartment_*GaGTP*Sst2*v8_k8;
-  v9: GaGDP + Gbc -> Gabc; compartment_*GaGDP*Gbc*v9_k9;
-  v10: Gbc + complexC -> complexD; compartment_*Gbc*complexC*v10_k10;
-  v11: complexD -> Gbc + complexC; compartment_*complexD*v11_k11;
-  v12: Ste11 + Ste5 -> complexA; compartment_*Ste5*Ste11*v12_k12;
-  v13: complexA -> Ste11 + Ste5; compartment_*complexA*v13_k13;
-  v14: Fus3 + Ste7 -> complexB; compartment_*Ste7*Fus3*v14_k14;
-  v15: complexB -> Fus3 + Ste7; compartment_*complexB*v15_k15;
-  v16: complexA + complexB -> complexC; compartment_*complexA*complexB*v16_k16;
-  v17: complexC -> Fus3 + Ste11 + Ste7 + Ste5; compartment_*complexC*v17_k17;
-  v18: complexD + Ste20 -> complexE; compartment_*complexD*Ste20*v18_k18;
-  v19: complexE -> complexD + Ste20; compartment_*complexE*v19_k19;
-  v20: complexE -> complexF; compartment_*complexE*v20_k20;
-  v21: complexE -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexE*v21_k21;
-  v22: complexF -> complexG; compartment_*complexF*v22_k22;
-  v23: complexF -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexF*v23_k23;
-  v24: complexG -> complexH; compartment_*complexG*v24_k24;
-  v25: complexG -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexG*v25_k25;
-  v26: complexH -> complexI; compartment_*complexH*v26_k26;
-  v27: complexH -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexH*v27_k27;
-  v28: complexI -> complexL + Fus3PP; compartment_*complexI*v28_k28;
-  v29: complexL + Fus3 -> complexK; compartment_*complexL*Fus3*v29_k29;
-  v30: complexK -> complexL + Fus3; compartment_*complexK*v30_k30;
-  v31: complexK -> complexI; compartment_*complexK*v31_k31;
-  v32: complexL -> Gbc + Ste7 + Ste5 + Ste20 + Ste11; compartment_*complexL*v32_k32;
-  v33: Fus3PP -> Fus3; compartment_*Fus3PP*v33_k33;
-  v34: Ste12 + Fus3PP -> Ste12a; compartment_*Ste12*Fus3PP*v34_k34;
-  v35: Ste12a -> Ste12 + Fus3PP; compartment_*Ste12a*v35_k35;
-  v36: Bar1 -> Bar1a; compartment_*Ste12a*Bar1*v36_k36;
-  v37: Bar1a -> Bar1; compartment_*Bar1a*v37_k37;
-  v38: Bar1a -> Bar1aex; compartment_*Bar1a*v38_k38;
-  v39: Far1 -> Far1PP; compartment_*(Far1*Fus3PP*Fus3PP/(100*100 + Fus3PP*Fus3PP))*v39_k39;
-  v40: Far1PP -> Far1; compartment_*Far1PP*v40_k40;
-  v41: Far1 -> Far1U; compartment_*Far1*Cdc28*v41_k41;
-  v42: Gbc + Far1PP -> complexM; compartment_*Gbc*Far1PP*v42_k42;
-  v43: complexM -> Gbc + Far1PP; compartment_*complexM*v43_k43;
-  v44: complexN -> Cdc28 + Far1PP; compartment_*complexN*v44_k44;
-  v45: Cdc28 + Far1PP -> complexN; compartment_*Far1PP*Cdc28*v45_k45;
-  v46: $p -> Sst2; compartment_*(Fus3PP^2/(4^2 + Fus3PP^2))*v46_k46;
-  v47: Sst2 -> $p; compartment_*Sst2*v47_k47;
-
-  // Species initializations:
-  alpha = 100;
-  Ste2 = 1666.6666667;
-  Ste2a = 0;
-  Gabc = 1666.6666667;
-  GaGTP = 0;
-  Gbc = 0;
-  GaGDP = 0;
-  complexC = 235.724935791903;
-  complexD = 0;
-  Ste5 = 158.33176608789;
-  Ste11 = 158.33176608789;
-  complexA = 105.943298120207;
-  Ste7 = 36.3997016405141;
-  Fus3 = 686.399701640513;
-  complexB = 77.8753625675829;
-  Ste20 = 1000;
-  complexE = 0;
-  complexF = 0;
-  complexG = 0;
-  complexH = 0;
-  complexI = 0;
-  complexL = 0;
-  Fus3PP = 0;
-  complexK = 0;
-  Ste12 = 200;
-  Ste12a = 0;
-  Bar1 = 200;
-  Bar1a = 0;
-  Bar1aex = 0;
-  Far1 = 500;
-  Far1PP = 0;
-  Far1U = 0;
-  complexM = 0;
-  complexN = 0;
-  Cdc28 = 300;
-  Sst2 = 0;
-  p = 0;
-
-  // Compartment initializations:
-  Extracellular = 1;
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1 = 0.03;
-  v1_k1 has min_inv_nM_inv;
-  v2_k2 = 0.0012;
-  v2_k2 has min_inv_nM_inv;
-  v3_k3 = 0.6;
-  v3_k3 has min_inv;
-  v4_k4 = 0.24;
-  v4_k4 has min_inv;
-  v5_k5 = 0.024;
-  v5_k5 has min_inv;
-  v6_k6 = 0.0036;
-  v6_k6 has min_inv_nM_inv;
-  v7_k7 = 0.24;
-  v7_k7 has min_inv;
-  v8_k8 = 0.033;
-  v8_k8 has min_inv_nM_inv;
-  v9_k9 = 2000;
-  v9_k9 has min_inv_nM_inv;
-  v10_k10 = 0.1;
-  v10_k10 has min_inv_nM_inv;
-  v11_k11 = 5;
-  v11_k11 has min_inv;
-  v12_k12 = 1;
-  v12_k12 has min_inv_nM_inv;
-  v13_k13 = 3;
-  v13_k13 has min_inv;
-  v14_k14 = 1;
-  v14_k14 has min_inv_nM_inv;
-  v15_k15 = 3;
-  v15_k15 has min_inv;
-  v16_k16 = 3;
-  v16_k16 has min_inv_nM_inv;
-  v17_k17 = 100;
-  v17_k17 has min_inv;
-  v18_k18 = 5;
-  v18_k18 has min_inv_nM_inv;
-  v19_k19 = 1;
-  v19_k19 has min_inv;
-  v20_k20 = 10;
-  v20_k20 has min_inv;
-  v21_k21 = 5;
-  v21_k21 has min_inv;
-  v22_k22 = 47;
-  v22_k22 has min_inv;
-  v23_k23 = 5;
-  v23_k23 has min_inv;
-  v24_k24 = 345;
-  v24_k24 has min_inv;
-  v25_k25 = 5;
-  v25_k25 has min_inv;
-  v26_k26 = 50;
-  v26_k26 has min_inv;
-  v27_k27 = 5;
-  v27_k27 has min_inv;
-  v28_k28 = 140;
-  v28_k28 has min_inv;
-  v29_k29 = 10;
-  v29_k29 has min_inv_nM_inv;
-  v30_k30 = 1;
-  v30_k30 has min_inv;
-  v31_k31 = 250;
-  v31_k31 has min_inv;
-  v32_k32 = 5;
-  v32_k32 has min_inv;
-  v33_k33 = 50;
-  v33_k33 has min_inv;
-  v34_k34 = 18;
-  v34_k34 has min_inv_nM_inv;
-  v35_k35 = 10;
-  v35_k35 has min_inv;
-  v36_k36 = 0.1;
-  v36_k36 has min_inv_nM_inv;
-  v37_k37 = 0.1;
-  v37_k37 has min_inv;
-  v38_k38 = 0.01;
-  v38_k38 has min_inv;
-  v39_k39 = 18;
-  v39_k39 has min_inv;
-  v40_k40 = 1;
-  v40_k40 has min_inv;
-  v41_k41 = 0.02;
-  v41_k41 has min_inv_nM_inv;
-  v42_k42 = 0.1;
-  v42_k42 has min_inv_nM_inv;
-  v43_k43 = 0.01;
-  v43_k43 has min_inv;
-  v44_k44 = 0.01;
-  v44_k44 has min_inv;
-  v45_k45 = 0.1;
-  v45_k45 has min_inv_nM_inv;
-  v46_k46 = 200;
-  v46_k46 has nM_min_inv;
-  v47_k47 = 1;
-  v47_k47 has min_inv;
-
-  // Other declarations:
-  const Extracellular, compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 60 second;
-  unit nanoMolar = 1e-9 mole / litre;
-  unit min_inv = 1 / 60 second;
-  unit min_inv_nM_inv = litre / (1e-9 mole * 60 second);
-  unit nM_min_inv = 1e-9 mole / (litre * 60 second);
-
-  // Display Names:
-  substance is "nanomole (default)";
-  time_unit is "minute (default)";
-  compartment_ is "cell";
-  alpha is "α-factor";
-  Ste2a is "Ste2active";
-  Gabc is "Gαβγ";
-  GaGTP is "GαGTP";
-  Gbc is "Gβγ";
-  GaGDP is "GαGDP";
-  Ste12a is "Ste12active";
-  Bar1a is "Bar1active";
-  Bar1aex is "Bar1activeEx";
-  Far1U is "Far1ubiquitin";
-  v1 is "alpha degradation";
-
-  // CV terms:
-  Extracellular hypernym "http://identifiers.org/go/GO:0005615"
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  Ste2 identity "http://identifiers.org/uniprot/P06842"
-  Ste2a identity "http://identifiers.org/uniprot/P06842"
-  Gabc part "http://identifiers.org/uniprot/P08539",
-            "http://identifiers.org/uniprot/P18851",
-            "http://identifiers.org/uniprot/P18852"
-  GaGTP identity "http://identifiers.org/uniprot/P08539"
-  Gbc part "http://identifiers.org/uniprot/P18851",
-           "http://identifiers.org/uniprot/P18852"
-  Gbc identity "http://identifiers.org/bind/50058"
-  GaGDP identity "http://identifiers.org/uniprot/P08539"
-  complexC part "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P32917"
-  complexC identity "http://identifiers.org/bind/133390"
-  complexD part "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P32917",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P18852"
-  Ste5 identity "http://identifiers.org/uniprot/P32917"
-  Ste11 identity "http://identifiers.org/uniprot/P23561"
-  complexA part "http://identifiers.org/uniprot/P32917",
-                "http://identifiers.org/uniprot/P23561"
-  Ste7 identity "http://identifiers.org/uniprot/P06784"
-  Fus3 identity "http://identifiers.org/uniprot/P16892"
-  complexB part "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P16892"
-  complexB identity "http://identifiers.org/bind/130661"
-  Ste20 identity "http://identifiers.org/uniprot/Q03497"
-  complexE part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  complexF part "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P32917",
-                "http://identifiers.org/uniprot/P23561"
-  complexG part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P32917"
-  complexH part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P32917"
-  complexI part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  complexL part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  Fus3PP identity "http://identifiers.org/uniprot/P16892"
-  complexK part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  Ste12 identity "http://identifiers.org/uniprot/P13574"
-  Ste12a identity "http://identifiers.org/uniprot/P13574"
-  Bar1 identity "http://identifiers.org/uniprot/P12630"
-  Bar1a identity "http://identifiers.org/uniprot/P12630"
-  Bar1aex identity "http://identifiers.org/uniprot/P12630"
-  Far1 identity "http://identifiers.org/uniprot/P21268"
-  Far1PP identity "http://identifiers.org/uniprot/P21268"
-  Far1U identity "http://identifiers.org/uniprot/P21268"
-  complexM part "http://identifiers.org/uniprot/P21268",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P18852"
-  complexN part "http://identifiers.org/uniprot/P21268",
-                "http://identifiers.org/uniprot/P00546"
-  Cdc28 identity "http://identifiers.org/uniprot/P00546"
-  Sst2 identity "http://identifiers.org/uniprot/P11972"
-  v1 hypernym "http://identifiers.org/go/GO:0030163"
-  v2 identity "http://identifiers.org/intact/EBI-904275"
-  v2 hypernym "http://identifiers.org/go/GO:0004934"
-  v3 identity "http://identifiers.org/intact/EBI-904275"
-  v4 hypernym "http://identifiers.org/go/GO:0030163"
-  v5 hypernym "http://identifiers.org/go/GO:0030163"
-  v6 version "http://identifiers.org/intact/EBI-380703",
-             "http://identifiers.org/intact/EBI-48387",
-             "http://identifiers.org/intact/EBI-877237"
-  v6 hypernym "http://identifiers.org/go/GO:0004930"
-  v7 hypernym "http://identifiers.org/go/GO:0003924"
-  v8 hypernym "http://identifiers.org/go/GO:0005096"
-  v8 identity "http://identifiers.org/intact/EBI-904406"
-  v9 version "http://identifiers.org/intact/EBI-877243",
-             "http://identifiers.org/intact/EBI-380703"
-  v10 hypernym "http://identifiers.org/go/GO:0005078"
-  v10 identity "http://identifiers.org/intact/EBI-903953"
-  v11 hypernym "http://identifiers.org/go/GO:0043241"
-  v12 identity "http://identifiers.org/intact/EBI-877414"
-  v13 hypernym "http://identifiers.org/go/GO:0043241"
-  v14 hypernym "http://identifiers.org/go/GO:0051019"
-  v14 identity "http://identifiers.org/intact/EBI-877260"
-  v15 hypernym "http://identifiers.org/go/GO:0043241"
-  v16 hypernym "http://identifiers.org/go/GO:0005078"
-  v16 part "http://identifiers.org/intact/EBI-895753",
-           "http://identifiers.org/intact/EBI-877421",
-           "http://identifiers.org/intact/EBI-877417"
-  v17 hypernym "http://identifiers.org/go/GO:0043241"
-  v18 hypernym "http://identifiers.org/go/GO:0004674"
-  v18 identity "http://identifiers.org/intact/EBI-903992"
-  v19 hypernym "http://identifiers.org/go/GO:0043241"
-  v20 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-               "http://identifiers.org/go/GO:0000185",
-               "http://identifiers.org/go/GO:0008349"
-  v21 hypernym "http://identifiers.org/go/GO:0043241"
-  v22 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-               "http://identifiers.org/go/GO:0000186",
-               "http://identifiers.org/go/GO:0004709"
-  v23 hypernym "http://identifiers.org/go/GO:0043241"
-  v24 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0004708",
-               "http://identifiers.org/go/GO:0000187"
-  v25 hypernym "http://identifiers.org/go/GO:0043241"
-  v26 hypernym "http://identifiers.org/go/GO:0006468"
-  v27 hypernym "http://identifiers.org/go/GO:0043241"
-  v28 hypernym "http://identifiers.org/go/GO:0043241"
-  v29 hypernym "http://identifiers.org/go/GO:0051019"
-  v29 part "http://identifiers.org/intact/EBI-877260",
-           "http://identifiers.org/intact/EBI-877421"
-  v30 hypernym "http://identifiers.org/go/GO:0043241"
-  v31 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0004708",
-               "http://identifiers.org/go/GO:0000187"
-  v32 hypernym "http://identifiers.org/go/GO:0043241"
-  v33 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0016311",
-               "http://identifiers.org/go/GO:0000188"
-  v34 hypernym "http://identifiers.org/go/GO:0004707",
-               "http://identifiers.org/go/GO:0051019"
-  v35 hypernym "http://identifiers.org/go/GO:0043241"
-  v36 hypernym "http://identifiers.org/go/GO:0003700"
-  v37 hypernym "http://identifiers.org/go/GO:0043241"
-  v38 hypernym "http://identifiers.org/go/GO:0006611"
-  v39 hypernym "http://identifiers.org/ec-code/2.7.11.24",
-               "http://identifiers.org/go/GO:0004707"
-  v40 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0016311"
-  v41 hypernym "http://identifiers.org/go/GO:0016567"
-  v43 hypernym "http://identifiers.org/go/GO:0043241"
-  v44 hypernym "http://identifiers.org/go/GO:0043241"
-  v45 hypernym "http://identifiers.org/go/GO:0004861"
-  v46 hypernym "http://identifiers.org/ec-code/2.7.11.24",
-               "http://identifiers.org/go/GO:0004707"
-end
-
-Kofahl2004_PheromonePathway is "Kofahl2004_PheromonePathway"
-
-Kofahl2004_PheromonePathway model_entity_is "http://identifiers.org/biomodels.db/MODEL6618819961"
-Kofahl2004_PheromonePathway model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000032"
-Kofahl2004_PheromonePathway description "http://identifiers.org/pubmed/15300679"
-Kofahl2004_PheromonePathway hypernym "http://identifiers.org/go/GO:0019236"
-Kofahl2004_PheromonePathway taxon "http://identifiers.org/taxonomy/4932"
-Kofahl2004_PheromonePathway part "http://identifiers.org/go/GO:0000165"
diff --git a/BioModelsRAG/data/BIOMD0000000033.txt b/BioModelsRAG/data/BIOMD0000000033.txt
deleted file mode 100644
index dc54ef5491023c0f1e64497854ed9bfc37537cf9..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000033.txt
+++ /dev/null
@@ -1,278 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Brown2004_NGF_EGF_signaling()
-
-  // Compartments and Species:
-  compartment cell;
-  species EGF in cell, NGF in cell, freeEGFReceptor in cell, boundEGFReceptor in cell;
-  species freeNGFReceptor in cell, boundNGFReceptor in cell, SosInactive in cell;
-  species SosActive in cell, P90RskInactive in cell, P90RskActive in cell;
-  species RasInactive in cell, RasActive in cell, $RasGapActive in cell, Raf1Inactive in cell;
-  species Raf1Active in cell, BRafInactive in cell, BRafActive in cell, MekInactive in cell;
-  species MekActive in cell, ErkInactive in cell, ErkActive in cell, PI3KInactive in cell;
-  species PI3KActive in cell, AktInactive in cell, AktActive in cell, C3GInactive in cell;
-  species C3GActive in cell, Rap1Inactive in cell, Rap1Active in cell, $RapGapActive in cell;
-  species $PP2AActive in cell, $Raf1PPtase in cell;
-
-  // Reactions:
-  EGFBindingReaction: EGF + freeEGFReceptor => boundEGFReceptor; cell*krbEGF*EGF*freeEGFReceptor;
-  EGFUnbindingReaction: boundEGFReceptor => EGF + freeEGFReceptor; cell*kruEGF*boundEGFReceptor;
-  NGFBindingReaction: NGF + freeNGFReceptor => boundNGFReceptor; krbNGF*NGF*freeNGFReceptor*cell;
-  NGFUnbindingReaction: boundNGFReceptor => NGF + freeNGFReceptor; kruNGF*boundNGFReceptor*cell;
-  SosActivationByEGFReaction: SosInactive -> SosActive; cell*(kEGF*boundEGFReceptor*SosInactive/(SosInactive + KmEGF));
-  SosActivationByNGFReaction: SosInactive -> SosActive; cell*(kNGF*boundNGFReceptor*SosInactive/(SosInactive + KmNGF));
-  SosDeactivationReaction: SosActive -> SosInactive; cell*(kdSos*P90RskActive*SosActive/(SosActive + KmdSos));
-  RasActivationReaction: RasInactive -> RasActive; cell*(kSos*SosActive*RasInactive/(RasInactive + KmSos));
-  RasDeactivationReaction: RasActive -> RasInactive; cell*(kRasGap*RasGapActive*RasActive/(RasActive + KmRasGap));
-  Raf1ByRasActivationReaction: Raf1Inactive -> Raf1Active; cell*(kRasToRaf1*RasActive*Raf1Inactive/(Raf1Inactive + KmRasToRaf1));
-  MekbyRaf1ActivationReaction: MekInactive -> MekActive; cell*(kpRaf1*Raf1Active*MekInactive/(MekInactive + KmpRaf1));
-  MekbyBRafActivationReaction: MekInactive -> MekActive; cell*(kpBRaf*BRafActive*MekInactive/(MekInactive + KmpBRaf));
-  ErkActivationReaction: ErkInactive -> ErkActive; cell*(kpMekCytoplasmic*MekActive*ErkInactive/(ErkInactive + KmpMekCytoplasmic));
-  MekDeactivationReaction: MekActive -> MekInactive; cell*(kdMek*PP2AActive*MekActive/(MekActive + KmdMek));
-  ErkDeactivationReaction: ErkActive -> ErkInactive; cell*(kdErk*PP2AActive*ErkActive/(ErkActive + KmdErk));
-  Raf1byPPtaseDeactivationReaction: Raf1Active -> Raf1Inactive; cell*(kdRaf1*Raf1PPtase*Raf1Active/(Raf1Active + KmdRaf1));
-  P90RskActivationReaction: P90RskInactive -> P90RskActive; cell*(kpP90Rsk*ErkActive*P90RskInactive/(P90RskInactive + KmpP90Rsk));
-  PI3KbyEGFRActivationReaction: PI3KInactive -> PI3KActive; cell*(kPI3K*boundEGFReceptor*PI3KInactive/(PI3KInactive + KmPI3K));
-  PI3KbyRasActivationReaction: PI3KInactive -> PI3KActive; cell*(kPI3KRas*RasActive*PI3KInactive/(PI3KInactive + KmPI3KRas));
-  AktActivationReaction: AktInactive -> AktActive; cell*(kAkt*PI3KActive*AktInactive/(AktInactive + KmAkt));
-  Raf1ByAktDeactivationReaction: Raf1Active -> Raf1Inactive; cell*(kdRaf1ByAkt*AktActive*Raf1Active/(Raf1Active + KmRaf1ByAkt));
-  C3GActivationReaction: C3GInactive -> C3GActive; cell*(kC3GNGF*boundNGFReceptor*C3GInactive/(C3GInactive + KmC3GNGF));
-  Rap1ActivationReaction: Rap1Inactive -> Rap1Active; cell*(kC3G*C3GActive*Rap1Inactive/(Rap1Inactive + KmC3G));
-  Rap1DeactivationReaction: Rap1Active -> Rap1Inactive; cell*(kRapGap*RapGapActive*Rap1Active/(Rap1Active + KmRapGap));
-  BRafByRap1ActivationReaction: BRafInactive -> BRafActive; cell*(kRap1ToBRaf*Rap1Active*BRafInactive/(BRafInactive + KmRap1ToBRaf));
-  BRafbyPPtaseDeactivationReaction: BRafActive -> BRafInactive; cell*(kdBRaf*Raf1PPtase*BRafActive/(BRafActive + KmdBRaf));
-
-  // Species initializations:
-  EGF = 10002000;
-  NGF = 456000;
-  freeEGFReceptor = 80000;
-  boundEGFReceptor = 0;
-  freeNGFReceptor = 10000;
-  boundNGFReceptor = 0;
-  SosInactive = 120000;
-  SosActive = 0;
-  P90RskInactive = 120000;
-  P90RskActive = 0;
-  RasInactive = 120000;
-  RasActive = 0;
-  RasGapActive = 120000;
-  Raf1Inactive = 120000;
-  Raf1Active = 0;
-  BRafInactive = 120000;
-  BRafActive = 0;
-  MekInactive = 600000;
-  MekActive = 0;
-  ErkInactive = 600000;
-  ErkActive = 0;
-  PI3KInactive = 120000;
-  PI3KActive = 0;
-  AktInactive = 120000;
-  AktActive = 0;
-  C3GInactive = 120000;
-  C3GActive = 0;
-  Rap1Inactive = 120000;
-  Rap1Active = 0;
-  RapGapActive = 120000;
-  PP2AActive = 120000;
-  Raf1PPtase = 120000;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  krbEGF = 2.18503e-05;
-  kruEGF = 0.0121008;
-  krbNGF = 1.38209e-07;
-  kruNGF = 0.00723811;
-  kEGF = 694.731;
-  KmEGF = 6086070;
-  kNGF = 389.428;
-  KmNGF = 2112.66;
-  kdSos = 1611.97;
-  KmdSos = 896896;
-  kSos = 32.344;
-  KmSos = 35954.3;
-  kRasGap = 1509.36;
-  KmRasGap = 1432410;
-  kRasToRaf1 = 0.884096;
-  KmRasToRaf1 = 62464.6;
-  kpRaf1 = 185.759;
-  KmpRaf1 = 4768350;
-  kpBRaf = 125.089;
-  KmpBRaf = 157948;
-  kdMek = 2.83243;
-  KmdMek = 518753;
-  kpMekCytoplasmic = 9.85367;
-  KmpMekCytoplasmic = 1007340;
-  kdErk = 8.8912;
-  KmdErk = 3496490;
-  kpP90Rsk = 0.0213697;
-  KmpP90Rsk = 763523;
-  kPI3K = 10.6737;
-  KmPI3K = 184912;
-  kPI3KRas = 0.0771067;
-  KmPI3KRas = 272056;
-  kAkt = 0.0566279;
-  KmAkt = 653951;
-  kdRaf1ByAkt = 15.1212;
-  KmRaf1ByAkt = 119355;
-  kC3GNGF = 146.912;
-  KmC3GNGF = 12876.2;
-  kC3G = 1.40145;
-  KmC3G = 10965.6;
-  kRapGap = 27.265;
-  KmRapGap = 295990;
-  kRap1ToBRaf = 2.20995;
-  KmRap1ToBRaf = 1025460;
-  kdRaf1 = 0.126329;
-  KmdRaf1 = 1061.71;
-  kdBRaf = 441.287;
-  KmdBRaf = 10879500;
-
-  // Other declarations:
-  const cell, krbEGF, kruEGF, krbNGF, kruNGF, kEGF, KmEGF, kNGF, KmNGF, kdSos;
-  const KmdSos, kSos, KmSos, kRasGap, KmRasGap, kRasToRaf1, KmRasToRaf1, kpRaf1;
-  const KmpRaf1, kpBRaf, KmpBRaf, kdMek, KmdMek, kpMekCytoplasmic, KmpMekCytoplasmic;
-  const kdErk, KmdErk, kpP90Rsk, KmpP90Rsk, kPI3K, KmPI3K, kPI3KRas, KmPI3KRas;
-  const kAkt, KmAkt, kdRaf1ByAkt, KmRaf1ByAkt, kC3GNGF, KmC3GNGF, kC3G, KmC3G;
-  const kRapGap, KmRapGap, kRap1ToBRaf, KmRap1ToBRaf, kdRaf1, KmdRaf1, kdBRaf;
-  const KmdBRaf;
-
-  // Unit definitions:
-  unit substance = item;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "item (default)";
-  time_unit is "minute (default)";
-  EGFBindingReaction is "EGF binding";
-  EGFUnbindingReaction is "EFG unbinding";
-  NGFBindingReaction is "NGF binding";
-  NGFUnbindingReaction is "NGF unbinding";
-  SosActivationByEGFReaction is "SOS activation by EGF";
-  SosActivationByNGFReaction is "SOS activation by NGF";
-  SosDeactivationReaction is "SOS deactivation";
-  RasActivationReaction is "Ras activation";
-  RasDeactivationReaction is "Ras deactivation";
-  Raf1ByRasActivationReaction is "Raf1 activation by Ras";
-  MekbyRaf1ActivationReaction is "Mek activation by Raf1";
-  MekbyBRafActivationReaction is "Mek activation by B-Raf";
-  ErkActivationReaction is "Erk activation";
-  MekDeactivationReaction is "Mek deactivation";
-  ErkDeactivationReaction is "Erk deactivation";
-  Raf1byPPtaseDeactivationReaction is "Raf1 deactivation by PPase";
-  P90RskActivationReaction is "P90Rsk activation";
-  PI3KbyEGFRActivationReaction is "PI3K activation by EGFR";
-  PI3KbyRasActivationReaction is "PI3K activation by Ras";
-  AktActivationReaction is "Akt activation";
-  Raf1ByAktDeactivationReaction is "Raf1 deactivation by Akt";
-  C3GActivationReaction is "C3G activation";
-  Rap1ActivationReaction is "Rap1 activation";
-  Rap1DeactivationReaction is "Rap1 deactivation";
-  BRafByRap1ActivationReaction is "BRaf activation by Rap1";
-  BRafbyPPtaseDeactivationReaction is "BRaf deactivation by PPase";
-
-  // CV terms:
-  cell identity "http://identifiers.org/go/GO:0005623"
-  EGF identity "http://identifiers.org/uniprot/P07522"
-  NGF identity "http://identifiers.org/uniprot/P25427"
-  freeEGFReceptor identity "http://identifiers.org/uniprot/Q9QX70"
-  boundEGFReceptor part "http://identifiers.org/uniprot/Q9QX70",
-                        "http://identifiers.org/uniprot/P07522"
-  freeNGFReceptor identity "http://identifiers.org/uniprot/P35739"
-  boundNGFReceptor part "http://identifiers.org/uniprot/P35739",
-                        "http://identifiers.org/uniprot/P25427"
-  SosInactive hypernym "http://identifiers.org/ensembl/ENSRNOP00000009359",
-                       "http://identifiers.org/uniprot/Q9Z1I1"
-  SosActive hypernym "http://identifiers.org/ensembl/ENSRNOP00000009359",
-                     "http://identifiers.org/uniprot/Q9Z1I1"
-  P90RskInactive version "http://identifiers.org/uniprot/Q9Z1I2",
-                         "http://identifiers.org/uniprot/Q63531"
-  P90RskActive version "http://identifiers.org/uniprot/Q9Z1I2",
-                       "http://identifiers.org/uniprot/Q63531"
-  RasInactive hypernym "http://identifiers.org/interpro/IPR003577"
-  RasActive hypernym "http://identifiers.org/interpro/IPR003577"
-  RasGapActive identity "http://identifiers.org/uniprot/P50904"
-  Raf1Inactive hypernym "http://identifiers.org/uniprot/P11345"
-  Raf1Active hypernym "http://identifiers.org/uniprot/P11345"
-  BRafInactive hypernym "http://identifiers.org/uniprot/Q99MC6"
-  BRafActive hypernym "http://identifiers.org/uniprot/Q99MC6"
-  MekInactive hypernym "http://identifiers.org/uniprot/Q01986",
-                       "http://identifiers.org/uniprot/P36506"
-  MekActive hypernym "http://identifiers.org/uniprot/Q01986",
-                     "http://identifiers.org/uniprot/P36506"
-  ErkInactive hypernym "http://identifiers.org/uniprot/P21708",
-                       "http://identifiers.org/uniprot/P63086"
-  ErkActive hypernym "http://identifiers.org/uniprot/P21708",
-                     "http://identifiers.org/uniprot/P63086"
-  PI3KInactive part "http://identifiers.org/interpro/IPR015433"
-  PI3KInactive hypernym "http://identifiers.org/go/GO:0005942"
-  PI3KActive part "http://identifiers.org/interpro/IPR015433"
-  PI3KActive hypernym "http://identifiers.org/go/GO:0005942"
-  AktInactive version "http://identifiers.org/uniprot/P47196",
-                      "http://identifiers.org/uniprot/P47197",
-                      "http://identifiers.org/uniprot/Q63484"
-  AktActive version "http://identifiers.org/uniprot/P47196",
-                    "http://identifiers.org/uniprot/P47197",
-                    "http://identifiers.org/uniprot/Q63484"
-  C3GInactive hypernym "http://identifiers.org/uniprot/Q9QYV3"
-  C3GActive hypernym "http://identifiers.org/uniprot/Q9QYV3"
-  Rap1Inactive version "http://identifiers.org/uniprot/P10113",
-                       "http://identifiers.org/uniprot/Q62636"
-  Rap1Active version "http://identifiers.org/uniprot/P10113",
-                     "http://identifiers.org/uniprot/Q62636"
-  RapGapActive identity "http://identifiers.org/uniprot/P47736"
-  PP2AActive identity "http://identifiers.org/go/GO:0000159"
-  EGFBindingReaction identity "http://identifiers.org/go/GO:0048408"
-  EGFBindingReaction hypernym "http://identifiers.org/go/GO:0045741"
-  EGFUnbindingReaction hypernym "http://identifiers.org/go/GO:0007175"
-  NGFBindingReaction hypernym "http://identifiers.org/go/GO:0051396"
-  NGFBindingReaction identity "http://identifiers.org/go/GO:0048406"
-  NGFUnbindingReaction hypernym "http://identifiers.org/go/GO:0051395"
-  SosActivationByEGFReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                      "http://identifiers.org/go/GO:0004716"
-  SosActivationByNGFReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                      "http://identifiers.org/go/GO:0004716"
-  SosDeactivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37"
-  RasActivationReaction identity "http://identifiers.org/go/GO:0046579"
-  RasDeactivationReaction identity "http://identifiers.org/go/GO:0046580"
-  Raf1ByRasActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0008349",
-                                       "http://identifiers.org/go/GO:0000185"
-  MekbyRaf1ActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0004709",
-                                       "http://identifiers.org/go/GO:0000186"
-  MekbyBRafActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0004709",
-                                       "http://identifiers.org/go/GO:0000186"
-  ErkActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                 "http://identifiers.org/go/GO:0000187",
-                                 "http://identifiers.org/go/GO:0004708"
-  MekDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  ErkDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                                   "http://identifiers.org/go/GO:0000188"
-  Raf1byPPtaseDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  P90RskActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                    "http://identifiers.org/go/GO:0004707"
-  PI3KbyEGFRActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37"
-  PI3KbyRasActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0008349"
-  AktActivationReaction hypernym "http://identifiers.org/go/GO:0045860"
-  Raf1ByAktDeactivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37"
-  C3GActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                 "http://identifiers.org/go/GO:0004716"
-  Rap1ActivationReaction identity "http://identifiers.org/go/GO:0046582"
-  BRafByRap1ActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                        "http://identifiers.org/go/GO:0000185"
-  BRafbyPPtaseDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16"
-end
-
-Brown2004_NGF_EGF_signaling is "Brown2004 - NGF and EGF signaling"
-
-Brown2004_NGF_EGF_signaling model_entity_is "http://identifiers.org/biomodels.db/MODEL6619514794"
-Brown2004_NGF_EGF_signaling model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000033"
-Brown2004_NGF_EGF_signaling description "http://identifiers.org/pubmed/16204838"
-Brown2004_NGF_EGF_signaling hypernym "http://identifiers.org/go/GO:0070371"
-Brown2004_NGF_EGF_signaling taxon "http://identifiers.org/taxonomy/131567"
-Brown2004_NGF_EGF_signaling property "http://identifiers.org/mamo/MAMO_0000046"
-Brown2004_NGF_EGF_signaling part "http://identifiers.org/go/GO:0048011",
-                                 "http://identifiers.org/go/GO:0007173"
diff --git a/BioModelsRAG/data/BIOMD0000000034.txt b/BioModelsRAG/data/BIOMD0000000034.txt
deleted file mode 100644
index 820d14a610278a1c8d740cff3a3c46ed791a1bf8..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000034.txt
+++ /dev/null
@@ -1,259 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment compartment_0000002, compartment_0000001;
-  species species_0000001 in compartment_0000001, species_0000002 in compartment_0000001;
-  species species_0000003 in compartment_0000001, species_0000004 in compartment_0000002;
-  species species_0000005 in compartment_0000002, species_0000006 in compartment_0000002;
-  species species_0000007 in compartment_0000001, species_0000008 in compartment_0000001;
-  species species_0000009 in compartment_0000001;
-
-  // Rate Rules:
-  parameter_0000001' = parameter_0000017*(species_0000008/(species_0000008 + parameter_0000011))*(parameter_0000005/(parameter_0000005 + species_0000001 + species_0000002 + species_0000003))*(1 - parameter_0000001) - parameter_0000014*parameter_0000001;
-  parameter_0000002' = parameter_0000018*(species_0000008/(species_0000008 + parameter_0000012))*(parameter_0000006/(parameter_0000006 + species_0000001 + species_0000002 + species_0000003))*(1 - parameter_0000002) - parameter_0000015*parameter_0000002;
-  parameter_0000003' = parameter_0000019*(species_0000008/(species_0000008 + parameter_0000013))*(parameter_0000007/(parameter_0000007 + species_0000001 + species_0000002 + species_0000003))*(1 - parameter_0000003) - parameter_0000016*parameter_0000003;
-  parameter_0000020' = (parameter_0000001^parameter_0000026 - parameter_0000020)/parameter_0000023;
-  parameter_0000021' = (parameter_0000002^parameter_0000026 - parameter_0000021)/parameter_0000024;
-  parameter_0000022' = (parameter_0000003^parameter_0000026 - parameter_0000022)/parameter_0000025;
-
-  // Reactions:
-  reaction_0000001:  => species_0000004; compartment_0000002*(parameter_0000027*parameter_0000021 + parameter_0000031);
-  reaction_0000002:  => species_0000007; compartment_0000001*(parameter_0000028*parameter_0000020 + parameter_0000032);
-  reaction_0000003:  => species_0000009; compartment_0000001*delay(parameter_0000029*parameter_0000022 + parameter_0000034, parameter_0000039);
-  reaction_0000004:  => species_0000008; compartment_0000001*(parameter_0000030*(species_0000009^2/(species_0000009^2 + parameter_0000010^2))*(parameter_0000008^2/(species_0000007^2 + parameter_0000008^2)) + parameter_0000033);
-  reaction_0000005: species_0000008 => ; compartment_0000001*parameter_0000036*species_0000008;
-  reaction_0000006: species_0000009 => ; compartment_0000001*parameter_0000038*species_0000009;
-  reaction_0000007: species_0000007 => ; compartment_0000001*parameter_0000037*species_0000007;
-  reaction_0000008: species_0000004 => species_0000005; compartment_0000002*(parameter_0000040*species_0000004/(parameter_0000041 + species_0000004));
-  reaction_0000009: species_0000005 => species_0000006; compartment_0000002*(parameter_0000040*species_0000005/(parameter_0000041 + species_0000005));
-  reaction_0000010: species_0000006 => species_0000001; compartment_0000002*(parameter_0000044*species_0000006/(parameter_0000045 + species_0000006));
-  reaction_0000011: species_0000001 => species_0000002; compartment_0000001*(parameter_0000042*species_0000001/(parameter_0000043 + species_0000001));
-  reaction_0000012: species_0000002 => species_0000003; compartment_0000001*(parameter_0000042*species_0000002/(parameter_0000043 + species_0000002));
-  reaction_0000013: species_0000003 => ; compartment_0000001*(parameter_0000046*species_0000003/(parameter_0000047 + species_0000003));
-  reaction_0000014: species_0000008 => ; compartment_0000001*parameter_0000048*species_0000008;
-  reaction_0000015: species_0000009 => ; compartment_0000001*parameter_0000048*species_0000009;
-  reaction_0000016: species_0000007 => ; compartment_0000001*parameter_0000048*species_0000007;
-  reaction_0000017: species_0000004 => ; compartment_0000002*parameter_0000048*species_0000004;
-  reaction_0000018: species_0000005 => ; compartment_0000002*parameter_0000048*species_0000005;
-  reaction_0000019: species_0000006 => ; compartment_0000002*parameter_0000048*species_0000006;
-  reaction_0000020: species_0000001 => ; compartment_0000001*parameter_0000048*species_0000001;
-  reaction_0000021: species_0000002 => ; compartment_0000001*parameter_0000048*species_0000002;
-  reaction_0000022: species_0000003 => ; compartment_0000001*parameter_0000048*species_0000003;
-
-  // Species initializations:
-  species_0000001 = 0.001;
-  species_0000002 = 0.001;
-  species_0000003 = 0.001;
-  species_0000004 = 0.001;
-  species_0000005 = 0.001;
-  species_0000006 = 0.001;
-  species_0000007 = 0.001;
-  species_0000008 = 0.001;
-  species_0000009 = 0.001;
-
-  // Compartment initializations:
-  compartment_0000002 = 1;
-  compartment_0000001 = 1;
-
-  // Variable initializations:
-  parameter_0000001 = ;
-  parameter_0000017 = 1.062;
-  parameter_0000011 = 0.083;
-  parameter_0000005 = 0.2;
-  parameter_0000014 = 0.2124;
-  parameter_0000002 = ;
-  parameter_0000018 = 1.062;
-  parameter_0000012 = 0.134;
-  parameter_0000006 = 0.24;
-  parameter_0000015 = 0.2124;
-  parameter_0000003 = ;
-  parameter_0000019 = 1.062;
-  parameter_0000013 = 0.248;
-  parameter_0000007 = 0.1;
-  parameter_0000016 = 0.2124;
-  parameter_0000008 = 0.54;
-  parameter_0000010 = 0.54;
-  parameter_0000020 = ;
-  parameter_0000026 = 5;
-  parameter_0000023 = 2.8249;
-  parameter_0000021 = ;
-  parameter_0000024 = 2.8249;
-  parameter_0000022 = ;
-  parameter_0000025 = 2.8249;
-  parameter_0000027 = 10.62;
-  parameter_0000028 = 76.464;
-  parameter_0000029 = 344.09;
-  parameter_0000030 = 1.062;
-  parameter_0000031 = 0.02124;
-  parameter_0000032 = 0.19116;
-  parameter_0000033 = 0.001062;
-  parameter_0000034 = 0.38232;
-  parameter_0000036 = 0.2124;
-  parameter_0000037 = 0.7434;
-  parameter_0000038 = 0.6903;
-  parameter_0000039 = 2.8249;
-  parameter_0000040 = 1.6992;
-  parameter_0000041 = 0.25;
-  parameter_0000042 = 0.3186;
-  parameter_0000043 = 0.001;
-  parameter_0000044 = 1.6992;
-  parameter_0000045 = 0.25;
-  parameter_0000046 = 5.31;
-  parameter_0000047 = 0.01;
-  parameter_0000048 = 0.00531;
-
-  // Other declarations:
-  var parameter_0000001, parameter_0000002, parameter_0000003, parameter_0000020;
-  var parameter_0000021, parameter_0000022;
-  const compartment_0000002, compartment_0000001, parameter_0000017, parameter_0000011;
-  const parameter_0000005, parameter_0000014, parameter_0000018, parameter_0000012;
-  const parameter_0000006, parameter_0000015, parameter_0000019, parameter_0000013;
-  const parameter_0000007, parameter_0000016, parameter_0000008, parameter_0000010;
-  const parameter_0000026, parameter_0000023, parameter_0000024, parameter_0000025;
-  const parameter_0000027, parameter_0000028, parameter_0000029, parameter_0000030;
-  const parameter_0000031, parameter_0000032, parameter_0000033, parameter_0000034;
-  const parameter_0000036, parameter_0000037, parameter_0000038, parameter_0000039;
-  const parameter_0000040, parameter_0000041, parameter_0000042, parameter_0000043;
-  const parameter_0000044, parameter_0000045, parameter_0000046, parameter_0000047;
-  const parameter_0000048;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  time_unit is "hour";
-  substance is "nanomole";
-  compartment_0000002 is "cytoplasm";
-  compartment_0000001 is "nucleus";
-  species_0000001 is "P0nuc";
-  species_0000002 is "P1nuc";
-  species_0000003 is "P2nuc";
-  species_0000004 is "P0cyt";
-  species_0000005 is "P1cyt";
-  species_0000006 is "P2cyt";
-  species_0000007 is "VRI";
-  species_0000008 is "CLK";
-  species_0000009 is "PDP";
-  parameter_0000001 is "ACvri";
-  parameter_0000017 is "Fv";
-  parameter_0000011 is "Kcv";
-  parameter_0000005 is "Kpv";
-  parameter_0000014 is "Kvdeac";
-  parameter_0000002 is "ACper";
-  parameter_0000018 is "Fp";
-  parameter_0000012 is "Kcp";
-  parameter_0000006 is "Kpp";
-  parameter_0000015 is "Kpdeac";
-  parameter_0000003 is "ACpdp";
-  parameter_0000019 is "Fpd";
-  parameter_0000013 is "Kcpd";
-  parameter_0000007 is "Kppd";
-  parameter_0000016 is "Kpddeac";
-  parameter_0000008 is "Kvc";
-  parameter_0000010 is "Kpdc";
-  parameter_0000020 is "OPvri";
-  parameter_0000026 is "N";
-  parameter_0000023 is "Tvriop";
-  parameter_0000021 is "OPper";
-  parameter_0000024 is "Tperop";
-  parameter_0000022 is "OPpdp";
-  parameter_0000025 is "Tpdpop";
-  parameter_0000027 is "Vper";
-  parameter_0000028 is "Vvri";
-  parameter_0000029 is "Vpdp";
-  parameter_0000030 is "Vclk";
-  parameter_0000031 is "Rpbas";
-  parameter_0000032 is "Rvbas";
-  parameter_0000033 is "Rcbas";
-  parameter_0000034 is "Rpdbas";
-  parameter_0000036 is "Vdclk";
-  parameter_0000037 is "vdvri";
-  parameter_0000038 is "vdpdp";
-  parameter_0000039 is "Tdelay";
-  parameter_0000040 is "Vpcyt";
-  parameter_0000041 is "Kpcyt";
-  parameter_0000042 is "Vpnuc";
-  parameter_0000043 is "Kpnuc";
-  parameter_0000044 is "Vtrans";
-  parameter_0000045 is "Ktrans";
-  parameter_0000046 is "Vdegp";
-  parameter_0000047 is "Kdegp";
-  parameter_0000048 is "kd";
-  reaction_0000001 is "Per production";
-  reaction_0000002 is "Vri production";
-  reaction_0000003 is "Pdp production";
-  reaction_0000004 is "Clk production";
-  reaction_0000005 is "Clk specific degradation";
-  reaction_0000006 is "Pdp specific degradation";
-  reaction_0000007 is "Vri specific degradation";
-  reaction_0000008 is "first cytoplasmic Per phosphorylation";
-  reaction_0000009 is "second cytoplasmic Per phosphorylation";
-  reaction_0000010 is "Per nuclear transport";
-  reaction_0000011 is "first nuclear Per phosphorylation";
-  reaction_0000012 is "second nuclear Rer phosphorylation";
-  reaction_0000013 is "Per specific degradation";
-  reaction_0000014 is "Clk aspecific degradation";
-  reaction_0000015 is "Pdp aspecific degradation";
-  reaction_0000016 is "Vri aspecific degradation";
-  reaction_0000017 is "Per_cyt aspecific degradation";
-  reaction_0000018 is "Per-P_cyt aspecific degradation";
-  reaction_0000019 is "Per-PP_cyt aspecific degradation";
-  reaction_0000020 is "Per_nuc aspecific degradation";
-  reaction_0000021 is "Per-P_nuc aspecific degradation";
-  reaction_0000022 is "Per-PP_nuc aspecific degradation";
-
-  // CV terms:
-  compartment_0000002 identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000001 identity "http://identifiers.org/go/GO:0005634"
-  species_0000001 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000002 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000003 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000004 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000005 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000006 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000007 identity "http://identifiers.org/uniprot/O18660"
-  species_0000008 part "http://identifiers.org/uniprot/O61735",
-                       "http://identifiers.org/uniprot/P07663"
-  species_0000009 identity "http://identifiers.org/uniprot/Q9TVS7"
-  reaction_0000001 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000002 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000003 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000004 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000005 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000006 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000007 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000008 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000009 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000010 hypernym "http://identifiers.org/go/GO:0006606"
-  reaction_0000011 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000012 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000013 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000014 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000015 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000016 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000017 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000018 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000019 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000020 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000021 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000022 hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-model_0000001 is "Smolen2004_CircClock"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6619579403"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000034"
-model_0000001 description "http://identifiers.org/pubmed/15111397"
-model_0000001 taxon "http://identifiers.org/taxonomy/7227"
-model_0000001 identity "http://identifiers.org/kegg.pathway/dme04710"
-model_0000001 hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000035.txt b/BioModelsRAG/data/BIOMD0000000035.txt
deleted file mode 100644
index edc7981451e91509fa042f155f32e04ecabee62a..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000035.txt
+++ /dev/null
@@ -1,103 +0,0 @@
-// Created by libAntimony v2.13.0
-model *vilarOscillator()
-
-  // Compartments and Species:
-  compartment deterministicOscillator;
-  substanceOnly species $EmptySet in deterministicOscillator, A in deterministicOscillator;
-  substanceOnly species C in deterministicOscillator, DA in deterministicOscillator;
-  substanceOnly species DAp in deterministicOscillator, DR in deterministicOscillator;
-  substanceOnly species DRp in deterministicOscillator, MA in deterministicOscillator;
-  substanceOnly species MR in deterministicOscillator, R in deterministicOscillator;
-
-  // Reactions:
-  Reaction1: A + R => C; A*R*Reaction1_gammaC;
-  Reaction2: A => $EmptySet; A*Reaction2_deltaA;
-  Reaction3: C => R; C*Reaction3_deltaA;
-  Reaction4: R => $EmptySet; R*Reaction4_deltaR;
-  Reaction5: A + DA => DAp; A*DA*Reaction5_gammaA;
-  Reaction6: DAp => A + DA; DAp*Reaction6_thetaA;
-  Reaction7: DA => DA + MA; DA*Reaction7_alphaA;
-  Reaction8: DAp => DAp + MA; DAp*Reaction8_alphaAp;
-  Reaction9: MA => $EmptySet; MA*Reaction9_deltaMA;
-  Reaction10: MA => A + MA; MA*Reaction10_betaA;
-  Reaction11: A + DR => DRp; A*DR*Reaction11_gammaR;
-  Reaction12: DRp => A + DR; DRp*Reaction12_thetaR;
-  Reaction13: DR => DR + MR; DR*Reaction13_alphaR;
-  Reaction14: DRp => DRp + MR; DRp*Reaction14_alphaRp;
-  Reaction15: MR => $EmptySet; MR*Reaction15_deltaMR;
-  Reaction16: MR => MR + R; MR*Reaction16_betaR;
-
-  // Species initializations:
-  EmptySet = 0;
-  A = 0;
-  C = 0;
-  DA = 1/deterministicOscillator;
-  DAp = 0;
-  DR = 1/deterministicOscillator;
-  DRp = 0;
-  MA = 0;
-  MR = 0;
-  R = 0;
-
-  // Compartment initializations:
-  deterministicOscillator = 1;
-
-  // Variable initializations:
-  Reaction1_gammaC = 2;
-  Reaction2_deltaA = 1;
-  Reaction3_deltaA = 1;
-  Reaction4_deltaR = 0.2;
-  Reaction5_gammaA = 1;
-  Reaction6_thetaA = 50;
-  Reaction7_alphaA = 50;
-  Reaction8_alphaAp = 500;
-  Reaction9_deltaMA = 10;
-  Reaction10_betaA = 50;
-  Reaction11_gammaR = 1;
-  Reaction12_thetaR = 100;
-  Reaction13_alphaR = 0.01;
-  Reaction14_alphaRp = 50;
-  Reaction15_deltaMR = 0.5;
-  Reaction16_betaR = 5;
-
-  // Other declarations:
-  const deterministicOscillator;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour";
-
-  // CV terms:
-  A hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  C hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  MA hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  MR hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  R hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0006461"
-  Reaction2 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction3 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction4 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction5 hypernym "http://identifiers.org/obo.go/GO:0016563"
-  Reaction6 hypernym "http://identifiers.org/obo.go/GO:0032986"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction9 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction10 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction11 hypernym "http://identifiers.org/obo.go/GO:0016563",
-                      "http://identifiers.org/obo.go/GO:0010843"
-  Reaction12 hypernym "http://identifiers.org/obo.go/GO:0032986"
-  Reaction13 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction14 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction15 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction16 hypernym "http://identifiers.org/obo.go/GO:0006412"
-end
-
-vilarOscillator is "Vilar2002_Oscillator"
-
-vilarOscillator model_entity_is "http://identifiers.org/biomodels.db/MODEL6619651140"
-vilarOscillator model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000035"
-vilarOscillator description "http://identifiers.org/pubmed/11972055"
-vilarOscillator hypernym "http://identifiers.org/obo.go/GO:0042752"
-vilarOscillator taxon "http://identifiers.org/taxonomy/131567"
diff --git a/BioModelsRAG/data/BIOMD0000000036.txt b/BioModelsRAG/data/BIOMD0000000036.txt
deleted file mode 100644
index 9236435635a85bc2c2da148838c1eb0cb790437c..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000036.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Tyson1999()
-
-  // Compartments and Species:
-  compartment default, CYTOPLASM;
-  species $EmptySet in default, M in CYTOPLASM, P in CYTOPLASM;
-
-  // Reactions:
-  TC: $EmptySet => M; CYTOPLASM*(TC_Vm/(1 + (P*(1 - 2/(1 + (1 + 8*TC_Keq*P)^0.5))/(2*TC_Pcrit))^2));
-  TL: $EmptySet => P; TL_V*M*CYTOPLASM;
-  mRNAD: M => $EmptySet; mRNAD_D*M*CYTOPLASM;
-  ProteinD: P => $EmptySet; ProteinD_D*P*CYTOPLASM;
-  DBT: P => $EmptySet; CYTOPLASM*((DBT_k1*P*(2/(1 + (1 + 8*DBT_Keq*P)^0.5)) + DBT_k2*P)/(DBT_J + P));
-
-  // Species initializations:
-  EmptySet = 0;
-  M = 1/CYTOPLASM;
-  P = 1/CYTOPLASM;
-
-  // Compartment initializations:
-  default = 1;
-  CYTOPLASM = 1;
-
-  // Variable initializations:
-  N_A = 6.0221367e+23;
-  TC_Vm = 1;
-  TC_Pcrit = 0.1;
-  TC_Keq = 200;
-  TL_V = 0.5;
-  mRNAD_D = 0.1;
-  ProteinD_D = 0.1;
-  DBT_k1 = 10;
-  DBT_k2 = 0.03;
-  DBT_J = 0.05;
-  DBT_Keq = 200;
-
-  // Other declarations:
-  const default, CYTOPLASM, N_A;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour";
-  P is "Pt";
-  TC is "transcription";
-  TL is "translation";
-  mRNAD is "mRNA degradation";
-  ProteinD is "protein degradation";
-  DBT is "Per phosphorylation and degradation";
-
-  // CV terms:
-  CYTOPLASM hypernym "http://identifiers.org/go/GO:0005737"
-  P identity "http://identifiers.org/uniprot/P07663"
-  TC hypernym "http://identifiers.org/go/GO:0006355",
-              "http://identifiers.org/go/GO:0009299"
-  TL hypernym "http://identifiers.org/go/GO:0006412"
-  mRNAD hypernym "http://identifiers.org/go/GO:0006402"
-  ProteinD hypernym "http://identifiers.org/go/GO:0030163"
-  DBT hypernym "http://identifiers.org/ec-code/2.7.1.37",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0030163"
-end
-
-Tyson1999 is "Tyson1999_CircClock"
-
-Tyson1999 model_entity_is "http://identifiers.org/biomodels.db/MODEL6619720081"
-Tyson1999 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000036"
-Tyson1999 description "http://identifiers.org/pubmed/20540926"
-Tyson1999 identity "http://identifiers.org/kegg.pathway/dme04710"
-Tyson1999 taxon "http://identifiers.org/taxonomy/7227"
-Tyson1999 hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000037.txt b/BioModelsRAG/data/BIOMD0000000037.txt
deleted file mode 100644
index 26a37d840ee424fc6173f9141add713a3888d195..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000037.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000037()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Pfr in compartment_, Pr in compartment_, Xi in compartment_, Xa in compartment_;
-  species prepreS in compartment_, preS in compartment_, Ya in compartment_;
-  species S in compartment_, $Gluc in compartment_, Yi in compartment_, V in compartment_;
-  species Pi in compartment_;
-
-  // Reactions:
-  Photoreceptor_activation: Pfr => Pr; compartment_*Pfr*Photoreceptor_activation_IfrSfrPfr;
-  Photoreceptor_inactivation: Pr => Pfr; Photoreceptor_inactivation_IrSrPr*Pr*compartment_;
-  Transducer_activation: Xi => Xa; Xi*Transducer_activation_kia*Pr*compartment_;
-  Transducer_inactivation: Xa => Xi; Transducer_inactivation_kai*Xa*compartment_;
-  preS_formation: prepreS => preS; prepreS*preS_formation_kx*Xa*compartment_;
-  S_generation: preS => S; preS*S_generation_ky*Ya*compartment_;
-  Glucose_sensor_inactivation: Ya + $Gluc => Yi; Glucose_sensor_inactivation_kG*Ya*Gluc*compartment_;
-  S_formation:  => S; compartment_*(S_formation_alpha1/(1 + V^3));
-  V_formation:  => V; compartment_*(V_formation_alpha2/(1 + S^3));
-  S_degradation: S => ; S_degradation_kd_s*S*compartment_;
-  V_degradation: V => ; compartment_*V*V_degradation_kd_v;
-  Photoreceptor_decay: Pr => Pi; compartment_*Photoreceptor_decay_kd*Pr;
-
-  // Species initializations:
-  Pfr = 10/compartment_;
-  Pr = 0;
-  Xi = 6/compartment_;
-  Xa = 0;
-  prepreS = 200/compartment_;
-  preS = 0;
-  Ya = 0.9/compartment_;
-  S = 0;
-  Gluc = 0;
-  Yi = 0;
-  V = 30/compartment_;
-  Pi = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  Photoreceptor_activation_IfrSfrPfr = 0.1;
-  Photoreceptor_inactivation_IrSrPr = 0;
-  Transducer_activation_kia = 0.1;
-  Transducer_inactivation_kai = 0.8;
-  preS_formation_kx = 0.2;
-  S_generation_ky = 1;
-  Glucose_sensor_inactivation_kG = 0.1;
-  S_formation_alpha1 = 30;
-  V_formation_alpha2 = 50;
-  S_degradation_kd_s = 1;
-  V_degradation_kd_v = 1;
-  Photoreceptor_decay_kd = 0.1;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour";
-
-  // CV terms:
-  Pfr version "http://identifiers.org/chebi/CHEBI:35799",
-              "http://identifiers.org/interpro/IPR001294"
-  Pr version "http://identifiers.org/chebi/CHEBI:35799",
-             "http://identifiers.org/interpro/IPR001294"
-  Gluc identity "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  Photoreceptor_activation hypernym "http://identifiers.org/go/GO:0031516"
-  Photoreceptor_inactivation hypernym "http://identifiers.org/go/GO:0031517"
-  S_formation hypernym "http://identifiers.org/go/GO:0009299",
-                       "http://identifiers.org/go/GO:0006412"
-  V_formation hypernym "http://identifiers.org/go/GO:0009299",
-                       "http://identifiers.org/go/GO:0006412"
-  S_degradation hypernym "http://identifiers.org/go/GO:0006402"
-  V_degradation hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-BIOMD0000000037 is "Marwan2003 - Genetics, regulatory hierarchy between genes"
-
-BIOMD0000000037 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000037"
-BIOMD0000000037 model_entity_is "http://identifiers.org/biomodels.db/MODEL6621175859"
-BIOMD0000000037 description "http://identifiers.org/pubmed/12750324"
-BIOMD0000000037 hypernym "http://identifiers.org/go/GO:0010018",
-                         "http://identifiers.org/go/GO:0042173"
-BIOMD0000000037 taxon "http://identifiers.org/taxonomy/5791"
diff --git a/BioModelsRAG/data/BIOMD0000000038.txt b/BioModelsRAG/data/BIOMD0000000038.txt
deleted file mode 100644
index 7d74487ccf6364e016ee1f950a3126fb6fb1850d..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000038.txt
+++ /dev/null
@@ -1,158 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Rohwer2000_Phosphotransferase_System()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species EI in compartment_, PyrPI in compartment_, EIP in compartment_;
-  species HPr in compartment_, EIPHPr in compartment_, HPrP in compartment_;
-  species EIIA in compartment_, HPrPIIA in compartment_, EIIAP in compartment_;
-  species EIICB in compartment_, EIIAPIICB in compartment_, EIICBP in compartment_;
-  species EIICBPGlc in compartment_, $PEP in compartment_, $Pyr in compartment_;
-  species $GlcP in compartment_, $Glc in compartment_;
-
-  // Reactions:
-  v1: $PEP + EI -> PyrPI; compartment_*(v1_k1f*PEP*EI - v1_k1r*PyrPI);
-  v2: PyrPI -> EIP + $Pyr; compartment_*(v2_k2f*PyrPI - v2_k2r*Pyr*EIP);
-  v3: HPr + EIP -> EIPHPr; compartment_*(v3_k3f*EIP*HPr - v3_k3r*EIPHPr);
-  v4: EIPHPr -> HPrP + EI; compartment_*(v4_k4f*EIPHPr - v4_k4r*EI*HPrP);
-  v5: HPrP + EIIA -> HPrPIIA; compartment_*(v5_k5f*HPrP*EIIA - v5_k5r*HPrPIIA);
-  v6: HPrPIIA -> EIIAP + HPr; compartment_*(v6_k6f*HPrPIIA - v6_k6r*HPr*EIIAP);
-  v7: EIICB + EIIAP -> EIIAPIICB; compartment_*(v7_k7f*EIIAP*EIICB - v7_k7r*EIIAPIICB);
-  v8: EIIAPIICB -> EIICBP + EIIA; compartment_*(v8_k8f*EIIAPIICB - v8_k8r*EIIA*EIICBP);
-  v9: EIICBP + $Glc -> EIICBPGlc; compartment_*(v9_k9f*EIICBP*Glc - v9_k9r*EIICBPGlc);
-  v10: EIICBPGlc -> EIICB + $GlcP; compartment_*(v10_k10f*EIICBPGlc - v10_k10r*EIICB*GlcP);
-
-  // Species initializations:
-  EI = 3;
-  PyrPI = 0;
-  EIP = 2;
-  HPr = 25;
-  EIPHPr = 0;
-  HPrP = 25;
-  EIIA = 20;
-  HPrPIIA = 0;
-  EIIAP = 20;
-  EIICB = 5;
-  EIIAPIICB = 0;
-  EIICBP = 5;
-  EIICBPGlc = 0;
-  PEP = 2800;
-  Pyr = 900;
-  GlcP = 50;
-  Glc = 500;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1f = 1960;
-  v1_k1r = 480000;
-  v2_k2f = 108000;
-  v2_k2r = 294;
-  v3_k3f = 14000;
-  v3_k3r = 14000;
-  v4_k4f = 84000;
-  v4_k4r = 3360;
-  v5_k5f = 21960;
-  v5_k5r = 21960;
-  v6_k6f = 4392;
-  v6_k6r = 3384;
-  v7_k7f = 880;
-  v7_k7r = 880;
-  v8_k8f = 2640;
-  v8_k8r = 960;
-  v9_k9f = 260;
-  v9_k9r = 389;
-  v10_k10f = 4800;
-  v10_k10r = 0.0054;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-  compartment_ is "cell";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  EI hypernym "http://identifiers.org/uniprot/P08839"
-  PyrPI part "http://identifiers.org/uniprot/P08839",
-             "http://identifiers.org/kegg.compound/C00074",
-             "http://identifiers.org/chebi/CHEBI:18021"
-  PyrPI part "http://identifiers.org/chebi/CHEBI:18021",
-             "http://identifiers.org/uniprot/P08839",
-             "http://identifiers.org/kegg.compound/C00615"
-  EIP hypernym "http://identifiers.org/uniprot/P08839"
-  HPr identity "http://identifiers.org/uniprot/P07006"
-  EIPHPr part "http://identifiers.org/uniprot/P07006",
-              "http://identifiers.org/uniprot/P08839"
-  HPrP part "http://identifiers.org/uniprot/P07006",
-            "http://identifiers.org/kegg.compound/C00615"
-  EIIA identity "http://identifiers.org/uniprot/P69783"
-  HPrPIIA part "http://identifiers.org/uniprot/P07006",
-               "http://identifiers.org/uniprot/P69783"
-  EIIAP identity "http://identifiers.org/uniprot/P69783"
-  EIICB identity "http://identifiers.org/uniprot/P69786"
-  EIIAPIICB identity "http://identifiers.org/uniprot/P69786",
-                     "http://identifiers.org/uniprot/P69783"
-  EIICBP identity "http://identifiers.org/uniprot/P69786"
-  EIICBPGlc part "http://identifiers.org/chebi/CHEBI:17234",
-                 "http://identifiers.org/uniprot/P69786",
-                 "http://identifiers.org/kegg.compound/C00293"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021",
-               "http://identifiers.org/kegg.compound/C00074"
-  Pyr identity "http://identifiers.org/chebi/CHEBI:15361",
-               "http://identifiers.org/kegg.compound/C00022"
-  GlcP identity "http://identifiers.org/chebi/CHEBI:14314",
-                "http://identifiers.org/kegg.compound/C00092"
-  Glc identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.3.9",
-              "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0008965",
-              "http://identifiers.org/go/GO:0016772"
-  v1 identity "http://identifiers.org/kegg.reaction/R02628"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.3.9",
-              "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0008965",
-              "http://identifiers.org/go/GO:0018106"
-  v2 identity "http://identifiers.org/kegg.reaction/R02628"
-  v3 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0018106"
-  v3 identity "http://identifiers.org/intact/EBI-902828"
-  v4 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0018106"
-  v4 identity "http://identifiers.org/intact/EBI-902828"
-  v5 hypernym "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0016772"
-  v5 identity "http://identifiers.org/intact/EBI-903339"
-  v6 hypernym "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0016772"
-  v6 identity "http://identifiers.org/intact/EBI-903339"
-  v7 hypernym "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0016772"
-  v7 identity "http://identifiers.org/intact/EBI-903826"
-  v8 identity "http://identifiers.org/intact/EBI-903826"
-  v8 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0018106"
-  v9 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0046835"
-  v10 hypernym "http://identifiers.org/go/GO:0016772",
-               "http://identifiers.org/go/GO:0046835"
-end
-
-Rohwer2000_Phosphotransferase_System is "Rohwer2000_Phosphotransferase_System"
-
-Rohwer2000_Phosphotransferase_System model_entity_is "http://identifiers.org/biomodels.db/MODEL6621395815"
-Rohwer2000_Phosphotransferase_System model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000038"
-Rohwer2000_Phosphotransferase_System description "http://identifiers.org/pubmed/10889194"
-Rohwer2000_Phosphotransferase_System identity "http://identifiers.org/kegg.pathway/eco02060"
-Rohwer2000_Phosphotransferase_System hypernym "http://identifiers.org/go/GO:0009401",
-                                              "http://identifiers.org/go/GO:0010827"
-Rohwer2000_Phosphotransferase_System taxon "http://identifiers.org/taxonomy/562"
-Rohwer2000_Phosphotransferase_System property "http://identifiers.org/mamo/MAMO_0000046"
diff --git a/BioModelsRAG/data/BIOMD0000000039.txt b/BioModelsRAG/data/BIOMD0000000039.txt
deleted file mode 100644
index 490f122b72b13fc46fe79b8f8bd6792548b6f7fb..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000039.txt
+++ /dev/null
@@ -1,95 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins()
-
-  // Compartments and Species:
-  compartment Cytosol, Endoplasmic_Reticulum, Mitochondria;
-  species Ca_cyt in Cytosol, CaER in Endoplasmic_Reticulum, CaM in Mitochondria;
-  species CaPr in Cytosol, Pr in Cytosol;
-
-  // Reactions:
-  v1: 0.25 CaER => Ca_cyt; Cytosol*(v1_Kch*Ca_cyt^2*(CaER - Ca_cyt)/(v1_K1^2 + Ca_cyt^2));
-  v3: 0.25 CaER => Ca_cyt; Cytosol*v3_Kleak*(CaER - Ca_cyt);
-  v5: Ca_cyt => 0.25 CaER; Endoplasmic_Reticulum*v5_Kpump*Ca_cyt;
-  v7: 0.25 CaM => Ca_cyt; Cytosol*CaM*(v7_Kout*Ca_cyt^2/(v7_K3^2 + Ca_cyt^2) + v7_Km);
-  v9: Ca_cyt => 0.25 CaM; Mitochondria*(v9_Kin*Ca_cyt^8/(v9_K2^8 + Ca_cyt^8));
-  v11: CaPr => Pr + Ca_cyt; Cytosol*v11_Kminus*CaPr;
-  v12: Pr + Ca_cyt => CaPr; Cytosol*v12_Kplus*Ca_cyt*Pr;
-
-  // Species initializations:
-  Ca_cyt = 0.35;
-  CaER = 0.76;
-  CaM = 0.29;
-  CaPr = 85.45;
-  Pr = 34.55;
-
-  // Compartment initializations:
-  Cytosol = 1;
-  Endoplasmic_Reticulum = 1;
-  Mitochondria = 1;
-
-  // Variable initializations:
-  v1_Kch = 4100;
-  v1_K1 = 5;
-  v3_Kleak = 0.05;
-  v5_Kpump = 20;
-  v7_Kout = 125;
-  v7_K3 = 5;
-  v7_Km = 0.00625;
-  v9_Kin = 300;
-  v9_K2 = 0.8;
-  v11_Kminus = 0.01;
-  v12_Kplus = 0.1;
-
-  // Other declarations:
-  const Cytosol, Endoplasmic_Reticulum, Mitochondria;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole (default)";
-  v1 is "Jch";
-  v3 is "Jleak";
-  v5 is "Jpump";
-  v7 is "Jout";
-  v9 is "Jin";
-  v11 is "dissociation of CaPr";
-  v12 is "binding of Ca on Pr";
-
-  // CV terms:
-  Cytosol identity "http://identifiers.org/go/GO:0005829"
-  Endoplasmic_Reticulum identity "http://identifiers.org/go/GO:0005790"
-  Mitochondria identity "http://identifiers.org/go/GO:0005739"
-  Ca_cyt identity "http://identifiers.org/chebi/CHEBI:29108"
-  CaER identity "http://identifiers.org/chebi/CHEBI:29108"
-  CaM identity "http://identifiers.org/chebi/CHEBI:29108"
-  CaPr part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/kegg.compound/C00017"
-  Pr hypernym "http://identifiers.org/kegg.compound/C00017",
-              "http://identifiers.org/chebi/CHEBI:16541"
-  v1 hypernym "http://identifiers.org/go/GO:0051482",
-              "http://identifiers.org/go/GO:0006816"
-  v3 hypernym "http://identifiers.org/go/GO:0006816",
-              "http://identifiers.org/go/GO:0007204"
-  v5 hypernym "http://identifiers.org/go/GO:0051481",
-              "http://identifiers.org/go/GO:0006816"
-  v7 identity "http://identifiers.org/go/GO:0006816",
-              "http://identifiers.org/go/GO:0007204"
-  v9 hypernym "http://identifiers.org/go/GO:0006816",
-              "http://identifiers.org/go/GO:0051481"
-  v11 hypernym "http://identifiers.org/go/GO:0007204"
-  v12 hypernym "http://identifiers.org/go/GO:0005509",
-               "http://identifiers.org/go/GO:0051481"
-end
-
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins is "Marhl2000_CaOscillations"
-
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins model_entity_is "http://identifiers.org/biomodels.db/MODEL6621933497"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000039"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins description "http://identifiers.org/pubmed/11004387"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins origin "http://identifiers.org/pubmed/17029696",
-                                                                              "http://identifiers.org/pubmed/12362939"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins taxon "http://identifiers.org/taxonomy/8355"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins identity "http://identifiers.org/kegg.pathway/hsa04020",
-                                                                                "http://identifiers.org/go/GO:0019722",
-                                                                                "http://identifiers.org/go/GO:0048016"
diff --git a/BioModelsRAG/data/BIOMD0000000040.txt b/BioModelsRAG/data/BIOMD0000000040.txt
deleted file mode 100644
index 6eb433a1e3e28d842399fb2265041b233e86c51b..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000040.txt
+++ /dev/null
@@ -1,61 +0,0 @@
-// Created by libAntimony v2.13.0
-
-// Warnings from automatic translation:
-//    Unable to set the stoichiometry math for the product Br in reaction Reaction5 because stoichiometry math is not a defined concept in Antimony.
-
-model *Field1974_Oregonator()
-
-  // Compartments and Species:
-  compartment BZ;
-  species Br in BZ, $BrO3 in BZ, Ce in BZ, HBrO2 in BZ, $HOBr in BZ;
-
-  // Reactions:
-  Reaction1: Br + $BrO3 => HBrO2 + $HOBr; Br*BrO3*Reaction1_k1*BZ;
-  Reaction2: Br + HBrO2 => 2 $HOBr; Br*HBrO2*Reaction2_k2*BZ;
-  Reaction3: $BrO3 + HBrO2 => Ce + 2 HBrO2; BrO3*HBrO2*Reaction3_k3*BZ;
-  Reaction4: 2 HBrO2 => $BrO3 + $HOBr; HBrO2^2*Reaction4_k4*BZ;
-  Reaction5: Ce => Br; Ce*Reaction5_k5*BZ;
-
-  // Species initializations:
-  Br = 1e-07;
-  BrO3 = 0.06;
-  Ce = 0.05;
-  HBrO2 = 5e-11;
-  HOBr = 0;
-
-  // Compartment initializations:
-  BZ = 1;
-
-  // Variable initializations:
-  f = 1;
-  Reaction1_k1 = 1.34;
-  Reaction2_k2 = 1600000000;
-  Reaction3_k3 = 8000;
-  Reaction4_k4 = 40000000;
-  Reaction5_k5 = 1;
-
-  // Other declarations:
-  const BZ, f;
-
-  // Display Names:
-  Br is "Br-";
-  BrO3 is "BrO3-";
-  Ce is "Ce4+";
-  Reaction1 is "M1";
-  Reaction2 is "M2";
-  Reaction3 is "M3";
-  Reaction4 is "M4";
-  Reaction5 is "M5";
-
-  // CV terms:
-  Br identity "http://identifiers.org/chebi/CHEBI:15858"
-  BrO3 identity "http://identifiers.org/chebi/CHEBI:29223"
-end
-
-Field1974_Oregonator is "Field1974_Oregonator"
-
-Field1974_Oregonator model_entity_is "http://identifiers.org/biomodels.db/MODEL6622000424"
-Field1974_Oregonator model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000040"
-Field1974_Oregonator description "http://identifiers.org/doi/10.1063/1.1681288"
-Field1974_Oregonator taxon "http://identifiers.org/taxonomy/131567"
-Field1974_Oregonator hypernym "http://identifiers.org/go/GO:0007622"
diff --git a/BioModelsRAG/data/BIOMD0000000041.txt b/BioModelsRAG/data/BIOMD0000000041.txt
deleted file mode 100644
index 4460529e5a9c3b76a17fb5ade2c79958b9307a13..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000041.txt
+++ /dev/null
@@ -1,127 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Kongas___Van_Beek()
-
-  // Compartments and Species:
-  compartment IMS, CYT;
-  species ADPi in IMS, ATPi in IMS, Cri in IMS, PCri in IMS, PCr in CYT, ADP in CYT;
-  species ATP in CYT, Cr in CYT, Pi in IMS, P in CYT;
-
-  // Reactions:
-  OxPhos: ADPi + Pi -> ATPi; IMS*(OxPhos_V_1*ADPi*Pi/(OxPhos_Ka_1*OxPhos_Kb_1*(1 + ADPi/OxPhos_Ka_1 + Pi/OxPhos_Kb_1 + ADPi*Pi/(OxPhos_Ka_1*OxPhos_Kb_1))));
-  MiCK: ATPi + Cri -> ADPi + PCri; IMS*((MiCK_Vf_2*ATPi*Cri/(MiCK_Kia_2*MiCK_Kb_2) - MiCK_Vb_2*ADPi*PCri/(MiCK_Kic_2*MiCK_Kd_2))/(1 + Cri/MiCK_Kib_2 + PCri/MiCK_Kid_2 + ATPi*(1/MiCK_Kia_2 + Cri/(MiCK_Kia_2*MiCK_Kb_2)) + ADPi*(1/MiCK_Kic_2 + Cri/(MiCK_Kic_2*MiCK_Kib_2) + PCri/(MiCK_Kid_2*(MiCK_Kic_2*MiCK_Kd_2/MiCK_Kid_2)))));
-  MMCK: ATP + Cr -> PCr + ADP; CYT*((MMCK_Vf_3*ATP*Cr/(MMCK_Kia_3*MMCK_Kb_3) - MMCK_Vb_3*ADP*PCr/(MMCK_Kic_3*MMCK_Kd_3))/(1 + Cr/MMCK_Kib_3 + PCr/MMCK_Kid_3 + ATP*(1/MMCK_Kia_3 + Cr/(MMCK_Kia_3*MMCK_Kb_3)) + ADP*(1/MMCK_Kic_3 + Cr/(MMCK_Kic_3*MMCK_Kib_3) + PCr/(MMCK_Kid_3*(MMCK_Kic_3*MMCK_Kd_3/MMCK_Kid_3)))));
-  ATPase: ATP => ADP + P; CYT*ATPase_v_4*ATP;
-  Pi_diffusion: Pi -> P; IMS*Pi_diffusion_k2_5*Pi - CYT*Pi_diffusion_k2_5*P;
-  Cr_diffusion: Cri -> Cr; IMS*Cr_diffusion_k1_6*Cri - CYT*Cr_diffusion_k1_6*Cr;
-  ADP_diffusion: ADPi -> ADP; IMS*ADP_diffusion_k1_7*ADPi - CYT*ADP_diffusion_k1_7*ADP;
-  PCr_diffusion: PCri -> PCr; IMS*PCr_diffusion_k1_8*PCri - CYT*PCr_diffusion_k1_8*PCr;
-  ATP_diffusion: ATPi -> ATP; IMS*ATP_diffusion_k1_9*ATPi - CYT*ATP_diffusion_k1_9*ATP;
-
-  // Species initializations:
-  ADPi = 0;
-  ATPi = 0;
-  Cri = 0;
-  PCri = 0;
-  PCr = 0;
-  ADP = 0;
-  ATP = 9700;
-  Cr = 26000;
-  Pi = 32000;
-  P = 0;
-
-  // Compartment initializations:
-  IMS = 0.0625;
-  CYT = 0.75;
-
-  // Variable initializations:
-  OxPhos_V_1 = 4600;
-  OxPhos_Ka_1 = 800;
-  OxPhos_Kb_1 = 20;
-  MiCK_Vf_2 = 2658;
-  MiCK_Kia_2 = 750;
-  MiCK_Kb_2 = 5200;
-  MiCK_Vb_2 = 11160;
-  MiCK_Kic_2 = 204.8;
-  MiCK_Kd_2 = 500;
-  MiCK_Kib_2 = 28800;
-  MiCK_Kid_2 = 1600;
-  MMCK_Vf_3 = 6966;
-  MMCK_Kia_3 = 900;
-  MMCK_Kb_3 = 15500;
-  MMCK_Vb_3 = 29250;
-  MMCK_Kic_3 = 222.4;
-  MMCK_Kd_3 = 1670;
-  MMCK_Kib_3 = 34900;
-  MMCK_Kid_3 = 4730;
-  ATPase_v_4 = 4600;
-  Pi_diffusion_k2_5 = 18.4;
-  Cr_diffusion_k1_6 = 14.6;
-  ADP_diffusion_k1_7 = 8.16;
-  PCr_diffusion_k1_8 = 14.6;
-  ATP_diffusion_k1_9 = 8.16;
-
-  // Other declarations:
-  const IMS, CYT;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  Pi is "Pii";
-  P is "Pi";
-  OxPhos is "Vsyn";
-  MiCK is "Vmick";
-  MMCK is "Vmmck";
-  ATPase is "Vhyd";
-  Pi_diffusion is "Jpi";
-  Cr_diffusion is "Jcr";
-  ADP_diffusion is "Jadp";
-  PCr_diffusion is "Jpcr";
-  ATP_diffusion is "Jatp";
-
-  // CV terms:
-  IMS hypernym "http://identifiers.org/go/GO:0005758"
-  CYT hypernym "http://identifiers.org/go/GO:0005829"
-  ADPi identity "http://identifiers.org/chebi/CHEBI:16761",
-                "http://identifiers.org/kegg.compound/C00008"
-  ATPi identity "http://identifiers.org/chebi/CHEBI:15422",
-                "http://identifiers.org/kegg.compound/C00002"
-  Cri identity "http://identifiers.org/chebi/CHEBI:16919",
-               "http://identifiers.org/kegg.compound/C00300"
-  PCri identity "http://identifiers.org/chebi/CHEBI:17287",
-                "http://identifiers.org/kegg.compound/C02305"
-  PCr identity "http://identifiers.org/chebi/CHEBI:17287",
-               "http://identifiers.org/kegg.compound/C02305"
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  Cr identity "http://identifiers.org/chebi/CHEBI:16919",
-              "http://identifiers.org/kegg.compound/C00300"
-  Pi identity "http://identifiers.org/chebi/CHEBI:18367",
-              "http://identifiers.org/kegg.compound/C00009"
-  P identity "http://identifiers.org/chebi/CHEBI:18367",
-             "http://identifiers.org/kegg.compound/C00009"
-  OxPhos hypernym "http://identifiers.org/go/GO:0006119"
-  MiCK hypernym "http://identifiers.org/ec-code/2.7.3.2",
-                "http://identifiers.org/go/GO:0004111"
-  MMCK hypernym "http://identifiers.org/ec-code/2.7.3.2",
-                "http://identifiers.org/go/GO:0004111"
-  ATPase hypernym "http://identifiers.org/go/GO:0016887"
-  Pi_diffusion hypernym "http://identifiers.org/go/GO:0006817"
-  Cr_diffusion hypernym "http://identifiers.org/go/GO:0015881"
-  ADP_diffusion hypernym "http://identifiers.org/go/GO:0015866"
-  PCr_diffusion hypernym "http://identifiers.org/go/GO:0015881"
-  ATP_diffusion hypernym "http://identifiers.org/go/GO:0015867"
-end
-
-Kongas___Van_Beek is "Kongas2007 - Creatine Kinase in energy metabolic signaling in muscle"
-
-Kongas___Van_Beek model_entity_is "http://identifiers.org/biomodels.db/MODEL6622188656"
-Kongas___Van_Beek model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000041"
-Kongas___Van_Beek description "http://identifiers.org/doi/10.1038/npre.2007.1317.1"
-Kongas___Van_Beek origin "http://identifiers.org/pubmed/10751324"
-Kongas___Van_Beek hypernym "http://identifiers.org/go/GO:0006600",
-                           "http://identifiers.org/go/GO:0046034"
-Kongas___Van_Beek taxon "http://identifiers.org/taxonomy/9984"
diff --git a/BioModelsRAG/data/BIOMD0000000042.txt b/BioModelsRAG/data/BIOMD0000000042.txt
deleted file mode 100644
index a070201a42fcc3a9ef2840f6c972544ba8a96ff9..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000042.txt
+++ /dev/null
@@ -1,189 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Glycolysis_Nielsen()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species ATP in compartment_, ADP in compartment_, AMP in compartment_, GLC in compartment_;
-  species F6P in compartment_, FBP in compartment_, GAP in compartment_, NAD in compartment_;
-  species NADH in compartment_, DPG in compartment_, PEP in compartment_;
-  species PYR in compartment_, ACA in compartment_, EtOH in compartment_;
-  species P in compartment_;
-
-  // Reactions:
-  ATPflow:  -> ATP; compartment_*(3.5 - ATP)*flow;
-  ADPflow:  -> ADP; compartment_*(1.1 - ADP)*flow;
-  NADHflow:  -> NADH; compartment_*(0.24 - NADH)*flow;
-  NADflow:  -> NAD; compartment_*(4 - NAD)*flow;
-  GLCflow:  -> GLC; compartment_*(50 - GLC)*flow;
-  F6Pflow: F6P => ; compartment_*F6P*flow;
-  FBPflow: FBP => ; compartment_*FBP*flow;
-  GAPflow: GAP => ; compartment_*GAP*flow;
-  DPGflow: DPG => ; compartment_*DPG*flow;
-  PEPflow: PEP => ; compartment_*PEP*flow;
-  PYRflow: PYR => ; compartment_*PYR*flow;
-  ACAflow: ACA => ; compartment_*ACA*flow;
-  EtOHflow: EtOH => ; compartment_*EtOH*flow;
-  AMPflow: AMP => ; compartment_*AMP*flow;
-  Pflow: P => ; compartment_*P*flow;
-  reaction_1: GLC + ATP => F6P + ADP; compartment_*(V1*ATP*GLC/((K1GLC + GLC)*(K1ATP + ATP)));
-  reaction_2: F6P + ATP => FBP + ADP; compartment_*(V2*ATP*F6P^2/((K2*(1 + k2*(ATP/AMP)^2) + F6P^2)*(K2ATP + ATP)));
-  reaction_3: FBP -> 2 GAP; compartment_*(k3f*FBP - k3b*GAP^2);
-  reaction_4: GAP + NAD => DPG + NADH; compartment_*(V4*NAD*GAP/((K4GAP + GAP)*(K4NAD + NAD)));
-  reaction_5: DPG + ADP -> PEP + ATP; compartment_*(k5f*DPG*ADP - k5b*PEP*ATP);
-  reaction_6: PEP + ADP => PYR + ATP; compartment_*(V6*ADP*PEP/((K6PEP + PEP)*(K6ADP + ADP)));
-  reaction_7: PYR => ACA; compartment_*(V7*PYR/(K7PYR + PYR));
-  reaction_8: ACA + NADH -> EtOH + NAD; compartment_*(k8f*NADH*ACA - k8b*NAD*EtOH);
-  reaction_9: AMP + ATP -> 2 ADP; compartment_*(k9f*AMP*ATP - k9b*ADP^2);
-  reaction_10: F6P => P; compartment_*k10*F6P;
-
-  // Species initializations:
-  ATP = 4.49064/compartment_;
-  ADP = 0.108367/compartment_;
-  AMP = 0.00261149/compartment_;
-  GLC = 0.0112817/compartment_;
-  F6P = 0.65939/compartment_;
-  FBP = 0.00770135/compartment_;
-  GAP = 0.00190919/compartment_;
-  NAD = 3.62057/compartment_;
-  NADH = 0.616118/compartment_;
-  DPG = 0.299109/compartment_;
-  PEP = 0.0021125/compartment_;
-  PYR = 0.00422702/compartment_;
-  ACA = 0.0738334/compartment_;
-  EtOH = 0.33981/compartment_;
-  P = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  V1 = 0.5;
-  K1GLC = 0.1;
-  K1ATP = 0.063;
-  V2 = 1.5;
-  K2 = 0.0016;
-  k2 = 0.017;
-  K2ATP = 0.01;
-  k3f = 1;
-  k3b = 50;
-  V4 = 10;
-  K4GAP = 1;
-  K4NAD = 1;
-  k5f = 1;
-  k5b = 0.5;
-  V6 = 10;
-  K6PEP = 0.2;
-  K6ADP = 0.3;
-  V7 = 2;
-  K7PYR = 0.3;
-  k8f = 1;
-  k8b = 0.000143;
-  k9f = 10;
-  k9b = 10;
-  k10 = 0.05;
-  flow = 0.011;
-
-  // Other declarations:
-  const compartment_, V1, K1GLC, K1ATP, V2, K2, k2, K2ATP, k3f, k3b, V4, K4GAP;
-  const K4NAD, k5f, k5b, V6, K6PEP, K6ADP, V7, K7PYR, k8f, k8b, k9f, k9b;
-  const k10, flow;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "minute";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005737"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  AMP identity "http://identifiers.org/chebi/CHEBI:16027",
-               "http://identifiers.org/kegg.compound/C00020"
-  GLC identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  F6P identity "http://identifiers.org/chebi/CHEBI:20935",
-               "http://identifiers.org/kegg.compound/C05345"
-  FBP identity "http://identifiers.org/chebi/CHEBI:16905",
-               "http://identifiers.org/kegg.compound/C05378"
-  GAP identity "http://identifiers.org/chebi/CHEBI:29052",
-               "http://identifiers.org/kegg.compound/C00118"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  DPG identity "http://identifiers.org/chebi/CHEBI:16001",
-               "http://identifiers.org/kegg.compound/C00236"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021",
-               "http://identifiers.org/kegg.compound/C00074"
-  PYR identity "http://identifiers.org/chebi/CHEBI:15361",
-               "http://identifiers.org/kegg.compound/C00022"
-  ACA identity "http://identifiers.org/chebi/CHEBI:15343",
-               "http://identifiers.org/kegg.compound/C00084"
-  EtOH identity "http://identifiers.org/chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  ATPflow hypernym "http://identifiers.org/go/GO:0006754"
-  ADPflow hypernym "http://identifiers.org/go/GO:0006172"
-  NADHflow hypernym "http://identifiers.org/go/GO:0006735"
-  NADflow hypernym "http://identifiers.org/go/GO:0009435"
-  GLCflow hypernym "http://identifiers.org/go/GO:0046323"
-  F6Pflow hypernym "http://identifiers.org/go/GO:0006002"
-  FBPflow hypernym "http://identifiers.org/go/GO:0030388"
-  GAPflow hypernym "http://identifiers.org/go/GO:0019683"
-  PYRflow hypernym "http://identifiers.org/go/GO:0042867"
-  ACAflow hypernym "http://identifiers.org/go/GO:0046187"
-  EtOHflow hypernym "http://identifiers.org/go/GO:0006068"
-  AMPflow hypernym "http://identifiers.org/go/GO:0006196"
-  reaction_1 homolog "http://identifiers.org/reactome/REACT_1164"
-  reaction_1 part "http://identifiers.org/ec-code/2.7.1.2",
-                  "http://identifiers.org/ec-code/5.3.1.9"
-  reaction_1 part "http://identifiers.org/kegg.reaction/R00771",
-                  "http://identifiers.org/kegg.reaction/R00299"
-  reaction_2 homolog "http://identifiers.org/reactome/REACT_1840"
-  reaction_2 hypernym "http://identifiers.org/ec-code/2.7.1.11",
-                      "http://identifiers.org/kegg.reaction/R00756"
-  reaction_3 homolog "http://identifiers.org/reactome/REACT_1693"
-  reaction_3 part "http://identifiers.org/kegg.reaction/R01070",
-                  "http://identifiers.org/kegg.reaction/R01015"
-  reaction_3 part "http://identifiers.org/ec-code/5.3.1.1",
-                  "http://identifiers.org/ec-code/4.1.2.13"
-  reaction_4 homolog "http://identifiers.org/reactome/REACT_587"
-  reaction_4 hypernym "http://identifiers.org/ec-code/1.2.1.12",
-                      "http://identifiers.org/kegg.reaction/R01061"
-  reaction_5 part "http://identifiers.org/ec-code/5.4.2.1",
-                  "http://identifiers.org/ec-code/2.7.2.3",
-                  "http://identifiers.org/ec-code/4.2.1.11"
-  reaction_5 part "http://identifiers.org/kegg.reaction/R00658",
-                  "http://identifiers.org/kegg.reaction/R01512",
-                  "http://identifiers.org/kegg.reaction/R01518"
-  reaction_5 part "http://identifiers.org/reactome/REACT_1771",
-                  "http://identifiers.org/reactome/REACT_1400"
-  reaction_6 version "http://identifiers.org/ec-code/2.7.1.40",
-                     "http://identifiers.org/kegg.reaction/R00200"
-  reaction_6 homolog "http://identifiers.org/reactome/REACT_1911"
-  reaction_7 hypernym "http://identifiers.org/ec-code/4.1.1.1",
-                      "http://identifiers.org/kegg.reaction/R00224"
-  reaction_8 hypernym "http://identifiers.org/ec-code/1.1.1.71",
-                      "http://identifiers.org/kegg.reaction/R00754"
-  reaction_8 homolog "http://identifiers.org/reactome/REACT_799"
-  reaction_9 hypernym "http://identifiers.org/ec-code/2.7.4.3",
-                      "http://identifiers.org/kegg.reaction/R00127"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0006001"
-  reaction_10 homolog "http://identifiers.org/reactome/REACT_1571"
-end
-
-Glycolysis_Nielsen is "Nielsen1998_Glycolysis"
-
-Glycolysis_Nielsen model_entity_is "http://identifiers.org/biomodels.db/MODEL6622455387"
-Glycolysis_Nielsen model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000042"
-Glycolysis_Nielsen description "http://identifiers.org/pubmed/17029704"
-Glycolysis_Nielsen origin "http://identifiers.org/pubmed/6454892",
-                          "http://identifiers.org/pubmed/8061224"
-Glycolysis_Nielsen homolog "http://identifiers.org/reactome/REACT_1383"
-Glycolysis_Nielsen taxon "http://identifiers.org/taxonomy/4932"
-Glycolysis_Nielsen identity "http://identifiers.org/kegg.pathway/sce00010"
-Glycolysis_Nielsen hypernym "http://identifiers.org/go/GO:0006096"
diff --git a/BioModelsRAG/data/BIOMD0000000043.txt b/BioModelsRAG/data/BIOMD0000000043.txt
deleted file mode 100644
index 487ce8eb29ea2838cf5687693547e4971df59e4c..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000043.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular;
-  species EC in extracellular, Z in cytosol, Rho in cytosol, Y in intravesicular;
-  species Fraction_Inactive_Channels in cytosol;
-
-  // Reactions:
-  vin: EC => Z; cytosol*(vin_v0 + vin_v1*beta);
-  v2: Z => Y; intravesicular*(v2_Vm2*Z^2/(v2_K2^2 + Z^2));
-  v3: Y => Z; cytosol*(beta*(Rho*(a/d)*Z^4/(1 + (a/d)*Z^4))*v3_Vm3*Y^2/(v3_Ky^2 + Y^2));
-  v4: Y => Z; cytosol*v4_Kf*Y;
-  v5: Z => EC; extracellular*v5_K*Z;
-  v6: Rho => Fraction_Inactive_Channels; cytosol*v6_Kd*Z^4*Rho;
-  v7: Fraction_Inactive_Channels => Rho; cytosol*v7_Kr*(1 - Rho);
-
-  // Species initializations:
-  EC = 0;
-  Z = 0;
-  Rho = 0;
-  Y = 0.36;
-  Fraction_Inactive_Channels = 0;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular = 1;
-
-  // Variable initializations:
-  a = 40000;
-  d = 100;
-  beta = 1;
-  vin_v0 = 1;
-  vin_v1 = 1;
-  v2_Vm2 = 6.5;
-  v2_K2 = 0.1;
-  v3_Vm3 = 50;
-  v3_Ky = 0.2;
-  v4_Kf = 1;
-  v5_K = 10;
-  v6_Kd = 5000;
-  v7_Kr = 5;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular, a, d, beta;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005615"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  intravesicular hypernym "http://identifiers.org/obo.go/GO:0005790"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Rho hypernym "http://identifiers.org/interpro/IPR016093",
-               "http://identifiers.org/interpro/IPR000493"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Fraction_Inactive_Channels hypernym "http://identifiers.org/interpro/IPR000493",
-                                      "http://identifiers.org/pirsf/PIRSF002433"
-  vin hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v3 hypernym "http://identifiers.org/obo.go/GO:0007204"
-  v4 hypernym "http://identifiers.org/obo.go/GO:0007204"
-  v5 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v6 hypernym "http://identifiers.org/obo.go/GO:0005220"
-  v7 hypernym "http://identifiers.org/obo.go/GO:0005220"
-end
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition is "Borghans1997 - Calcium Oscillation - Model 1"
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition model_entity_is "http://identifiers.org/biomodels.db/MODEL6622689184"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000043"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition description "http://identifiers.org/pubmed/17029867"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition hypernym "http://identifiers.org/obo.go/GO:0048016",
-                                                                               "http://identifiers.org/obo.go/GO:0019722"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition identity "http://identifiers.org/kegg.pathway/rno04020"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition taxon "http://identifiers.org/taxonomy/10114"
diff --git a/BioModelsRAG/data/BIOMD0000000044.txt b/BioModelsRAG/data/BIOMD0000000044.txt
deleted file mode 100644
index 80162dbe39ebba50cbe5d6dc9562bd99e7603774..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000044.txt
+++ /dev/null
@@ -1,129 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular;
-  species EC in extracellular, Z in cytosol, A in cytosol, Y in intravesicular;
-
-  // Reactions:
-  vin: EC => Z; cytosol*(vin_v0 + vin_v1*beta);
-  v2: Z => Y; intravesicular*(v2_Vm2*Z^2/(v2_K2^2 + Z^2));
-  v3: Y => Z; cytosol*v3_Vm3*A^4*Y^2*Z^4/((v3_Ka^4 + A^4)*(v3_Ky^2 + Y^2)*(v3_Kz^4 + Z^4));
-  v4: Y => Z; cytosol*v4_Kf*Y;
-  v5: Z => EC; extracellular*v5_K*Z;
-  v6:  => A; cytosol*beta*v6_Vp;
-  v7: A => ; cytosol*v7_Vd*A^2*Z^v7_n/((v7_Kp^2 + A^2)*(v7_Kd^v7_n + Z^v7_n));
-  v8: A => ; cytosol*v8_epsilon*A;
-
-  // Species initializations:
-  EC = 1000;
-  Z = 0;
-  A = 0.45;
-  Y = 0.36;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular = 1;
-
-  // Variable initializations:
-  beta = 0.5;
-  vin_v0 = 2;
-  vin_v1 = 1;
-  v2_Vm2 = 6.5;
-  v2_K2 = 0.1;
-  v3_Vm3 = 19.5;
-  v3_Ka = 0.2;
-  v3_Ky = 0.2;
-  v3_Kz = 0.3;
-  v4_Kf = 1;
-  v5_K = 10;
-  v6_Vp = 2.5;
-  v7_Vd = 80;
-  v7_Kp = 1;
-  v7_Kd = 0.4;
-  v7_n = 4;
-  v8_epsilon = 0.1;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular, beta;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-  v6 is "Agonist stimulated production of IP3";
-  v7 is "Ca dependent IP3 degradation";
-  v8 is "Ca independent IP3 degradation";
-
-  // SBO terms:
-  extracellular.sboTerm = 290
-  cytosol.sboTerm = 290
-  intravesicular.sboTerm = 290
-  EC.sboTerm = 327
-  Z.sboTerm = 327
-  A.sboTerm = 327
-  Y.sboTerm = 327
-  beta.sboTerm = 498
-  vin.sboTerm = 185
-  vin_v0.sboTerm = 485
-  vin_v1.sboTerm = 162
-  v2.sboTerm = 185
-  v2_Vm2.sboTerm = 186
-  v2_K2.sboTerm = 424
-  v3.sboTerm = 185
-  v3_Vm3.sboTerm = 186
-  v3_Ka.sboTerm = 194
-  v3_Ky.sboTerm = 424
-  v3_Kz.sboTerm = 423
-  v4.sboTerm = 185
-  v4_Kf.sboTerm = 35
-  v5.sboTerm = 185
-  v5_K.sboTerm = 35
-  v6.sboTerm = 393
-  v6_Vp.sboTerm = 48
-  v7.sboTerm = 179
-  v7_Vd.sboTerm = 324
-  v7_Kp.sboTerm = 424
-  v7_Kd.sboTerm = 194
-  v7_n.sboTerm = 190
-  v8.sboTerm = 179
-  v8_epsilon.sboTerm = 498
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005615"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  intravesicular hypernym "http://identifiers.org/obo.go/GO:0005790"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  A identity "http://identifiers.org/chebi/CHEBI:16595",
-             "http://identifiers.org/kegg.compound/C01245"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  vin hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v3 hypernym "http://identifiers.org/obo.go/GO:0006816",
-              "http://identifiers.org/obo.go/GO:0051482"
-  v4 hypernym "http://identifiers.org/obo.go/GO:0007204"
-  v5 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v6 hypernym "http://identifiers.org/obo.go/GO:0006021",
-              "http://identifiers.org/obo.go/GO:0007200"
-  v7 hypernym "http://identifiers.org/obo.go/GO:0019310"
-  v8 hypernym "http://identifiers.org/obo.go/GO:0019310"
-end
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 is "Borghans1997 - Calcium Oscillation - Model 2"
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 model_entity_is "http://identifiers.org/biomodels.db/MODEL6622948601"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000044"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 description "http://identifiers.org/pubmed/17029867"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 hypernym "http://identifiers.org/obo.go/GO:0019722",
-                                                                                         "http://identifiers.org/obo.go/GO:0048016"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 parthood "http://identifiers.org/kegg.pathway/rno04020"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 taxon "http://identifiers.org/taxonomy/10114"
diff --git a/BioModelsRAG/data/BIOMD0000000045.txt b/BioModelsRAG/data/BIOMD0000000045.txt
deleted file mode 100644
index db8d00c66254dd15cee0befebdc7cda34a353163..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000045.txt
+++ /dev/null
@@ -1,97 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular1, intravesicular2;
-  species EC in extracellular, Z in cytosol, Y in intravesicular2, X in intravesicular1;
-
-  // Reactions:
-  vin: EC => Z; cytosol*(vin_v0 + vin_v1*beta);
-  v2i: Z => Y; intravesicular2*v2i_Vm2i*Z^2/(v2i_K2i^2 + Z^2);
-  v3i: Y => Z; cytosol*v3i_Vm3i*Y^2*Z^2/((v3i_K3y^2 + Y^2)*(v3i_K3z^2 + Z^2));
-  v4: Y => Z; cytosol*v4_Kf*Y;
-  v5: Z => EC; extracellular*v5_K*Z;
-  v6: X => Z; cytosol*v6_Kf*X;
-  v2s: Z => X; intravesicular1*v2s_Vm2s*Z^2/(v2s_K2s^2 + Z^2);
-  v3s: X => Z; cytosol*beta*v3s_Vm3s*X^2/(v3s_K3s^2 + X^2);
-
-  // Species initializations:
-  EC = 0;
-  Z = 0;
-  Y = 0;
-  X = 0.5;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular1 = 1;
-  intravesicular2 = 1;
-
-  // Variable initializations:
-  beta = 1;
-  vin_v0 = 0.015;
-  vin_v1 = 0.012;
-  v2i_Vm2i = 3.1;
-  v2i_K2i = 0.005;
-  v3i_Vm3i = 25;
-  v3i_K3y = 0.065;
-  v3i_K3z = 0.022;
-  v4_Kf = 0.5;
-  v5_K = 1;
-  v6_Kf = 0.5;
-  v2s_Vm2s = 1.5;
-  v2s_K2s = 0.0265;
-  v3s_Vm3s = 0.169;
-  v3s_K3s = 0.1;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular1, intravesicular2, beta;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005615"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  intravesicular1 hypernym "http://identifiers.org/obo.go/GO:0005790"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  X identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  vin hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v2i hypernym "http://identifiers.org/obo.go/GO:0051481",
-               "http://identifiers.org/obo.go/GO:0006816"
-  v3i hypernym "http://identifiers.org/obo.go/GO:0005219",
-               "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v4 hypernym "http://identifiers.org/obo.go/GO:0006816",
-              "http://identifiers.org/obo.go/GO:0007204"
-  v5 hypernym "http://identifiers.org/obo.go/GO:0051481",
-              "http://identifiers.org/obo.go/GO:0006816"
-  v6 hypernym "http://identifiers.org/obo.go/GO:0006816",
-              "http://identifiers.org/obo.go/GO:0007204"
-  v2s hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0051481"
-  v3s hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0051482"
-end
-
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model is "Borghans1997 - Calcium Oscillation - Model 3"
-
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model model_entity_is "http://identifiers.org/biomodels.db/MODEL6623009547"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000045"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model description "http://identifiers.org/pubmed/17029867"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model hypernym "http://identifiers.org/obo.go/GO:0048016",
-                                                                       "http://identifiers.org/obo.go/GO:0019722"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model taxon "http://identifiers.org/taxonomy/10114"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model identity "http://identifiers.org/kegg.pathway/rno04020"
diff --git a/BioModelsRAG/data/BIOMD0000000046.txt b/BioModelsRAG/data/BIOMD0000000046.txt
deleted file mode 100644
index 616db6882572302b4aef724feae359dd2516aff0..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000046.txt
+++ /dev/null
@@ -1,127 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Olsen2003_peroxidase()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species NADH in compartment_, O2 in compartment_, H2O2 in compartment_;
-  species per3 in compartment_, coI in compartment_, ArH in compartment_;
-  species coII in compartment_, Ar in compartment_, NADrad in compartment_;
-  species super in compartment_, coIII in compartment_, per2 in compartment_;
-  species $NAD2 in compartment_, $NAD in compartment_, $O2g in compartment_;
-  species $NADHres in compartment_;
-
-  // Reactions:
-  v1: NADH + O2 => H2O2 + $NAD; compartment_*v1_k1*NADH*O2;
-  v2: per3 + H2O2 => coI; compartment_*v2_k2*H2O2*per3;
-  v3: ArH + coI => Ar + coII; compartment_*v3_k3*coI*ArH;
-  v4: coII + ArH => per3 + Ar; compartment_*v4_k4*coII*ArH;
-  v5: NADrad + O2 => $NAD + super; compartment_*v5_k5*NADrad*O2;
-  v6: per3 + super => coIII; compartment_*v6_k6*super*per3;
-  v7: 2 super => H2O2 + O2; compartment_*v7_k7*super*super;
-  v8: NADrad + coIII => $NAD + coI; compartment_*v8_k8*coIII*NADrad;
-  v9: 2 NADrad => $NAD2; compartment_*v9_k9*NADrad*NADrad;
-  v10: per3 + NADrad => per2 + $NAD; compartment_*v10_k10*per3*NADrad;
-  v11: per2 + O2 => coIII; compartment_*v11_k11*per2*O2;
-  v12: $NADHres => NADH; compartment_*v12_k12;
-  v131: $O2g => O2; compartment_*v131_k13f*O2g;
-  v132: O2 => $O2g; compartment_*v132_k13b*O2;
-  v14: NADH + Ar => NADrad + ArH; compartment_*v14_k14*Ar*NADH;
-
-  // Species initializations:
-  NADH = 0;
-  O2 = 0;
-  H2O2 = 0;
-  per3 = 1.4;
-  coI = 0;
-  ArH = 500;
-  coII = 0;
-  Ar = 0;
-  NADrad = 0;
-  super = 0;
-  coIII = 0;
-  per2 = 0;
-  NAD2 = 0;
-  NAD = 0;
-  O2g = 12;
-  NADHres = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1 = 3e-06;
-  v2_k2 = 18;
-  v3_k3 = 0.15;
-  v4_k4 = 0.0052;
-  v5_k5 = 20;
-  v6_k6 = 17;
-  v7_k7 = 20;
-  v8_k8 = 40;
-  v9_k9 = 60;
-  v10_k10 = 1.8;
-  v11_k11 = 0.1;
-  v12_k12 = 0.08;
-  v131_k13f = 0.006;
-  v132_k13b = 0.006;
-  v14_k14 = 0.7;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-
-  // CV terms:
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  O2 identity "http://identifiers.org/chebi/CHEBI:15379",
-              "http://identifiers.org/kegg.compound/C00007"
-  H2O2 identity "http://identifiers.org/chebi/CHEBI:16240",
-                "http://identifiers.org/kegg.compound/C00027"
-  per3 hypernym "http://identifiers.org/interpro/IPR000823",
-                "http://identifiers.org/pirsf/PIRSF000293"
-  coI hypernym "http://identifiers.org/interpro/IPR000823",
-               "http://identifiers.org/pirsf/PIRSF000293"
-  ArH version "http://identifiers.org/chebi/CHEBI:30763",
-              "http://identifiers.org/chebi/CHEBI:16796"
-  ArH version "http://identifiers.org/kegg.compound/C00156",
-              "http://identifiers.org/kegg.compound/C01598"
-  coII hypernym "http://identifiers.org/interpro/IPR000823",
-                "http://identifiers.org/pirsf/PIRSF000293"
-  Ar version "http://identifiers.org/chebi/CHEBI:17879",
-             "http://identifiers.org/chebi/CHEBI:16796"
-  Ar version "http://identifiers.org/kegg.compound/C00156",
-             "http://identifiers.org/kegg.compound/C01598"
-  NADrad hypernym "http://identifiers.org/chebi/CHEBI:15846",
-                  "http://identifiers.org/kegg.compound/C00003"
-  super identity "http://identifiers.org/chebi/CHEBI:18421",
-                 "http://identifiers.org/kegg.compound/C00704"
-  coIII hypernym "http://identifiers.org/interpro/IPR000823",
-                 "http://identifiers.org/pirsf/PIRSF000293"
-  per2 hypernym "http://identifiers.org/interpro/IPR000823",
-                "http://identifiers.org/pirsf/PIRSF000293"
-  NAD2 part "http://identifiers.org/chebi/CHEBI:15846"
-  NAD2 part "http://identifiers.org/kegg.compound/C00003"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  O2g identity "http://identifiers.org/chebi/CHEBI:15379",
-               "http://identifiers.org/kegg.compound/C00007"
-  NADHres identity "http://identifiers.org/chebi/CHEBI:16908",
-                   "http://identifiers.org/kegg.compound/C00004"
-  v1 identity "http://identifiers.org/kegg.reaction/R07171"
-  v1 hypernym "http://identifiers.org/ec-code/1.6.3.1"
-  v7 identity "http://identifiers.org/kegg.reaction/R00275"
-  v7 hypernym "http://identifiers.org/ec-code/1.15.1.1"
-end
-
-Olsen2003_peroxidase is "Olsen2003_peroxidase"
-
-Olsen2003_peroxidase model_entity_is "http://identifiers.org/biomodels.db/MODEL6623265463"
-Olsen2003_peroxidase model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000046"
-Olsen2003_peroxidase description "http://identifiers.org/pubmed/12823550"
-Olsen2003_peroxidase origin "http://identifiers.org/pubmed/11901676"
-Olsen2003_peroxidase taxon "http://identifiers.org/taxonomy/3704"
-Olsen2003_peroxidase hypernym "http://identifiers.org/go/GO:0016692"
diff --git a/BioModelsRAG/data/BIOMD0000000047.txt b/BioModelsRAG/data/BIOMD0000000047.txt
deleted file mode 100644
index 07cf65ea7c3f1c16a5eff6c7ae93b91b57af48ac..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000047.txt
+++ /dev/null
@@ -1,80 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Oxhamre_Bacteria_induced_Ca_oscillations()
-
-  // Compartments and Species:
-  compartment Cytosol, Endoplasmic_Reticulum;
-  species CaER in Endoplasmic_Reticulum, Ca_Cyt in Cytosol;
-
-  // Assignment Rules:
-  n := n0*(exp(-kbN*time) + kappa*(1 - exp(-kbN*time)));
-  p1 := p11 + p12*n/(K1 + n);
-  p2 := Ca_Cyt/(K2 + Ca_Cyt);
-
-  // Rate Rules:
-  p3' = -(k31*Ca_Cyt*p3) + k31*K3*(1 - p3);
-
-  // Reactions:
-  Jch: CaER => Ca_Cyt; Jch_Fch_0*p1*p2*p3;
-  Jleak: CaER => Ca_Cyt; Jleak_Fleak;
-  Jpump: Ca_Cyt => CaER; Jpump_Fpump_0*Ca_Cyt/(Jpump_Kpump + Ca_Cyt);
-
-  // Species initializations:
-  CaER = 0;
-  Ca_Cyt = 0;
-
-  // Compartment initializations:
-  Cytosol = 1;
-  Endoplasmic_Reticulum = 1;
-
-  // Variable initializations:
-  n0 = 1;
-  kbN = 0.5;
-  kappa = 5;
-  p11 = 0.2;
-  p12 = 0.8;
-  K1 = 5;
-  K2 = 0.7;
-  p3 = 0.95;
-  k31 = 0.5;
-  K3 = 0.7;
-  Jch_Fch_0 = 8;
-  Jleak_Fleak = 0.5;
-  Jpump_Fpump_0 = 2;
-  Jpump_Kpump = 0.1;
-
-  // Other declarations:
-  var n, p1, p2, p3;
-  const Cytosol, Endoplasmic_Reticulum, n0, kbN, kappa, p11, p12, K1, K2;
-  const k31, K3;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  Cytosol hypernym "http://identifiers.org/go/GO:0005829"
-  Endoplasmic_Reticulum hypernym "http://identifiers.org/go/GO:0005790"
-  CaER hypernym "http://identifiers.org/chebi/CHEBI:29108"
-  Ca_Cyt hypernym "http://identifiers.org/chebi/CHEBI:29108"
-  Jch hypernym "http://identifiers.org/go/GO:0006816",
-               "http://identifiers.org/go/GO:0051482"
-  Jleak hypernym "http://identifiers.org/go/GO:0007204",
-                 "http://identifiers.org/go/GO:0006816"
-  Jpump hypernym "http://identifiers.org/go/GO:0051481",
-                 "http://identifiers.org/go/GO:0006816"
-end
-
-Oxhamre_Bacteria_induced_Ca_oscillations is "Oxhamre2005_Ca_oscillation"
-
-Oxhamre_Bacteria_induced_Ca_oscillations model_entity_is "http://identifiers.org/biomodels.db/MODEL6623415355"
-Oxhamre_Bacteria_induced_Ca_oscillations model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000047"
-Oxhamre_Bacteria_induced_Ca_oscillations description "http://identifiers.org/pubmed/15596518"
-Oxhamre_Bacteria_induced_Ca_oscillations origin "http://identifiers.org/pubmed/11874447"
-Oxhamre_Bacteria_induced_Ca_oscillations identity "http://identifiers.org/kegg.pathway/rno04020"
-Oxhamre_Bacteria_induced_Ca_oscillations taxon "http://identifiers.org/taxonomy/10114"
-Oxhamre_Bacteria_induced_Ca_oscillations hypernym "http://identifiers.org/go/GO:0048016",
-                                                  "http://identifiers.org/go/GO:0019722"
diff --git a/BioModelsRAG/data/BIOMD0000000048.txt b/BioModelsRAG/data/BIOMD0000000048.txt
deleted file mode 100644
index 9a087375fef45816260c504492e90b2a58073938..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000048.txt
+++ /dev/null
@@ -1,277 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Kholodenko1999_-_EGFR_signaling()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species EGF in compartment_, R in compartment_, Ra in compartment_, R2 in compartment_;
-  species RP in compartment_, PLCg in compartment_, RPLCg in compartment_;
-  species RPLCgP in compartment_, PLCgP in compartment_, Grb in compartment_;
-  species RG in compartment_, SOS in compartment_, RGS in compartment_, GS in compartment_;
-  species Shc in compartment_, RSh in compartment_, RShP in compartment_;
-  species ShP in compartment_, RShG in compartment_, ShG in compartment_;
-  species RShGS in compartment_, ShGS in compartment_, PLCgl in compartment_;
-
-  // Reactions:
-  v1: R + EGF -> Ra; (v1_k1f*R*EGF - v1_k1b*Ra)*compartment_;
-  v2: 2 Ra -> R2; (v2_k2f*Ra*Ra - v2_k2b*R2)*compartment_;
-  v3: R2 -> RP; (v3_k3f*R2 - v3_k3b*RP)*compartment_;
-  v4: RP => R2; (v4_V4*RP/(v4_K4 + RP))*compartment_;
-  v5: RP + PLCg -> RPLCg; (v5_k5f*RP*PLCg - v5_k5b*RPLCg)*compartment_;
-  v6: RPLCg -> RPLCgP; (v6_k6f*RPLCg - v6_k6b*RPLCgP)*compartment_;
-  v7: RPLCgP -> PLCgP + RP; (v7_k7f*RPLCgP - v7_k7b*RP*PLCgP)*compartment_;
-  v8: PLCgP => PLCg; (v8_V8*PLCgP/(v8_K8 + PLCgP))*compartment_;
-  v9: Grb + RP -> RG; (v9_k9f*RP*Grb - v9_k9b*RG)*compartment_;
-  v10: RG + SOS -> RGS; (v10_k10f*RG*SOS - v10_k10b*RGS)*compartment_;
-  v11: RGS -> GS + RP; (v11_k11f*RGS - v11_k11b*RP*GS)*compartment_;
-  v12: GS -> Grb + SOS; (v12_k12f*GS - v12_k12b*Grb*SOS)*compartment_;
-  v13: Shc + RP -> RSh; (v13_k13f*RP*Shc - v13_k13b*RSh)*compartment_;
-  v14: RSh -> RShP; (v14_k14f*RSh - v14_k14b*RShP)*compartment_;
-  v15: RShP -> RP + ShP; (v15_k15f*RShP - v15_k15b*ShP*RP)*compartment_;
-  v16: ShP => Shc; (v16_V16*ShP/(v16_K16 + ShP))*compartment_;
-  v17: RShP + Grb -> RShG; (v17_k17f*RShP*Grb - v17_k17b*RShG)*compartment_;
-  v18: RShG -> ShG + RP; (v18_k18f*RShG - v18_k18b*RP*ShG)*compartment_;
-  v19: SOS + RShG -> RShGS; (v19_k19f*RShG*SOS - v19_k19b*RShGS)*compartment_;
-  v20: RShGS -> ShGS + RP; (v20_k20f*RShGS - v20_k20b*ShGS*RP)*compartment_;
-  v21: Grb + ShP -> ShG; (v21_k21f*ShP*Grb - v21_k21b*ShG)*compartment_;
-  v22: ShG + SOS -> ShGS; (v22_k22f*ShG*SOS - v22_k22b*ShGS)*compartment_;
-  v23: ShGS -> GS + ShP; (v23_k23f*ShGS - v23_k23b*ShP*GS)*compartment_;
-  v24: RShP + GS -> RShGS; (v24_k24f*RShP*GS - v24_k24b*RShGS)*compartment_;
-  v25: PLCgP -> PLCgl; (v25_k25f*PLCgP - v25_k25b*PLCgl)*compartment_;
-
-  // Species initializations:
-  EGF = 680;
-  R = 100;
-  Ra = 0;
-  R2 = 0;
-  RP = 0;
-  PLCg = 105;
-  RPLCg = 0;
-  RPLCgP = 0;
-  PLCgP = 0;
-  Grb = 85;
-  RG = 0;
-  SOS = 34;
-  RGS = 0;
-  GS = 0;
-  Shc = 150;
-  RSh = 0;
-  RShP = 0;
-  ShP = 0;
-  RShG = 0;
-  ShG = 0;
-  RShGS = 0;
-  ShGS = 0;
-  PLCgl = 0;
-
-  // Compartment initializations:
-  compartment_ = 3e-12;
-
-  // Variable initializations:
-  v1_k1f = 0.003;
-  v1_k1b = 0.06;
-  v2_k2f = 0.01;
-  v2_k2b = 0.1;
-  v3_k3f = 1;
-  v3_k3b = 0.01;
-  v4_V4 = 450;
-  v4_K4 = 50;
-  v5_k5f = 0.06;
-  v5_k5b = 0.2;
-  v6_k6f = 1;
-  v6_k6b = 0.05;
-  v7_k7f = 0.3;
-  v7_k7b = 0.006;
-  v8_V8 = 1;
-  v8_K8 = 100;
-  v9_k9f = 0.003;
-  v9_k9b = 0.05;
-  v10_k10f = 0.01;
-  v10_k10b = 0.06;
-  v11_k11f = 0.03;
-  v11_k11b = 0.0045;
-  v12_k12f = 0.0015;
-  v12_k12b = 0.0001;
-  v13_k13f = 0.09;
-  v13_k13b = 0.6;
-  v14_k14f = 6;
-  v14_k14b = 0.06;
-  v15_k15f = 0.3;
-  v15_k15b = 0.0009;
-  v16_V16 = 1.7;
-  v16_K16 = 340;
-  v17_k17f = 0.003;
-  v17_k17b = 0.1;
-  v18_k18f = 0.3;
-  v18_k18b = 0.0009;
-  v19_k19f = 0.01;
-  v19_k19b = 0.0214;
-  v20_k20f = 0.12;
-  v20_k20b = 0.00024;
-  v21_k21f = 0.003;
-  v21_k21b = 0.1;
-  v22_k22f = 0.03;
-  v22_k22b = 0.064;
-  v23_k23f = 0.1;
-  v23_k23b = 0.021;
-  v24_k24f = 0.009;
-  v24_k24b = 0.0429;
-  v25_k25f = 1;
-  v25_k25b = 0.03;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole";
-  compartment_ is "cytoplasm";
-  EGF is "Epidermal_Growth_Factor";
-  R is "EGFR";
-  Ra is "EGF_EGFR";
-  R2 is "(EGF_EGFR)2";
-  RP is "(EGF_EGFR)2-P";
-  RPLCg is "(EGF_EGFR)2_PLCg";
-  RPLCgP is "(EGF_EGFR)2_PLCg-P";
-  PLCgP is "PLCg-P";
-  Grb is "Grb2";
-  RG is "(EGF_EGFR)2_Grb2";
-  RGS is "(EGF_EGFR)2_Grb2_SOS";
-  GS is "Grb2_SOS";
-  RSh is "(EGF_EGFR)2_Shc";
-  RShP is "(EGF_EGFR)_Shc-P";
-  ShP is "Shc-P";
-  RShG is "(EGF_EGFR)2_Shc_Grb2";
-  ShG is "Shc_Grb2";
-  RShGS is "(EGF_EGFR)2_Shc_Grb2_SOS";
-  ShGS is "Shc_Grb2_SOS";
-  PLCgl is "PLCgP-I";
-  v1 is "EGF_binds_to_EGFR";
-  v2 is "association_of_2_Ra_into_dimer";
-  v3 is "phosphorylation_of_R2";
-  v4 is "dephosphorylation_of_RP";
-  v5 is "binding_of_PLCg_to_RP";
-  v6 is "phosphorylation_of_PLCg";
-  v7 is "dissociation_of_RPLCgP";
-  v8 is "dephosphorylation_of_PLCgP";
-  v9 is "binding_of_Grb2_to_RP";
-  v10 is "binding_of_SOS_to_RG";
-  v11 is "dissociation_of_RGS";
-  v12 is "dissociation_of_GS";
-  v13 is "binding_of_Shc_to_RP";
-  v14 is "phosphorylation_of_RSh";
-  v15 is "dissociation_of_RShp";
-  v16 is "dephosphorylation_of_ShP";
-  v17 is "binding_of_Grb2_to_RShP";
-  v18 is "dissociation_of_RShG";
-  v19 is "binding_of_SOS_to_RShG";
-  v20 is "dissociation_of_RShGS";
-  v21 is "binding_of_Grb2_to_ShP";
-  v22 is "binding_of_SOS_to_ShG";
-  v23 is "dissociation_of_ShGS";
-  v24 is "association_of_RShP_and_GS";
-  v25 is "translocation_of_PLCgP";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005737"
-  EGF identity "http://identifiers.org/uniprot/P07522"
-  R hypernym "http://identifiers.org/uniprot/Q9QX70"
-  Ra part "http://identifiers.org/uniprot/Q9QX70",
-          "http://identifiers.org/uniprot/P07522"
-  R2 part "http://identifiers.org/uniprot/P07522",
-          "http://identifiers.org/uniprot/Q9QX70"
-  RP hypernym "http://identifiers.org/uniprot/Q9QX70"
-  PLCg hypernym "http://identifiers.org/interpro/IPR001192"
-  PLCg version "http://identifiers.org/uniprot/P10686",
-               "http://identifiers.org/uniprot/P24135"
-  RPLCg version "http://identifiers.org/uniprot/P10686",
-                "http://identifiers.org/uniprot/P24135",
-                "http://identifiers.org/uniprot/Q9QX70"
-  RPLCgP version "http://identifiers.org/uniprot/P24135",
-                 "http://identifiers.org/uniprot/P10686",
-                 "http://identifiers.org/uniprot/Q9QX70"
-  PLCgP version "http://identifiers.org/interpro/IPR001192"
-  PLCgP hypernym "http://identifiers.org/uniprot/P24135",
-                 "http://identifiers.org/uniprot/P10686"
-  Grb identity "http://identifiers.org/uniprot/P62994"
-  RG part "http://identifiers.org/uniprot/P62994",
-          "http://identifiers.org/uniprot/Q9QX70"
-  SOS identity "http://identifiers.org/uniprot/Q9Z1I1"
-  RGS part "http://identifiers.org/uniprot/Q9QX70",
-           "http://identifiers.org/uniprot/P62994",
-           "http://identifiers.org/uniprot/Q9Z1I1"
-  GS part "http://identifiers.org/uniprot/P62994",
-          "http://identifiers.org/uniprot/Q9Z1I1"
-  Shc hypernym "http://identifiers.org/uniprot/Q5M824"
-  RSh part "http://identifiers.org/uniprot/Q9QX70",
-           "http://identifiers.org/uniprot/Q5M824"
-  RShP part "http://identifiers.org/uniprot/Q5M824",
-            "http://identifiers.org/uniprot/Q9QX70"
-  ShP hypernym "http://identifiers.org/uniprot/Q5M824"
-  RShG part "http://identifiers.org/uniprot/Q5M824",
-            "http://identifiers.org/uniprot/P62994",
-            "http://identifiers.org/uniprot/Q9QX70"
-  ShG part "http://identifiers.org/uniprot/Q5M824",
-           "http://identifiers.org/uniprot/P62994"
-  RShGS part "http://identifiers.org/uniprot/P62994",
-             "http://identifiers.org/uniprot/Q5M824",
-             "http://identifiers.org/uniprot/Q9Z1I1",
-             "http://identifiers.org/uniprot/Q9QX70"
-  ShGS part "http://identifiers.org/uniprot/Q5M824",
-            "http://identifiers.org/uniprot/P62994",
-            "http://identifiers.org/uniprot/Q9Z1I1"
-  PLCgl hypernym "http://identifiers.org/interpro/IPR001192"
-  PLCgl version "http://identifiers.org/uniprot/P24135",
-                "http://identifiers.org/uniprot/P10686"
-  v1 identity "http://identifiers.org/go/GO:0005154",
-              "http://identifiers.org/go/GO:0048408"
-  v1 parthood "http://identifiers.org/go/GO:0045741"
-  v2 hypernym "http://identifiers.org/go/GO:0046983"
-  v3 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-              "http://identifiers.org/go/GO:0006468",
-              "http://identifiers.org/go/GO:0004716"
-  v4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-  v5 hypernym "http://identifiers.org/go/GO:0051425",
-              "http://identifiers.org/go/GO:0042169"
-  v6 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-              "http://identifiers.org/go/GO:0006468",
-              "http://identifiers.org/go/GO:0004716"
-  v8 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-  v9 hypernym "http://identifiers.org/go/GO:0042169",
-              "http://identifiers.org/go/GO:0051425"
-  v10 hypernym "http://identifiers.org/go/GO:0005070",
-               "http://identifiers.org/go/GO:0017124",
-               "http://identifiers.org/go/GO:0005068"
-  v13 hypernym "http://identifiers.org/go/GO:0051425",
-               "http://identifiers.org/go/GO:0042169"
-  v14 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004716"
-  v16 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  v17 hypernym "http://identifiers.org/go/GO:0051425",
-               "http://identifiers.org/go/GO:0042169"
-  v19 hypernym "http://identifiers.org/go/GO:0017124",
-               "http://identifiers.org/go/GO:0005070",
-               "http://identifiers.org/go/GO:0005068"
-  v21 hypernym "http://identifiers.org/go/GO:0051425",
-               "http://identifiers.org/go/GO:0042169"
-  v22 hypernym "http://identifiers.org/go/GO:0017124",
-               "http://identifiers.org/go/GO:0005070"
-  v24 hypernym "http://identifiers.org/go/GO:0051425",
-               "http://identifiers.org/go/GO:0042169"
-  v25 hypernym "http://identifiers.org/go/GO:0030845"
-end
-
-Kholodenko1999_-_EGFR_signaling is "Kholodenko1999 - EGFR signaling"
-
-Kholodenko1999_-_EGFR_signaling model_entity_is "http://identifiers.org/biomodels.db/MODEL6624193277"
-Kholodenko1999_-_EGFR_signaling model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000048"
-Kholodenko1999_-_EGFR_signaling description "http://identifiers.org/pubmed/10514507"
-Kholodenko1999_-_EGFR_signaling model_entity_is "http://identifiers.org/biomodels.db/MODEL6624193277"
-Kholodenko1999_-_EGFR_signaling model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000048"
-Kholodenko1999_-_EGFR_signaling container "http://identifiers.org/go/GO:0007173"
-Kholodenko1999_-_EGFR_signaling taxon "http://identifiers.org/taxonomy/10116"
diff --git a/BioModelsRAG/data/BIOMD0000000049.txt b/BioModelsRAG/data/BIOMD0000000049.txt
deleted file mode 100644
index 04cfa50ae8f2d36fdbfb470421d713d0f6733363..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000049.txt
+++ /dev/null
@@ -1,1102 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Sasagawa2005_MAPK()
-
-  // Compartments and Species:
-  compartment compartment_, c1;
-  species EGFR in compartment_, L_EGFR in compartment_, L_EGFR_dimer in compartment_;
-  species SOS in c1, L_dpEGFR in compartment_, pSOS in c1, SOS_Grb2 in c1;
-  species Grb2 in c1, Dok in c1, pDok in c1, Crk in c1, FRS2 in c1, Shc in c1;
-  species pSOS_Grb2 in c1, Rap1_GDP in c1, MEK in c1, MKP3 in c1, pShc_dpEGFR in c1;
-  species dpEGFR_c_Cbl in c1, B_Raf_Rap1_GTP in c1, pShc_dpEGFR_c_Cbl in c1;
-  species pFRS2_dpEGFR_c_Cbl in c1, Shc_dpEGFR in c1, c_Cbl in c1, RasGAP in c1;
-  species c_Raf in c1, B_Raf in c1, ERK in c1, PP2A in c1, Ras_GDP in c1;
-  species Rap1GAP in c1, C3G in c1, NGFR in compartment_, pShc in c1, pFRS2_dpEGFR in c1;
-  species pTrkA_endo in c1, MEK_ERK in c1, pMEK_ERK in c1, FRS2_dpEGFR_c_Cbl_ubiq in c1;
-  species Crk_C3G_pFRS2_dpEGFR_c_Cbl in c1, pShc_dpEGFR_c_Cbl_ubiq in c1;
-  species Crk_C3G_pFRS2_dpEGFR in c1, Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq in c1;
-  species Grb2_SOS_pShc_dpEGFR_c_Cbl in c1, Shc_dpEGFR_c_Cbl_ubiq in c1, dpEGFR_c_Cbl_ubiq in c1;
-  species proteosome in c1, Grb2_SOS_pShc in c1, Shc_dpEGFR_c_Cbl in c1, Grb2_SOS_pShc_dpEGFR in c1;
-  species pFRS2 in c1, FRS2_dpEGFR in c1, pDok_RasGAP in c1, pMEK in c1, FRS2_dpEGFR_c_Cbl in c1;
-  species pFRS2_dpEGFR_c_Cbl_ubiq in c1, Ras_GTP in c1, Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq in c1;
-  species c_Raf_Ras_GTP in c1, B_Raf_Ras_GTP in c1, ppMEK in c1, ppERK in c1;
-  species pTrkA in compartment_, Crk_C3G in c1, Rap1_GTP in c1, L_NGFR in compartment_;
-  species ppMEK_ERK in c1, dppERK in c1, Shc_pTrkA in c1, Shc_pTrkA_endo in c1;
-  species pShc_pTrkA in c1, pFRS2_pTrkA in c1, FRS2_pTrkA in c1, pShc_pTrkA_endo in c1;
-  species FRS2_pTrkA_endo in c1, pFRS2_pTrkA_endo in c1, Crk_C3G_pFRS2_pTrkA_endo in c1;
-  species Grb2_SOS_pShc_pTrkA in c1, Crk_C3G_pFRS2_pTrkA in c1, Grb2_SOS_pShc_pTrkA_endo in c1;
-  species c_Raf_Ras_GTP_MEK in c1, c_Raf_Ras_GTP_pMEK in c1, c_Raf_Ras_GTP_MEK_ERK in c1;
-  species c_Raf_Ras_GTP_pMEK_ERK in c1, B_Raf_Ras_GTP_MEK in c1, B_Raf_Ras_GTP_pMEK in c1;
-  species B_Raf_Ras_GTP_MEK_ERK in c1, B_Raf_Ras_GTP_pMEK_ERK in c1, B_Raf_Rap1_GTP_MEK in c1;
-  species B_Raf_Rap1_GTP_pMEK in c1, B_Raf_Rap1_GTP_MEK_ERK in c1, B_Raf_Rap1_GTP_pMEK_ERK in c1;
-  species ppERK_MKP3 in c1, dppERK_MKP3 in c1, $pro_TrkA in c1, $NGF in compartment_;
-  species $EGF in compartment_, $pro_EGFR in c1, $degradation in c1;
-
-  // Reactions:
-  re1: $pro_EGFR -> EGFR; compartment_*(re1_re1_k1*pro_EGFR - re1_re1_k2*EGFR);
-  re2: $EGF + EGFR -> L_EGFR; compartment_*(re2_re2_k1*EGF*EGFR - re2_re2_k2*L_EGFR);
-  re8: 2 L_EGFR -> L_EGFR_dimer; compartment_*(re8_re8_k1*L_EGFR*L_EGFR - re8_re8_k2*L_EGFR_dimer);
-  J3: SOS + Grb2 -> SOS_Grb2; c1*(J3_J3_k1*SOS*Grb2 - J3_J3_k2*SOS_Grb2);
-  J4: Grb2 + pSOS -> pSOS_Grb2; c1*(J4_J4_k1*Grb2*pSOS - J4_J4_k2*pSOS_Grb2);
-  J5: L_EGFR_dimer -> L_dpEGFR; compartment_*(J5_J5_k1*L_EGFR_dimer - J5_J5_k2*L_dpEGFR);
-  J6: L_dpEGFR + c_Cbl -> dpEGFR_c_Cbl; c1*(J6_J6_k1*L_dpEGFR*c_Cbl - J6_J6_k2*dpEGFR_c_Cbl);
-  J7: L_dpEGFR + pShc -> pShc_dpEGFR; c1*(J7_J7_k1*L_dpEGFR*pShc - J7_J7_k2*pShc_dpEGFR);
-  J8: pDok -> Dok; c1*(J8_J8_k1*pDok - J8_J8_k2*Dok);
-  J9: c_Cbl + pShc_dpEGFR -> pShc_dpEGFR_c_Cbl; c1*(J9_J9_k1*c_Cbl*pShc_dpEGFR - J9_J9_k2*pShc_dpEGFR_c_Cbl);
-  J10: pSOS => SOS; c1*J10_J10_k*pSOS;
-  J11: pSOS_Grb2 => SOS_Grb2; c1*J11_J11_k*pSOS_Grb2;
-  J12: L_dpEGFR + Shc -> Shc_dpEGFR; c1*(J12_J12_k1*L_dpEGFR*Shc - J12_J12_k2*Shc_dpEGFR);
-  J13: Shc_dpEGFR => pShc_dpEGFR; c1*J13_J13_k*Shc_dpEGFR;
-  J14: dpEGFR_c_Cbl => dpEGFR_c_Cbl_ubiq; c1*J14_J14_k*dpEGFR_c_Cbl;
-  J15: dpEGFR_c_Cbl_ubiq => proteosome + c_Cbl; c1*J15_J15_k*dpEGFR_c_Cbl_ubiq;
-  J16: c_Cbl + Shc_dpEGFR -> Shc_dpEGFR_c_Cbl; c1*(J16_J16_k1*c_Cbl*Shc_dpEGFR - J16_J16_k2*Shc_dpEGFR_c_Cbl);
-  J17: Shc_dpEGFR_c_Cbl => Shc_dpEGFR_c_Cbl_ubiq; c1*J17_J17_k*Shc_dpEGFR_c_Cbl;
-  J18: Shc_dpEGFR_c_Cbl_ubiq => proteosome + c_Cbl + Shc; c1*J18_J18_k*Shc_dpEGFR_c_Cbl_ubiq;
-  J19: pShc_dpEGFR_c_Cbl => pShc_dpEGFR_c_Cbl_ubiq; c1*J19_J19_k*pShc_dpEGFR_c_Cbl;
-  J20: pShc_dpEGFR_c_Cbl_ubiq => proteosome + c_Cbl + pShc; c1*J20_J20_k*pShc_dpEGFR_c_Cbl_ubiq;
-  J21: Shc_dpEGFR_c_Cbl => pShc_dpEGFR_c_Cbl; c1*J21_J21_k*Shc_dpEGFR_c_Cbl;
-  J22: pShc + SOS_Grb2 -> Grb2_SOS_pShc; c1*(J22_J22_k1*pShc*SOS_Grb2 - J22_J22_k2*Grb2_SOS_pShc);
-  J23: L_dpEGFR + Grb2_SOS_pShc -> Grb2_SOS_pShc_dpEGFR; c1*(J23_J23_k1*L_dpEGFR*Grb2_SOS_pShc - J23_J23_k2*Grb2_SOS_pShc_dpEGFR);
-  J24: pShc_dpEGFR + SOS_Grb2 -> Grb2_SOS_pShc_dpEGFR; c1*(J24_J24_k1*pShc_dpEGFR*SOS_Grb2 - J24_J24_k2*Grb2_SOS_pShc_dpEGFR);
-  J25: c_Cbl + Grb2_SOS_pShc_dpEGFR -> Grb2_SOS_pShc_dpEGFR_c_Cbl; c1*(J25_J25_k1*c_Cbl*Grb2_SOS_pShc_dpEGFR - J25_J25_k2*Grb2_SOS_pShc_dpEGFR_c_Cbl);
-  J27: dpEGFR_c_Cbl + Grb2_SOS_pShc -> Grb2_SOS_pShc_dpEGFR_c_Cbl; c1*(J27_J27_k1*dpEGFR_c_Cbl*Grb2_SOS_pShc - J27_J27_k2*Grb2_SOS_pShc_dpEGFR_c_Cbl);
-  J28: Grb2_SOS_pShc_dpEGFR_c_Cbl => Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq; c1*J28_J28_k*Grb2_SOS_pShc_dpEGFR_c_Cbl;
-  J29: Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq => proteosome + c_Cbl + Grb2_SOS_pShc; c1*J29_J29_k*Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq;
-  J30: Grb2_SOS_pShc => Shc + SOS_Grb2; J30_J30_k*Grb2_SOS_pShc;
-  J31: Dok => pDok; c1*(J31_J31_Vmax*Dok*(L_dpEGFR + Shc_dpEGFR + pShc_dpEGFR + Grb2_SOS_pShc_dpEGFR + dpEGFR_c_Cbl + Shc_dpEGFR_c_Cbl + pShc_dpEGFR_c_Cbl + Grb2_SOS_pShc_dpEGFR_c_Cbl + FRS2_dpEGFR + pFRS2_dpEGFR + Crk_C3G_pFRS2_dpEGFR + FRS2_dpEGFR_c_Cbl + Crk_C3G_pFRS2_dpEGFR_c_Cbl)/(J31_J31_Km1 + Dok));
-  J32: pShc => Shc; c1*J32_J32_k*pShc;
-  J33: pFRS2 => FRS2; c1*J33_J33_k*pFRS2;
-  J34: Crk + C3G -> Crk_C3G; c1*(J34_J34_k1*Crk*C3G - J34_J34_k2*Crk_C3G);
-  J35: L_dpEGFR + FRS2 -> FRS2_dpEGFR; c1*(J35_J35_k1*L_dpEGFR*FRS2 - J35_J35_k2*FRS2_dpEGFR);
-  J36: L_dpEGFR + pFRS2 -> pFRS2_dpEGFR; c1*(J36_J36_k1*L_dpEGFR*pFRS2 - J36_J36_k2*pFRS2_dpEGFR);
-  J37: FRS2_dpEGFR => pFRS2_dpEGFR; c1*J37_J37_k*FRS2_dpEGFR;
-  J38: pFRS2_dpEGFR + Crk_C3G -> Crk_C3G_pFRS2_dpEGFR; c1*(J38_J38_k1*pFRS2_dpEGFR*Crk_C3G - J38_J38_k2*Crk_C3G_pFRS2_dpEGFR);
-  J39: FRS2_dpEGFR + c_Cbl -> FRS2_dpEGFR_c_Cbl; c1*(J39_J39_k1*FRS2_dpEGFR*c_Cbl - J39_J39_k2*FRS2_dpEGFR_c_Cbl);
-  J40: c_Cbl + pFRS2_dpEGFR -> pFRS2_dpEGFR_c_Cbl; c1*(J40_J40_k1*c_Cbl*pFRS2_dpEGFR - J40_J40_k2*pFRS2_dpEGFR_c_Cbl);
-  J41: pFRS2_dpEGFR_c_Cbl => pFRS2_dpEGFR_c_Cbl_ubiq; c1*J41_J41_k*pFRS2_dpEGFR_c_Cbl;
-  J42: FRS2_dpEGFR_c_Cbl => FRS2_dpEGFR_c_Cbl_ubiq; c1*J42_J42_k*FRS2_dpEGFR_c_Cbl;
-  J43: FRS2_dpEGFR_c_Cbl => pFRS2_dpEGFR_c_Cbl; c1*J43_J43_k*FRS2_dpEGFR_c_Cbl;
-  J44: pFRS2_dpEGFR_c_Cbl + Crk_C3G -> Crk_C3G_pFRS2_dpEGFR_c_Cbl; c1*(J44_J44_k1*pFRS2_dpEGFR_c_Cbl*Crk_C3G - J44_J44_k2*Crk_C3G_pFRS2_dpEGFR_c_Cbl);
-  J45: Crk_C3G_pFRS2_dpEGFR_c_Cbl => Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq; c1*J45_J45_k*Crk_C3G_pFRS2_dpEGFR_c_Cbl;
-  J46: FRS2_dpEGFR_c_Cbl_ubiq => proteosome + c_Cbl + FRS2; c1*J46_J46_k*FRS2_dpEGFR_c_Cbl_ubiq;
-  J47: pFRS2_dpEGFR_c_Cbl_ubiq => proteosome + c_Cbl + pFRS2; c1*J47_J47_k*pFRS2_dpEGFR_c_Cbl_ubiq;
-  J49: pDok + RasGAP -> pDok_RasGAP; c1*(J49_J49_k1*pDok*RasGAP - J49_J49_k2*pDok_RasGAP);
-  J50: SOS_Grb2 => pSOS_Grb2; c1*(J50_J50_Vmax*SOS_Grb2*dppERK/(J50_J50_Km1 + SOS_Grb2));
-  J51: SOS => pSOS; c1*(J51_J51_Vmax*SOS*dppERK/(J51_J51_Km1 + SOS));
-  J52: c_Raf + Ras_GTP -> c_Raf_Ras_GTP; c1*(J52_J52_k1*c_Raf*Ras_GTP - J52_J52_k2*c_Raf_Ras_GTP);
-  J53: Rap1_GTP + B_Raf -> B_Raf_Rap1_GTP; c1*(J53_J53_k1*Rap1_GTP*B_Raf - J53_J53_k2*B_Raf_Rap1_GTP);
-  J54: Ras_GTP + B_Raf -> B_Raf_Ras_GTP; c1*(J54_J54_k1*Ras_GTP*B_Raf - J54_J54_k2*B_Raf_Ras_GTP);
-  J57: ppMEK => pMEK; J57_J57_Vmax*ppMEK*PP2A/(J57_J57_Km1 + ppMEK);
-  J58: pMEK => MEK; c1*(J58_J58_Vmax*pMEK*PP2A/(J58_J58_Km1 + pMEK));
-  J61: ppMEK_ERK => pMEK_ERK; c1*(J61_J61_Vmax*ppMEK_ERK*PP2A/(J61_J61_Km1 + ppMEK_ERK));
-  J62: pMEK_ERK => MEK_ERK; c1*(J62_J62_Vmax*pMEK_ERK*PP2A/(J62_J62_Km1 + pMEK_ERK));
-  J63: 2 ppERK -> dppERK; c1*(J63_J63_k1*ppERK*ppERK - J63_J63_k2*dppERK);
-  J66: Ras_GTP => Ras_GDP; c1*J66_J66_k*Ras_GTP;
-  J67: Rap1_GTP => Rap1_GDP; c1*J67_J67_k*Rap1_GTP;
-  J68: Rap1_GDP => Rap1_GTP; c1*(J68_J68_Vmax*Rap1_GDP*(Crk_C3G_pFRS2_dpEGFR + Crk_C3G_pFRS2_dpEGFR_c_Cbl + Crk_C3G_pFRS2_pTrkA_endo)/(J68_J68_Km1 + Rap1_GDP));
-  J69: Ras_GDP => Ras_GTP; c1*(J69_J69_Vmax*Ras_GDP*(Grb2_SOS_pShc_dpEGFR + Grb2_SOS_pShc_dpEGFR_c_Cbl + Grb2_SOS_pShc_pTrkA)/(J69_J69_Km1 + Ras_GDP));
-  J70: $NGF + NGFR -> L_NGFR; compartment_*(J70_J70_k1*NGF*NGFR - J70_J70_k2*L_NGFR);
-  J71: L_NGFR => pTrkA; compartment_*J71_J71_k*L_NGFR;
-  J72: pTrkA => pTrkA_endo; c1*J72_J72_k*pTrkA;
-  J73: pTrkA_endo => $degradation; c1*J73_J73_k*pTrkA_endo;
-  J74: pTrkA => $degradation; c1*J74_J74_k*pTrkA;
-  J75: Shc + pTrkA -> Shc_pTrkA; c1*(J75_J75_k1*Shc*pTrkA - J75_J75_k2*Shc_pTrkA);
-  J76: pShc + pTrkA -> pShc_pTrkA; c1*(J76_J76_k1*pShc*pTrkA - J76_J76_k2*pShc_pTrkA);
-  J77: FRS2 + pTrkA -> FRS2_pTrkA; c1*(J77_J77_k1*FRS2*pTrkA - J77_J77_k2*FRS2_pTrkA);
-  J78: pFRS2 + pTrkA -> pFRS2_pTrkA; c1*(J78_J78_k1*pFRS2*pTrkA - J78_J78_k2*pFRS2_pTrkA);
-  J79: pTrkA_endo + Shc -> Shc_pTrkA_endo; c1*(J79_J79_k1*pTrkA_endo*Shc - J79_J79_k2*Shc_pTrkA_endo);
-  J80: pTrkA_endo + pShc -> pShc_pTrkA_endo; c1*(J80_J80_k1*pTrkA_endo*pShc - J80_J80_k2*pShc_pTrkA_endo);
-  J81: Shc_pTrkA_endo => pShc_pTrkA_endo; c1*J81_J81_k*Shc_pTrkA_endo;
-  J82: Shc_pTrkA => pShc_pTrkA; c1*J82_J82_k*Shc_pTrkA;
-  J83: FRS2_pTrkA => pFRS2_pTrkA; c1*J83_J83_k*FRS2_pTrkA;
-  J84: pTrkA_endo + FRS2 -> FRS2_pTrkA_endo; c1*(J84_J84_k1*pTrkA_endo*FRS2 - J84_J84_k2*FRS2_pTrkA_endo);
-  J85: pTrkA_endo + pFRS2 -> pFRS2_pTrkA_endo; c1*(J85_J85_k1*pTrkA_endo*pFRS2 - J85_J85_k2*pFRS2_pTrkA_endo);
-  J86: FRS2_pTrkA_endo => pFRS2_pTrkA_endo; c1*J86_J86_k*FRS2_pTrkA_endo;
-  J87: FRS2_pTrkA => $degradation + FRS2; c1*J87_J87_k*FRS2_pTrkA;
-  J88: pFRS2_pTrkA => $degradation + pFRS2; c1*J88_J88_k*pFRS2_pTrkA;
-  J89: Shc_pTrkA => $degradation + Shc; c1*J89_J89_k*Shc_pTrkA;
-  J90: pShc_pTrkA => $degradation + pShc; c1*J90_J90_k*pShc_pTrkA;
-  J92: FRS2_pTrkA_endo => $degradation + FRS2; c1*J92_J92_k*FRS2_pTrkA_endo;
-  J93: Shc_pTrkA_endo => $degradation + Shc; c1*J93_J93_k*Shc_pTrkA_endo;
-  J94: pShc_pTrkA_endo => $degradation + pShc; c1*J94_J94_k*pShc_pTrkA_endo;
-  J95: SOS_Grb2 + pShc_pTrkA_endo -> Grb2_SOS_pShc_pTrkA_endo; c1*(J95_J95_k1*SOS_Grb2*pShc_pTrkA_endo - J95_J95_k2*Grb2_SOS_pShc_pTrkA_endo);
-  J96: SOS_Grb2 + pShc_pTrkA -> Grb2_SOS_pShc_pTrkA; c1*(J96_J96_k1*SOS_Grb2*pShc_pTrkA - J96_J96_k2*Grb2_SOS_pShc_pTrkA);
-  J97: Grb2_SOS_pShc_pTrkA => Grb2_SOS_pShc_pTrkA_endo; c1*J97_J97_k*Grb2_SOS_pShc_pTrkA;
-  J98: Crk_C3G_pFRS2_pTrkA => Crk_C3G_pFRS2_pTrkA_endo; c1*J98_J98_k*Crk_C3G_pFRS2_pTrkA;
-  J99: pFRS2_pTrkA => pFRS2_pTrkA_endo; c1*J99_J99_k*pFRS2_pTrkA;
-  J100: FRS2_pTrkA => FRS2_pTrkA_endo; c1*J100_J100_k*FRS2_pTrkA;
-  J101: pShc_pTrkA => pShc_pTrkA_endo; c1*J101_J101_k*pShc_pTrkA;
-  J102: Shc_pTrkA => Shc_pTrkA_endo; c1*J102_J102_k*Shc_pTrkA;
-  J103: Crk_C3G + pFRS2_pTrkA -> Crk_C3G_pFRS2_pTrkA; c1*(J103_J103_k1*Crk_C3G*pFRS2_pTrkA - J103_J103_k2*Crk_C3G_pFRS2_pTrkA);
-  J104: Crk_C3G + pFRS2_pTrkA_endo -> Crk_C3G_pFRS2_pTrkA_endo; c1*(J104_J104_k1*Crk_C3G*pFRS2_pTrkA_endo - J104_J104_k2*Crk_C3G_pFRS2_pTrkA_endo);
-  J105: Grb2_SOS_pShc + pTrkA -> Grb2_SOS_pShc_pTrkA; c1*(J105_J105_k1*Grb2_SOS_pShc*pTrkA - J105_J105_k2*Grb2_SOS_pShc_pTrkA);
-  J106: Grb2_SOS_pShc + pTrkA_endo -> Grb2_SOS_pShc_pTrkA_endo; c1*(J106_J106_k1*Grb2_SOS_pShc*pTrkA_endo - J106_J106_k2*Grb2_SOS_pShc_pTrkA_endo);
-  J107: Crk_C3G_pFRS2_pTrkA => $degradation + pFRS2 + Crk_C3G; c1*J107_J107_k*Crk_C3G_pFRS2_pTrkA;
-  J108: Crk_C3G_pFRS2_pTrkA_endo => $degradation + Crk_C3G + pFRS2; c1*J108_J108_k*Crk_C3G_pFRS2_pTrkA_endo;
-  J109: Grb2_SOS_pShc_pTrkA => $degradation + Grb2_SOS_pShc; c1*J109_J109_k*Grb2_SOS_pShc_pTrkA;
-  J110: Grb2_SOS_pShc_pTrkA_endo => $degradation + Grb2_SOS_pShc; c1*J110_J110_k*Grb2_SOS_pShc_pTrkA_endo;
-  J112: pFRS2_pTrkA_endo => $degradation + pFRS2; J112_J112_k*pFRS2_pTrkA_endo;
-  J113: $pro_TrkA -> NGFR; compartment_*(J113_J113_k1*pro_TrkA - J113_J113_k2*NGFR);
-  J115: Shc + dpEGFR_c_Cbl -> Shc_dpEGFR_c_Cbl; c1*(J115_J115_k1*Shc*dpEGFR_c_Cbl - J115_J115_k2*Shc_dpEGFR_c_Cbl);
-  J116: dpEGFR_c_Cbl + pShc -> pShc_dpEGFR_c_Cbl; c1*(J116_J116_k1*dpEGFR_c_Cbl*pShc - J116_J116_k2*pShc_dpEGFR_c_Cbl);
-  J117: pShc_dpEGFR_c_Cbl + SOS_Grb2 -> Grb2_SOS_pShc_dpEGFR_c_Cbl; c1*(J117_J117_k1*pShc_dpEGFR_c_Cbl*SOS_Grb2 - J117_J117_k2*Grb2_SOS_pShc_dpEGFR_c_Cbl);
-  J119: c_Cbl + Crk_C3G_pFRS2_dpEGFR -> Crk_C3G_pFRS2_dpEGFR_c_Cbl; c1*(J119_J119_k1*c_Cbl*Crk_C3G_pFRS2_dpEGFR - J119_J119_k2*Crk_C3G_pFRS2_dpEGFR_c_Cbl);
-  J118: dpEGFR_c_Cbl + FRS2 -> FRS2_dpEGFR_c_Cbl; c1*(J118_J118_k1*dpEGFR_c_Cbl*FRS2 - J118_J118_k2*FRS2_dpEGFR_c_Cbl);
-  J120: dpEGFR_c_Cbl + pFRS2 -> pFRS2_dpEGFR_c_Cbl; c1*(J120_J120_k1*dpEGFR_c_Cbl*pFRS2 - J120_J120_k2*pFRS2_dpEGFR_c_Cbl);
-  J121: Ras_GTP => Ras_GDP; c1*(J121_J121_Vmax*Ras_GTP*pDok_RasGAP/(J121_J121_Km1 + Ras_GTP));
-  J122: Rap1_GTP => Rap1_GDP; c1*(J122_J122_Vmax*Rap1_GTP*Rap1GAP/(J122_J122_Km1 + Rap1_GTP));
-  J123: Dok => pDok; c1*(J123_J123_Vmax*Dok*(pTrkA + Shc_pTrkA + pShc_pTrkA + Grb2_SOS_pShc_pTrkA + FRS2_pTrkA + pFRS2_pTrkA + Crk_C3G_pFRS2_pTrkA)/(J123_J123_Km1 + Dok));
-  J124: Grb2_SOS_pShc => pShc + pSOS_Grb2; c1*(J124_J124_Vmax*Grb2_SOS_pShc*dppERK/(J124_J124_Km1 + Grb2_SOS_pShc));
-  J133: ERK + MEK -> MEK_ERK; c1*(J133_J133_k1*ERK*MEK - J133_J133_k2*MEK_ERK);
-  J134: ERK + pMEK -> pMEK_ERK; c1*(J134_J134_k1*ERK*pMEK - J134_J134_k2*pMEK_ERK);
-  J135: ERK + ppMEK -> ppMEK_ERK; c1*(J135_J135_k1*ERK*ppMEK - J135_J135_k2*ppMEK_ERK);
-  J136: ppMEK_ERK => ppERK + ppMEK; c1*J136_J136_k*ppMEK_ERK;
-  J137: c_Raf_Ras_GTP => c_Raf + Ras_GDP; c1*(J137_J137_Vmax*c_Raf_Ras_GTP*pDok_RasGAP/(J137_J137_Km1 + c_Raf_Ras_GTP));
-  J138: B_Raf_Ras_GTP => B_Raf + Ras_GDP; c1*(J138_J138_Vmax*B_Raf_Ras_GTP*pDok_RasGAP/(J138_J138_Km1 + B_Raf_Ras_GTP));
-  J139: B_Raf_Rap1_GTP => B_Raf + Rap1_GDP; c1*(J139_J139_Vmax*B_Raf_Rap1_GTP*Rap1GAP/(J139_J139_Km1 + B_Raf_Rap1_GTP));
-  J140: c_Raf_Ras_GTP + MEK => c_Raf_Ras_GTP_MEK; c1*(J140_J140_k1*c_Raf_Ras_GTP*MEK - J140_J140_k2*c_Raf_Ras_GTP_MEK);
-  J141: c_Raf_Ras_GTP + pMEK -> c_Raf_Ras_GTP_pMEK; c1*(J141_J141_k1*c_Raf_Ras_GTP*pMEK - J141_J141_k2*c_Raf_Ras_GTP_pMEK);
-  J142: c_Raf_Ras_GTP + MEK_ERK -> c_Raf_Ras_GTP_MEK_ERK; c1*(J142_J142_k1*c_Raf_Ras_GTP*MEK_ERK - J142_J142_k2*c_Raf_Ras_GTP_MEK_ERK);
-  J143: c_Raf_Ras_GTP + pMEK_ERK -> c_Raf_Ras_GTP_pMEK_ERK; c1*(J143_J143_k1*c_Raf_Ras_GTP*pMEK_ERK - J143_J143_k2*c_Raf_Ras_GTP_pMEK_ERK);
-  J144: B_Raf_Ras_GTP + MEK -> B_Raf_Ras_GTP_MEK; c1*(J144_J144_k1*B_Raf_Ras_GTP*MEK - J144_J144_k2*B_Raf_Ras_GTP_MEK);
-  J145: B_Raf_Ras_GTP + pMEK -> B_Raf_Ras_GTP_pMEK; c1*(J145_J145_k1*B_Raf_Ras_GTP*pMEK - J145_J145_k2*B_Raf_Ras_GTP_pMEK);
-  J146: B_Raf_Ras_GTP + MEK_ERK -> B_Raf_Ras_GTP_MEK_ERK; c1*(J146_J146_k1*B_Raf_Ras_GTP*MEK_ERK - J146_J146_k2*B_Raf_Ras_GTP_MEK_ERK);
-  J147: B_Raf_Ras_GTP + pMEK_ERK -> B_Raf_Ras_GTP_pMEK_ERK; c1*(J147_J147_k1*B_Raf_Ras_GTP*pMEK_ERK - J147_J147_k2*B_Raf_Ras_GTP_pMEK_ERK);
-  J148: B_Raf_Rap1_GTP + MEK -> B_Raf_Rap1_GTP_MEK; c1*(J148_J148_k1*B_Raf_Rap1_GTP*MEK - J148_J148_k2*B_Raf_Rap1_GTP_MEK);
-  J149: B_Raf_Rap1_GTP + pMEK -> B_Raf_Rap1_GTP_pMEK; c1*(J149_J149_k1*B_Raf_Rap1_GTP*pMEK - J149_J149_k2*B_Raf_Rap1_GTP_pMEK);
-  J150: B_Raf_Rap1_GTP + MEK_ERK -> B_Raf_Rap1_GTP_MEK_ERK; c1*(J150_J150_k1*B_Raf_Rap1_GTP*MEK_ERK - J150_J150_k2*B_Raf_Rap1_GTP_MEK_ERK);
-  J151: B_Raf_Rap1_GTP + pMEK_ERK -> B_Raf_Rap1_GTP_pMEK_ERK; c1*(J151_J151_k1*B_Raf_Rap1_GTP*pMEK_ERK - J151_J151_k2*B_Raf_Rap1_GTP_pMEK_ERK);
-  J152: c_Raf_Ras_GTP_MEK => c_Raf_Ras_GTP + pMEK; c1*J152_J152_k*c_Raf_Ras_GTP_MEK;
-  J153: c_Raf_Ras_GTP_pMEK => c_Raf_Ras_GTP + ppMEK; c1*J153_J153_k*c_Raf_Ras_GTP_pMEK;
-  J154: c_Raf_Ras_GTP_MEK_ERK => c_Raf_Ras_GTP + pMEK_ERK; c1*J154_J154_k*c_Raf_Ras_GTP_MEK_ERK;
-  J155: c_Raf_Ras_GTP_pMEK_ERK => c_Raf_Ras_GTP + ppMEK_ERK; c1*J155_J155_k*c_Raf_Ras_GTP_pMEK_ERK;
-  J156: B_Raf_Ras_GTP_MEK => B_Raf_Ras_GTP + pMEK; c1*J156_J156_k*B_Raf_Ras_GTP_MEK;
-  J157: B_Raf_Ras_GTP_pMEK => B_Raf_Ras_GTP + ppMEK; c1*J157_J157_k*B_Raf_Ras_GTP_pMEK;
-  J158: B_Raf_Ras_GTP_MEK_ERK => B_Raf_Ras_GTP + pMEK_ERK; c1*J158_J158_k*B_Raf_Ras_GTP_MEK_ERK;
-  J159: B_Raf_Ras_GTP_pMEK_ERK => B_Raf_Ras_GTP + ppMEK_ERK; c1*J159_J159_k*B_Raf_Ras_GTP_pMEK_ERK;
-  J160: B_Raf_Rap1_GTP_MEK => B_Raf_Rap1_GTP + pMEK; c1*J160_J160_k*B_Raf_Rap1_GTP_MEK;
-  J161: B_Raf_Rap1_GTP_pMEK => B_Raf_Rap1_GTP + ppMEK; c1*J161_J161_k*B_Raf_Rap1_GTP_pMEK;
-  J162: B_Raf_Rap1_GTP_MEK_ERK => B_Raf_Rap1_GTP + pMEK_ERK; c1*J162_J162_k*B_Raf_Rap1_GTP_MEK_ERK;
-  J163: B_Raf_Rap1_GTP_pMEK_ERK => B_Raf_Rap1_GTP + ppMEK_ERK; c1*J163_J163_k*B_Raf_Rap1_GTP_pMEK_ERK;
-  J164: Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq => c_Cbl + pFRS2 + Crk_C3G; c1*J164_J164_k*Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq;
-  J165: MKP3 + dppERK => dppERK_MKP3; c1*(J165_J165_k1*MKP3*dppERK - J165_J165_k2*dppERK_MKP3);
-  J166: MKP3 + ppERK -> ppERK_MKP3; c1*(J166_J166_k1*MKP3*ppERK - J166_J166_k2*ppERK_MKP3);
-  J167: ppERK_MKP3 => ERK + MKP3; c1*J167_J167_k*ppERK_MKP3;
-  J168: dppERK_MKP3 => ppERK + ERK + MKP3; c1*J168_J168_k*dppERK_MKP3;
-
-  // Species initializations:
-  EGFR = 0.3;
-  L_EGFR = 0;
-  L_EGFR_dimer = 0;
-  SOS = 0.1;
-  L_dpEGFR = 0;
-  pSOS = 0;
-  SOS_Grb2 = 0;
-  Grb2 = 1;
-  Dok = 0.3;
-  pDok = 0;
-  Crk = 1;
-  FRS2 = 1;
-  Shc = 1;
-  pSOS_Grb2 = 0;
-  Rap1_GDP = 0.2;
-  MEK = 0.68;
-  MKP3 = 0.018;
-  pShc_dpEGFR = 0;
-  dpEGFR_c_Cbl = 0;
-  B_Raf_Rap1_GTP = 0;
-  pShc_dpEGFR_c_Cbl = 0;
-  pFRS2_dpEGFR_c_Cbl = 0;
-  Shc_dpEGFR = 0;
-  c_Cbl = 0.5;
-  RasGAP = 0.1;
-  c_Raf = 0.5;
-  B_Raf = 0.2;
-  ERK = 0.26;
-  PP2A = 0.24;
-  Ras_GDP = 0.1;
-  Rap1GAP = 0.012;
-  C3G = 0.5;
-  NGFR = 0.061894;
-  pShc = 0;
-  pFRS2_dpEGFR = 0;
-  pTrkA_endo = 0;
-  MEK_ERK = 0;
-  pMEK_ERK = 0;
-  FRS2_dpEGFR_c_Cbl_ubiq = 0;
-  Crk_C3G_pFRS2_dpEGFR_c_Cbl = 0;
-  pShc_dpEGFR_c_Cbl_ubiq = 0;
-  Crk_C3G_pFRS2_dpEGFR = 0;
-  Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq = 0;
-  Grb2_SOS_pShc_dpEGFR_c_Cbl = 0;
-  Shc_dpEGFR_c_Cbl_ubiq = 0;
-  dpEGFR_c_Cbl_ubiq = 0;
-  proteosome = 0;
-  Grb2_SOS_pShc = 0;
-  Shc_dpEGFR_c_Cbl = 0;
-  Grb2_SOS_pShc_dpEGFR = 0;
-  pFRS2 = 0;
-  FRS2_dpEGFR = 0;
-  pDok_RasGAP = 0;
-  pMEK = 0;
-  FRS2_dpEGFR_c_Cbl = 0;
-  pFRS2_dpEGFR_c_Cbl_ubiq = 0;
-  Ras_GTP = 0;
-  Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq = 0;
-  c_Raf_Ras_GTP = 0;
-  B_Raf_Ras_GTP = 0;
-  ppMEK = 0;
-  ppERK = 0;
-  pTrkA = 0;
-  Crk_C3G = 0;
-  Rap1_GTP = 0;
-  L_NGFR = 0;
-  ppMEK_ERK = 0;
-  dppERK = 0;
-  Shc_pTrkA = 0;
-  Shc_pTrkA_endo = 0;
-  pShc_pTrkA = 0;
-  pFRS2_pTrkA = 0;
-  FRS2_pTrkA = 0;
-  pShc_pTrkA_endo = 0;
-  FRS2_pTrkA_endo = 0;
-  pFRS2_pTrkA_endo = 0;
-  Crk_C3G_pFRS2_pTrkA_endo = 0;
-  Grb2_SOS_pShc_pTrkA = 0;
-  Crk_C3G_pFRS2_pTrkA = 0;
-  Grb2_SOS_pShc_pTrkA_endo = 0;
-  c_Raf_Ras_GTP_MEK = 0;
-  c_Raf_Ras_GTP_pMEK = 0;
-  c_Raf_Ras_GTP_MEK_ERK = 0;
-  c_Raf_Ras_GTP_pMEK_ERK = 0;
-  B_Raf_Ras_GTP_MEK = 0;
-  B_Raf_Ras_GTP_pMEK = 0;
-  B_Raf_Ras_GTP_MEK_ERK = 0;
-  B_Raf_Ras_GTP_pMEK_ERK = 0;
-  B_Raf_Rap1_GTP_MEK = 0;
-  B_Raf_Rap1_GTP_pMEK = 0;
-  B_Raf_Rap1_GTP_MEK_ERK = 0;
-  B_Raf_Rap1_GTP_pMEK_ERK = 0;
-  ppERK_MKP3 = 0;
-  dppERK_MKP3 = 0;
-  pro_TrkA = 0.020631;
-  NGF = 0;
-  EGF = 0.001613;
-  pro_EGFR = 0.3;
-  degradation = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-  c1 = 1;
-
-  // Variable initializations:
-  re1_re1_k1 = 0.0001;
-  re1_re1_k2 = 0.0001;
-  re2_re2_k1 = 2.2833;
-  re2_re2_k2 = 0.0029666;
-  re8_re8_k1 = 10;
-  re8_re8_k2 = 0.02;
-  J3_J3_k1 = 0.03;
-  J3_J3_k2 = 0.0168;
-  J4_J4_k1 = 0.03;
-  J4_J4_k2 = 0.0168;
-  J5_J5_k1 = 4;
-  J5_J5_k2 = 0.001;
-  J6_J6_k1 = 0.5;
-  J6_J6_k2 = 0.2;
-  J7_J7_k1 = 10;
-  J7_J7_k2 = 0.2;
-  J8_J8_k1 = 0.002;
-  J8_J8_k2 = 1e-05;
-  J9_J9_k1 = 0.5;
-  J9_J9_k2 = 0.2;
-  J10_J10_k = 0.002;
-  J11_J11_k = 0.002;
-  J12_J12_k1 = 10;
-  J12_J12_k2 = 0.2;
-  J13_J13_k = 1;
-  J14_J14_k = 0.05;
-  J15_J15_k = 0.001;
-  J16_J16_k1 = 0.5;
-  J16_J16_k2 = 0.2;
-  J17_J17_k = 0.05;
-  J18_J18_k = 0.001;
-  J19_J19_k = 0.05;
-  J20_J20_k = 0.001;
-  J21_J21_k = 1;
-  J22_J22_k1 = 10;
-  J22_J22_k2 = 0.2;
-  J23_J23_k1 = 10;
-  J23_J23_k2 = 0.2;
-  J24_J24_k1 = 10;
-  J24_J24_k2 = 0.2;
-  J25_J25_k1 = 0.5;
-  J25_J25_k2 = 0.2;
-  J27_J27_k1 = 10;
-  J27_J27_k2 = 0.2;
-  J28_J28_k = 0.05;
-  J29_J29_k = 0.001;
-  J30_J30_k = 0.005;
-  J31_J31_Vmax = 0.2;
-  J31_J31_Km1 = 0.1;
-  J32_J32_k = 0.005;
-  J33_J33_k = 0.005;
-  J34_J34_k1 = 1;
-  J34_J34_k2 = 0.002;
-  J35_J35_k1 = 1;
-  J35_J35_k2 = 0.2;
-  J36_J36_k1 = 1;
-  J36_J36_k2 = 0.2;
-  J37_J37_k = 1;
-  J38_J38_k1 = 1;
-  J38_J38_k2 = 0.2;
-  J39_J39_k1 = 0.5;
-  J39_J39_k2 = 0.2;
-  J40_J40_k1 = 0.5;
-  J40_J40_k2 = 0.2;
-  J41_J41_k = 0.05;
-  J42_J42_k = 0.05;
-  J43_J43_k = 1;
-  J44_J44_k1 = 1;
-  J44_J44_k2 = 0.2;
-  J45_J45_k = 0.05;
-  J46_J46_k = 0.001;
-  J47_J47_k = 0.001;
-  J49_J49_k1 = 0.12;
-  J49_J49_k2 = 0.01;
-  J50_J50_Vmax = 1;
-  J50_J50_Km1 = 25.641;
-  J51_J51_Vmax = 1;
-  J51_J51_Km1 = 25.641;
-  J52_J52_k1 = 60;
-  J52_J52_k2 = 0.5;
-  J53_J53_k1 = 60;
-  J53_J53_k2 = 0.5;
-  J54_J54_k1 = 60;
-  J54_J54_k2 = 0.5;
-  J57_J57_Vmax = 3;
-  J57_J57_Km1 = 15.657;
-  J58_J58_Vmax = 3;
-  J58_J58_Km1 = 15.657;
-  J61_J61_Vmax = 3;
-  J61_J61_Km1 = 15.657;
-  J62_J62_Vmax = 3;
-  J62_J62_Km1 = 15.657;
-  J63_J63_k1 = 10;
-  J63_J63_k2 = 0.075;
-  J66_J66_k = 0.0001667;
-  J67_J67_k = 0.0001166;
-  J68_J68_Vmax = 0.024;
-  J68_J68_Km1 = 0.01;
-  J69_J69_Vmax = 2;
-  J69_J69_Km1 = 0.02;
-  J70_J70_k1 = 6.2;
-  J70_J70_k2 = 6.4e-05;
-  J71_J71_k = 1;
-  J72_J72_k = 0.00063;
-  J73_J73_k = 0.00042;
-  J74_J74_k = 0.0022;
-  J75_J75_k1 = 10;
-  J75_J75_k2 = 0.2;
-  J76_J76_k1 = 10;
-  J76_J76_k2 = 0.2;
-  J77_J77_k1 = 5;
-  J77_J77_k2 = 0.1;
-  J78_J78_k1 = 5;
-  J78_J78_k2 = 0.1;
-  J79_J79_k1 = 10;
-  J79_J79_k2 = 0.2;
-  J80_J80_k1 = 10;
-  J80_J80_k2 = 0.2;
-  J81_J81_k = 0.1;
-  J82_J82_k = 0.1;
-  J83_J83_k = 2;
-  J84_J84_k1 = 5;
-  J84_J84_k2 = 0.1;
-  J85_J85_k1 = 5;
-  J85_J85_k2 = 0.1;
-  J86_J86_k = 2;
-  J87_J87_k = 0.0022;
-  J88_J88_k = 0.0022;
-  J89_J89_k = 0.0022;
-  J90_J90_k = 0.0022;
-  J92_J92_k = 0.00042;
-  J93_J93_k = 0.00042;
-  J94_J94_k = 0.00042;
-  J95_J95_k1 = 10;
-  J95_J95_k2 = 0.2;
-  J96_J96_k1 = 10;
-  J96_J96_k2 = 0.2;
-  J97_J97_k = 0.00063;
-  J98_J98_k = 0.00063;
-  J99_J99_k = 0.00063;
-  J100_J100_k = 0.00063;
-  J101_J101_k = 0.00063;
-  J102_J102_k = 0.00063;
-  J103_J103_k1 = 1;
-  J103_J103_k2 = 0.2;
-  J104_J104_k1 = 1;
-  J104_J104_k2 = 0.2;
-  J105_J105_k1 = 10;
-  J105_J105_k2 = 0.2;
-  J106_J106_k1 = 10;
-  J106_J106_k2 = 0.2;
-  J107_J107_k = 0.0022;
-  J108_J108_k = 0.00042;
-  J109_J109_k = 0.0022;
-  J110_J110_k = 0.00042;
-  J112_J112_k = 0.00042;
-  J113_J113_k1 = 0.0008333;
-  J113_J113_k2 = 0.00027778;
-  J115_J115_k1 = 10;
-  J115_J115_k2 = 0.2;
-  J116_J116_k1 = 10;
-  J116_J116_k2 = 0.2;
-  J117_J117_k1 = 10;
-  J117_J117_k2 = 0.2;
-  J119_J119_k1 = 0.5;
-  J119_J119_k2 = 0.2;
-  J118_J118_k1 = 1;
-  J118_J118_k2 = 0.2;
-  J120_J120_k1 = 1;
-  J120_J120_k2 = 0.2;
-  J121_J121_Vmax = 10;
-  J121_J121_Km1 = 1;
-  J122_J122_Vmax = 2;
-  J122_J122_Km1 = 1;
-  J123_J123_Vmax = 0.02;
-  J123_J123_Km1 = 0.1;
-  J124_J124_Vmax = 1;
-  J124_J124_Km1 = 25.641;
-  J133_J133_k1 = 16.304;
-  J133_J133_k2 = 0.6;
-  J134_J134_k1 = 16.304;
-  J134_J134_k2 = 0.6;
-  J135_J135_k1 = 16.304;
-  J135_J135_k2 = 0.6;
-  J136_J136_k = 0.15;
-  J137_J137_Vmax = 10;
-  J137_J137_Km1 = 1;
-  J138_J138_Vmax = 10;
-  J138_J138_Km1 = 1;
-  J139_J139_Vmax = 2;
-  J139_J139_Km1 = 1;
-  J140_J140_k1 = 15.625;
-  J140_J140_k2 = 2;
-  J141_J141_k1 = 15.625;
-  J141_J141_k2 = 2;
-  J142_J142_k1 = 15.625;
-  J142_J142_k2 = 2;
-  J143_J143_k1 = 15.625;
-  J143_J143_k2 = 2;
-  J144_J144_k1 = 6.25;
-  J144_J144_k2 = 0.8;
-  J145_J145_k1 = 6.25;
-  J145_J145_k2 = 0.8;
-  J146_J146_k1 = 6.25;
-  J146_J146_k2 = 0.8;
-  J147_J147_k1 = 6.25;
-  J147_J147_k2 = 0.8;
-  J148_J148_k1 = 9.375;
-  J148_J148_k2 = 1.2;
-  J149_J149_k1 = 9.375;
-  J149_J149_k2 = 1.2;
-  J150_J150_k1 = 9.375;
-  J150_J150_k2 = 1.2;
-  J151_J151_k1 = 9.375;
-  J151_J151_k2 = 1.2;
-  J152_J152_k = 0.5;
-  J153_J153_k = 0.5;
-  J154_J154_k = 0.5;
-  J155_J155_k = 0.5;
-  J156_J156_k = 0.2;
-  J157_J157_k = 0.2;
-  J158_J158_k = 0.2;
-  J159_J159_k = 0.2;
-  J160_J160_k = 0.3;
-  J161_J161_k = 0.3;
-  J162_J162_k = 0.3;
-  J163_J163_k = 0.3;
-  J164_J164_k = 0.001;
-  J165_J165_k1 = 15;
-  J165_J165_k2 = 0.24;
-  J166_J166_k1 = 15;
-  J166_J166_k2 = 0.24;
-  J167_J167_k = 0.06;
-  J168_J168_k = 0.06;
-
-  // Other declarations:
-  const compartment_, c1;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "microMole";
-  proteosome is "proteasome";
-  re1 is "form_EGFreceptor";
-  re2 is "EGFbinding";
-  re8 is "dimerization";
-  J3 is "binding_SOS_Grb2";
-  J4 is "binding_pSOS_Grb2";
-  J5 is "EGFRphosphorylation";
-  J6 is "binding_cCbI_dpEGFR";
-  J7 is "binding_pShc_LdpEGFR";
-  J8 is "pDOKdephosphorylation";
-  J9 is "binding_cCbl_pShc_dpEGFR";
-  J10 is "SOSdephosphorylation";
-  J11 is "pSOS_Grb2_dephosphorylation";
-  J12 is "binding_Shc_LdpEGFR";
-  J13 is "Shc_dpEGFR_phosphorylation";
-  J14 is "dpEGFR_c_Cbl_ubiquitination";
-  J15 is "dpEGFR_cCbl_degrad";
-  J16 is "binding_cCbl_Shc_dpEGFR";
-  J17 is "Shc_dpEGFR_c_CBl_Ubiquitination";
-  J18 is "Shc_dpEGFR_c_Cbl_ubiq_Degradation";
-  J19 is "pShc_dpEGFR_c_Cbl_ubiquitination";
-  J20 is "pShc_dpEGFR_c_Cbl_ubiq_degradation";
-  J21 is "Shc_dpEGFR_c_Cblphosphorylation";
-  J22 is "binding_Grb2_SOS_pShc";
-  J23 is "binding_Grb2_SOS_pShc_dpEGFR";
-  J24 is "binding_Grb2_SOS_pShc_dpEGFR";
-  J25 is "binding_c_Cbl_Grb2_SOS_pShc_dpEGFR";
-  J27 is "binding_Grb2_SOS_pShc_to_dpEGFR_c_Cbl";
-  J28 is "Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiquitination";
-  J29 is "Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq_degradation";
-  J30 is "Grb2_SOS_pShc_Dissociation";
-  J32 is "pShc_dephosphorylation";
-  J33 is "pFRS2_dephosphorylation";
-  J34 is "binding_Crk_to_C3G";
-  J35 is "binding_L_dpEGFR_to_FRS2";
-  J36 is "binding_pFRS2_to_L_dpEGFR";
-  J37 is "FRS2_dpEGFRphsphorylation";
-  J38 is "binding_Crk_C3G_to_pFRS2_pRTK";
-  J39 is "binding_c_Cbl_to_FRS2_dpEGFR";
-  J40 is "binding_c_Cbl_to_pFRS2_dpEGFR";
-  J41 is "pFRS2_dpEGFR_c_Cbl_ubiquitiation";
-  J42 is "FRS2_dpEGFR_c_Cbl_ubiquitination";
-  J43 is "FRS2_dpEGFR_c_Cbl_phosphorylation";
-  J44 is "binding_Crk_C3G_to_pFRS2_pFRS2_dpEGFR_c_Cbl";
-  J45 is "Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiquitination";
-  J46 is "FRS2_dpEGFR_c_Cbl_ubiq_dissociation";
-  J47 is "pFRS2_dpEGFR_c_Cbl_ubiq_dissociation";
-  J49 is "binding_RasGAP_to_pDOK";
-  J50 is "SOS_Grb2_phosphorylation";
-  J51 is "SOS_phosphorylation";
-  J52 is "binding_c_Raf_to_Ras_GTP";
-  J53 is "binding_B_Raf_to_Rap1_GTP";
-  J54 is "binding_B_Raf_to_Ras_GTP";
-  J57 is "ppMEK_dephosphorylation";
-  J58 is "pMEK_dephosphorylation";
-  J61 is "ppMEK_ERK";
-  J62 is "pMEK_ERK_dephosphorylation";
-  J63 is "ppERK_dimerization";
-  J66 is "Ras_GTP_dephosphorylation";
-  J67 is "Rap1_GTP_dephosphorylation";
-  J68 is "Rap1_GTP_phosphorylation";
-  J69 is "Ras_GDP_phosphorylation";
-  J70 is "binding_NGF_to_NGFR";
-  J71 is "TrkA_phosphorylation";
-  J72 is "pTrkA_intermalization";
-  J73 is "pTrkA_endo_degradation";
-  J74 is "pTrkA_degradation";
-  J75 is "binding_Shc_to_pTrkA";
-  J76 is "binding_pShc_to_pTrkA";
-  J77 is "binding_FRS2_to_pTrkA";
-  J78 is "binding_pFRS2_to_pTrkA";
-  J79 is "binding_Shc_to_pTrkA_endo";
-  J80 is "binding_pShc_to_pTrkA_endo";
-  J81 is "Shc_pTrkA_endo_phosphorylation";
-  J82 is "Shc_pTrkA_phosphorylation";
-  J83 is "pFRS2_pTrkA_phosphorylation";
-  J84 is "binding_FRS2_to_pTrkA_endo";
-  J85 is "binding_pFRS2_to_pTrkA_endo";
-  J86 is "FRS2_pTrkA_endo_phosphorylation";
-  J87 is "FRS2_pTrkA_degradation";
-  J88 is "pFRS2_pTrkA_degradation";
-  J89 is "Shc_pTrkA_degradation";
-  J90 is "pShc_pTrkA_degradation";
-  J92 is "FRS2_pTrkA_endo_degradation";
-  J93 is "Shc_pTrkA_endo_degradation";
-  J94 is "pShc_pTrkA_endo_degradation";
-  J95 is "binding_Grb2_SOS_to_pShc_pTrkA_endo";
-  J96 is "binding_Grb2_SOS_to_pShc_pTrkA";
-  J97 is "Grb2_SOS_pShc_pTrkA_ubiquitination";
-  J98 is "Crk_C3G_pFRS2_pTrkA_ubiquitination";
-  J99 is "pFRS2_pTrkA_ubiquitination";
-  J100 is "FRS2_pTrkA_ubiquitination";
-  J101 is "pShc_pTrkA_ubiquitination";
-  J102 is "Shc_pTrkA_ubiquitination";
-  J103 is "binding_Crk_C3G_to_pFRS2_pTrkA";
-  J104 is "binding_Crk_C3G_to_pFRS2_pTrkA_endo";
-  J105 is "binding_Grb2_SOS_pShc_to_pTrkA";
-  J106 is "binding_Grb2_SOS_pShc_to_pTrkA_endo";
-  J107 is "Crk_C3G_pFRS2_pTrkA_degradation";
-  J108 is "Crk_C3G_pFRS2_pTrkA_endo_degradation";
-  J109 is "Grb2_SOS_pShc_pTrkA_degradation";
-  J110 is "Grb2_SOS_pShc_pTrkA_endo_degradation";
-  J112 is "pFRS2_pTrkA_endo_degradation";
-  J113 is "form_NGFreceptor";
-  J115 is "binding_Shc_to_dpEGFR_c_Cbl";
-  J116 is "binding_pShc_to_dpEGFR_c_Cbl";
-  J117 is "binding_SOS_Grb2_to_pShc_dpEGFR_c_Cbl";
-  J119 is "binding_c_Cbl_to_Crk_C3G_pFRS2_dpEGFR";
-  J118 is "binding_FRS2_to_dpEGFR_c_Cbl";
-  J120 is "binding_pFRS2_to_dpEGFR_c_Cbl";
-  J121 is "Ras_GTP_dephosphorylation";
-  J122 is "RAP1_GTP_dephosphorylation";
-  J123 is "Dok_phosphorylation";
-  J124 is "Grb1_SOS_pShc_dissociation";
-  J133 is "binding_MEK_to_ERK";
-  J134 is "binding_ERK_to_pMEK";
-  J135 is "binding_ERK_to_ppMEK";
-  J136 is "ppMEK_ERK_dissociation";
-  J137 is "c_Raf_Ras_GTP_dissociation";
-  J138 is "B_Raf_Ras_GTP_dissociation";
-  J139 is "B_Raf_Rap1_GTP_dissociation";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0009898"
-  c1 hypernym "http://identifiers.org/go/GO:0005737"
-  EGFR parthood "http://identifiers.org/uniprot/Q9QX70"
-  L_EGFR part "http://identifiers.org/uniprot/P07522",
-              "http://identifiers.org/uniprot/Q9QX70"
-  L_EGFR_dimer part "http://identifiers.org/uniprot/P07522",
-                    "http://identifiers.org/uniprot/Q9QX70"
-  SOS hypernym "http://identifiers.org/uniprot/Q9Z1I1"
-  L_dpEGFR part "http://identifiers.org/uniprot/Q9QX70",
-                "http://identifiers.org/uniprot/P07522"
-  pSOS hypernym "http://identifiers.org/uniprot/Q9Z1I1"
-  SOS_Grb2 part "http://identifiers.org/uniprot/Q9Z1I1",
-                "http://identifiers.org/uniprot/P62994"
-  Grb2 identity "http://identifiers.org/uniprot/P62994"
-  Dok hypernym "http://identifiers.org/uniprot/Q4QQV2",
-               "http://identifiers.org/interpro/IPR002404"
-  pDok hypernym "http://identifiers.org/uniprot/Q4QQV2",
-                "http://identifiers.org/interpro/IPR002404"
-  pDok hypernym "http://identifiers.org/kegg.compound/C00562"
-  Crk identity "http://identifiers.org/uniprot/Q63768"
-  FRS2 hypernym "http://identifiers.org/uniprot/D4A244"
-  Shc hypernym "http://identifiers.org/uniprot/Q5M824"
-  pSOS_Grb2 part "http://identifiers.org/uniprot/Q9Z1I1",
-                 "http://identifiers.org/uniprot/P62994"
-  Rap1_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-                "http://identifiers.org/uniprot/Q62636"
-  MEK version "http://identifiers.org/uniprot/Q01986"
-  MKP3 identity "http://identifiers.org/uniprot/Q64346"
-  pShc_dpEGFR part "http://identifiers.org/uniprot/P07522",
-                   "http://identifiers.org/uniprot/Q5M824",
-                   "http://identifiers.org/uniprot/Q9QX70"
-  dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q8K4S7",
-                    "http://identifiers.org/uniprot/Q9QX70"
-  B_Raf_Rap1_GTP part "http://identifiers.org/chebi/CHEBI:15996",
-                      "http://identifiers.org/uniprot/Q62636",
-                      "http://identifiers.org/uniprot/Q99MC6"
-  pShc_dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q8K4S7",
-                         "http://identifiers.org/uniprot/Q5M824",
-                         "http://identifiers.org/uniprot/Q9QX70"
-  pFRS2_dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q9QX70",
-                          "http://identifiers.org/uniprot/D4A244",
-                          "http://identifiers.org/uniprot/Q8K4S7"
-  Shc_dpEGFR part "http://identifiers.org/uniprot/Q5M824",
-                  "http://identifiers.org/uniprot/P07522",
-                  "http://identifiers.org/uniprot/Q9QX70"
-  c_Cbl homolog "http://identifiers.org/uniprot/Q8K4S7"
-  RasGAP identity "http://identifiers.org/interpro/IPR011575"
-  c_Raf identity "http://identifiers.org/uniprot/P11345"
-  B_Raf identity "http://identifiers.org/uniprot/Q99MC6"
-  ERK identity "http://identifiers.org/uniprot/P63086"
-  PP2A version "http://identifiers.org/uniprot/P62716",
-               "http://identifiers.org/uniprot/P63331"
-  Ras_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/interpro/IPR003577"
-  Rap1GAP version "http://identifiers.org/uniprot/P47736"
-  C3G identity "http://identifiers.org/uniprot/Q9QYV3"
-  NGFR identity "http://identifiers.org/uniprot/P35739"
-  pShc hypernym "http://identifiers.org/uniprot/Q5M824"
-  pFRS2_dpEGFR part "http://identifiers.org/uniprot/Q8C180",
-                    "http://identifiers.org/uniprot/P07522",
-                    "http://identifiers.org/uniprot/Q9QX70"
-  pTrkA_endo hypernym "http://identifiers.org/uniprot/P35739"
-  MEK_ERK part "http://identifiers.org/uniprot/P63086",
-               "http://identifiers.org/uniprot/Q01986"
-  pMEK_ERK part "http://identifiers.org/uniprot/P63086",
-                "http://identifiers.org/uniprot/Q01986"
-  FRS2_dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/Q9QX70",
-                              "http://identifiers.org/uniprot/D4A244",
-                              "http://identifiers.org/uniprot/Q8K4S7"
-  Crk_C3G_pFRS2_dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q9QYV3",
-                                  "http://identifiers.org/uniprot/Q9QX70",
-                                  "http://identifiers.org/uniprot/Q63768",
-                                  "http://identifiers.org/uniprot/D4A244",
-                                  "http://identifiers.org/uniprot/Q8K4S7"
-  pShc_dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/Q9QX70",
-                              "http://identifiers.org/uniprot/Q5M824",
-                              "http://identifiers.org/uniprot/Q8K4S7"
-  Crk_C3G_pFRS2_dpEGFR part "http://identifiers.org/uniprot/Q9QX70",
-                            "http://identifiers.org/uniprot/Q9QYV3",
-                            "http://identifiers.org/uniprot/Q63768",
-                            "http://identifiers.org/uniprot/D4A244"
-  Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/Q8K4S7",
-                                       "http://identifiers.org/uniprot/Q9QX70",
-                                       "http://identifiers.org/uniprot/Q5M824",
-                                       "http://identifiers.org/uniprot/P62994",
-                                       "http://identifiers.org/uniprot/Q9Z1I1"
-  Grb2_SOS_pShc_dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q8K4S7",
-                                  "http://identifiers.org/uniprot/Q9QX70",
-                                  "http://identifiers.org/uniprot/Q5M824",
-                                  "http://identifiers.org/uniprot/P62994",
-                                  "http://identifiers.org/uniprot/Q9Z1I1"
-  Shc_dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/Q8K4S7",
-                             "http://identifiers.org/uniprot/Q9QX70",
-                             "http://identifiers.org/uniprot/Q5M824"
-  dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/Q8K4S7",
-                         "http://identifiers.org/uniprot/Q9QX70"
-  proteosome hypernym "http://identifiers.org/go/GO:0000502"
-  Grb2_SOS_pShc part "http://identifiers.org/uniprot/P62994",
-                     "http://identifiers.org/uniprot/Q5M824",
-                     "http://identifiers.org/uniprot/Q9Z1I1"
-  Shc_dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q5M824",
-                        "http://identifiers.org/uniprot/Q8K4S7",
-                        "http://identifiers.org/uniprot/Q9QX70"
-  Grb2_SOS_pShc_dpEGFR part "http://identifiers.org/uniprot/Q9QX70",
-                            "http://identifiers.org/uniprot/Q9Z1I1",
-                            "http://identifiers.org/uniprot/Q5M824",
-                            "http://identifiers.org/uniprot/P62994"
-  pFRS2 hypernym "http://identifiers.org/uniprot/D4A244",
-                 "http://identifiers.org/kegg.compound/C00562"
-  FRS2_dpEGFR part "http://identifiers.org/uniprot/Q9QX70",
-                   "http://identifiers.org/uniprot/D4A244"
-  pDok_RasGAP part "http://identifiers.org/uniprot/Q4QQV2",
-                   "http://identifiers.org/interpro/IPR011575"
-  pMEK hypernym "http://identifiers.org/uniprot/Q01986"
-  FRS2_dpEGFR_c_Cbl part "http://identifiers.org/uniprot/Q9QX70",
-                         "http://identifiers.org/uniprot/D4A244",
-                         "http://identifiers.org/uniprot/Q8K4S7"
-  pFRS2_dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/D4A244",
-                               "http://identifiers.org/uniprot/Q8K4S7",
-                               "http://identifiers.org/uniprot/Q9QX70"
-  Ras_GTP identity "http://identifiers.org/interpro/IPR003577"
-  Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq part "http://identifiers.org/uniprot/D4A244",
-                                       "http://identifiers.org/uniprot/Q9QX70",
-                                       "http://identifiers.org/uniprot/Q9QYV3",
-                                       "http://identifiers.org/uniprot/Q63768",
-                                       "http://identifiers.org/uniprot/Q8K4S7"
-  c_Raf_Ras_GTP part "http://identifiers.org/uniprot/P11345",
-                     "http://identifiers.org/interpro/IPR003577"
-  B_Raf_Ras_GTP part "http://identifiers.org/uniprot/P28028",
-                     "http://identifiers.org/interpro/IPR003577"
-  ppMEK hypernym "http://identifiers.org/uniprot/Q01986"
-  ppERK hypernym "http://identifiers.org/uniprot/P63086"
-  pTrkA hypernym "http://identifiers.org/uniprot/P35739"
-  Crk_C3G part "http://identifiers.org/uniprot/Q63768",
-               "http://identifiers.org/uniprot/Q9QYV3"
-  Rap1_GTP hypernym "http://identifiers.org/uniprot/Q62636"
-  L_NGFR part "http://identifiers.org/uniprot/P35739",
-              "http://identifiers.org/uniprot/P25427"
-  ppMEK_ERK part "http://identifiers.org/uniprot/Q01986",
-                 "http://identifiers.org/uniprot/P63086"
-  dppERK hypernym "http://identifiers.org/uniprot/P63086"
-  Shc_pTrkA part "http://identifiers.org/uniprot/P35739",
-                 "http://identifiers.org/uniprot/Q5M824"
-  Shc_pTrkA_endo part "http://identifiers.org/uniprot/P35739",
-                      "http://identifiers.org/uniprot/Q5M824"
-  pShc_pTrkA part "http://identifiers.org/uniprot/P35739",
-                  "http://identifiers.org/uniprot/Q5M824"
-  pFRS2_pTrkA part "http://identifiers.org/uniprot/P35739",
-                   "http://identifiers.org/uniprot/D4A244"
-  FRS2_pTrkA part "http://identifiers.org/uniprot/D4A244",
-                  "http://identifiers.org/uniprot/P35739"
-  pShc_pTrkA_endo part "http://identifiers.org/uniprot/Q5M824",
-                       "http://identifiers.org/uniprot/P35739"
-  FRS2_pTrkA_endo part "http://identifiers.org/uniprot/D4A244",
-                       "http://identifiers.org/uniprot/P35739"
-  pFRS2_pTrkA_endo part "http://identifiers.org/uniprot/P35739",
-                        "http://identifiers.org/uniprot/D4A244"
-  Crk_C3G_pFRS2_pTrkA_endo part "http://identifiers.org/uniprot/P35739",
-                                "http://identifiers.org/uniprot/Q9QYV3",
-                                "http://identifiers.org/uniprot/Q63768",
-                                "http://identifiers.org/uniprot/D4A244"
-  Grb2_SOS_pShc_pTrkA part "http://identifiers.org/uniprot/Q5M824",
-                           "http://identifiers.org/uniprot/Q9Z1I1",
-                           "http://identifiers.org/uniprot/P62994",
-                           "http://identifiers.org/uniprot/P35739"
-  Crk_C3G_pFRS2_pTrkA part "http://identifiers.org/uniprot/P35739",
-                           "http://identifiers.org/uniprot/Q9QYV3",
-                           "http://identifiers.org/uniprot/Q63768",
-                           "http://identifiers.org/uniprot/D4A244"
-  Grb2_SOS_pShc_pTrkA_endo part "http://identifiers.org/uniprot/Q9Z1I1",
-                                "http://identifiers.org/uniprot/P35739",
-                                "http://identifiers.org/uniprot/Q5M824",
-                                "http://identifiers.org/uniprot/P62994"
-  c_Raf_Ras_GTP_MEK part "http://identifiers.org/uniprot/Q01986",
-                         "http://identifiers.org/uniprot/P11345",
-                         "http://identifiers.org/interpro/IPR003577"
-  c_Raf_Ras_GTP_pMEK part "http://identifiers.org/uniprot/P11345",
-                          "http://identifiers.org/uniprot/P36506",
-                          "http://identifiers.org/interpro/IPR003577"
-  c_Raf_Ras_GTP_MEK_ERK part "http://identifiers.org/uniprot/P63086",
-                             "http://identifiers.org/uniprot/P11345",
-                             "http://identifiers.org/uniprot/Q01986",
-                             "http://identifiers.org/interpro/IPR003577"
-  c_Raf_Ras_GTP_pMEK_ERK part "http://identifiers.org/uniprot/P63086",
-                              "http://identifiers.org/uniprot/Q01986",
-                              "http://identifiers.org/uniprot/P11345",
-                              "http://identifiers.org/interpro/IPR003577"
-  B_Raf_Ras_GTP_MEK part "http://identifiers.org/uniprot/Q01986",
-                         "http://identifiers.org/uniprot/Q99MC6",
-                         "http://identifiers.org/interpro/IPR003577"
-  B_Raf_Ras_GTP_pMEK part "http://identifiers.org/uniprot/Q01986",
-                          "http://identifiers.org/uniprot/Q99MC6",
-                          "http://identifiers.org/interpro/IPR003577"
-  B_Raf_Ras_GTP_MEK_ERK part "http://identifiers.org/uniprot/P63086",
-                             "http://identifiers.org/uniprot/Q01986",
-                             "http://identifiers.org/uniprot/Q99MC6",
-                             "http://identifiers.org/interpro/IPR003577"
-  B_Raf_Ras_GTP_pMEK_ERK part "http://identifiers.org/uniprot/Q01986",
-                              "http://identifiers.org/uniprot/P63086",
-                              "http://identifiers.org/uniprot/Q99MC6",
-                              "http://identifiers.org/interpro/IPR003577"
-  B_Raf_Rap1_GTP_MEK part "http://identifiers.org/chebi/CHEBI:15996",
-                          "http://identifiers.org/uniprot/Q01986",
-                          "http://identifiers.org/uniprot/Q99MC6",
-                          "http://identifiers.org/uniprot/Q62636"
-  B_Raf_Rap1_GTP_pMEK part "http://identifiers.org/chebi/CHEBI:15996",
-                           "http://identifiers.org/uniprot/Q01986",
-                           "http://identifiers.org/uniprot/Q62636",
-                           "http://identifiers.org/uniprot/Q99MC6"
-  B_Raf_Rap1_GTP_MEK_ERK part "http://identifiers.org/chebi/CHEBI:15996",
-                              "http://identifiers.org/uniprot/P63086",
-                              "http://identifiers.org/uniprot/Q01986",
-                              "http://identifiers.org/uniprot/Q62636",
-                              "http://identifiers.org/uniprot/Q99MC6"
-  B_Raf_Rap1_GTP_pMEK_ERK part "http://identifiers.org/chebi/CHEBI:15996",
-                               "http://identifiers.org/uniprot/P63086",
-                               "http://identifiers.org/uniprot/Q01986",
-                               "http://identifiers.org/uniprot/Q62636",
-                               "http://identifiers.org/uniprot/Q99MC6"
-  ppERK_MKP3 part "http://identifiers.org/uniprot/Q64346",
-                  "http://identifiers.org/uniprot/P63086"
-  dppERK_MKP3 part "http://identifiers.org/uniprot/Q64346",
-                   "http://identifiers.org/uniprot/Q01986"
-  pro_TrkA hypernym "http://identifiers.org/uniprot/P35739"
-  NGF identity "http://identifiers.org/uniprot/P25427"
-  EGF identity "http://identifiers.org/uniprot/P07522"
-  pro_EGFR hypernym "http://identifiers.org/uniprot/Q9QX70"
-  re1 parthood "http://identifiers.org/go/GO:0045741"
-  re2 parthood "http://identifiers.org/go/GO:0045741"
-  re2 identity "http://identifiers.org/go/GO:0005154",
-               "http://identifiers.org/go/GO:0048408"
-  re8 hypernym "http://identifiers.org/go/GO:0005154"
-  J3 hypernym "http://identifiers.org/go/GO:0005068",
-              "http://identifiers.org/go/GO:0005070",
-              "http://identifiers.org/go/GO:0017124"
-  J4 hypernym "http://identifiers.org/go/GO:0017124",
-              "http://identifiers.org/go/GO:0005070",
-              "http://identifiers.org/go/GO:0005068"
-  J5 hypernym "http://identifiers.org/go/GO:0004716"
-  J6 hypernym "http://identifiers.org/go/GO:0051425"
-  J7 hypernym "http://identifiers.org/go/GO:0051425",
-              "http://identifiers.org/go/GO:0042169"
-  J8 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-  J9 identity "http://identifiers.org/go/GO:0031625",
-              "http://identifiers.org/go/GO:0017124"
-  J10 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J11 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J12 hypernym "http://identifiers.org/go/GO:0042169"
-  J13 hypernym "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004716"
-  J14 hypernym "http://identifiers.org/go/GO:0016567"
-  J15 identity "http://identifiers.org/go/GO:0043161"
-  J16 identity "http://identifiers.org/go/GO:0031625",
-               "http://identifiers.org/go/GO:0017124"
-  J17 hypernym "http://identifiers.org/go/GO:0016567"
-  J18 identity "http://identifiers.org/go/GO:0043161"
-  J19 hypernym "http://identifiers.org/go/GO:0016567"
-  J20 identity "http://identifiers.org/go/GO:0043161"
-  J21 hypernym "http://identifiers.org/go/GO:0004716",
-               "http://identifiers.org/go/GO:0006468"
-  J22 hypernym "http://identifiers.org/go/GO:0005070"
-  J23 hypernym "http://identifiers.org/go/GO:0042169"
-  J24 hypernym "http://identifiers.org/go/GO:0005070"
-  J25 identity "http://identifiers.org/go/GO:0031625",
-               "http://identifiers.org/go/GO:0017124"
-  J27 hypernym "http://identifiers.org/go/GO:0042169"
-  J28 hypernym "http://identifiers.org/go/GO:0016567"
-  J29 identity "http://identifiers.org/go/GO:0043161"
-  J30 hypernym "http://identifiers.org/go/GO:0043241"
-  J31 hypernym "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004716"
-  J32 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J33 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J34 hypernym "http://identifiers.org/go/GO:0006461"
-  J35 identity "http://identifiers.org/go/GO:0051425"
-  J36 identity "http://identifiers.org/go/GO:0051425"
-  J37 hypernym "http://identifiers.org/go/GO:0004716"
-  J38 hypernym "http://identifiers.org/go/GO:0042169"
-  J39 hypernym "http://identifiers.org/go/GO:0031625"
-  J40 hypernym "http://identifiers.org/go/GO:0031625"
-  J41 hypernym "http://identifiers.org/go/GO:0016567"
-  J42 hypernym "http://identifiers.org/go/GO:0016567"
-  J43 hypernym "http://identifiers.org/go/GO:0004716",
-               "http://identifiers.org/go/GO:0006468"
-  J44 hypernym "http://identifiers.org/go/GO:0042169"
-  J45 hypernym "http://identifiers.org/go/GO:0016567"
-  J46 hypernym "http://identifiers.org/go/GO:0043161"
-  J47 hypernym "http://identifiers.org/go/GO:0043161"
-  J49 parthood "http://identifiers.org/go/GO:0046580"
-  J50 hypernym "http://identifiers.org/go/GO:0006468"
-  J51 hypernym "http://identifiers.org/go/GO:0006468"
-  J52 hypernym "http://identifiers.org/go/GO:0000185"
-  J53 hypernym "http://identifiers.org/go/GO:0000185"
-  J54 hypernym "http://identifiers.org/go/GO:0000185"
-  J57 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J57 parthood "http://identifiers.org/go/GO:0051389"
-  J58 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J58 parthood "http://identifiers.org/go/GO:0051389"
-  J61 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J61 parthood "http://identifiers.org/go/GO:0051389"
-  J62 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J62 parthood "http://identifiers.org/go/GO:0051389"
-  J63 hypernym "http://identifiers.org/go/GO:0005154"
-  J66 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J66 parthood "http://identifiers.org/go/GO:0046580"
-  J67 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  J68 hypernym "http://identifiers.org/go/GO:0005085",
-               "http://identifiers.org/go/GO:0006468"
-  J69 hypernym "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0005085"
-  J70 hypernym "http://identifiers.org/go/GO:0048406",
-               "http://identifiers.org/go/GO:0051396"
-  J71 hypernym "http://identifiers.org/go/GO:0004716",
-               "http://identifiers.org/go/GO:0006468"
-  J72 hypernym "http://identifiers.org/go/GO:0031623"
-  J73 hypernym "http://identifiers.org/go/GO:0043241"
-  J74 hypernym "http://identifiers.org/go/GO:0043241"
-  J75 hypernym "http://identifiers.org/go/GO:0042169",
-               "http://identifiers.org/go/GO:0051425"
-  J76 hypernym "http://identifiers.org/go/GO:0051425",
-               "http://identifiers.org/go/GO:0042169"
-  J77 hypernym "http://identifiers.org/go/GO:0051425"
-  J78 hypernym "http://identifiers.org/go/GO:0051425"
-  J79 hypernym "http://identifiers.org/go/GO:0051425",
-               "http://identifiers.org/go/GO:0042169"
-  J80 hypernym "http://identifiers.org/go/GO:0042169",
-               "http://identifiers.org/go/GO:0051425"
-  J81 hypernym "http://identifiers.org/go/GO:0006468"
-  J82 hypernym "http://identifiers.org/go/GO:0006468"
-  J83 hypernym "http://identifiers.org/go/GO:0006468"
-  J84 hypernym "http://identifiers.org/go/GO:0051425"
-  J85 hypernym "http://identifiers.org/go/GO:0051425"
-  J86 hypernym "http://identifiers.org/go/GO:0006468"
-  J87 hypernym "http://identifiers.org/go/GO:0043241"
-  J88 hypernym "http://identifiers.org/go/GO:0043241"
-  J89 hypernym "http://identifiers.org/go/GO:0043241"
-  J90 hypernym "http://identifiers.org/go/GO:0043241"
-  J92 hypernym "http://identifiers.org/go/GO:0043241"
-  J93 hypernym "http://identifiers.org/go/GO:0043241"
-  J94 hypernym "http://identifiers.org/go/GO:0043241"
-  J95 hypernym "http://identifiers.org/go/GO:0005070"
-  J96 hypernym "http://identifiers.org/go/GO:0005070"
-  J97 hypernym "http://identifiers.org/go/GO:0016567"
-  J98 hypernym "http://identifiers.org/go/GO:0016567"
-  J99 hypernym "http://identifiers.org/go/GO:0016567"
-  J100 hypernym "http://identifiers.org/go/GO:0016567"
-  J101 hypernym "http://identifiers.org/go/GO:0016567"
-  J102 hypernym "http://identifiers.org/go/GO:0016567"
-  J103 hypernym "http://identifiers.org/go/GO:0042169"
-  J104 hypernym "http://identifiers.org/go/GO:0042169"
-  J105 hypernym "http://identifiers.org/go/GO:0051425",
-                "http://identifiers.org/go/GO:0042169"
-  J106 hypernym "http://identifiers.org/go/GO:0051425",
-                "http://identifiers.org/go/GO:0042169"
-  J107 hypernym "http://identifiers.org/go/GO:0043241"
-  J108 hypernym "http://identifiers.org/go/GO:0043241"
-  J109 hypernym "http://identifiers.org/go/GO:0043241"
-  J110 hypernym "http://identifiers.org/go/GO:0043241"
-  J112 hypernym "http://identifiers.org/go/GO:0043241"
-  J113 parthood "http://identifiers.org/go/GO:0051396"
-  J115 hypernym "http://identifiers.org/go/GO:0042169",
-                "http://identifiers.org/go/GO:0051425"
-  J116 hypernym "http://identifiers.org/go/GO:0042169",
-                "http://identifiers.org/go/GO:0051425"
-  J117 hypernym "http://identifiers.org/go/GO:0005070"
-  J119 hypernym "http://identifiers.org/go/GO:0031625"
-  J118 hypernym "http://identifiers.org/go/GO:0051425"
-  J120 hypernym "http://identifiers.org/go/GO:0051425"
-  J121 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470"
-  J122 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470"
-  J123 hypernym "http://identifiers.org/go/GO:0006468"
-  J124 hypernym "http://identifiers.org/go/GO:0043241"
-  J133 parthood "http://identifiers.org/go/GO:0000187"
-  J134 parthood "http://identifiers.org/go/GO:0000187"
-  J135 parthood "http://identifiers.org/go/GO:0000187"
-  J136 hypernym "http://identifiers.org/go/GO:0043241"
-  J137 hypernym "http://identifiers.org/go/GO:0043241"
-  J138 hypernym "http://identifiers.org/go/GO:0043241"
-  J139 hypernym "http://identifiers.org/go/GO:0043241"
-  J140 hypernym "http://identifiers.org/go/GO:0019899"
-  J141 hypernym "http://identifiers.org/go/GO:0019899"
-  J142 hypernym "http://identifiers.org/go/GO:0019899"
-  J143 hypernym "http://identifiers.org/go/GO:0019899"
-  J144 hypernym "http://identifiers.org/go/GO:0019899"
-  J145 hypernym "http://identifiers.org/go/GO:0019899"
-  J146 hypernym "http://identifiers.org/go/GO:0019899"
-  J147 hypernym "http://identifiers.org/go/GO:0019899"
-  J148 hypernym "http://identifiers.org/go/GO:0019899"
-  J149 hypernym "http://identifiers.org/go/GO:0019899"
-  J150 hypernym "http://identifiers.org/go/GO:0019899"
-  J151 hypernym "http://identifiers.org/go/GO:0019899"
-  J152 hypernym "http://identifiers.org/go/GO:0004709"
-  J153 hypernym "http://identifiers.org/go/GO:0004709"
-  J154 hypernym "http://identifiers.org/go/GO:0004709"
-  J155 hypernym "http://identifiers.org/go/GO:0004709"
-  J156 hypernym "http://identifiers.org/go/GO:0004709"
-  J157 hypernym "http://identifiers.org/go/GO:0004709"
-  J158 hypernym "http://identifiers.org/go/GO:0004709"
-  J159 hypernym "http://identifiers.org/go/GO:0004709"
-  J160 hypernym "http://identifiers.org/go/GO:0004709"
-  J161 hypernym "http://identifiers.org/go/GO:0004709"
-  J162 hypernym "http://identifiers.org/go/GO:0004709"
-  J163 hypernym "http://identifiers.org/go/GO:0004709"
-  J164 hypernym "http://identifiers.org/go/GO:0043241"
-  J165 parthood "http://identifiers.org/go/GO:0000188"
-  J166 parthood "http://identifiers.org/go/GO:0000188"
-  J167 parthood "http://identifiers.org/go/GO:0043241"
-  J167 parthood "http://identifiers.org/go/GO:0000188"
-  J168 parthood "http://identifiers.org/go/GO:0000188"
-  J168 parthood "http://identifiers.org/go/GO:0043241"
-end
-
-Sasagawa2005_MAPK is "Sasagawa2005_MAPK"
-
-Sasagawa2005_MAPK model_entity_is "http://identifiers.org/biomodels.db/MODEL6624243033"
-Sasagawa2005_MAPK model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000049"
-Sasagawa2005_MAPK description "http://identifiers.org/pubmed/15793571"
-Sasagawa2005_MAPK origin "http://identifiers.org/biomodels.db/MODEL9071122126",
-                         "http://identifiers.org/biomodels.db/BIOMD0000000019",
-                         "http://identifiers.org/biomodels.db/MODEL9070467164",
-                         "http://identifiers.org/biomodels.db/MODEL9079179924",
-                         "http://identifiers.org/biomodels.db/BIOMD0000000146",
-                         "http://identifiers.org/pubmed/11024454",
-                         "http://identifiers.org/pubmed/11832340",
-                         "http://identifiers.org/pubmed/14751248"
-Sasagawa2005_MAPK taxon "http://identifiers.org/taxonomy/10114"
-Sasagawa2005_MAPK part "http://identifiers.org/go/GO:0007173",
-                       "http://identifiers.org/go/GO:0007265",
-                       "http://identifiers.org/go/GO:0048011",
-                       "http://identifiers.org/go/GO:0000165"
-Sasagawa2005_MAPK property "http://identifiers.org/mamo/MAMO_0000046"
-Sasagawa2005_MAPK hypernym "http://identifiers.org/go/GO:0070371"
diff --git a/BioModelsRAG/data/BIOMD0000000050.txt b/BioModelsRAG/data/BIOMD0000000050.txt
deleted file mode 100644
index 00c41f48fb8ec458fc06445bb3fc1f488ac68fb4..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000050.txt
+++ /dev/null
@@ -1,101 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Kinetic_modelling_of_Amadori_degradation()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species DFG in compartment_, E1 in compartment_, E2 in compartment_, Cn in compartment_;
-  species Gly in compartment_, _3DG in compartment_, FA in compartment_, _1DG in compartment_;
-  species AA in compartment_, Man in compartment_, Glu in compartment_, MG in compartment_;
-  species Mel in compartment_, Fru in compartment_;
-
-  // Reactions:
-  v1: DFG => E1; v1_k1*DFG;
-  v2: DFG => E2; v2_k2*DFG;
-  v3: DFG => Gly + Cn; v3_k3*DFG;
-  v4: E1 => Gly + _3DG; v4_k4*E1;
-  v5: _3DG => Cn; v5_k5*_3DG;
-  v6: _3DG => FA; v6_k6*_3DG;
-  v7: E2 => Gly + _1DG; v7_k7*E2;
-  v8: _1DG => Cn; v8_k8*_1DG;
-  v9: _1DG => AA; v9_k9*_1DG;
-  v10: E1 => Gly + Man; v10_k10*E1;
-  v11: E1 => Gly + Glu; v11_k11*E1;
-  v12: Man => Glu; v12_k12*Man;
-  v13: Glu => _3DG; v13_k13*Glu;
-  v14: Gly + Cn => Mel; v14_k14*Cn*Gly;
-  v15: Cn => AA + FA + MG; v15_k15*Cn;
-  v16: E2 => Gly + Fru; v16_k16*E2;
-
-  // Species initializations:
-  DFG = 9;
-  E1 = 0;
-  E2 = 0;
-  Cn = 0;
-  Gly = 0;
-  _3DG = 0;
-  FA = 0;
-  _1DG = 0;
-  AA = 0;
-  Man = 0;
-  Glu = 0;
-  MG = 0;
-  Mel = 0;
-  Fru = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1 = 0.0057;
-  v2_k2 = 0.0156;
-  v3_k3 = 0.0155;
-  v4_k4 = 0.0794;
-  v5_k5 = 0.0907;
-  v6_k6 = 0.0274;
-  v7_k7 = 0.2125;
-  v8_k8 = 0;
-  v9_k9 = 1.9085;
-  v10_k10 = 0.0707;
-  v11_k11 = 0.1131;
-  v12_k12 = 0.0008;
-  v13_k13 = 0.0022;
-  v14_k14 = 0.0034;
-  v15_k15 = 0.0159;
-  v16_k16 = 0.0134;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  Cn hypernym "http://identifiers.org/chebi/CHEBI:23008"
-  Gly identity "http://identifiers.org/chebi/CHEBI:15428",
-               "http://identifiers.org/kegg.compound/C00037"
-  FA identity "http://identifiers.org/chebi/CHEBI:30751",
-              "http://identifiers.org/kegg.compound/C00058"
-  AA identity "http://identifiers.org/chebi/CHEBI:15366",
-              "http://identifiers.org/kegg.compound/C00033"
-  Man identity "http://identifiers.org/chebi/CHEBI:14575",
-               "http://identifiers.org/kegg.compound/C00159"
-  Glu identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  MG identity "http://identifiers.org/chebi/CHEBI:17158",
-              "http://identifiers.org/kegg.compound/C00546"
-  Fru identity "http://identifiers.org/chebi/CHEBI:28757",
-               "http://identifiers.org/kegg.compound/C01496"
-end
-
-Kinetic_modelling_of_Amadori_degradation is "Martins2003_AmadoriDegradation"
-
-Kinetic_modelling_of_Amadori_degradation model_entity_is "http://identifiers.org/biomodels.db/MODEL7981660691"
-Kinetic_modelling_of_Amadori_degradation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000050"
-Kinetic_modelling_of_Amadori_degradation description "http://identifiers.org/pubmed/12873422"
-Kinetic_modelling_of_Amadori_degradation taxon "http://identifiers.org/taxonomy/131567"
-Kinetic_modelling_of_Amadori_degradation hypernym "http://identifiers.org/go/GO:1901575"
diff --git a/BioModelsRAG/data/BIOMD0000000051.txt b/BioModelsRAG/data/BIOMD0000000051.txt
deleted file mode 100644
index afeb2e15833d3a6887008b79e7611339edb0faad..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000051.txt
+++ /dev/null
@@ -1,601 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Chassagnole2002_Carbon_Metabolism()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol;
-  species cpep in cytosol, cglcex in extracellular, cg6p in cytosol, cpyr in cytosol;
-  species cf6p in cytosol, cg1p in cytosol, cpg in cytosol, cfdp in cytosol;
-  species csed7p in cytosol, cgap in cytosol, ce4p in cytosol, cxyl5p in cytosol;
-  species crib5p in cytosol, cdhap in cytosol, cpgp in cytosol, cpg3 in cytosol;
-  species cpg2 in cytosol, cribu5p in cytosol;
-
-  // Assignment Rules:
-  catp := 4.27 - 4.163*(time/(0.657 + 1.43*time + 0.0364*time^2));
-  cadp := 0.582 + 1.73*2.731^(-0.15*time)*(0.12*time + 0.000214*time^3);
-  camp := 0.123 + 7.25*(time/(7.25 + 1.47*time + 0.17*time^2)) + 1.073/(1.29 + 8.05*time);
-  cnadp := (0.159 - 0.00554*(time/((2.8 - 0.271*time) + 0.01*time^2))) + 0.182/(4.82 + 0.526*time);
-  cnadph := 0.062 + 0.332*2.718^(-0.464*time)*(0.0166*time^1.58 + 0.000166*time^4.73 + 0.1312*10^-9*time^7.89 + 0.1362*10^-12*time^11 + 0.1233*10^-15*time^14.2);
-  cnad := 1.314 + 1.314*2.73^(-0.0435*time - 0.342) - (time + 7.871)*(2.73^(-0.0218*time - 0.171)/(8.481 + time));
-  cnadh := 0.0934 + 0.00111*2.371^(-0.123*time)*(0.844*time + 0.104*time^3);
-
-  // Reactions:
-  vPTS: cglcex + 65 cpep -> 65 cg6p + 65 cpyr; extracellular*vPTS_rmaxPTS*cglcex*(cpep/cpyr)/((vPTS_KPTSa1 + vPTS_KPTSa2*(cpep/cpyr) + vPTS_KPTSa3*cglcex + cglcex*(cpep/cpyr))*(1 + cg6p^vPTS_nPTSg6p/vPTS_KPTSg6p));
-  vPGI: cg6p -> cf6p; cytosol*vPGI_rmaxPGI*(cg6p - cf6p/vPGI_KPGIeq)/(vPGI_KPGIg6p*(1 + cf6p/(vPGI_KPGIf6p*(1 + cpg/vPGI_KPGIf6ppginh)) + cpg/vPGI_KPGIg6ppginh) + cg6p);
-  vPGM: cg6p -> cg1p; cytosol*vPGM_rmaxPGM*(cg6p - cg1p/vPGM_KPGMeq)/(vPGM_KPGMg6p*(1 + cg1p/vPGM_KPGMg1p) + cg6p);
-  vG6PDH: cg6p -> cpg; cytosol*vG6PDH_rmaxG6PDH*cg6p*cnadp/((cg6p + vG6PDH_KG6PDHg6p)*(1 + cnadph/vG6PDH_KG6PDHnadphg6pinh)*(vG6PDH_KG6PDHnadp*(1 + cnadph/vG6PDH_KG6PDHnadphnadpinh) + cnadp));
-  vPFK: cf6p -> cfdp; cytosol*vPFK_rmaxPFK*catp*cf6p/((catp + vPFK_KPFKatps*(1 + cadp/vPFK_KPFKadpc))*(cf6p + vPFK_KPFKf6ps*(1 + cpep/vPFK_KPFKpep + cadp/vPFK_KPFKadpb + camp/vPFK_KPFKampb)/(1 + cadp/vPFK_KPFKadpa + camp/vPFK_KPFKampa))*(1 + vPFK_LPFK/(1 + cf6p*(1 + cadp/vPFK_KPFKadpa + camp/vPFK_KPFKampa)/(vPFK_KPFKf6ps*(1 + cpep/vPFK_KPFKpep + cadp/vPFK_KPFKadpb + camp/vPFK_KPFKampb)))^vPFK_nPFK));
-  vTA: cgap + csed7p -> cf6p + ce4p; cytosol*vTA_rmaxTA*(cgap*csed7p - ce4p*cf6p/vTA_KTAeq);
-  vTKA: crib5p + cxyl5p -> cgap + csed7p; cytosol*vTKA_rmaxTKa*(crib5p*cxyl5p - csed7p*cgap/vTKA_KTKaeq);
-  vTKB: ce4p + cxyl5p -> cgap + cf6p; cytosol*vTKB_rmaxTKb*(cxyl5p*ce4p - cf6p*cgap/vTKB_KTKbeq);
-  vMURSyNTH: 2 cf6p -> ; cytosol*vMURSyNTH_rmaxMurSynth;
-  vALDO: cfdp -> cdhap + cgap; cytosol*vALDO_rmaxALDO*(cfdp - cgap*cdhap/vALDO_kALDOeq)/(vALDO_kALDOfdp + cfdp + vALDO_kALDOgap*cdhap/(vALDO_kALDOeq*vALDO_VALDOblf) + vALDO_kALDOdhap*cgap/(vALDO_kALDOeq*vALDO_VALDOblf) + cfdp*cgap/vALDO_kALDOgapinh + cgap*cdhap/(vALDO_VALDOblf*vALDO_kALDOeq));
-  vGAPDH: cgap -> cpgp; cytosol*vGAPDH_rmaxGAPDH*(cgap*cnad - cpgp*cnadh/vGAPDH_KGAPDHeq)/((vGAPDH_KGAPDHgap*(1 + cpgp/vGAPDH_KGAPDHpgp) + cgap)*(vGAPDH_KGAPDHnad*(1 + cnadh/vGAPDH_KGAPDHnadh) + cnad));
-  vTIS: cdhap -> cgap; cytosol*vTIS_rmaxTIS*(cdhap - cgap/vTIS_kTISeq)/(vTIS_kTISdhap*(1 + cgap/vTIS_kTISgap) + cdhap);
-  vTRPSYNTH:  -> cpyr + cgap; cytosol*vTRPSYNTH_rmaxTrpSynth;
-  vG3PDH: cdhap -> ; cytosol*vG3PDH_rmaxG3PDH*cdhap/(vG3PDH_KG3PDHdhap + cdhap);
-  vPGK: cpgp -> cpg3; cytosol*vPGK_rmaxPGK*(cadp*cpgp - catp*cpg3/vPGK_KPGKeq)/((vPGK_KPGKadp*(1 + catp/vPGK_KPGKatp) + cadp)*(vPGK_KPGKpgp*(1 + cpg3/vPGK_KPGKpg3) + cpgp));
-  vsersynth: cpg3 -> ; cytosol*vsersynth_rmaxSerSynth*cpg3/(vsersynth_KSerSynthpg3 + cpg3);
-  vrpGluMu: cpg3 -> cpg2; cytosol*vrpGluMu_rmaxPGluMu*(cpg3 - cpg2/vrpGluMu_KPGluMueq)/(vrpGluMu_KPGluMupg3*(1 + cpg2/vrpGluMu_KPGluMupg2) + cpg3);
-  vENO: cpg2 -> cpep; cytosol*vENO_rmaxENO*(cpg2 - cpep/vENO_KENOeq)/(vENO_KENOpg2*(1 + cpep/vENO_KENOpep) + cpg2);
-  vPK: cpep -> cpyr; cytosol*vPK_rmaxPK*cpep*(cpep/vPK_KPKpep + 1)^(vPK_nPK - 1)*cadp/(vPK_KPKpep*(vPK_LPK*((1 + catp/vPK_KPKatp)/(cfdp/vPK_KPKfdp + camp/vPK_KPKamp + 1))^vPK_nPK + (cpep/vPK_KPKpep + 1)^vPK_nPK)*(cadp + vPK_KPKadp));
-  vpepCxylase: cpep -> ; cytosol*vpepCxylase_rmaxpepCxylase*cpep*(1 + (cfdp/vpepCxylase_KpepCxylasefdp)^vpepCxylase_npepCxylasefdp)/(vpepCxylase_KpepCxylasepep + cpep);
-  vSynth1: cpep -> ; cytosol*vSynth1_rmaxSynth1*cpep/(vSynth1_KSynth1pep + cpep);
-  vSynth2: cpyr -> ; cytosol*vSynth2_rmaxSynth2*cpyr/(vSynth2_KSynth2pyr + cpyr);
-  vDAHPS: ce4p + cpep -> ; cytosol*vDAHPS_rmaxDAHPS*ce4p^vDAHPS_nDAHPSe4p*cpep^vDAHPS_nDAHPSpep/((vDAHPS_KDAHPSe4p + ce4p^vDAHPS_nDAHPSe4p)*(vDAHPS_KDAHPSpep + cpep^vDAHPS_nDAHPSpep));
-  vPDH: cpyr -> ; cytosol*vPDH_rmaxPDH*cpyr^vPDH_nPDH/(vPDH_KPDHpyr + cpyr^vPDH_nPDH);
-  vMethSynth:  -> cpyr; cytosol*vMethSynth_rmaxMetSynth;
-  vPGDH: cpg -> cribu5p; cytosol*vPGDH_rmaxPGDH*cpg*cnadp/((cpg + vPGDH_KPGDHpg)*(cnadp + vPGDH_KPGDHnadp*(1 + cnadph/vPGDH_KPGDHnadphinh)*(1 + catp/vPGDH_KPGDHatpinh)));
-  vR5PI: cribu5p -> crib5p; cytosol*vR5PI_rmaxR5PI*(cribu5p - crib5p/vR5PI_KR5PIeq);
-  vRu5P: cribu5p -> cxyl5p; cytosol*vRu5P_rmaxRu5P*(cribu5p - cxyl5p/vRu5P_KRu5Peq);
-  vPPK: crib5p -> ; cytosol*vPPK_rmaxRPPK*crib5p/(vPPK_KRPPKrib5p + crib5p);
-  vG1PAT: cg1p -> ; cytosol*vG1PAT_rmaxG1PAT*cg1p*catp*(1 + (cfdp/vG1PAT_KG1PATfdp)^vG1PAT_nG1PATfdp)/((vG1PAT_KG1PATatp + catp)*(vG1PAT_KG1PATg1p + cg1p));
-  vG6P: cg6p -> ; cytosol*vG6P_mu*cg6p;
-  vf6P: cf6p -> ; cytosol*vf6P_mu*cf6p;
-  vfdP: cfdp -> ; cytosol*vfdP_mu*cfdp;
-  vGAP: cgap -> ; cytosol*vGAP_mu*cgap;
-  vDHAP: cdhap -> ; cytosol*vDHAP_mu*cdhap;
-  vPGP: cpgp -> ; cytosol*vPGP_mu*cpgp;
-  vPG3: cpg3 -> ; cytosol*vPG3_mu*cpg3;
-  vpg2: cpg2 -> ; cytosol*vpg2_mu*cpg2;
-  vPEP: cpep -> ; cytosol*vPEP_mu*cpep;
-  vRibu5p: cribu5p -> ; cytosol*vRibu5p_mu*cribu5p;
-  vRIB5P: crib5p -> ; cytosol*vRIB5P_mu*crib5p;
-  vXYL5P: cxyl5p -> ; cytosol*vXYL5P_mu*cxyl5p;
-  vSED7P: csed7p -> ; cytosol*vSED7P_mu*csed7p;
-  vpyr: cpyr -> ; cytosol*vpyr_mu*cpyr;
-  vPG: cpg -> ; cytosol*vPG_mu*cpg;
-  vE4P: ce4p -> ; cytosol*vE4P_mu*ce4p;
-  vGLP: cg1p -> ; cytosol*vGLP_mu*cg1p;
-  vEXTER:  -> cglcex; extracellular*vEXTER_Dil*(vEXTER_cfeed - cglcex);
-
-  // Species initializations:
-  cpep = 2.67;
-  cglcex = 2;
-  cg6p = 3.48;
-  cpyr = 2.67;
-  cf6p = 0.6;
-  cg1p = 0.653;
-  cpg = 0.808;
-  cfdp = 0.272;
-  csed7p = 0.276;
-  cgap = 0.218;
-  ce4p = 0.098;
-  cxyl5p = 0.138;
-  crib5p = 0.398;
-  cdhap = 0.167;
-  cpgp = 0.008;
-  cpg3 = 2.13;
-  cpg2 = 0.399;
-  cribu5p = 0.111;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  catp has mM;
-  cadp has mM;
-  camp has mM;
-  cnadp has mM;
-  cnadph has mM;
-  cnad has mM;
-  cnadh has mM;
-
-  // Variable initializations:
-  vPTS_rmaxPTS = 7829.78;
-  vPTS_rmaxPTS has mM_per_second;
-  vPTS_KPTSa1 = 3082.3;
-  vPTS_KPTSa1 has mM;
-  vPTS_KPTSa2 = 0.01;
-  vPTS_KPTSa2 has mM;
-  vPTS_KPTSa3 = 245.3;
-  vPTS_KPTSa3 has dimensionless;
-  vPTS_nPTSg6p = 3.66;
-  vPTS_nPTSg6p has dimensionless;
-  vPTS_KPTSg6p = 2.15;
-  vPTS_KPTSg6p has mM;
-  vPGI_rmaxPGI = 650.9878687;
-  vPGI_rmaxPGI has mM_per_second;
-  vPGI_KPGIeq = 0.1725;
-  vPGI_KPGIeq has dimensionless;
-  vPGI_KPGIg6p = 2.9;
-  vPGI_KPGIg6p has mM;
-  vPGI_KPGIf6p = 0.266;
-  vPGI_KPGIf6p has mM;
-  vPGI_KPGIf6ppginh = 0.2;
-  vPGI_KPGIf6ppginh has mM;
-  vPGI_KPGIg6ppginh = 0.2;
-  vPGI_KPGIg6ppginh has mM;
-  vPGM_rmaxPGM = 0.8398242773;
-  vPGM_rmaxPGM has mM_per_second;
-  vPGM_KPGMeq = 0.196;
-  vPGM_KPGMeq has dimensionless;
-  vPGM_KPGMg6p = 1.038;
-  vPGM_KPGMg6p has mM;
-  vPGM_KPGMg1p = 0.0136;
-  vPGM_KPGMg1p has mM;
-  vG6PDH_rmaxG6PDH = 1.380196955;
-  vG6PDH_rmaxG6PDH has mM_per_second;
-  vG6PDH_KG6PDHg6p = 14.4;
-  vG6PDH_KG6PDHg6p has mM;
-  vG6PDH_KG6PDHnadphg6pinh = 6.43;
-  vG6PDH_KG6PDHnadphg6pinh has mM;
-  vG6PDH_KG6PDHnadp = 0.0246;
-  vG6PDH_KG6PDHnadp has mM;
-  vG6PDH_KG6PDHnadphnadpinh = 0.01;
-  vG6PDH_KG6PDHnadphnadpinh has mM;
-  vPFK_rmaxPFK = 1840.584747;
-  vPFK_rmaxPFK has mM_per_second;
-  vPFK_KPFKatps = 0.123;
-  vPFK_KPFKatps has mM;
-  vPFK_KPFKadpc = 4.14;
-  vPFK_KPFKadpc has mM;
-  vPFK_KPFKf6ps = 0.325;
-  vPFK_KPFKf6ps has mM;
-  vPFK_KPFKpep = 3.26;
-  vPFK_KPFKpep has mM;
-  vPFK_KPFKadpb = 3.89;
-  vPFK_KPFKadpb has mM;
-  vPFK_KPFKampb = 3.2;
-  vPFK_KPFKampb has mM;
-  vPFK_KPFKadpa = 128;
-  vPFK_KPFKadpa has mM;
-  vPFK_KPFKampa = 19.1;
-  vPFK_KPFKampa has mM;
-  vPFK_LPFK = 5629067;
-  vPFK_LPFK has dimensionless;
-  vPFK_nPFK = 11.1;
-  vPFK_nPFK has dimensionless;
-  vTA_rmaxTA = 10.87164108;
-  vTA_rmaxTA has per_mM_per_second;
-  vTA_KTAeq = 1.05;
-  vTA_KTAeq has dimensionless;
-  vTKA_rmaxTKa = 9.473384783;
-  vTKA_rmaxTKa has per_mM_per_second;
-  vTKA_KTKaeq = 1.2;
-  vTKA_KTKaeq has dimensionless;
-  vTKB_rmaxTKb = 86.55855855;
-  vTKB_rmaxTKb has per_mM_per_second;
-  vTKB_KTKbeq = 10;
-  vTKB_KTKbeq has dimensionless;
-  vMURSyNTH_rmaxMurSynth = 0.00043711;
-  vMURSyNTH_rmaxMurSynth has mM_per_second;
-  vALDO_rmaxALDO = 17.41464425;
-  vALDO_rmaxALDO has mM_per_second;
-  vALDO_kALDOeq = 0.144;
-  vALDO_kALDOeq has mM;
-  vALDO_kALDOfdp = 1.75;
-  vALDO_kALDOfdp has mM;
-  vALDO_kALDOgap = 0.088;
-  vALDO_kALDOgap has mM;
-  vALDO_VALDOblf = 2;
-  vALDO_VALDOblf has dimensionless;
-  vALDO_kALDOdhap = 0.088;
-  vALDO_kALDOdhap has mM;
-  vALDO_kALDOgapinh = 0.6;
-  vALDO_kALDOgapinh has mM;
-  vGAPDH_rmaxGAPDH = 921.5942861;
-  vGAPDH_rmaxGAPDH has mM_per_second;
-  vGAPDH_KGAPDHeq = 0.63;
-  vGAPDH_KGAPDHeq has dimensionless;
-  vGAPDH_KGAPDHgap = 0.683;
-  vGAPDH_KGAPDHgap has mM;
-  vGAPDH_KGAPDHpgp = 1.04e-05;
-  vGAPDH_KGAPDHpgp has mM;
-  vGAPDH_KGAPDHnad = 0.252;
-  vGAPDH_KGAPDHnad has mM;
-  vGAPDH_KGAPDHnadh = 1.09;
-  vGAPDH_KGAPDHnadh has mM;
-  vTIS_rmaxTIS = 68.67474392;
-  vTIS_rmaxTIS has mM_per_second;
-  vTIS_kTISeq = 1.39;
-  vTIS_kTISeq has dimensionless;
-  vTIS_kTISdhap = 2.8;
-  vTIS_kTISdhap has mM;
-  vTIS_kTISgap = 0.3;
-  vTIS_kTISgap has mM;
-  vTRPSYNTH_rmaxTrpSynth = 0.001037;
-  vTRPSYNTH_rmaxTrpSynth has mM_per_second;
-  vG3PDH_rmaxG3PDH = 0.01162042696;
-  vG3PDH_rmaxG3PDH has mM_per_second;
-  vG3PDH_KG3PDHdhap = 1;
-  vG3PDH_KG3PDHdhap has mM;
-  vPGK_rmaxPGK = 3021.773771;
-  vPGK_rmaxPGK has mM_per_second;
-  vPGK_KPGKeq = 1934.4;
-  vPGK_KPGKeq has dimensionless;
-  vPGK_KPGKadp = 0.185;
-  vPGK_KPGKadp has mM;
-  vPGK_KPGKatp = 0.653;
-  vPGK_KPGKatp has mM;
-  vPGK_KPGKpgp = 0.0468;
-  vPGK_KPGKpgp has mM;
-  vPGK_KPGKpg3 = 0.473;
-  vPGK_KPGKpg3 has mM;
-  vsersynth_rmaxSerSynth = 0.025712107;
-  vsersynth_rmaxSerSynth has mM_per_second;
-  vsersynth_KSerSynthpg3 = 1;
-  vsersynth_KSerSynthpg3 has mM;
-  vrpGluMu_rmaxPGluMu = 89.04965407;
-  vrpGluMu_rmaxPGluMu has mM_per_second;
-  vrpGluMu_KPGluMueq = 0.188;
-  vrpGluMu_KPGluMueq has dimensionless;
-  vrpGluMu_KPGluMupg3 = 0.2;
-  vrpGluMu_KPGluMupg3 has mM;
-  vrpGluMu_KPGluMupg2 = 0.369;
-  vrpGluMu_KPGluMupg2 has mM;
-  vENO_rmaxENO = 330.4476151;
-  vENO_rmaxENO has mM_per_second;
-  vENO_KENOeq = 6.73;
-  vENO_KENOeq has mM;
-  vENO_KENOpg2 = 0.1;
-  vENO_KENOpg2 has mM;
-  vENO_KENOpep = 0.135;
-  vENO_KENOpep has mM;
-  vPK_rmaxPK = 0.06113150238;
-  vPK_rmaxPK has mM_per_second;
-  vPK_KPKpep = 0.31;
-  vPK_KPKpep has mM;
-  vPK_nPK = 4;
-  vPK_nPK has dimensionless;
-  vPK_LPK = 1000;
-  vPK_LPK has dimensionless;
-  vPK_KPKatp = 22.5;
-  vPK_KPKatp has mM;
-  vPK_KPKfdp = 0.19;
-  vPK_KPKfdp has mM;
-  vPK_KPKamp = 0.2;
-  vPK_KPKamp has mM;
-  vPK_KPKadp = 0.26;
-  vPK_KPKadp has mM;
-  vpepCxylase_rmaxpepCxylase = 0.1070205858;
-  vpepCxylase_rmaxpepCxylase has mM_per_second;
-  vpepCxylase_KpepCxylasefdp = 0.7;
-  vpepCxylase_KpepCxylasefdp has mM;
-  vpepCxylase_npepCxylasefdp = 4.21;
-  vpepCxylase_npepCxylasefdp has dimensionless;
-  vpepCxylase_KpepCxylasepep = 4.07;
-  vpepCxylase_KpepCxylasepep has mM;
-  vSynth1_rmaxSynth1 = 0.01953897003;
-  vSynth1_rmaxSynth1 has mM_per_second;
-  vSynth1_KSynth1pep = 1;
-  vSynth1_KSynth1pep has mM;
-  vSynth2_rmaxSynth2 = 0.07361855055;
-  vSynth2_rmaxSynth2 has mM_per_second;
-  vSynth2_KSynth2pyr = 1;
-  vSynth2_KSynth2pyr has mM;
-  vDAHPS_rmaxDAHPS = 0.1079531227;
-  vDAHPS_rmaxDAHPS has mM_per_second;
-  vDAHPS_nDAHPSe4p = 2.6;
-  vDAHPS_nDAHPSe4p has dimensionless;
-  vDAHPS_nDAHPSpep = 2.2;
-  vDAHPS_nDAHPSpep has dimensionless;
-  vDAHPS_KDAHPSe4p = 0.035;
-  vDAHPS_KDAHPSe4p has mM;
-  vDAHPS_KDAHPSpep = 0.0053;
-  vDAHPS_KDAHPSpep has mM;
-  vPDH_rmaxPDH = 6.059531017;
-  vPDH_rmaxPDH has mM_per_second;
-  vPDH_nPDH = 3.68;
-  vPDH_nPDH has dimensionless;
-  vPDH_KPDHpyr = 1159;
-  vPDH_KPDHpyr has mM;
-  vMethSynth_rmaxMetSynth = 0.0022627;
-  vMethSynth_rmaxMetSynth has mM_per_second;
-  vPGDH_rmaxPGDH = 16.23235977;
-  vPGDH_rmaxPGDH has mM_per_second;
-  vPGDH_KPGDHpg = 37.5;
-  vPGDH_KPGDHpg has mM;
-  vPGDH_KPGDHnadp = 0.0506;
-  vPGDH_KPGDHnadp has mM;
-  vPGDH_KPGDHnadphinh = 0.0138;
-  vPGDH_KPGDHnadphinh has mM;
-  vPGDH_KPGDHatpinh = 208;
-  vPGDH_KPGDHatpinh has mM;
-  vR5PI_rmaxR5PI = 4.83841193;
-  vR5PI_rmaxR5PI has second_inverse;
-  vR5PI_KR5PIeq = 4;
-  vR5PI_KR5PIeq has dimensionless;
-  vRu5P_rmaxRu5P = 6.739029475;
-  vRu5P_rmaxRu5P has second_inverse;
-  vRu5P_KRu5Peq = 1.4;
-  vRu5P_KRu5Peq has dimensionless;
-  vPPK_rmaxRPPK = 0.01290045226;
-  vPPK_rmaxRPPK has mM_per_second;
-  vPPK_KRPPKrib5p = 0.1;
-  vPPK_KRPPKrib5p has mM;
-  vG1PAT_rmaxG1PAT = 0.007525458026;
-  vG1PAT_rmaxG1PAT has mM_per_second;
-  vG1PAT_KG1PATfdp = 0.119;
-  vG1PAT_KG1PATfdp has mM;
-  vG1PAT_nG1PATfdp = 1.2;
-  vG1PAT_nG1PATfdp has mM;
-  vG1PAT_KG1PATatp = 4.42;
-  vG1PAT_KG1PATatp has mM;
-  vG1PAT_KG1PATg1p = 3.2;
-  vG1PAT_KG1PATg1p has mM;
-  vG6P_mu = 2.78e-05;
-  vG6P_mu has second_inverse;
-  vf6P_mu = 2.78e-05;
-  vf6P_mu has second_inverse;
-  vfdP_mu = 2.78e-05;
-  vfdP_mu has second_inverse;
-  vGAP_mu = 2.78e-05;
-  vGAP_mu has second_inverse;
-  vDHAP_mu = 2.78e-05;
-  vDHAP_mu has second_inverse;
-  vPGP_mu = 2.78e-05;
-  vPGP_mu has second_inverse;
-  vPG3_mu = 2.78e-05;
-  vPG3_mu has second_inverse;
-  vpg2_mu = 2.78e-05;
-  vpg2_mu has second_inverse;
-  vPEP_mu = 2.78e-05;
-  vPEP_mu has second_inverse;
-  vRibu5p_mu = 2.78e-05;
-  vRibu5p_mu has second_inverse;
-  vRIB5P_mu = 2.78e-05;
-  vRIB5P_mu has second_inverse;
-  vXYL5P_mu = 2.78e-05;
-  vXYL5P_mu has second_inverse;
-  vSED7P_mu = 2.78e-05;
-  vSED7P_mu has second_inverse;
-  vpyr_mu = 2.78e-05;
-  vpyr_mu has second_inverse;
-  vPG_mu = 2.78e-05;
-  vPG_mu has second_inverse;
-  vE4P_mu = 2.78e-05;
-  vE4P_mu has second_inverse;
-  vGLP_mu = 2.78e-05;
-  vGLP_mu has second_inverse;
-  vEXTER_Dil = 2.78e-05;
-  vEXTER_Dil has second_inverse;
-  vEXTER_cfeed = 110.96;
-  vEXTER_cfeed has mM;
-
-  // Other declarations:
-  var catp, cadp, camp, cnadp, cnadph, cnad, cnadh;
-  const extracellular, cytosol;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit mM = 1e-3 mole / litre;
-  unit second_inverse = 1 / second;
-  unit mM_per_second = 1e-3 mole / (litre * second);
-  unit per_mM_per_second = litre / (1e-3 mole * second);
-
-  // Display Names:
-  substance is "millimole";
-  mM is "milli Molar";
-  second_inverse is "second inverse";
-  mM_per_second is "mM per second";
-  per_mM_per_second is "per mM per second";
-  cpep is "Phosphoenol pyruvate";
-  cglcex is "Extracellular Glucose";
-  cg6p is "Glucose-6-Phosphate";
-  cpyr is "Pyruvate";
-  cf6p is "Fructose-6-Phosphate";
-  cg1p is "Glucose-1-Phosphate";
-  cpg is "6-Phosphogluconate";
-  cfdp is "Fructose-1,6-bisphosphate";
-  csed7p is "sedoheptulose-7-phosphate";
-  cgap is "Glyceraldehyde-3-Phosphate";
-  ce4p is "Erythrose-4-phosphate";
-  cxyl5p is "Xylulose-5-phosphate";
-  crib5p is "Ribose-5-phosphate";
-  cdhap is "Dihydroxyacetonephosphate";
-  cpgp is "1,3-diphosphosphoglycerate";
-  cpg3 is "3-Phosphoglycerate";
-  cpg2 is "2-Phosphoglycerate";
-  cribu5p is "Ribulose-5-phosphate";
-  vPTS is "Phosphotransferase system";
-  vPGI is "Glucose-6-phosphate isomerase";
-  vPGM is "Phosphoglucomutase";
-  vG6PDH is "Glucose-6-phosphate dehydrogenase";
-  vPFK is "Phosphofructokinase";
-  vTA is "Transaldolase";
-  vTKA is "Transketolase a";
-  vTKB is "Transketolase b";
-  vMURSyNTH is "Mureine synthesis";
-  vALDO is "Aldolase";
-  vGAPDH is "Glyceraldehyde-3-phosphate dehydrogenase";
-  vTIS is "Triosephosphate isomerase";
-  vTRPSYNTH is "Tryptophan synthesis";
-  vG3PDH is "Glycerol-3-phosphate dehydrogenase";
-  vPGK is "Phosphoglycerate kinase";
-  vsersynth is "Serine synthesis";
-  vrpGluMu is "Phosphoglycerate mutase";
-  vENO is "Enolase";
-  vPK is "Pyruvate kinase";
-  vpepCxylase is "PEP carboxylase";
-  vSynth1 is "Synthesis 1";
-  vSynth2 is "Synthesis 2";
-  vDAHPS is "DAHP synthesis";
-  vPDH is "Pyruvate dehydrogenase";
-  vMethSynth is "Methionine synthesis";
-  vPGDH is "6-Phosphogluconate dehydrogenase";
-  vR5PI is "Ribose-phosphate isomerase";
-  vRu5P is "Ribulose-phosphate epimerase";
-  vPPK is "Ribose phosphate pyrophosphokinase";
-  vG1PAT is "Glucose-1-phosphate adenyltransferase";
-  vG6P is "G6P degradation";
-  vf6P is "F6P degradation";
-  vfdP is "FDP degradation";
-  vGAP is "GAP degradation";
-  vDHAP is "DHAP degradation";
-  vPGP is "PGP degradation";
-  vPG3 is "PG3 degradation";
-  vpg2 is "PG2 degradation";
-  vPEP is "PEP degradation";
-  vRibu5p is "Ribu5P dilution";
-  vRIB5P is "Rib5P dilution";
-  vXYL5P is "XYL5P dilution";
-  vSED7P is "SED7P dilution";
-  vpyr is "Pyruvate dilution";
-  vPG is "PG dilution";
-  vE4P is "E4P dilution";
-  vGLP is "GLP dilution";
-  vEXTER is "Extracellular glucose kinetics";
-
-  // CV terms:
-  extracellular identity "http://identifiers.org/go/GO:0005576"
-  cytosol identity "http://identifiers.org/go/GO:0005829"
-  cpep identity "http://identifiers.org/chebi/CHEBI:18021",
-                "http://identifiers.org/kegg.compound/C00074"
-  cglcex identity "http://identifiers.org/chebi/CHEBI:4167"
-  cglcex identity "http://identifiers.org/kegg.compound/C00031",
-                  "http://identifiers.org/chebi/CHEBI:4167"
-  cglcex hypernym "http://identifiers.org/chebi/CHEBI:17234",
-                  "http://identifiers.org/kegg.compound/C00293"
-  cg6p identity "http://identifiers.org/chebi/CHEBI:17665",
-                "http://identifiers.org/kegg.compound/C00668"
-  cpyr identity "http://identifiers.org/chebi/CHEBI:15361",
-                "http://identifiers.org/kegg.compound/C00022"
-  cf6p identity "http://identifiers.org/kegg.compound/C05345",
-                "http://identifiers.org/chebi/CHEBI:16084"
-  cf6p hypernym "http://identifiers.org/kegg.compound/C00085",
-                "http://identifiers.org/chebi/CHEBI:15946"
-  cf6p hypernym "http://identifiers.org/chebi/CHEBI:15946"
-  cg1p identity "http://identifiers.org/chebi/CHEBI:16077",
-                "http://identifiers.org/kegg.compound/C00103"
-  cpg identity "http://identifiers.org/chebi/CHEBI:16863",
-               "http://identifiers.org/kegg.compound/C00345"
-  cfdp identity "http://identifiers.org/chebi/CHEBI:16905",
-                "http://identifiers.org/kegg.compound/C00354"
-  csed7p identity "http://identifiers.org/chebi/CHEBI:15721",
-                  "http://identifiers.org/kegg.compound/C00281"
-  cgap identity "http://identifiers.org/chebi/CHEBI:17138",
-                "http://identifiers.org/kegg.compound/C00661"
-  ce4p identity "http://identifiers.org/chebi/CHEBI:48153",
-                "http://identifiers.org/kegg.compound/C00279"
-  cxyl5p identity "http://identifiers.org/chebi/CHEBI:16332",
-                  "http://identifiers.org/kegg.compound/C00231"
-  crib5p identity "http://identifiers.org/chebi/CHEBI:17797",
-                  "http://identifiers.org/kegg.compound/C00117"
-  cdhap identity "http://identifiers.org/chebi/CHEBI:16108",
-                 "http://identifiers.org/kegg.compound/C00111"
-  cpgp identity "http://identifiers.org/chebi/CHEBI:16001",
-                "http://identifiers.org/kegg.compound/C00236"
-  cpg3 identity "http://identifiers.org/chebi/CHEBI:17794",
-                "http://identifiers.org/kegg.compound/C00197"
-  cpg2 identity "http://identifiers.org/chebi/CHEBI:17835",
-                "http://identifiers.org/kegg.compound/C00631"
-  cribu5p identity "http://identifiers.org/chebi/CHEBI:17363",
-                   "http://identifiers.org/kegg.compound/C00199"
-  vPTS identity "http://identifiers.org/kegg.pathway/eco02060"
-  vPGI homolog "http://identifiers.org/reactome/REACT_1255"
-  vPGI identity "http://identifiers.org/kegg.reaction/R00771"
-  vPGI hypernym "http://identifiers.org/ec-code/5.3.1.9",
-                "http://identifiers.org/go/GO:0004347"
-  vPGM homolog "http://identifiers.org/reactome/REACT_605"
-  vPGM identity "http://identifiers.org/kegg.reaction/R00959"
-  vPGM hypernym "http://identifiers.org/ec-code/5.4.2.2"
-  vG6PDH part "http://identifiers.org/kegg.reaction/R00835",
-              "http://identifiers.org/kegg.reaction/R02035"
-  vG6PDH part "http://identifiers.org/ec-code/1.1.1.49",
-              "http://identifiers.org/ec-code/3.1.1.31"
-  vPFK homolog "http://identifiers.org/reactome/REACT_736"
-  vPFK identity "http://identifiers.org/kegg.reaction/R00756"
-  vPFK hypernym "http://identifiers.org/ec-code/2.7.1.11"
-  vTA homolog "http://identifiers.org/reactome/REACT_1272"
-  vTA identity "http://identifiers.org/kegg.reaction/R01827"
-  vTA hypernym "http://identifiers.org/ec-code/2.2.1.2"
-  vTKA homolog "http://identifiers.org/reactome/REACT_162"
-  vTKA identity "http://identifiers.org/kegg.reaction/R01641"
-  vTKA hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  vTKB homolog "http://identifiers.org/reactome/REACT_1811"
-  vTKB identity "http://identifiers.org/kegg.reaction/R01067"
-  vTKB hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  vMURSyNTH hypernym "http://identifiers.org/go/GO:0006002"
-  vALDO homolog "http://identifiers.org/reactome/REACT_1602"
-  vALDO identity "http://identifiers.org/kegg.reaction/R01070"
-  vALDO hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  vGAPDH homolog "http://identifiers.org/reactome/REACT_1847"
-  vGAPDH identity "http://identifiers.org/kegg.reaction/R01061"
-  vGAPDH hypernym "http://identifiers.org/ec-code/1.2.1.12"
-  vTIS homolog "http://identifiers.org/reactome/REACT_469"
-  vTIS identity "http://identifiers.org/kegg.reaction/R01015"
-  vTIS hypernym "http://identifiers.org/ec-code/5.3.1.1"
-  vTRPSYNTH hypernym "http://identifiers.org/go/GO:0000162"
-  vG3PDH homolog "http://identifiers.org/reactome/REACT_16938"
-  vG3PDH identity "http://identifiers.org/kegg.reaction/R00842"
-  vG3PDH hypernym "http://identifiers.org/ec-code/1.1.1.8"
-  vPGK homolog "http://identifiers.org/reactome/REACT_1186"
-  vPGK identity "http://identifiers.org/kegg.reaction/R01512"
-  vPGK hypernym "http://identifiers.org/ec-code/2.7.2.3"
-  vsersynth hypernym "http://identifiers.org/go/GO:0009070"
-  vrpGluMu homolog "http://identifiers.org/reactome/REACT_576"
-  vrpGluMu identity "http://identifiers.org/kegg.reaction/R01518"
-  vrpGluMu hypernym "http://identifiers.org/ec-code/5.4.2.1"
-  vENO homolog "http://identifiers.org/reactome/REACT_1400"
-  vENO identity "http://identifiers.org/kegg.reaction/R00658"
-  vENO hypernym "http://identifiers.org/ec-code/4.2.1.11"
-  vPK homolog "http://identifiers.org/reactome/REACT_1524"
-  vPK identity "http://identifiers.org/kegg.reaction/R00200"
-  vPK hypernym "http://identifiers.org/ec-code/2.7.1.40"
-  vpepCxylase identity "http://identifiers.org/kegg.reaction/R00345"
-  vpepCxylase hypernym "http://identifiers.org/ec-code/4.1.1.31"
-  vSynth1 hypernym "http://identifiers.org/go/GO:0009423"
-  vSynth2 part "http://identifiers.org/go/GO:0006523",
-               "http://identifiers.org/go/GO:0009097",
-               "http://identifiers.org/go/GO:0019877"
-  vDAHPS identity "http://identifiers.org/kegg.reaction/R01826"
-  vDAHPS hypernym "http://identifiers.org/ec-code/2.5.1.54"
-  vPDH hypernym "http://identifiers.org/ec-code/1.2.1.51"
-  vPDH identity "http://identifiers.org/kegg.reaction/R00209"
-  vPDH parthood "http://identifiers.org/kegg.pathway/rn00620"
-  vMethSynth hypernym "http://identifiers.org/go/GO:0042866"
-  vPGDH hypernym "http://identifiers.org/ec-code/1.1.1.44"
-  vPGDH identity "http://identifiers.org/kegg.reaction/R01528"
-  vPGDH homolog "http://identifiers.org/reactome/REACT_611"
-  vR5PI hypernym "http://identifiers.org/ec-code/5.3.1.6"
-  vR5PI identity "http://identifiers.org/kegg.reaction/R01056"
-  vR5PI homolog "http://identifiers.org/reactome/REACT_6907"
-  vRu5P identity "http://identifiers.org/kegg.reaction/R01529"
-  vRu5P hypernym "http://identifiers.org/ec-code/5.1.3.1"
-  vRu5P homolog "http://identifiers.org/reactome/REACT_1522"
-  vPPK identity "http://identifiers.org/kegg.reaction/R01049"
-  vPPK hypernym "http://identifiers.org/ec-code/2.7.6.1"
-  vPPK homolog "http://identifiers.org/reactome/REACT_2023"
-  vG1PAT identity "http://identifiers.org/kegg.reaction/R00948"
-  vG1PAT hypernym "http://identifiers.org/ec-code/2.7.7.27"
-  vG6P hypernym "http://identifiers.org/go/GO:0044275"
-  vf6P hypernym "http://identifiers.org/go/GO:0044275"
-  vfdP hypernym "http://identifiers.org/go/GO:0044275"
-  vGAP hypernym "http://identifiers.org/go/GO:0019683"
-  vDHAP hypernym "http://identifiers.org/go/GO:0044275"
-  vPGP hypernym "http://identifiers.org/go/GO:0044275"
-  vPG3 hypernym "http://identifiers.org/go/GO:0044275"
-  vpg2 hypernym "http://identifiers.org/go/GO:0044275"
-  vPEP hypernym "http://identifiers.org/go/GO:0046395"
-end
-
-Chassagnole2002_Carbon_Metabolism is "Chassagnole2002_Carbon_Metabolism"
-
-Chassagnole2002_Carbon_Metabolism model_entity_is "http://identifiers.org/biomodels.db/MODEL6624119661"
-Chassagnole2002_Carbon_Metabolism model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000051"
-Chassagnole2002_Carbon_Metabolism description "http://identifiers.org/pubmed/17590932"
-Chassagnole2002_Carbon_Metabolism part "http://identifiers.org/kegg.pathway/map00030",
-                                       "http://identifiers.org/kegg.pathway/map00010"
-Chassagnole2002_Carbon_Metabolism part "http://identifiers.org/go/GO:0009401",
-                                       "http://identifiers.org/go/GO:0006098",
-                                       "http://identifiers.org/go/GO:0006096"
-Chassagnole2002_Carbon_Metabolism taxon "http://identifiers.org/taxonomy/562"
diff --git a/BioModelsRAG/data/BIOMD0000000052.txt b/BioModelsRAG/data/BIOMD0000000052.txt
deleted file mode 100644
index fc265ecb3be00727a2a62b84279ca26fd84c090c..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000052.txt
+++ /dev/null
@@ -1,85 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MODEL8177704759()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Glu in compartment_, Fru in compartment_, Formic_acid in compartment_;
-  species Triose in compartment_, Acetic_acid in compartment_, Cn in compartment_;
-  species Amadori in compartment_, AMP in compartment_, C5 in compartment_;
-  species lys_R in compartment_, Melanoidin in compartment_;
-
-  // Reactions:
-  _J1: Glu => Fru; _J1_K1*Glu;
-  _J2: Fru => Glu; _J2_K2*Fru;
-  _J3: Glu => C5 + Formic_acid; _J3_K3*Glu;
-  _J4: Fru => C5 + Formic_acid; _J4_K4*Fru;
-  _J5: Fru => 2 Triose; _J5_K5*Fru;
-  _J6: Triose => Cn + Acetic_acid; _J6_K6*Triose;
-  _J7: lys_R + Glu => Amadori; _J7_K7*Glu*lys_R;
-  _J8: Amadori => Acetic_acid + lys_R; _J8_K8*Amadori;
-  _J9: Amadori => AMP; _J9_K9*Amadori;
-  _J10: lys_R + Fru => AMP; _J10_K10*Fru*lys_R;
-  _J11: AMP => Melanoidin; _J11_K11*AMP;
-
-  // Species initializations:
-  Glu = 160;
-  Fru = 0;
-  Formic_acid = 0;
-  Triose = 0;
-  Acetic_acid = 0;
-  Cn = 0;
-  Amadori = 0;
-  AMP = 0;
-  C5 = 0;
-  lys_R = 15;
-  Melanoidin = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  _J1_K1 = 0.01;
-  _J2_K2 = 0.00509;
-  _J3_K3 = 0.00047;
-  _J4_K4 = 0.0011;
-  _J5_K5 = 0.00712;
-  _J6_K6 = 0.00439;
-  _J7_K7 = 0.00018;
-  _J8_K8 = 0.11134;
-  _J9_K9 = 0.14359;
-  _J10_K10 = 0.00015;
-  _J11_K11 = 0.12514;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  Glu identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  Fru identity "http://identifiers.org/chebi/CHEBI:28757",
-               "http://identifiers.org/kegg.compound/C01496"
-  Formic_acid identity "http://identifiers.org/chebi/CHEBI:30751",
-                       "http://identifiers.org/kegg.compound/C00058"
-  Acetic_acid identity "http://identifiers.org/chebi/CHEBI:15366",
-                       "http://identifiers.org/kegg.compound/C00033"
-  lys_R identity "http://identifiers.org/chebi/CHEBI:32568"
-end
-
-MODEL8177704759 is "Brands2002 - Monosaccharide-casein systems"
-
-MODEL8177704759 model_entity_is "http://identifiers.org/biomodels.db/MODEL8177704759"
-MODEL8177704759 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000052"
-MODEL8177704759 description "http://identifiers.org/pubmed/12405768"
-MODEL8177704759 origin "http://identifiers.org/pubmed/11600005"
-MODEL8177704759 taxon "http://identifiers.org/taxonomy/131567"
-MODEL8177704759 hypernym "http://identifiers.org/go/GO:0046364",
-                         "http://identifiers.org/go/GO:0048029"
-MODEL8177704759 property "http://identifiers.org/mamo/MAMO_0000046"
diff --git a/BioModelsRAG/data/BIOMD0000000053.txt b/BioModelsRAG/data/BIOMD0000000053.txt
deleted file mode 100644
index 63be9c8ae31598c91716c5190425135231ee1f93..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000053.txt
+++ /dev/null
@@ -1,96 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Ferreira_CML_generation()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Glucose in compartment_, Lysine in compartment_, Schiff in compartment_;
-  species Amadori in compartment_, Glyoxal in compartment_, CML in compartment_;
-
-  // Assignment Rules:
-  Fraction_Amadori := Amadori/0.0034;
-  Fraction_CML := CML/0.0034;
-
-  // Reactions:
-  v1a: Lysine + Glucose => Schiff; compartment_*v1a_p1*v1a_k1a*Glucose*Lysine;
-  v1b: Schiff => Lysine + Glucose; compartment_*v1b_k1b*Schiff;
-  v2a: Schiff => Amadori; compartment_*v2a_p2*v2a_k2a*Schiff;
-  v2b: Amadori => Schiff; compartment_*v2b_p2*v2b_k2b*Amadori;
-  v3: Glucose => Glyoxal; compartment_*v3_ox*v3_p3*v3_k3*(Glucose/0.25)^0.36;
-  v4: Amadori => CML; compartment_*v4_ox*v4_p4*v4_k4*Amadori;
-  v5: Lysine + Glyoxal => CML; compartment_*v5_ox*v5_p5*v5_k5*Glyoxal*Lysine;
-  v5b: Glyoxal => ; compartment_*v5b_k5b*Glyoxal;
-  v6: Schiff => CML; compartment_*v6_ox*v6_p6*v6_k3*(Schiff/0.25)^0.36;
-  v7a:  => Lysine; compartment_*0.05*v7a_ox*v7a_p7*v7a_k3*(Schiff/0.25)^0.36;
-  v7b:  => Glyoxal; compartment_*0.005*v7b_ox*v7b_p7*v7b_k3*(Schiff/0.25)^0.36;
-  v7c: Schiff => ; compartment_*v7c_ox*v7c_p7*v7c_k3*(Schiff/0.25)^0.36;
-
-  // Species initializations:
-  Glucose = 0.25;
-  Lysine = 0.0034;
-  Schiff = 0;
-  Amadori = 0;
-  Glyoxal = 0;
-  CML = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1a_p1 = 0.115;
-  v1a_k1a = 0.09;
-  v1b_k1b = 0.36;
-  v2a_p2 = 0.75;
-  v2a_k2a = 0.033;
-  v2b_p2 = 0.75;
-  v2b_k2b = 0.0012;
-  v3_ox = 1;
-  v3_p3 = 1;
-  v3_k3 = 7.92e-07;
-  v4_ox = 1;
-  v4_p4 = 1;
-  v4_k4 = 8.6e-05;
-  v5_ox = 1;
-  v5_p5 = 1;
-  v5_k5 = 0.019;
-  v5b_k5b = 0.0017;
-  v6_ox = 1;
-  v6_p6 = 2.7;
-  v6_k3 = 7.92e-07;
-  v7a_ox = 1;
-  v7a_p7 = 60;
-  v7a_k3 = 7.92e-07;
-  v7b_ox = 1;
-  v7b_p7 = 60;
-  v7b_k3 = 7.92e-07;
-  v7c_ox = 1;
-  v7c_p7 = 60;
-  v7c_k3 = 7.92e-07;
-
-  // Other declarations:
-  var Fraction_Amadori, Fraction_CML;
-  const compartment_;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour (default)";
-
-  // CV terms:
-  Glucose identity "http://identifiers.org/chebi/CHEBI:17234",
-                   "http://identifiers.org/kegg.compound/C00293"
-  Lysine identity "http://identifiers.org/chebi/CHEBI:25094"
-  Glyoxal identity "http://identifiers.org/kegg.compound/C14448",
-                   "http://identifiers.org/chebi/CHEBI:34779"
-end
-
-Ferreira_CML_generation is "Ferreira2003_CML_generation2"
-
-Ferreira_CML_generation model_entity_is "http://identifiers.org/biomodels.db/MODEL0733584307"
-Ferreira_CML_generation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000053"
-Ferreira_CML_generation description "http://identifiers.org/pubmed/12911334"
-Ferreira_CML_generation taxon "http://identifiers.org/taxonomy/131567"
-Ferreira_CML_generation part "http://identifiers.org/go/GO:0018205",
-                             "http://identifiers.org/go/GO:0005518"
-Ferreira_CML_generation property "http://identifiers.org/doid/DOID:9120",
-                                 "http://identifiers.org/doid/DOID:9351"
diff --git a/BioModelsRAG/data/BIOMD0000000054.txt b/BioModelsRAG/data/BIOMD0000000054.txt
deleted file mode 100644
index 0d3e7de6e618667eb31032bb15f37baf9ff1a8ba..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000054.txt
+++ /dev/null
@@ -1,106 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Ataullahkhanov1996_Adenylate()
-
-  // Compartments and Species:
-  compartment cell;
-  species I in cell, E in cell, A in cell;
-
-  // Assignment Rules:
-  T := (A + 3*E - ((6*A*E - 3*E^2) + A^2)^0.5)/6;
-  M := (7*A - 3*E - ((6*A*E - 3*E^2) + A^2)^0.5)/6;
-
-  // Reactions:
-  U1:  => I; cell*P*J;
-  U2: 3 I + E => ; cell*W2*I*T;
-  U3:  => E; cell*W3*T^0.52*M^0.41;
-  U6_plus_3U7: E => ; cell*2*U;
-  U6_plus_U7_minus_U8:  => A; cell*U*(1 - W*T^n*M^k);
-
-  // Species initializations:
-  I = 10;
-  E = 2.1;
-  A = 1.11;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  P = 0.121;
-  J = 100;
-  W2 = 0.2;
-  W3 = 13.48;
-  U = 0.02;
-  W = 0.01;
-  n = 1.2;
-  k = -1;
-
-  // Other declarations:
-  var T, M;
-  const cell, P, J, W2, W3, U, W, n, k;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "millimole (default)";
-  time_unit is "hour (default)";
-  cell is "Erythrocyte";
-  I is "Ions";
-  E is "Energy pool";
-  A is "Adenylate pool";
-  T is "ATP";
-  M is "AMP";
-  P is "Membrane permeability";
-  J is "Extracellular ion concentration";
-  W2 is "Ion pump activity";
-  W3 is "Glycolytic activity";
-  U is "de novo AMP synthesis";
-  W is "AMP degradation";
-  n is "Dependence of AMP degradation on ATP";
-  k is "Dependence of AMP degradation on AMP";
-  U1 is "Passive ion influx";
-  U2 is "ATP consumption by ion pump";
-  U3 is "ATP from glycolysis";
-  U6_plus_3U7 is "AMP synthesis de novo";
-  U6_plus_U7_minus_U8 is "Adenylate pool";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  I identity "http://identifiers.org/obo.chebi/CHEBI:29101",
-             "http://identifiers.org/kegg.compound/C01330"
-  E version "http://identifiers.org/obo.chebi/CHEBI:15422",
-            "http://identifiers.org/obo.chebi/CHEBI:16761"
-  E version "http://identifiers.org/kegg.compound/C00008",
-            "http://identifiers.org/kegg.compound/C00002"
-  A version "http://identifiers.org/kegg.compound/C00020",
-            "http://identifiers.org/kegg.compound/C00008",
-            "http://identifiers.org/kegg.compound/C00002"
-  A version "http://identifiers.org/obo.chebi/CHEBI:16027",
-            "http://identifiers.org/obo.chebi/CHEBI:16761",
-            "http://identifiers.org/obo.chebi/CHEBI:15422"
-  U1 hypernym "http://identifiers.org/obo.go/GO:0006814"
-  U2 part "http://identifiers.org/obo.go/GO:0042623",
-          "http://identifiers.org/obo.go/GO:0006814"
-  U3 hypernym "http://identifiers.org/obo.go/GO:0006754"
-  U6_plus_3U7 part "http://identifiers.org/obo.go/GO:0003999",
-                   "http://identifiers.org/obo.go/GO:0004001"
-  U6_plus_3U7 part "http://identifiers.org/ec-code/2.7.1.20",
-                   "http://identifiers.org/ec-code/2.4.2.7"
-  U6_plus_U7_minus_U8 part "http://identifiers.org/ec-code/2.4.2.7",
-                           "http://identifiers.org/ec-code/3.5.4.6",
-                           "http://identifiers.org/ec-code/2.7.1.20"
-  U6_plus_U7_minus_U8 part "http://identifiers.org/obo.go/GO:0003876",
-                           "http://identifiers.org/obo.go/GO:0004001",
-                           "http://identifiers.org/obo.go/GO:0003999"
-end
-
-Ataullahkhanov1996_Adenylate is "Ataullahkhanov1996_Adenylate"
-
-Ataullahkhanov1996_Adenylate model_entity_is "http://identifiers.org/biomodels.db/MODEL4770526315"
-Ataullahkhanov1996_Adenylate model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000054"
-Ataullahkhanov1996_Adenylate description "http://identifiers.org/pubmed/8733433"
-Ataullahkhanov1996_Adenylate taxon "http://identifiers.org/taxonomy/9606"
-Ataullahkhanov1996_Adenylate part "http://identifiers.org/obo.go/GO:0002028",
-                                  "http://identifiers.org/obo.go/GO:0006167",
-                                  "http://identifiers.org/obo.go/GO:0006110"
diff --git a/BioModelsRAG/data/BIOMD0000000055.txt b/BioModelsRAG/data/BIOMD0000000055.txt
deleted file mode 100644
index d18756abec1f33d03df7df9576c5d4f44ca958cf..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000055.txt
+++ /dev/null
@@ -1,362 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Locke2005_CircadianClock()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species cLm in compartment_, cLc in compartment_, cLn in compartment_, cTm in compartment_;
-  species cTc in compartment_, cTn in compartment_, cXm in compartment_, cXc in compartment_;
-  species cXn in compartment_, cYm in compartment_, cYc in compartment_, cYn in compartment_;
-  species cPn in compartment_;
-
-  // Reactions:
-  one11:  => cLm; compartment_*ceil(sin(pi*time/dayLength + 0.001)/2)*q1*cPn;
-  two11:  => cLm; compartment_*(n1*cXn^a/(g1^a + cXn^a));
-  three11: cLm => ; compartment_*(m1*cLm/(k1 + cLm));
-  one12:  => cLc; compartment_*p1*cLm;
-  three12: cLn => cLc; compartment_*r2*cLn;
-  four12: cLc => ; compartment_*(m2*cLc/(k2 + cLc));
-  one13: cLc => cLn; compartment_*r1*cLc;
-  three13: cLn => ; compartment_*(m3*cLn/(k3 + cLn));
-  one14:  => cTm; compartment_*(n2*cYn^b/(g2^b + cYn^b))*(g3^c/(g3^c + cLn^c));
-  two14: cTm => ; compartment_*(m4*cTm/(k4 + cTm));
-  one15:  => cTc; compartment_*p2*cTm;
-  three15: cTn => cTc; compartment_*r4*cTn;
-  four15: cTc => ; compartment_*((1 - ceil(sin(pi*time/dayLength + 0.001)/2))*m5 + m6)*(cTc/(k5 + cTc));
-  one16: cTc => cTn; compartment_*r3*cTc;
-  three16: cTn => ; compartment_*((1 - ceil(sin(pi*time/dayLength + 0.001)/2))*m7 + m8)*(cTn/(k6 + cTn));
-  one17:  => cXm; compartment_*(n3*cTn^d/(g4^d + cTn^d));
-  two17: cXm => ; compartment_*(m9*cXm/(k7 + cXm));
-  one18:  => cXc; compartment_*p3*cXm;
-  three18: cXn => cXc; compartment_*r6*cXn;
-  four18: cXc => ; compartment_*(m10*cXc/(k8 + cXc));
-  one19: cXc => cXn; compartment_*r5*cXc;
-  three19: cXn => ; compartment_*(m11*cXn/(k9 + cXn));
-  one20:  => cYm; compartment_*(ceil(sin(pi*time/dayLength + 0.001)/2)*q2*cPn + (ceil(sin(pi*time/dayLength + 0.001)/2)*n4 + n5)*g5^e/(g5^e + cTn^e))*(g6^f/(g6^f + cLn^f));
-  two20: cYm => ; compartment_*(m12*cYm/(k10 + cYm));
-  one21:  => cYc; compartment_*p4*cYm;
-  three21: cYn => cYc; compartment_*r8*cYn;
-  four21: cYc => ; compartment_*(m13*cYc/(k11 + cYc));
-  one22: cYc => cYn; compartment_*r7*cYc;
-  three22: cYn => ; compartment_*(m14*cYn/(k12 + cYn));
-  one23:  => cPn; compartment_*(1 - ceil(sin(pi*time/dayLength + 0.001)/2))*p5;
-  two23: cPn => ; compartment_*(m15*cPn/(k13 + cPn));
-  three23: cPn => ; compartment_*q3*ceil(sin(pi*time/dayLength + 0.001)/2)*cPn;
-
-  // Species initializations:
-  cLm = 0.539;
-  cLc = 0.015;
-  cLn = 0.0855;
-  cTm = 0.456;
-  cTc = 8.7;
-  cTn = 0.4;
-  cXm = 0.08;
-  cXc = 1.34;
-  cXn = 0.4;
-  cYm = 0.037;
-  cYc = 0.004;
-  cYn = 0.013;
-  cPn = 0.835;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  q1 = 2.4514;
-  n1 = 5.1694;
-  a = 3.3064;
-  g1 = 0.876738488;
-  m1 = 1.5283;
-  k1 = 1.817;
-  p1 = 0.8295;
-  r1 = 16.8363;
-  r2 = 0.1687;
-  m2 = 20.44;
-  k2 = 1.5644;
-  m3 = 3.6888;
-  k3 = 1.2765;
-  n2 = 3.0087;
-  b = 1.0258;
-  g2 = 0.036805783;
-  g3 = 0.26593318;
-  c = 1.0258;
-  m4 = 3.8231;
-  k4 = 2.5734;
-  p2 = 4.324;
-  r3 = 0.3166;
-  r4 = 2.1509;
-  m5 = 0.0013;
-  m6 = 3.1741;
-  k5 = 2.7454;
-  m7 = 0.0492;
-  m8 = 4.0424;
-  k6 = 0.4033;
-  n3 = 0.2431;
-  d = 1.4422;
-  g4 = 0.538811228;
-  m9 = 10.1132;
-  k7 = 6.5585;
-  p3 = 2.147;
-  r5 = 1.0352;
-  r6 = 3.3017;
-  m10 = 0.2179;
-  k8 = 0.6632;
-  m11 = 3.3442;
-  k9 = 17.1111;
-  q2 = 2.40178;
-  n4 = 0.0857;
-  n5 = 0.1649;
-  g5 = 1.17803247;
-  g6 = 0.064455137;
-  f = 1.0237;
-  e = 3.6064;
-  m12 = 4.297;
-  k10 = 1.7303;
-  p4 = 0.2485;
-  r7 = 2.2123;
-  r8 = 0.2002;
-  m13 = 0.1347;
-  k11 = 1.8258;
-  m14 = 0.6114;
-  k12 = 1.8066;
-  p5 = 0.5;
-  k13 = 1.2;
-  q3 = 1;
-  m15 = 1.2;
-  Lmax = 1;
-  Lmin = 0;
-  CP = 24;
-  dayLength = 12;
-  two11_Fch_0 = 8;
-  four12_Fch_0 = 8;
-
-  // Other declarations:
-  const compartment_, q1, n1, a, g1, m1, k1, p1, r1, r2, m2, k2, m3, k3, n2;
-  const b, g2, g3, c, m4, k4, p2, r3, r4, m5, m6, k5, m7, m8, k6, n3, d, g4;
-  const m9, k7, p3, r5, r6, m10, k8, m11, k9, q2, n4, n5, g5, g6, f, e, m12;
-  const k10, p4, r7, r8, m13, k11, m14, k12, p5, k13, q3, m15, Lmax, Lmin;
-  const CP, dayLength;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "nM (default)";
-  time_unit is "hour (default)";
-  cLm is "LHY mRNA";
-  cLc is "LHY protein in cytoplasm";
-  cLn is "LHY protein in nucleus";
-  cTm is "TOC1 mRNA";
-  cTc is "TOC1 protein in cytoplasm";
-  cTn is "TOC1 protein in nucleus";
-  cXm is "X mRNA";
-  cXc is "X protein in cytoplasm";
-  cXn is "X protein in nucleus";
-  cYm is "Y mRNA";
-  cYc is "Y protein in cytoplasm";
-  cYn is "Y protein in nucleus";
-  cPn is "light sensitive protein P";
-  one11 is "LHY transcription by light activation";
-  two11 is "Light independent LHY transcription";
-  three11 is "LHY mRNA degradation";
-  one12 is "LHY translation";
-  three12 is "LHY transport out of nucleus";
-  four12 is "Cytoplasmic LHY degradation";
-  one13 is "LHY transport into nucleus";
-  three13 is "Nuclear LHY degradation";
-  one14 is "TOC1 transcription";
-  two14 is "TOC mRNA degradation";
-  one15 is "TOC1 translation";
-  three15 is "TOC1 transport out of nucleus";
-  four15 is "Cytoplasmic TOC1 degradation";
-  one16 is "TOC1 movement into nucleus";
-  three16 is "Nuclear TOC1 degradation";
-  one17 is "Protein X transcription";
-  two17 is "Protein X degradation";
-  one18 is "Protein X translation";
-  three18 is "ProteinX movement out of nucleus";
-  four18 is "Cytoplasmic Protein X degradation";
-  one19 is "Protein X movement into nucleus";
-  three19 is "Nuclear Protein X degradation";
-  one20 is "Protein Y transcription";
-  two20 is "Protein Y mRNA degradation";
-  one21 is "Protein Y translation";
-  three21 is "Protein Y out of nucleus";
-  four21 is "Cytoplasmic Protein Y degradation";
-  one22 is "Protein Y into nucleus";
-  three22 is "Nuclear Protein Y degradation";
-  one23 is "Light dependent production of Protein P";
-  two23 is "Protein P degradation";
-  three23 is "Light activated Protein P degradation";
-
-  // SBO terms:
-  compartment_.sboTerm = 290
-  cLm.sboTerm = 278
-  cLc.sboTerm = 245
-  cLn.sboTerm = 245
-  cTm.sboTerm = 278
-  cTc.sboTerm = 245
-  cTn.sboTerm = 245
-  cXm.sboTerm = 278
-  cXc.sboTerm = 245
-  cXn.sboTerm = 245
-  cYm.sboTerm = 278
-  cYc.sboTerm = 245
-  cYn.sboTerm = 245
-  cPn.sboTerm = 245
-  q1.sboTerm = 337
-  n1.sboTerm = 186
-  a.sboTerm = 190
-  g1.sboTerm = 363
-  m1.sboTerm = 324
-  k1.sboTerm = 27
-  p1.sboTerm = 153
-  r1.sboTerm = 153
-  r2.sboTerm = 156
-  m2.sboTerm = 324
-  k2.sboTerm = 26
-  m3.sboTerm = 324
-  k3.sboTerm = 27
-  n2.sboTerm = 186
-  b.sboTerm = 190
-  g2.sboTerm = 363
-  g3.sboTerm = 261
-  c.sboTerm = 190
-  m4.sboTerm = 324
-  k4.sboTerm = 27
-  p2.sboTerm = 153
-  r3.sboTerm = 153
-  r4.sboTerm = 156
-  m5.sboTerm = 324
-  m6.sboTerm = 324
-  k5.sboTerm = 27
-  m7.sboTerm = 324
-  m8.sboTerm = 324
-  k6.sboTerm = 27
-  n3.sboTerm = 186
-  d.sboTerm = 190
-  g4.sboTerm = 363
-  m9.sboTerm = 324
-  k7.sboTerm = 27
-  p3.sboTerm = 153
-  r5.sboTerm = 153
-  r6.sboTerm = 156
-  m10.sboTerm = 324
-  k8.sboTerm = 27
-  m11.sboTerm = 324
-  k9.sboTerm = 27
-  q2.sboTerm = 337
-  n4.sboTerm = 186
-  n5.sboTerm = 186
-  g5.sboTerm = 261
-  g6.sboTerm = 261
-  f.sboTerm = 190
-  e.sboTerm = 190
-  m12.sboTerm = 324
-  k10.sboTerm = 27
-  p4.sboTerm = 153
-  r7.sboTerm = 153
-  r8.sboTerm = 158
-  m13.sboTerm = 324
-  k11.sboTerm = 27
-  m14.sboTerm = 324
-  k12.sboTerm = 27
-  p5.sboTerm = 153
-  k13.sboTerm = 27
-  q3.sboTerm = 337
-  m15.sboTerm = 324
-  one11.sboTerm = 183
-  two11.sboTerm = 183
-  three11.sboTerm = 179
-  one12.sboTerm = 184
-  three12.sboTerm = 185
-  four12.sboTerm = 179
-  one13.sboTerm = 185
-  three13.sboTerm = 179
-  one14.sboTerm = 183
-  two14.sboTerm = 179
-  one15.sboTerm = 184
-  three15.sboTerm = 185
-  four15.sboTerm = 179
-  one16.sboTerm = 185
-  three16.sboTerm = 179
-  one17.sboTerm = 183
-  two17.sboTerm = 179
-  one18.sboTerm = 184
-  three18.sboTerm = 185
-  four18.sboTerm = 179
-  one19.sboTerm = 185
-  three19.sboTerm = 179
-  one20.sboTerm = 183
-  two20.sboTerm = 179
-  one21.sboTerm = 184
-  three21.sboTerm = 185
-  four21.sboTerm = 179
-  one22.sboTerm = 185
-  three22.sboTerm = 179
-  one23.sboTerm = 393
-  two23.sboTerm = 179
-  three23.sboTerm = 179
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005623"
-  cLm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cLc identity "http://identifiers.org/uniprot/O81713"
-  cLn identity "http://identifiers.org/uniprot/O81713"
-  cTm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cTc identity "http://identifiers.org/uniprot/Q9LKL2"
-  cTn identity "http://identifiers.org/uniprot/Q9LKL2"
-  cXm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cXn hypernym "http://identifiers.org/go/GO:0005667"
-  cYm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cYn hypernym "http://identifiers.org/go/GO:0005667"
-  one11 hypernym "http://identifiers.org/go/GO:0009642",
-                 "http://identifiers.org/go/GO:0006351"
-  two11 hypernym "http://identifiers.org/go/GO:0006351"
-  three11 hypernym "http://identifiers.org/go/GO:0006402"
-  one12 hypernym "http://identifiers.org/go/GO:0006412"
-  three12 hypernym "http://identifiers.org/go/GO:0006886"
-  four12 hypernym "http://identifiers.org/go/GO:0030163"
-  one13 hypernym "http://identifiers.org/go/GO:0006886"
-  three13 hypernym "http://identifiers.org/go/GO:0030163"
-  one14 hypernym "http://identifiers.org/go/GO:0006351"
-  two14 hypernym "http://identifiers.org/go/GO:0006402"
-  one15 hypernym "http://identifiers.org/go/GO:0006412"
-  three15 hypernym "http://identifiers.org/go/GO:0006886"
-  four15 hypernym "http://identifiers.org/go/GO:0030163"
-  one16 hypernym "http://identifiers.org/go/GO:0006886"
-  three16 hypernym "http://identifiers.org/go/GO:0030163"
-  one17 hypernym "http://identifiers.org/go/GO:0006351"
-  two17 hypernym "http://identifiers.org/go/GO:0006402"
-  one18 hypernym "http://identifiers.org/go/GO:0006412"
-  three18 hypernym "http://identifiers.org/go/GO:0006886"
-  four18 hypernym "http://identifiers.org/go/GO:0030163"
-  one19 hypernym "http://identifiers.org/go/GO:0006886"
-  three19 hypernym "http://identifiers.org/go/GO:0030163"
-  one20 hypernym "http://identifiers.org/go/GO:0006351"
-  two20 hypernym "http://identifiers.org/go/GO:0006402"
-  one21 hypernym "http://identifiers.org/go/GO:0006412"
-  three21 hypernym "http://identifiers.org/go/GO:0006886"
-  four21 hypernym "http://identifiers.org/go/GO:0030163"
-  one22 hypernym "http://identifiers.org/go/GO:0006886"
-  three22 hypernym "http://identifiers.org/go/GO:0030163"
-  one23 hypernym "http://identifiers.org/go/GO:0009642",
-                 "http://identifiers.org/go/GO:0006412"
-  two23 hypernym "http://identifiers.org/go/GO:0030163"
-  three23 hypernym "http://identifiers.org/go/GO:0045732",
-                   "http://identifiers.org/go/GO:0009642"
-end
-
-Locke2005_CircadianClock is "Locke2005 - Circadian Clock"
-
-Locke2005_CircadianClock model_entity_is "http://identifiers.org/biomodels.db/MODEL0737170531"
-Locke2005_CircadianClock model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000055"
-Locke2005_CircadianClock description "http://identifiers.org/pubmed/16729048"
-Locke2005_CircadianClock origin "http://identifiers.org/pubmed/15784272"
-Locke2005_CircadianClock hypernym "http://identifiers.org/go/GO:0042752"
-Locke2005_CircadianClock taxon "http://identifiers.org/taxonomy/3701"
-Locke2005_CircadianClock identity "http://identifiers.org/kegg.pathway/ath04710"
diff --git a/BioModelsRAG/data/BIOMD0000000056.txt b/BioModelsRAG/data/BIOMD0000000056.txt
deleted file mode 100644
index 0999d83633432af1880ae12ceec56bfc1f9ea177..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000056.txt
+++ /dev/null
@@ -1,817 +0,0 @@
-// Created by libAntimony v2.13.0
-function BB_218(A1, A2, A3, A4)
-  (A2 - A1) + A3*A2 + A4*A1;
-end
-
-BB_218 is "BB"
-
-function GK_219(A1, A2, A3, A4)
-  2*A4*A1/((A2 - A1) + A3*A2 + A4*A1 + root(2, ((A2 - A1) + A3*A2 + A4*A1)^2 - 4*(A2 - A1)*A4*A1));
-end
-
-GK_219 is "GK"
-
-function MichaelisMenten_220(M1, J1, k1, S1)
-  k1*S1*M1/(J1 + S1);
-end
-
-MichaelisMenten_220 is "Michaelis-Menten"
-
-function Mass_Action_2_221(k1, S1, S2)
-  k1*S1*S2;
-end
-
-Mass_Action_2_221 is "Mass_Action_2"
-
-function Mass_Action_1_222(k1, S1)
-  k1*S1;
-end
-
-Mass_Action_1_222 is "Mass_Action_1"
-
-
-model *BIOMD0000000056()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species $BCK2 in cell, MASS in cell, BUB2 in cell, BUD in cell;
-  substanceOnly species C2 in cell, C2P in cell, C5 in cell, C5P in cell;
-  substanceOnly species CDC14 in cell, $CDC14T in cell, RENT in cell, RENTP in cell;
-  substanceOnly species CDC15 in cell, $CDC15i in cell, CDC20 in cell, CDC20i in cell;
-  substanceOnly species CDC6 in cell, CDC6P in cell, $CDC6T in cell, F2 in cell;
-  substanceOnly species F5 in cell, F2P in cell, F5P in cell, CDH1 in cell;
-  substanceOnly species CDH1i in cell, $CKIT in cell, $SIC1T in cell, CLB2 in cell;
-  substanceOnly species $CLB2T in cell, CLB5 in cell, $CLB5T in cell, CLN2 in cell;
-  substanceOnly species $CLN3 in cell, ESP1 in cell, $IE in cell, IEP in cell;
-  substanceOnly species LTE1 in cell, MAD2 in cell, $MCM1 in cell, NET1 in cell;
-  substanceOnly species NET1P in cell, $NET1T in cell, ORI in cell, PDS1 in cell;
-  substanceOnly species $PE in cell, PPX in cell, $SBF in cell, SIC1 in cell;
-  substanceOnly species SIC1P in cell, SPN in cell, SWI5 in cell, SWI5P in cell;
-  substanceOnly species $TEM1GDP in cell, TEM1GTP in cell;
-
-  // Assignment Rules:
-  BCK2 := b0*MASS;
-  CDC14T := CDC14 + RENT + RENTP;
-  CDC15i := CDC15T - CDC15;
-  CDC6T := CDC6 + F2 + F5 + CDC6P + F2P + F5P;
-  CKIT := SIC1T + CDC6T;
-  SIC1T := SIC1 + C2 + C5 + SIC1P + C2P + C5P;
-  CLB2T := CLB2 + C2 + C2P + F2 + F2P;
-  CLB5T := CLB5 + C5 + C5P + F5 + F5P;
-  CLN3 := C0*Dn3*MASS/(Jn3 + Dn3*MASS);
-  IE := IET - IEP;
-  MCM1 := GK_219(kamcm*CLB2, kimcm, Jamcm, Jimcm);
-  NET1T := NET1 + NET1P + RENT + RENTP;
-  PE := ESP1T - ESP1;
-  SBF := GK_219(Vasbf, Visbf, Jasbf, Jisbf);
-  Vasbf := kasbf*(esbfn2*CLN2 + esbfn3*(CLN3 + BCK2) + esbfb5*CLB5);
-  Visbf := kisbf_p + kisbf_p_p*CLB2;
-  TEM1GDP := TEM1T - TEM1GTP;
-  F := exp(-mu*D);
-  D := 1.026/mu - 32;
-  mu := ln(2)/mdt;
-  Vdb5 := kdb5_p + kdb5_p_p*CDC20;
-  Vdb2 := kdb2_p + kdb2_p_p*CDH1 + kdb2p*CDC20;
-  Vkpc1 := kd1c1 + Vd2c1/(Jd2c1 + SIC1 + C2 + C5 + SIC1P + C2P + C5P);
-  Vd2c1 := kd2c1*(ec1n3*CLN3 + ec1k2*BCK2 + ec1n2*CLN2 + ec1b5*CLB5 + ec1b2*CLB2);
-  Vkpf6 := kd1f6 + Vd2f6/(Jd2f6 + CDC6 + F2 + F5 + CDC6P + F2P + F5P);
-  Vd2f6 := kd2f6*(ef6n3*CLN3 + ef6k2*BCK2 + ef6n2*CLN2 + ef6b5*CLB5 + ef6b2*CLB2);
-  Vacdh := kacdh_p + kacdh_p_p*CDC14;
-  Vicdh := kicdh_p + kicdh_p_p*(eicdhn3*CLN3 + eicdhn2*CLN2 + eicdhb5*CLB5 + eicdhb2*CLB2);
-  Vppnet := kppnet_p + kppnet_p_p*PPX;
-  Vkpnet := (kkpnet_p + kkpnet_p_p*CDC15)*MASS;
-  Vdppx := kdppx_p + kdppx_p_p*(J20ppx + CDC20)*Jpds/(Jpds + PDS1);
-  Vdpds := kd1pds_p + kd2pds_p_p*CDC20 + kd3pds_p_p*CDH1;
-  Vaiep := kaiep*CLB2;
-  Vppc1 := kppc1*CDC14;
-  Vppf6 := kppf6*CDC14;
-
-  // Reactions:
-  Growth:  => MASS; mu*MASS;
-  Synthesis_of_CLN2:  => CLN2; (ksn2_p + ksn2_p_p*SBF)*MASS;
-  Degradation_of_CLN2: CLN2 => ; Mass_Action_1_222(kdn2, CLN2);
-  Synthesis_of_CLB2:  => CLB2; (ksb2_p + ksb2_p_p*MCM1)*MASS;
-  Degradation_of_CLB2: CLB2 => ; Mass_Action_1_222(Vdb2, CLB2);
-  Synthesis_of_CLB5:  => CLB5; (ksb5_p + ksb5_p_p*SBF)*MASS;
-  Degradation_of_CLB5: CLB5 => ; Mass_Action_1_222(Vdb5, CLB5);
-  Synthesis_of_SIC1:  => SIC1; ksc1_p + ksc1_p_p*SWI5;
-  Phosphorylation_of_SIC1: SIC1 => SIC1P; Mass_Action_1_222(Vkpc1, SIC1);
-  Dephosphorylation_of_SIC1: SIC1P => SIC1; Mass_Action_1_222(Vppc1, SIC1P);
-  Fast_Degradation_of_SIC1P: SIC1P => ; Mass_Action_1_222(kd3c1, SIC1P);
-  Assoc_of_CLB2_and_SIC1: CLB2 + SIC1 => C2; Mass_Action_2_221(kasb2, CLB2, SIC1);
-  Dissoc_of_CLB2SIC1_complex: C2 => CLB2 + SIC1; Mass_Action_1_222(kdib2, C2);
-  Assoc_of_CLB5_and_SIC1: CLB5 + SIC1 => C5; Mass_Action_2_221(kasb5, CLB5, SIC1);
-  Dissoc_of_CLB5SIC1: C5 => CLB5 + SIC1; Mass_Action_1_222(kdib5, C5);
-  Phosphorylation_of_C2: C2 => C2P; Mass_Action_1_222(Vkpc1, C2);
-  Dephosphorylation_of_C2P: C2P => C2; Mass_Action_1_222(Vppc1, C2P);
-  Phosphorylation_of_C5: C5 => C5P; Mass_Action_1_222(Vkpc1, C5);
-  Dephosphorylation_of_C5P: C5P => C5; Mass_Action_1_222(Vppc1, C5P);
-  Degradation_of_CLB2_in_C2: C2 => SIC1; Mass_Action_1_222(Vdb2, C2);
-  Degradation_of_CLB5_in_C5: C5 => SIC1; Mass_Action_1_222(Vdb5, C5);
-  Degradation_of_SIC1_in_C2P: C2P => CLB2; Mass_Action_1_222(kd3c1, C2P);
-  Degradation_of_SIC1P_in_C5P_: C5P => CLB5; Mass_Action_1_222(kd3c1, C5P);
-  Degradation_of_CLB2_in_C2P: C2P => SIC1P; Mass_Action_1_222(Vdb2, C2P);
-  Degradation_of_CLB5_in_C5P: C5P => SIC1P; Mass_Action_1_222(Vdb5, C5P);
-  CDC6_synthesis:  => CDC6; ksf6_p + ksf6_p_p*SWI5 + ksf6_p_p_p*SBF;
-  Phosphorylation_of_CDC6: CDC6 => CDC6P; Mass_Action_1_222(Vkpf6, CDC6);
-  Dephosphorylation_of_CDC6: CDC6P => CDC6; Mass_Action_1_222(Vppf6, CDC6P);
-  Degradation_of_CDC6P: CDC6P => ; Mass_Action_1_222(kd3f6, CDC6P);
-  CLB2CDC6_complex_formation: CLB2 + CDC6 => F2; Mass_Action_2_221(kasf2, CLB2, CDC6);
-  CLB2CDC6_dissociation: F2 => CLB2 + CDC6; Mass_Action_1_222(kdif2, F2);
-  CLB5CDC6_complex_formation: CLB5 + CDC6 => F5; Mass_Action_2_221(kasf5, CLB5, CDC6);
-  CLB5CDC6_dissociation: F5 => CLB5 + CDC6; Mass_Action_1_222(kdif5, F5);
-  F2_phosphorylation: F2 => F2P; Mass_Action_1_222(Vkpf6, F2);
-  F2P_dephosphorylation: F2P => F2; Mass_Action_1_222(Vppf6, F2P);
-  F5_phosphorylation: F5 => F5P; Mass_Action_1_222(Vkpf6, F5);
-  F5P_dephosphorylation: F5P => F5; Mass_Action_1_222(Vppf6, F5P);
-  CLB2_degradation_in_F2: F2 => CDC6; Mass_Action_1_222(Vdb2, F2);
-  CLB5_degradation_in_F5: F5 => CDC6; Mass_Action_1_222(Vdb5, F5);
-  CDC6_degradation_in_F2P: F2P => CLB2; Mass_Action_1_222(kd3f6, F2P);
-  CDC6_degradation_in_F5P: F5P => CLB5; Mass_Action_1_222(kd3f6, F5P);
-  CLB2_degradation_in_F2P: F2P => CDC6P; Mass_Action_1_222(Vdb2, F2P);
-  CLB5_degradation_in_F5P: F5P => CDC6P; Mass_Action_1_222(Vdb5, F5P);
-  Synthesis_of_SWI5:  => SWI5; ksswi_p + ksswi_p_p*MCM1;
-  Degradation_of_SWI5: SWI5 => ; Mass_Action_1_222(kdswi, SWI5);
-  Degradation_of_SWI5P: SWI5P => ; Mass_Action_1_222(kdswi, SWI5P);
-  Activation_of_SWI5: SWI5P => SWI5; Mass_Action_1_222(kaswi*CDC14, SWI5P);
-  Inactivation_of_SWI5: SWI5 => SWI5P; Mass_Action_1_222(kiswi*CLB2, SWI5);
-  Activation_of_IEP: $IE => IEP; MichaelisMenten_220(Vaiep, Jaiep, 1, IE);
-  Inactivation_1: IEP => $IE; MichaelisMenten_220(1, Jiiep, kiiep, IEP);
-  Synthesis_of_inactive_CDC20:  => CDC20i; ks20_p + ks20_p_p*MCM1;
-  Degradation_of_inactiveCDC20: CDC20i => ; Mass_Action_1_222(kd20, CDC20i);
-  Degradation_of_active_CDC20: CDC20 => ; Mass_Action_1_222(kd20, CDC20);
-  Activation_of_CDC20: CDC20i => CDC20; Mass_Action_1_222(ka20_p + ka20_p_p*IEP, CDC20i);
-  Inactivation_2: CDC20 => CDC20i; Inactivation_2_k*Mass_Action_1_222(MAD2, CDC20);
-  CDH1_synthesis:  => CDH1; kscdh;
-  CDH1_degradation: CDH1 => ; Mass_Action_1_222(kdcdh, CDH1);
-  CDH1i_degradation: CDH1i => ; Mass_Action_1_222(kdcdh, CDH1i);
-  CDH1i_activation: CDH1i => CDH1; MichaelisMenten_220(Vacdh, Jacdh, 1, CDH1i);
-  Inactivation_3: CDH1 => CDH1i; MichaelisMenten_220(Vicdh, Jicdh, 1, CDH1);
-  CDC14_synthesis:  => CDC14; ks14;
-  CDC14_degradation: CDC14 => ; Mass_Action_1_222(kd14, CDC14);
-  Assoc_with_NET1_to_form_RENT: CDC14 + NET1 => RENT; Mass_Action_2_221(kasrent, CDC14, NET1);
-  Dissoc_from_RENT: RENT => NET1 + CDC14; Mass_Action_1_222(kdirent, RENT);
-  Assoc_with_NET1P_to_form_RENTP: CDC14 + NET1P => RENTP; Mass_Action_2_221(kasrentp, CDC14, NET1P);
-  Dissoc_from_RENP: RENTP => CDC14 + NET1P; Mass_Action_1_222(kdirentp, RENTP);
-  Net1_synthesis:  => NET1; ksnet;
-  Net1_degradation: NET1 => ; Mass_Action_1_222(kdnet, NET1);
-  Net1P_degradation: NET1P => ; Mass_Action_1_222(kdnet, NET1P);
-  NET1_phosphorylation: NET1 => NET1P; Mass_Action_1_222(Vkpnet, NET1);
-  dephosphorylation_1: NET1P => NET1; Mass_Action_1_222(Vppnet, NET1P);
-  RENT_phosphorylation: RENT => RENTP; Mass_Action_1_222(Vkpnet, RENT);
-  dephosphorylation_2: RENTP => RENT; Mass_Action_1_222(Vppnet, RENTP);
-  Degradation_of_NET1_in_RENT: RENT => CDC14; Mass_Action_1_222(kdnet, RENT);
-  Degradation_of_NET1P_in_RENTP: RENTP => CDC14; Mass_Action_1_222(kdnet, RENTP);
-  Degradation_of_CDC14_in_RENT: RENT => NET1; Mass_Action_1_222(kd14, RENT);
-  Degradation_of_CDC14_in_RENTP: RENTP => NET1P; Mass_Action_1_222(kd14, RENTP);
-  TEM1_activation: $TEM1GDP => TEM1GTP; MichaelisMenten_220(LTE1, Jatem, 1, TEM1GDP);
-  inactivation_1: TEM1GTP => $TEM1GDP; MichaelisMenten_220(BUB2, Jitem, 1, TEM1GTP);
-  CDC15_activation: $CDC15i => CDC15; Mass_Action_1_222(ka15_p*TEM1GDP + ka15_p_p*TEM1GTP + ka15p*CDC14, CDC15i);
-  inactivation_2: CDC15 => $CDC15i; Mass_Action_1_222(ki15, CDC15);
-  PPX_synthesis:  => PPX; ksppx;
-  degradation_1: PPX => ; Mass_Action_1_222(Vdppx, PPX);
-  PDS1_synthesis:  => PDS1; kspds_p + ks1pds_p_p*SBF + ks2pds_p_p*MCM1;
-  degradation_2: PDS1 => ; Mass_Action_1_222(Vdpds, PDS1);
-  Degradation_of_PDS1_in_PE: $PE => ESP1; Mass_Action_1_222(Vdpds, PE);
-  Assoc_with_ESP1_to_form_PE: PDS1 + ESP1 => $PE; Mass_Action_2_221(kasesp, PDS1, ESP1);
-  Disso_from_PE: $PE => PDS1 + ESP1; Mass_Action_1_222(kdiesp, PE);
-  DNA_synthesis:  => ORI; ksori*(eorib5*CLB5 + eorib2*CLB2);
-  Negative_regulation_of_DNA_synthesis: ORI => ; Mass_Action_1_222(kdori, ORI);
-  Budding:  => BUD; ksbud*(ebudn2*CLN2 + ebudn3*CLN3 + ebudb5*CLB5);
-  Negative_regulation_of_Cell_budding: BUD => ; Mass_Action_1_222(kdbud, BUD);
-  Spindle_formation:  => SPN; ksspn*CLB2/(Jspn + CLB2);
-  Spindle_disassembly: SPN => ; Mass_Action_1_222(kdspn, SPN);
-
-  // Events:
-  reset_ORI: at (CLB2 + CLB5 - KEZ2) < 0: ORI = 0;
-  start_S: at (ORI - 1) > 0: BUB2 = bub2h, MAD2 = mad2h;
-  spindle_checkpoint: at (SPN - 1) > 0: BUB2 = bub2l, LTE1 = lte1h, MAD2 = mad2l;
-  cell_division: at (CLB2 - KEZ) < 0: SPN = 0, BUD = 0, LTE1 = lte1l, MASS = F*MASS;
-
-  // Species initializations:
-  MASS = 1.206019/cell;
-  BUB2 = 0.2/cell;
-  BUD = 0.008473/cell;
-  C2 = 0.238404/cell;
-  C2P = 0.024034/cell;
-  C5 = 0.070081/cell;
-  C5P = 0.006878/cell;
-  CDC14 = 0.468344/cell;
-  RENT = 1.04954/cell;
-  RENTP = 0.6/cell;
-  CDC15 = 0.656533/cell;
-  CDC20 = 0.444296/cell;
-  CDC20i = 1.472044/cell;
-  CDC6 = 0.10758/cell;
-  CDC6P = 0.015486/cell;
-  F2 = 0.236058/cell;
-  F5 = 7.24e-05/cell;
-  F2P = 0.0273938/cell;
-  F5P = 7.91e-05/cell;
-  CDH1 = 0.930499/cell;
-  CDH1i = 0.0695/cell;
-  CLB2 = 0.1469227/cell;
-  CLB5 = 0.0518014/cell;
-  CLN2 = 0.0652511/cell;
-  ESP1 = 0.301313/cell;
-  IEP = 0.1015/cell;
-  LTE1 = 0.1/cell;
-  MAD2 = 0.01/cell;
-  NET1 = 0.018645/cell;
-  NET1P = 0.970271/cell;
-  ORI = 0.000909/cell;
-  PDS1 = 0.025612/cell;
-  PPX = 0.123179/cell;
-  SIC1 = 0.0228776/cell;
-  SIC1P = 0.00641/cell;
-  SPN = 0.03/cell;
-  SWI5 = 0.95/cell;
-  SWI5P = 0.02/cell;
-  TEM1GTP = 0.9/cell;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  b0 = 0.054;
-  CDC15T = 1;
-  C0 = 0.4;
-  Dn3 = 1;
-  Jn3 = 6;
-  IET = 1;
-  kamcm = 1;
-  kimcm = 0.15;
-  Jamcm = 0.1;
-  Jimcm = 0.1;
-  ESP1T = 1;
-  Jasbf = 0.01;
-  Jisbf = 0.01;
-  TEM1T = 1;
-  KEZ2 = 0.2;
-  mad2h = 8;
-  bub2h = 1;
-  mad2l = 0.01;
-  lte1h = 1;
-  bub2l = 0.2;
-  KEZ = 0.3;
-  lte1l = 0.1;
-  ebudb5 = 1;
-  ebudn2 = 0.25;
-  ebudn3 = 0.05;
-  ec1b2 = 0.45;
-  ec1b5 = 0.1;
-  ec1k2 = 0.03;
-  ec1n2 = 0.06;
-  ec1n3 = 0.3;
-  ef6b2 = 0.55;
-  ef6b5 = 0.1;
-  ef6k2 = 0.03;
-  ef6n2 = 0.06;
-  ef6n3 = 0.3;
-  eicdhb2 = 1.2;
-  eicdhb5 = 8;
-  eicdhn2 = 0.4;
-  eicdhn3 = 0.25;
-  eorib2 = 0.45;
-  eorib5 = 0.9;
-  esbfb5 = 2;
-  esbfn2 = 2;
-  esbfn3 = 10;
-  J20ppx = 0.15;
-  Jacdh = 0.03;
-  Jaiep = 0.1;
-  Jatem = 0.1;
-  Jd2c1 = 0.05;
-  Jd2f6 = 0.05;
-  Jicdh = 0.03;
-  Jiiep = 0.1;
-  Jitem = 0.1;
-  Jpds = 0.04;
-  Jspn = 0.14;
-  ka15_p = 0.002;
-  ka15_p_p = 1;
-  ka15p = 0.001;
-  ka20_p = 0.05;
-  ka20_p_p = 0.2;
-  kacdh_p = 0.01;
-  kacdh_p_p = 0.8;
-  kaiep = 0.1;
-  kasb2 = 50;
-  kasb5 = 50;
-  kasbf = 0.38;
-  kasesp = 50;
-  kasf2 = 15;
-  kasf5 = 0.01;
-  kasrent = 200;
-  kasrentp = 1;
-  kaswi = 2;
-  kd14 = 0.1;
-  kd1c1 = 0.01;
-  kd1f6 = 0.01;
-  kd1pds_p = 0.01;
-  kd20 = 0.3;
-  kd2c1 = 1;
-  kd2f6 = 1;
-  kd2pds_p_p = 0.2;
-  kd3c1 = 1;
-  kd3f6 = 1;
-  kd3pds_p_p = 0.04;
-  kdb2_p = 0.003;
-  kdb2_p_p = 0.4;
-  kdb2p = 0.15;
-  kdb5_p = 0.01;
-  kdb5_p_p = 0.16;
-  kdbud = 0.06;
-  kdcdh = 0.01;
-  kdib2 = 0.05;
-  kdib5 = 0.06;
-  kdiesp = 0.5;
-  kdif2 = 0.5;
-  kdif5 = 0.01;
-  kdirent = 1;
-  kdirentp = 2;
-  kdn2 = 0.12;
-  kdnet = 0.03;
-  kdori = 0.06;
-  kdppx_p = 0.17;
-  kdppx_p_p = 2;
-  kdspn = 0.06;
-  kdswi = 0.08;
-  ki15 = 0.5;
-  kicdh_p = 0.001;
-  kicdh_p_p = 0.08;
-  kiiep = 0.15;
-  kisbf_p = 0.6;
-  kisbf_p_p = 8;
-  kiswi = 0.05;
-  kkpnet_p = 0.01;
-  kkpnet_p_p = 0.6;
-  kppc1 = 4;
-  kppf6 = 4;
-  kppnet_p = 0.05;
-  kppnet_p_p = 3;
-  ks14 = 0.2;
-  ks1pds_p_p = 0.03;
-  ks20_p = 0.006;
-  ks20_p_p = 0.6;
-  ks2pds_p_p = 0.055;
-  ksb2_p = 0.001;
-  ksb2_p_p = 0.04;
-  ksb5_p = 0.0008;
-  ksb5_p_p = 0.005;
-  ksbud = 0.2;
-  ksc1_p = 0.012;
-  ksc1_p_p = 0.12;
-  kscdh = 0.01;
-  ksf6_p = 0.024;
-  ksf6_p_p = 0.12;
-  ksf6_p_p_p = 0.004;
-  ksn2_p = 0;
-  ksn2_p_p = 0.15;
-  ksnet = 0.084;
-  ksori = 2;
-  kspds_p = 0;
-  ksppx = 0.1;
-  ksspn = 0.1;
-  ksswi_p = 0.005;
-  ksswi_p_p = 0.08;
-  mdt = 90;
-  Inactivation_2_k = 1;
-
-  // Other declarations:
-  var CDC15T, IET, ESP1T, Vasbf, Visbf, TEM1T, KEZ2, mad2l, lte1h, bub2l;
-  var KEZ, F, lte1l, D, mu, Vdb5, Vdb2, Vkpc1, Vd2c1, Vkpf6, Vd2f6, Vacdh;
-  var Vicdh, Vppnet, Vkpnet, Vdppx, Vdpds, Vaiep, Vppc1, Vppf6;
-  const cell, b0, C0, Dn3, Jn3, kamcm, kimcm, Jamcm, Jimcm, Jasbf, Jisbf;
-  const mad2h, bub2h, ebudb5, ebudn2, ebudn3, ec1b2, ec1b5, ec1k2, ec1n2;
-  const ec1n3, ef6b2, ef6b5, ef6k2, ef6n2, ef6n3, eicdhb2, eicdhb5, eicdhn2;
-  const eicdhn3, eorib2, eorib5, esbfb5, esbfn2, esbfn3, J20ppx, Jacdh, Jaiep;
-  const Jatem, Jd2c1, Jd2f6, Jicdh, Jiiep, Jitem, Jpds, Jspn, ka15_p, ka15_p_p;
-  const ka15p, ka20_p, ka20_p_p, kacdh_p, kacdh_p_p, kaiep, kasb2, kasb5;
-  const kasbf, kasesp, kasf2, kasf5, kasrent, kasrentp, kaswi, kd14, kd1c1;
-  const kd1f6, kd1pds_p, kd20, kd2c1, kd2f6, kd2pds_p_p, kd3c1, kd3f6, kd3pds_p_p;
-  const kdb2_p, kdb2_p_p, kdb2p, kdb5_p, kdb5_p_p, kdbud, kdcdh, kdib2, kdib5;
-  const kdiesp, kdif2, kdif5, kdirent, kdirentp, kdn2, kdnet, kdori, kdppx_p;
-  const kdppx_p_p, kdspn, kdswi, ki15, kicdh_p, kicdh_p_p, kiiep, kisbf_p;
-  const kisbf_p_p, kiswi, kkpnet_p, kkpnet_p_p, kppc1, kppf6, kppnet_p, kppnet_p_p;
-  const ks14, ks1pds_p_p, ks20_p, ks20_p_p, ks2pds_p_p, ksb2_p, ksb2_p_p;
-  const ksb5_p, ksb5_p_p, ksbud, ksc1_p, ksc1_p_p, kscdh, ksf6_p, ksf6_p_p;
-  const ksf6_p_p_p, ksn2_p, ksn2_p_p, ksnet, ksori, kspds_p, ksppx, ksspn;
-  const ksswi_p, ksswi_p_p, mdt;
-
-  // Unit definitions:
-  unit time_unit = 60 second;
-
-  // Display Names:
-  time_unit is "min";
-  reset_ORI is "reset ORI";
-  start_S is "start DNA synthesis";
-  spindle_checkpoint is "spindle checkpoint";
-  cell_division is "cell division";
-  ka15_p is "ka15'";
-  ka15_p_p is "ka15''";
-  ka20_p is "ka20'";
-  ka20_p_p is "ka20''";
-  kacdh_p is "kacdh'";
-  kacdh_p_p is "kacdh''";
-  kd1pds_p is "kd1pds'";
-  kd2pds_p_p is "kd2pds''";
-  kd3pds_p_p is "kd3pds''";
-  kdb2_p is "kdb2'";
-  kdb2_p_p is "kdb2''";
-  kdb5_p is "kdb5'";
-  kdb5_p_p is "kdb5''";
-  kdppx_p is "kdppx'";
-  kdppx_p_p is "kdppx''";
-  kicdh_p is "kicdh'";
-  kicdh_p_p is "kicdh''";
-  kisbf_p is "kisbf'";
-  kisbf_p_p is "kisbf''";
-  kkpnet_p is "kkpnet'";
-  kkpnet_p_p is "kkpnet''";
-  kppnet_p is "kppnet'";
-  kppnet_p_p is "kppnet''";
-  ks1pds_p_p is "ks1pds''";
-  ks20_p is "ks20'";
-  ks20_p_p is "ks20''";
-  ks2pds_p_p is "ks2pds''";
-  ksb2_p is "ksb2'";
-  ksb2_p_p is "ksb2''";
-  ksb5_p is "ksb5'";
-  ksb5_p_p is "ksb5''";
-  ksc1_p is "ksc1'";
-  ksc1_p_p is "ksc1''";
-  ksf6_p is "ksf6'";
-  ksf6_p_p is "ksf6''";
-  ksf6_p_p_p is "ksf6'''";
-  ksn2_p is "ksn2'";
-  ksn2_p_p is "ksn2''";
-  kspds_p is "kspds'";
-  ksswi_p is "ksswi'";
-  ksswi_p_p is "ksswi''";
-  Synthesis_of_CLN2 is "Synthesis of CLN2";
-  Degradation_of_CLN2 is "Degradation of CLN2";
-  Synthesis_of_CLB2 is "Synthesis of CLB2";
-  Degradation_of_CLB2 is "Degradation of CLB2";
-  Synthesis_of_CLB5 is "Synthesis of CLB5";
-  Degradation_of_CLB5 is "Degradation of CLB5";
-  Synthesis_of_SIC1 is "Synthesis of SIC1";
-  Phosphorylation_of_SIC1 is "Phosphorylation of SIC1";
-  Dephosphorylation_of_SIC1 is "Dephosphorylation of SIC1";
-  Fast_Degradation_of_SIC1P is "Fast Degradation of SIC1P";
-  Assoc_of_CLB2_and_SIC1 is "Assoc. of CLB2 and SIC1";
-  Dissoc_of_CLB2SIC1_complex is "Dissoc. of CLB2/SIC1 complex";
-  Assoc_of_CLB5_and_SIC1 is "Assoc. of CLB5 and SIC1";
-  Dissoc_of_CLB5SIC1 is "Dissoc. of CLB5/SIC1";
-  Phosphorylation_of_C2 is "Phosphorylation of C2";
-  Dephosphorylation_of_C2P is "Dephosphorylation of C2P";
-  Phosphorylation_of_C5 is "Phosphorylation of C5";
-  Dephosphorylation_of_C5P is "Dephosphorylation of C5P";
-  Degradation_of_CLB2_in_C2 is "Degradation of CLB2 in C2";
-  Degradation_of_CLB5_in_C5 is "Degradation of CLB5 in C5";
-  Degradation_of_SIC1_in_C2P is "Degradation of SIC1 in C2P";
-  Degradation_of_SIC1P_in_C5P_ is "Degradation of SIC1P in C5P";
-  Degradation_of_CLB2_in_C2P is "Degradation of CLB2 in C2P";
-  Degradation_of_CLB5_in_C5P is "Degradation of CLB5 in C5P";
-  CDC6_synthesis is "CDC6 synthesis";
-  Phosphorylation_of_CDC6 is "Phosphorylation of CDC6";
-  Dephosphorylation_of_CDC6 is "Dephosphorylation of CDC6";
-  Degradation_of_CDC6P is "Degradation of CDC6P";
-  CLB2CDC6_complex_formation is "CLB2/CDC6 complex formation";
-  CLB2CDC6_dissociation is "CLB2/CDC6 dissociation";
-  CLB5CDC6_complex_formation is "CLB5/CDC6 complex formation";
-  CLB5CDC6_dissociation is "CLB5/CDC6 dissociation";
-  F2_phosphorylation is "F2 phosphorylation";
-  F2P_dephosphorylation is "F2P dephosphorylation";
-  F5_phosphorylation is "F5 phosphorylation";
-  F5P_dephosphorylation is "F5P dephosphorylation";
-  CLB2_degradation_in_F2 is "CLB2 degradation in F2";
-  CLB5_degradation_in_F5 is "CLB5 degradation in F5";
-  CDC6_degradation_in_F2P is "CDC6 degradation in F2P";
-  CDC6_degradation_in_F5P is "CDC6 degradation in F5P";
-  CLB2_degradation_in_F2P is "CLB2 degradation in F2P";
-  CLB5_degradation_in_F5P is "CLB5 degradation in F5P";
-  Synthesis_of_SWI5 is "Synthesis of SWI5";
-  Degradation_of_SWI5 is "Degradation of SWI5";
-  Degradation_of_SWI5P is "Degradation of SWI5P";
-  Activation_of_SWI5 is "Activation of SWI5";
-  Inactivation_of_SWI5 is "Inactivation of SWI5";
-  Activation_of_IEP is "Activation of IEP";
-  Inactivation_1 is "Inactivation";
-  Synthesis_of_inactive_CDC20 is "Synthesis of inactive CDC20";
-  Degradation_of_inactiveCDC20 is "Degradation of inactiveCDC20";
-  Degradation_of_active_CDC20 is "Degradation of active CDC20";
-  Activation_of_CDC20 is "Activation of CDC20";
-  Inactivation_2 is "Inactivation";
-  CDH1_synthesis is "CDH1 synthesis";
-  CDH1_degradation is "CDH1 degradation";
-  CDH1i_degradation is "CDH1i degradation";
-  CDH1i_activation is "CDH1i activation";
-  Inactivation_3 is "Inactivation";
-  CDC14_synthesis is "CDC14 synthesis";
-  CDC14_degradation is "CDC14 degradation";
-  Assoc_with_NET1_to_form_RENT is "Assoc. with NET1 to form RENT";
-  Dissoc_from_RENT is "Dissoc. from RENT";
-  Assoc_with_NET1P_to_form_RENTP is "Assoc with NET1P to form RENTP";
-  Dissoc_from_RENP is "Dissoc. from RENP";
-  Net1_synthesis is "Net1 synthesis";
-  Net1_degradation is "Net1 degradation";
-  Net1P_degradation is "Net1P degradation";
-  NET1_phosphorylation is "NET1 phosphorylation";
-  dephosphorylation_1 is "dephosphorylation";
-  RENT_phosphorylation is "RENT phosphorylation";
-  dephosphorylation_2 is "dephosphorylation";
-  Degradation_of_NET1_in_RENT is "Degradation of NET1 in RENT";
-  Degradation_of_NET1P_in_RENTP is "Degradation of NET1P in RENTP";
-  Degradation_of_CDC14_in_RENT is "Degradation of CDC14 in RENT";
-  Degradation_of_CDC14_in_RENTP is "Degradation of CDC14 in RENTP";
-  TEM1_activation is "TEM1 activation";
-  inactivation_1 is "inactivation";
-  CDC15_activation is "CDC15 activation";
-  inactivation_2 is "inactivation";
-  PPX_synthesis is "PPX synthesis";
-  degradation_1 is "degradation";
-  PDS1_synthesis is "PDS1 synthesis";
-  degradation_2 is "degradation";
-  Degradation_of_PDS1_in_PE is "Degradation of PDS1 in PE";
-  Assoc_with_ESP1_to_form_PE is "Assoc. with ESP1 to form PE";
-  Disso_from_PE is "Disso. from PE";
-  DNA_synthesis is "DNA synthesis";
-  Negative_regulation_of_DNA_synthesis is "Negative regulation of DNA synthesis";
-  Negative_regulation_of_Cell_budding is "Negative regulation of Cell budding";
-  Spindle_formation is "Spindle formation";
-  Spindle_disassembly is "Spindle disassembly";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/obo.go/GO:0005623"
-  BCK2 identity "http://identifiers.org/uniprot/P33306"
-  MASS hypernym "http://identifiers.org/obo.fma/FMA:86557"
-  BUB2 identity "http://identifiers.org/uniprot/P26448"
-  BUD hypernym "http://identifiers.org/cco/CCO:C0000485"
-  C2 part "http://identifiers.org/uniprot/P38634",
-          "http://identifiers.org/uniprot/P24869",
-          "http://identifiers.org/uniprot/P24868"
-  C2P part "http://identifiers.org/uniprot/P24868",
-           "http://identifiers.org/uniprot/P24869",
-           "http://identifiers.org/uniprot/P38634"
-  C5 part "http://identifiers.org/uniprot/P38634",
-          "http://identifiers.org/uniprot/P32943",
-          "http://identifiers.org/uniprot/P30283"
-  C5P part "http://identifiers.org/uniprot/P38634",
-           "http://identifiers.org/uniprot/P32943",
-           "http://identifiers.org/uniprot/P30283"
-  CDC14 identity "http://identifiers.org/uniprot/Q00684"
-  CDC14T identity "http://identifiers.org/uniprot/Q00684"
-  RENT identity "http://identifiers.org/obo.go/GO:0030869"
-  RENT part "http://identifiers.org/uniprot/P47035",
-            "http://identifiers.org/uniprot/P06700",
-            "http://identifiers.org/uniprot/Q00684"
-  RENTP identity "http://identifiers.org/obo.go/GO:0030869"
-  RENTP part "http://identifiers.org/uniprot/P06700",
-             "http://identifiers.org/uniprot/P47035",
-             "http://identifiers.org/uniprot/Q00684"
-  CDC15 identity "http://identifiers.org/uniprot/P27636"
-  CDC15i identity "http://identifiers.org/uniprot/P27636"
-  CDC20 identity "http://identifiers.org/uniprot/P26309"
-  CDC20i identity "http://identifiers.org/uniprot/P26309"
-  CDC6 identity "http://identifiers.org/uniprot/P09119"
-  CDC6P identity "http://identifiers.org/uniprot/P09119"
-  CDC6T identity "http://identifiers.org/uniprot/P09119"
-  F2 part "http://identifiers.org/uniprot/P09119",
-          "http://identifiers.org/uniprot/P24868",
-          "http://identifiers.org/uniprot/P24869"
-  F5 part "http://identifiers.org/uniprot/P32943",
-          "http://identifiers.org/uniprot/P30283",
-          "http://identifiers.org/uniprot/P09119"
-  F2P part "http://identifiers.org/uniprot/P09119",
-           "http://identifiers.org/uniprot/P24868",
-           "http://identifiers.org/uniprot/P24869"
-  F5P part "http://identifiers.org/uniprot/P09119",
-           "http://identifiers.org/uniprot/P30283",
-           "http://identifiers.org/uniprot/P32943"
-  CDH1 identity "http://identifiers.org/uniprot/P53197"
-  CDH1i identity "http://identifiers.org/uniprot/P53197"
-  CKIT part "http://identifiers.org/uniprot/P38634",
-            "http://identifiers.org/uniprot/P09119"
-  SIC1T identity "http://identifiers.org/uniprot/P38634"
-  CLB2 part "http://identifiers.org/uniprot/P24869",
-            "http://identifiers.org/uniprot/P24868"
-  CLB2T part "http://identifiers.org/uniprot/P24869",
-             "http://identifiers.org/uniprot/P24868"
-  CLB5 part "http://identifiers.org/uniprot/P32943",
-            "http://identifiers.org/uniprot/P30283"
-  CLB5T part "http://identifiers.org/uniprot/P32943",
-             "http://identifiers.org/uniprot/P30283"
-  CLN2 part "http://identifiers.org/uniprot/P20438",
-            "http://identifiers.org/uniprot/P20437"
-  CLN3 identity "http://identifiers.org/uniprot/P13365"
-  ESP1 identity "http://identifiers.org/uniprot/Q03018"
-  IE identity "http://identifiers.org/obo.go/GO:0005680"
-  IEP identity "http://identifiers.org/obo.go/GO:0005680"
-  LTE1 identity "http://identifiers.org/uniprot/P07866"
-  MAD2 identity "http://identifiers.org/uniprot/P40958"
-  MCM1 identity "http://identifiers.org/uniprot/P11746"
-  NET1 identity "http://identifiers.org/uniprot/P47035"
-  NET1P identity "http://identifiers.org/uniprot/P47035"
-  NET1T identity "http://identifiers.org/uniprot/P47035"
-  PDS1 identity "http://identifiers.org/uniprot/P40316"
-  PE identity "http://identifiers.org/uniprot/Q03018"
-  PPX identity "http://identifiers.org/uniprot/P38698"
-  SBF identity "http://identifiers.org/uniprot/P11938"
-  SIC1 identity "http://identifiers.org/uniprot/P38634"
-  SIC1P identity "http://identifiers.org/uniprot/P38634"
-  SPN hypernym "http://identifiers.org/cco/CCO:P0000392"
-  SWI5 identity "http://identifiers.org/uniprot/P08153"
-  SWI5P identity "http://identifiers.org/uniprot/P08153"
-  TEM1GDP identity "http://identifiers.org/uniprot/P38987"
-  TEM1GTP identity "http://identifiers.org/uniprot/P38987"
-  Growth hypernym "http://identifiers.org/obo.go/GO:0016049"
-  Synthesis_of_CLN2 hypernym "http://identifiers.org/kegg.pathway/sce04110",
-                             "http://identifiers.org/obo.go/GO:0006412"
-  Degradation_of_CLN2 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  Synthesis_of_CLB2 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Degradation_of_CLB2 hypernym "http://identifiers.org/obo.go/GO:0051437",
-                               "http://identifiers.org/obo.go/GO:0008054"
-  Synthesis_of_CLB5 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Degradation_of_CLB5 hypernym "http://identifiers.org/obo.go/GO:0008054",
-                               "http://identifiers.org/obo.go/GO:0051437"
-  Synthesis_of_SIC1 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Phosphorylation_of_SIC1 hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                                   "http://identifiers.org/obo.go/GO:0004693",
-                                   "http://identifiers.org/obo.go/GO:0006468"
-  Dephosphorylation_of_SIC1 hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                                     "http://identifiers.org/obo.go/GO:0004721",
-                                     "http://identifiers.org/obo.go/GO:0006470"
-  Fast_Degradation_of_SIC1P hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Assoc_of_CLB2_and_SIC1 hypernym "http://identifiers.org/obo.go/GO:0005515",
-                                  "http://identifiers.org/obo.go/GO:0043623"
-  Dissoc_of_CLB2SIC1_complex hypernym "http://identifiers.org/obo.go/GO:0043624"
-  Assoc_of_CLB5_and_SIC1 hypernym "http://identifiers.org/obo.go/GO:0043623",
-                                  "http://identifiers.org/obo.go/GO:0005515"
-  Dissoc_of_CLB5SIC1 hypernym "http://identifiers.org/obo.go/GO:0043624"
-  Phosphorylation_of_C2 hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                                 "http://identifiers.org/obo.go/GO:0006468",
-                                 "http://identifiers.org/obo.go/GO:0004693"
-  Dephosphorylation_of_C2P hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                                    "http://identifiers.org/obo.go/GO:0006470",
-                                    "http://identifiers.org/obo.go/GO:0004721"
-  Phosphorylation_of_C5 hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                                 "http://identifiers.org/obo.go/GO:0006468",
-                                 "http://identifiers.org/obo.go/GO:0004693"
-  Dephosphorylation_of_C5P hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                                    "http://identifiers.org/obo.go/GO:0006470",
-                                    "http://identifiers.org/obo.go/GO:0004721"
-  Degradation_of_CLB2_in_C2 hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                     "http://identifiers.org/obo.go/GO:0008054"
-  Degradation_of_CLB5_in_C5 hypernym "http://identifiers.org/obo.go/GO:0008054",
-                                     "http://identifiers.org/obo.go/GO:0051437"
-  Degradation_of_SIC1_in_C2P hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_SIC1P_in_C5P_ hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_CLB2_in_C2P hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                      "http://identifiers.org/obo.go/GO:0008054"
-  Degradation_of_CLB5_in_C5P hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                      "http://identifiers.org/obo.go/GO:0008054"
-  CDC6_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Phosphorylation_of_CDC6 hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                                   "http://identifiers.org/obo.go/GO:0004693",
-                                   "http://identifiers.org/obo.go/GO:0006468"
-  Dephosphorylation_of_CDC6 hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                                     "http://identifiers.org/obo.go/GO:0004721",
-                                     "http://identifiers.org/obo.go/GO:0006470"
-  Degradation_of_CDC6P hypernym "http://identifiers.org/obo.go/GO:0030163"
-  CLB2CDC6_complex_formation hypernym "http://identifiers.org/obo.go/GO:0043623",
-                                      "http://identifiers.org/obo.go/GO:0005515"
-  CLB2CDC6_dissociation hypernym "http://identifiers.org/obo.go/GO:0043624"
-  CLB5CDC6_complex_formation hypernym "http://identifiers.org/obo.go/GO:0043623",
-                                      "http://identifiers.org/obo.go/GO:0005515"
-  CLB5CDC6_dissociation hypernym "http://identifiers.org/obo.go/GO:0043624"
-  F2_phosphorylation hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                              "http://identifiers.org/obo.go/GO:0006468",
-                              "http://identifiers.org/obo.go/GO:0004693"
-  F2P_dephosphorylation hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                                 "http://identifiers.org/obo.go/GO:0006470",
-                                 "http://identifiers.org/obo.go/GO:0004721"
-  F5_phosphorylation hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                              "http://identifiers.org/obo.go/GO:0006468",
-                              "http://identifiers.org/obo.go/GO:0004693"
-  F5P_dephosphorylation hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                                 "http://identifiers.org/obo.go/GO:0006470",
-                                 "http://identifiers.org/obo.go/GO:0004721"
-  CLB2_degradation_in_F2 hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                  "http://identifiers.org/obo.go/GO:0008054"
-  CLB5_degradation_in_F5 hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                  "http://identifiers.org/obo.go/GO:0008054"
-  CDC6_degradation_in_F2P hypernym "http://identifiers.org/obo.go/GO:0030163"
-  CDC6_degradation_in_F5P hypernym "http://identifiers.org/obo.go/GO:0030163"
-  CLB2_degradation_in_F2P hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                   "http://identifiers.org/obo.go/GO:0008054"
-  CLB5_degradation_in_F5P hypernym "http://identifiers.org/obo.go/GO:0051437",
-                                   "http://identifiers.org/obo.go/GO:0008054"
-  Synthesis_of_SWI5 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Degradation_of_SWI5 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_SWI5P hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Activation_of_SWI5 hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                              "http://identifiers.org/obo.go/GO:0006470",
-                              "http://identifiers.org/obo.go/GO:0051091",
-                              "http://identifiers.org/obo.go/GO:0004721"
-  Inactivation_of_SWI5 hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                                "http://identifiers.org/obo.go/GO:0006468",
-                                "http://identifiers.org/obo.go/GO:0004693",
-                                "http://identifiers.org/obo.go/GO:0043433"
-  Activation_of_IEP hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                             "http://identifiers.org/obo.go/GO:0006468",
-                             "http://identifiers.org/obo.go/GO:0004693"
-  Inactivation_1 hypernym "http://identifiers.org/obo.go/GO:0001100",
-                          "http://identifiers.org/obo.go/GO:0006470"
-  Synthesis_of_inactive_CDC20 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Degradation_of_inactiveCDC20 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_active_CDC20 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Activation_of_CDC20 hypernym "http://identifiers.org/obo.go/GO:0031536"
-  Inactivation_2 hypernym "http://identifiers.org/obo.go/GO:0001100"
-  CDH1_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  CDH1_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
-  CDH1i_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
-  CDH1i_activation hypernym "http://identifiers.org/ec-code/3.1.3.48",
-                            "http://identifiers.org/obo.go/GO:0004721",
-                            "http://identifiers.org/obo.go/GO:0006470",
-                            "http://identifiers.org/obo.go/GO:0031536"
-  Inactivation_3 hypernym "http://identifiers.org/ec-code/2.7.11.22",
-                          "http://identifiers.org/obo.go/GO:0004693",
-                          "http://identifiers.org/obo.go/GO:0001100",
-                          "http://identifiers.org/obo.go/GO:0006468"
-  CDC14_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  CDC14_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Assoc_with_NET1_to_form_RENT hypernym "http://identifiers.org/obo.go/GO:0030869",
-                                        "http://identifiers.org/obo.go/GO:0005515",
-                                        "http://identifiers.org/obo.go/GO:0043623"
-  Dissoc_from_RENT hypernym "http://identifiers.org/obo.go/GO:0043624"
-  Assoc_with_NET1P_to_form_RENTP part "http://identifiers.org/kegg.pathway/ko04111"
-  Assoc_with_NET1P_to_form_RENTP hypernym "http://identifiers.org/obo.go/GO:0043623",
-                                          "http://identifiers.org/obo.go/GO:0005515"
-  Dissoc_from_RENP hypernym "http://identifiers.org/obo.go/GO:0043624"
-  Net1_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Net1_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Net1P_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
-  NET1_phosphorylation hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                                "http://identifiers.org/obo.go/GO:0004672",
-                                "http://identifiers.org/obo.go/GO:0006468",
-                                "http://identifiers.org/obo.go/GO:0031536"
-  dephosphorylation_1 hypernym "http://identifiers.org/ec-code/3.6.1.11",
-                               "http://identifiers.org/obo.go/GO:0004309",
-                               "http://identifiers.org/obo.go/GO:0006470"
-  RENT_phosphorylation hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                                "http://identifiers.org/obo.go/GO:0031536",
-                                "http://identifiers.org/obo.go/GO:0006468",
-                                "http://identifiers.org/obo.go/GO:0004672"
-  dephosphorylation_2 hypernym "http://identifiers.org/ec-code/3.6.1.11",
-                               "http://identifiers.org/obo.go/GO:0006470",
-                               "http://identifiers.org/obo.go/GO:0004309"
-  Degradation_of_NET1_in_RENT hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_NET1P_in_RENTP hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_CDC14_in_RENT hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_CDC14_in_RENTP hypernym "http://identifiers.org/obo.go/GO:0030163"
-  TEM1_activation hypernym "http://identifiers.org/obo.go/GO:0005525",
-                           "http://identifiers.org/obo.go/GO:0031536",
-                           "http://identifiers.org/obo.go/GO:0005515"
-  inactivation_1 hypernym "http://identifiers.org/obo.go/GO:0005096",
-                          "http://identifiers.org/obo.go/GO:0007094",
-                          "http://identifiers.org/obo.go/GO:0005515"
-  CDC15_activation hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                            "http://identifiers.org/ec-code/3.1.3.48",
-                            "http://identifiers.org/obo.go/GO:0004721",
-                            "http://identifiers.org/obo.go/GO:0031536",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  inactivation_2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                          "http://identifiers.org/obo.go/GO:0006469",
-                          "http://identifiers.org/obo.go/GO:0001100"
-  PPX_synthesis hypernym "http://identifiers.org/ec-code/3.6.1.11",
-                         "http://identifiers.org/obo.go/GO:0006412"
-  degradation_1 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  PDS1_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  degradation_2 hypernym "http://identifiers.org/obo.go/GO:0051437",
-                         "http://identifiers.org/obo.go/GO:0030163"
-  Degradation_of_PDS1_in_PE hypernym "http://identifiers.org/obo.go/GO:0030163",
-                                     "http://identifiers.org/obo.go/GO:0051437"
-  Assoc_with_ESP1_to_form_PE hypernym "http://identifiers.org/obo.go/GO:0043623",
-                                      "http://identifiers.org/obo.go/GO:0005515",
-                                      "http://identifiers.org/obo.go/GO:0043027"
-  Disso_from_PE hypernym "http://identifiers.org/obo.go/GO:0043280",
-                         "http://identifiers.org/obo.go/GO:0043624"
-  DNA_synthesis hypernym "http://identifiers.org/obo.go/GO:0006261",
-                         "http://identifiers.org/obo.go/GO:0000082"
-  Negative_regulation_of_DNA_synthesis hypernym "http://identifiers.org/obo.go/GO:0008156"
-  Budding hypernym "http://identifiers.org/obo.go/GO:0045782"
-  Negative_regulation_of_Cell_budding hypernym "http://identifiers.org/obo.go/GO:0045781"
-  Spindle_formation hypernym "http://identifiers.org/obo.go/GO:0051225"
-  Spindle_disassembly hypernym "http://identifiers.org/obo.go/GO:0051228"
-end
-
-BIOMD0000000056 is "Chen2004 - Cell Cycle Regulation"
-
-BIOMD0000000056 model_entity_is "http://identifiers.org/biomodels.db/MODEL6624073334"
-BIOMD0000000056 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000056"
-BIOMD0000000056 description "http://identifiers.org/pubmed/15169868"
-BIOMD0000000056 identity "http://identifiers.org/kegg.pathway/sce04111"
-BIOMD0000000056 hypernym "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000056 homolog "http://identifiers.org/reactome/REACT_152"
-BIOMD0000000056 taxon "http://identifiers.org/taxonomy/4932"
diff --git a/BioModelsRAG/data/BIOMD0000000057.txt b/BioModelsRAG/data/BIOMD0000000057.txt
deleted file mode 100644
index 646f6989c97221e9276ec84889ec5f5d575bd46b..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000057.txt
+++ /dev/null
@@ -1,110 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Sneyd2002_dynamic_model_of_IP3_Receptor()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species R in compartment_, O in compartment_, I1 in compartment_, S in compartment_;
-  species A in compartment_, I2 in compartment_;
-
-  // Assignment Rules:
-  open_probability := (0.1*O + 0.9*A)^4;
-  Phi1 := (k1*L1 + l2)*c/(L1 + c*(1 + L1/L3));
-  Phi2 := (k2*L3 + l4*c)/(L3 + c*(1 + L3/L1));
-  Phi_minus2 := (kminus2 + lminus4*c)/(1 + c/L5);
-  Phi3 := k3*L5/(L5 + c);
-  Phi4 := (k4*L5 + l6)*c/(L5 + c);
-  Phi_minus4 := L1*(kminus4 + lminus6)/(L1 + c);
-  Phi5 := (k1*L1 + l2)*c/(L1 + c);
-
-  // Reactions:
-  v1: R -> O; compartment_*(Phi2*v1_IP3*R - Phi_minus2*O);
-  v2: R -> I1; compartment_*(Phi1*R - (v2_kminus1 + v2_lminus2)*I1);
-  v3: O -> S; compartment_*(Phi3*O - v3_kminus3*S);
-  v4: O -> A; compartment_*(Phi4*O - Phi_minus4*A);
-  v5: A -> I2; compartment_*(Phi5*A - (v5_kminus1 + v5_lminus2)*I2);
-
-  // Species initializations:
-  R = 1;
-  O = 0;
-  I1 = 0;
-  S = 0;
-  A = 0;
-  I2 = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  k1 = 0.64;
-  L1 = 0.12;
-  l2 = 1.7;
-  c = 10;
-  L3 = 0.025;
-  lminus2 = 0.8;
-  k2 = 37.4;
-  l4 = 1.7;
-  kminus2 = 1.4;
-  lminus4 = 2.5;
-  L5 = 54.7;
-  kminus1 = 0.04;
-  kminus3 = 29.8;
-  k3 = 0.11;
-  k4 = 4;
-  l6 = 4707;
-  kminus4 = 0.54;
-  lminus6 = 11.4;
-  IP3 = 10;
-  v1_IP3 = 10;
-  v2_kminus1 = 0.04;
-  v2_lminus2 = 0.8;
-  v3_kminus3 = 29.8;
-  v5_kminus1 = 0.04;
-  v5_lminus2 = 0.8;
-
-  // Other declarations:
-  var open_probability, Phi1, Phi2, Phi_minus2, Phi3, Phi4, Phi_minus4, Phi5;
-  const compartment_, k1, L1, l2, c, L3, lminus2, k2, l4, kminus2, lminus4;
-  const L5, kminus1, kminus3, k3, k4, l6, kminus4, lminus6, IP3;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  R is "Receptor";
-  O is "Open State";
-  I1 is "Inactivated State 1";
-  S is "Shut State";
-  A is "Activated State";
-  I2 is "Inactivated State 2";
-  v1 is "Receptor-Open state transition";
-  v2 is "Receptor-Inactivated state 1 transition";
-  v3 is "Open-Shut state transition";
-  v4 is "Open-Activated state transition";
-  v5 is "Activated-Inactivated state 2 transition";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005829"
-  R hypernym "http://identifiers.org/interpro/IPR000493"
-  O hypernym "http://identifiers.org/interpro/IPR000493"
-  I1 hypernym "http://identifiers.org/interpro/IPR000493"
-  S hypernym "http://identifiers.org/interpro/IPR000493"
-  A hypernym "http://identifiers.org/interpro/IPR000493"
-  I2 hypernym "http://identifiers.org/interpro/IPR000493"
-  v1 hypernym "http://identifiers.org/go/GO:0031587",
-              "http://identifiers.org/go/GO:0005220"
-  v2 hypernym "http://identifiers.org/go/GO:0031586"
-  v3 hypernym "http://identifiers.org/go/GO:0031586"
-  v4 hypernym "http://identifiers.org/go/GO:0031587"
-  v5 hypernym "http://identifiers.org/go/GO:0031586"
-end
-
-Sneyd2002_dynamic_model_of_IP3_Receptor is "Sneyd2002_IP3_Receptor"
-
-Sneyd2002_dynamic_model_of_IP3_Receptor model_entity_is "http://identifiers.org/biomodels.db/MODEL9098147664"
-Sneyd2002_dynamic_model_of_IP3_Receptor model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000057"
-Sneyd2002_dynamic_model_of_IP3_Receptor description "http://identifiers.org/pubmed/11842185"
-Sneyd2002_dynamic_model_of_IP3_Receptor taxon "http://identifiers.org/taxonomy/10117"
-Sneyd2002_dynamic_model_of_IP3_Receptor identity "http://identifiers.org/kegg.pathway/map04020"
-Sneyd2002_dynamic_model_of_IP3_Receptor hypernym "http://identifiers.org/go/GO:0048016",
-                                                 "http://identifiers.org/go/GO:0019722"
diff --git a/BioModelsRAG/data/BIOMD0000000058.txt b/BioModelsRAG/data/BIOMD0000000058.txt
deleted file mode 100644
index 23df4745d84a8d51e5e63a42d055990d3c2088cc..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000058.txt
+++ /dev/null
@@ -1,124 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Bindschadler_Ca_Oscillator()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species c1 in compartment_, h1 in compartment_, c2 in compartment_, h2 in compartment_;
-
-  // Assignment Rules:
-  Phi1_c1 := r2*c1/(R1 + c1);
-  Phi_minus1_c1 := k1/(R3 + c1);
-  Phi2_c1 := (k2 + r4*c1)/(R3 + c1);
-  Phi3_c1 := k3/(R5 + c1);
-  Phi1_c2 := r2*c2/(R1 + c2);
-  Phi_minus1_c2 := k1/(R3 + c2);
-  Phi2_c2 := (k2 + r4*c2)/(R3 + c2);
-  Phi3_c2 := k3/(R5 + c2);
-
-  // Reactions:
-  Jreceptor_Cell1:  => c1; compartment_*Jreceptor_Cell1_kf*(Jreceptor_Cell1_p*h1*Phi1_c1/(Phi1_c1*Jreceptor_Cell1_p + Phi_minus1_c1))^4;
-  Jpump_Cell1: c1 => ; compartment_*(Jpump_Cell1_Vp*c1^2/(Jpump_Cell1_Kp^2 + c1^2));
-  Jleak_Cell1:  => c1; compartment_*Jleak_Cell1_Jleak;
-  Inactivated_to_S_Cell1:  => h1; compartment_*Phi3_c1*(1 - h1);
-  Open_to_Inactivated_Cell1: h1 => ; compartment_*Phi1_c1*Phi2_c1*h1*Open_to_Inactivated_Cell1_p/(Phi1_c1*Open_to_Inactivated_Cell1_p + Phi_minus1_c1);
-  Jreceptor_Cell2:  => c2; compartment_*Jreceptor_Cell2_kf*(Jreceptor_Cell2_p*h2*Phi1_c2/(Phi1_c2*Jreceptor_Cell2_p + Phi_minus1_c2))^4;
-  Jpump_Cell2: c2 => ; compartment_*Jpump_Cell2_Vp*c2^2/(Jpump_Cell2_Kp^2 + c2^2);
-  Jleak_Cell2:  => c2; compartment_*Jleak_Cell2_Jleak;
-  Inactivated_to_S_Cell2:  => h2; compartment_*Phi3_c2*(1 - h2);
-  Open_to_Inactivated_Cell2: h2 => ; compartment_*Phi1_c2*Phi2_c2*h2*Open_to_Inactivated_Cell2_p/(Phi1_c2*Open_to_Inactivated_Cell2_p + Phi_minus1_c2);
-  diffusion: c2 => c1; compartment_*diffusion_D*(c2 - c1);
-
-  // Species initializations:
-  c1 = 0.3;
-  h1 = 0.8;
-  c2 = 0.1;
-  h2 = 0.1;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  r2 = 100;
-  R1 = 6;
-  k1 = 44;
-  R3 = 50;
-  k2 = 26.5;
-  r4 = 20;
-  k3 = 1.6;
-  R5 = 1.6;
-  Jreceptor_Cell1_kf = 28;
-  Jreceptor_Cell1_p = 0.2778;
-  Jpump_Cell1_Vp = 1.2;
-  Jpump_Cell1_Kp = 0.18;
-  Jleak_Cell1_Jleak = 0.2;
-  Open_to_Inactivated_Cell1_p = 0.2778;
-  Jreceptor_Cell2_kf = 28;
-  Jreceptor_Cell2_p = 0.2778;
-  Jpump_Cell2_Vp = 1.2;
-  Jpump_Cell2_Kp = 0.18;
-  Jleak_Cell2_Jleak = 0.2;
-  Open_to_Inactivated_Cell2_p = 0.2778;
-  diffusion_D = 0.01;
-
-  // Other declarations:
-  var Phi1_c1, Phi_minus1_c1, Phi2_c1, Phi3_c1, Phi1_c2, Phi_minus1_c2, Phi2_c2;
-  var Phi3_c2;
-  const compartment_, r2, R1, k1, R3, k2, r4, k3, R5;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  c1 is "Calcium ion Cell1";
-  h1 is "Receptor fraction Cell1";
-  c2 is "Calcium ion Cell2";
-  h2 is "Receptor fraction Cell2";
-  Jreceptor_Cell1 is "IP3R mediated Ca release Cell1";
-  Jpump_Cell1 is "ATPase pump mediated Ca efflux Cell1";
-  Jleak_Cell1 is "IP3R independent Ca release Cell1";
-  Inactivated_to_S_Cell1 is "Inactivated to Shut state transition Cell1";
-  Open_to_Inactivated_Cell1 is "Open to Inactivated state transition Cell1";
-  Jreceptor_Cell2 is "IP3R mediated Ca release Cell2";
-  Jpump_Cell2 is "ATPase pump mediated Ca efflux Cell2";
-  Jleak_Cell2 is "IP3R independent Ca release Cell2";
-  Inactivated_to_S_Cell2 is "Inactivated to Shut state transition Cell2";
-  Open_to_Inactivated_Cell2 is "Open to Inactivated state transition Cell2";
-  diffusion is "Diffusion of Ca between cells";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005829"
-  c1 identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  h1 hypernym "http://identifiers.org/interpro/IPR000493"
-  c2 identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  h2 hypernym "http://identifiers.org/interpro/IPR000493"
-  Jreceptor_Cell1 identity "http://identifiers.org/go/GO:0005220"
-  Jreceptor_Cell1 hypernym "http://identifiers.org/go/GO:0007204"
-  Jpump_Cell1 identity "http://identifiers.org/go/GO:0005388"
-  Jleak_Cell1 hypernym "http://identifiers.org/go/GO:0007204"
-  Jleak_Cell1 hypernym "http://identifiers.org/go/GO:0051209"
-  Inactivated_to_S_Cell1 hypernym "http://identifiers.org/go/GO:0031586"
-  Open_to_Inactivated_Cell1 hypernym "http://identifiers.org/go/GO:0031586"
-  Jreceptor_Cell2 identity "http://identifiers.org/go/GO:0005220"
-  Jreceptor_Cell2 hypernym "http://identifiers.org/go/GO:0007204"
-  Jpump_Cell2 identity "http://identifiers.org/go/GO:0005388"
-  Jleak_Cell2 hypernym "http://identifiers.org/go/GO:0007204"
-  Jleak_Cell2 hypernym "http://identifiers.org/go/GO:0051209"
-  Inactivated_to_S_Cell2 hypernym "http://identifiers.org/go/GO:0031586"
-  Open_to_Inactivated_Cell2 hypernym "http://identifiers.org/go/GO:0031586"
-  diffusion hypernym "http://identifiers.org/go/GO:0015085"
-end
-
-Bindschadler_Ca_Oscillator is "Bindschadler2001_coupled_Ca_oscillators"
-
-Bindschadler_Ca_Oscillator model_entity_is "http://identifiers.org/biomodels.db/MODEL9107330008"
-Bindschadler_Ca_Oscillator model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000058"
-Bindschadler_Ca_Oscillator description "http://identifiers.org/pubmed/12779457"
-Bindschadler_Ca_Oscillator origin "http://identifiers.org/biomodels.db/MODEL9200487367"
-Bindschadler_Ca_Oscillator container "http://identifiers.org/bto/BTO:0000028"
-Bindschadler_Ca_Oscillator identity "http://identifiers.org/kegg.pathway/map04020"
-Bindschadler_Ca_Oscillator part "http://identifiers.org/go/GO:0019722",
-                                "http://identifiers.org/go/GO:0048016"
-Bindschadler_Ca_Oscillator taxon "http://identifiers.org/taxonomy/10116"
diff --git a/BioModelsRAG/data/BIOMD0000000059.txt b/BioModelsRAG/data/BIOMD0000000059.txt
deleted file mode 100644
index bef3829ca86287a54a73735caa3b3a597418479e..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000059.txt
+++ /dev/null
@@ -1,348 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Fridlyand2003_Ca_flux_pancreatic_cells()
-
-  // Compartments and Species:
-  compartment Cytoplasm, ER;
-  species Ca_cyt in Cytoplasm, Ca_er in ER, IP3_cyt in Cytoplasm, Na_cyt in Cytoplasm;
-  species ATP_cyt in Cytoplasm, $ADP_cyt in Cytoplasm;
-
-  // Assignment Rules:
-  ADP_cyt := 4000 - ATP_cyt;
-  n_infinity := 1/(1 + exp((Vn - V)/Sn));
-  tau_n := c/(exp((V - Vtau)/a) + exp((Vtau - V)/b));
-  I_Vca := gmvca*pvca*(V - Vca);
-  I_CaPump := Pmcap*Ca_cyt^2/(Kcap^2 + Ca_cyt^2);
-  I_NaCa := gnaca*Ca_cyt^5*(V - Vnaca)/(Ca_cyt^5 + Knaca^5);
-  I_CRAN := f_CRAN*p_CRAN*(V - Vna);
-  I_Na := gmna*pna*(V - Vna);
-  I_NaK := Pnak*(F1*f_2*f_3*F4*F5*f_6 - b_1*B2*B3*B4*b_5*B6)/D;
-  I_KDr := gmKDr*n*(V - Vk);
-  I_KCa := gmkca*f_Ca*(V - Vk);
-  I_KATP := gmkatp*Okatp*(V - Vk);
-  Vca := (TV/2)*ln(Ca_ec/Ca_cyt);
-  Vk := TV*ln(K_ec/K_cyt);
-  Vna := TV*ln(Na_ec/Na_cyt);
-  Vnaca := TV*(3*ln(Na_ec/Na_cyt) - ln(Ca_ec/Ca_cyt));
-  pvca := 1/(1 + exp((Vcah - V)/Kcah));
-  f_CRAN := -gm_CRAN/(1 + exp((Ca_er - Kcar)/3));
-  p_CRAN := V - V_CRAN;
-  pna := 1/(1 + exp((104 + V)/8));
-  f_5 := f5_ast*exp(V/(2*TV));
-  b_5 := b5_ast*exp(-V/(2*TV));
-  F1 := f_1*Na_cyt^3;
-  F4 := f_4*K_ec^2;
-  F5 := f_5*ATP_cyt;
-  B2 := b_2*ADP_cyt;
-  B3 := b_3*Na_ec^3;
-  B4 := b_4*P;
-  B6 := b_6*Ksup^2;
-  D := f_2*f_3*F4*F5*f_6 + b_1*f_3*F4*F5*f_6 + b_1*B2*F4*F5*f_6 + b_1*B2*B3*F5*f_6 + b_1*B2*B3*B4*f_6 + b_1*B2*B3*B4*b_5;
-  f_Ca := Ca_cyt^4/(Ca_cyt^4 + Kkca^4);
-  Okatp := (0.08*(1 + 0.33*(ADP_cyt/Kdd)) + 0.89*(0.165*(ADP_cyt/Kdd))^2)/((1 + 0.165*(ADP_cyt/Kdd))^2*(1 + 0.135*(ADP_cyt/Ktd) + 0.05*(ATP_cyt/Ktt)));
-  Jerp := Pcaer*Ca_cyt^2/(Ca_cyt^2 + Kcarp^2);
-  O_infinity := Ca_cyt*IP3_cyt^3/((Ca_cyt + Krca)*(IP3_cyt^3 + Kip3^3));
-  Jout := (Pleak + Pip3*O_infinity)*(Ca_er - Ca_cyt);
-
-  // Rate Rules:
-  n' = (n_infinity - n)/tau_n;
-  V' = (0 - (I_Vca + I_CaPump + I_NaCa + I_CRAN + I_Na + I_NaK + I_KDr + I_KCa + I_KATP))/Cm;
-
-  // Reactions:
-  Calcium_cyt_Ivca:  => Ca_cyt; fi*-I_Vca/(2*F);
-  Calcium_cyt_Inaca:  => Ca_cyt; fi*2*I_NaCa/(2*F);
-  Calcium_cyt_Icapump: Ca_cyt => ; fi*2*I_CaPump/(2*F);
-  Calcium_cyt_Jerp: 0.01 Ca_cyt => 0.03 Ca_er; Cytoplasm*Jerp;
-  Calcium_cyt_Jout: 0.03 Ca_er => 0.01 Ca_cyt; Jout;
-  Calcium_cyt_sequestration: Ca_cyt => ; Cytoplasm*ksg*Ca_cyt;
-  IP3_synthesis:  => IP3_cyt; Cytoplasm*kip*Ca_cyt^2/(Ca_cyt^2 + Kipca^2);
-  IP3_degradation: IP3_cyt => ; Cytoplasm*kdip*IP3_cyt;
-  Na_Inaca: Na_cyt => ; 3*I_NaCa/F;
-  Na_Inak: Na_cyt => ; 3*I_NaK/F;
-  Na_Ina:  => Na_cyt; -I_Na/F;
-  Na_Icran:  => Na_cyt; -I_CRAN/F;
-  ATP_production:  => ATP_cyt; Cytoplasm*kadp*ADP_cyt;
-  ATP_NaKATPase: ATP_cyt => ; I_NaK/F;
-  ATP_Capump: ATP_cyt => ; I_CaPump/F;
-  ATP_Jerp: ATP_cyt => ; Cytoplasm*Jerp/2;
-  ATP_Ca_dependent_consumption: ATP_cyt => ; Cytoplasm*katpca*Ca_cyt*ATP_cyt;
-  ATP_consumption: ATP_cyt => ; Cytoplasm*katp*ATP_cyt;
-
-  // Species initializations:
-  Ca_cyt = 0.085;
-  Ca_er = 22.8;
-  IP3_cyt = 0.33;
-  Na_cyt = 9858;
-  ATP_cyt = 932.1;
-
-  // Compartment initializations:
-  Cytoplasm = 7.64e-13;
-  ER = 2.8e-13;
-
-  // Variable initializations:
-  n = 0.00123;
-  n_infinity has dimensionless;
-  tau_n has time_unit;
-  V = -60.9;
-  V has millivolt;
-  I_Vca has femtoampere;
-  I_CaPump has femtoampere;
-  I_NaCa has femtoampere;
-  I_CRAN has femtoampere;
-  I_Na has femtoampere;
-  I_NaK has femtoampere;
-  I_KDr has femtoampere;
-  I_KCa has femtoampere;
-  I_KATP has femtoampere;
-  Cm = 6158;
-  Cm has femtofarad;
-  Vca has millivolt;
-  TV = 26.73;
-  TV has millivolt;
-  Ca_ec = 2600;
-  Ca_ec has micromole_per_litre;
-  Vk has millivolt;
-  K_ec = 8000;
-  K_ec has micromole_per_litre;
-  K_cyt = 132400;
-  K_cyt has micromole_per_litre;
-  Vna has millivolt;
-  Na_ec = 140000;
-  Na_ec has micromole_per_litre;
-  Vnaca has millivolt;
-  Vcah = -19;
-  Vcah has millivolt;
-  Kcah = 9.5;
-  Kcah has millivolt;
-  gm_CRAN = 0.7;
-  gm_CRAN has picosiemens_per_millivolt;
-  Kcar = 200;
-  Kcar has micromole_per_litre;
-  p_CRAN has millivolt;
-  V_CRAN = 0;
-  V_CRAN has millivolt;
-  pna has dimensionless;
-  f5_ast = 0.002;
-  f5_ast has per_microM_per_millisecond;
-  b5_ast = 0.03;
-  b5_ast has per_millisecond;
-  f_1 = 2.5e-10;
-  f_1 has per_microMcube_per_millisecond;
-  f_4 = 1.5e-08;
-  f_4 has per_microMsquare_per_millisecond;
-  b_2 = 0.0001;
-  b_2 has per_microM_per_millisecond;
-  b_3 = 1.72e-17;
-  b_3 has per_microMcube_per_millisecond;
-  b_4 = 0.0002;
-  b_4 has per_microM_per_millisecond;
-  P = 4950;
-  P has micromole_per_litre;
-  b_6 = 6e-07;
-  b_6 has per_microM_per_millisecond;
-  Ksup = 150400;
-  Ksup has micromole_per_litre;
-  f_2 = 10;
-  f_2 has per_millisecond;
-  f_3 = 0.172;
-  f_3 has per_millisecond;
-  f_6 = 11.5;
-  f_6 has per_millisecond;
-  b_1 = 100;
-  b_1 has per_millisecond;
-  f_Ca has dimensionless;
-  Kkca = 0.1;
-  Kkca has micromole_per_litre;
-  Okatp has dimensionless;
-  Kdd = 17;
-  Kdd has micromole_per_litre;
-  Ktd = 26;
-  Ktd has micromole_per_litre;
-  Ktt = 1;
-  Ktt has micromole_per_litre;
-  Vn = -14;
-  Vn has millivolt;
-  Sn = 7;
-  Sn has millivolt;
-  c = 20;
-  c has time_unit;
-  Vtau = -75;
-  Vtau has millivolt;
-  a = 65;
-  a has millivolt;
-  b = 20;
-  b has millivolt;
-  gmvca = 770;
-  gmvca has picosiemens;
-  Pmcap = 2000;
-  Pmcap has femtoampere;
-  Kcap = 0.1;
-  Kcap has micromole_per_litre;
-  gnaca = 271;
-  gnaca has picosiemens;
-  Knaca = 0.75;
-  Knaca has micromole_per_litre;
-  gmna = 1200;
-  gmna has picosiemens;
-  Pnak = 600;
-  Pnak has femtoampere;
-  gmKDr = 3000;
-  gmKDr has picosiemens;
-  gmkca = 130;
-  gmkca has picosiemens;
-  gmkatp = 24000;
-  gmkatp has picosiemens;
-  Jerp has microM_per_millisecond;
-  Pcaer = 0.105;
-  Pcaer has microM_per_millisecond;
-  Kcarp = 0.5;
-  Kcarp has micromole_per_litre;
-  O_infinity has dimensionless;
-  Krca = 0.077;
-  Krca has micromole_per_litre;
-  Kip3 = 3.2;
-  Kip3 has micromole_per_litre;
-  Jout has micromole_per_millisecond;
-  Pleak = 1e-16;
-  Pleak has litres_per_millisecond;
-  Pip3 = 1.2e-15;
-  Pip3 has litres_per_millisecond;
-  fi = 0.01;
-  fi has dimensionless;
-  F = 9.6485e+16;
-  F has fA_msec_per_micromole;
-  ksg = 0.0001;
-  ksg has per_millisecond;
-  fer = 0.03;
-  fer has dimensionless;
-  kip = 0.0003;
-  kip has microM_per_millisecond;
-  Kipca = 0.4;
-  Kipca has micromole_per_litre;
-  kdip = 4e-05;
-  kdip has per_millisecond;
-  kadp = 0.00037;
-  kadp has per_millisecond;
-  katpca = 5e-05;
-  katpca has per_microM_per_millisecond;
-  katp = 5e-05;
-  katp has per_millisecond;
-
-  // Other declarations:
-  var n, n_infinity, tau_n, V, I_Vca, I_CaPump, I_NaCa, I_CRAN, I_Na, I_NaK;
-  var I_KDr, I_KCa, I_KATP, Vca, Vk, Vna, Vnaca, pvca, f_CRAN, p_CRAN, pna;
-  var f_5, b_5, F1, F4, F5, B2, B3, B4, B6, D, f_Ca, Okatp, Jerp, Pcaer, O_infinity;
-  var Jout;
-  const Cytoplasm, ER, Cm, TV, Ca_ec, K_ec, K_cyt, Na_ec, Vcah, Kcah, gm_CRAN;
-  const Kcar, V_CRAN, f5_ast, b5_ast, f_1, f_4, b_2, b_3, b_4, P, b_6, Ksup;
-  const f_2, f_3, f_6, b_1, Kkca, Kdd, Ktd, Ktt, Vn, Sn, c, Vtau, a, b, gmvca;
-  const Pmcap, Kcap, gnaca, Knaca, gmna, Pnak, gmKDr, gmkca, gmkatp, Kcarp;
-  const Krca, Kip3, Pleak, Pip3, fi, F, ksg, fer, kip, Kipca, kdip, kadp;
-  const katpca, katp;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 1e-3 second;
-  unit millivolt = 1e-3 volt;
-  unit femtoampere = 1e-15 ampere;
-  unit micromole_per_litre = 1e-6 mole / litre;
-  unit picosiemens = 1e-12 siemens;
-  unit femtofarad = 1e-15 farad;
-  unit per_millisecond = 1 / 1e-3 second;
-  unit picosiemens_per_millivolt = 1e-12 siemens / 1e-3 volt;
-  unit micromole_per_millisecond = 1e-6 mole / 1e-3 second;
-  unit microM_per_millisecond = 1e-6 mole / (1e-3 second * litre);
-  unit litres_per_millisecond = litre / 1e-3 second;
-  unit per_microM_per_millisecond = litre / (1e-6 mole * 1e-3 second);
-  unit per_microMcube_per_millisecond = litre^3 / ((1e-6 mole)^3 * 1e-3 second);
-  unit per_microMsquare_per_millisecond = litre^2 / ((1e-6 mole)^2 * 1e-3 second);
-  unit per_microM = litre / 1e-6 mole;
-  unit fA_msec_per_micromole = 1e-15 ampere * 1e-3 second / 1e-6 mole;
-
-  // Display Names:
-  substance is "Micromole";
-  time_unit is "milliseconds";
-  millivolt is "Voltage";
-  femtoampere is "Current";
-  micromole_per_litre is "Concentration";
-  picosiemens is "Conductance";
-  femtofarad is "Capacitance";
-  per_millisecond is "Time inverse";
-  picosiemens_per_millivolt is "Conductance coefficient";
-  micromole_per_millisecond is "amount per time";
-  microM_per_millisecond is "concentration per time";
-  litres_per_millisecond is "volume per time";
-  per_microM_per_millisecond is "per concentration per time";
-  per_microMcube_per_millisecond is "per concentration cubed per time";
-  per_microMsquare_per_millisecond is "per Concentration square per time";
-  per_microM is "per concentration";
-  fA_msec_per_micromole is "Faraday constant";
-  Cytoplasm is "cytoplasm";
-  ER is "endoplasmic reticulum";
-  Ca_cyt is "Cytosolic Calcium";
-  Ca_er is "ER Calcium";
-  IP3_cyt is "Cytosolic IP3";
-  Na_cyt is "Cytosolic Sodium";
-  ATP_cyt is "Cytosolic ATP";
-  ADP_cyt is "Cytosolic ADP";
-  F is "Faraday's constant";
-  kip is "IP3 production rate constant";
-  Kipca is "half activation cytosolic Ca";
-  kdip is "IP3 degradation rate constant";
-  kadp is "ATP production rate constant";
-  katpca is "Ca dependent ATP consumption";
-  katp is "Rate constant of ATP consumption";
-
-  // CV terms:
-  Cytoplasm identity "http://identifiers.org/go/GO:0005737"
-  ER identity "http://identifiers.org/go/GO:0005783"
-  Ca_cyt identity "http://identifiers.org/chebi/CHEBI:29108",
-                  "http://identifiers.org/kegg.compound/C00076"
-  Ca_er identity "http://identifiers.org/chebi/CHEBI:29108",
-                 "http://identifiers.org/kegg.compound/C00076"
-  IP3_cyt identity "http://identifiers.org/chebi/CHEBI:16595",
-                   "http://identifiers.org/kegg.compound/C01245"
-  Na_cyt identity "http://identifiers.org/chebi/CHEBI:29101",
-                  "http://identifiers.org/kegg.compound/C01330"
-  ATP_cyt identity "http://identifiers.org/chebi/CHEBI:15422",
-                   "http://identifiers.org/kegg.compound/C00002"
-  ADP_cyt identity "http://identifiers.org/chebi/CHEBI:16761",
-                   "http://identifiers.org/kegg.compound/C00008"
-  Calcium_cyt_Ivca hypernym "http://identifiers.org/go/GO:0005245"
-  Calcium_cyt_Inaca hypernym "http://identifiers.org/go/GO:0005432"
-  Calcium_cyt_Icapump identity "http://identifiers.org/ec-code/3.6.3.8"
-  Calcium_cyt_Icapump part "http://identifiers.org/go/GO:0005388",
-                           "http://identifiers.org/go/GO:0005524"
-  Calcium_cyt_Jerp identity "http://identifiers.org/ec-code/3.6.3.8"
-  Calcium_cyt_Jerp part "http://identifiers.org/go/GO:0005388",
-                        "http://identifiers.org/go/GO:0005524"
-  Calcium_cyt_Jout part "http://identifiers.org/go/GO:0007204",
-                        "http://identifiers.org/go/GO:0005220"
-  Calcium_cyt_sequestration identity "http://identifiers.org/go/GO:0051208"
-  IP3_synthesis identity "http://identifiers.org/ec-code/3.1.4.11",
-                         "http://identifiers.org/go/GO:0004435"
-  Na_Inaca identity "http://identifiers.org/go/GO:0005432"
-  Na_Inak identity "http://identifiers.org/ec-code/3.6.3.9",
-                   "http://identifiers.org/go/GO:0005391"
-  Na_Ina hypernym "http://identifiers.org/go/GO:0005248"
-  Na_Icran hypernym "http://identifiers.org/go/GO:0005227"
-  ATP_production identity "http://identifiers.org/go/GO:0006754"
-  ATP_NaKATPase identity "http://identifiers.org/ec-code/3.6.3.9",
-                         "http://identifiers.org/go/GO:0005391"
-  ATP_Capump identity "http://identifiers.org/ec-code/3.6.3.8",
-                      "http://identifiers.org/go/GO:0005388"
-  ATP_Jerp identity "http://identifiers.org/ec-code/3.6.3.8",
-                    "http://identifiers.org/go/GO:0005388"
-  ATP_Ca_dependent_consumption identity "http://identifiers.org/go/GO:0030899"
-  ATP_consumption identity "http://identifiers.org/go/GO:0006200"
-end
-
-Fridlyand2003_Ca_flux_pancreatic_cells is "Fridlyand2003_Calcium_flux"
-
-Fridlyand2003_Ca_flux_pancreatic_cells model_entity_is "http://identifiers.org/biomodels.db/MODEL0928773489"
-Fridlyand2003_Ca_flux_pancreatic_cells model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000059"
-Fridlyand2003_Ca_flux_pancreatic_cells description "http://identifiers.org/pubmed/12644446"
-Fridlyand2003_Ca_flux_pancreatic_cells taxon "http://identifiers.org/taxonomy/10090"
-Fridlyand2003_Ca_flux_pancreatic_cells identity "http://identifiers.org/kegg.pathway/map04020"
-Fridlyand2003_Ca_flux_pancreatic_cells part "http://identifiers.org/go/GO:0050848",
-                                            "http://identifiers.org/go/GO:0050796"
-Fridlyand2003_Ca_flux_pancreatic_cells container "http://identifiers.org/bto/BTO:0000783"
diff --git a/BioModelsRAG/data/BIOMD0000000060.txt b/BioModelsRAG/data/BIOMD0000000060.txt
deleted file mode 100644
index bab99ae6c925c256bc68c8c9deb0a58d35908083..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000060.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Keizer1996_Ryanodine_receptor_adaptation()
-
-  // Compartments and Species:
-  compartment compartment_;
-  substanceOnly species Pc1 in compartment_, Po2 in compartment_, Po1 in compartment_;
-  substanceOnly species Pc2 in compartment_;
-
-  // Assignment Rules:
-  Open_probability := Po1 + Po2;
-
-  // Reactions:
-  Closed_state_1: Po1 -> Pc1; Closed_state_1_ka_minus*Po1 - Closed_state_1_ka_plus*Closed_state_1_Ca^Closed_state_1_n*Pc1;
-  Open_state_2: Po1 -> Po2; Open_state_2_kb_plus*Open_state_2_Ca^Open_state_2_m*Po1 - Open_state_2_kb_minus*Po2;
-  Closed_State_2: Po1 -> Pc2; Closed_State_2_kc_plus*Po1 - Closed_State_2_kc_minus*Pc2;
-
-  // Species initializations:
-  Pc1 = 0.963/compartment_;
-  Po2 = 0;
-  Po1 = 0;
-  Pc2 = 0.037/compartment_;
-
-  // Compartment initializations:
-  compartment_ = 1;
-  Open_probability has dimensionless;
-
-  // Variable initializations:
-  Closed_state_1_ka_minus = 28.8;
-  Closed_state_1_ka_minus has per_second;
-  Closed_state_1_ka_plus = 1500;
-  Closed_state_1_ka_plus has per_microM4sec;
-  Closed_state_1_Ca = 0.9;
-  Closed_state_1_Ca has microM;
-  Closed_state_1_n = 4;
-  Closed_state_1_n has dimensionless;
-  Open_state_2_kb_plus = 1500;
-  Open_state_2_kb_plus has per_microM3sec;
-  Open_state_2_Ca = 0.9;
-  Open_state_2_Ca has microM;
-  Open_state_2_m = 3;
-  Open_state_2_m has dimensionless;
-  Open_state_2_kb_minus = 385.9;
-  Open_state_2_kb_minus has per_second;
-  Closed_State_2_kc_plus = 1.75;
-  Closed_State_2_kc_plus has per_second;
-  Closed_State_2_kc_minus = 0.1;
-  Closed_State_2_kc_minus has per_second;
-
-  // Other declarations:
-  var Open_probability;
-  const compartment_;
-
-  // Unit definitions:
-  unit per_microM4sec = litre^4 / ((1e-6 mole)^4 * second);
-  unit per_microM3sec = litre^3 / ((1e-6 mole)^3 * second);
-  unit per_second = 1 / second;
-  unit microM = 1e-6 mole / litre;
-  unit substance = dimensionless;
-
-  // Display Names:
-  per_microM4sec is "microM-4sec-1";
-  per_microM3sec is "microM-3sec-1";
-  substance is "normalized substance";
-  Closed_State_2 is "Closed State 2";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005623"
-  Pc1 hypernym "http://identifiers.org/uniprot/P21817"
-  Po2 hypernym "http://identifiers.org/uniprot/P21817"
-  Po1 hypernym "http://identifiers.org/uniprot/P21817"
-  Pc2 hypernym "http://identifiers.org/uniprot/P21817"
-  Closed_state_1 hypernym "http://identifiers.org/go/GO:0005219"
-  Open_state_2 hypernym "http://identifiers.org/go/GO:0005219"
-  Closed_State_2 hypernym "http://identifiers.org/go/GO:0005219"
-end
-
-Keizer1996_Ryanodine_receptor_adaptation is "Keizer1996_Ryanodine_receptor_adaptation"
-
-Keizer1996_Ryanodine_receptor_adaptation model_entity_is "http://identifiers.org/biomodels.db/MODEL0332756009"
-Keizer1996_Ryanodine_receptor_adaptation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000060"
-Keizer1996_Ryanodine_receptor_adaptation description "http://identifiers.org/pubmed/8968617"
-Keizer1996_Ryanodine_receptor_adaptation taxon "http://identifiers.org/taxonomy/131567"
-Keizer1996_Ryanodine_receptor_adaptation identity "http://identifiers.org/kegg.pathway/map04020"
-Keizer1996_Ryanodine_receptor_adaptation part "http://identifiers.org/go/GO:0005219",
-                                              "http://identifiers.org/go/GO:0048763",
-                                              "http://identifiers.org/go/GO:0019722"
-Keizer1996_Ryanodine_receptor_adaptation property "http://identifiers.org/mamo/MAMO_0000046"
diff --git a/BioModelsRAG/data/BIOMD0000000061.txt b/BioModelsRAG/data/BIOMD0000000061.txt
deleted file mode 100644
index 8841eb4a4aeff0b8a0785fdeb3ec7814f970b348..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000061.txt
+++ /dev/null
@@ -1,384 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Hynne2001_Glycolysis()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol;
-  species GlcX in extracellular, Glc in cytosol, ATP in cytosol, G6P in cytosol;
-  species ADP in cytosol, F6P in cytosol, FBP in cytosol, GAP in cytosol;
-  species DHAP in cytosol, NAD in cytosol, BPG in cytosol, NADH in cytosol;
-  species PEP in cytosol, Pyr in cytosol, ACA in cytosol, EtOH in cytosol;
-  species EtOHX in extracellular, Glyc in cytosol, GlycX in extracellular;
-  species ACAX in extracellular, CNX in extracellular, AMP in cytosol, $P in extracellular;
-  species $CNX0 in extracellular, $GlcX0 in extracellular;
-
-  // Reactions:
-  vinGlc: $GlcX0 -> GlcX; extracellular*vinGlc_k0*(GlcX0 - GlcX);
-  vGlcTrans: GlcX -> 59 Glc; (extracellular*vGlcTrans_V2f/vGlcTrans_Yvol)*(GlcX/vGlcTrans_K2Glc/(1 + GlcX/vGlcTrans_K2Glc + ((vGlcTrans_P2*(GlcX/vGlcTrans_K2Glc) + 1)/(vGlcTrans_P2*(Glc/vGlcTrans_K2Glc) + 1))*(1 + Glc/vGlcTrans_K2Glc + G6P/vGlcTrans_K2IG6P + Glc*G6P/(vGlcTrans_K2Glc*vGlcTrans_K2IIG6P)))) - (cytosol*vGlcTrans_V2r/vGlcTrans_Yvol)*(Glc/vGlcTrans_K2Glc/(1 + Glc/vGlcTrans_K2Glc + ((vGlcTrans_P2*(Glc/vGlcTrans_K2Glc) + 1)/(vGlcTrans_P2*(GlcX/vGlcTrans_K2Glc) + 1))*(1 + GlcX/vGlcTrans_K2Glc) + G6P/vGlcTrans_K2IG6P + Glc*G6P/(vGlcTrans_K2Glc*vGlcTrans_K2IIG6P)));
-  vHK: ATP + Glc -> G6P + ADP; cytosol*vHK_V3m*ATP*Glc/(vHK_K3DGlc*vHK_K3ATP + vHK_K3Glc*ATP + vHK_K3ATP*Glc + Glc*ATP);
-  vPGI: G6P -> F6P; cytosol*(vPGI_V4f*G6P/(vPGI_K4G6P + G6P + (vPGI_K4G6P/vPGI_K4F6P)*F6P) - vPGI_V4r*(F6P/vPGI_K4eq)/(vPGI_K4G6P + G6P + (vPGI_K4G6P/vPGI_K4F6P)*F6P));
-  vPFK: F6P + ATP -> FBP + ADP; cytosol*(vPFK_V5m*F6P^2/(vPFK_K5*(1 + vPFK_kappa5*(ATP/AMP)*(ATP/AMP)) + F6P^2));
-  vALD: FBP -> GAP + DHAP; cytosol*(vALD_V6f*FBP/(vALD_K6FBP + FBP + GAP*vALD_K6DHAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + DHAP*vALD_K6GAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + FBP*GAP/vALD_K6IGAP + GAP*DHAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6)) - vALD_V6f*GAP*DHAP/vALD_K6eq/(vALD_K6FBP + FBP + GAP*vALD_K6DHAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + DHAP*vALD_K6GAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + FBP*GAP/vALD_K6IGAP + GAP*DHAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6)));
-  vTIM: DHAP -> GAP; cytosol*(vTIM_V7f*DHAP/(vTIM_K7DHAP + DHAP + (vTIM_K7DHAP/vTIM_K7GAP)*GAP) - vTIM_V7r*(GAP/vTIM_K7eq)/(vTIM_K7DHAP + DHAP + (vTIM_K7DHAP/vTIM_K7GAP)*GAP));
-  vGAPDH: GAP + NAD -> NADH + BPG; cytosol*(vGAPDH_V8f*GAP*NAD/vGAPDH_K8GAP/vGAPDH_K8NAD/((1 + GAP/vGAPDH_K8GAP + BPG/vGAPDH_K8BPG)*(1 + NAD/vGAPDH_K8NAD + NADH/vGAPDH_K8NADH)) - vGAPDH_V8r*BPG*NADH/vGAPDH_K8eq/vGAPDH_K8GAP/vGAPDH_K8NAD/((1 + GAP/vGAPDH_K8GAP + BPG/vGAPDH_K8BPG)*(1 + NAD/vGAPDH_K8NAD + NADH/vGAPDH_K8NADH)));
-  vlpPEP: BPG + ADP -> PEP + ATP; cytosol*(vlpPEP_k9f*BPG*ADP - vlpPEP_k9r*PEP*ATP);
-  vPK: ADP + PEP -> Pyr + ATP; cytosol*(vPK_V10m*ADP*PEP/((vPK_K10PEP + PEP)*(vPK_K10ADP + ADP)));
-  vPDC: Pyr -> ACA; cytosol*(vPDC_V11m*Pyr/(vPDC_K11 + Pyr));
-  vADH: NADH + ACA -> NAD + EtOH; cytosol*(vADH_V12m*ACA*NADH/((vADH_K12NADH + NADH)*(vADH_K12ACA + ACA)));
-  vdifEtOH: 59 EtOH -> EtOHX; (vdifEtOH_k13/vdifEtOH_Yvol)*(cytosol*EtOH - extracellular*EtOHX);
-  voutEtOH: EtOHX -> $P; extracellular*voutEtOH_k0*EtOHX;
-  vlpGlyc: DHAP + NADH -> Glyc + NAD; cytosol*(vlpGlyc_V15m*DHAP/(vlpGlyc_K15DHAP*(1 + (vlpGlyc_K15INADH/NADH)*(1 + NAD/vlpGlyc_K15INAD)) + DHAP*(1 + (vlpGlyc_K15NADH/NADH)*(1 + NAD/vlpGlyc_K15INAD))));
-  vdifGlyc: 59 Glyc -> GlycX; (vdifGlyc_k16/vdifGlyc_Yvol)*(cytosol*Glyc - extracellular*GlycX);
-  voutGlyc: GlycX -> $P; extracellular*voutGlyc_k0*GlycX;
-  vdifACA: 59 ACA -> ACAX; (vdifACA_k18/vdifACA_Yvol)*(cytosol*ACA - extracellular*ACAX);
-  voutACA: ACAX -> $P; extracellular*voutACA_k0*ACAX;
-  vlacto: CNX + ACAX -> $P; extracellular*vlacto_k20*ACAX*CNX;
-  vinCN: $CNX0 -> CNX; extracellular*vinCN_k0*(CNX0 - CNX);
-  vstorage: ATP + G6P -> ADP; cytosol*vstorage_k22*ATP*G6P;
-  vconsum: ATP -> ADP; cytosol*vconsum_k23*ATP;
-  vAK: ATP + AMP -> 2 ADP; cytosol*(vAK_k24f*AMP*ATP - vAK_k24r*ADP^2);
-
-  // Species initializations:
-  GlcX = 6.7;
-  Glc = 0.573074;
-  ATP = 2.1;
-  G6P = 4.2;
-  ADP = 1.5;
-  F6P = 0.49;
-  FBP = 4.64;
-  GAP = 0.115;
-  DHAP = 2.95;
-  NAD = 0.65;
-  BPG = 0.00027;
-  NADH = 0.33;
-  PEP = 0.04;
-  Pyr = 8.7;
-  ACA = 1.48153;
-  EtOH = 19.2379;
-  EtOHX = 16.4514;
-  Glyc = 4.196;
-  GlycX = 1.68478;
-  ACAX = 1.28836;
-  CNX = 5.20358;
-  AMP = 0.33;
-  P = 0;
-  CNX0 = 5.6;
-  GlcX0 = 24;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-
-  // Variable initializations:
-  vinGlc_k0 = 0.048;
-  vinGlc_k0 has min_inverse;
-  vGlcTrans_V2f = 1014.96;
-  vGlcTrans_V2f has mM_per_minute;
-  vGlcTrans_Yvol = 59;
-  vGlcTrans_Yvol has dimensionless;
-  vGlcTrans_K2Glc = 1.7;
-  vGlcTrans_K2Glc has mM;
-  vGlcTrans_P2 = 1;
-  vGlcTrans_P2 has dimensionless;
-  vGlcTrans_K2IG6P = 1.2;
-  vGlcTrans_K2IG6P has mM;
-  vGlcTrans_K2IIG6P = 7.2;
-  vGlcTrans_K2IIG6P has mM;
-  vGlcTrans_V2r = 1014.96;
-  vGlcTrans_V2r has mM_per_minute;
-  vHK_V3m = 51.7547;
-  vHK_V3m has mM_per_minute;
-  vHK_K3DGlc = 0.37;
-  vHK_K3DGlc has mM;
-  vHK_K3ATP = 0.1;
-  vHK_K3ATP has mM;
-  vHK_K3Glc = 0;
-  vHK_K3Glc has mM;
-  vPGI_V4f = 496.042;
-  vPGI_V4f has mM_per_minute;
-  vPGI_K4G6P = 0.8;
-  vPGI_K4G6P has mM;
-  vPGI_K4F6P = 0.15;
-  vPGI_K4F6P has mM;
-  vPGI_V4r = 496.042;
-  vPGI_V4r has mM_per_minute;
-  vPGI_K4eq = 0.13;
-  vPGI_K4eq has dimensionless;
-  vPFK_V5m = 45.4327;
-  vPFK_V5m has mM_per_minute;
-  vPFK_K5 = 0.021;
-  vPFK_K5 has mM_squared;
-  vPFK_kappa5 = 0.15;
-  vPFK_kappa5 has dimensionless;
-  vALD_V6f = 2207.82;
-  vALD_V6f has mM_per_minute;
-  vALD_K6FBP = 0.3;
-  vALD_K6FBP has mM;
-  vALD_K6DHAP = 2;
-  vALD_K6DHAP has mM;
-  vALD_K6eq = 0.081;
-  vALD_K6eq has mM;
-  vALD_ratio6 = 5;
-  vALD_ratio6 has dimensionless;
-  vALD_K6GAP = 4;
-  vALD_K6GAP has mM;
-  vALD_K6IGAP = 10;
-  vALD_K6IGAP has mM;
-  vTIM_V7f = 116.365;
-  vTIM_V7f has mM_per_minute;
-  vTIM_K7DHAP = 1.23;
-  vTIM_K7DHAP has mM;
-  vTIM_K7GAP = 1.27;
-  vTIM_K7GAP has mM;
-  vTIM_V7r = 116.365;
-  vTIM_V7r has mM_per_minute;
-  vTIM_K7eq = 0.055;
-  vTIM_K7eq has dimensionless;
-  vGAPDH_V8f = 833.858;
-  vGAPDH_V8f has mM_per_minute;
-  vGAPDH_K8GAP = 0.6;
-  vGAPDH_K8GAP has mM;
-  vGAPDH_K8NAD = 0.1;
-  vGAPDH_K8NAD has mM;
-  vGAPDH_K8BPG = 0.01;
-  vGAPDH_K8BPG has mM;
-  vGAPDH_K8NADH = 0.06;
-  vGAPDH_K8NADH has mM;
-  vGAPDH_V8r = 833.858;
-  vGAPDH_V8r has mM_per_minute;
-  vGAPDH_K8eq = 0.0055;
-  vGAPDH_K8eq has dimensionless;
-  vlpPEP_k9f = 443866;
-  vlpPEP_k9f has mM_inverse_min_inverse;
-  vlpPEP_k9r = 1528.62;
-  vlpPEP_k9r has mM_inverse_min_inverse;
-  vPK_V10m = 343.096;
-  vPK_V10m has mM_per_minute;
-  vPK_K10PEP = 0.2;
-  vPK_K10PEP has mM;
-  vPK_K10ADP = 0.17;
-  vPK_K10ADP has mM;
-  vPDC_V11m = 53.1328;
-  vPDC_V11m has mM_per_minute;
-  vPDC_K11 = 0.3;
-  vPDC_K11 has mM;
-  vADH_V12m = 89.8023;
-  vADH_V12m has mM_per_minute;
-  vADH_K12NADH = 0.1;
-  vADH_K12NADH has mM;
-  vADH_K12ACA = 0.71;
-  vADH_K12ACA has mM;
-  vdifEtOH_k13 = 16.72;
-  vdifEtOH_k13 has min_inverse;
-  vdifEtOH_Yvol = 59;
-  vdifEtOH_Yvol has dimensionless;
-  voutEtOH_k0 = 0.048;
-  voutEtOH_k0 has min_inverse;
-  vlpGlyc_V15m = 81.4797;
-  vlpGlyc_V15m has mM_per_minute;
-  vlpGlyc_K15DHAP = 25;
-  vlpGlyc_K15DHAP has mM;
-  vlpGlyc_K15INADH = 0.034;
-  vlpGlyc_K15INADH has mM;
-  vlpGlyc_K15INAD = 0.13;
-  vlpGlyc_K15INAD has mM;
-  vlpGlyc_K15NADH = 0.13;
-  vlpGlyc_K15NADH has mM;
-  vdifGlyc_k16 = 1.9;
-  vdifGlyc_k16 has min_inverse;
-  vdifGlyc_Yvol = 59;
-  vdifGlyc_Yvol has dimensionless;
-  voutGlyc_k0 = 0.048;
-  voutGlyc_k0 has min_inverse;
-  vdifACA_k18 = 24.7;
-  vdifACA_k18 has min_inverse;
-  vdifACA_Yvol = 59;
-  vdifACA_Yvol has dimensionless;
-  voutACA_k0 = 0.048;
-  voutACA_k0 has min_inverse;
-  vlacto_k20 = 0.00283828;
-  vlacto_k20 has mM_inverse_min_inverse;
-  vinCN_k0 = 0.048;
-  vinCN_k0 has min_inverse;
-  vstorage_k22 = 2.25932;
-  vstorage_k22 has mM_inverse_min_inverse;
-  vconsum_k23 = 3.2076;
-  vconsum_k23 has min_inverse;
-  vAK_k24f = 432.9;
-  vAK_k24f has mM_inverse_min_inverse;
-  vAK_k24r = 133.333;
-  vAK_k24r has mM_inverse_min_inverse;
-
-  // Other declarations:
-  const extracellular, cytosol;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-  unit mM_per_minute = 1e-3 mole / (litre * 60 second);
-  unit min_inverse = 1 / 60 second;
-  unit mM_inverse_min_inverse = litre / (1e-3 mole * 60 second);
-  unit mM_squared = (1e-3 mole)^2 / litre^2;
-  unit mM = 1e-3 mole / litre;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "minute";
-  mM_per_minute is "mM per minute";
-  min_inverse is "minute inverse";
-  mM_inverse_min_inverse is "mM inverse min inverse";
-  mM_squared is "mM squared";
-  mM is "milliMolar";
-  GlcX is "Extracellular glucose";
-  Glc is "Cytosolic glucose";
-  G6P is "Glucose-6-Phosphate";
-  F6P is "Fructose-6-Phosphate";
-  FBP is "Fructose 1,6-bisphosphate";
-  GAP is "Glyceraldehyde 3-phosphate";
-  DHAP is "Dihydroxyacetone phosphate";
-  BPG is "1,3-Bisphosphoglycerate";
-  PEP is "Phosphoenolpyruvate";
-  Pyr is "Pyruvate";
-  ACA is "Acetaldehyde";
-  EtOHX is "Extracellular ethanol";
-  Glyc is "Glycerol";
-  GlycX is "Extracellular glycerol";
-  ACAX is "Extracellular acetaldehyde";
-  CNX is "Extracellular cyanide";
-  CNX0 is "Mixed flow cyanide";
-  GlcX0 is "Mixed flow glucose";
-  vinGlc is "Glucose Mixed flow to extracellular medium";
-  vGlcTrans is "Glucose uptake";
-  vHK is "Hexokinase";
-  vPGI is "Phosphoglucoisomerase";
-  vPFK is "Phosphofructokinase";
-  vALD is "Aldolase";
-  vTIM is "Triosephosphate isomerase";
-  vGAPDH is "Glyceraldehyde 3-phosphate dehydrogenase";
-  vlpPEP is "Phosphoenolpyruvate synthesis";
-  vPK is "Pyruvate kinase";
-  vPDC is "Pyruvate decarboxylase";
-  vADH is "Alcohol dehydrogenase";
-  vdifEtOH is "Ethanol out";
-  voutEtOH is "Ethanol flow";
-  vlpGlyc is "Glycerol synthesis";
-  vdifGlyc is "Glycerol out";
-  voutGlyc is "Glycerol flow";
-  vdifACA is "Acetaldehyde out";
-  voutACA is "Acetaldehyde flow";
-  vlacto is "Cyanide-Acetaldehyde flow";
-  vinCN is "Cyanide flow";
-  vstorage is "Storage";
-  vconsum is "ATP consumption";
-  vAK is "Adenylate kinase";
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005576"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  GlcX identity "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  Glc identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  G6P identity "http://identifiers.org/chebi/CHEBI:15954",
-               "http://identifiers.org/kegg.compound/C00092"
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  F6P identity "http://identifiers.org/chebi/CHEBI:20935",
-               "http://identifiers.org/kegg.compound/C00085"
-  FBP identity "http://identifiers.org/chebi/CHEBI:16905",
-               "http://identifiers.org/kegg.compound/C00354"
-  GAP identity "http://identifiers.org/chebi/CHEBI:29052",
-               "http://identifiers.org/kegg.compound/C00118"
-  DHAP identity "http://identifiers.org/chebi/CHEBI:16108",
-                "http://identifiers.org/kegg.compound/C00111"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  BPG identity "http://identifiers.org/chebi/CHEBI:16001",
-               "http://identifiers.org/kegg.compound/C00236"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  PEP identity "http://identifiers.org/kegg.compound/C00074",
-               "http://identifiers.org/chebi/CHEBI:18021"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021"
-  Pyr identity "http://identifiers.org/chebi/CHEBI:15361"
-  Pyr identity "http://identifiers.org/kegg.compound/C00022",
-               "http://identifiers.org/chebi/CHEBI:32816"
-  ACA identity "http://identifiers.org/chebi/CHEBI:15343",
-               "http://identifiers.org/kegg.compound/C00084"
-  EtOH identity "http://identifiers.org/chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  EtOHX identity "http://identifiers.org/chebi/CHEBI:16236",
-                 "http://identifiers.org/kegg.compound/C000469"
-  Glyc identity "http://identifiers.org/chebi/CHEBI:17754",
-                "http://identifiers.org/kegg.compound/C00116"
-  GlycX identity "http://identifiers.org/chebi/CHEBI:17754",
-                 "http://identifiers.org/kegg.compound/C00116"
-  ACAX identity "http://identifiers.org/chebi/CHEBI:15343",
-                "http://identifiers.org/kegg.compound/C00084"
-  CNX identity "http://identifiers.org/chebi/CHEBI:17514",
-               "http://identifiers.org/kegg.compound/C00177"
-  AMP identity "http://identifiers.org/chebi/CHEBI:16027",
-               "http://identifiers.org/kegg.compound/C00020"
-  CNX0 identity "http://identifiers.org/chebi/CHEBI:17514",
-                "http://identifiers.org/kegg.compound/C00177"
-  GlcX0 identity "http://identifiers.org/chebi/CHEBI:17234",
-                 "http://identifiers.org/kegg.compound/C00293"
-  vinGlc hypernym "http://identifiers.org/obo.go/GO:0015758"
-  vGlcTrans homolog "http://identifiers.org/reactome/REACT_212"
-  vGlcTrans hypernym "http://identifiers.org/obo.go/GO:0046323"
-  vHK homolog "http://identifiers.org/reactome/REACT_1318"
-  vHK identity "http://identifiers.org/ec-code/2.7.1.2",
-               "http://identifiers.org/kegg.reaction/R00299"
-  vPGI identity "http://identifiers.org/ec-code/5.3.1.9",
-                "http://identifiers.org/kegg.reaction/R00771"
-  vPGI homolog "http://identifiers.org/reactome/REACT_1164"
-  vPFK identity "http://identifiers.org/ec-code/2.7.1.11",
-                "http://identifiers.org/kegg.reaction/R00756"
-  vPFK homolog "http://identifiers.org/reactome/REACT_1840"
-  vALD identity "http://identifiers.org/ec-code/4.1.2.13",
-                "http://identifiers.org/kegg.reaction/R01070"
-  vTIM homolog "http://identifiers.org/reactome/REACT_1693"
-  vTIM identity "http://identifiers.org/ec-code/5.3.1.1",
-                "http://identifiers.org/kegg.reaction/R01015"
-  vGAPDH homolog "http://identifiers.org/reactome/REACT_587"
-  vGAPDH identity "http://identifiers.org/ec-code/1.2.1.12",
-                  "http://identifiers.org/kegg.reaction/R01061"
-  vlpPEP homolog "http://identifiers.org/reactome/REACT_1771"
-  vlpPEP part "http://identifiers.org/kegg.reaction/R01512",
-              "http://identifiers.org/kegg.reaction/R01518",
-              "http://identifiers.org/kegg.reaction/R00658"
-  vlpPEP part "http://identifiers.org/ec-code/2.7.2.3",
-              "http://identifiers.org/ec-code/5.4.2.1",
-              "http://identifiers.org/ec-code/4.2.1.11"
-  vPK homolog "http://identifiers.org/reactome/REACT_1911"
-  vPK identity "http://identifiers.org/ec-code/2.7.1.40",
-               "http://identifiers.org/kegg.reaction/R00200"
-  vPDC identity "http://identifiers.org/ec-code/4.1.1.1",
-                "http://identifiers.org/kegg.reaction/R00224"
-  vADH identity "http://identifiers.org/ec-code/1.1.1.1",
-                "http://identifiers.org/kegg.reaction/R00754"
-  vADH homolog "http://identifiers.org/reactome/REACT_799"
-  vdifEtOH hypernym "http://identifiers.org/obo.go/GO:0015850"
-  voutEtOH hypernym "http://identifiers.org/obo.go/GO:0015850"
-  vlpGlyc part "http://identifiers.org/kegg.reaction/R01034",
-               "http://identifiers.org/kegg.reaction/R01011"
-  vlpGlyc part "http://identifiers.org/ec-code/1.1.1.6",
-               "http://identifiers.org/ec-code/2.7.1.29"
-  vdifGlyc hypernym "http://identifiers.org/obo.go/GO:0015850"
-  voutGlyc hypernym "http://identifiers.org/obo.go/GO:0015850"
-  vstorage hypernym "http://identifiers.org/obo.go/GO:0043211"
-  vconsum hypernym "http://identifiers.org/obo.go/GO:0006200"
-  vAK hypernym "http://identifiers.org/ec-code/2.7.4.3",
-               "http://identifiers.org/obo.go/GO:0004017"
-end
-
-Hynne2001_Glycolysis is "Hynne2001_Glycolysis"
-
-Hynne2001_Glycolysis model_entity_is "http://identifiers.org/biomodels.db/MODEL6624167348"
-Hynne2001_Glycolysis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000061"
-Hynne2001_Glycolysis description "http://identifiers.org/pubmed/11744196"
-Hynne2001_Glycolysis taxon "http://identifiers.org/taxonomy/4932"
-Hynne2001_Glycolysis homolog "http://identifiers.org/reactome/REACT_1383"
-Hynne2001_Glycolysis hypernym "http://identifiers.org/obo.go/GO:0006096"
-Hynne2001_Glycolysis identity "http://identifiers.org/kegg.pathway/sce00010"
diff --git a/BioModelsRAG/data/BIOMD0000000062.txt b/BioModelsRAG/data/BIOMD0000000062.txt
deleted file mode 100644
index 2d9b124a9e1e8e67f3f0394d266f30585835822f..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000062.txt
+++ /dev/null
@@ -1,111 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Bhartiya2003_Tryptophan_operon()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Enz in compartment_, Ts in compartment_, $Tt in compartment_, $To in compartment_;
-
-  // Assignment Rules:
-  Tt := To + Ts;
-  To := Tomax*Tex/(Tex*(1 + Ts/f_val) + e_val);
-  Ts_norm := Ts/82;
-  To_norm := To/82;
-  Tt_norm := Tt/82;
-  Enz_norm := Enz/1;
-
-  // Reactions:
-  Enzyme_synthesis:  -> Enz; compartment_*Enzyme_synthesis_k1*Enzyme_synthesis_ki1^Enzyme_synthesis_nH*Enzyme_synthesis_Ot/(Enzyme_synthesis_ki1^Enzyme_synthesis_nH + Tt^Enzyme_synthesis_nH);
-  Enzyme_dilution: Enz -> ; compartment_*Enzyme_dilution_mu*Enz;
-  tryptophan_synthesis:  -> Ts; compartment_*tryptophan_synthesis_k2*Enz*tryptophan_synthesis_Ki2/(tryptophan_synthesis_Ki2 + Tt);
-  tryptophan_consumption: Ts -> ; compartment_*tryptophan_consumption_g*Ts/(tryptophan_consumption_Kg + Ts);
-  tryptophan_dilution: Ts -> ; compartment_*tryptophan_dilution_mu*Ts;
-
-  // Species initializations:
-  Enz = 0;
-  Ts = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  Tomax = 100;
-  Tomax has concentration;
-  Tex = 0.14;
-  Tex has concentration;
-  f_val = 380;
-  f_val has concentration;
-  e_val = 0.9;
-  e_val has concentration;
-  Ts_norm has dimensionless;
-  To_norm has dimensionless;
-  Tt_norm has dimensionless;
-  Enz_norm has dimensionless;
-  Enzyme_synthesis_k1 = 65;
-  Enzyme_synthesis_k1 has time_inverse;
-  Enzyme_synthesis_ki1 = 3.53;
-  Enzyme_synthesis_ki1 has concentration;
-  Enzyme_synthesis_nH = 1.92;
-  Enzyme_synthesis_nH has dimensionless;
-  Enzyme_synthesis_Ot = 0.0033;
-  Enzyme_synthesis_Ot has concentration;
-  Enzyme_dilution_mu = 0.01;
-  Enzyme_dilution_mu has time_inverse;
-  tryptophan_synthesis_k2 = 25;
-  tryptophan_synthesis_k2 has time_inverse;
-  tryptophan_synthesis_Ki2 = 810;
-  tryptophan_synthesis_Ki2 has concentration;
-  tryptophan_consumption_g = 25;
-  tryptophan_consumption_g has Concentration_per_time;
-  tryptophan_consumption_Kg = 0.2;
-  tryptophan_consumption_Kg has concentration;
-  tryptophan_dilution_mu = 0.01;
-  tryptophan_dilution_mu has time_inverse;
-
-  // Other declarations:
-  var Ts_norm, To_norm, Tt_norm, Enz_norm;
-  const compartment_, Tomax, Tex, f_val, e_val;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-  unit concentration = 1e-6 mole / litre;
-  unit Concentration_per_time = 1e-6 mole / (litre * 60 second);
-  unit time_inverse = 1 / 60 second;
-
-  // Display Names:
-  substance is "micromole";
-  time_unit is "minutes";
-  concentration is "microM";
-  Concentration_per_time is "microM_per_min";
-  time_inverse is "per_min";
-  compartment_ is "cell";
-  Enz is "Anthranilate synthase";
-  Ts is "Synthesized tryptophan";
-  Tt is "Total tryptophan";
-  To is "exog. Trp";
-  Enzyme_synthesis is "Anthranilate synthase synthesis";
-  Enzyme_dilution is "Enzyme dilution due to cell growth";
-  tryptophan_synthesis is "Tryptophan synthesis";
-  tryptophan_consumption is "Tryptophan consumption for protein synthesis";
-  tryptophan_dilution is "Tryptophan dilution due to cell growth";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  Enz identity "http://identifiers.org/uniprot/P00895"
-  Ts identity "http://identifiers.org/chebi/CHEBI:27897",
-              "http://identifiers.org/kegg.compound/C00806"
-  Tt identity "http://identifiers.org/chebi/CHEBI:27897",
-              "http://identifiers.org/kegg.compound/C00806"
-  Enzyme_synthesis hypernym "http://identifiers.org/go/GO:0006417"
-  tryptophan_synthesis hypernym "http://identifiers.org/go/GO:0000162"
-  tryptophan_consumption hypernym "http://identifiers.org/go/GO:0006412"
-end
-
-Bhartiya2003_Tryptophan_operon is "Bhartiya2003_Tryptophan_operon"
-
-Bhartiya2003_Tryptophan_operon model_entity_is "http://identifiers.org/biomodels.db/MODEL6624111460"
-Bhartiya2003_Tryptophan_operon model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000062"
-Bhartiya2003_Tryptophan_operon description "http://identifiers.org/pubmed/12787031"
-Bhartiya2003_Tryptophan_operon origin "http://identifiers.org/pubmed/11171956"
-Bhartiya2003_Tryptophan_operon hypernym "http://identifiers.org/go/GO:0000162"
-Bhartiya2003_Tryptophan_operon taxon "http://identifiers.org/taxonomy/562"
diff --git a/BioModelsRAG/data/BIOMD0000000063.txt b/BioModelsRAG/data/BIOMD0000000063.txt
deleted file mode 100644
index da82a5791cc403bb6b65d86bcf5f0f49ddc28e5b..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000063.txt
+++ /dev/null
@@ -1,267 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Galazzo1990_FermentationPathwayKinetics()
-
-  // Compartments and Species:
-  compartment extracellular, cytoplasm;
-  species Glci in cytoplasm, ATP in cytoplasm, G6P in cytoplasm, FDP in cytoplasm;
-  species PEP in cytoplasm, $Gly in cytoplasm, $EtOH in cytoplasm, $Carbo in cytoplasm;
-  species $Glco in extracellular;
-
-  // Assignment Rules:
-  VappGly := parameter_4*G6P^parameter_5/(parameter_6^parameter_5 + G6P^parameter_5);
-  VratioVmax := Vhk/(cytoplasm*parameter_7);
-
-  // Reactions:
-  Vhk: ATP + Glci -> G6P; cytoplasm*Vhk_Vm2/(1 + Vhk_Km2Glc/Glci + Vhk_Km2ATP/ATP + Vhk_Ks2Glc*Vhk_Km2ATP/(Glci*ATP));
-  Vin: $Glco -> Glci; cytoplasm*(Vin_Vm1 - Vin_Ki1G6P*G6P);
-  Vpol: ATP + G6P -> $Carbo; cytoplasm*1.1*Vpol_Vm3*G6P^Vpol_n3/(Vpol_K3Gly^Vpol_n3 + G6P^Vpol_n3)/(1 + (Vpol_Km30/0.7)*(1 + Vpol_Km3G6P/G6P));
-  Vpfk: ATP + G6P -> FDP; ((cytoplasm*Vpfk_Vm4*Vpfk_g4R*0.3*G6P/Vpfk_K4F6P)*ATP/Vpfk_K4ATP)*(1 + 0.3*G6P/Vpfk_K4F6P + ATP/Vpfk_K4ATP + (Vpfk_g4R*0.3*G6P/Vpfk_K4F6P)*ATP/Vpfk_K4ATP)/((1 + 0.3*G6P/Vpfk_K4F6P + ATP/Vpfk_K4ATP + (Vpfk_g4R*0.3*G6P/Vpfk_K4F6P)*ATP/Vpfk_K4ATP)^2 + Vpfk_L40*((1 + Vpfk_c4AMP*(3 - ATP - 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5))/Vpfk_K4AMP)/(1 + (3 - ATP - 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5))/Vpfk_K4AMP))^2*(1 + Vpfk_c4F6P*0.3*G6P/Vpfk_K4F6P + Vpfk_c4ATP*ATP/Vpfk_K4ATP + (Vpfk_gT*Vpfk_c4F6P*0.3*G6P/Vpfk_K4F6P)*Vpfk_c4ATP*ATP/Vpfk_K4ATP)^2);
-  Vgapd: FDP -> 2 ATP + 2 PEP; cytoplasm*Vgapd_Vm5/(1 + Vgapd_K5G3P/(0.01*FDP) + (Vgapd_K5NAD/Vgapd_NAD + Vgapd_K5G3P*Vgapd_K5NAD/(Vgapd_NAD*0.01*FDP) + Vgapd_K5G3P*Vgapd_K5NAD*Vgapd_NADH/(Vgapd_NAD*0.01*FDP*Vgapd_K5NADH))*(1 + 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgapd_K5ADP + (3 - ATP - 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5))/Vgapd_K5AMP + ATP/Vgapd_K5ATP));
-  Vpk: PEP -> ATP + $EtOH; cytoplasm*Vpk_Vm6*((PEP/Vpk_K6PEP)*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP)*(Vpk_g6R*(1 + PEP/Vpk_K6PEP + 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP + (Vpk_g6R*PEP/Vpk_K6PEP)*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP) + ((Vpk_q6*Vpk_L60*((1 + Vpk_c6FDP*FDP/Vpk_K6FDP)/(1 + FDP/Vpk_K6FDP))^2*Vpk_g6T*Vpk_c6PEP*PEP/Vpk_K6PEP)*Vpk_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP)*(1 + Vpk_c6PEP*PEP/Vpk_K6PEP + Vpk_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP + (Vpk_g6T*Vpk_c6PEP*PEP/Vpk_K6PEP)*Vpk_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP))/((1 + 9.55*10^-9/Vpk_h6)*((1 + PEP/Vpk_K6PEP + 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP + (Vpk_g6R*PEP/Vpk_K6PEP)*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP)^2 + Vpk_L60*((1 + Vpk_c6FDP*FDP/Vpk_K6FDP)/(1 + FDP/Vpk_K6FDP))^2*(1 + Vpk_c6PEP*PEP/Vpk_K6PEP + Vpk_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP + (Vpk_g6T*Vpk_c6PEP*PEP/Vpk_K6PEP)*Vpk_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vpk_K6ADP)^2));
-  Vgol: 0.5 FDP -> $Gly; Vgol_Vm7*cytoplasm*((PEP/Vgol_K6PEP)*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP)*(Vgol_g6R*(1 + PEP/Vgol_K6PEP + 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP + (Vgol_g6R*PEP/Vgol_K6PEP)*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP) + ((Vgol_q6*Vgol_L60*((1 + Vgol_c6FDP*FDP/Vgol_K6FDP)/(1 + FDP/Vgol_K6FDP))^2*Vgol_g6T*Vgol_c6PEP*PEP/Vgol_K6PEP)*Vgol_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP)*(1 + Vgol_c6PEP*PEP/Vgol_K6PEP + Vgol_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP + (Vgol_g6T*Vgol_c6PEP*PEP/Vgol_K6PEP)*Vgol_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP))/((1 + 9.55*10^-9/Vgol_h6)*((1 + PEP/Vgol_K6PEP + 0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP + (Vgol_g6R*PEP/Vgol_K6PEP)*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP)^2 + Vgol_L60*((1 + Vgol_c6FDP*FDP/Vgol_K6FDP)/(1 + FDP/Vgol_K6FDP))^2*(1 + Vgol_c6PEP*PEP/Vgol_K6PEP + Vgol_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP + (Vgol_g6T*Vgol_c6PEP*PEP/Vgol_K6PEP)*Vgol_c6ADP*0.5*(-ATP + (12*ATP - 3*ATP^2)^0.5)/Vgol_K6ADP)^2));
-  Vatpase: ATP -> ; cytoplasm*Vatpase_Vm8*ATP;
-
-  // Species initializations:
-  Glci = 0.0345;
-  ATP = 1.19;
-  G6P = 1.011;
-  FDP = 9.144;
-  PEP = 0.0095;
-  Gly = 0;
-  EtOH = 0;
-  Carbo = 0;
-  Glco = 1;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytoplasm = 1;
-  VappGly has mM_per_minute;
-
-  // Variable initializations:
-  parameter_4 = 14.31;
-  parameter_4 has mM_per_minute;
-  parameter_5 = 8.25;
-  parameter_5 has dimensionless;
-  parameter_6 = 2;
-  parameter_6 has mM;
-  VratioVmax has dimensionless;
-  parameter_7 = 68.5;
-  parameter_7 has mM_per_minute;
-  Vin_Vm1 = 19.7;
-  Vin_Vm1 has mM_per_minute;
-  Vin_Ki1G6P = 3.7;
-  Vin_Ki1G6P has min_inv;
-  Vhk_Vm2 = 68.5;
-  Vhk_Vm2 has mM_per_minute;
-  Vhk_Km2Glc = 0.11;
-  Vhk_Km2Glc has mM;
-  Vhk_Km2ATP = 0.1;
-  Vhk_Km2ATP has mM;
-  Vhk_Ks2Glc = 0.0062;
-  Vhk_Ks2Glc has mM;
-  Vpol_Vm3 = 14.31;
-  Vpol_Vm3 has mM_per_minute;
-  Vpol_n3 = 8.25;
-  Vpol_n3 has dimensionless;
-  Vpol_K3Gly = 2;
-  Vpol_K3Gly has mM;
-  Vpol_Km30 = 1;
-  Vpol_Km30 has mM;
-  Vpol_Km3G6P = 1.1;
-  Vpol_Km3G6P has mM;
-  Vpfk_Vm4 = 31.7;
-  Vpfk_Vm4 has mM_per_minute;
-  Vpfk_g4R = 10;
-  Vpfk_g4R has dimensionless;
-  Vpfk_K4F6P = 1;
-  Vpfk_K4F6P has mM;
-  Vpfk_K4ATP = 0.06;
-  Vpfk_K4ATP has mM;
-  Vpfk_L40 = 3342;
-  Vpfk_L40 has dimensionless;
-  Vpfk_c4AMP = 0.019;
-  Vpfk_c4AMP has dimensionless;
-  Vpfk_K4AMP = 0.025;
-  Vpfk_K4AMP has mM;
-  Vpfk_c4F6P = 0.0005;
-  Vpfk_c4F6P has dimensionless;
-  Vpfk_c4ATP = 1;
-  Vpfk_c4ATP has dimensionless;
-  Vpfk_gT = 1;
-  Vpfk_gT has dimensionless;
-  Vgapd_Vm5 = 49.9;
-  Vgapd_Vm5 has mM_per_minute;
-  Vgapd_K5G3P = 0.0025;
-  Vgapd_K5G3P has mM;
-  Vgapd_K5NAD = 0.18;
-  Vgapd_K5NAD has dimensionless;
-  Vgapd_NAD = 1.91939;
-  Vgapd_NAD has mM;
-  Vgapd_NADH = 0.0806142;
-  Vgapd_NADH has mM;
-  Vgapd_K5NADH = 0.0003;
-  Vgapd_K5NADH has mM;
-  Vgapd_K5ADP = 1.5;
-  Vgapd_K5ADP has mM;
-  Vgapd_K5AMP = 1.1;
-  Vgapd_K5AMP has mM;
-  Vgapd_K5ATP = 2.5;
-  Vgapd_K5ATP has mM;
-  Vpk_Vm6 = 3440;
-  Vpk_Vm6 has mM_per_minute;
-  Vpk_K6PEP = 0.00793966;
-  Vpk_K6PEP has mM;
-  Vpk_K6ADP = 5;
-  Vpk_K6ADP has mM;
-  Vpk_g6R = 0.1;
-  Vpk_g6R has dimensionless;
-  Vpk_q6 = 1;
-  Vpk_q6 has dimensionless;
-  Vpk_L60 = 164.084;
-  Vpk_L60 has dimensionless;
-  Vpk_c6FDP = 0.01;
-  Vpk_c6FDP has dimensionless;
-  Vpk_K6FDP = 0.2;
-  Vpk_K6FDP has mM;
-  Vpk_g6T = 1;
-  Vpk_g6T has dimensionless;
-  Vpk_c6PEP = 0.000158793;
-  Vpk_c6PEP has dimensionless;
-  Vpk_c6ADP = 1;
-  Vpk_c6ADP has dimensionless;
-  Vpk_h6 = 1.14815e-07;
-  Vpk_h6 has dimensionless;
-  Vgol_Vm7 = 203;
-  Vgol_Vm7 has mM_per_minute;
-  Vgol_K6PEP = 0.00793966;
-  Vgol_K6PEP has mM;
-  Vgol_K6ADP = 5;
-  Vgol_K6ADP has mM;
-  Vgol_g6R = 0.1;
-  Vgol_g6R has dimensionless;
-  Vgol_q6 = 1;
-  Vgol_q6 has dimensionless;
-  Vgol_L60 = 164.084;
-  Vgol_L60 has dimensionless;
-  Vgol_c6FDP = 0.01;
-  Vgol_c6FDP has dimensionless;
-  Vgol_K6FDP = 0.2;
-  Vgol_K6FDP has mM;
-  Vgol_g6T = 1;
-  Vgol_g6T has dimensionless;
-  Vgol_c6PEP = 0.000158793;
-  Vgol_c6PEP has dimensionless;
-  Vgol_c6ADP = 1;
-  Vgol_c6ADP has dimensionless;
-  Vgol_h6 = 1.14815e-07;
-  Vgol_h6 has dimensionless;
-  Vatpase_Vm8 = 25.1;
-  Vatpase_Vm8 has min_inv;
-
-  // Other declarations:
-  var VappGly, VratioVmax;
-  const extracellular, cytoplasm, parameter_4, parameter_5, parameter_6, parameter_7;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-  unit mM = 1e-3 mole / litre;
-  unit mM_per_minute = 1e-3 mole / (litre * 60 second);
-  unit min_inv = 1 / 60 second;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "minute";
-  mM is "milliMolar";
-  mM_per_minute is "mM per minute";
-  min_inv is "minute_inverse";
-  extracellular is "Extracellular";
-  cytoplasm is "Cytoplasm";
-  Glci is "Glucose inside the cell";
-  G6P is "Glucose 6-phosphate";
-  FDP is "Fructose 1,6-phosphate";
-  PEP is "Phosphoenol pyruvate";
-  Gly is "Glycerol";
-  EtOH is "Ethanol";
-  Carbo is "Glycogen and Trehalose";
-  Glco is "Glucose outside the cell";
-  parameter_4 is "Trehalose and Glycogen formation_Vm3";
-  parameter_5 is "Trehalose and Glycogen formation_n3";
-  parameter_6 is "Trehalose and Glycogen formation_K3Gly";
-  VratioVmax is "VratioVmax_ATP";
-  Vhk is "Hexokinase";
-  parameter_7 is "Hexokinase_Vm2";
-  Vin is "Glucose in";
-  Vpol is "Trehalose and Glycogen formation";
-  Vpfk is "Phosphofructokinase";
-  Vgapd is "GAPD";
-  Vpk is "Pyruvate kinase";
-  Vgol is "Glycerol synthesis";
-  Vatpase is "ATPase";
-
-  // CV terms:
-  extracellular identity "http://identifiers.org/go/GO:0005576"
-  cytoplasm identity "http://identifiers.org/go/GO:0005737"
-  Glci identity "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  G6P identity "http://identifiers.org/chebi/CHEBI:17665",
-               "http://identifiers.org/kegg.compound/C00668"
-  FDP identity "http://identifiers.org/chebi/CHEBI:16905",
-               "http://identifiers.org/kegg.compound/C00354"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021",
-               "http://identifiers.org/kegg.compound/C00074"
-  Gly identity "http://identifiers.org/chebi/CHEBI:17754",
-               "http://identifiers.org/kegg.compound/C00116"
-  EtOH identity "http://identifiers.org/chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  Carbo part "http://identifiers.org/chebi/CHEBI:28087",
-             "http://identifiers.org/chebi/CHEBI:27082"
-  Carbo part "http://identifiers.org/kegg.compound/C00182",
-             "http://identifiers.org/kegg.compound/C01083",
-             "http://identifiers.org/chebi/CHEBI:28087"
-  Glco identity "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  Vhk homolog "http://identifiers.org/reactome/REACT_1318"
-  Vhk identity "http://identifiers.org/ec-code/2.7.1.2",
-               "http://identifiers.org/kegg.reaction/R00299"
-  Vin homolog "http://identifiers.org/reactome/REACT_2092"
-  Vin identity "http://identifiers.org/go/GO:0046323"
-  Vpol homolog "http://identifiers.org/reactome/REACT_1736"
-  Vpol part "http://identifiers.org/go/GO:0005978",
-            "http://identifiers.org/go/GO:0005992"
-  Vpfk part "http://identifiers.org/reactome/REACT_736",
-            "http://identifiers.org/reactome/REACT_1164"
-  Vpfk part "http://identifiers.org/kegg.reaction/R00771",
-            "http://identifiers.org/kegg.reaction/R00756"
-  Vgapd part "http://identifiers.org/kegg.reaction/R00658",
-             "http://identifiers.org/kegg.reaction/R01518",
-             "http://identifiers.org/kegg.reaction/R01512",
-             "http://identifiers.org/kegg.reaction/R01061",
-             "http://identifiers.org/kegg.reaction/R01015",
-             "http://identifiers.org/kegg.reaction/R01070"
-  Vgapd part "http://identifiers.org/ec-code/2.7.2.3",
-             "http://identifiers.org/ec-code/5.4.2.1",
-             "http://identifiers.org/ec-code/1.2.1.12",
-             "http://identifiers.org/ec-code/5.3.1.1",
-             "http://identifiers.org/ec-code/4.1.2.13",
-             "http://identifiers.org/ec-code/4.2.1.11"
-  Vpk hypernym "http://identifiers.org/go/GO:0043458"
-  Vpk identity "http://identifiers.org/ec-code/2.7.1.40"
-  Vgol hypernym "http://identifiers.org/go/GO:0006114"
-  Vatpase hypernym "http://identifiers.org/ec-code/3.6.1.3",
-                   "http://identifiers.org/go/GO:0016887"
-end
-
-Galazzo1990_FermentationPathwayKinetics is "Galazzo1990_FermentationPathwayKinetics"
-
-Galazzo1990_FermentationPathwayKinetics model_entity_is "http://identifiers.org/biomodels.db/MODEL6624154196"
-Galazzo1990_FermentationPathwayKinetics model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000063"
-Galazzo1990_FermentationPathwayKinetics description "http://identifiers.org/doi/10.1016/0141-0229(90)90033-M"
-Galazzo1990_FermentationPathwayKinetics homolog "http://identifiers.org/reactome/REACT_723"
-Galazzo1990_FermentationPathwayKinetics identity "http://identifiers.org/kegg.pathway/sce00010"
-Galazzo1990_FermentationPathwayKinetics hypernym "http://identifiers.org/go/GO:0019660"
-Galazzo1990_FermentationPathwayKinetics property "http://identifiers.org/mamo/MAMO_0000046"
-Galazzo1990_FermentationPathwayKinetics taxon "http://identifiers.org/taxonomy/4932"
-Galazzo1990_FermentationPathwayKinetics part "http://identifiers.org/go/GO:0006096"
diff --git a/BioModelsRAG/data/BIOMD0000000064.txt b/BioModelsRAG/data/BIOMD0000000064.txt
deleted file mode 100644
index ac7e5c3e0afc5bf1749bf4ec5bb0d86c006c54fe..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000064.txt
+++ /dev/null
@@ -1,434 +0,0 @@
-// Created by libAntimony v2.13.0
-function L_PFK(L, CiATP, KiATP, CAMP, KAMP, CF26BP, KF26BP, CF16BP, KF16BP, AT, AM, F16, F26)
-  L*((1 + CiATP*(AT/KiATP))/(1 + AT/KiATP))^2*((1 + CAMP*(AM/KAMP))/(1 + AM/KAMP))^2*((1 + CF26BP*F26/KF26BP + CF16BP*F16/KF16BP)/(1 + F26/KF26BP + F16/KF16BP))^2;
-end
-
-L_PFK is "L_PFK"
-
-function R_PFK(KmF6P, KmATP, g, AT, F6)
-  1 + F6/KmF6P + AT/KmATP + g*(F6/KmF6P)*(AT/KmATP);
-end
-
-R_PFK is "R_PFK"
-
-function T_PFK(CATP, KmATP, AT)
-  1 + CATP*(AT/KmATP);
-end
-
-T_PFK is "T_PFK"
-
-
-model *Teusink2000_Glycolysis()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol;
-  species GLCi in cytosol, G6P in cytosol, F6P in cytosol, F16P in cytosol;
-  species TRIO in cytosol, BPG in cytosol, P3G in cytosol, P2G in cytosol;
-  species PEP in cytosol, PYR in cytosol, ACE in cytosol, P in cytosol, NAD in cytosol;
-  species NADH in cytosol, $Glyc in cytosol, $Trh in cytosol, $CO2 in cytosol;
-  species $SUCC in cytosol, $GLCo in extracellular, $ETOH in cytosol, $GLY in cytosol;
-  species $ATP in cytosol, $ADP in cytosol, $SUM_P in cytosol, $AMP in cytosol;
-  species $F26BP in cytosol;
-
-  // Assignment Rules:
-  ATP := (P - ADP)/2;
-  ADP := (SUM_P - (P^2*(1 - 4*KeqAK) + 2*SUM_P*P*(4*KeqAK - 1) + SUM_P^2)^0.5)/(1 - 4*KeqAK);
-  AMP := SUM_P - ATP - ADP;
-
-  // Reactions:
-  vGLK: GLCi + P -> G6P; (cytosol*vGLK_VmGLK/(vGLK_KmGLKGLCi*vGLK_KmGLKATP))*(GLCi*ATP - G6P*ADP/vGLK_KeqGLK)/((1 + GLCi/vGLK_KmGLKGLCi + G6P/vGLK_KmGLKG6P)*(1 + ATP/vGLK_KmGLKATP + ADP/vGLK_KmGLKADP));
-  vPGI: G6P -> F6P; (cytosol*vPGI_VmPGI_2/vPGI_KmPGIG6P_2)*(G6P - F6P/vPGI_KeqPGI_2)/(1 + G6P/vPGI_KmPGIG6P_2 + F6P/vPGI_KmPGIF6P_2);
-  vGLYCO: G6P + P => $Glyc; cytosol*vGLYCO_KGLYCOGEN_3;
-  vTreha: 2 G6P + P => $Trh; cytosol*vTreha_KTREHALOSE;
-  vPFK: F6P + P => F16P; cytosol*vPFK_VmPFK*gR*(F6P/KmPFKF6P)*(ATP/KmPFKATP)*R_PFK(KmPFKF6P, KmPFKATP, gR, ATP, F6P)/(R_PFK(KmPFKF6P, KmPFKATP, gR, ATP, F6P)^2 + L_PFK(Lzero, CiPFKATP, KiPFKATP, CPFKAMP, KPFKAMP, CPFKF26BP, KPFKF26BP, CPFKF16BP, KPFKF16BP, ATP, AMP, F16P, F26BP)*T_PFK(CPFKATP, KmPFKATP, ATP)^2);
-  vALD: F16P -> 2 TRIO; (cytosol*vALD_VmALD/vALD_KmALDF16P)*(F16P - (KeqTPI/(1 + KeqTPI))*TRIO*(1/(1 + KeqTPI))*TRIO/vALD_KeqALD)/(1 + F16P/vALD_KmALDF16P + (KeqTPI/(1 + KeqTPI))*TRIO/vALD_KmALDGAP + (1/(1 + KeqTPI))*TRIO/vALD_KmALDDHAP + (KeqTPI/(1 + KeqTPI))*TRIO*(1/(1 + KeqTPI))*TRIO/(vALD_KmALDGAP*vALD_KmALDDHAP) + F16P*(KeqTPI/(1 + KeqTPI))*TRIO/(vALD_KmALDGAPi*vALD_KmALDF16P));
-  vGAPDH: TRIO + NAD -> BPG + NADH; cytosol*(vGAPDH_VmGAPDHf*(KeqTPI/(1 + KeqTPI))*TRIO*NAD/(vGAPDH_KmGAPDHGAP*vGAPDH_KmGAPDHNAD) - vGAPDH_VmGAPDHr*BPG*NADH/(vGAPDH_KmGAPDHBPG*vGAPDH_KmGAPDHNADH))/((1 + (KeqTPI/(1 + KeqTPI))*TRIO/vGAPDH_KmGAPDHGAP + BPG/vGAPDH_KmGAPDHBPG)*(1 + NAD/vGAPDH_KmGAPDHNAD + NADH/vGAPDH_KmGAPDHNADH));
-  vPGK: BPG -> P3G + P; (cytosol*vPGK_VmPGK/(vPGK_KmPGKP3G*vPGK_KmPGKATP))*(vPGK_KeqPGK*BPG*ADP - P3G*ATP)/((1 + BPG/vPGK_KmPGKBPG + P3G/vPGK_KmPGKP3G)*(1 + ATP/vPGK_KmPGKATP + ADP/vPGK_KmPGKADP));
-  vPGM: P3G -> P2G; (cytosol*vPGM_VmPGM/vPGM_KmPGMP3G)*(P3G - P2G/vPGM_KeqPGM)/(1 + P3G/vPGM_KmPGMP3G + P2G/vPGM_KmPGMP2G);
-  vENO: P2G -> PEP; (cytosol*vENO_VmENO/vENO_KmENOP2G)*(P2G - PEP/vENO_KeqENO)/(1 + P2G/vENO_KmENOP2G + PEP/vENO_KmENOPEP);
-  vPYK: PEP -> PYR + P; (cytosol*vPYK_VmPYK/(vPYK_KmPYKPEP*vPYK_KmPYKADP))*(PEP*ADP - PYR*ATP/vPYK_KeqPYK)/((1 + PEP/vPYK_KmPYKPEP + PYR/vPYK_KmPYKPYR)*(1 + ATP/vPYK_KmPYKATP + ADP/vPYK_KmPYKADP));
-  vPDC: PYR => ACE + $CO2; cytosol*vPDC_VmPDC*(PYR^vPDC_nPDC/vPDC_KmPDCPYR^vPDC_nPDC)/(1 + PYR^vPDC_nPDC/vPDC_KmPDCPYR^vPDC_nPDC);
-  vSUC: 2 ACE + 3 NAD + 4 P => 3 NADH + $SUCC; cytosol*vSUC_KSUCC*ACE;
-  vGLT: $GLCo -> GLCi; (vGLT_VmGLT/vGLT_KmGLTGLCo)*(GLCo - GLCi/vGLT_KeqGLT)/(1 + GLCo/vGLT_KmGLTGLCo + GLCi/vGLT_KmGLTGLCi + 0.91*GLCo*GLCi/(vGLT_KmGLTGLCo*vGLT_KmGLTGLCi));
-  vADH: ACE + NADH -> NAD + $ETOH; -cytosol*((vADH_VmADH/(vADH_KiADHNAD*vADH_KmADHETOH))*(NAD*ETOH - NADH*ACE/vADH_KeqADH)/(1 + NAD/vADH_KiADHNAD + vADH_KmADHNAD*ETOH/(vADH_KiADHNAD*vADH_KmADHETOH) + vADH_KmADHNADH*ACE/(vADH_KiADHNADH*vADH_KmADHACE) + NADH/vADH_KiADHNADH + NAD*ETOH/(vADH_KiADHNAD*vADH_KmADHETOH) + vADH_KmADHNADH*NAD*ACE/(vADH_KiADHNAD*vADH_KiADHNADH*vADH_KmADHACE) + vADH_KmADHNAD*ETOH*NADH/(vADH_KiADHNAD*vADH_KmADHETOH*vADH_KiADHNADH) + NADH*ACE/(vADH_KiADHNADH*vADH_KmADHACE) + NAD*ETOH*ACE/(vADH_KiADHNAD*vADH_KmADHETOH*vADH_KiADHACE) + ETOH*NADH*ACE/(vADH_KiADHETOH*vADH_KiADHNADH*vADH_KmADHACE)));
-  vG3PDH: TRIO + NADH => NAD + $GLY; (cytosol*vG3PDH_VmG3PDH/(vG3PDH_KmG3PDHDHAP*vG3PDH_KmG3PDHNADH))*((1/(1 + KeqTPI))*TRIO*NADH - GLY*NAD/vG3PDH_KeqG3PDH)/((1 + (1/(1 + KeqTPI))*TRIO/vG3PDH_KmG3PDHDHAP + GLY/vG3PDH_KmG3PDHGLY)*(1 + NADH/vG3PDH_KmG3PDHNADH + NAD/vG3PDH_KmG3PDHNAD));
-  vATP: P -> ; cytosol*vATP_KATPASE*ATP;
-
-  // Species initializations:
-  GLCi = 0.087;
-  G6P = 2.45;
-  F6P = 0.62;
-  F16P = 5.51;
-  TRIO = 0.96;
-  BPG = 0;
-  P3G = 0.9;
-  P2G = 0.12;
-  PEP = 0.07;
-  PYR = 1.85;
-  ACE = 0.17;
-  P = 6.31;
-  NAD = 1.2;
-  NADH = 0.39;
-  Glyc = 0;
-  Trh = 0;
-  CO2 = 1;
-  SUCC = 0;
-  GLCo = 50;
-  ETOH = 50;
-  GLY = 0.15;
-  SUM_P = 4.1;
-  F26BP = 0.02;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-
-  // Variable initializations:
-  KeqAK = 0.45;
-  KeqAK has dimensionless;
-  gR = 5.12;
-  gR has dimensionless;
-  KmPFKF6P = 0.1;
-  KmPFKF6P has mM;
-  KmPFKATP = 0.71;
-  KmPFKATP has mM;
-  Lzero = 0.66;
-  Lzero has dimensionless;
-  CiPFKATP = 100;
-  CiPFKATP has dimensionless;
-  KiPFKATP = 0.65;
-  KiPFKATP has mM;
-  CPFKAMP = 0.0845;
-  CPFKAMP has dimensionless;
-  KPFKAMP = 0.0995;
-  KPFKAMP has mM;
-  CPFKF26BP = 0.0174;
-  CPFKF26BP has dimensionless;
-  KPFKF26BP = 0.000682;
-  KPFKF26BP has mM;
-  CPFKF16BP = 0.397;
-  CPFKF16BP has dimensionless;
-  KPFKF16BP = 0.111;
-  KPFKF16BP has mM;
-  CPFKATP = 3;
-  CPFKATP has dimensionless;
-  KeqTPI = 0.045;
-  KeqTPI has dimensionless;
-  vGLK_VmGLK = 226.452;
-  vGLK_VmGLK has mMpermin;
-  vGLK_KmGLKGLCi = 0.08;
-  vGLK_KmGLKGLCi has mM;
-  vGLK_KmGLKATP = 0.15;
-  vGLK_KmGLKATP has mM;
-  vGLK_KeqGLK = 3800;
-  vGLK_KeqGLK has dimensionless;
-  vGLK_KmGLKG6P = 30;
-  vGLK_KmGLKG6P has mM;
-  vGLK_KmGLKADP = 0.23;
-  vGLK_KmGLKADP has mM;
-  vPGI_VmPGI_2 = 339.677;
-  vPGI_VmPGI_2 has mMpermin;
-  vPGI_KmPGIG6P_2 = 1.4;
-  vPGI_KmPGIG6P_2 has mM;
-  vPGI_KeqPGI_2 = 0.314;
-  vPGI_KeqPGI_2 has dimensionless;
-  vPGI_KmPGIF6P_2 = 0.3;
-  vPGI_KmPGIF6P_2 has mM;
-  vGLYCO_KGLYCOGEN_3 = 6;
-  vGLYCO_KGLYCOGEN_3 has mMpermin;
-  vTreha_KTREHALOSE = 2.4;
-  vTreha_KTREHALOSE has mMpermin;
-  vPFK_VmPFK = 182.903;
-  vPFK_VmPFK has mMpermin;
-  vALD_VmALD = 322.258;
-  vALD_VmALD has mMpermin;
-  vALD_KmALDF16P = 0.3;
-  vALD_KmALDF16P has mM;
-  vALD_KeqALD = 0.069;
-  vALD_KeqALD has dimensionless;
-  vALD_KmALDGAP = 2;
-  vALD_KmALDGAP has mM;
-  vALD_KmALDDHAP = 2.4;
-  vALD_KmALDDHAP has mM;
-  vALD_KmALDGAPi = 10;
-  vALD_KmALDGAPi has mM;
-  vGAPDH_VmGAPDHf = 1184.52;
-  vGAPDH_VmGAPDHf has mMpermin;
-  vGAPDH_KmGAPDHGAP = 0.21;
-  vGAPDH_KmGAPDHGAP has mM;
-  vGAPDH_KmGAPDHNAD = 0.09;
-  vGAPDH_KmGAPDHNAD has mM;
-  vGAPDH_VmGAPDHr = 6549.8;
-  vGAPDH_VmGAPDHr has mMpermin;
-  vGAPDH_KmGAPDHBPG = 0.0098;
-  vGAPDH_KmGAPDHBPG has mM;
-  vGAPDH_KmGAPDHNADH = 0.06;
-  vGAPDH_KmGAPDHNADH has mM;
-  vPGK_VmPGK = 1306.45;
-  vPGK_VmPGK has mMpermin;
-  vPGK_KmPGKP3G = 0.53;
-  vPGK_KmPGKP3G has mM;
-  vPGK_KmPGKATP = 0.3;
-  vPGK_KmPGKATP has mM;
-  vPGK_KeqPGK = 3200;
-  vPGK_KeqPGK has dimensionless;
-  vPGK_KmPGKBPG = 0.003;
-  vPGK_KmPGKBPG has mM;
-  vPGK_KmPGKADP = 0.2;
-  vPGK_KmPGKADP has mM;
-  vPGM_VmPGM = 2525.81;
-  vPGM_VmPGM has mMpermin;
-  vPGM_KmPGMP3G = 1.2;
-  vPGM_KmPGMP3G has mM;
-  vPGM_KeqPGM = 0.19;
-  vPGM_KeqPGM has dimensionless;
-  vPGM_KmPGMP2G = 0.08;
-  vPGM_KmPGMP2G has mM;
-  vENO_VmENO = 365.806;
-  vENO_VmENO has mMpermin;
-  vENO_KmENOP2G = 0.04;
-  vENO_KmENOP2G has mM;
-  vENO_KeqENO = 6.7;
-  vENO_KeqENO has dimensionless;
-  vENO_KmENOPEP = 0.5;
-  vENO_KmENOPEP has mM;
-  vPYK_VmPYK = 1088.71;
-  vPYK_VmPYK has mMpermin;
-  vPYK_KmPYKPEP = 0.14;
-  vPYK_KmPYKPEP has mM;
-  vPYK_KmPYKADP = 0.53;
-  vPYK_KmPYKADP has mM;
-  vPYK_KeqPYK = 6500;
-  vPYK_KeqPYK has dimensionless;
-  vPYK_KmPYKPYR = 21;
-  vPYK_KmPYKPYR has mM;
-  vPYK_KmPYKATP = 1.5;
-  vPYK_KmPYKATP has mM;
-  vPDC_VmPDC = 174.194;
-  vPDC_VmPDC has mMpermin;
-  vPDC_nPDC = 1.9;
-  vPDC_nPDC has dimensionless;
-  vPDC_KmPDCPYR = 4.33;
-  vPDC_KmPDCPYR has mM;
-  vSUC_KSUCC = 21.4;
-  vGLT_VmGLT = 97.264;
-  vGLT_VmGLT has mmolepermin;
-  vGLT_KmGLTGLCo = 1.1918;
-  vGLT_KmGLTGLCo has mM;
-  vGLT_KeqGLT = 1;
-  vGLT_KeqGLT has mM;
-  vGLT_KmGLTGLCi = 1.1918;
-  vGLT_KmGLTGLCi has mM;
-  vADH_VmADH = 810;
-  vADH_VmADH has mMpermin;
-  vADH_KiADHNAD = 0.92;
-  vADH_KiADHNAD has mM;
-  vADH_KmADHETOH = 17;
-  vADH_KmADHETOH has mM;
-  vADH_KeqADH = 6.9e-05;
-  vADH_KeqADH has dimensionless;
-  vADH_KmADHNAD = 0.17;
-  vADH_KmADHNAD has mM;
-  vADH_KmADHNADH = 0.11;
-  vADH_KmADHNADH has mM;
-  vADH_KiADHNADH = 0.031;
-  vADH_KiADHNADH has mM;
-  vADH_KmADHACE = 1.11;
-  vADH_KmADHACE has mM;
-  vADH_KiADHACE = 1.1;
-  vADH_KiADHACE has mM;
-  vADH_KiADHETOH = 90;
-  vADH_KiADHETOH has mM;
-  vG3PDH_VmG3PDH = 70.15;
-  vG3PDH_VmG3PDH has mMpermin;
-  vG3PDH_KmG3PDHDHAP = 0.4;
-  vG3PDH_KmG3PDHDHAP has mM;
-  vG3PDH_KmG3PDHNADH = 0.023;
-  vG3PDH_KmG3PDHNADH has mM;
-  vG3PDH_KeqG3PDH = 4300;
-  vG3PDH_KeqG3PDH has dimensionless;
-  vG3PDH_KmG3PDHGLY = 1;
-  vG3PDH_KmG3PDHGLY has mM;
-  vG3PDH_KmG3PDHNAD = 0.93;
-  vG3PDH_KmG3PDHNAD has mM;
-  vATP_KATPASE = 33.7;
-  vATP_KATPASE has permin;
-
-  // Other declarations:
-  const extracellular, cytosol, KeqAK, gR, KmPFKF6P, KmPFKATP, Lzero, CiPFKATP;
-  const KiPFKATP, CPFKAMP, KPFKAMP, CPFKF26BP, KPFKF26BP, CPFKF16BP, KPFKF16BP;
-  const CPFKATP, KeqTPI;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-  unit mM = 1e-3 mole / litre;
-  unit mMpermin = 1e-3 mole / (litre * 60 second);
-  unit permin = 1 / 60 second;
-  unit mmolepermin = 1e-3 mole / 60 second;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "minute";
-  GLCi is "Glucose in Cytosol";
-  G6P is "Glucose 6 Phosphate";
-  F6P is "Fructose 6 Phosphate";
-  F16P is "Fructose-1,6 bisphosphate";
-  TRIO is "Triose-phosphate";
-  BPG is "1,3-bisphosphoglycerate";
-  P3G is "3-phosphoglycerate";
-  P2G is "2-phosphoglycerate";
-  PEP is "Phosphoenolpyruvate";
-  PYR is "Pyruvate";
-  ACE is "Acetaldehyde";
-  P is "High energy phosphates";
-  Glyc is "Glycogen";
-  Trh is "Trehalose";
-  SUCC is "Succinate";
-  GLCo is "Extracellular Glucose";
-  ETOH is "Ethanol";
-  GLY is "Glycerol";
-  ATP is "ATP concentration";
-  ADP is "ADP concentration";
-  SUM_P is "sum of AXP conc";
-  KeqAK is "AK eq constant";
-  AMP is "AMP concentration";
-  F26BP is "F2,6P";
-  KeqTPI is "TPI eq constant";
-  vGLK is "Hexokinase";
-  vPGI is "Glucose-6-phosphate isomerase";
-  vGLYCO is "Glycogen synthesis";
-  vTreha is "Trehalose 6-phosphate synthase";
-  vPFK is "Phosphofructokinase";
-  vALD is "Aldolase";
-  vGAPDH is "Glyceraldehyde 3-phosphate dehydrogenase";
-  vPGK is "Phosphoglycerate kinase";
-  vPGM is "Phosphoglycerate mutase";
-  vENO is "Enolase";
-  vPYK is "Pyruvate kinase";
-  vPDC is "Pyruvate decarboxylase";
-  vSUC is "Succinate synthesis";
-  vGLT is "Glucose transport";
-  vADH is "Alcohol dehydrogenase";
-  vG3PDH is "Glycerol 3-phosphate dehydrogenase";
-  vATP is "ATPase activity";
-
-  // CV terms:
-  extracellular identity "http://identifiers.org/obo.go/GO:0005576"
-  cytosol identity "http://identifiers.org/obo.go/GO:0005829"
-  GLCi identity "http://identifiers.org/obo.chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  G6P identity "http://identifiers.org/obo.chebi/CHEBI:17665",
-               "http://identifiers.org/kegg.compound/C00668"
-  F6P identity "http://identifiers.org/obo.chebi/CHEBI:15946",
-               "http://identifiers.org/kegg.compound/C05345"
-  F16P identity "http://identifiers.org/obo.chebi/CHEBI:16905",
-                "http://identifiers.org/kegg.compound/C00354"
-  TRIO part "http://identifiers.org/obo.chebi/CHEBI:16108",
-            "http://identifiers.org/obo.chebi/CHEBI:29052"
-  TRIO part "http://identifiers.org/kegg.compound/C00118",
-            "http://identifiers.org/kegg.compound/C00111",
-            "http://identifiers.org/chebi/CHEBI:29052"
-  BPG identity "http://identifiers.org/obo.chebi/CHEBI:16001",
-               "http://identifiers.org/kegg.compound/C00236"
-  P3G identity "http://identifiers.org/obo.chebi/CHEBI:17794",
-               "http://identifiers.org/kegg.compound/C00197"
-  P2G identity "http://identifiers.org/obo.chebi/CHEBI:17835",
-               "http://identifiers.org/kegg.compound/C00631"
-  PEP identity "http://identifiers.org/kegg.compound/C00074",
-               "http://identifiers.org/chebi/CHEBI:18021"
-  PEP identity "http://identifiers.org/obo.chebi/CHEBI:18021"
-  PYR identity "http://identifiers.org/obo.chebi/CHEBI:15361"
-  PYR identity "http://identifiers.org/kegg.compound/C00022",
-               "http://identifiers.org/chebi/CHEBI:32816"
-  ACE identity "http://identifiers.org/obo.chebi/CHEBI:15343",
-               "http://identifiers.org/kegg.compound/C00084"
-  P part "http://identifiers.org/kegg.compound/C00008",
-         "http://identifiers.org/kegg.compound/C00002",
-         "http://identifiers.org/chebi/CHEBI:16761"
-  P part "http://identifiers.org/obo.chebi/CHEBI:16761",
-         "http://identifiers.org/obo.chebi/CHEBI:15422"
-  NAD identity "http://identifiers.org/obo.chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  NADH identity "http://identifiers.org/obo.chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  Glyc identity "http://identifiers.org/obo.chebi/CHEBI:28087",
-                "http://identifiers.org/kegg.compound/C00182"
-  Trh identity "http://identifiers.org/obo.chebi/CHEBI:27082",
-               "http://identifiers.org/kegg.compound/C01083"
-  CO2 identity "http://identifiers.org/obo.chebi/CHEBI:16526",
-               "http://identifiers.org/kegg.compound/C00011"
-  SUCC identity "http://identifiers.org/obo.chebi/CHEBI:30031"
-  GLCo identity "http://identifiers.org/obo.chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  ETOH identity "http://identifiers.org/obo.chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  GLY identity "http://identifiers.org/obo.chebi/CHEBI:17754",
-               "http://identifiers.org/kegg.compound/C00116"
-  ATP identity "http://identifiers.org/obo.chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  ADP identity "http://identifiers.org/obo.chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  SUM_P part "http://identifiers.org/obo.chebi/CHEBI:15422",
-             "http://identifiers.org/obo.chebi/CHEBI:16761",
-             "http://identifiers.org/obo.chebi/CHEBI:16027"
-  SUM_P part "http://identifiers.org/kegg.compound/C00002",
-             "http://identifiers.org/kegg.compound/C00008",
-             "http://identifiers.org/kegg.compound/C00020",
-             "http://identifiers.org/chebi/CHEBI:15422"
-  AMP identity "http://identifiers.org/obo.chebi/CHEBI:16027",
-               "http://identifiers.org/kegg.compound/C00020"
-  F26BP identity "http://identifiers.org/obo.chebi/CHEBI:28602",
-                 "http://identifiers.org/kegg.compound/C00665"
-  vGLK identity "http://identifiers.org/ec-code/2.7.1.2",
-                "http://identifiers.org/kegg.reaction/R00299"
-  vGLK homolog "http://identifiers.org/reactome/REACT_1318"
-  vPGI identity "http://identifiers.org/ec-code/5.3.1.9",
-                "http://identifiers.org/kegg.reaction/R00771"
-  vPGI homolog "http://identifiers.org/reactome/REACT_116"
-  vGLYCO hypernym "http://identifiers.org/obo.go/GO:0005978"
-  vGLYCO homolog "http://identifiers.org/reactome/REACT_1736"
-  vTreha hypernym "http://identifiers.org/obo.go/GO:0005992"
-  vPFK identity "http://identifiers.org/ec-code/2.7.1.11",
-                "http://identifiers.org/kegg.reaction/R00756"
-  vPFK homolog "http://identifiers.org/reactome/REACT_736"
-  vALD identity "http://identifiers.org/ec-code/4.1.2.13",
-                "http://identifiers.org/kegg.reaction/R01070"
-  vALD homolog "http://identifiers.org/reactome/REACT_1602"
-  vGAPDH identity "http://identifiers.org/ec-code/1.2.1.12",
-                  "http://identifiers.org/kegg.reaction/R01061"
-  vGAPDH homolog "http://identifiers.org/reactome/REACT_1847"
-  vPGK identity "http://identifiers.org/ec-code/2.7.2.3",
-                "http://identifiers.org/kegg.reaction/R01512"
-  vPGK homolog "http://identifiers.org/reactome/REACT_1771"
-  vPGM identity "http://identifiers.org/ec-code/5.4.2.1",
-                "http://identifiers.org/kegg.reaction/R01518"
-  vPGM homolog "http://identifiers.org/reactome/REACT_576"
-  vENO identity "http://identifiers.org/ec-code/4.2.1.11",
-                "http://identifiers.org/kegg.reaction/R00658"
-  vENO homolog "http://identifiers.org/reactome/REACT_1400"
-  vPYK identity "http://identifiers.org/ec-code/2.7.1.40",
-                "http://identifiers.org/kegg.reaction/R00200"
-  vPYK homolog "http://identifiers.org/reactome/REACT_1911"
-  vPDC identity "http://identifiers.org/ec-code/4.1.1.1",
-                "http://identifiers.org/kegg.reaction/R00224"
-  vSUC hypernym "http://identifiers.org/obo.go/GO:0006105"
-  vGLT hypernym "http://identifiers.org/obo.go/GO:0046323"
-  vGLT homolog "http://identifiers.org/reactome/REACT_2092"
-  vADH homolog "http://identifiers.org/reactome/REACT_799"
-  vADH hypernym "http://identifiers.org/ec-code/1.1.1.2",
-                "http://identifiers.org/kegg.reaction/R00746"
-  vG3PDH hypernym "http://identifiers.org/ec-code/1.1.1.8"
-  vATP hypernym "http://identifiers.org/ec-code/3.6.1.3",
-                "http://identifiers.org/obo.go/GO:0016887"
-end
-
-Teusink2000_Glycolysis is "Teusink2000_Glycolysis"
-
-Teusink2000_Glycolysis model_entity_is "http://identifiers.org/biomodels.db/MODEL6623915522"
-Teusink2000_Glycolysis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000064"
-Teusink2000_Glycolysis description "http://identifiers.org/pubmed/10951190"
-Teusink2000_Glycolysis taxon "http://identifiers.org/taxonomy/4932"
-Teusink2000_Glycolysis identity "http://identifiers.org/kegg.pathway/sce00010",
-                                "http://identifiers.org/obo.go/GO:0006096"
-Teusink2000_Glycolysis homolog "http://identifiers.org/reactome/REACT_723"
diff --git a/BioModelsRAG/data/BIOMD0000000065.txt b/BioModelsRAG/data/BIOMD0000000065.txt
deleted file mode 100644
index 5ad7aba7124712dce476693bc25dab288d85d2ae..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000065.txt
+++ /dev/null
@@ -1,140 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Yildirim2003_Lac_operon()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, B in cell, A in cell, L in cell, P in cell, I1 in cell;
-  species I2 in cell, I3 in cell, $L_e in cell;
-
-  // Reactions:
-  r_m1:  => M; cell*gamma_0;
-  r_m2: M => ; cell*M*(gamma_M + mu);
-  r_m3_i1: I1 => M; cell*I1/tau_M;
-  r_i1:  => I1; cell*alpha_M*((K_1*exp(mu*tau_M*-2)*A^2 + 1)/(K + K_1*exp(-2*mu*tau_M)*A^2));
-  r_b1: B => ; cell*B*(gamma_B + mu);
-  r_b2_i2: I2 => B; cell*I2/tau_B;
-  r_i2:  => I2; cell*alpha_B*M*exp(-(mu*tau_B));
-  r_a1: A => ; cell*A*(gamma_A + mu);
-  r_a2: A => ; cell*beta_A*B*(A/(K_A + A));
-  r_a3_l1: L => A; cell*alpha_A*B*(L/(K_L + L));
-  r_l2: L => ; cell*L*(gamma_L + mu);
-  r_l3: L => ; cell*beta_L1*P*(L/(K_L1 + L));
-  r_l4:  => L; cell*alpha_L*P*(L_e/(K_Le + L_e));
-  r_p1: P => ; cell*P*(gamma_P + mu);
-  r_p2_i3: I3 => P; cell*I3/(tau_B + tau_P);
-  r_i3:  => I3; cell*alpha_P*M*exp(-1*mu*(tau_B + tau_P));
-
-  // Species initializations:
-  M = 0.000626;
-  B = 0;
-  A = 0.038;
-  L = 0.372;
-  P = 0.0149;
-  I1 = 0;
-  I2 = 0;
-  I3 = 0;
-  L_e = 0.08;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  mu = 0.0226;
-  gamma_M = 0.411;
-  gamma_B = 0.000833;
-  gamma_A = 0.52;
-  gamma_0 = 7.25e-07;
-  K = 7200;
-  alpha_M = 0.000997;
-  tau_B = 2;
-  alpha_A = 17600;
-  K_L1 = 1.81;
-  alpha_B = 0.0166;
-  K_A = 1.95;
-  beta_A = 21500;
-  tau_M = 0.1;
-  K_L = 0.97;
-  gamma_L = 0;
-  gamma_P = 0.65;
-  alpha_L = 2880;
-  alpha_P = 10;
-  tau_P = 0.83;
-  beta_L1 = 2650;
-  K_Le = 0.26;
-  K_1 = 25200;
-
-  // Other declarations:
-  const cell, mu, gamma_M, gamma_B, gamma_A, gamma_0, K, alpha_M, tau_B, alpha_A;
-  const K_L1, alpha_B, K_A, beta_A, tau_M, K_L, gamma_L, gamma_P, alpha_L;
-  const alpha_P, tau_P, beta_L1, K_Le, K_1;
-
-  // Unit definitions:
-  unit time_unit = 60 second;
-  unit substance = 1e-3 mole;
-
-  // Display Names:
-  time_unit is "minute";
-  substance is "millimoles";
-  M is "mRNA";
-  B is "Betagalactosidase";
-  A is "allolactose";
-  L is "lactose_internal";
-  P is "permease";
-  I1 is "PartialmRNA";
-  I2 is "PartialBetagalactosidase";
-  I3 is "PartialPermease";
-  L_e is "External_Lactose";
-  r_m1 is "Basal_mRNA_Synthesis";
-  r_m2 is "mRNA_Degradation";
-  r_m3_i1 is "allolactose_controlled_mRNA_synthesis";
-  r_i1 is "allolactose_controlled_partial_mRNA_synthesis";
-  r_b1 is "Beta_galactosidase_Degradation";
-  r_b2_i2 is "Beta_galactosidase_synthesis";
-  r_i2 is "Partial_Beta_galactosidase_synthesis";
-  r_a1 is "Basal_Allolactose_Degradation";
-  r_a2 is "Betagalactosidase_mediated_Allolactose_Degradation";
-  r_a3_l1 is "Beta_galactosidase_reaction";
-  r_l2 is "lactose_degradation";
-  r_l3 is "Lactose_transport_out";
-  r_l4 is "Lactose_transport_in";
-  r_p1 is "permease_degradation";
-  r_p2_i3 is "permease_synthesis";
-  r_i3 is "partial_permease_synthesis";
-
-  // CV terms:
-  cell identity "http://identifiers.org/go/GO:0005623"
-  M identity "http://identifiers.org/chebi/CHEBI:33699"
-  B identity "http://identifiers.org/uniprot/P00722"
-  A part "http://identifiers.org/chebi/CHEBI:36229"
-  L identity "http://identifiers.org/chebi/CHEBI:17716",
-             "http://identifiers.org/kegg.compound/C00243"
-  P identity "http://identifiers.org/uniprot/P02920"
-  L_e identity "http://identifiers.org/chebi/CHEBI:17716",
-               "http://identifiers.org/kegg.compound/C00243"
-  r_m1 hypernym "http://identifiers.org/go/GO:0006351"
-  r_m2 identity "http://identifiers.org/go/GO:0006402"
-  r_m3_i1 hypernym "http://identifiers.org/go/GO:0009299"
-  r_i1 hypernym "http://identifiers.org/go/GO:0009299"
-  r_b1 hypernym "http://identifiers.org/go/GO:0044257"
-  r_b2_i2 hypernym "http://identifiers.org/go/GO:0006412"
-  r_i2 hypernym "http://identifiers.org/go/GO:0006412"
-  r_a1 hypernym "http://identifiers.org/go/GO:0046352"
-  r_a2 hypernym "http://identifiers.org/go/GO:0046352"
-  r_a3_l1 identity "http://identifiers.org/ec-code/3.2.1.108",
-                   "http://identifiers.org/go/GO:0004565"
-  r_l2 identity "http://identifiers.org/go/GO:0005990"
-  r_l3 identity "http://identifiers.org/go/GO:0015155"
-  r_l4 identity "http://identifiers.org/go/GO:0015155"
-  r_p1 hypernym "http://identifiers.org/go/GO:0044257"
-  r_p2_i3 hypernym "http://identifiers.org/go/GO:0006412"
-  r_i3 hypernym "http://identifiers.org/go/GO:0006412"
-end
-
-Yildirim2003_Lac_operon is "Yildirim2003_Lac_Operon"
-
-Yildirim2003_Lac_operon model_entity_is "http://identifiers.org/biomodels.db/MODEL6624248569"
-Yildirim2003_Lac_operon model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000065"
-Yildirim2003_Lac_operon description "http://identifiers.org/pubmed/12719218"
-Yildirim2003_Lac_operon origin "http://identifiers.org/pubmed/9104037"
-Yildirim2003_Lac_operon hypernym "http://identifiers.org/go/GO:0045990"
-Yildirim2003_Lac_operon taxon "http://identifiers.org/taxonomy/562"
diff --git a/BioModelsRAG/data/BIOMD0000000066.txt b/BioModelsRAG/data/BIOMD0000000066.txt
deleted file mode 100644
index 6d69a7df2a6b0652f302891f1c898542cab990a4..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000066.txt
+++ /dev/null
@@ -1,217 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Chassagnole2001_Threonine_Synthesis()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species aspp in compartment_, asa in compartment_, hs in compartment_, hsp in compartment_;
-  species phos in compartment_, thr in compartment_, asp in compartment_;
-  species nadp in compartment_, nadph in compartment_, adp in compartment_;
-  species atp in compartment_;
-
-  // Reactions:
-  vak: atp + asp -> aspp + adp; compartment_*(vak_vm11*(asp*atp - aspp*adp/vak_keqak)/((vak_k11*(1 + (thr/vak_k1thr)^vak_nak1)/(1 + (thr/(vak_alpha*vak_k1thr))^vak_nak1) + vak_k11*aspp/vak_k1aspp + asp)*(vak_k1atp*(1 + adp/vak_k1adp) + atp)) + vak_vm13*(asp*atp - aspp*adp/vak_keqak)/((1 + (vak_lys/vak_k1lys)^vak_nak3)*(vak_k13*(1 + aspp/vak_k13aspp) + asp)*(vak_k13atp*(1 + adp/vak_k13adp) + atp)));
-  vasd: nadph + aspp -> nadp + phos + asa; compartment_*(vasd_vm2f*(aspp*nadph - asa*nadp*phos/vasd_k2eq)/((vasd_k2aspp*(1 + asa/vasd_k2asa)*(1 + phos/vasd_k2p) + aspp)*(vasd_k2nadph*(1 + nadp/vasd_k2nadp) + nadph)));
-  vhdh: nadph + asa -> hs + nadp; compartment_*(vhdh_vm3f*(asa*nadph - hs*nadp/vhdh_k3eq)/(((1 + (thr/vhdh_k3thr)^vhdh_nhdh1)/(1 + (thr/(vhdh_alpha3*vhdh_k3thr))^vhdh_nhdh1))*(vhdh_k3asa + asa + hs*vhdh_k3asa/vhdh_k3hs)*(vhdh_k3nadph*(1 + nadp/vhdh_k3nadp) + nadph)));
-  vtsy: hsp -> thr + phos; compartment_*vtsy_vm5*hsp/(hsp + vtsy_k5hsp);
-  vhk: hs + atp -> hsp + adp; compartment_*(vhk_vm4f*hs*atp/((1 + vhk_lys/vhk_k4lys)*(atp + vhk_k4atp*(1 + hs/vhk_k4ihs))*(hs + vhk_k4hs*(1 + thr/vhk_k4thr)*(1 + atp/vhk_k4iatp))));
-  vnadph_endo: nadph -> nadp; compartment_*vnadph_endo_prot*vnadph_endo_knadph*nadph;
-  vatpase: atp -> adp + phos; compartment_*vatpase_prot*vatpase_katpase;
-
-  // Species initializations:
-  aspp = 0;
-  asa = 0;
-  hs = 0;
-  hsp = 0;
-  phos = 0;
-  thr = 2;
-  asp = 2;
-  nadp = 0;
-  nadph = 2;
-  adp = 0;
-  atp = 10;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  vak_vm11 = 0.15;
-  vak_vm11 has mM_per_min;
-  vak_keqak = 0.00064;
-  vak_keqak has dimensionless;
-  vak_k11 = 0.97;
-  vak_k11 has mM;
-  vak_k1thr = 0.167;
-  vak_k1thr has mM;
-  vak_nak1 = 4.09;
-  vak_nak1 has dimensionless;
-  vak_alpha = 2.47;
-  vak_alpha has dimensionless;
-  vak_k1aspp = 0.017;
-  vak_k1aspp has mM;
-  vak_k1atp = 0.98;
-  vak_k1atp has mM;
-  vak_k1adp = 0.25;
-  vak_k1adp has mM;
-  vak_vm13 = 0.0722;
-  vak_vm13 has mM_per_min;
-  vak_lys = 0.46;
-  vak_lys has mM;
-  vak_k1lys = 0.391;
-  vak_k1lys has mM;
-  vak_nak3 = 2.8;
-  vak_nak3 has dimensionless;
-  vak_k13 = 0.32;
-  vak_k13 has mM;
-  vak_k13aspp = 0.017;
-  vak_k13aspp has mM;
-  vak_k13atp = 0.22;
-  vak_k13atp has mM;
-  vak_k13adp = 0.25;
-  vak_k13adp has mM;
-  vasd_vm2f = 0.1812;
-  vasd_vm2f has mM_per_min;
-  vasd_k2eq = 56.4150334574039;
-  vasd_k2eq has dimensionless;
-  vasd_k2aspp = 0.022;
-  vasd_k2aspp has mM;
-  vasd_k2asa = 0.11;
-  vasd_k2asa has mM;
-  vasd_k2p = 10;
-  vasd_k2p has mM;
-  vasd_k2nadph = 0.029;
-  vasd_k2nadph has mM;
-  vasd_k2nadp = 0.144;
-  vasd_k2nadp has mM;
-  vhdh_vm3f = 1.001;
-  vhdh_vm3f has mM_per_min;
-  vhdh_k3eq = 3162.27766016838;
-  vhdh_k3eq has dimensionless;
-  vhdh_k3thr = 0.097;
-  vhdh_k3thr has mM;
-  vhdh_nhdh1 = 1.41;
-  vhdh_nhdh1 has dimensionless;
-  vhdh_alpha3 = 3.93;
-  vhdh_alpha3 has dimensionless;
-  vhdh_k3asa = 0.24;
-  vhdh_k3asa has mM;
-  vhdh_k3hs = 3.39;
-  vhdh_k3hs has mM;
-  vhdh_k3nadph = 0.037;
-  vhdh_k3nadph has mM;
-  vhdh_k3nadp = 0.067;
-  vhdh_k3nadp has mM;
-  vtsy_vm5 = 0.0434;
-  vtsy_vm5 has mM_per_min;
-  vtsy_k5hsp = 0.31;
-  vtsy_k5hsp has mM;
-  vhk_vm4f = 0.1;
-  vhk_vm4f has mM_per_min;
-  vhk_lys = 0.46;
-  vhk_lys has mM;
-  vhk_k4lys = 9.45;
-  vhk_k4lys has mM;
-  vhk_k4atp = 0.072;
-  vhk_k4atp has mM;
-  vhk_k4ihs = 4.7;
-  vhk_k4ihs has mM;
-  vhk_k4hs = 0.11;
-  vhk_k4hs has mM;
-  vhk_k4thr = 1.09;
-  vhk_k4thr has mM;
-  vhk_k4iatp = 4.35;
-  vhk_k4iatp has mM;
-  vnadph_endo_knadph = 5.4e-06;
-  vnadph_endo_knadph has litre_per_mg_per_min;
-  vnadph_endo_prot = 202;
-  vnadph_endo_prot has mg_per_litre;
-  vatpase_katpase = 4.1e-05;
-  vatpase_katpase has millimole_per_mg_per_min;
-  vatpase_prot = 202;
-  vatpase_prot has mg_per_litre;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-  unit mM = 1e-3 mole / litre;
-  unit mM_per_min = 1e-3 mole / (litre * 60 second);
-  unit litre_per_mg_per_min = litre / (1e-3 gram * 60 second);
-  unit millimole_per_mg_per_min = 1e-3 mole / (1e-3 gram * 60 second);
-  unit mg_per_litre = 1e-3 gram / litre;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "min";
-  aspp is "Aspartyl phosphate";
-  asa is "Aspartate beta-semialdehyde";
-  hs is "Homoserine";
-  hsp is "O-Phospho-homoserine";
-  phos is "Phos";
-  thr is "Threonine";
-  asp is "Aspartate";
-  nadp is "NADP";
-  nadph is "NADPH";
-  adp is "ADP";
-  atp is "ATP";
-  vak is "Aspartate Kinase";
-  vasd is "Aspartate semialdehyde dehydrogenase";
-  vhdh is "Homoserine dehydrogenase";
-  vtsy is "Threonine synthase";
-  vhk is "Homoserine kinase";
-  vnadph_endo is "Endogenous consumption of NADPH";
-  vatpase is "ATPase";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005623"
-  aspp identity "http://identifiers.org/obo.chebi/CHEBI:15836",
-                "http://identifiers.org/kegg.compound/C03082"
-  asa identity "http://identifiers.org/obo.chebi/CHEBI:18051",
-               "http://identifiers.org/kegg.compound/C00441"
-  hs identity "http://identifiers.org/obo.chebi/CHEBI:15699",
-              "http://identifiers.org/kegg.compound/C00263"
-  hsp identity "http://identifiers.org/obo.chebi/CHEBI:15961",
-               "http://identifiers.org/kegg.compound/C01102"
-  phos identity "http://identifiers.org/obo.chebi/CHEBI:18367",
-                "http://identifiers.org/kegg.compound/C00009"
-  thr identity "http://identifiers.org/obo.chebi/CHEBI:16857",
-               "http://identifiers.org/kegg.compound/C00188"
-  asp identity "http://identifiers.org/obo.chebi/CHEBI:17053",
-               "http://identifiers.org/kegg.compound/C00049"
-  nadp identity "http://identifiers.org/obo.chebi/CHEBI:18009",
-                "http://identifiers.org/kegg.compound/C00006"
-  nadph identity "http://identifiers.org/obo.chebi/CHEBI:16474",
-                 "http://identifiers.org/kegg.compound/C00005"
-  adp identity "http://identifiers.org/obo.chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  atp identity "http://identifiers.org/obo.chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  vak identity "http://identifiers.org/kegg.reaction/R00480"
-  vak hypernym "http://identifiers.org/ec-code/2.7.2.4",
-               "http://identifiers.org/obo.go/GO:0004072"
-  vasd hypernym "http://identifiers.org/ec-code/1.2.1.11",
-                "http://identifiers.org/obo.go/GO:0004073"
-  vasd identity "http://identifiers.org/kegg.reaction/R02291"
-  vhdh hypernym "http://identifiers.org/ec-code/1.1.1.3",
-                "http://identifiers.org/obo.go/GO:0004412"
-  vhdh identity "http://identifiers.org/kegg.reaction/R01775"
-  vtsy identity "http://identifiers.org/kegg.reaction/R01466"
-  vtsy hypernym "http://identifiers.org/ec-code/4.2.3.1",
-                "http://identifiers.org/obo.go/GO:0004795"
-  vhk hypernym "http://identifiers.org/ec-code/2.7.1.39",
-               "http://identifiers.org/obo.go/GO:0004413"
-  vhk identity "http://identifiers.org/kegg.reaction/R01771"
-  vnadph_endo hypernym "http://identifiers.org/obo.go/GO:0006739"
-  vatpase identity "http://identifiers.org/obo.go/GO:0016887"
-end
-
-Chassagnole2001_Threonine_Synthesis is "Chassagnole2001_Threonine Synthesis"
-
-Chassagnole2001_Threonine_Synthesis model_entity_is "http://identifiers.org/biomodels.db/MODEL6624131052"
-Chassagnole2001_Threonine_Synthesis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000066"
-Chassagnole2001_Threonine_Synthesis description "http://identifiers.org/pubmed/11368770"
-Chassagnole2001_Threonine_Synthesis part "http://identifiers.org/obo.go/GO:0009088",
-                                         "http://identifiers.org/obo.go/GO:0006531"
-Chassagnole2001_Threonine_Synthesis taxon "http://identifiers.org/taxonomy/83333"
-Chassagnole2001_Threonine_Synthesis hypernym "http://identifiers.org/kegg.pathway/map00260"
diff --git a/BioModelsRAG/data/BIOMD0000000067.txt b/BioModelsRAG/data/BIOMD0000000067.txt
deleted file mode 100644
index 36e49c7f7f3c68b7dacf067f610bb6e9861bf9e8..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000067.txt
+++ /dev/null
@@ -1,131 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Fung2005_Metabolator()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species AcCoA in compartment_, AcP in compartment_, OAc in compartment_;
-  species HOAc in compartment_, LacI in compartment_, Acs in compartment_;
-  species Pta in compartment_, $HOAc_E in compartment_;
-
-  // Reactions:
-  V_gly:  => AcCoA; compartment_*S0;
-  V_TCA: AcCoA => ; compartment_*kTCA*AcCoA;
-  V_out: HOAc -> $HOAc_E; compartment_*k3*(HOAc - HOAc_E);
-  V_Pta: AcCoA => AcP; compartment_*k1*Pta*AcCoA/(KM1 + AcCoA);
-  V_Ack: AcP -> OAc; compartment_*(kAck_f*AcP - kAck_r*OAc);
-  V_Acs: OAc => AcCoA; compartment_*k2*Acs*OAc/(KM2 + OAc);
-  V_Ace: OAc -> HOAc; compartment_*C*(OAc*H - Keq*HOAc);
-  R_LacI:  => LacI; compartment_*(alpha1*(AcP/Kg1)^n/(1 + (AcP/Kg1)^n) + alpha0);
-  R_Acs:  => Acs; compartment_*(alpha2*(AcP/Kg2)^n/(1 + (AcP/Kg2)^n) + alpha0);
-  R_Pta:  => Pta; alpha3/(1 + (LacI/Kg3)^n) + alpha0;
-  R_dLacI: LacI => ; compartment_*kd*LacI;
-  R_dAcs: Acs => ; compartment_*kd*Acs;
-  R_dPta: Pta => ; compartment_*kd*Pta;
-
-  // Species initializations:
-  AcCoA = 0;
-  AcP = 0;
-  OAc = 0;
-  HOAc = 0;
-  LacI = 0;
-  Acs = 0;
-  Pta = 0;
-  HOAc_E = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  S0 = 0.5;
-  kTCA = 10;
-  k1 = 80;
-  KM1 = 0.06;
-  k2 = 0.8;
-  KM2 = 0.1;
-  kAck_f = 1;
-  kAck_r = 1;
-  C = 100;
-  H = 1e-07;
-  Keq = 0.0005;
-  k3 = 0.01;
-  alpha0 = 0;
-  alpha1 = 0.1;
-  alpha2 = 2;
-  alpha3 = 2;
-  Kg1 = 10;
-  Kg2 = 10;
-  Kg3 = 0.001;
-  n = 2;
-  kd = 0.06;
-
-  // Other declarations:
-  const compartment_, S0, kTCA, k1, KM1, k2, KM2, kAck_f, kAck_r, C, H, Keq;
-  const k3, alpha0, alpha1, alpha2, alpha3, Kg1, Kg2, Kg3, n, kd;
-
-  // Display Names:
-  compartment_ is "Intracellular";
-  AcCoA is "Acetyl-CoA";
-  AcP is "Acetyl phosphate";
-  OAc is "Acetate";
-  HOAc is "protonated acetate";
-  LacI is "lac repressor";
-  Acs is "Acetyl-CoA synthase";
-  Pta is "Phosphate acetyl transferase";
-  HOAc_E is "acetate export";
-  V_gly is "Glycolytic flux";
-  V_TCA is "Flux to TCA cycle";
-  V_out is "Intercellular transport of Acetate";
-  V_Pta is "Phosphate acetyl transferase flux";
-  V_Ack is "Acetate kinase";
-  V_Acs is "Acetyl-CoA synthase flux";
-  V_Ace is "Acid-base equilibrium";
-  R_LacI is "LacI synthesis";
-  R_Acs is "Acetyl-CoA synthase synthesis";
-  R_Pta is "Phosphate acetyl transferase synthase";
-  R_dLacI is "LacI degradation";
-  R_dAcs is "Acs degradation";
-  R_dPta is "Pta degradation";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005622"
-  AcCoA identity "http://identifiers.org/obo.chebi/CHEBI:15351",
-                 "http://identifiers.org/kegg.compound/C00024"
-  AcP identity "http://identifiers.org/obo.chebi/CHEBI:15350",
-               "http://identifiers.org/kegg.compound/C00227"
-  OAc identity "http://identifiers.org/obo.chebi/CHEBI:30089",
-               "http://identifiers.org/kegg.compound/C00033"
-  HOAc hypernym "http://identifiers.org/obo.chebi/CHEBI:30089",
-                "http://identifiers.org/kegg.compound/C00033"
-  LacI parthood "http://identifiers.org/obo.go/GO:0017053"
-  Acs identity "http://identifiers.org/uniprot/P27550"
-  Pta identity "http://identifiers.org/uniprot/P0A9M8"
-  HOAc_E hypernym "http://identifiers.org/obo.chebi/CHEBI:30089",
-                  "http://identifiers.org/kegg.compound/C00033"
-  V_gly version "http://identifiers.org/obo.go/GO:0006096"
-  V_TCA version "http://identifiers.org/obo.go/GO:0006099"
-  V_out hypernym "http://identifiers.org/obo.go/GO:0015123"
-  V_Pta identity "http://identifiers.org/ec-code/2.3.1.8",
-                 "http://identifiers.org/kegg.reaction/R00230"
-  V_Ack hypernym "http://identifiers.org/ec-code/2.7.2.1",
-                 "http://identifiers.org/obo.go/GO:0008776"
-  V_Acs hypernym "http://identifiers.org/ec-code/6.2.1.1",
-                 "http://identifiers.org/obo.go/GO:0019427"
-  V_Acs identity "http://identifiers.org/kegg.reaction/R00235"
-  R_LacI part "http://identifiers.org/obo.go/GO:0006351",
-              "http://identifiers.org/obo.go/GO:0006412"
-  R_Acs part "http://identifiers.org/obo.go/GO:0006351",
-             "http://identifiers.org/obo.go/GO:0006412"
-  R_Pta part "http://identifiers.org/obo.go/GO:0006351",
-             "http://identifiers.org/obo.go/GO:0006412"
-  R_dLacI hypernym "http://identifiers.org/obo.go/GO:0030163"
-  R_dAcs hypernym "http://identifiers.org/obo.go/GO:0030163"
-  R_dPta hypernym "http://identifiers.org/obo.go/GO:0030163"
-end
-
-Fung2005_Metabolator is "Fung2005_Metabolic_Oscillator"
-
-Fung2005_Metabolator model_entity_is "http://identifiers.org/biomodels.db/MODEL6624231052"
-Fung2005_Metabolator model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000067"
-Fung2005_Metabolator description "http://identifiers.org/pubmed/15875027"
-Fung2005_Metabolator hypernym "http://identifiers.org/obo.go/GO:0045990"
-Fung2005_Metabolator taxon "http://identifiers.org/taxonomy/83333"
diff --git a/BioModelsRAG/data/BIOMD0000000068.txt b/BioModelsRAG/data/BIOMD0000000068.txt
deleted file mode 100644
index dc450fed86b1bab6b61d25160232711440a42a26..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000068.txt
+++ /dev/null
@@ -1,104 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Curien2003_MetThr_synthesis()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Phser in compartment_, $Thr in compartment_, $Cystathionine in compartment_;
-  species $Hser in compartment_, $Phi in compartment_, $Cys in compartment_;
-  species $AdoMet in compartment_, $CGS in compartment_, $TS in compartment_;
-
-  // Reactions:
-  v1: $Hser -> Phser; compartment_*v1_V0;
-  vCys: Phser + $Cys -> $Cystathionine + $Phi; CGS*(vCys_kcat2/(1 + vCys_KmCYS/Cys))*Phser/(Phser + vCys_KmPHSER*(1 + Phi/vCys_Ki2)/(1 + vCys_KmCYS/Cys));
-  vThr: Phser -> $Thr + $Phi; TS*(5.9e-4 + 0.062*AdoMet^2.9/(32^2.9 + AdoMet^2.9))*Phser/(1 + Phi/vThr_Ki3);
-
-  // Species initializations:
-  Phser = 0;
-  Thr = 0;
-  Cystathionine = 0;
-  Hser = 0;
-  Phi = 10000;
-  Cys = 15;
-  AdoMet = 20;
-  CGS = 0.7;
-  TS = 5;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_V0 = 1;
-  v1_V0 has microM_per_second;
-  vCys_kcat2 = 30;
-  vCys_kcat2 has microM;
-  vCys_KmCYS = 460;
-  vCys_KmCYS has microM;
-  vCys_KmPHSER = 2500;
-  vCys_KmPHSER has microM;
-  vCys_Ki2 = 2000;
-  vCys_Ki2 has microM;
-  vThr_Ki3 = 1000;
-  vThr_Ki3 has microM;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit microM = 1e-6 mole / litre;
-  unit sec_inverse = 1 / second;
-  unit microM_per_second = 1e-6 mole / (litre * second);
-
-  // Display Names:
-  substance is "micromole";
-  compartment_ is "Cell";
-  Phser is "Phosphohomoserine";
-  Thr is "Threonine";
-  Hser is "Homoserine";
-  Phi is "Inorganic phosphate";
-  Cys is "Cysteine";
-  AdoMet is "S-adenosylmethionine";
-  CGS is "Cystathionine gamma-synthase";
-  TS is "Threonine synthase";
-  v1 is "Phosphohomoserine synthesis";
-  vCys is "Cystathionine gamma-synthase";
-  vThr is "Threonine Synthase";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005623"
-  Phser identity "http://identifiers.org/obo.chebi/CHEBI:15961",
-                 "http://identifiers.org/kegg.compound/C01102"
-  Thr identity "http://identifiers.org/obo.chebi/CHEBI:16857",
-               "http://identifiers.org/kegg.compound/C00188"
-  Cystathionine identity "http://identifiers.org/obo.chebi/CHEBI:17482",
-                         "http://identifiers.org/kegg.compound/C02291"
-  Hser identity "http://identifiers.org/obo.chebi/CHEBI:15699",
-                "http://identifiers.org/kegg.compound/C00263"
-  Phi identity "http://identifiers.org/obo.chebi/CHEBI:18367",
-               "http://identifiers.org/kegg.compound/C00009"
-  Cys identity "http://identifiers.org/obo.chebi/CHEBI:17561",
-               "http://identifiers.org/kegg.compound/C00097"
-  AdoMet identity "http://identifiers.org/obo.chebi/CHEBI:15414",
-                  "http://identifiers.org/kegg.compound/C00019"
-  CGS hypernym "http://identifiers.org/uniprot/P55217"
-  TS hypernym "http://identifiers.org/uniprot/Q9S7B5"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.1.39",
-              "http://identifiers.org/obo.go/GO:0004413"
-  v1 identity "http://identifiers.org/kegg.reaction/R01775"
-  vCys hypernym "http://identifiers.org/ec-code/2.5.1.48",
-                "http://identifiers.org/obo.go/GO:0003962"
-  vThr identity "http://identifiers.org/kegg.reaction/R01466"
-  vThr hypernym "http://identifiers.org/ec-code/4.2.3.1",
-                "http://identifiers.org/obo.go/GO:0004795"
-end
-
-Curien2003_MetThr_synthesis is "Curien2003_MetThr_synthesis"
-
-Curien2003_MetThr_synthesis model_entity_is "http://identifiers.org/biomodels.db/MODEL6624146302"
-Curien2003_MetThr_synthesis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000068"
-Curien2003_MetThr_synthesis description "http://identifiers.org/pubmed/14622248"
-Curien2003_MetThr_synthesis part "http://identifiers.org/obo.go/GO:0019283",
-                                 "http://identifiers.org/obo.go/GO:0009088"
-Curien2003_MetThr_synthesis part "http://identifiers.org/kegg.pathway/map00260",
-                                 "http://identifiers.org/kegg.pathway/map00271"
-Curien2003_MetThr_synthesis taxon "http://identifiers.org/taxonomy/3702"
diff --git a/BioModelsRAG/data/BIOMD0000000069.txt b/BioModelsRAG/data/BIOMD0000000069.txt
deleted file mode 100644
index bde99e43d205b32509545c8b02c7a5ecf69e977b..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000069.txt
+++ /dev/null
@@ -1,99 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Src_MitoticActivation()
-
-  // Compartments and Species:
-  compartment default;
-  species srci in default, srco in default, srca in default, srcc in default;
-  species Cbp_P_CSK in default, CSK_cytoplasm in default, PTP in default;
-  species PTP_pY789 in default, Cbp in default, Cbp_P in default;
-
-  // Assignment Rules:
-  ptp_activity := PTP_background + Kser*PTP_pY789;
-  src_activity := rho_srco*srco + rho_srca*srca + src_background + rho_srcc*srcc;
-
-  // Reactions:
-  v1: srci -> srco; (k2*ptp_activity*srci - k1*Cbp_P_CSK*srco)*default;
-  v2: srco -> srca; (k3*src_activity*srco - p1*srca)*default;
-  v3: srca -> srcc; (k1*Cbp_P_CSK*srca - k2*ptp_activity*srcc)*default;
-  v4: srcc => srci; default*k4*p1*srcc;
-  CSK_translocation: CSK_cytoplasm + Cbp_P -> Cbp_P_CSK; (Cbp_P*kCSKon*CSK_cytoplasm - kCSKoff*Cbp_P_CSK)*default;
-  PTP_phosphorylation: PTP -> PTP_pY789; default*((kPTP*src_activity + p3)*PTP - p2*PTP_pY789);
-  Cbp_phosphorylation: Cbp => Cbp_P; kCbp*src_activity*Cbp*default;
-
-  // Species initializations:
-  srci = 1;
-  srco = 0;
-  srca = 0;
-  srcc = 0;
-  Cbp_P_CSK = 0;
-  CSK_cytoplasm = 1;
-  PTP = 1;
-  PTP_pY789 = 0;
-  Cbp = 1;
-  Cbp_P = 0;
-
-  // Compartment initializations:
-  default = 1;
-
-  // Variable initializations:
-  k1 = 1;
-  k2 = 0.8;
-  k3 = 1;
-  k4 = 10;
-  kPTP = 1;
-  kCbp = 1;
-  p1 = 0.05;
-  p2 = 0.15;
-  p3 = 0.035;
-  src_background = 0.0001;
-  PTP_background = 0;
-  kCSKon = 0.1;
-  kCSKoff = 0.01;
-  rho_srca = 1;
-  rho_srco = 0;
-  rho_srcc = 1;
-  Kser = 1;
-  acsk0 = 0;
-
-  // Other declarations:
-  var ptp_activity, src_activity;
-  const default, k1, k2, k3, k4, kPTP, kCbp, p1, p2, p3, src_background, PTP_background;
-  const kCSKon, kCSKoff, rho_srca, rho_srco, rho_srcc, Kser, acsk0;
-
-  // CV terms:
-  default identity "http://identifiers.org/go/GO:0005623"
-  srci hypernym "http://identifiers.org/uniprot/P12931"
-  srco hypernym "http://identifiers.org/uniprot/P12931"
-  srca hypernym "http://identifiers.org/uniprot/P12931"
-  srcc hypernym "http://identifiers.org/uniprot/P12931"
-  Cbp_P_CSK part "http://identifiers.org/uniprot/P41240",
-                 "http://identifiers.org/uniprot/Q9NWQ8"
-  CSK_cytoplasm identity "http://identifiers.org/uniprot/P41240"
-  PTP hypernym "http://identifiers.org/uniprot/P18433"
-  PTP_pY789 hypernym "http://identifiers.org/uniprot/P18433"
-  Cbp hypernym "http://identifiers.org/uniprot/Q9NWQ8"
-  Cbp_P hypernym "http://identifiers.org/uniprot/Q9NWQ8"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-              "http://identifiers.org/go/GO:0004713"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-              "http://identifiers.org/go/GO:0004713"
-  v3 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-              "http://identifiers.org/go/GO:0004713"
-  v4 hypernym "http://identifiers.org/ec-code/3.1.3.48",
-              "http://identifiers.org/go/GO:0004725"
-  CSK_translocation part "http://identifiers.org/go/GO:0006461",
-                         "http://identifiers.org/go/GO:0006612"
-  PTP_phosphorylation hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                               "http://identifiers.org/go/GO:0004713"
-  Cbp_phosphorylation hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                               "http://identifiers.org/go/GO:0004713"
-end
-
-Src_MitoticActivation is "Fuss2006_MitoticActivation"
-
-Src_MitoticActivation model_entity_is "http://identifiers.org/biomodels.db/MODEL7146478294"
-Src_MitoticActivation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000069"
-Src_MitoticActivation description "http://identifiers.org/pubmed/16873466"
-Src_MitoticActivation taxon "http://identifiers.org/taxonomy/9606"
-Src_MitoticActivation hypernym "http://identifiers.org/reactome/REACT_152",
-                               "http://identifiers.org/go/GO:0000278"
diff --git a/BioModelsRAG/data/BIOMD0000000070.txt b/BioModelsRAG/data/BIOMD0000000070.txt
deleted file mode 100644
index 0a0c289cf10585b668f29ef12081f9d22737518a..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000070.txt
+++ /dev/null
@@ -1,754 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Holzhutter2004_Erythrocyte_Metabolism()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Glcin in compartment_, MgATP in compartment_, Glc6P in compartment_;
-  species MgADP in compartment_, Fru6P in compartment_, Fru16P2 in compartment_;
-  species GraP in compartment_, DHAP in compartment_, Phi in compartment_;
-  species NAD in compartment_, Gri13P2 in compartment_, NADH in compartment_;
-  species Gri3P in compartment_, Gri23P2f in compartment_, Gri2P in compartment_;
-  species PEP in compartment_, Pyr in compartment_, Lac in compartment_, NADPHf in compartment_;
-  species NADPf in compartment_, AMPf in compartment_, ADPf in compartment_;
-  species GlcA6P in compartment_, Rul5P in compartment_, GSSG in compartment_;
-  species GSH in compartment_, Xul5P in compartment_, Rib5P in compartment_;
-  species Sed7P in compartment_, E4P in compartment_, MgAMP in compartment_;
-  species ATPf in compartment_, Mgf in compartment_, MgGri23P2 in compartment_;
-  species P1NADP in compartment_, P1f in compartment_, P1NADPH in compartment_;
-  species P2NADP in compartment_, P2f in compartment_, P2NADPH in compartment_;
-  species $PRPP in compartment_, $Lacex in compartment_, $Pyrex in compartment_;
-  species $Glcout in compartment_, $Phiex in compartment_;
-
-  // Reactions:
-  vGLT: $Glcout -> Glcin; compartment_*((vGLT_Vmaxv0/vGLT_KMoutv0)*(Glcout - Glcin/vGLT_Keqv0)/(1 + Glcout/vGLT_KMoutv0 + Glcin/vGLT_KMinv0 + vGLT_alfav0*Glcout*Glcin/vGLT_KMoutv0/vGLT_KMinv0));
-  vHEX: Glcin + MgATP -> Glc6P + MgADP; compartment_*((vHEX_Inhibv1*Glcin/(Glcin + vHEX_KMGlcv1))*(vHEX_Vmax1v1/vHEX_KMgATPv1)*(MgATP + (vHEX_Vmax2v1/vHEX_Vmax1v1)*MgATP*Mgf/vHEX_KMgATPMgv1 - Glc6P*MgADP/vHEX_Keqv1)/(1 + (MgATP/vHEX_KMgATPv1)*(1 + Mgf/vHEX_KMgATPMgv1) + Mgf/vHEX_KMgv1 + (1.55 + Glc6P/vHEX_KGlc6Pv1)*(1 + Mgf/vHEX_KMgv1) + (Gri23P2f + MgGri23P2)/vHEX_K23P2Gv1 + Mgf*(Gri23P2f + MgGri23P2)/(vHEX_KMgv1*vHEX_KMg23P2Gv1)));
-  vGPI: Glc6P -> Fru6P; compartment_*(vGPI_Vmaxv2*(Glc6P - Fru6P/vGPI_Keqv2)/(Glc6P + vGPI_KGlc6Pv2*(1 + Fru6P/vGPI_KFru6Pv2)));
-  vPFK: MgATP + Fru6P -> Fru16P2 + MgADP; compartment_*(vPFK_Vmaxv3*(Fru6P*MgATP - Fru16P2*MgADP/vPFK_Keqv3)/((Fru6P + vPFK_KFru6Pv3)*(MgATP + vPFK_KMgATPv3)*(1 + vPFK_L0v3*((1 + ATPf/vPFK_KATPv3)*(1 + Mgf/vPFK_KMgv3)/((1 + (AMPf + MgAMP)/vPFK_KAMPv3)*(1 + Fru6P/vPFK_KFru6Pv3)))^4)));
-  vALD: Fru16P2 -> GraP + DHAP; compartment_*((vALD_Vmaxv4/vALD_KFru16P2v4)*(Fru16P2 - GraP*DHAP/vALD_Keqv4)/(1 + Fru16P2/vALD_KFru16P2v4 + GraP/vALD_KiGraPv4 + DHAP*(GraP + vALD_KGraPv4)/(vALD_KDHAPv4*vALD_KiGraPv4) + Fru16P2*GraP/(vALD_KFru16P2v4*vALD_KiiGraPv4)));
-  vTPI: DHAP -> GraP; compartment_*(vTPI_Vmaxv5*(DHAP - GraP/vTPI_Keqv5)/(DHAP + vTPI_KDHAPv5*(1 + GraP/vTPI_KGraPv5)));
-  vGAPDH: GraP + Phi + NAD -> NADH + Gri13P2; compartment_*((vGAPDH_Vmaxv6/(vGAPDH_KNADv6*vGAPDH_KGraPv6*vGAPDH_KPv6))*(NAD*GraP*Phi - Gri13P2*NADH/vGAPDH_Keqv6)/((1 + NAD/vGAPDH_KNADv6)*(1 + GraP/vGAPDH_KGraPv6)*(1 + Phi/vGAPDH_KPv6) + (1 + NADH/vGAPDH_KNADHv6)*(1 + Gri13P2/vGAPDH_K13P2Gv6) - 1));
-  vPGK: MgADP + Gri13P2 -> MgATP + Gri3P; compartment_*((vPGK_Vmaxv7/(vPGK_KMgADPv7*vPGK_K13P2Gv7))*(MgADP*Gri13P2 - MgATP*Gri3P/vPGK_Keqv7)/((1 + MgADP/vPGK_KMgADPv7)*(1 + Gri13P2/vPGK_K13P2Gv7) + (1 + MgATP/vPGK_KMgATPv7)*(1 + Gri3P/vPGK_K3PGv7) - 1));
-  vBPGM: Gri13P2 -> Gri23P2f; compartment_*(vBPGM_kDPGMv8*(Gri13P2 - (Gri23P2f + MgGri23P2)/vBPGM_Keqv8)/(1 + (Gri23P2f + MgGri23P2)/vBPGM_K23P2Gv8));
-  vBPGP: Gri23P2f -> Gri3P + Phi; compartment_*(vBPGP_Vmaxv9*(Gri23P2f + MgGri23P2 - Gri3P/vBPGP_Keqv9)/(Gri23P2f + MgGri23P2 + vBPGP_K23P2Gv9));
-  vPGM: Gri3P -> Gri2P; compartment_*(vPGM_Vmaxv10*(Gri3P - Gri2P/vPGM_Keqv10)/(Gri3P + vPGM_K3PGv10*(1 + Gri2P/vPGM_K2PGv10)));
-  vENO: Gri2P -> PEP; compartment_*(vENO_Vmaxv11*(Gri2P - PEP/vENO_Keqv11)/(Gri2P + vENO_K2PGv11*(1 + PEP/vENO_KPEPv11)));
-  vPK: PEP + MgADP -> MgATP + Pyr; compartment_*(vPK_Vmaxv12*(PEP*MgADP - Pyr*MgATP/vPK_Keqv12)/((PEP + vPK_KPEPv12)*(MgADP + vPK_KMgADPv12)*(1 + vPK_L0v12*(1 + (ATPf + MgATP)/vPK_KATPv12)^4/((1 + PEP/vPK_KPEPv12)^4*(1 + Fru16P2/vPK_KFru16P2v12)^4))));
-  vLDHNADH: NADH + Pyr -> Lac + NAD; compartment_*vLDHNADH_Vmaxv13*(Pyr*NADH - Lac*NAD/vLDHNADH_Keqv13);
-  vLDHNADPH: Pyr + NADPHf -> Lac + NADPf; compartment_*vLDHNADPH_kLDHv14*(Pyr*NADPHf - Lac*NADPf/vLDHNADPH_Keqv14);
-  vATPase: MgATP -> Phi + MgADP; compartment_*vATPase_kATPasev15*MgATP;
-  vAK: MgATP + AMPf -> ADPf + MgADP; compartment_*((vAK_Vmaxv16/(vAK_KATPv16*vAK_KAMPv16))*(MgATP*AMPf - MgADP*ADPf/vAK_Keqv16)/((1 + MgATP/vAK_KATPv16)*(1 + AMPf/vAK_KAMPv16) + (MgADP + ADPf)/vAK_KADPv16 + MgADP*ADPf/vAK_KADPv16^2));
-  vG6PDH: Glc6P + NADPf -> GlcA6P + NADPHf; compartment_*((vG6PDH_Vmaxv17/vG6PDH_KG6Pv17/vG6PDH_KNADPv17)*(Glc6P*NADPf - GlcA6P*NADPHf/vG6PDH_Keqv17)/(1 + NADPf*(1 + Glc6P/vG6PDH_KG6Pv17)/vG6PDH_KNADPv17 + (ATPf + MgATP)/vG6PDH_KATPv17 + NADPHf/vG6PDH_KNADPHv17 + (Gri23P2f + MgGri23P2)/vG6PDH_KPGA23v17));
-  vPGLDH: GlcA6P + NADPf -> Rul5P + NADPHf; compartment_*((vPGLDH_Vmaxv18/vPGLDH_K6PG1v18/vPGLDH_KNADPv18)*(GlcA6P*NADPf - Rul5P*NADPHf/vPGLDH_Keqv18)/((1 + NADPf/vPGLDH_KNADPv18)*(1 + GlcA6P/vPGLDH_K6PG1v18 + (Gri23P2f + MgGri23P2)/vPGLDH_KPGA23v18) + (ATPf + MgATP)/vPGLDH_KATPv18 + NADPHf*(1 + GlcA6P/vPGLDH_K6PG2v18)/vPGLDH_KNADPHv18));
-  vGSSGRD: GSSG + NADPHf -> 2 GSH + NADPf; compartment_*(vGSSGRD_Vmaxv19*(GSSG*NADPHf/(vGSSGRD_KGSSGv19*vGSSGRD_KNADPHv19) - (GSH^2/vGSSGRD_KGSHv19^2)*NADPf/(vGSSGRD_KNADPv19*vGSSGRD_Keqv19))/(1 + NADPHf*(1 + GSSG/vGSSGRD_KGSSGv19)/vGSSGRD_KNADPHv19 + (NADPf/vGSSGRD_KNADPv19)*(1 + GSH*(1 + GSH/vGSSGRD_KGSHv19)/vGSSGRD_KGSHv19)));
-  vGSHox: 2 GSH -> GSSG; compartment_*vGSHox_Kv20*GSH;
-  vRibPepi: Rul5P -> Xul5P; compartment_*(vRibPepi_Vmaxv21*(Rul5P - Xul5P/vRibPepi_Keqv21)/(Rul5P + vRibPepi_KRu5Pv21*(1 + Xul5P/vRibPepi_KX5Pv21)));
-  vRibPiso: Rul5P -> Rib5P; compartment_*(vRibPiso_Vmaxv22*(Rul5P - Rib5P/vRibPiso_Keqv22)/(Rul5P + vRibPiso_KRu5Pv22*(1 + Rib5P/vRibPiso_KR5Pv22)));
-  vTrKet1: Xul5P + Rib5P -> GraP + Sed7P; compartment_*(vTrKet1_Vmaxv23*(Rib5P*Xul5P - GraP*Sed7P/vTrKet1_Keqv23)/((vTrKet1_K1v23 + Rib5P)*Xul5P + (vTrKet1_K2v23 + vTrKet1_K6v23*Sed7P)*Rib5P + (vTrKet1_K3v23 + vTrKet1_K5v23*Sed7P)*GraP + vTrKet1_K4v23*Sed7P + vTrKet1_K7v23*Xul5P*GraP));
-  vTrAld: GraP + Sed7P -> E4P + Fru6P; compartment_*(vTrAld_Vmaxv24*(Sed7P*GraP - E4P*Fru6P/vTrAld_Keqv24)/((vTrAld_K1v24 + GraP)*Sed7P + (vTrAld_K2v24 + vTrAld_K6v24*Fru6P)*GraP + (vTrAld_K3v24 + vTrAld_K5v24*Fru6P)*E4P + vTrAld_K4v24*Fru6P + vTrAld_K7v24*Sed7P*E4P));
-  vPPRPPS: MgATP + Rib5P -> MgAMP + $PRPP; compartment_*(vPPRPPS_Vmaxv25*(Rib5P*MgATP - PRPP*MgAMP/vPPRPPS_Keqv25)/((vPPRPPS_KATPv25 + MgATP)*(vPPRPPS_KR5Pv25 + Rib5P)));
-  vTrKet2: Xul5P + E4P -> GraP + Fru6P; compartment_*(vTrKet2_Vmaxv26*(E4P*Xul5P - GraP*Fru6P/vTrKet2_Keqv26)/((vTrKet2_K1v26 + E4P)*Xul5P + (vTrKet2_K2v26 + vTrKet2_K6v26*Fru6P)*E4P + (vTrKet2_K3v26 + vTrKet2_K5v26*Fru6P)*GraP + vTrKet2_K4v26*Fru6P + vTrKet2_K7v26*Xul5P*GraP));
-  vPhiexch: $Phiex -> Phi; compartment_*vPhiexch_Vmaxv27*(Phiex - Phi/vPhiexch_Keqv27);
-  vLacexch: $Lacex -> Lac; compartment_*vLacexch_Vmaxv28*(Lacex - Lac/vLacexch_Keqv28);
-  vPyrexch: $Pyrex -> Pyr; compartment_*vPyrexch_Vmaxv29*(Pyrex - Pyr/vPyrexch_Keqv29);
-  vMgATP: MgATP -> Mgf + ATPf; compartment_*vMgATP_EqMult*(MgATP - Mgf*ATPf/vMgATP_KdATP);
-  vMgADP: MgADP -> Mgf + ADPf; compartment_*vMgADP_EqMult*(MgADP - Mgf*ADPf/vMgADP_KdADP);
-  vMgAMP: MgAMP -> Mgf + AMPf; compartment_*vMgAMP_EqMult*(MgAMP - Mgf*AMPf/vMgAMP_KdAMP);
-  vMgGri23P2: MgGri23P2 -> Mgf + Gri23P2f; compartment_*vMgGri23P2_EqMult*(MgGri23P2 - Mgf*Gri23P2f/vMgGri23P2_Kd23P2G);
-  vP1NADP: P1NADP -> P1f + NADPf; compartment_*vP1NADP_EqMult*(P1NADP - P1f*NADPf/vP1NADP_Kd1);
-  vP1NADPH: P1NADPH -> P1f + NADPHf; compartment_*vP1NADPH_EqMult*(P1NADPH - P1f*NADPHf/vP1NADPH_Kd3);
-  vP2NADP: P2NADP -> P2f + NADPf; compartment_*vP2NADP_EqMult*(P2NADP - P2f*NADPf/vP2NADP_Kd2);
-  vP2NADPH: P2NADPH -> P2f + NADPHf; compartment_*vP2NADPH_EqMult*(P2NADPH - P2f*NADPHf/vP2NADPH_Kd4);
-
-  // Species initializations:
-  Glcin = 4.5663;
-  MgATP = 1.4;
-  Glc6P = 0.0394;
-  MgADP = 0.1;
-  Fru6P = 0.0153;
-  Fru16P2 = 0.0097;
-  GraP = 0.0061;
-  DHAP = 0.1492;
-  Phi = 0.9992;
-  NAD = 0.0653;
-  Gri13P2 = 0.0005;
-  NADH = 0.0002;
-  Gri3P = 0.0658;
-  Gri23P2f = 2.0601;
-  Gri2P = 0.0084;
-  PEP = 0.0109;
-  Pyr = 0.084;
-  Lac = 1.6803;
-  NADPHf = 0.004;
-  NADPf = 0;
-  AMPf = 0;
-  ADPf = 0.25;
-  GlcA6P = 0.025;
-  Rul5P = 0.0047;
-  GSSG = 0.0004;
-  GSH = 3.1136;
-  Xul5P = 0.0127;
-  Rib5P = 0.014;
-  Sed7P = 0.0154;
-  E4P = 0.0063;
-  MgAMP = 0;
-  ATPf = 0.25;
-  Mgf = 0.8;
-  MgGri23P2 = 0.5;
-  P1NADP = 0;
-  P1f = 0;
-  P1NADPH = 0.024;
-  P2NADP = 0;
-  P2f = 0;
-  P2NADPH = 0.024;
-  PRPP = 1;
-  Lacex = 1.68;
-  Pyrex = 0.084;
-  Glcout = 5;
-  Phiex = 1;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  vGLT_Vmaxv0 = 33.6;
-  vGLT_Vmaxv0 has mM_per_hour;
-  vGLT_KMoutv0 = 1.7;
-  vGLT_KMoutv0 has mM;
-  vGLT_Keqv0 = 1;
-  vGLT_Keqv0 has dimensionless;
-  vGLT_KMinv0 = 6.9;
-  vGLT_KMinv0 has mM;
-  vGLT_alfav0 = 0.54;
-  vGLT_alfav0 has dimensionless;
-  vHEX_Inhibv1 = 1;
-  vHEX_Inhibv1 has dimensionless;
-  vHEX_KMGlcv1 = 0.1;
-  vHEX_KMGlcv1 has mM;
-  vHEX_Vmax1v1 = 15.8;
-  vHEX_Vmax1v1 has mM_per_hour;
-  vHEX_KMgATPv1 = 1.44;
-  vHEX_KMgATPv1 has mM;
-  vHEX_Vmax2v1 = 33.2;
-  vHEX_Vmax2v1 has mM_per_hour;
-  vHEX_KMgATPMgv1 = 1.14;
-  vHEX_KMgATPMgv1 has mM;
-  vHEX_Keqv1 = 3900;
-  vHEX_Keqv1 has mM;
-  vHEX_KMgv1 = 1.03;
-  vHEX_KMgv1 has mM;
-  vHEX_KGlc6Pv1 = 0.0045;
-  vHEX_KGlc6Pv1 has mM;
-  vHEX_K23P2Gv1 = 2.7;
-  vHEX_K23P2Gv1 has mM;
-  vHEX_KMg23P2Gv1 = 3.44;
-  vHEX_KMg23P2Gv1 has mM;
-  vGPI_Vmaxv2 = 935;
-  vGPI_Vmaxv2 has mM_per_hour;
-  vGPI_Keqv2 = 0.3925;
-  vGPI_Keqv2 has dimensionless;
-  vGPI_KGlc6Pv2 = 0.182;
-  vGPI_KGlc6Pv2 has mM;
-  vGPI_KFru6Pv2 = 0.071;
-  vGPI_KFru6Pv2 has mM;
-  vPFK_Vmaxv3 = 239;
-  vPFK_Vmaxv3 has mM_per_hour;
-  vPFK_Keqv3 = 100000;
-  vPFK_Keqv3 has dimensionless;
-  vPFK_KFru6Pv3 = 0.1;
-  vPFK_KFru6Pv3 has mM;
-  vPFK_KMgATPv3 = 0.068;
-  vPFK_KMgATPv3 has mM;
-  vPFK_L0v3 = 0.001072;
-  vPFK_L0v3 has dimensionless;
-  vPFK_KATPv3 = 0.01;
-  vPFK_KATPv3 has mM;
-  vPFK_KMgv3 = 0.44;
-  vPFK_KMgv3 has mM;
-  vPFK_KAMPv3 = 0.033;
-  vPFK_KAMPv3 has mM;
-  vALD_Vmaxv4 = 98.91000366;
-  vALD_Vmaxv4 has mM_per_hour;
-  vALD_KFru16P2v4 = 0.0071;
-  vALD_KFru16P2v4 has mM;
-  vALD_Keqv4 = 0.114;
-  vALD_Keqv4 has mM;
-  vALD_KiGraPv4 = 0.0572;
-  vALD_KiGraPv4 has mM;
-  vALD_KGraPv4 = 0.1906;
-  vALD_KGraPv4 has mM;
-  vALD_KDHAPv4 = 0.0364;
-  vALD_KDHAPv4 has mM;
-  vALD_KiiGraPv4 = 0.176;
-  vALD_KiiGraPv4 has mM;
-  vTPI_Vmaxv5 = 5456.600098;
-  vTPI_Vmaxv5 has mM_per_hour;
-  vTPI_Keqv5 = 0.0407;
-  vTPI_Keqv5 has dimensionless;
-  vTPI_KDHAPv5 = 0.838;
-  vTPI_KDHAPv5 has mM;
-  vTPI_KGraPv5 = 0.428;
-  vTPI_KGraPv5 has mM;
-  vGAPDH_Vmaxv6 = 4300;
-  vGAPDH_Vmaxv6 has mM_per_hour;
-  vGAPDH_KNADv6 = 0.05;
-  vGAPDH_KNADv6 has mM;
-  vGAPDH_KGraPv6 = 0.005;
-  vGAPDH_KGraPv6 has mM;
-  vGAPDH_KPv6 = 3.9;
-  vGAPDH_KPv6 has mM;
-  vGAPDH_Keqv6 = 0.000192;
-  vGAPDH_Keqv6 has dimensionless;
-  vGAPDH_KNADHv6 = 0.0083;
-  vGAPDH_KNADHv6 has mM;
-  vGAPDH_K13P2Gv6 = 0.0035;
-  vGAPDH_K13P2Gv6 has mM;
-  vPGK_Vmaxv7 = 5000;
-  vPGK_Vmaxv7 has mM_per_hour;
-  vPGK_KMgADPv7 = 0.35;
-  vPGK_KMgADPv7 has mM;
-  vPGK_K13P2Gv7 = 0.002;
-  vPGK_K13P2Gv7 has mM;
-  vPGK_Keqv7 = 1455;
-  vPGK_Keqv7 has dimensionless;
-  vPGK_KMgATPv7 = 0.48;
-  vPGK_KMgATPv7 has mM;
-  vPGK_K3PGv7 = 1.2;
-  vPGK_K3PGv7 has mM;
-  vBPGM_kDPGMv8 = 76000;
-  vBPGM_kDPGMv8 has hour_inverse;
-  vBPGM_Keqv8 = 100000;
-  vBPGM_Keqv8 has dimensionless;
-  vBPGM_K23P2Gv8 = 0.04;
-  vBPGM_K23P2Gv8 has mM;
-  vBPGP_Vmaxv9 = 0.53;
-  vBPGP_Vmaxv9 has mM_per_hour;
-  vBPGP_Keqv9 = 100000;
-  vBPGP_Keqv9 has dimensionless;
-  vBPGP_K23P2Gv9 = 0.2;
-  vBPGP_K23P2Gv9 has mM;
-  vPGM_Vmaxv10 = 2000;
-  vPGM_Vmaxv10 has mM_per_hour;
-  vPGM_Keqv10 = 0.145;
-  vPGM_Keqv10 has dimensionless;
-  vPGM_K3PGv10 = 5;
-  vPGM_K3PGv10 has mM;
-  vPGM_K2PGv10 = 1;
-  vPGM_K2PGv10 has mM;
-  vENO_Vmaxv11 = 1500;
-  vENO_Vmaxv11 has mM_per_hour;
-  vENO_Keqv11 = 1.7;
-  vENO_Keqv11 has dimensionless;
-  vENO_K2PGv11 = 1;
-  vENO_K2PGv11 has mM;
-  vENO_KPEPv11 = 1;
-  vENO_KPEPv11 has mM;
-  vPK_Vmaxv12 = 570;
-  vPK_Vmaxv12 has mM_per_hour;
-  vPK_Keqv12 = 13790;
-  vPK_Keqv12 has dimensionless;
-  vPK_KPEPv12 = 0.225;
-  vPK_KPEPv12 has mM;
-  vPK_KMgADPv12 = 0.474;
-  vPK_KMgADPv12 has mM;
-  vPK_L0v12 = 19;
-  vPK_L0v12 has dimensionless;
-  vPK_KATPv12 = 3.39;
-  vPK_KATPv12 has mM;
-  vPK_KFru16P2v12 = 0.005;
-  vPK_KFru16P2v12 has mM;
-  vLDHNADH_Vmaxv13 = 2800000;
-  vLDHNADH_Vmaxv13 has per_mM_hour;
-  vLDHNADH_Keqv13 = 9090;
-  vLDHNADH_Keqv13 has dimensionless;
-  vLDHNADPH_kLDHv14 = 243.4;
-  vLDHNADPH_kLDHv14 has per_mM_hour;
-  vLDHNADPH_Keqv14 = 14181.8;
-  vLDHNADPH_Keqv14 has dimensionless;
-  vATPase_kATPasev15 = 1.68;
-  vATPase_kATPasev15 has hour_inverse;
-  vAK_Vmaxv16 = 1380;
-  vAK_Vmaxv16 has mM_per_hour;
-  vAK_KATPv16 = 0.09;
-  vAK_KATPv16 has mM;
-  vAK_KAMPv16 = 0.08;
-  vAK_KAMPv16 has mM;
-  vAK_Keqv16 = 0.25;
-  vAK_Keqv16 has dimensionless;
-  vAK_KADPv16 = 0.11;
-  vAK_KADPv16 has mM;
-  vG6PDH_Vmaxv17 = 162;
-  vG6PDH_Vmaxv17 has mM_per_hour;
-  vG6PDH_KG6Pv17 = 0.0667;
-  vG6PDH_KG6Pv17 has mM;
-  vG6PDH_KNADPv17 = 0.00367;
-  vG6PDH_KNADPv17 has mM;
-  vG6PDH_Keqv17 = 2000;
-  vG6PDH_Keqv17 has dimensionless;
-  vG6PDH_KATPv17 = 0.749;
-  vG6PDH_KATPv17 has mM;
-  vG6PDH_KNADPHv17 = 0.00312;
-  vG6PDH_KNADPHv17 has mM;
-  vG6PDH_KPGA23v17 = 2.289;
-  vG6PDH_KPGA23v17 has mM;
-  vPGLDH_Vmaxv18 = 1575;
-  vPGLDH_Vmaxv18 has mM_per_hour;
-  vPGLDH_K6PG1v18 = 0.01;
-  vPGLDH_K6PG1v18 has mM;
-  vPGLDH_KNADPv18 = 0.018;
-  vPGLDH_KNADPv18 has mM;
-  vPGLDH_Keqv18 = 141.7;
-  vPGLDH_Keqv18 has dimensionless;
-  vPGLDH_KPGA23v18 = 0.12;
-  vPGLDH_KPGA23v18 has mM;
-  vPGLDH_KATPv18 = 0.154;
-  vPGLDH_KATPv18 has mM;
-  vPGLDH_K6PG2v18 = 0.058;
-  vPGLDH_K6PG2v18 has mM;
-  vPGLDH_KNADPHv18 = 0.0045;
-  vPGLDH_KNADPHv18 has mM;
-  vGSSGRD_Vmaxv19 = 90;
-  vGSSGRD_Vmaxv19 has mM_per_hour;
-  vGSSGRD_KGSSGv19 = 0.0652;
-  vGSSGRD_KGSSGv19 has mM;
-  vGSSGRD_KNADPHv19 = 0.00852;
-  vGSSGRD_KNADPHv19 has mM;
-  vGSSGRD_KGSHv19 = 20;
-  vGSSGRD_KGSHv19 has mM;
-  vGSSGRD_KNADPv19 = 0.07;
-  vGSSGRD_KNADPv19 has mM;
-  vGSSGRD_Keqv19 = 1.04;
-  vGSSGRD_Keqv19 has dimensionless;
-  vGSHox_Kv20 = 0.03;
-  vGSHox_Kv20 has hour_inverse;
-  vRibPepi_Vmaxv21 = 4634;
-  vRibPepi_Vmaxv21 has mM_per_hour;
-  vRibPepi_Keqv21 = 2.7;
-  vRibPepi_Keqv21 has dimensionless;
-  vRibPepi_KRu5Pv21 = 0.19;
-  vRibPepi_KRu5Pv21 has mM;
-  vRibPepi_KX5Pv21 = 0.5;
-  vRibPepi_KX5Pv21 has mM;
-  vRibPiso_Vmaxv22 = 730;
-  vRibPiso_Vmaxv22 has mM_per_hour;
-  vRibPiso_Keqv22 = 3;
-  vRibPiso_Keqv22 has dimensionless;
-  vRibPiso_KRu5Pv22 = 0.78;
-  vRibPiso_KRu5Pv22 has mM;
-  vRibPiso_KR5Pv22 = 2.2;
-  vRibPiso_KR5Pv22 has mM;
-  vTrKet1_Vmaxv23 = 23.5;
-  vTrKet1_Vmaxv23 has mM_per_hour;
-  vTrKet1_Keqv23 = 1.05;
-  vTrKet1_Keqv23 has dimensionless;
-  vTrKet1_K1v23 = 0.4177;
-  vTrKet1_K1v23 has mM;
-  vTrKet1_K2v23 = 0.3055;
-  vTrKet1_K2v23 has mM;
-  vTrKet1_K6v23 = 0.00774;
-  vTrKet1_K6v23 has dimensionless;
-  vTrKet1_K3v23 = 12.432;
-  vTrKet1_K3v23 has mM;
-  vTrKet1_K5v23 = 0.41139;
-  vTrKet1_K5v23 has dimensionless;
-  vTrKet1_K4v23 = 0.00496;
-  vTrKet1_K4v23 has mM;
-  vTrKet1_K7v23 = 48.8;
-  vTrKet1_K7v23 has dimensionless;
-  vTrAld_Vmaxv24 = 27.2;
-  vTrAld_Vmaxv24 has mM_per_hour;
-  vTrAld_Keqv24 = 1.05;
-  vTrAld_Keqv24 has dimensionless;
-  vTrAld_K1v24 = 0.00823;
-  vTrAld_K1v24 has mM;
-  vTrAld_K2v24 = 0.04765;
-  vTrAld_K2v24 has mM;
-  vTrAld_K6v24 = 0.4653;
-  vTrAld_K6v24 has dimensionless;
-  vTrAld_K3v24 = 0.1733;
-  vTrAld_K3v24 has mM;
-  vTrAld_K5v24 = 0.8683;
-  vTrAld_K5v24 has dimensionless;
-  vTrAld_K4v24 = 0.006095;
-  vTrAld_K4v24 has mM;
-  vTrAld_K7v24 = 2.524;
-  vTrAld_K7v24 has dimensionless;
-  vPPRPPS_Vmaxv25 = 1.1;
-  vPPRPPS_Vmaxv25 has mM_per_hour;
-  vPPRPPS_Keqv25 = 100000;
-  vPPRPPS_Keqv25 has dimensionless;
-  vPPRPPS_KATPv25 = 0.03;
-  vPPRPPS_KATPv25 has mM;
-  vPPRPPS_KR5Pv25 = 0.57;
-  vPPRPPS_KR5Pv25 has mM;
-  vTrKet2_Vmaxv26 = 23.5;
-  vTrKet2_Vmaxv26 has mM_per_hour;
-  vTrKet2_Keqv26 = 1.2;
-  vTrKet2_Keqv26 has dimensionless;
-  vTrKet2_K1v26 = 0.00184;
-  vTrKet2_K1v26 has mM;
-  vTrKet2_K2v26 = 0.3055;
-  vTrKet2_K2v26 has mM;
-  vTrKet2_K6v26 = 0.122;
-  vTrKet2_K6v26 has dimensionless;
-  vTrKet2_K3v26 = 0.0548;
-  vTrKet2_K3v26 has mM;
-  vTrKet2_K5v26 = 0.0287;
-  vTrKet2_K5v26 has dimensionless;
-  vTrKet2_K4v26 = 0.0003;
-  vTrKet2_K4v26 has mM;
-  vTrKet2_K7v26 = 0.215;
-  vTrKet2_K7v26 has dimensionless;
-  vPhiexch_Vmaxv27 = 100;
-  vPhiexch_Vmaxv27 has hour_inverse;
-  vPhiexch_Keqv27 = 1;
-  vPhiexch_Keqv27 has dimensionless;
-  vLacexch_Vmaxv28 = 10000;
-  vLacexch_Vmaxv28 has hour_inverse;
-  vLacexch_Keqv28 = 1;
-  vLacexch_Keqv28 has dimensionless;
-  vPyrexch_Vmaxv29 = 10000;
-  vPyrexch_Vmaxv29 has hour_inverse;
-  vPyrexch_Keqv29 = 1;
-  vPyrexch_Keqv29 has dimensionless;
-  vMgATP_EqMult = 10000000;
-  vMgATP_EqMult has hour_inverse;
-  vMgATP_KdATP = 0.072;
-  vMgATP_KdATP has mM;
-  vMgADP_EqMult = 10000000;
-  vMgADP_EqMult has hour_inverse;
-  vMgADP_KdADP = 0.76;
-  vMgADP_KdADP has mM;
-  vMgAMP_EqMult = 10000000;
-  vMgAMP_EqMult has hour_inverse;
-  vMgAMP_KdAMP = 16.64;
-  vMgAMP_KdAMP has mM;
-  vMgGri23P2_EqMult = 10000000;
-  vMgGri23P2_EqMult has hour_inverse;
-  vMgGri23P2_Kd23P2G = 1.667;
-  vMgGri23P2_Kd23P2G has mM;
-  vP1NADP_EqMult = 10000000;
-  vP1NADP_EqMult has hour_inverse;
-  vP1NADP_Kd1 = 0.0002;
-  vP1NADP_Kd1 has mM;
-  vP1NADPH_EqMult = 10000000;
-  vP1NADPH_EqMult has hour_inverse;
-  vP1NADPH_Kd3 = 1e-05;
-  vP1NADPH_Kd3 has mM;
-  vP2NADP_EqMult = 10000000;
-  vP2NADP_EqMult has hour_inverse;
-  vP2NADP_Kd2 = 1e-05;
-  vP2NADP_Kd2 has mM;
-  vP2NADPH_EqMult = 10000000;
-  vP2NADPH_EqMult has hour_inverse;
-  vP2NADPH_Kd4 = 0.0002;
-  vP2NADPH_Kd4 has mM;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 3600 second;
-  unit mM = 1e-3 mole / litre;
-  unit mM_per_hour = 1e-3 mole / (litre * 3600 second);
-  unit hour_inverse = 1 / 3600 second;
-  unit per_mM_hour = litre / (1e-3 mole * 3600 second);
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "hour";
-  compartment_ is "cytoplasm";
-  Glcin is "Glucose in";
-  Glc6P is "Glucose 6-phosphate";
-  Fru6P is "Fructose 6-phosphate";
-  Fru16P2 is "Fructose 1,6-phosphate";
-  GraP is "Glyceraldehyde 3-phosphate";
-  DHAP is "Dihydroxyacetone phosphate";
-  Phi is "Phosphate";
-  Gri13P2 is "1,3-Bisphospho-D-glycerate";
-  Gri3P is "3-Phospho-D-glycerate";
-  Gri23P2f is "2,3-Bisphospho-D-glycerate";
-  Gri2P is "2-Phospho-D-glycerate";
-  PEP is "Phosphoenolpyruvate";
-  Pyr is "Pyruvate";
-  Lac is "Lactate";
-  NADPHf is "NADPH";
-  NADPf is "NADP";
-  AMPf is "AMP";
-  ADPf is "ADP";
-  GlcA6P is "Phospho-D-glucono-1,5-lactone";
-  Rul5P is "Ribulose 5-phosphate";
-  GSSG is "Oxidized Glutathione";
-  GSH is "Reduced Glutathione";
-  Xul5P is "Xylulose 5-phosphate";
-  Rib5P is "Ribose 5-phosphate";
-  Sed7P is "Sedoheptulose 7-phosphate";
-  E4P is "Erythrose 4-phosphate";
-  ATPf is "ATP";
-  Mgf is "Mg";
-  P1NADP is "Protein1 bound NADP";
-  P1f is "Protein1";
-  P1NADPH is "Protein1 bound NADPH";
-  P2NADP is "Protein2 bound NADP";
-  P2f is "Protein2";
-  P2NADPH is "Protein2 bound NADPH";
-  Lacex is "External Lactate";
-  Pyrex is "External Pyruvate";
-  Glcout is "Glucose outside";
-  Phiex is "Phosphate external";
-  vGLT is "Glucose transport";
-  vHEX is "Hexokinase";
-  vGPI is "Glucosephosphate isomerase";
-  vPFK is "Phosphofructokinase";
-  vALD is "Aldolase";
-  vTPI is "Triosephosphate isomerase";
-  vGAPDH is "Glyceraldehyde 3-phosphate dehydrogenase";
-  vPGK is "Phosphoglycerate kinase";
-  vBPGM is "Bisphosphoglycerate mutase";
-  vBPGP is "Bisphosphoglycerate phosphatase";
-  vPGM is "Phosphoglycerate mutase";
-  vENO is "Enolase";
-  vPK is "Pyruvate kinase";
-  vLDHNADH is "Lactate dehydrogenase";
-  vLDHNADPH is "Lactate dehydrogenase";
-  vATPase is "ATPase";
-  vAK is "Adenylate kinase";
-  vG6PDH is "Glucose 6-phosphate dehydrogenase";
-  vPGLDH is "Phosphogluconate dehydrogenase";
-  vGSSGRD is "Glutathione reductase";
-  vGSHox is "Glutathione oxidation";
-  vRibPepi is "Phosphoribulose epimerase";
-  vRibPiso is "Ribose phosphate isomerase";
-  vTrKet1 is "Transketolase 1";
-  vTrAld is "Transaldolase";
-  vPPRPPS is "Phosphoribosylpyrophosphate synthetase";
-  vTrKet2 is "Transketolase 2";
-  vPhiexch is "Phosphate exchange";
-  vLacexch is "Lactate exchange";
-  vPyrexch is "Pyruvate exchange";
-  vMgATP is "MgATP dissociation";
-  vMgADP is "MgADP dissociation";
-  vMgAMP is "MgAMP dissociation";
-  vMgGri23P2 is "MgGri23P2 dissociation";
-  vP1NADP is "P1NADP dissociation";
-  vP1NADPH is "P1NADPH dissociation";
-  vP2NADP is "P2NADP dissociation";
-  vP2NADPH is "P2NADPH dissociation";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005737"
-  Glcin identity "http://identifiers.org/chebi/CHEBI:17234",
-                 "http://identifiers.org/kegg.compound/C00293"
-  MgATP part "http://identifiers.org/chebi/CHEBI:25107",
-             "http://identifiers.org/chebi/CHEBI:15422"
-  MgATP part "http://identifiers.org/kegg.compound/C00305",
-             "http://identifiers.org/kegg.compound/C00002",
-             "http://identifiers.org/chebi/CHEBI:18420"
-  Glc6P identity "http://identifiers.org/chebi/CHEBI:17665",
-                 "http://identifiers.org/kegg.compound/C00668"
-  MgADP part "http://identifiers.org/chebi/CHEBI:25107",
-             "http://identifiers.org/chebi/CHEBI:16761"
-  MgADP part "http://identifiers.org/kegg.compound/C00305",
-             "http://identifiers.org/kegg.compound/C00008",
-             "http://identifiers.org/chebi/CHEBI:18420"
-  Fru6P identity "http://identifiers.org/chebi/CHEBI:16084",
-                 "http://identifiers.org/kegg.compound/C05345"
-  Fru16P2 identity "http://identifiers.org/chebi/CHEBI:28013",
-                   "http://identifiers.org/kegg.compound/C05378"
-  GraP identity "http://identifiers.org/chebi/CHEBI:29052",
-                "http://identifiers.org/kegg.compound/C00118"
-  DHAP identity "http://identifiers.org/chebi/CHEBI:16108",
-                "http://identifiers.org/kegg.compound/C00111"
-  Phi identity "http://identifiers.org/chebi/CHEBI:35780"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  Gri13P2 identity "http://identifiers.org/chebi/CHEBI:16001",
-                   "http://identifiers.org/kegg.compound/C00236"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  Gri3P identity "http://identifiers.org/chebi/CHEBI:17794",
-                 "http://identifiers.org/kegg.compound/C00197"
-  Gri23P2f identity "http://identifiers.org/chebi/CHEBI:17720",
-                    "http://identifiers.org/kegg.compound/C01159"
-  Gri2P identity "http://identifiers.org/chebi/CHEBI:17835",
-                 "http://identifiers.org/kegg.compound/C00631"
-  PEP identity "http://identifiers.org/kegg.compound/C00074",
-               "http://identifiers.org/chebi/CHEBI:18021"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021"
-  Pyr identity "http://identifiers.org/chebi/CHEBI:15361"
-  Pyr identity "http://identifiers.org/kegg.compound/C00022",
-               "http://identifiers.org/chebi/CHEBI:32816"
-  Lac identity "http://identifiers.org/kegg.compound/C00256",
-               "http://identifiers.org/chebi/CHEBI:42111"
-  NADPHf identity "http://identifiers.org/chebi/CHEBI:16474",
-                  "http://identifiers.org/kegg.compound/C00005"
-  NADPf identity "http://identifiers.org/chebi/CHEBI:18009",
-                 "http://identifiers.org/kegg.compound/C00006"
-  AMPf identity "http://identifiers.org/chebi/CHEBI:16027",
-                "http://identifiers.org/kegg.compound/C00020"
-  ADPf identity "http://identifiers.org/chebi/CHEBI:16761",
-                "http://identifiers.org/kegg.compound/C00008"
-  GlcA6P identity "http://identifiers.org/chebi/CHEBI:16938",
-                  "http://identifiers.org/kegg.compound/C01236"
-  Rul5P identity "http://identifiers.org/chebi/CHEBI:17363",
-                 "http://identifiers.org/kegg.compound/C00199"
-  GSSG identity "http://identifiers.org/chebi/CHEBI:17858",
-                "http://identifiers.org/kegg.compound/C00127"
-  GSH identity "http://identifiers.org/chebi/CHEBI:16856",
-               "http://identifiers.org/kegg.compound/C00051"
-  Xul5P identity "http://identifiers.org/chebi/CHEBI:16332",
-                 "http://identifiers.org/kegg.compound/C00231"
-  Rib5P identity "http://identifiers.org/chebi/CHEBI:17797",
-                 "http://identifiers.org/kegg.compound/C00117"
-  Sed7P identity "http://identifiers.org/kegg.compound/C05382",
-                 "http://identifiers.org/chebi/CHEBI:15721"
-  E4P identity "http://identifiers.org/chebi/CHEBI:16897",
-               "http://identifiers.org/kegg.compound/C00279"
-  MgAMP part "http://identifiers.org/chebi/CHEBI:25107",
-             "http://identifiers.org/chebi/CHEBI:16027"
-  MgAMP part "http://identifiers.org/kegg.compound/C00305",
-             "http://identifiers.org/kegg.compound/C00020",
-             "http://identifiers.org/chebi/CHEBI:18420"
-  ATPf identity "http://identifiers.org/chebi/CHEBI:15422",
-                "http://identifiers.org/kegg.compound/C00002"
-  Mgf identity "http://identifiers.org/chebi/CHEBI:25107",
-               "http://identifiers.org/kegg.compound/C00305"
-  MgGri23P2 part "http://identifiers.org/chebi/CHEBI:25107",
-                 "http://identifiers.org/chebi/CHEBI:17720"
-  MgGri23P2 part "http://identifiers.org/kegg.compound/C00305",
-                 "http://identifiers.org/kegg.compound/C01159",
-                 "http://identifiers.org/chebi/CHEBI:18420"
-  P1NADP part "http://identifiers.org/chebi/CHEBI:36080",
-              "http://identifiers.org/chebi/CHEBI:18009"
-  P1NADP part "http://identifiers.org/kegg.compound/C00006",
-              "http://identifiers.org/kegg.compound/C00017",
-              "http://identifiers.org/chebi/CHEBI:18009"
-  P1f hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  P1f hypernym "http://identifiers.org/kegg.compound/C00017",
-               "http://identifiers.org/chebi/CHEBI:16541"
-  P1NADPH part "http://identifiers.org/chebi/CHEBI:16474",
-               "http://identifiers.org/chebi/CHEBI:36080"
-  P1NADPH part "http://identifiers.org/kegg.compound/C00005",
-               "http://identifiers.org/kegg.compound/C00017",
-               "http://identifiers.org/chebi/CHEBI:16474"
-  P2NADP part "http://identifiers.org/chebi/CHEBI:18009",
-              "http://identifiers.org/chebi/CHEBI:36080"
-  P2NADP part "http://identifiers.org/kegg.compound/C00006",
-              "http://identifiers.org/kegg.compound/C00017",
-              "http://identifiers.org/chebi/CHEBI:18009"
-  P2f hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  P2f hypernym "http://identifiers.org/kegg.compound/C00017",
-               "http://identifiers.org/chebi/CHEBI:16541"
-  P2NADPH part "http://identifiers.org/chebi/CHEBI:16474",
-               "http://identifiers.org/chebi/CHEBI:36080"
-  P2NADPH part "http://identifiers.org/kegg.compound/C00005",
-               "http://identifiers.org/kegg.compound/C00017",
-               "http://identifiers.org/chebi/CHEBI:16474"
-  PRPP identity "http://identifiers.org/chebi/CHEBI:17111",
-                "http://identifiers.org/kegg.compound/C00119"
-  Lacex identity "http://identifiers.org/kegg.compound/C00256",
-                 "http://identifiers.org/chebi/CHEBI:42111"
-  Pyrex identity "http://identifiers.org/chebi/CHEBI:32816",
-                 "http://identifiers.org/kegg.compound/C00022"
-  Glcout identity "http://identifiers.org/chebi/CHEBI:17234",
-                  "http://identifiers.org/kegg.compound/C00293"
-  Phiex identity "http://identifiers.org/chebi/CHEBI:35780"
-  vGLT hypernym "http://identifiers.org/go/GO:0046323"
-  vGLT identity "http://identifiers.org/reactome/REACT_2092"
-  vHEX hypernym "http://identifiers.org/ec-code/2.7.1.2"
-  vHEX identity "http://identifiers.org/kegg.reaction/R00299",
-                "http://identifiers.org/reactome/REACT_1318"
-  vGPI hypernym "http://identifiers.org/ec-code/5.3.1.9"
-  vGPI identity "http://identifiers.org/kegg.reaction/R00771",
-                "http://identifiers.org/reactome/REACT_1164"
-  vPFK hypernym "http://identifiers.org/ec-code/2.7.1.11"
-  vPFK identity "http://identifiers.org/kegg.reaction/R00756",
-                "http://identifiers.org/reactome/REACT_736"
-  vALD hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  vALD identity "http://identifiers.org/kegg.reaction/R01070",
-                "http://identifiers.org/reactome/REACT_1602"
-  vTPI hypernym "http://identifiers.org/ec-code/5.3.1.1"
-  vTPI identity "http://identifiers.org/kegg.reaction/R01015",
-                "http://identifiers.org/reactome/REACT_775"
-  vGAPDH identity "http://identifiers.org/kegg.reaction/R01061",
-                  "http://identifiers.org/reactome/REACT_1847"
-  vGAPDH hypernym "http://identifiers.org/ec-code/1.2.1.12"
-  vPGK identity "http://identifiers.org/kegg.reaction/R01512",
-                "http://identifiers.org/reactome/REACT_1186"
-  vPGK hypernym "http://identifiers.org/ec-code/2.7.2.3"
-  vBPGM hypernym "http://identifiers.org/ec-code/5.4.2.4"
-  vBPGM identity "http://identifiers.org/kegg.reaction/R01662"
-  vBPGP identity "http://identifiers.org/kegg.reaction/R01516"
-  vBPGP hypernym "http://identifiers.org/ec-code/3.1.3.13"
-  vPGM hypernym "http://identifiers.org/ec-code/5.4.2.1"
-  vPGM identity "http://identifiers.org/kegg.reaction/R01518",
-                "http://identifiers.org/reactome/REACT_576"
-  vENO hypernym "http://identifiers.org/ec-code/4.2.1.11"
-  vENO identity "http://identifiers.org/kegg.reaction/R00658",
-                "http://identifiers.org/reactome/REACT_1400"
-  vPK identity "http://identifiers.org/kegg.reaction/R00200",
-               "http://identifiers.org/reactome/REACT_1911"
-  vPK hypernym "http://identifiers.org/ec-code/2.7.1.40"
-  vLDHNADH identity "http://identifiers.org/kegg.reaction/R00703",
-                    "http://identifiers.org/reactome/REACT_178"
-  vLDHNADH hypernym "http://identifiers.org/ec-code/1.1.1.27"
-  vLDHNADPH hypernym "http://identifiers.org/ec-code/1.1.1.27"
-  vATPase identity "http://identifiers.org/kegg.reaction/R00086"
-  vATPase hypernym "http://identifiers.org/ec-code/3.6.1.3"
-  vAK hypernym "http://identifiers.org/ec-code/2.7.4.3"
-  vAK identity "http://identifiers.org/kegg.reaction/R00127"
-  vG6PDH hypernym "http://identifiers.org/ec-code/1.1.1.49"
-  vG6PDH version "http://identifiers.org/reactome/REACT_1868",
-                 "http://identifiers.org/reactome/REACT_1125"
-  vG6PDH identity "http://identifiers.org/kegg.reaction/R00835"
-  vPGLDH hypernym "http://identifiers.org/ec-code/1.1.1.44"
-  vPGLDH part "http://identifiers.org/kegg.reaction/R02035",
-              "http://identifiers.org/kegg.reaction/R01528"
-  vPGLDH part "http://identifiers.org/reactome/REACT_2072",
-              "http://identifiers.org/reactome/REACT_611"
-  vGSSGRD identity "http://identifiers.org/kegg.reaction/R00094",
-                   "http://identifiers.org/reactome/REACT_2220"
-  vGSSGRD hypernym "http://identifiers.org/ec-code/1.8.1.7"
-  vGSHox hypernym "http://identifiers.org/ec-code/1.8.1.7"
-  vGSHox identity "http://identifiers.org/reactome/REACT_2037"
-  vRibPepi identity "http://identifiers.org/kegg.reaction/R01529",
-                    "http://identifiers.org/reactome/REACT_1522"
-  vRibPepi hypernym "http://identifiers.org/ec-code/5.1.3.1"
-  vRibPiso identity "http://identifiers.org/ec-code/5.3.1.6"
-  vRibPiso identity "http://identifiers.org/kegg.reaction/R01056",
-                    "http://identifiers.org/reactome/REACT_2033"
-  vTrKet1 hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  vTrKet1 identity "http://identifiers.org/kegg.reaction/R01641",
-                   "http://identifiers.org/reactome/REACT_1629"
-  vTrAld hypernym "http://identifiers.org/ec-code/2.2.1.2"
-  vTrAld identity "http://identifiers.org/kegg.reaction/R01827",
-                  "http://identifiers.org/reactome/REACT_479"
-  vPPRPPS hypernym "http://identifiers.org/ec-code/2.7.6.1"
-  vPPRPPS identity "http://identifiers.org/kegg.reaction/R01049",
-                   "http://identifiers.org/reactome/REACT_2023"
-  vTrKet2 identity "http://identifiers.org/kegg.reaction/R01830",
-                   "http://identifiers.org/reactome/REACT_1811"
-  vTrKet2 hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  vPhiexch hypernym "http://identifiers.org/go/GO:0009935"
-  vLacexch hypernym "http://identifiers.org/go/GO:0009935"
-  vPyrexch hypernym "http://identifiers.org/go/GO:0009935"
-  vMgATP hypernym "http://identifiers.org/go/GO:0006754"
-  vP1NADPH hypernym "http://identifiers.org/go/GO:0006740"
-  vP2NADPH hypernym "http://identifiers.org/go/GO:0006735"
-end
-
-Holzhutter2004_Erythrocyte_Metabolism is "Holzhutter2004_Erythrocyte_Metabolism"
-
-Holzhutter2004_Erythrocyte_Metabolism model_entity_is "http://identifiers.org/biomodels.db/MODEL6624180840"
-Holzhutter2004_Erythrocyte_Metabolism model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000070"
-Holzhutter2004_Erythrocyte_Metabolism description "http://identifiers.org/pubmed/15233787"
-Holzhutter2004_Erythrocyte_Metabolism part "http://identifiers.org/go/GO:0006096",
-                                           "http://identifiers.org/go/GO:0006098",
-                                           "http://identifiers.org/go/GO:0006749"
-Holzhutter2004_Erythrocyte_Metabolism part "http://identifiers.org/kegg.pathway/hsa00010",
-                                           "http://identifiers.org/kegg.pathway/hsa00030",
-                                           "http://identifiers.org/kegg.pathway/hsa00480"
-Holzhutter2004_Erythrocyte_Metabolism part "http://identifiers.org/reactome/REACT_1383",
-                                           "http://identifiers.org/reactome/REACT_2220",
-                                           "http://identifiers.org/reactome/REACT_1859"
-Holzhutter2004_Erythrocyte_Metabolism taxon "http://identifiers.org/taxonomy/9606"
diff --git a/BioModelsRAG/data/BIOMD0000000071.txt b/BioModelsRAG/data/BIOMD0000000071.txt
deleted file mode 100644
index fbe16c62d7b5ecca2ec2d28d1f2130df73f6ca7e..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000071.txt
+++ /dev/null
@@ -1,376 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Bakker2001_Glycolysis()
-
-  // Compartments and Species:
-  compartment tot_cell, glycosome, cytosol, extracellular;
-  species GlcI in tot_cell, Pg in glycosome, Glc6P in glycosome, Fru6P in glycosome;
-  species Fru16BP in glycosome, DHAP in tot_cell, GAP in glycosome, NAD in glycosome;
-  species BPGA13 in glycosome, NADH in glycosome, Pyr in cytosol, Nb in tot_cell;
-  species Pc in cytosol, $PyrE in extracellular, $Gly in glycosome, $GlcE in extracellular;
-  species $Gly3P in tot_cell, $Gly3Pc in cytosol, $Gly3Pg in glycosome, $ATPc in cytosol;
-  species $ADPc in cytosol, $ATPg in glycosome, $ADPg in glycosome, $DHAPg in glycosome;
-  species $DHAPc in cytosol, $PGAg in glycosome, $PEPc in cytosol;
-
-  // Assignment Rules:
-  Gly3P := (Gly3Pc*cytosol + Gly3Pg*glycosome)/tot_cell;
-  Gly3Pc := sumc5 - DHAPc;
-  Gly3Pg := Gly3Pc*DHAPg/(Keq_anti*DHAPc);
-  ATPc := ((Pc*(1 - 4*KeqAK) - sumAc) + ((sumAc - (1 - 4*KeqAK)*Pc)^2 + 4*(1 - 4*KeqAK)*KeqAK*Pc^2)^0.5)/(2*(1 - 4*KeqAK));
-  ADPc := Pc - 2*ATPc;
-  ATPg := ((Pg*(1 - 4*KeqAK) - sumAg) + ((sumAg - (1 - 4*KeqAK)*Pg)^2 + 4*(1 - 4*KeqAK)*KeqAK*Pg^2)^0.5)/(2*(1 - 4*KeqAK));
-  ADPg := Pg - 2*ATPg;
-  DHAPg := (DHAP*Vt - DHAPc*Vc)/Vg;
-  DHAPc := sumc5*(1 + Vc/Vg)*DHAP/(sumc4 + sumc5*Vc/Vg - (BPGA13 + 2*Fru16BP + Fru6P + GAP + Glc6P + Pg));
-  Vc := cytosol*Vt/tot_cell;
-  Vg := glycosome*Vt/tot_cell;
-  PGAg := Nb*(1 + Vc/Vg)/(1 + (1 + Keq_PGM + Keq_PGM*Keq_ENO)*Vc/Vg);
-  PEPc := Keq_ENO*Keq_PGM*PGAg;
-
-  // Reactions:
-  vGlcTr: $GlcE -> GlcI; (tot_cell/Vt)*vGlcTr_Vm1*(GlcE - GlcI)/(vGlcTr_K1Glc + GlcE + GlcI + vGlcTr_afac*GlcE*GlcI/vGlcTr_K1Glc);
-  vHK: Pg + GlcI => Glc6P; (tot_cell/Vt)*vHK_Vm2*GlcI*ATPg/(vHK_K2ATPg*vHK_K2GlcI*(1 + Glc6P/vHK_K2Glc6P + GlcI/vHK_K2GlcI)*(1 + ATPg/vHK_K2ATPg + ADPg/vHK_K2ADPg));
-  vPGI: Glc6P -> Fru6P; (tot_cell/Vt)*vPGI_Vm3*(Glc6P/vPGI_K3Glc6P - Fru6P/vPGI_K3Fru6P)/(1 + Glc6P/vPGI_K3Glc6P + Fru6P/vPGI_K3Fru6P);
-  vPFK: Pg + Fru6P => Fru16BP; (tot_cell/Vt)*vPFK_K4i1Fru16BP*vPFK_Vm4*Fru6P*ATPg/(vPFK_K4ATPg*vPFK_K4Fru6P*(vPFK_K4i1Fru16BP + Fru16BP)*(1 + Fru16BP/vPFK_K4i2Fru16BP + Fru6P/vPFK_K4Fru6P)*(1 + ATPg/vPFK_K4ATPg));
-  vALD: Fru16BP -> GAP + DHAP; (tot_cell/Vt)*(vALD_Vm5f*Fru16BP/(0.009*(1 + ATPg/0.68 + ADPg/1.51 + (sumAg - (ATPg + ADPg))/3.65)) - vALD_Vm5r*GAP*DHAPg/(vALD_K5DHAP*vALD_K5GAP))/(1 + GAP/vALD_K5GAP + DHAPg/vALD_K5DHAP + GAP*DHAPg/(vALD_K5DHAP*vALD_K5GAP) + Fru16BP/(0.009*(1 + ATPg/0.68 + ADPg/1.51 + (sumAg - (ATPg + ADPg))/3.65)) + Fru16BP*GAP/(vALD_K5GAPi*0.009*(1 + ATPg/0.68 + ADPg/1.51 + (sumAg - (ATPg + ADPg))/3.65)));
-  vTPI: DHAP -> GAP; (tot_cell/Vt)*TPIact*vTPI_Vm6*(DHAPg/vTPI_K6DHAPg - 5.7*GAP/vTPI_K6GAP)/(1 + GAP/vTPI_K6GAP + DHAPg/vTPI_K6DHAPg);
-  vGAPdh: GAP + NAD -> NADH + BPGA13; (tot_cell/Vt)*vGAPdh_Vm7*(vGAPdh_Vm7f*(GAP*(NAD/vGAPdh_K7GAP/vGAPdh_K7NAD) - (vGAPdh_Vm7r/vGAPdh_Vm7f)*(BPGA13*NADH/vGAPdh_K7BPGA13/vGAPdh_K7NADH))/((1 + GAP/vGAPdh_K7GAP + BPGA13/vGAPdh_K7BPGA13)*(1 + NAD/vGAPdh_K7NAD + NADH/vGAPdh_K7NADH)));
-  vGDH: DHAP + NADH -> NAD + $Gly3P; (tot_cell/Vt)*vGDH_Vm8*vGDH_Vm8f*(NADH*DHAPg/(vGDH_K8DHAPg*vGDH_K8NADH) - vGDH_Vm8r*NAD*Gly3Pg/(vGDH_K8Gly3Pg*vGDH_K8NAD*vGDH_Vm8f))/((1 + NAD/vGDH_K8NAD + NADH/vGDH_K8NADH)*(1 + DHAPg/vGDH_K8DHAPg + Gly3Pg/vGDH_K8Gly3Pg));
-  vGPO: $Gly3P => DHAP; (tot_cell/Vt)*vGPO_Vm9*Gly3Pc/(vGPO_K9Gly3Pc*1 + Gly3Pc);
-  vPyrTr: Pyr => $PyrE; (tot_cell/Vt)*vPyrTr_Vm10*Pyr/vPyrTr_K10Pyr/(1 + Pyr/vPyrTr_K10Pyr);
-  vPGK: BPGA13 -> Nb + Pg; (tot_cell/Vt)*vPGK_Vm11*vPGK_Vm11f*(-vPGK_Vm11r*PGAg*ATPg/(vPGK_K11ATPg*vPGK_K11PGA3*vPGK_Vm11f) + BPGA13*ADPg/(vPGK_K11ADPg*vPGK_K11BPGA13))/((1 + BPGA13/vPGK_K11BPGA13 + PGAg/vPGK_K11PGA3)*(1 + ATPg/vPGK_K11ATPg + ADPg/vPGK_K11ADPg));
-  vPK: Nb => Pc + Pyr; (tot_cell/Vt)*vPK_Vm12*(PEPc/(0.34*(1 + ADPc/0.57 + ATPc/0.64)))^vPK_n12*ADPc/vPK_K12ADP/((1 + (PEPc/(0.34*(1 + ADPc/0.57 + ATPc/0.64)))^vPK_n12)*(1 + ADPc/vPK_K12ADP));
-  vATPase: Pc => ; (tot_cell/Vt)*vATPase_K13*ATPc/ADPc;
-  vGlyK: $Gly3P -> Pg + $Gly; (tot_cell/Vt)*vGlyK_Vm14*(vGlyK_Vm14f*ADPg*Gly3Pg/(vGlyK_K14ADPg*vGlyK_K14Gly3Pg) - Gly*vGlyK_Vm14r*ATPg/(vGlyK_K14ATPg*vGlyK_K14Gly))/((1 + Gly/vGlyK_K14Gly + Gly3Pg/vGlyK_K14Gly3Pg)*(1 + ATPg/vGlyK_K14ATPg + ADPg/vGlyK_K14ADPg));
-
-  // Species initializations:
-  GlcI = 0.0340009;
-  Pg = 7.63936;
-  Glc6P = 2.07199;
-  Fru6P = 0.511773;
-  Fru16BP = 16.5371;
-  DHAP = 3.89921;
-  GAP = 0.0399329;
-  NAD = 3.95514;
-  BPGA13 = 0.0326745;
-  NADH = 0.0448639;
-  Pyr = 4.77413;
-  Nb = 1.59603;
-  Pc = 6.51839;
-  PyrE = 0;
-  Gly = 0;
-  GlcE = 5;
-
-  // Compartment initializations:
-  tot_cell = 5.7;
-  glycosome = 0.2446;
-  cytosol = 5.4554;
-  extracellular = 1;
-
-  // Variable initializations:
-  KeqAK = 0.442;
-  KeqAK has dimensionless;
-  sumAc = 3.9;
-  sumAc has mM;
-  sumAg = 6;
-  sumAg has mM;
-  Vt = 5.7;
-  Vt has microlitre_per_mg;
-  Vc has microlitre_per_mg;
-  Vg has microlitre_per_mg;
-  sumc5 = 5;
-  sumc5 has mM;
-  sumc4 = 45;
-  sumc4 has mM;
-  Keq_anti = 1;
-  Keq_anti has dimensionless;
-  Keq_PGM = 0.187;
-  Keq_PGM has dimensionless;
-  Keq_ENO = 6.7;
-  Keq_ENO has dimensionless;
-  TPIact = 1;
-  TPIact has dimensionless;
-  vGlcTr_Vm1 = 106.2;
-  vGlcTr_Vm1 has nanomole_per_min_per_mg;
-  vGlcTr_K1Glc = 2;
-  vGlcTr_K1Glc has mM;
-  vGlcTr_afac = 0.75;
-  vGlcTr_afac has dimensionless;
-  vHK_Vm2 = 625;
-  vHK_Vm2 has nanomole_per_min_per_mg;
-  vHK_K2ATPg = 0.116;
-  vHK_K2ATPg has mM;
-  vHK_K2GlcI = 0.1;
-  vHK_K2GlcI has mM;
-  vHK_K2Glc6P = 12;
-  vHK_K2Glc6P has mM;
-  vHK_K2ADPg = 0.126;
-  vHK_K2ADPg has mM;
-  vPGI_Vm3 = 848;
-  vPGI_Vm3 has nanomole_per_min_per_mg;
-  vPGI_K3Glc6P = 0.4;
-  vPGI_K3Glc6P has mM;
-  vPGI_K3Fru6P = 0.12;
-  vPGI_K3Fru6P has mM;
-  vPFK_K4i1Fru16BP = 15.8;
-  vPFK_K4i1Fru16BP has mM;
-  vPFK_Vm4 = 780;
-  vPFK_Vm4 has nanomole_per_min_per_mg;
-  vPFK_K4ATPg = 0.026;
-  vPFK_K4ATPg has mM;
-  vPFK_K4Fru6P = 0.82;
-  vPFK_K4Fru6P has mM;
-  vPFK_K4i2Fru16BP = 10.7;
-  vPFK_K4i2Fru16BP has mM;
-  vALD_Vm5r = 219.555;
-  vALD_Vm5r has nanomole_per_min_per_mg;
-  vALD_K5DHAP = 0.015;
-  vALD_K5DHAP has mM;
-  vALD_K5GAP = 0.067;
-  vALD_K5GAP has mM;
-  vALD_Vm5f = 184.5;
-  vALD_Vm5f has nanomole_per_min_per_mg;
-  vALD_K5GAPi = 0.098;
-  vALD_K5GAPi has mM;
-  vTPI_Vm6 = 842;
-  vTPI_Vm6 has nanomole_per_min_per_mg;
-  vTPI_K6GAP = 0.25;
-  vTPI_K6GAP has mM;
-  vTPI_K6DHAPg = 1.2;
-  vTPI_K6DHAPg has mM;
-  vGAPdh_Vm7 = 1;
-  vGAPdh_Vm7 has dimensionless;
-  vGAPdh_Vm7f = 1470;
-  vGAPdh_Vm7f has nanomole_per_min_per_mg;
-  vGAPdh_K7GAP = 0.15;
-  vGAPdh_K7GAP has mM;
-  vGAPdh_K7NAD = 0.45;
-  vGAPdh_K7NAD has mM;
-  vGAPdh_Vm7r = 984.9;
-  vGAPdh_Vm7r has nanomole_per_min_per_mg;
-  vGAPdh_K7BPGA13 = 0.1;
-  vGAPdh_K7BPGA13 has mM;
-  vGAPdh_K7NADH = 0.02;
-  vGAPdh_K7NADH has mM;
-  vGDH_Vm8 = 1;
-  vGDH_Vm8 has dimensionless;
-  vGDH_Vm8f = 533;
-  vGDH_Vm8f has nanomole_per_min_per_mg;
-  vGDH_K8DHAPg = 0.1;
-  vGDH_K8DHAPg has mM;
-  vGDH_K8NADH = 0.01;
-  vGDH_K8NADH has mM;
-  vGDH_Vm8r = 149.24;
-  vGDH_Vm8r has nanomole_per_min_per_mg;
-  vGDH_K8Gly3Pg = 2;
-  vGDH_K8Gly3Pg has mM;
-  vGDH_K8NAD = 0.4;
-  vGDH_K8NAD has mM;
-  vGPO_Vm9 = 368;
-  vGPO_Vm9 has nanomole_per_min_per_mg;
-  vGPO_K9Gly3Pc = 1.7;
-  vGPO_K9Gly3Pc has mM;
-  vPyrTr_Vm10 = 200;
-  vPyrTr_Vm10 has nanomole_per_min_per_mg;
-  vPyrTr_K10Pyr = 1.96;
-  vPyrTr_K10Pyr has mM;
-  vPGK_Vm11 = 1;
-  vPGK_Vm11 has dimensionless;
-  vPGK_Vm11f = 640;
-  vPGK_Vm11f has nanomole_per_min_per_mg;
-  vPGK_Vm11r = 18.56;
-  vPGK_Vm11r has nanomole_per_min_per_mg;
-  vPGK_K11ATPg = 0.29;
-  vPGK_K11ATPg has mM;
-  vPGK_K11PGA3 = 1.62;
-  vPGK_K11PGA3 has mM;
-  vPGK_K11ADPg = 0.1;
-  vPGK_K11ADPg has dimensionless;
-  vPGK_K11BPGA13 = 0.05;
-  vPGK_K11BPGA13 has dimensionless;
-  vPK_n12 = 2.5;
-  vPK_n12 has dimensionless;
-  vPK_Vm12 = 2600;
-  vPK_Vm12 has nanomole_per_min_per_mg;
-  vPK_K12ADP = 0.114;
-  vPK_K12ADP has mM;
-  vATPase_K13 = 50;
-  vATPase_K13 has nanomole_per_min_per_mg;
-  vGlyK_Vm14 = 1;
-  vGlyK_Vm14 has dimensionless;
-  vGlyK_Vm14r = 33400;
-  vGlyK_Vm14r has nanomole_per_min_per_mg;
-  vGlyK_K14ATPg = 0.19;
-  vGlyK_K14ATPg has mM;
-  vGlyK_K14Gly = 0.12;
-  vGlyK_K14Gly has mM;
-  vGlyK_Vm14f = 200;
-  vGlyK_Vm14f has nanomole_per_min_per_mg;
-  vGlyK_K14ADPg = 0.12;
-  vGlyK_K14ADPg has mM;
-  vGlyK_K14Gly3Pg = 5.1;
-  vGlyK_K14Gly3Pg has mM;
-
-  // Other declarations:
-  var Vc, Vg;
-  const tot_cell, glycosome, cytosol, extracellular, KeqAK, sumAc, sumAg;
-  const Vt, sumc5, sumc4, Keq_anti, Keq_PGM, Keq_ENO, TPIact;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit volume = 1e-6 litre;
-  unit microlitre_per_mg = 1e-6 litre / 1e-3 gram;
-  unit nanomole_per_min_per_mg = 1e-9 mole / (60 second * 1e-3 gram);
-  unit time_unit = 60 second;
-  unit mM = 1e-9 mole / 1e-6 litre;
-
-  // Display Names:
-  substance is "nanomole";
-  volume is "microlitre";
-  time_unit is "minute";
-  tot_cell is "total cell";
-  GlcI is "Glucose";
-  Pg is "Phosphates in Glycosome";
-  Glc6P is "Glucose 6-phosphate";
-  Fru6P is "Fructose 6-phosphate";
-  Fru16BP is "Fructose 1,6-bisphosphate";
-  DHAP is "Dihydroxyacetone phosphate";
-  GAP is "Glyceraldehyde 3-phosphate";
-  BPGA13 is "1,3-bisphosphoglycerate";
-  Pyr is "Pyruvate";
-  Nb is "3-PGA 2-PGA PEP";
-  Pc is "Phosphates cytosol";
-  PyrE is "Pyruvate external";
-  Gly is "Glycerol";
-  GlcE is "Glucose external";
-  Gly3P is "Glycerol 3-phosphate";
-  Gly3Pc is "Gy3P c.";
-  Gly3Pg is "Gy3P g.";
-  ATPc is "ATP cyt.";
-  ADPc is "ADP cyt.";
-  ATPg is "ATP gly.";
-  ADPg is "ADP gly.";
-  DHAPg is "DHAP gly.";
-  Vt is "tot volume per mg protein";
-  DHAPc is "DHAP cyt.";
-  PGAg is "3-PGA g.";
-  PEPc is "PEP c.";
-  vGlcTr is "Glucose transport";
-  vHK is "Hexokinase";
-  vPGI is "Glucose-phosphate isomerase";
-  vPFK is "Phosphofructokinase";
-  vALD is "Aldolase";
-  vTPI is "Triosephosphate isomerase";
-  vGAPdh is "Glyceraldehyde 3-phosphate dehydrogenase";
-  vGDH is "Glycerol 3-phosphate dehydrogenase";
-  vGPO is "Glycerol 3-phosphate oxidase";
-  vPyrTr is "Pyruvate transport";
-  vPGK is "Phosphoglycerate kinase";
-  vPK is "Pyruvate kinase";
-  vATPase is "ATPase";
-  vGlyK is "Glycerol kinase";
-
-  // CV terms:
-  glycosome identity "http://identifiers.org/go/GO:0020015"
-  cytosol identity "http://identifiers.org/go/GO:0005829"
-  extracellular identity "http://identifiers.org/go/GO:0005576"
-  GlcI hypernym "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  Pg hypernym "http://identifiers.org/chebi/CHEBI:35780"
-  Glc6P identity "http://identifiers.org/chebi/CHEBI:17665",
-                 "http://identifiers.org/kegg.compound/C00668"
-  Fru6P identity "http://identifiers.org/chebi/CHEBI:16084",
-                 "http://identifiers.org/kegg.compound/C05345"
-  Fru16BP identity "http://identifiers.org/chebi/CHEBI:28013",
-                   "http://identifiers.org/kegg.compound/C05378"
-  DHAP identity "http://identifiers.org/chebi/CHEBI:16108",
-                "http://identifiers.org/kegg.compound/C00111"
-  GAP identity "http://identifiers.org/chebi/CHEBI:29052",
-               "http://identifiers.org/kegg.compound/C00118"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  BPGA13 identity "http://identifiers.org/chebi/CHEBI:16001",
-                  "http://identifiers.org/kegg.compound/C00236"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  Pyr identity "http://identifiers.org/chebi/CHEBI:15361",
-               "http://identifiers.org/kegg.compound/C00022"
-  Nb part "http://identifiers.org/kegg.compound/C00197",
-          "http://identifiers.org/kegg.compound/C00631",
-          "http://identifiers.org/kegg.compound/C00074"
-  Nb part "http://identifiers.org/chebi/CHEBI:18021",
-          "http://identifiers.org/chebi/CHEBI:17794",
-          "http://identifiers.org/chebi/CHEBI:17835"
-  Pc hypernym "http://identifiers.org/chebi/CHEBI:35780"
-  PyrE hypernym "http://identifiers.org/chebi/CHEBI:32816",
-                "http://identifiers.org/kegg.compound/C00022"
-  Gly identity "http://identifiers.org/chebi/CHEBI:17754",
-               "http://identifiers.org/kegg.compound/C00116"
-  GlcE hypernym "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  Gly3P identity "http://identifiers.org/chebi/CHEBI:15978",
-                 "http://identifiers.org/kegg.compound/C00093"
-  Gly3Pc identity "http://identifiers.org/chebi/CHEBI:15978",
-                  "http://identifiers.org/kegg.compound/C00093"
-  Gly3Pg identity "http://identifiers.org/chebi/CHEBI:15978",
-                  "http://identifiers.org/kegg.compound/C00093"
-  ATPc identity "http://identifiers.org/chebi/CHEBI:15422",
-                "http://identifiers.org/kegg.compound/C00002"
-  ADPc identity "http://identifiers.org/chebi/CHEBI:16761",
-                "http://identifiers.org/kegg.compound/C00008"
-  ATPg identity "http://identifiers.org/chebi/CHEBI:15422",
-                "http://identifiers.org/kegg.compound/C00002"
-  ADPg identity "http://identifiers.org/chebi/CHEBI:16761",
-                "http://identifiers.org/kegg.compound/C00008"
-  DHAPg identity "http://identifiers.org/chebi/CHEBI:16108",
-                 "http://identifiers.org/kegg.compound/C00111"
-  DHAPc identity "http://identifiers.org/chebi/CHEBI:16108",
-                 "http://identifiers.org/kegg.compound/C00111"
-  PGAg identity "http://identifiers.org/chebi/CHEBI:18021",
-                "http://identifiers.org/kegg.compound/C00074"
-  PEPc identity "http://identifiers.org/chebi/CHEBI:18021",
-                "http://identifiers.org/kegg.compound/C00074"
-  vGlcTr hypernym "http://identifiers.org/go/GO:0046323"
-  vGlcTr homolog "http://identifiers.org/reactome/REACT_2092"
-  vHK identity "http://identifiers.org/kegg.reaction/R00299"
-  vHK hypernym "http://identifiers.org/ec-code/2.7.1.2"
-  vHK homolog "http://identifiers.org/reactome/REACT_1318"
-  vPGI identity "http://identifiers.org/kegg.reaction/R00771"
-  vPGI hypernym "http://identifiers.org/ec-code/5.3.1.9"
-  vPGI homolog "http://identifiers.org/reactome/REACT_1164"
-  vPFK identity "http://identifiers.org/kegg.reaction/R00756"
-  vPFK hypernym "http://identifiers.org/ec-code/2.7.1.11"
-  vPFK homolog "http://identifiers.org/reactome/REACT_736"
-  vALD identity "http://identifiers.org/kegg.reaction/R01070"
-  vALD hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  vALD homolog "http://identifiers.org/reactome/REACT_1602"
-  vTPI identity "http://identifiers.org/kegg.reaction/R01015"
-  vTPI hypernym "http://identifiers.org/ec-code/5.3.1.1"
-  vTPI homolog "http://identifiers.org/reactome/REACT_775"
-  vGAPdh identity "http://identifiers.org/kegg.reaction/R01061"
-  vGAPdh hypernym "http://identifiers.org/ec-code/1.2.1.12"
-  vGAPdh homolog "http://identifiers.org/reactome/REACT_1847"
-  vGDH identity "http://identifiers.org/kegg.reaction/R00841"
-  vGDH hypernym "http://identifiers.org/ec-code/3.1.3.21"
-  vGDH homolog "http://identifiers.org/reactome/REACT_1146"
-  vGPO identity "http://identifiers.org/kegg.reaction/R00846"
-  vGPO hypernym "http://identifiers.org/ec-code/1.1.3.21"
-  vPGK hypernym "http://identifiers.org/ec-code/2.7.2.3"
-  vPK hypernym "http://identifiers.org/ec-code/2.7.1.40"
-  vPK identity "http://identifiers.org/kegg.reaction/R00200"
-  vPK homolog "http://identifiers.org/reactome/REACT_1911"
-  vATPase hypernym "http://identifiers.org/go/GO:0006200"
-  vGlyK identity "http://identifiers.org/kegg.reaction/R00847"
-  vGlyK hypernym "http://identifiers.org/ec-code/2.7.1.30"
-end
-
-Bakker2001_Glycolysis is "Bakker2001_Glycolysis"
-
-Bakker2001_Glycolysis model_entity_is "http://identifiers.org/biomodels.db/MODEL6624099213"
-Bakker2001_Glycolysis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000071"
-Bakker2001_Glycolysis description "http://identifiers.org/pubmed/11415442"
-Bakker2001_Glycolysis origin "http://identifiers.org/biomodels.db/MODEL1101100000",
-                             "http://identifiers.org/pubmed/10468568"
-Bakker2001_Glycolysis taxon "http://identifiers.org/taxonomy/5691"
-Bakker2001_Glycolysis identity "http://identifiers.org/kegg.pathway/tbr00010"
-Bakker2001_Glycolysis hypernym "http://identifiers.org/go/GO:0006096"
-Bakker2001_Glycolysis homolog "http://identifiers.org/reactome/REACT_1383"
diff --git a/BioModelsRAG/data/BIOMD0000000072.txt b/BioModelsRAG/data/BIOMD0000000072.txt
deleted file mode 100644
index 1bd28ae80ad6624b3b3bbad22aad6317a7da3786..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000072.txt
+++ /dev/null
@@ -1,102 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Model_1()
-
-  // Compartments and Species:
-  compartment cell;
-  species L in cell, R in cell, G in cell, Gbg in cell, Gd in cell, Ga in cell;
-  species RL in cell;
-
-  // Reactions:
-  reaction_0: L + R -> RL; cell*(reaction_0_k1*L*R - reaction_0_k2*RL);
-  reaction_1:  => R; cell*reaction_1_v;
-  reaction_2: R => ; cell*reaction_2_k1*R;
-  reaction_3: Gd + Gbg => G; cell*reaction_3_k1*Gd*Gbg;
-  reaction_4: G => Ga + Gbg; cell*reaction_4_k1*RL*G;
-  reaction_5: RL => ; cell*reaction_5_k1*RL;
-  reaction_6: Ga => Gd; cell*reaction_6_k1*Ga;
-
-  // Species initializations:
-  L = 6.02e+17;
-  R = 10000;
-  G = 7000;
-  Gbg = 3000;
-  Gd = 3000;
-  Ga = 0;
-  RL = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  reaction_0_k1 = 3.32e-18;
-  reaction_0_k2 = 0.01;
-  reaction_1_v = 4;
-  reaction_2_k1 = 0.0004;
-  reaction_3_k1 = 1;
-  reaction_4_k1 = 1e-05;
-  reaction_5_k1 = 0.004;
-  reaction_6_k1 = 0.11;
-
-  // Other declarations:
-  const cell;
-
-  // Unit definitions:
-  unit substance = item;
-
-  // Display Names:
-  L is "Ligand";
-  R is "Receptor";
-  G is "Inactive heterotrimeric G-protein";
-  Gbg is "Free levels of G-beta-gamma";
-  Gd is "G-alpha-GDP";
-  Ga is "G-alpha-GTP";
-  RL is "Receptor-Ligand";
-  reaction_0 is "Ligand-Receptor Association";
-  reaction_1 is "Receptor Synthesis";
-  reaction_2 is "Receptor Degradation";
-  reaction_3 is "Heterotrimeric G-Protein Formation";
-  reaction_4 is "G-protein Activation";
-  reaction_5 is "Receptor-Ligand Degradation";
-  reaction_6 is "G-protein Inactivation ";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005623"
-  L version "http://identifiers.org/uniprot/P34165",
-            "http://identifiers.org/uniprot/P34166"
-  L hypernym "http://identifiers.org/interpro/IPR006742"
-  R identity "http://identifiers.org/uniprot/P06842"
-  G hypernym "http://identifiers.org/go/GO:0005834"
-  Gbg identity "http://identifiers.org/go/GO:0031680"
-  Gd part "http://identifiers.org/interpro/IPR001019",
-          "http://identifiers.org/kegg.compound/C00035"
-  Gd part "http://identifiers.org/chebi/CHEBI:17552",
-          "http://identifiers.org/interpro/IPR001019"
-  Ga part "http://identifiers.org/interpro/IPR001019",
-          "http://identifiers.org/kegg.compound/C00044"
-  Ga part "http://identifiers.org/chebi/CHEBI:15996",
-          "http://identifiers.org/interpro/IPR001019"
-  RL hypernym "http://identifiers.org/go/GO:0043235"
-  RL part "http://identifiers.org/uniprot/P34165",
-          "http://identifiers.org/uniprot/P06842"
-  RL part "http://identifiers.org/uniprot/P34166",
-          "http://identifiers.org/uniprot/P06842"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0004934",
-                      "http://identifiers.org/go/GO:0001664",
-                      "http://identifiers.org/go/GO:0005102"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0001965",
-                      "http://identifiers.org/go/GO:0031683"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0004930",
-                      "http://identifiers.org/go/GO:0043241"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_6 hypernym "http://identifiers.org/go/GO:0003924"
-end
-
-Model_1 is "Yi2003_GproteinCycle"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL9468910329"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000072"
-Model_1 description "http://identifiers.org/pubmed/12960402"
-Model_1 hypernym "http://identifiers.org/go/GO:0031684"
-Model_1 taxon "http://identifiers.org/taxonomy/4932"
diff --git a/BioModelsRAG/data/BIOMD0000000073.txt b/BioModelsRAG/data/BIOMD0000000073.txt
deleted file mode 100644
index 949d653f1bff3ee88f6518a6d51895026221ff7f..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000073.txt
+++ /dev/null
@@ -1,364 +0,0 @@
-// Created by libAntimony v2.13.0
-function function_3(Vs, B, n, K)
-  Vs*B^n/(K^n + B^n);
-end
-
-function_3 is "Activation of gene"
-
-function function_2(V, substrate, Km)
-  V*substrate/(Km + substrate);
-end
-
-function_2 is "Michaelis-Menten(irreversible)"
-
-function function_1(k, mRNA)
-  k*mRNA;
-end
-
-function_1 is "mRNA translated into protein"
-
-function function_0(vsb, K, m, Bn)
-  vsb*K^m/(K^m + Bn^m);
-end
-
-function_0 is "Inhibition of gene"
-
-
-model *Model_1()
-
-  // Compartments and Species:
-  compartment cell;
-  species species_0 in cell, species_1 in cell, species_2 in cell, species_3 in cell;
-  species species_4 in cell, species_5 in cell, species_6 in cell, species_7 in cell;
-  species species_8 in cell, species_9 in cell, species_10 in cell, species_11 in cell;
-  species species_12 in cell, species_13 in cell, species_14 in cell, species_15 in cell;
-
-  // Reactions:
-  reaction_0:  => species_0; cell*function_0(reaction_0_vsb, reaction_0_K, reaction_0_m, species_3);
-  reaction_1:  => species_1; cell*function_1(reaction_1_k, species_0);
-  reaction_2: species_0 => ; cell*reaction_2_k1*species_0;
-  reaction_3: species_1 => species_2; cell*function_2(reaction_3_V, species_1, reaction_3_Km);
-  reaction_4: species_1 -> species_3; cell*(reaction_4_k1*species_1 - reaction_4_k2*species_3);
-  reaction_5:  => species_4; cell*function_1(reaction_5_k, species_5);
-  reaction_6: species_5 => ; cell*reaction_6_k1*species_5;
-  reaction_7: species_4 => species_6; cell*function_2(reaction_7_V, species_4, reaction_7_Km);
-  reaction_8: species_6 => ; cell*function_2(reaction_8_V, species_6, reaction_8_Km);
-  reaction_9:  => species_7; cell*function_3(reaction_9_Vs, species_3, reaction_9_n, reaction_9_K);
-  reaction_10:  => species_8; cell*function_1(reaction_10_k, species_7);
-  reaction_11: species_9 => ; cell*function_2(reaction_11_V, species_9, reaction_11_Km);
-  reaction_12: species_8 => species_9; cell*function_2(reaction_12_V, species_8, reaction_12_Km);
-  reaction_13: species_4 + species_8 -> species_10; cell*(reaction_13_k1*species_4*species_8 - reaction_13_k2*species_10);
-  reaction_14: species_10 => species_11; cell*function_2(reaction_14_V, species_10, reaction_14_Km);
-  reaction_15: species_11 => ; cell*function_2(reaction_15_V, species_11, reaction_15_Km);
-  reaction_16: species_10 -> species_12; cell*(reaction_16_k1*species_10 - reaction_16_k2*species_12);
-  reaction_17: species_14 => ; cell*reaction_17_k1*species_14;
-  reaction_18: species_2 => ; cell*reaction_18_k1*species_2;
-  reaction_19: species_13 => ; cell*reaction_19_k1*species_13;
-  reaction_20:  => species_5; cell*function_3(reaction_20_Vs, species_3, reaction_20_n, reaction_20_K);
-  reaction_21: species_12 => species_14; cell*function_2(reaction_21_V, species_12, reaction_21_Km);
-  reaction_22: species_7 => ; cell*reaction_22_k1*species_7;
-  reaction_23: species_12 + species_3 -> species_15; cell*(reaction_23_k1*species_12*species_3 - reaction_23_k2*species_15);
-  reaction_24: species_0 => ; cell*function_2(reaction_24_V, species_0, reaction_24_Km);
-  reaction_25: species_5 => ; cell*function_2(reaction_25_V, species_5, reaction_25_Km);
-  reaction_26: species_7 => ; cell*function_2(reaction_26_V, species_7, reaction_26_Km);
-  reaction_27: species_8 => ; cell*reaction_27_k1*species_8;
-  reaction_28: species_4 => ; cell*reaction_28_k1*species_4;
-  reaction_29: species_9 => ; cell*reaction_29_k1*species_9;
-  reaction_30: species_6 => ; cell*reaction_30_k1*species_6;
-  reaction_31: species_11 => ; cell*reaction_31_k1*species_11;
-  reaction_32: species_10 => ; cell*reaction_32_k1*species_10;
-  reaction_33: species_14 => ; cell*function_2(reaction_33_V, species_14, reaction_33_Km);
-  reaction_34: species_1 => ; cell*reaction_34_k1*species_1;
-  reaction_35: species_2 => ; cell*function_2(reaction_35_V, species_2, reaction_35_Km);
-  reaction_36: species_3 => species_13; cell*function_2(reaction_36_V, species_3, reaction_36_Km);
-  reaction_37: species_13 => ; cell*function_2(reaction_37_V, species_13, reaction_37_Km);
-  reaction_38: species_15 => ; cell*reaction_38_k1*species_15;
-  reaction_39: species_15 => ; cell*function_2(reaction_39_V, species_15, reaction_39_Km);
-  reaction_40: species_3 => ; cell*reaction_40_k1*species_3;
-  reaction_41: species_2 => species_1; cell*function_2(reaction_41_V, species_2, reaction_41_Km);
-  reaction_42: species_13 => species_3; cell*function_2(reaction_42_V, species_13, reaction_42_Km);
-  reaction_43: species_6 => species_4; cell*function_2(reaction_43_V, species_6, reaction_43_Km);
-  reaction_44: species_9 => species_8; cell*function_2(reaction_44_V, species_9, reaction_44_Km);
-  reaction_45: species_14 => species_12; cell*function_2(reaction_45_V, species_14, reaction_45_Km);
-  reaction_46: species_12 => ; cell*reaction_46_k1*species_12;
-  reaction_47: species_11 => species_10; cell*function_2(reaction_47_V, species_11, reaction_47_Km);
-
-  // Species initializations:
-  species_0 = 9;
-  species_1 = 2;
-  species_2 = 0;
-  species_3 = 1.9;
-  species_4 = 0;
-  species_5 = 1.4;
-  species_6 = 0;
-  species_7 = 1.6;
-  species_8 = 0;
-  species_9 = 0;
-  species_10 = 0;
-  species_11 = 0;
-  species_12 = 1;
-  species_13 = 0;
-  species_14 = 0;
-  species_15 = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  reaction_0_vsb = 1;
-  reaction_0_K = 2.2;
-  reaction_0_m = 2;
-  reaction_1_k = 0.12;
-  reaction_2_k1 = 0.01;
-  reaction_3_V = 0.5;
-  reaction_3_Km = 0.1;
-  reaction_4_k1 = 0.4;
-  reaction_4_k2 = 0.2;
-  reaction_5_k = 1.6;
-  reaction_6_k1 = 0.01;
-  reaction_7_V = 0.6;
-  reaction_7_Km = 0.1;
-  reaction_8_V = 0.7;
-  reaction_8_Km = 0.3;
-  reaction_9_Vs = 1.5;
-  reaction_9_n = 4;
-  reaction_9_K = 0.7;
-  reaction_10_k = 0.6;
-  reaction_11_V = 0.7;
-  reaction_11_Km = 0.3;
-  reaction_12_V = 0.4;
-  reaction_12_Km = 0.1;
-  reaction_13_k1 = 0.4;
-  reaction_13_k2 = 0.2;
-  reaction_14_V = 0.4;
-  reaction_14_Km = 0.1;
-  reaction_15_V = 0.7;
-  reaction_15_Km = 0.3;
-  reaction_16_k1 = 0.4;
-  reaction_16_k2 = 0.2;
-  reaction_17_k1 = 0.01;
-  reaction_18_k1 = 0.01;
-  reaction_19_k1 = 0.01;
-  reaction_20_Vs = 1.1;
-  reaction_20_n = 4;
-  reaction_20_K = 0.6;
-  reaction_21_V = 0.4;
-  reaction_21_Km = 0.1;
-  reaction_22_k1 = 0.01;
-  reaction_23_k1 = 0.5;
-  reaction_23_k2 = 0.1;
-  reaction_24_V = 0.8;
-  reaction_24_Km = 0.4;
-  reaction_25_V = 1;
-  reaction_25_Km = 0.4;
-  reaction_26_V = 1.1;
-  reaction_26_Km = 0.31;
-  reaction_27_k1 = 0.01;
-  reaction_28_k1 = 0.12;
-  reaction_29_k1 = 0.01;
-  reaction_30_k1 = 0.01;
-  reaction_31_k1 = 0.01;
-  reaction_32_k1 = 0.01;
-  reaction_33_V = 0.7;
-  reaction_33_Km = 0.3;
-  reaction_34_k1 = 0.01;
-  reaction_35_V = 0.5;
-  reaction_35_Km = 0.3;
-  reaction_36_V = 0.5;
-  reaction_36_Km = 0.1;
-  reaction_37_V = 0.6;
-  reaction_37_Km = 0.3;
-  reaction_38_k1 = 0.01;
-  reaction_39_V = 0.8;
-  reaction_39_Km = 0.3;
-  reaction_40_k1 = 0.01;
-  reaction_41_V = 0.1;
-  reaction_41_Km = 0.1;
-  reaction_42_V = 0.2;
-  reaction_42_Km = 0.1;
-  reaction_43_V = 0.1;
-  reaction_43_Km = 0.1;
-  reaction_44_V = 0.3;
-  reaction_44_Km = 0.1;
-  reaction_45_V = 0.1;
-  reaction_45_Km = 0.1;
-  reaction_46_k1 = 0.01;
-  reaction_47_V = 0.1;
-  reaction_47_Km = 0.1;
-
-  // Other declarations:
-  const cell;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  species_0 is "Mb";
-  species_1 is "Bc";
-  species_2 is "Bcp";
-  species_3 is "Bn";
-  species_4 is "Cc";
-  species_5 is "Mc";
-  species_6 is "Ccp";
-  species_7 is "Mp";
-  species_8 is "Pc";
-  species_9 is "Pcp";
-  species_10 is "PCc";
-  species_11 is "PCcp";
-  species_12 is "PCn";
-  species_13 is "Bnp";
-  species_14 is "PCnp";
-  species_15 is "In";
-  reaction_0 is "Mb synthesized";
-  reaction_1 is "Mb translated into protein";
-  reaction_2 is "Mb nonspecific degradation";
-  reaction_3 is "Bc phosphorylation";
-  reaction_4 is "Bc transfered from cytosolic to nuclear";
-  reaction_5 is "Mc translated into protein";
-  reaction_6 is "Mc nonspecific degradation";
-  reaction_7 is "Cc phosphorylation";
-  reaction_8 is "Ccp specific degradation";
-  reaction_9 is "Mp synthesis";
-  reaction_10 is "Mp translated into protein";
-  reaction_11 is "Pcp specific degradation";
-  reaction_12 is "Pc phosphorylation";
-  reaction_13 is "Cc and Pc produce complex Per_Cry";
-  reaction_14 is "PCc phosphorylation";
-  reaction_15 is "PCcp specific degradation";
-  reaction_16 is "PCc transfered into nuclear";
-  reaction_17 is "PCnp nonspecific degradation";
-  reaction_18 is "Bcp nonspecific degradation";
-  reaction_19 is "Bnp nonspecific degradation";
-  reaction_20 is "Mc synthesis";
-  reaction_21 is "PCn phosphorylation";
-  reaction_22 is "Mp nonspecific degradation";
-  reaction_23 is "Per_Cry and Clock_Bmal form inactive complex";
-  reaction_24 is "Mb specific degradation";
-  reaction_25 is "Mc specific degradation";
-  reaction_26 is "Mp specific degradation";
-  reaction_27 is "Pc nonspecific degradation";
-  reaction_28 is "Cc nonspecific degradation";
-  reaction_29 is "Pcp nonspecific degradation";
-  reaction_30 is "Ccp nonspecific degradation";
-  reaction_31 is "PCcp nonspecific degradation";
-  reaction_32 is "PCc nonspecific degradation";
-  reaction_33 is "PCnp specific degradation";
-  reaction_34 is "Bc nonspecific degradation";
-  reaction_35 is "Bcp specific degradation";
-  reaction_36 is "Bn phosphorylation";
-  reaction_37 is "Bnp specific degradation";
-  reaction_38 is "In nonspecific degration";
-  reaction_39 is "In specific degradation";
-  reaction_40 is "Bn nonspecific degradation";
-  reaction_41 is "Bcp dephosphorylation";
-  reaction_42 is "Bnp dephosphorylation";
-  reaction_43 is "Ccp dephosphorylation";
-  reaction_44 is "Pcp dephosphorylation";
-  reaction_45 is "PCnp dephosphorylation";
-  reaction_46 is "PCn nonspecific degradation";
-  reaction_47 is "PCcp dephosphorylation";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005622"
-  species_0 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_1 version "http://identifiers.org/uniprot/O00327"
-  species_2 version "http://identifiers.org/uniprot/O00327"
-  species_3 identity "http://identifiers.org/uniprot/O00327"
-  species_4 version "http://identifiers.org/uniprot/Q16526",
-                    "http://identifiers.org/uniprot/Q8IV71"
-  species_5 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_6 version "http://identifiers.org/uniprot/Q16526",
-                    "http://identifiers.org/uniprot/Q8IV71"
-  species_7 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_8 version "http://identifiers.org/uniprot/O15534",
-                    "http://identifiers.org/uniprot/O15055",
-                    "http://identifiers.org/uniprot/P56645"
-  species_9 version "http://identifiers.org/uniprot/O15534",
-                    "http://identifiers.org/uniprot/O15055",
-                    "http://identifiers.org/uniprot/P56645"
-  species_10 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_10 part "http://identifiers.org/uniprot/O15055",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_10 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_11 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_11 part "http://identifiers.org/uniprot/O15055",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_11 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_12 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_12 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_12 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_13 version "http://identifiers.org/uniprot/O00327"
-  species_14 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_14 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_14 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0045892"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_6 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_7 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_8 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_9 identity "http://identifiers.org/go/GO:0045893"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_11 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_12 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_13 hypernym "http://identifiers.org/go/GO:0043623"
-  reaction_14 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_15 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_16 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_17 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_18 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_19 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_20 hypernym "http://identifiers.org/go/GO:0045893"
-  reaction_21 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_22 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_23 hypernym "http://identifiers.org/go/GO:0043623"
-  reaction_24 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_25 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_26 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_27 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_28 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_29 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_30 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_31 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_32 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_33 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_34 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_35 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_36 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_37 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_38 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_39 parthood "http://identifiers.org/go/GO:0008233"
-  reaction_40 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_41 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_42 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_43 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_44 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_45 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_46 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_47 hypernym "http://identifiers.org/go/GO:0006470",
-                       "http://identifiers.org/go/GO:0016311"
-end
-
-Model_1 is "Leloup2003_CircClock_DD"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL1109528188"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000073"
-Model_1 description "http://identifiers.org/pubmed/12775757"
-Model_1 origin "http://identifiers.org/biomodels.db/BIOMD0000000021"
-Model_1 taxon "http://identifiers.org/taxonomy/40674"
-Model_1 version "http://identifiers.org/kegg.pathway/hsa04710"
-Model_1 hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000074.txt b/BioModelsRAG/data/BIOMD0000000074.txt
deleted file mode 100644
index 23c41b7421dbae25dc28076ef262660ed06c3570..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000074.txt
+++ /dev/null
@@ -1,411 +0,0 @@
-// Created by libAntimony v2.13.0
-function function_3(Vs, B, n, K)
-  Vs*B^n/(K^n + B^n);
-end
-
-function_3 is "Activation of gene"
-
-function function_2(V, substrate, Km)
-  V*substrate/(Km + substrate);
-end
-
-function_2 is "Michaelis-Menten (irreversible)"
-
-function function_1(k, mRNA)
-  k*mRNA;
-end
-
-function_1 is "mRNA translated into protein"
-
-function function_0(vsb, K, m, Bn)
-  vsb*K^m/(K^m + Bn^m);
-end
-
-function_0 is "Inhibition of gene"
-
-
-model *Model_1()
-
-  // Compartments and Species:
-  compartment compartment_0;
-  species species_0 in compartment_0, species_1 in compartment_0, species_2 in compartment_0;
-  species species_3 in compartment_0, species_4 in compartment_0, species_5 in compartment_0;
-  species species_6 in compartment_0, species_7 in compartment_0, species_8 in compartment_0;
-  species species_9 in compartment_0, species_10 in compartment_0, species_11 in compartment_0;
-  species species_12 in compartment_0, species_13 in compartment_0, species_14 in compartment_0;
-  species species_15 in compartment_0, species_16 in compartment_0, species_17 in compartment_0;
-  species species_18 in compartment_0;
-
-  // Reactions:
-  reaction_0:  => species_0; compartment_0*function_0(reaction_0_vsb, reaction_0_K, reaction_0_m, species_18);
-  reaction_1:  => species_1; compartment_0*function_1(reaction_1_k, species_0);
-  reaction_2: species_0 => ; compartment_0*reaction_2_k1*species_0;
-  reaction_3: species_1 => species_2; compartment_0*function_2(reaction_3_V, species_1, reaction_3_Km);
-  reaction_4: species_1 -> species_3; compartment_0*(reaction_4_k1*species_1 - reaction_4_k2*species_3);
-  reaction_5:  => species_4; compartment_0*function_1(reaction_5_k, species_5);
-  reaction_6: species_5 => ; compartment_0*reaction_6_k1*species_5;
-  reaction_7: species_4 => species_6; compartment_0*function_2(reaction_7_V, species_4, reaction_7_Km);
-  reaction_8: species_6 => ; compartment_0*function_2(reaction_8_V, species_6, reaction_8_Km);
-  reaction_9:  => species_7; compartment_0*function_3(reaction_9_Vs, species_3, reaction_9_n, reaction_9_K);
-  reaction_10:  => species_8; compartment_0*function_1(reaction_10_k, species_7);
-  reaction_11: species_9 => ; compartment_0*function_2(reaction_11_V, species_9, reaction_11_Km);
-  reaction_12: species_8 => species_9; compartment_0*function_2(reaction_12_V, species_8, reaction_12_Km);
-  reaction_13: species_4 + species_8 -> species_10; compartment_0*(reaction_13_k1*species_4*species_8 - reaction_13_k2*species_10);
-  reaction_14: species_10 => species_11; compartment_0*function_2(reaction_14_V, species_10, reaction_14_Km);
-  reaction_15: species_11 => ; compartment_0*function_2(reaction_15_V, species_11, reaction_15_Km);
-  reaction_16: species_10 -> species_12; compartment_0*(reaction_16_k1*species_10 - reaction_16_k2*species_12);
-  reaction_17: species_14 => ; compartment_0*reaction_17_k1*species_14;
-  reaction_18: species_2 => ; compartment_0*reaction_18_k1*species_2;
-  reaction_19: species_13 => ; compartment_0*reaction_19_k1*species_13;
-  reaction_20:  => species_5; compartment_0*function_3(reaction_20_Vs, species_3, reaction_20_n, reaction_20_K);
-  reaction_21: species_12 => species_14; compartment_0*function_2(reaction_21_V, species_12, reaction_21_Km);
-  reaction_22: species_7 => ; compartment_0*reaction_22_k1*species_7;
-  reaction_23: species_12 + species_3 -> species_15; compartment_0*(reaction_23_k1*species_12*species_3 - reaction_23_k2*species_15);
-  reaction_24: species_0 => ; compartment_0*function_2(reaction_24_V, species_0, reaction_24_Km);
-  reaction_25: species_5 => ; compartment_0*function_2(reaction_25_V, species_5, reaction_25_Km);
-  reaction_26: species_7 => ; compartment_0*function_2(reaction_26_V, species_7, reaction_26_Km);
-  reaction_27: species_8 => ; compartment_0*reaction_27_k1*species_8;
-  reaction_28: species_4 => ; compartment_0*reaction_28_k1*species_4;
-  reaction_29: species_9 => ; compartment_0*reaction_29_k1*species_9;
-  reaction_30: species_6 => ; compartment_0*reaction_30_k1*species_6;
-  reaction_31: species_11 => ; compartment_0*reaction_31_k1*species_11;
-  reaction_32: species_10 => ; compartment_0*reaction_32_k1*species_10;
-  reaction_33: species_14 => ; compartment_0*function_2(reaction_33_V, species_14, reaction_33_Km);
-  reaction_34: species_1 => ; compartment_0*reaction_34_k1*species_1;
-  reaction_35: species_2 => ; compartment_0*function_2(reaction_35_V, species_2, reaction_35_Km);
-  reaction_36: species_3 => species_13; compartment_0*function_2(reaction_36_V, species_3, reaction_36_Km);
-  reaction_37: species_13 => ; compartment_0*function_2(reaction_37_V, species_13, reaction_37_Km);
-  reaction_38: species_15 => ; compartment_0*reaction_38_k1*species_15;
-  reaction_39: species_15 => ; compartment_0*function_2(reaction_39_V, species_15, reaction_39_Km);
-  reaction_40: species_3 => ; compartment_0*reaction_40_k1*species_3;
-  reaction_41: species_2 => species_1; compartment_0*function_2(reaction_41_V, species_2, reaction_41_Km);
-  reaction_42: species_13 => species_3; compartment_0*function_2(reaction_42_V, species_13, reaction_42_Km);
-  reaction_43: species_6 => species_4; compartment_0*function_2(reaction_43_V, species_6, reaction_43_Km);
-  reaction_44: species_9 => species_8; compartment_0*function_2(reaction_44_V, species_9, reaction_44_Km);
-  reaction_45: species_14 => species_12; compartment_0*function_2(reaction_45_V, species_14, reaction_45_Km);
-  reaction_46: species_12 => ; compartment_0*reaction_46_k1*species_12;
-  reaction_47: species_11 => species_10; compartment_0*function_2(reaction_47_V, species_11, reaction_47_Km);
-  reaction_48:  => species_16; compartment_0*function_3(reaction_48_Vs, species_3, reaction_48_n, reaction_48_K);
-  reaction_49: species_16 => ; compartment_0*reaction_49_k1*species_16;
-  reaction_50: species_16 => ; compartment_0*function_2(reaction_50_V, species_16, reaction_50_Km);
-  reaction_51:  => species_17; compartment_0*function_1(reaction_51_k, species_16);
-  reaction_52: species_17 -> species_18; compartment_0*(reaction_52_k1*species_17 - reaction_52_k2*species_18);
-  reaction_53: species_17 => ; compartment_0*function_2(reaction_53_V, species_17, reaction_53_Km);
-  reaction_54: species_17 => ; compartment_0*reaction_54_k1*species_17;
-  reaction_55: species_18 => ; compartment_0*function_2(reaction_55_V, species_18, reaction_55_Km);
-  reaction_56: species_18 => ; compartment_0*reaction_56_k1*species_18;
-
-  // Species initializations:
-  species_0 = 0;
-  species_1 = 0;
-  species_2 = 0;
-  species_3 = 0;
-  species_4 = 0;
-  species_5 = 0;
-  species_6 = 0;
-  species_7 = 0;
-  species_8 = 0;
-  species_9 = 0;
-  species_10 = 0;
-  species_11 = 0;
-  species_12 = 0;
-  species_13 = 0;
-  species_14 = 0;
-  species_15 = 0;
-  species_16 = 0;
-  species_17 = 0;
-  species_18 = 0;
-
-  // Compartment initializations:
-  compartment_0 = 1;
-
-  // Variable initializations:
-  reaction_0_vsb = 1.8;
-  reaction_0_K = 1;
-  reaction_0_m = 2;
-  reaction_1_k = 0.32;
-  reaction_2_k1 = 0.02;
-  reaction_3_V = 1.4;
-  reaction_3_Km = 1.006;
-  reaction_4_k1 = 0.8;
-  reaction_4_k2 = 0.4;
-  reaction_5_k = 3.2;
-  reaction_6_k1 = 0.02;
-  reaction_7_V = 1.2;
-  reaction_7_Km = 1.006;
-  reaction_8_V = 1.4;
-  reaction_8_Km = 0.3;
-  reaction_9_Vs = 2.4;
-  reaction_9_n = 2;
-  reaction_9_K = 0.6;
-  reaction_10_k = 1.2;
-  reaction_11_V = 3.4;
-  reaction_11_Km = 0.3;
-  reaction_12_V = 9.6;
-  reaction_12_Km = 1.006;
-  reaction_13_k1 = 0.8;
-  reaction_13_k2 = 0.4;
-  reaction_14_V = 2.4;
-  reaction_14_Km = 1.006;
-  reaction_15_V = 1.4;
-  reaction_15_Km = 0.3;
-  reaction_16_k1 = 0.8;
-  reaction_16_k2 = 0.4;
-  reaction_17_k1 = 0.02;
-  reaction_18_k1 = 0.02;
-  reaction_19_k1 = 0.02;
-  reaction_20_Vs = 2.2;
-  reaction_20_n = 2;
-  reaction_20_K = 0.6;
-  reaction_21_V = 2.4;
-  reaction_21_Km = 1.006;
-  reaction_22_k1 = 0.02;
-  reaction_23_k1 = 1;
-  reaction_23_k2 = 0.2;
-  reaction_24_V = 1.3;
-  reaction_24_Km = 0.4;
-  reaction_25_V = 2;
-  reaction_25_Km = 0.4;
-  reaction_26_V = 2.2;
-  reaction_26_Km = 0.3;
-  reaction_27_k1 = 0.02;
-  reaction_28_k1 = 0.02;
-  reaction_29_k1 = 0.02;
-  reaction_30_k1 = 0.02;
-  reaction_31_k1 = 0.02;
-  reaction_32_k1 = 0.02;
-  reaction_33_V = 1.4;
-  reaction_33_Km = 0.3;
-  reaction_34_k1 = 0.02;
-  reaction_35_V = 3;
-  reaction_35_Km = 0.3;
-  reaction_36_V = 1.4;
-  reaction_36_Km = 1.006;
-  reaction_37_V = 3;
-  reaction_37_Km = 0.3;
-  reaction_38_k1 = 0.02;
-  reaction_39_V = 1.6;
-  reaction_39_Km = 0.3;
-  reaction_40_k1 = 0.02;
-  reaction_41_V = 0.2;
-  reaction_41_Km = 0.1;
-  reaction_42_V = 0.4;
-  reaction_42_Km = 0.1;
-  reaction_43_V = 0.2;
-  reaction_43_Km = 0.1;
-  reaction_44_V = 0.6;
-  reaction_44_Km = 0.1;
-  reaction_45_V = 0.2;
-  reaction_45_Km = 0.1;
-  reaction_46_k1 = 0.02;
-  reaction_47_V = 0.2;
-  reaction_47_Km = 0.1;
-  reaction_48_Vs = 1.6;
-  reaction_48_n = 2;
-  reaction_48_K = 0.6;
-  reaction_49_k1 = 0.02;
-  reaction_50_V = 1.6;
-  reaction_50_Km = 0.4;
-  reaction_51_k = 1.7;
-  reaction_52_k1 = 0.8;
-  reaction_52_k2 = 0.4;
-  reaction_53_V = 4.4;
-  reaction_53_Km = 0.3;
-  reaction_54_k1 = 0.02;
-  reaction_55_V = 0.8;
-  reaction_55_Km = 0.3;
-  reaction_56_k1 = 0.02;
-
-  // Other declarations:
-  const compartment_0;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  compartment_0 is "cell";
-  species_0 is "Mb";
-  species_1 is "Bc";
-  species_2 is "Bcp";
-  species_3 is "Bn";
-  species_4 is "Cc";
-  species_5 is "Mc";
-  species_6 is "Ccp";
-  species_7 is "Mp";
-  species_8 is "Pc";
-  species_9 is "Pcp";
-  species_10 is "PCc";
-  species_11 is "PCcp";
-  species_12 is "PCn";
-  species_13 is "Bnp";
-  species_14 is "PCnp";
-  species_15 is "In";
-  species_16 is "Mr";
-  species_17 is "Rc";
-  species_18 is "Rn";
-  reaction_0 is "Mb synthesized";
-  reaction_1 is "Mb translated into protein";
-  reaction_2 is "Mb nonspecific degradation";
-  reaction_3 is "Bc phosphorylation";
-  reaction_4 is "Bc transfered from cytosolic to nuclear";
-  reaction_5 is "Mc translated into protein";
-  reaction_6 is "Mc nonspecific degradation";
-  reaction_7 is "Cc phosphorylation";
-  reaction_8 is "Ccp specific degradation";
-  reaction_9 is "Mp synthesis";
-  reaction_10 is "Mp translated into protein";
-  reaction_11 is "Pcp specific degradation";
-  reaction_12 is "Pc phospholation";
-  reaction_13 is "Cc and Pc produce PCc";
-  reaction_14 is "PCc phospholation";
-  reaction_15 is "PCcp specific degradation";
-  reaction_16 is "PCc transfered into nuclear";
-  reaction_17 is "PCnp nonspecific degradation";
-  reaction_18 is "Bcp nonspecific degradation";
-  reaction_19 is "Bnp nonspecific degradation";
-  reaction_20 is "Mc synthesis";
-  reaction_21 is "PCn phospholation";
-  reaction_22 is "Mp nonspecific degradation";
-  reaction_23 is "Per_Cry and Clock_Bmal form inactive complex";
-  reaction_24 is "Mb specific degradation";
-  reaction_25 is "Mc specific degradation";
-  reaction_26 is "Mp specific degradation";
-  reaction_27 is "Pc nonspecific degradation";
-  reaction_28 is "Cc nonspecific degradation";
-  reaction_29 is "Pcp nonspecific degradation";
-  reaction_30 is "Ccp nonspecific degradation";
-  reaction_31 is "PCcp nonspecific degradation";
-  reaction_32 is "PCc nonspecific degradation";
-  reaction_33 is "PCnp specific degradation";
-  reaction_34 is "Bc nonspecific degradation";
-  reaction_35 is "Bcp specific degradation";
-  reaction_36 is "Bn phospholation";
-  reaction_37 is "Bnp specific degradation";
-  reaction_38 is "In nonspecific degration";
-  reaction_39 is "In specific degradation";
-  reaction_40 is "Bn nonspecific degradation";
-  reaction_41 is "Bcp dephospholation";
-  reaction_42 is "Bnp dephospholation";
-  reaction_43 is "Ccp dephospholation";
-  reaction_44 is "Pcp dephospholation";
-  reaction_45 is "PCnp dephospholation";
-  reaction_46 is "PCn nonspecific degradation";
-  reaction_47 is "PCcp dephospholation";
-  reaction_48 is "Mr synthesized";
-  reaction_49 is "Mr nonspecific degradation";
-  reaction_50 is "Mr specific degradation";
-  reaction_51 is "Mr translated into protein";
-  reaction_52 is "Rc transfered into nuclear";
-  reaction_53 is "Rc specific degradation";
-  reaction_54 is "Rc nonspecific degradation";
-  reaction_55 is "Rn specific degradation";
-  reaction_56 is "Rn nonspecific degradation";
-
-  // CV terms:
-  compartment_0 hypernym "http://identifiers.org/go/GO:0005623"
-  species_0 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_1 version "http://identifiers.org/uniprot/O00327"
-  species_2 version "http://identifiers.org/uniprot/O00327"
-  species_3 version "http://identifiers.org/uniprot/O00327"
-  species_4 version "http://identifiers.org/uniprot/Q16526",
-                    "http://identifiers.org/uniprot/Q8IV71"
-  species_5 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_6 version "http://identifiers.org/uniprot/Q16526",
-                    "http://identifiers.org/uniprot/Q8IV71"
-  species_7 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_8 version "http://identifiers.org/uniprot/O15534",
-                    "http://identifiers.org/uniprot/O15055",
-                    "http://identifiers.org/uniprot/P56645"
-  species_9 version "http://identifiers.org/uniprot/O15534",
-                    "http://identifiers.org/uniprot/O15055",
-                    "http://identifiers.org/uniprot/P56645"
-  species_10 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_10 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_11 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_11 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_12 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_12 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_13 version "http://identifiers.org/uniprot/O00327"
-  species_14 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_14 part "http://identifiers.org/uniprot/O15055",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_14 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_16 hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  species_17 version "http://identifiers.org/uniprot/Q6EEZ7"
-  species_18 version "http://identifiers.org/uniprot/Q6EEZ7"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0045892"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_6 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_7 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_8 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_9 hypernym "http://identifiers.org/go/GO:0045893"
-  reaction_11 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_12 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_13 hypernym "http://identifiers.org/go/GO:0043623"
-  reaction_14 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_15 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_16 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_17 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_18 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_19 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_20 parthood "http://identifiers.org/go/GO:0045893"
-  reaction_21 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_22 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_23 hypernym "http://identifiers.org/go/GO:0043623"
-  reaction_24 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_25 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_26 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_27 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_28 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_29 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_30 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_31 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_32 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_33 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_34 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_35 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_36 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_37 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_38 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_39 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_40 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_41 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_42 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_43 parthood "http://identifiers.org/go/GO:0006470"
-  reaction_44 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_45 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_46 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_47 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_48 parthood "http://identifiers.org/go/GO:0045893"
-  reaction_49 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_50 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_51 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_52 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_53 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_54 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_55 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_56 hypernym "http://identifiers.org/go/GO:0044257"
-end
-
-Model_1 is "Leloup2003_CircClock_DD_REV-ERBalpha"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL1272626224"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000074"
-Model_1 description "http://identifiers.org/pubmed/12775757"
-Model_1 origin "http://identifiers.org/biomodels.db/BIOMD0000000021"
-Model_1 version "http://identifiers.org/kegg.pathway/hsa04710"
-Model_1 hypernym "http://identifiers.org/go/GO:0042752"
-Model_1 taxon "http://identifiers.org/taxonomy/40674"
diff --git a/BioModelsRAG/data/BIOMD0000000075.txt b/BioModelsRAG/data/BIOMD0000000075.txt
deleted file mode 100644
index 2cac405edf083b801c56a30a6c519e3b316afdc8..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000075.txt
+++ /dev/null
@@ -1,250 +0,0 @@
-// Created by libAntimony v2.13.0
-function Function_for_PIPSyn(PI_PM, Ratebasal_PIPsyn_PIPSyn, Ratestim_PIPsyn_PIPSyn)
-  (Ratebasal_PIPsyn_PIPSyn + Ratestim_PIPsyn_PIPSyn)*PI_PM;
-end
-
-Function_for_PIPSyn is "Function for PIPSyn"
-
-function Function_for_PLCact(KfPLCact, PLC_PM, PLC_act_PM, krPLCact, signal_PLCact, stim_PM)
-  KfPLCact*PLC_PM*stim_PM*signal_PLCact + -(krPLCact*PLC_act_PM);
-end
-
-Function_for_PLCact is "Function for PLCact"
-
-function Function_for_IP3_PHGFP(IP3_Cyt, IP3_PHGFP_Cyt, KMOLE, PH_GFP_Cyt, kf_IP3PH_IP3_PHGFP, kr_IP3PH_IP3_PHGFP)
-  (kf_IP3PH_IP3_PHGFP*0.00166112956810631*IP3_Cyt*0.00166112956810631*PH_GFP_Cyt + -(kr_IP3PH_IP3_PHGFP*0.00166112956810631*IP3_PHGFP_Cyt))*1*(1/KMOLE);
-end
-
-Function_for_IP3_PHGFP is "Function for IP3-PHGFP"
-
-function Function_for_PIP2_PH(PH_GFP_Cyt, PIP2_PHGFP_PM, PIP2_PM, PM, kf_PIP2PH_PIP2_PH, kr_PIP2PH_PIP2_PH)
-  (kf_PIP2PH_PIP2_PH*0.00166112956810631*PH_GFP_Cyt*PIP2_PM + -(kr_PIP2PH_PIP2_PH*PIP2_PHGFP_PM))*PM;
-end
-
-Function_for_PIP2_PH is "Function for PIP2_PH"
-
-function Function_for_PIP2_PH_hyd(PIP2_PHGFP_PM, PLC_act_PM, PM, k_PIP2PHhyd)
-  k_PIP2PHhyd*PLC_act_PM*PIP2_PHGFP_PM*PM;
-end
-
-Function_for_PIP2_PH_hyd is "Function for PIP2_PH_hyd"
-
-function Function_for_IP3deg(IP3_Cyt, IP3_basal, KMOLE, kIP3deg)
-  kIP3deg*(0.00166112956810631*IP3_Cyt + -IP3_basal)*1*(1/KMOLE);
-end
-
-Function_for_IP3deg is "Function for IP3deg"
-
-function Function_for_PIP2Syn(PIP_PM, Rate_PIP2SynStim_PIP2Syn, Rate_PIP2Synbasal_PIP2Syn)
-  (Rate_PIP2Synbasal_PIP2Syn + Rate_PIP2SynStim_PIP2Syn)*PIP_PM;
-end
-
-Function_for_PIP2Syn is "Function for PIP2Syn"
-
-function Function_for_PIP2_hyd(PIP2_PM, PLC_act_PM, PM, k_PIP2hyd)
-  k_PIP2hyd*PIP2_PM*PLC_act_PM*PM;
-end
-
-Function_for_PIP2_hyd is "Function for PIP2_hyd"
-
-
-model *Xu2003_Phosphoinositide_turnover()
-
-  // Compartments and Species:
-  compartment Extracellular, PM, Cytosol, NM, Nucleus;
-  species PIP2_PHGFP_PM in PM, PH_GFP_Cyt in Cytosol, PI_PM in PM, $stim_PM in PM;
-  species IP3_PHGFP_Cyt in Cytosol, PIP2_PM in PM, PIP_PM in PM, DAG_PM in PM;
-  species $hv_Cytosol in Cytosol, $IP3X_Cytosol in Cytosol, PLC_PM in PM;
-  species PLC_act_PM in PM, IP3_Cyt in Cytosol;
-
-  // Assignment Rules:
-  Ratebasal_PIPsyn_PIPSyn := piecewise(0.581*kBasalSynPIP_PIPSyn*(-1 + exp((PIP_basal_PIPSyn + -PIP_PM)*(1/PIP_basal_PIPSyn))), PIP_PM < PIP_basal_PIPSyn, 0);
-  Ratestim_PIPsyn_PIPSyn := piecewise(kStimSynPIP_PIPSyn*exp(-((time + -tauPIPsyn_PIPSyn)*(1/PIPsyndecay_PIPSyn))), time > tauPIPsyn_PIPSyn, 0);
-  signal_PLCact := piecewise(exp(-((time + -tau0_PLCact)*(1/stimdecay_PLCact))), time > tau0_PLCact, 0);
-  kr_PIP2PH_PIP2_PH := kf_PIP2PH_PIP2_PH*KdPIP2PH_PIP2_PH;
-  Rate_PIP2Synbasal_PIP2Syn := piecewise(0.581*kBasalSynPIP2_PIP2Syn*(-1 + exp((PIP2_basal_PIP2Syn + -PIP2_PM)*(1/PIP2_basal_PIP2Syn))), PIP2_PM < PIP2_basal_PIP2Syn, 0);
-  Rate_PIP2SynStim_PIP2Syn := piecewise(kStimSynPIP2_PIP2Syn*exp(-((time + -tauPIP2syn_PIP2Syn)*(1/PIP2syndecay_PIP2Syn))), time > tauPIP2syn_PIP2Syn, 0);
-  kr_IP3PH_IP3_PHGFP := kf_IP3PH_IP3_PHGFP*KdIP3PH_IP3_PHGFP;
-
-  // Reactions:
-  PIPSyn: PI_PM -> PIP_PM; PM*Function_for_PIPSyn(PI_PM, Ratebasal_PIPsyn_PIPSyn, Ratestim_PIPsyn_PIPSyn);
-  PIP2_hyd: PIP2_PM -> DAG_PM + IP3_Cyt; Function_for_PIP2_hyd(PIP2_PM, PLC_act_PM, PM, PIP2_hyd_k_PIP2hyd);
-  PLCact: PLC_PM -> PLC_act_PM; PM*Function_for_PLCact(PLCact_KfPLCact, PLC_PM, PLC_act_PM, PLCact_krPLCact, signal_PLCact, stim_PM);
-  PIP2_PH_hyd: PIP2_PHGFP_PM -> PH_GFP_Cyt + IP3_Cyt + DAG_PM; Function_for_PIP2_PH_hyd(PIP2_PHGFP_PM, PLC_act_PM, PM, PIP2_PH_hyd_k_PIP2PHhyd);
-  PIP2_PH: PH_GFP_Cyt + PIP2_PM -> PIP2_PHGFP_PM; Function_for_PIP2_PH(PH_GFP_Cyt, PIP2_PHGFP_PM, PIP2_PM, PM, kf_PIP2PH_PIP2_PH, kr_PIP2PH_PIP2_PH);
-  IP3deg: IP3_Cyt -> ; Cytosol*Function_for_IP3deg(IP3_Cyt, IP3deg_IP3_basal, KMOLE, IP3deg_kIP3deg);
-  PIP2Syn: PIP_PM -> PIP2_PM; PM*Function_for_PIP2Syn(PIP_PM, Rate_PIP2SynStim_PIP2Syn, Rate_PIP2Synbasal_PIP2Syn);
-  IP3_PHGFP: IP3_Cyt + PH_GFP_Cyt -> IP3_PHGFP_Cyt; Cytosol*Function_for_IP3_PHGFP(IP3_Cyt, IP3_PHGFP_Cyt, KMOLE, PH_GFP_Cyt, kf_IP3PH_IP3_PHGFP, kr_IP3PH_IP3_PHGFP);
-
-  // Species initializations:
-  PIP2_PHGFP_PM = 0;
-  PIP2_PHGFP_PM has substance_per_volume;
-  PH_GFP_Cyt = 0;
-  PH_GFP_Cyt has substance_per_volume;
-  PI_PM = 142857;
-  PI_PM has substance_per_volume;
-  stim_PM = 1;
-  stim_PM has substance_per_volume;
-  IP3_PHGFP_Cyt = 0;
-  IP3_PHGFP_Cyt has substance_per_volume;
-  PIP2_PM = 4000;
-  PIP2_PM has substance_per_volume;
-  PIP_PM = 2857;
-  PIP_PM has substance_per_volume;
-  DAG_PM = 2000;
-  DAG_PM has substance_per_volume;
-  hv_Cytosol = 0;
-  hv_Cytosol has substance_per_volume;
-  IP3X_Cytosol = 0;
-  IP3X_Cytosol has substance_per_volume;
-  PLC_PM = 100;
-  PLC_PM has substance_per_volume;
-  PLC_act_PM = 0;
-  PLC_act_PM has substance_per_volume;
-  IP3_Cyt = 96.32;
-  IP3_Cyt has substance_per_volume;
-
-  // Compartment initializations:
-  Extracellular = 0.277777777777778;
-  Extracellular has volume;
-  PM = 0.5555555555556;
-  PM has volume;
-  Cytosol = 1;
-  Cytosol has volume;
-  NM = 0.111111111111111;
-  NM has volume;
-  Nucleus = 0.111111111111111;
-  Nucleus has volume;
-
-  // Variable initializations:
-  KMOLE = 0.00166112956810631;
-  KMOLE has unit_0;
-  PIP_basal_PIPSyn = 2857;
-  PIP_basal_PIPSyn has unit_1;
-  kBasalSynPIP_PIPSyn = 0.0055;
-  kBasalSynPIP_PIPSyn has unit_2;
-  kStimSynPIP_PIPSyn = 0.019;
-  kStimSynPIP_PIPSyn has unit_2;
-  tauPIPsyn_PIPSyn = 0.05;
-  tauPIPsyn_PIPSyn has unit_3;
-  PIPsyndecay_PIPSyn = 1;
-  PIPsyndecay_PIPSyn has unit_3;
-  Ratebasal_PIPsyn_PIPSyn has unit_2;
-  Ratestim_PIPsyn_PIPSyn has unit_2;
-  tau0_PLCact = 0.05;
-  tau0_PLCact has unit_3;
-  stimdecay_PLCact = 1;
-  stimdecay_PLCact has unit_3;
-  signal_PLCact has unit_4;
-  kf_PIP2PH_PIP2_PH = 0.12;
-  kf_PIP2PH_PIP2_PH has unit_5;
-  KdPIP2PH_PIP2_PH = 2;
-  KdPIP2PH_PIP2_PH has unit_6;
-  kr_PIP2PH_PIP2_PH has unit_2;
-  kStimSynPIP2_PIP2Syn = 0.92;
-  kStimSynPIP2_PIP2Syn has unit_2;
-  tauPIP2syn_PIP2Syn = 0.05;
-  tauPIP2syn_PIP2Syn has unit_3;
-  PIP2syndecay_PIP2Syn = 1;
-  PIP2syndecay_PIP2Syn has unit_3;
-  PIP2_basal_PIP2Syn = 4000;
-  PIP2_basal_PIP2Syn has unit_1;
-  kBasalSynPIP2_PIP2Syn = 0.048;
-  kBasalSynPIP2_PIP2Syn has unit_2;
-  Rate_PIP2Synbasal_PIP2Syn has unit_2;
-  Rate_PIP2SynStim_PIP2Syn has unit_2;
-  kf_IP3PH_IP3_PHGFP = 10;
-  kf_IP3PH_IP3_PHGFP has unit_5;
-  KdIP3PH_IP3_PHGFP = 2;
-  KdIP3PH_IP3_PHGFP has unit_6;
-  kr_IP3PH_IP3_PHGFP has unit_2;
-  PIP2_hyd_k_PIP2hyd = 2.4;
-  PLCact_KfPLCact = 0.0005;
-  PLCact_krPLCact = 0.1;
-  PIP2_PH_hyd_k_PIP2PHhyd = 0;
-  IP3deg_IP3_basal = 0.16;
-  IP3deg_kIP3deg = 0.08;
-
-  // Other declarations:
-  var Ratebasal_PIPsyn_PIPSyn, Ratestim_PIPsyn_PIPSyn, signal_PLCact, kr_PIP2PH_PIP2_PH;
-  var Rate_PIP2Synbasal_PIP2Syn, Rate_PIP2SynStim_PIP2Syn, kr_IP3PH_IP3_PHGFP;
-  const Extracellular, PM, Cytosol, NM, Nucleus, KMOLE, PIP_basal_PIPSyn;
-  const kBasalSynPIP_PIPSyn, kStimSynPIP_PIPSyn, tauPIPsyn_PIPSyn, PIPsyndecay_PIPSyn;
-  const tau0_PLCact, stimdecay_PLCact, kf_PIP2PH_PIP2_PH, KdPIP2PH_PIP2_PH;
-  const kStimSynPIP2_PIP2Syn, tauPIP2syn_PIP2Syn, PIP2syndecay_PIP2Syn, PIP2_basal_PIP2Syn;
-  const kBasalSynPIP2_PIP2Syn, kf_IP3PH_IP3_PHGFP, KdIP3PH_IP3_PHGFP;
-
-  // Unit definitions:
-  unit length = metre;
-  unit area = (1e-6 metre)^2;
-  unit volume = litre;
-  unit time_unit = time_unit;
-  unit substance = item;
-  unit unit_0 = 1e-18 avogadro;
-  unit unit_1 = item / (1e6 metre)^2;
-  unit unit_2 = 1 / second;
-  unit unit_3 = second;
-  unit unit_4 = 1 / dimensionless^-0;
-  unit unit_5 = metre^3 / ((1e-9 dimensionless)^-0 * mole * second);
-  unit unit_6 = item * avogadro / ((1e-6 dimensionless)^-0 * litre);
-  unit extent = substance;
-  unit substance_per_volume = item / litre;
-
-  // Display Names:
-  time_unit is "time";
-  unit_0 is "aAvogadro";
-  unit_1 is "#/Mm²";
-  unit_2 is "1/s";
-  unit_3 is "s";
-  unit_4 is "1";
-  unit_5 is "µl/(mol*s)";
-  unit_6 is "µmol/l";
-  IP3_PHGFP is "IP3-PHGFP";
-
-  // CV terms:
-  Extracellular identity "http://identifiers.org/go/GO:0005576"
-  PM identity "http://identifiers.org/go/GO:0005886"
-  Cytosol identity "http://identifiers.org/go/GO:0005622"
-  NM identity "http://identifiers.org/go/GO:0031965"
-  Nucleus identity "http://identifiers.org/go/GO:0005634"
-  PIP2_PHGFP_PM part "http://identifiers.org/chebi/CHEBI:18348"
-  PIP2_PHGFP_PM part "http://identifiers.org/interpro/IPR011584"
-  PIP2_PHGFP_PM part "http://identifiers.org/interpro/IPR001849"
-  PH_GFP_Cyt part "http://identifiers.org/interpro/IPR001849"
-  PH_GFP_Cyt part "http://identifiers.org/interpro/IPR011584"
-  PI_PM hypernym "http://identifiers.org/chebi/CHEBI:28874"
-  stim_PM property "http://identifiers.org/opb/OPB_01072"
-  IP3_PHGFP_Cyt part "http://identifiers.org/interpro/IPR001849"
-  IP3_PHGFP_Cyt part "http://identifiers.org/chebi/CHEBI:16595"
-  IP3_PHGFP_Cyt part "http://identifiers.org/interpro/IPR011584"
-  PIP2_PM hypernym "http://identifiers.org/chebi/CHEBI:18348"
-  PIP_PM hypernym "http://identifiers.org/chebi/CHEBI:26034"
-  DAG_PM hypernym "http://identifiers.org/chebi/CHEBI:18035"
-  hv_Cytosol hypernym "http://identifiers.org/chebi/CHEBI:30212"
-  IP3X_Cytosol identity "http://identifiers.org/pato/PATO:0002355"
-  IP3X_Cytosol hypernym "http://identifiers.org/chebi/CHEBI:16595"
-  PLC_PM hypernym "http://identifiers.org/uniprot/Q8K4S1"
-  PLC_act_PM hypernym "http://identifiers.org/uniprot/Q8K4S1"
-  PLC_act_PM property "http://identifiers.org/ec-code/3.1.4.11"
-  IP3_Cyt hypernym "http://identifiers.org/chebi/CHEBI:16595"
-  PIPSyn hypernym "http://identifiers.org/biomodels.sbo/SBO:0000216"
-  PIP2_hyd hypernym "http://identifiers.org/biomodels.sbo/SBO:0000182"
-  PLCact hypernym "http://identifiers.org/biomodels.sbo/SBO:0000170"
-  PIP2_PH_hyd hypernym "http://identifiers.org/biomodels.sbo/SBO:0000182"
-  PIP2_PH hypernym "http://identifiers.org/biomodels.sbo/SBO:0000182"
-  IP3deg hypernym "http://identifiers.org/biomodels.sbo/SBO:0000179"
-  PIP2Syn hypernym "http://identifiers.org/biomodels.sbo/SBO:0000216"
-  IP3_PHGFP hypernym "http://identifiers.org/biomodels.sbo/SBO:0000182"
-end
-
-Xu2003_Phosphoinositide_turnover is "Xu2003 - Phosphoinositide turnover"
-
-Xu2003_Phosphoinositide_turnover model_entity_is "http://identifiers.org/biomodels.db/MODEL3095606944",
-                                                 "http://identifiers.org/biomodels.db/BIOMD0000000075"
-Xu2003_Phosphoinositide_turnover identity "http://identifiers.org/biomodels.db/MODEL3095606944"
-Xu2003_Phosphoinositide_turnover identity "http://identifiers.org/biomodels.db/BIOMD0000000075"
-Xu2003_Phosphoinositide_turnover parthood "http://identifiers.org/kegg.pathway/map04070"
-Xu2003_Phosphoinositide_turnover hypernym "http://identifiers.org/go/GO:0046488"
-Xu2003_Phosphoinositide_turnover container "http://identifiers.org/bto/BTO:0000931"
-Xu2003_Phosphoinositide_turnover taxon "http://identifiers.org/taxonomy/10090"
-Xu2003_Phosphoinositide_turnover description "http://identifiers.org/pubmed/12771127"
diff --git a/BioModelsRAG/data/BIOMD0000000076.txt b/BioModelsRAG/data/BIOMD0000000076.txt
deleted file mode 100644
index 5cef2d80124aaaa19830781a37f7814b80356884..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000076.txt
+++ /dev/null
@@ -1,97 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Cronwright2002_Glycerol_Synthesis()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species G3P in compartment_, $Gly in compartment_, $DHAP in compartment_;
-
-  // Reactions:
-  Gpd_p: $DHAP -> G3P; (compartment_*Gpd_p_Vf1/(Gpd_p_K1nadh*Gpd_p_K1dhap))*(Gpd_p_NADH*DHAP - Gpd_p_NAD*G3P/Gpd_p_Keq1)/((1 + Gpd_p_F16BP/Gpd_p_K1f16bp + Gpd_p_ATP/Gpd_p_K1atp + Gpd_p_ADP/Gpd_p_K1adp)*(1 + Gpd_p_NADH/Gpd_p_K1nadh + Gpd_p_NAD/Gpd_p_K1nad)*(1 + DHAP/Gpd_p_K1dhap + G3P/Gpd_p_K1g3p));
-  Gpp_p: G3P -> $Gly; compartment_*Gpp_p_V2*G3P/Gpp_p_K2g3p/((1 + G3P/Gpp_p_K2g3p)*(1 + Gpp_p_Phi/Gpp_p_K2phi));
-
-  // Species initializations:
-  G3P = 0;
-  Gly = 15.1;
-  DHAP = 0.59;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  Gpd_p_Vf1 = 47;
-  Gpd_p_Vf1 has mM_per_minute;
-  Gpd_p_K1nadh = 0.023;
-  Gpd_p_K1nadh has mM;
-  Gpd_p_K1dhap = 0.54;
-  Gpd_p_K1dhap has mM;
-  Gpd_p_NADH = 1.87;
-  Gpd_p_NADH has mM;
-  Gpd_p_NAD = 1.45;
-  Gpd_p_NAD has mM;
-  Gpd_p_Keq1 = 10000;
-  Gpd_p_Keq1 has dimensionless;
-  Gpd_p_F16BP = 6.01;
-  Gpd_p_F16BP has mM;
-  Gpd_p_K1f16bp = 4.8;
-  Gpd_p_K1f16bp has mM;
-  Gpd_p_ATP = 2.37;
-  Gpd_p_ATP has mM;
-  Gpd_p_K1atp = 0.73;
-  Gpd_p_K1atp has mM;
-  Gpd_p_ADP = 2.17;
-  Gpd_p_ADP has mM;
-  Gpd_p_K1adp = 2;
-  Gpd_p_K1adp has mM;
-  Gpd_p_K1nad = 0.93;
-  Gpd_p_K1nad has mM;
-  Gpd_p_K1g3p = 1.2;
-  Gpd_p_K1g3p has mM;
-  Gpp_p_V2 = 53;
-  Gpp_p_V2 has mM_per_minute;
-  Gpp_p_K2g3p = 3.5;
-  Gpp_p_K2g3p has mM;
-  Gpp_p_Phi = 1;
-  Gpp_p_Phi has mM;
-  Gpp_p_K2phi = 1;
-  Gpp_p_K2phi has mM;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-  unit mM_per_minute = 1e-3 mole / (litre * 60 second);
-  unit mM = 1e-3 mole / litre;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "minute";
-  compartment_ is "Cytoplasm";
-  G3P is "Glycerol 3-phosphate";
-  Gly is "Glycerol";
-  Gpd_p is "Glycerol 3-phosphate dehydrogenase";
-  Gpp_p is "Glycerol 3-phosphatase";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005737"
-  G3P identity "http://identifiers.org/obo.chebi/CHEBI:15978",
-               "http://identifiers.org/kegg.compound/C00093"
-  Gly identity "http://identifiers.org/obo.chebi/CHEBI:17754",
-               "http://identifiers.org/kegg.compound/C00116"
-  DHAP identity "http://identifiers.org/obo.chebi/CHEBI:16108",
-                "http://identifiers.org/kegg.compound/C00111"
-  Gpd_p identity "http://identifiers.org/ec-code/1.1.1.94",
-                 "http://identifiers.org/kegg.reaction/R00842"
-  Gpp_p identity "http://identifiers.org/ec-code/3.1.3.21",
-                 "http://identifiers.org/kegg.reaction/R00841"
-end
-
-Cronwright2002_Glycerol_Synthesis is "Cronwright2002_Glycerol_Synthesis"
-
-Cronwright2002_Glycerol_Synthesis model_entity_is "http://identifiers.org/biomodels.db/MODEL6624139162"
-Cronwright2002_Glycerol_Synthesis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000076"
-Cronwright2002_Glycerol_Synthesis description "http://identifiers.org/pubmed/12200299"
-Cronwright2002_Glycerol_Synthesis identity "http://identifiers.org/obo.go/GO:0006114"
-Cronwright2002_Glycerol_Synthesis parthood "http://identifiers.org/kegg.pathway/sce00561"
-Cronwright2002_Glycerol_Synthesis taxon "http://identifiers.org/taxonomy/4932"
diff --git a/BioModelsRAG/data/BIOMD0000000077.txt b/BioModelsRAG/data/BIOMD0000000077.txt
deleted file mode 100644
index 496497d7d6c03be5e57b33bc55101e0b6bcc42f1..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000077.txt
+++ /dev/null
@@ -1,96 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Model_1()
-
-  // Compartments and Species:
-  compartment cell;
-  species H in cell, HR in cell, R in cell, HRRH in cell, E in cell, GQ in cell;
-  species IP3 in cell, $CHO in cell;
-
-  // Assignment Rules:
-  CHO := 0.001*alpha*IP3*(0.3 + 0.3*beta*time*exp(1 - beta*time))/(1 + 0.001*alpha*IP3);
-
-  // Reactions:
-  reaction_0: H + R -> HR; cell*(reaction_0_k1*H*R - reaction_0_k2*HR);
-  reaction_1: 2 HR -> HRRH; cell*(reaction_1_k1*HR^2 - reaction_1_k2*HRRH);
-  reaction_2: HRRH + GQ -> E; cell*(reaction_2_k1*HRRH*GQ - reaction_2_k2*E);
-  reaction_3: IP3 => ; cell*reaction_3_k1*IP3;
-  reaction_4:  => IP3; cell*reaction_4_k*E;
-
-  // Events:
-  RemovalH: at time > 5: H = 0;
-
-  // Species initializations:
-  H = 1;
-  HR = 0;
-  R = 0.01;
-  HRRH = 0;
-  E = 0;
-  GQ = 0.1;
-  IP3 = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  alpha = 2;
-  alpha has substance;
-  beta = 4;
-  beta has unitDefinition_3;
-  reaction_0_k1 = 2.5;
-  reaction_0_k2 = 5;
-  reaction_1_k1 = 2500;
-  reaction_1_k2 = 5;
-  reaction_2_k1 = 4000;
-  reaction_2_k2 = 200;
-  reaction_3_k1 = 10;
-  reaction_4_k = 20000000;
-
-  // Other declarations:
-  const cell, alpha, beta;
-
-  // Unit definitions:
-  unit time_unit = 60 second;
-  unit substance = 1e-9 mole;
-  unit unitDefinition_3 = 1 / 60 second;
-
-  // Display Names:
-  unitDefinition_3 is "unit for beta";
-  RemovalH is "removal of hormone";
-  reaction_0 is "H binding to  R";
-  reaction_1 is "HR forming HRRH";
-  reaction_2 is "G protein react with dimer producing E";
-  reaction_3 is "IP3 converted into inactive metabolites";
-  reaction_4 is "Production of IP3";
-
-  // CV terms:
-  cell identity "http://identifiers.org/go/GO:0005623"
-  H version "http://identifiers.org/uniprot/P51924"
-  H version "http://identifiers.org/uniprot/P07490"
-  HR version "http://identifiers.org/uniprot/P07490",
-             "http://identifiers.org/uniprot/P30969"
-  R version "http://identifiers.org/uniprot/P30969"
-  HRRH hypernym "http://identifiers.org/go/GO:0043234"
-  E identity "http://identifiers.org/pirsf/PIRSF005483"
-  GQ version "http://identifiers.org/go/GO:0005834"
-  IP3 hypernym "http://identifiers.org/chebi/CHEBI:16595"
-  IP3 hypernym "http://identifiers.org/kegg.compound/C01245"
-  CHO hypernym "http://identifiers.org/interpro/IPR000699"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0051428",
-                      "http://identifiers.org/go/GO:0005102"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0004968"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0006461"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0007202"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0009056"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0004629"
-end
-
-Model_1 is "Blum2000_LHsecretion_1"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL3092061764"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000077"
-Model_1 description "http://identifiers.org/pubmed/10662710"
-Model_1 parthood "http://identifiers.org/go/GO:0032275",
-                 "http://identifiers.org/go/GO:0007200"
-Model_1 taxon "http://identifiers.org/taxonomy/131567"
-Model_1 hypernym "http://identifiers.org/go/GO:0097210"
-Model_1 property "http://identifiers.org/mamo/MAMO_0000046"
diff --git a/BioModelsRAG/data/BIOMD0000000078.txt b/BioModelsRAG/data/BIOMD0000000078.txt
deleted file mode 100644
index 750ad3b07bbfdbe215a921d9018314111998313f..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000078.txt
+++ /dev/null
@@ -1,374 +0,0 @@
-// Created by libAntimony v2.13.0
-function function_3(Vs, B, n, K)
-  Vs*B^n/(K^n + B^n);
-end
-
-function_3 is "Activation of gene"
-
-function function_2(V, substrate, Km)
-  V*substrate/(Km + substrate);
-end
-
-function_2 is "Michaelis-Menten(irreversible)"
-
-function function_1(k, mRNA)
-  k*mRNA;
-end
-
-function_1 is "mRNA translated into protein"
-
-function function_0(vsb, K, m, Bn)
-  vsb*K^m/(K^m + Bn^m);
-end
-
-function_0 is "Inhibition of gene"
-
-function functionDefinition_0000005(length, time_ref)
-  ceil(sin(pi*time_ref/ length + 0.001)/2);
-end
-
-functionDefinition_0000005 is "ceiling"
-
-
-model *Model_1()
-
-  // Compartments and Species:
-  compartment cell;
-  species species_0 in cell, species_1 in cell, species_2 in cell, species_3 in cell;
-  species species_4 in cell, species_5 in cell, species_6 in cell, species_7 in cell;
-  species species_8 in cell, species_9 in cell, species_10 in cell, species_11 in cell;
-  species species_12 in cell, species_13 in cell, species_14 in cell, species_15 in cell;
-
-  // Assignment Rules:
-  parameter_0000081 := functionDefinition_0000005(12, time);
-  parameter_0000082 := 1.5 + (1.8 - 1.5)*parameter_0000081;
-
-  // Reactions:
-  reaction_0:  => species_0; cell*function_0(reaction_0_vsb, reaction_0_K, reaction_0_m, species_3);
-  reaction_1:  => species_1; cell*function_1(reaction_1_k, species_0);
-  reaction_2: species_0 => ; cell*reaction_2_k1*species_0;
-  reaction_3: species_1 => species_2; cell*function_2(reaction_3_V, species_1, reaction_3_Km);
-  reaction_4: species_1 -> species_3; cell*(reaction_4_k1*species_1 - reaction_4_k2*species_3);
-  reaction_5:  => species_4; cell*function_1(reaction_5_k, species_5);
-  reaction_6: species_5 => ; cell*reaction_6_k1*species_5;
-  reaction_7: species_4 => species_6; cell*function_2(reaction_7_V, species_4, reaction_7_Km);
-  reaction_8: species_6 => ; cell*function_2(reaction_8_V, species_6, reaction_8_Km);
-  reaction_9:  => species_7; cell*function_3(parameter_0000082, species_3, reaction_9_n, reaction_9_K);
-  reaction_10:  => species_8; cell*function_1(reaction_10_k, species_7);
-  reaction_11: species_9 => ; cell*function_2(reaction_11_V, species_9, reaction_11_Km);
-  reaction_12: species_8 => species_9; cell*function_2(reaction_12_V, species_8, reaction_12_Km);
-  reaction_13: species_4 + species_8 -> species_10; cell*(reaction_13_k1*species_4*species_8 - reaction_13_k2*species_10);
-  reaction_14: species_10 => species_11; cell*function_2(reaction_14_V, species_10, reaction_14_Km);
-  reaction_15: species_11 => ; cell*function_2(reaction_15_V, species_11, reaction_15_Km);
-  reaction_16: species_10 -> species_12; cell*(reaction_16_k1*species_10 - reaction_16_k2*species_12);
-  reaction_17: species_14 => ; cell*reaction_17_k1*species_14;
-  reaction_18: species_2 => ; cell*reaction_18_k1*species_2;
-  reaction_19: species_13 => ; cell*reaction_19_k1*species_13;
-  reaction_20:  => species_5; cell*function_3(reaction_20_Vs, species_3, reaction_20_n, reaction_20_K);
-  reaction_21: species_12 => species_14; cell*function_2(reaction_21_V, species_12, reaction_21_Km);
-  reaction_22: species_7 => ; cell*reaction_22_k1*species_7;
-  reaction_23: species_12 + species_3 -> species_15; cell*(reaction_23_k1*species_12*species_3 - reaction_23_k2*species_15);
-  reaction_24: species_0 => ; cell*function_2(reaction_24_V, species_0, reaction_24_Km);
-  reaction_25: species_5 => ; cell*function_2(reaction_25_V, species_5, reaction_25_Km);
-  reaction_26: species_7 => ; cell*function_2(reaction_26_V, species_7, reaction_26_Km);
-  reaction_27: species_8 => ; cell*reaction_27_k1*species_8;
-  reaction_28: species_4 => ; cell*reaction_28_k1*species_4;
-  reaction_29: species_9 => ; cell*reaction_29_k1*species_9;
-  reaction_30: species_6 => ; cell*reaction_30_k1*species_6;
-  reaction_31: species_11 => ; cell*reaction_31_k1*species_11;
-  reaction_32: species_10 => ; cell*reaction_32_k1*species_10;
-  reaction_33: species_14 => ; cell*function_2(reaction_33_V, species_14, reaction_33_Km);
-  reaction_34: species_1 => ; cell*reaction_34_k1*species_1;
-  reaction_35: species_2 => ; cell*function_2(reaction_35_V, species_2, reaction_35_Km);
-  reaction_36: species_3 => species_13; cell*function_2(reaction_36_V, species_3, reaction_36_Km);
-  reaction_37: species_13 => ; cell*function_2(reaction_37_V, species_13, reaction_37_Km);
-  reaction_38: species_15 => ; cell*reaction_38_k1*species_15;
-  reaction_39: species_15 => ; cell*function_2(reaction_39_V, species_15, reaction_39_Km);
-  reaction_40: species_3 => ; cell*reaction_40_k1*species_3;
-  reaction_41: species_2 => species_1; cell*function_2(reaction_41_V, species_2, reaction_41_Km);
-  reaction_42: species_13 => species_3; cell*function_2(reaction_42_V, species_13, reaction_42_Km);
-  reaction_43: species_6 => species_4; cell*function_2(reaction_43_V, species_6, reaction_43_Km);
-  reaction_44: species_9 => species_8; cell*function_2(reaction_44_V, species_9, reaction_44_Km);
-  reaction_45: species_14 => species_12; cell*function_2(reaction_45_V, species_14, reaction_45_Km);
-  reaction_46: species_12 => ; cell*reaction_46_k1*species_12;
-  reaction_47: species_11 => species_10; cell*function_2(reaction_47_V, species_11, reaction_47_Km);
-
-  // Species initializations:
-  species_0 = 9.5;
-  species_1 = 2;
-  species_2 = 0;
-  species_3 = 1.9;
-  species_4 = 0;
-  species_5 = 1.7;
-  species_6 = 0;
-  species_7 = 2.5;
-  species_8 = 0;
-  species_9 = 0;
-  species_10 = 0;
-  species_11 = 0;
-  species_12 = 1;
-  species_13 = 0;
-  species_14 = 0;
-  species_15 = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  reaction_0_vsb = 1;
-  reaction_0_K = 2.2;
-  reaction_0_m = 2;
-  reaction_1_k = 0.12;
-  reaction_2_k1 = 0.01;
-  reaction_3_V = 0.5;
-  reaction_3_Km = 0.1;
-  reaction_4_k1 = 0.4;
-  reaction_4_k2 = 0.2;
-  reaction_5_k = 1.6;
-  reaction_6_k1 = 0.01;
-  reaction_7_V = 0.6;
-  reaction_7_Km = 0.1;
-  reaction_8_V = 0.7;
-  reaction_8_Km = 0.3;
-  reaction_9_n = 4;
-  reaction_9_K = 0.7;
-  reaction_10_k = 0.6;
-  reaction_11_V = 0.7;
-  reaction_11_Km = 0.3;
-  reaction_12_V = 0.4;
-  reaction_12_Km = 0.1;
-  reaction_13_k1 = 0.4;
-  reaction_13_k2 = 0.2;
-  reaction_14_V = 0.4;
-  reaction_14_Km = 0.1;
-  reaction_15_V = 0.7;
-  reaction_15_Km = 0.3;
-  reaction_16_k1 = 0.4;
-  reaction_16_k2 = 0.2;
-  reaction_17_k1 = 0.01;
-  reaction_18_k1 = 0.01;
-  reaction_19_k1 = 0.01;
-  reaction_20_Vs = 1.1;
-  reaction_20_n = 4;
-  reaction_20_K = 0.6;
-  reaction_21_V = 0.4;
-  reaction_21_Km = 0.1;
-  reaction_22_k1 = 0.01;
-  reaction_23_k1 = 0.5;
-  reaction_23_k2 = 0.1;
-  reaction_24_V = 0.8;
-  reaction_24_Km = 0.4;
-  reaction_25_V = 1;
-  reaction_25_Km = 0.4;
-  reaction_26_V = 1.1;
-  reaction_26_Km = 0.31;
-  reaction_27_k1 = 0.01;
-  reaction_28_k1 = 0.12;
-  reaction_29_k1 = 0.01;
-  reaction_30_k1 = 0.01;
-  reaction_31_k1 = 0.01;
-  reaction_32_k1 = 0.01;
-  reaction_33_V = 0.7;
-  reaction_33_Km = 0.3;
-  reaction_34_k1 = 0.01;
-  reaction_35_V = 0.5;
-  reaction_35_Km = 0.3;
-  reaction_36_V = 0.5;
-  reaction_36_Km = 0.1;
-  reaction_37_V = 0.6;
-  reaction_37_Km = 0.3;
-  reaction_38_k1 = 0.01;
-  reaction_39_V = 0.8;
-  reaction_39_Km = 0.3;
-  reaction_40_k1 = 0.01;
-  reaction_41_V = 0.1;
-  reaction_41_Km = 0.1;
-  reaction_42_V = 0.2;
-  reaction_42_Km = 0.1;
-  reaction_43_V = 0.1;
-  reaction_43_Km = 0.1;
-  reaction_44_V = 0.3;
-  reaction_44_Km = 0.1;
-  reaction_45_V = 0.1;
-  reaction_45_Km = 0.1;
-  reaction_46_k1 = 0.01;
-  reaction_47_V = 0.1;
-  reaction_47_Km = 0.1;
-
-  // Other declarations:
-  var parameter_0000081, parameter_0000082;
-  const cell;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  species_0 is "Mb";
-  species_1 is "Bc";
-  species_2 is "Bcp";
-  species_3 is "Bn";
-  species_4 is "Cc";
-  species_5 is "Mc";
-  species_6 is "Ccp";
-  species_7 is "Mp";
-  species_8 is "Pc";
-  species_9 is "Pcp";
-  species_10 is "PCc";
-  species_11 is "PCcp";
-  species_12 is "PCn";
-  species_13 is "Bnp";
-  species_14 is "PCnp";
-  species_15 is "In";
-  parameter_0000081 is "LD";
-  parameter_0000082 is "vsp";
-  reaction_0 is "Mb synthesized";
-  reaction_1 is "Mb translated into protein";
-  reaction_2 is "Mb nonspecific degradation";
-  reaction_3 is "Bc phosphorylation";
-  reaction_4 is "Bc transfered from cytosolic to nuclear";
-  reaction_5 is "Mc translated into protein";
-  reaction_6 is "Mc nonspecific degradation";
-  reaction_7 is "Cc phosphorylation";
-  reaction_8 is "Ccp specific degradation";
-  reaction_9 is "Mp synthesis";
-  reaction_10 is "Mp translated into protein";
-  reaction_11 is "Pcp specific degradation";
-  reaction_12 is "Pc phosphorylation";
-  reaction_13 is "Cc and Pc produce complex Per_Cry";
-  reaction_14 is "PCc phosphorylation";
-  reaction_15 is "PCcp specific degradation";
-  reaction_16 is "PCc transfered into nuclear";
-  reaction_17 is "PCnp nonspecific degradation";
-  reaction_18 is "Bcp nonspecific degradation";
-  reaction_19 is "Bnp nonspecific degradation";
-  reaction_20 is "Mc synthesis";
-  reaction_21 is "PCn phosphorylation";
-  reaction_22 is "Mp nonspecific degradation";
-  reaction_23 is "Per_Cry and Clock_Bmal form inactive complex";
-  reaction_24 is "Mb specific degradation";
-  reaction_25 is "Mc specific degradation";
-  reaction_26 is "Mp specific degradation";
-  reaction_27 is "Pc nonspecific degradation";
-  reaction_28 is "Cc nonspecific degradation";
-  reaction_29 is "Pcp nonspecific degradation";
-  reaction_30 is "Ccp nonspecific degradation";
-  reaction_31 is "PCcp nonspecific degradation";
-  reaction_32 is "PCc nonspecific degradation";
-  reaction_33 is "PCnp specific degradation";
-  reaction_34 is "Bc nonspecific degradation";
-  reaction_35 is "Bcp specific degradation";
-  reaction_36 is "Bn phosphorylation";
-  reaction_37 is "Bnp specific degradation";
-  reaction_38 is "In nonspecific degration";
-  reaction_39 is "In specific degradation";
-  reaction_40 is "Bn nonspecific degradation";
-  reaction_41 is "Bcp dephosphorylation";
-  reaction_42 is "Bnp dephosphorylation";
-  reaction_43 is "Ccp dephosphorylation";
-  reaction_44 is "Pcp dephosphorylation";
-  reaction_45 is "PCnp dephosphorylation";
-  reaction_46 is "PCn nonspecific degradation";
-  reaction_47 is "PCcp dephosphorylation";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/obo.go/GO:0005623"
-  species_0 hypernym "http://identifiers.org/obo.chebi/CHEBI:33699"
-  species_1 version "http://identifiers.org/uniprot/O00327"
-  species_2 version "http://identifiers.org/uniprot/O00327"
-  species_3 version "http://identifiers.org/uniprot/O00327"
-  species_4 version "http://identifiers.org/uniprot/Q8IV71",
-                    "http://identifiers.org/uniprot/Q16526"
-  species_5 parthood "http://identifiers.org/obo.chebi/CHEBI:33699"
-  species_6 version "http://identifiers.org/uniprot/Q8IV71",
-                    "http://identifiers.org/uniprot/Q16526"
-  species_7 hypernym "http://identifiers.org/obo.chebi/CHEBI:33699"
-  species_8 version "http://identifiers.org/uniprot/P56645",
-                    "http://identifiers.org/uniprot/O15055",
-                    "http://identifiers.org/uniprot/O15534"
-  species_9 version "http://identifiers.org/uniprot/P56645",
-                    "http://identifiers.org/uniprot/O15055",
-                    "http://identifiers.org/uniprot/O15534"
-  species_10 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_10 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_10 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_11 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_11 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_12 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_12 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_12 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  species_13 hypernym "http://identifiers.org/uniprot/O00327"
-  species_14 part "http://identifiers.org/uniprot/P56645",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_14 part "http://identifiers.org/uniprot/O15055",
-                  "http://identifiers.org/uniprot/Q8IV71"
-  species_14 part "http://identifiers.org/uniprot/O15534",
-                  "http://identifiers.org/uniprot/Q16526"
-  reaction_0 hypernym "http://identifiers.org/obo.go/GO:0045892"
-  reaction_1 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  reaction_2 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_3 hypernym "http://identifiers.org/obo.go/GO:0006468"
-  reaction_4 hypernym "http://identifiers.org/obo.go/GO:0000060"
-  reaction_5 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  reaction_6 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_7 hypernym "http://identifiers.org/obo.go/GO:0006468"
-  reaction_8 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_9 identity "http://identifiers.org/obo.go/GO:0045893"
-  reaction_10 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  reaction_11 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_12 hypernym "http://identifiers.org/obo.go/GO:0006468"
-  reaction_13 hypernym "http://identifiers.org/obo.go/GO:0043623"
-  reaction_14 hypernym "http://identifiers.org/obo.go/GO:0006468"
-  reaction_15 parthood "http://identifiers.org/obo.go/GO:0008233"
-  reaction_16 hypernym "http://identifiers.org/obo.go/GO:0000060"
-  reaction_17 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_18 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_19 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_20 hypernym "http://identifiers.org/obo.go/GO:0045893"
-  reaction_21 hypernym "http://identifiers.org/obo.go/GO:0006468"
-  reaction_22 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_23 hypernym "http://identifiers.org/obo.go/GO:0043623"
-  reaction_24 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_25 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_26 parthood "http://identifiers.org/obo.go/GO:0008233"
-  reaction_27 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_28 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_29 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_30 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_31 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_32 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_33 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_34 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_35 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_36 hypernym "http://identifiers.org/obo.go/GO:0006468"
-  reaction_37 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_38 hypernym "http://identifiers.org/obo.go/GO:0051261"
-  reaction_39 hypernym "http://identifiers.org/obo.go/GO:0008233"
-  reaction_40 parthood "http://identifiers.org/obo.go/GO:0051261"
-  reaction_41 hypernym "http://identifiers.org/obo.go/GO:0006470"
-  reaction_42 hypernym "http://identifiers.org/obo.go/GO:0006470"
-  reaction_43 hypernym "http://identifiers.org/obo.go/GO:0006470"
-  reaction_44 hypernym "http://identifiers.org/obo.go/GO:0006470"
-  reaction_45 hypernym "http://identifiers.org/obo.go/GO:0006470"
-  reaction_46 version "http://identifiers.org/obo.go/GO:0051261"
-  reaction_47 hypernym "http://identifiers.org/obo.go/GO:0006470",
-                       "http://identifiers.org/obo.go/GO:0016311"
-end
-
-Model_1 is "Leloup2003_CircClock_LD"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL4108701438"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000078"
-Model_1 description "http://identifiers.org/pubmed/12775757"
-Model_1 origin "http://identifiers.org/biomodels.db/BIOMD0000000021"
-Model_1 taxon "http://identifiers.org/taxonomy/40674"
-Model_1 hypernym "http://identifiers.org/obo.go/GO:0009649"
-Model_1 version "http://identifiers.org/kegg.pathway/hsa04710"
diff --git a/BioModelsRAG/data/BIOMD0000000079.txt b/BioModelsRAG/data/BIOMD0000000079.txt
deleted file mode 100644
index ca5b2d9e2e57dec1e1fa2cf02f6481e2f63a4ade..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000079.txt
+++ /dev/null
@@ -1,91 +0,0 @@
-// Created by libAntimony v2.13.0
-function function_4(P, V3, R, k3)
-  P*V3*(1 - R)/(k3 + (1 - R));
-end
-
-function function_3(V2, R, Q, K2)
-  V2*R*Q/(K2 + Q);
-end
-
-function function_2(V1, Q, K1)
-  V1*(1 - Q)/(K1 + (1 - Q));
-end
-
-function function_1(V, substrate, Km)
-  V*substrate/(Km + substrate);
-end
-
-function function_0(a, Q)
-  a*Q;
-end
-
-
-model *Model_0()
-
-  // Compartments and Species:
-  compartment body;
-  substanceOnly species P in body, Q in body, R in body;
-
-  // Reactions:
-  reaction_0:  => P; body*function_0(reaction_0_a, Q);
-  reaction_1: P => ; function_1(reaction_1_V, P, reaction_1_Km);
-  reaction_2:  => Q; function_2(reaction_2_V1, Q, reaction_2_K1);
-  reaction_3: Q => ; function_3(reaction_3_V2, R, Q, reaction_3_K2);
-  reaction_4:  => R; function_4(P, reaction_4_V3, R, reaction_4_k3);
-  reaction_5: R => ; function_1(reaction_5_V, R, reaction_5_Km);
-
-  // Species initializations:
-  P = 0.43;
-  Q = 0.8;
-  R = 0.55;
-
-  // Compartment initializations:
-  body = 1;
-
-  // Variable initializations:
-  reaction_0_a = 0.1;
-  reaction_1_V = 0.1;
-  reaction_1_Km = 0.2;
-  reaction_2_V1 = 1;
-  reaction_2_K1 = 0.01;
-  reaction_3_V2 = 1.5;
-  reaction_3_K2 = 0.01;
-  reaction_4_V3 = 6;
-  reaction_4_k3 = 0.01;
-  reaction_5_V = 2.5;
-  reaction_5_Km = 0.01;
-
-  // Other declarations:
-  const body;
-
-  // Unit definitions:
-  unit time_unit = 604800 second;
-  unit substance = dimensionless;
-
-  // Display Names:
-  time_unit is "weeks";
-  substance is "dimensionless";
-  reaction_0 is "Increase of  P";
-  reaction_1 is "Decrease of P";
-  reaction_2 is "Increase of Q";
-  reaction_3 is "Decrease of Q";
-  reaction_4 is "Increase of R";
-  reaction_5 is "Decrease of R";
-
-  // CV terms:
-  reaction_0 hypernym "http://identifiers.org/go/GO:0040018",
-                      "http://identifiers.org/go/GO:0035264"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0040015"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0007631"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0002023"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0048520"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0048521"
-end
-
-Model_0 is "Goldbeter2006_weightCycling"
-
-Model_0 model_entity_is "http://identifiers.org/biomodels.db/MODEL4644593552"
-Model_0 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000079"
-Model_0 description "http://identifiers.org/pubmed/16595882"
-Model_0 taxon "http://identifiers.org/taxonomy/9606"
-Model_0 hypernym "http://identifiers.org/go/GO:0040014"
diff --git a/BioModelsRAG/data/BIOMD0000000080.txt b/BioModelsRAG/data/BIOMD0000000080.txt
deleted file mode 100644
index 13e775ef0953016700a1caaa339dca9055cf9da9..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000080.txt
+++ /dev/null
@@ -1,123 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Model_1()
-
-  // Compartments and Species:
-  compartment cell;
-  species D in cell, DR in cell, DRG_GDP in cell, G_GDP in cell, DRG in cell;
-  species GDP in cell, DRG_GTP in cell, GTP in cell, G_GTP in cell, R in cell;
-
-  // Reactions:
-  Reaction_1: D + R -> DR; cell*(Reaction_1_k1*D*R - Reaction_1_k7*DR);
-  Reaction_2: DR + G_GDP -> DRG_GDP; cell*(Reaction_2_k2*DR*G_GDP - Reaction_2_k8*DRG_GDP);
-  Reaction_3: DRG_GDP -> GDP + DRG; cell*(Reaction_3_k3*DRG_GDP - Reaction_3_k9*GDP*DRG);
-  Reaction_4: DRG + GTP -> DRG_GTP; cell*(Reaction_4_k4*DRG*GTP - Reaction_4_k10*DRG_GTP);
-  Reaction_5: DRG_GTP => G_GTP + DR; cell*Reaction_5_k5*DRG_GTP;
-  Reaction_6: G_GTP => G_GDP; cell*Reaction_6_k6*G_GTP;
-
-  // Species initializations:
-  D = 3.1e-05;
-  DR = 0;
-  DRG_GDP = 0;
-  G_GDP = 1e-06;
-  DRG = 0;
-  GDP = 0;
-  DRG_GTP = 0;
-  GTP = 1e-05;
-  G_GTP = 0;
-  R = 1e-10;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  Reaction_1_k1 = 5000000;
-  Reaction_1_k7 = 10;
-  Reaction_2_k2 = 100000000;
-  Reaction_2_k8 = 0.1;
-  Reaction_3_k3 = 5;
-  Reaction_3_k9 = 100000;
-  Reaction_4_k4 = 5000000;
-  Reaction_4_k10 = 55;
-  Reaction_5_k5 = 1;
-  Reaction_6_k6 = 2;
-
-  // Other declarations:
-  const cell;
-
-  // Display Names:
-  Reaction_1 is "Forming DR";
-  Reaction_2 is "DR Binding with G_GDP produce DRG_GDP";
-  Reaction_3 is "GDP Releasing";
-  Reaction_4 is "GTP binding with DRG";
-  Reaction_5 is "G protein activation";
-  Reaction_6 is "Hydrolysis of GTP to GDP";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005623"
-  D identity "http://identifiers.org/chebi/CHEBI:35569"
-  DR part "http://identifiers.org/chebi/CHEBI:35569",
-          "http://identifiers.org/uniprot/P08913"
-  DR part "http://identifiers.org/chebi/CHEBI:35569",
-          "http://identifiers.org/uniprot/P18089"
-  DR part "http://identifiers.org/chebi/CHEBI:35569",
-          "http://identifiers.org/uniprot/P18825"
-  DRG_GDP part "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/uniprot/P08913",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GDP part "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/uniprot/P18089",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GDP part "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/uniprot/P18825",
-               "http://identifiers.org/go/GO:0005834"
-  G_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-             "http://identifiers.org/go/GO:0005834"
-  DRG part "http://identifiers.org/chebi/CHEBI:35569",
-           "http://identifiers.org/uniprot/P08913",
-           "http://identifiers.org/go/GO:0005834"
-  DRG part "http://identifiers.org/chebi/CHEBI:35569",
-           "http://identifiers.org/uniprot/P18089",
-           "http://identifiers.org/go/GO:0005834"
-  DRG part "http://identifiers.org/chebi/CHEBI:35569",
-           "http://identifiers.org/uniprot/P18825",
-           "http://identifiers.org/go/GO:0005834"
-  GDP identity "http://identifiers.org/chebi/CHEBI:17552"
-  DRG_GTP part "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/uniprot/P08913",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GTP part "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/uniprot/P18089",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GTP part "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/uniprot/P18825",
-               "http://identifiers.org/go/GO:0005834"
-  GTP identity "http://identifiers.org/chebi/CHEBI:15996"
-  G_GTP part "http://identifiers.org/chebi/CHEBI:15996",
-             "http://identifiers.org/go/GO:0005834"
-  R version "http://identifiers.org/uniprot/P08913",
-            "http://identifiers.org/uniprot/P18089",
-            "http://identifiers.org/uniprot/P18825"
-  Reaction_1 hypernym "http://identifiers.org/go/GO:0031690"
-  Reaction_2 hypernym "http://identifiers.org/go/GO:0001664"
-  Reaction_3 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction_4 hypernym "http://identifiers.org/go/GO:0005525",
-                      "http://identifiers.org/go/GO:0032403"
-  Reaction_5 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction_6 hypernym "http://identifiers.org/go/GO:0003924"
-end
-
-Model_1 is "Thomsen1989_AdenylateCyclase"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL1173806337"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000080"
-Model_1 description "http://identifiers.org/pubmed/2574993"
-Model_1 origin "http://identifiers.org/biomodels.db/BIOMD0000000082"
-Model_1 hypernym "http://identifiers.org/go/GO:0031684",
-                 "http://identifiers.org/go/GO:0007194"
-Model_1 taxon "http://identifiers.org/taxonomy/9606"
diff --git a/BioModelsRAG/data/BIOMD0000000081.txt b/BioModelsRAG/data/BIOMD0000000081.txt
deleted file mode 100644
index fa07279649acb166698857fe720ea1814f5a4d5e..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000081.txt
+++ /dev/null
@@ -1,373 +0,0 @@
-// Created by libAntimony v2.13.0
-function Function_for_PIP2_5Pase(MgSat20, PIP2_M, kPIP2Pase)
-  MgSat20*kPIP2Pase*PIP2_M;
-end
-
-Function_for_PIP2_5Pase is "Function for PIP2_5Pase"
-
-function Function_for_MgonGDPAIF4(GGDPAlF4_M, M, Mg2_C, kMgonAlF4)
-  kMgonAlF4*GGDPAlF4_M*Mg2_C*M;
-end
-
-Function_for_MgonGDPAIF4 is "Function for MgonGDPAIF4"
-
-function Function_for_MgGTPon(GGTP_M, M, Mg2_C, kMg2onGTP)
-  kMg2onGTP*GGTP_M*Mg2_C*M;
-end
-
-Function_for_MgGTPon is "Function for MgGTPon"
-
-function Function_for_PI4Kinase(ATPSat1000, M, MgSat20, PI_M, kPI4Kinase)
-  (0.2 + 0.8*MgSat20)*kPI4Kinase*PI_M*ATPSat1000*M;
-end
-
-Function_for_PI4Kinase is "Function for PI4Kinase"
-
-function Function_for_PIP2binding(KCNQsites_M, PIP2_M, PIP2xKCNQ_M, kPIP2off, kPIP2on)
-  kPIP2on*KCNQsites_M*PIP2_M + -(kPIP2off*PIP2xKCNQ_M);
-end
-
-Function_for_PIP2binding is "Function for PIP2binding"
-
-function Function_for_IP3Phosphatase(NA_micro, ip3_C, kIP3ase)
-  ip3_C*kIP3ase*NA_micro;
-end
-
-Function_for_IP3Phosphatase is "Function for IP3Phosphatase"
-
-function Function_for_PLC(M, PIP2_M, PLCspont, fGactive, kPLC)
-  kPLC*(fGactive + PLCspont)*PIP2_M*M;
-end
-
-Function_for_PLC is "Function for PLC"
-
-function Function_for_AIF4on(AlF4_C, GGDPAlF4_M, GGDP_M, M, kAlF4off, kAlF4on)
-  (kAlF4on*AlF4_C*GGDP_M + -(kAlF4off*GGDPAlF4_M))*M;
-end
-
-Function_for_AIF4on is "Function for AIF4on"
-
-function Function_for_GGTPase(GGTPMg_M, MgSat10, kGGTPase)
-  kGGTPase*MgSat10*GGTPMg_M;
-end
-
-Function_for_GGTPase is "Function for GGTPase"
-
-function Function_for_PIP5kinase(ATPSat300, MgSat20, PIP_M, kPIP5Kinase)
-  (0.2 + 0.8*MgSat20)*kPIP5Kinase*PIP_M*ATPSat300;
-end
-
-Function_for_PIP5kinase is "Function for PIP5kinase"
-
-function Function_for_GDPdissoc(GDP_C, GGDP_M, G_M, M, OxoSat, TonicAct, kGDPoff, kGDPon)
-  (kGDPoff*GGDP_M*(OxoSat + TonicAct) + -(kGDPon*GDP_C*G_M))*M;
-end
-
-Function_for_GDPdissoc is "Function for GDPdissoc"
-
-function Function_for_GTPon(GGTP_M, GTP_C, G_M, M, kGTPoff, kGTPon)
-  (kGTPon*G_M*GTP_C + -(kGTPoff*GGTP_M))*M;
-end
-
-Function_for_GTPon is "Function for GTPon"
-
-function Function_for_GTPgSon(GGTPgS_M, GTPgS_C, G_M, M, kGTPgSoff, kGTPgSon)
-  (kGTPgSon*G_M*GTPgS_C + -(kGTPgSoff*GGTPgS_M))*M;
-end
-
-Function_for_GTPgSon is "Function for GTPgSon"
-
-function Function_for_GDPbSon(GDPbS_C, GGDPbS_M, G_M, M, OxoSat, kGDPbSon, kGGDPbSoff)
-  (kGDPbSon*G_M*GDPbS_C + -(kGGDPbSoff*(1 + 20*OxoSat)*GGDPbS_M))*M;
-end
-
-Function_for_GDPbSon is "Function for GDPbSon"
-
-function Function_for_MgonGGTPgS(GGTPgS_M, M, Mg2_C, kMg2onGTPgS)
-  kMg2onGTPgS*GGTPgS_M*Mg2_C*M;
-end
-
-Function_for_MgonGGTPgS is "Function for MgonGGTPgS"
-
-
-model *Suh2004_KCNQ_regulation()
-
-  // Compartments and Species:
-  compartment EX, M, Cytoplasm;
-  species GTPgS_C in Cytoplasm, KCNQsites_M in M, PIP2_M in M, GGDPbS_M in M;
-  species $Mg2_C in Cytoplasm, ATP_C in Cytoplasm, oxoM_EX in EX, GDPbS_C in Cytoplasm;
-  species GGTPMg_M in M, GDP_C in Cytoplasm, $GTP_C in Cytoplasm, GGDPAlF4Mg_M in M;
-  species ip3_C in Cytoplasm, AlF4_C in Cytoplasm, G_M in M, GGTP_M in M;
-  species GGDPAlF4_M in M, GGTPgS_M in M, PI_M in M, PIP_M in M, PIP2xKCNQ_M in M;
-  species GGTPgSMg_M in M, GGDP_M in M;
-
-  // Assignment Rules:
-  GTP_C := 100 - 50*exp(-(0.00833333333333333*(290 + time)));
-  MgSat20 := 1*(1/(1 + 20*(1/Mg2_C)));
-  ATPSat300 := 1*(1/(1 + 300*(1/(0.5 + ATP_C))));
-  MgSat10 := 0.2 + 0.8*1*(1/(1 + KMgGTPase*(1/Mg2_C)));
-  OxoSat := 1*(1/(1 + Koxom*(1/(1e-5 + oxoM_EX))));
-  Gactive := GGTPMg_M + GGTPgSMg_M + GGDPAlF4Mg_M;
-  ATPSat1000 := 1*(1/(1 + 1000*(1/(0.5 + ATP_C))));
-  I_KCNQ := 1.33*(0.025*PIP2xKCNQ_M)^nHill;
-  fGactive := (GGTPMg_M + GGTPgSMg_M + GGDPAlF4Mg_M)/200;
-
-  // Reactions:
-  PIP5kinase: 0.0009967 ATP_C + PIP_M -> PIP2_M; Function_for_PIP5kinase(ATPSat300, MgSat20, PIP_M, PIP5kinase_kPIP5Kinase);
-  IP3Phosphatase: 1.66611e-18 ip3_C -> ; Cytoplasm*Function_for_IP3Phosphatase(NA_micro, ip3_C, IP3Phosphatase_kIP3ase);
-  PIP2binding: KCNQsites_M + PIP2_M -> PIP2xKCNQ_M; M*Function_for_PIP2binding(KCNQsites_M, PIP2_M, PIP2xKCNQ_M, PIP2binding_kPIP2off, PIP2binding_kPIP2on);
-  MgonGGTPgS: GGTPgS_M -> GGTPgSMg_M; Function_for_MgonGGTPgS(GGTPgS_M, M, Mg2_C, MgonGGTPgS_kMg2onGTPgS);
-  GGTPase: GGTPMg_M -> GGDP_M; M*Function_for_GGTPase(GGTPMg_M, MgSat10, GGTPase_kGGTPase);
-  GTPon: G_M -> GGTP_M; Function_for_GTPon(GGTP_M, GTP_C, G_M, M, GTPon_kGTPoff, GTPon_kGTPon);
-  GTPgSon: 0.0009967 GTPgS_C + G_M -> GGTPgS_M; Function_for_GTPgSon(GGTPgS_M, GTPgS_C, G_M, M, GTPgSon_kGTPgSoff, GTPgSon_kGTPgSon);
-  GDPbSon: G_M + 0.0009967 GDPbS_C -> GGDPbS_M; Function_for_GDPbSon(GDPbS_C, GGDPbS_M, G_M, M, OxoSat, GDPbSon_kGDPbSon, GDPbSon_kGGDPbSoff);
-  MgGTPon: GGTP_M -> GGTPMg_M; Function_for_MgGTPon(GGTP_M, M, Mg2_C, MgGTPon_kMg2onGTP);
-  GDPdissoc: GGDP_M -> 0.0009967 GDP_C + G_M; Function_for_GDPdissoc(GDP_C, GGDP_M, G_M, M, OxoSat, GDPdissoc_TonicAct, GDPdissoc_kGDPoff, GDPdissoc_kGDPon);
-  PIP2_5Pase: PIP2_M -> PIP_M; M*Function_for_PIP2_5Pase(MgSat20, PIP2_M, PIP2_5Pase_kPIP2Pase);
-  PLC: PIP2_M -> 0.0009967 ip3_C; Function_for_PLC(M, PIP2_M, PLC_PLCspont, fGactive, PLC_kPLC);
-  AlF4on: 0.0009967 AlF4_C + GGDP_M -> GGDPAlF4_M; Function_for_AIF4on(AlF4_C, GGDPAlF4_M, GGDP_M, M, AlF4on_kAlF4off, AlF4on_kAlF4on);
-  PI4Kinase: 0.0009967 ATP_C + PI_M -> PIP_M; Function_for_PI4Kinase(ATPSat1000, M, MgSat20, PI_M, PI4Kinase_kPI4Kinase);
-  MgonGDPAlF4: GGDPAlF4_M -> GGDPAlF4Mg_M; Function_for_MgonGDPAIF4(GGDPAlF4_M, M, Mg2_C, MgonGDPAlF4_kMgonAlF4);
-
-  // Events:
-  event_0000001_0: at 0 after time >= 3: oxoM_EX = 10;
-  event_0000002_0: at 0 after time >= 8: oxoM_EX = 0;
-
-  // Species initializations:
-  GTPgS_C = 0;
-  GTPgS_C has substance_per_volume;
-  KCNQsites_M = 6.7;
-  KCNQsites_M has substance_per_volume;
-  PIP2_M = 5000;
-  PIP2_M has substance_per_volume;
-  GGDPbS_M = 0;
-  GGDPbS_M has substance_per_volume;
-  Mg2_C = 2100;
-  Mg2_C has substance_per_volume;
-  ATP_C = 3000;
-  ATP_C has substance_per_volume;
-  oxoM_EX = 0;
-  oxoM_EX has substance_per_volume;
-  GDPbS_C = 0;
-  GDPbS_C has substance_per_volume;
-  GGTPMg_M = 0.1;
-  GGTPMg_M has substance_per_volume;
-  GDP_C = 0;
-  GDP_C has substance_per_volume;
-  GTP_C has substance_per_volume;
-  GGDPAlF4Mg_M = 0;
-  GGDPAlF4Mg_M has substance_per_volume;
-  ip3_C = 0.48;
-  ip3_C has substance_per_volume;
-  AlF4_C = 0;
-  AlF4_C has substance_per_volume;
-  G_M = 0.065;
-  G_M has substance_per_volume;
-  GGTP_M = 0.048;
-  GGTP_M has substance_per_volume;
-  GGDPAlF4_M = 0;
-  GGDPAlF4_M has substance_per_volume;
-  GGTPgS_M = 0;
-  GGTPgS_M has substance_per_volume;
-  PI_M = 200000;
-  PI_M has substance_per_volume;
-  PIP_M = 1150;
-  PIP_M has substance_per_volume;
-  PIP2xKCNQ_M = 33.3;
-  PIP2xKCNQ_M has substance_per_volume;
-  GGTPgSMg_M = 0;
-  GGTPgSMg_M has substance_per_volume;
-  GGDP_M = 200;
-  GGDP_M has substance_per_volume;
-
-  // Compartment initializations:
-  EX = 1;
-  EX has volume;
-  M = 1;
-  M has volume;
-  Cytoplasm = 1;
-  Cytoplasm has volume;
-  MgSat20 has unit_0;
-  ATPSat300 has unit_0;
-  MgSat10 has unit_0;
-
-  // Variable initializations:
-  KMgGTPase = 10;
-  KMgGTPase has unit_2;
-  OxoSat has unit_0;
-  Koxom = 8;
-  Koxom has unit_2;
-  Gactive has unit_1;
-  ATPSat1000 has unit_0;
-  I_KCNQ has unit_0;
-  nHill = 1.8;
-  nHill has unit_0;
-  fGactive has unit_0;
-  NA_micro = 6.022e+17;
-  NA_micro has unit_3;
-  PIP5kinase_kPIP5Kinase = 0.06;
-  IP3Phosphatase_kIP3ase = 0.3;
-  PIP2binding_kPIP2off = 0.25;
-  PIP2binding_kPIP2on = 0.00025;
-  MgonGGTPgS_kMg2onGTPgS = 0.002;
-  GGTPase_kGGTPase = 1.8;
-  GTPon_kGTPoff = 0.08;
-  GTPon_kGTPon = 0.45;
-  GTPgSon_kGTPgSoff = 0.005;
-  GTPgSon_kGTPgSon = 0.006;
-  GDPbSon_kGDPbSon = 0.28;
-  GDPbSon_kGGDPbSoff = 0.1;
-  MgGTPon_kMg2onGTP = 0.003;
-  GDPdissoc_TonicAct = 0.002;
-  GDPdissoc_kGDPoff = 0.5;
-  GDPdissoc_kGDPon = 0.003;
-  PIP2_5Pase_kPIP2Pase = 0.005;
-  PLC_PLCspont = 0.00075;
-  PLC_kPLC = 4.8;
-  AlF4on_kAlF4off = 0.005;
-  AlF4on_kAlF4on = 7e-06;
-  PI4Kinase_kPI4Kinase = 0.0001;
-  MgonGDPAlF4_kMgonAlF4 = 0.002;
-
-  // Other declarations:
-  var MgSat20, ATPSat300, MgSat10, OxoSat, Gactive, ATPSat1000, I_KCNQ, fGactive;
-  const EX, M, Cytoplasm, KMgGTPase, Koxom, nHill, NA_micro;
-
-  // Unit definitions:
-  unit length = metre;
-  unit area = (1e-6 metre)^2;
-  unit volume = litre;
-  unit time_unit = time_unit;
-  unit substance = item;
-  unit unit_0 = 1 / dimensionless^-0;
-  unit unit_1 = item / (1e6 metre)^2;
-  unit unit_2 = item * avogadro / ((1e-6 dimensionless)^-0 * litre);
-  unit unit_3 = 1 / 1e6 avogadro;
-  unit extent = substance;
-  unit substance_per_volume = item / litre;
-
-  // Display Names:
-  time_unit is "time";
-  unit_0 is "1";
-  unit_1 is "#/Mm²";
-  unit_2 is "µmol/l";
-  unit_3 is "1/MAvogadro";
-  EX is "Extracellular";
-  M is "Membrane";
-  GGDPAlF4Mg_M is "GGDPAIF4Mg_M";
-  ip3_C is "IP3_C";
-  AlF4_C is "AIF4_C";
-  GGDPAlF4_M is "GGDPAIF4_M";
-  event_0000001_0 is "event_0000001";
-  event_0000002_0 is "event_0000002";
-  NA_micro is "NA(micro)";
-  AlF4on is "AIF4on";
-  MgonGDPAlF4 is "MgonGDPAIF4";
-
-  // CV terms:
-  EX identity "http://identifiers.org/go/GO:0005576"
-  M identity "http://identifiers.org/go/GO:0005886"
-  Cytoplasm identity "http://identifiers.org/go/GO:0005737"
-  GTPgS_C identity "http://identifiers.org/kegg.compound/C01806"
-  GTPgS_C identity "http://identifiers.org/chebi/CHEBI:5235"
-  KCNQsites_M part "http://identifiers.org/uniprot/O88944"
-  KCNQsites_M part "http://identifiers.org/uniprot/O43526"
-  PIP2_M identity "http://identifiers.org/chebi/CHEBI:18348"
-  PIP2_M identity "http://identifiers.org/kegg.compound/C04637"
-  GGDPbS_M part "http://identifiers.org/chebi/CHEBI:38309"
-  GGDPbS_M part "http://identifiers.org/go/GO:0005834"
-  Mg2_C identity "http://identifiers.org/chebi/CHEBI:25107"
-  Mg2_C identity "http://identifiers.org/kegg.compound/C00305"
-  ATP_C identity "http://identifiers.org/kegg.compound/C00002"
-  ATP_C identity "http://identifiers.org/chebi/CHEBI:15422"
-  oxoM_EX identity "http://identifiers.org/chebi/CHEBI:38322"
-  GDPbS_C hypernym "http://identifiers.org/chebi/CHEBI:38309"
-  GGTPMg_M part "http://identifiers.org/kegg.compound/C00044"
-  GGTPMg_M part "http://identifiers.org/kegg.compound/C00305"
-  GGTPMg_M part "http://identifiers.org/go/GO:0005834"
-  GGTPMg_M part "http://identifiers.org/chebi/CHEBI:18420"
-  GGTPMg_M part "http://identifiers.org/chebi/CHEBI:15996"
-  GGTPMg_M part "http://identifiers.org/chebi/CHEBI:25107"
-  GDP_C identity "http://identifiers.org/kegg.compound/C00035"
-  GDP_C identity "http://identifiers.org/chebi/CHEBI:17552"
-  GTP_C identity "http://identifiers.org/chebi/CHEBI:15996"
-  GTP_C identity "http://identifiers.org/kegg.compound/C00044"
-  GGDPAlF4Mg_M part "http://identifiers.org/uniprot/P29992"
-  GGDPAlF4Mg_M part "http://identifiers.org/kegg.compound/C00305"
-  GGDPAlF4Mg_M part "http://identifiers.org/kegg.compound/C00035"
-  GGDPAlF4Mg_M part "http://identifiers.org/chebi/CHEBI:30111"
-  GGDPAlF4Mg_M part "http://identifiers.org/chebi/CHEBI:25107"
-  GGDPAlF4Mg_M part "http://identifiers.org/chebi/CHEBI:17552"
-  ip3_C identity "http://identifiers.org/chebi/CHEBI:16595"
-  ip3_C identity "http://identifiers.org/kegg.compound/C01245"
-  AlF4_C identity "http://identifiers.org/chebi/CHEBI:30111"
-  G_M identity "http://identifiers.org/go/GO:0005834"
-  GGTP_M part "http://identifiers.org/go/GO:0005834"
-  GGTP_M part "http://identifiers.org/chebi/CHEBI:15996"
-  GGTP_M part "http://identifiers.org/kegg.compound/C00044"
-  GGDPAlF4_M part "http://identifiers.org/kegg.compound/C00035"
-  GGDPAlF4_M part "http://identifiers.org/go/GO:0005834"
-  GGDPAlF4_M part "http://identifiers.org/chebi/CHEBI:17552"
-  GGDPAlF4_M part "http://identifiers.org/chebi/CHEBI:30111"
-  GGTPgS_M part "http://identifiers.org/go/GO:0005834"
-  GGTPgS_M part "http://identifiers.org/chebi/CHEBI:43000"
-  GGTPgS_M part "http://identifiers.org/chebi/CHEBI:5235"
-  GGTPgS_M part "http://identifiers.org/kegg.compound/C01806"
-  PI_M identity "http://identifiers.org/chebi/CHEBI:16749"
-  PI_M identity "http://identifiers.org/kegg.compound/C01194"
-  PIP_M identity "http://identifiers.org/chebi/CHEBI:17526"
-  PIP_M identity "http://identifiers.org/kegg.compound/C01277"
-  PIP2xKCNQ_M part "http://identifiers.org/uniprot/O88944"
-  PIP2xKCNQ_M part "http://identifiers.org/chebi/CHEBI:18348"
-  PIP2xKCNQ_M part "http://identifiers.org/kegg.compound/C04637"
-  PIP2xKCNQ_M part "http://identifiers.org/uniprot/O43526"
-  GGTPgSMg_M part "http://identifiers.org/kegg.compound/C00305"
-  GGTPgSMg_M part "http://identifiers.org/chebi/CHEBI:5235"
-  GGTPgSMg_M part "http://identifiers.org/chebi/CHEBI:25107"
-  GGTPgSMg_M part "http://identifiers.org/kegg.compound/C01806"
-  GGTPgSMg_M part "http://identifiers.org/go/GO:0005834"
-  GGTPgSMg_M part "http://identifiers.org/chebi/CHEBI:18420"
-  GGDP_M part "http://identifiers.org/go/GO:0005834"
-  GGDP_M part "http://identifiers.org/chebi/CHEBI:17552"
-  GGDP_M part "http://identifiers.org/kegg.compound/C00035"
-  PIP5kinase identity "http://identifiers.org/kegg.reaction/R03469"
-  PIP5kinase hypernym "http://identifiers.org/ec-code/2.7.1.68"
-  PIP5kinase hypernym "http://identifiers.org/go/GO:0016308"
-  IP3Phosphatase identity "http://identifiers.org/kegg.reaction/R03394"
-  IP3Phosphatase hypernym "http://identifiers.org/ec-code/3.1.3.56"
-  IP3Phosphatase hypernym "http://identifiers.org/go/GO:0004445"
-  PIP2binding hypernym "http://identifiers.org/go/GO:0005267"
-  PIP2binding hypernym "http://identifiers.org/go/GO:0005546"
-  MgonGGTPgS parthood "http://identifiers.org/go/GO:0031684"
-  GGTPase hypernym "http://identifiers.org/go/GO:0003924"
-  GTPon parthood "http://identifiers.org/go/GO:0031684"
-  GTPgSon parthood "http://identifiers.org/go/GO:0031684"
-  GDPbSon parthood "http://identifiers.org/go/GO:0031684"
-  MgGTPon parthood "http://identifiers.org/go/GO:0031684"
-  GDPdissoc parthood "http://identifiers.org/go/GO:0031684"
-  PIP2_5Pase identity "http://identifiers.org/kegg.reaction/R04404"
-  PIP2_5Pase hypernym "http://identifiers.org/ec-code/3.1.3.36"
-  PIP2_5Pase hypernym "http://identifiers.org/go/GO:0004439"
-  PLC identity "http://identifiers.org/kegg.reaction/R03435"
-  PLC hypernym "http://identifiers.org/ec-code/3.1.4.11"
-  PLC hypernym "http://identifiers.org/go/GO:0004435"
-  PLC hypernym "http://identifiers.org/go/GO:0007200"
-  AlF4on parthood "http://identifiers.org/go/GO:0031684"
-  PI4Kinase identity "http://identifiers.org/kegg.reaction/R03361"
-  PI4Kinase hypernym "http://identifiers.org/ec-code/2.7.1.67"
-  PI4Kinase hypernym "http://identifiers.org/go/GO:0004430"
-  MgonGDPAlF4 parthood "http://identifiers.org/go/GO:0031684"
-end
-
-Suh2004_KCNQ_regulation is "Suh2004_KCNQ_Regulation"
-
-Suh2004_KCNQ_regulation model_entity_is "http://identifiers.org/biomodels.db/MODEL4662889298",
-                                        "http://identifiers.org/biomodels.db/BIOMD0000000081"
-Suh2004_KCNQ_regulation part "http://identifiers.org/go/GO:0007207"
-Suh2004_KCNQ_regulation part "http://identifiers.org/go/GO:0006629"
-Suh2004_KCNQ_regulation identity "http://identifiers.org/biomodels.db/MODEL4662889298"
-Suh2004_KCNQ_regulation identity "http://identifiers.org/kegg.pathway/map04020"
-Suh2004_KCNQ_regulation identity "http://identifiers.org/biomodels.db/BIOMD0000000081"
-Suh2004_KCNQ_regulation identity "http://identifiers.org/kegg.pathway/map04070"
-Suh2004_KCNQ_regulation taxon "http://identifiers.org/taxonomy/9606"
-Suh2004_KCNQ_regulation description "http://identifiers.org/pubmed/15173220"
diff --git a/BioModelsRAG/data/BIOMD0000000082.txt b/BioModelsRAG/data/BIOMD0000000082.txt
deleted file mode 100644
index 78e3b5b7e521dc17e03724ae74b15c3c5d8866df..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000082.txt
+++ /dev/null
@@ -1,126 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Model_1()
-
-  // Compartments and Species:
-  compartment cell;
-  species agonist in cell, DR in cell, DRG_GDP in cell, DRG in cell, GDP in cell;
-  species DRG_GTP in cell, GTP in cell, Recptor in cell, G_GDP in cell, G_GTP in cell;
-
-  // Reactions:
-  Forming: agonist + Recptor -> DR; cell*(Forming_k1*agonist*Recptor - Forming_k7*DR);
-  reaction_1: DR + G_GDP -> DRG_GDP; cell*(reaction_1_k2*DR*G_GDP - reaction_1_k8*DRG_GDP);
-  reaction_2: DRG_GDP -> GDP + DRG; cell*(reaction_2_k3*DRG_GDP - reaction_2_k9*DRG*GDP);
-  reaction_3: DRG + GTP -> DRG_GTP; cell*(reaction_3_k4*DRG*GTP - reaction_3_k10*DRG_GTP);
-  reaction_4: DRG_GTP => G_GTP + DR; cell*reaction_4_k5*DRG_GTP;
-  reaction_5: G_GTP => G_GDP; cell*reaction_5_k6*G_GTP;
-
-  // Species initializations:
-  agonist = 1e-08;
-  DR = 0;
-  DRG_GDP = 0;
-  DRG = 0;
-  GDP = 0;
-  DRG_GTP = 0;
-  GTP = 1e-05;
-  Recptor = 1e-09;
-  G_GDP = 1e-09;
-  G_GTP = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  Forming_k1 = 5000000;
-  Forming_k7 = 0.5;
-  reaction_1_k2 = 100000000;
-  reaction_1_k8 = 0.1;
-  reaction_2_k3 = 0.1;
-  reaction_2_k9 = 100000;
-  reaction_3_k4 = 10000000;
-  reaction_3_k10 = 0.1;
-  reaction_4_k5 = 0.05;
-  reaction_5_k6 = 0.1;
-
-  // Other declarations:
-  const cell;
-
-  // Display Names:
-  agonist is "D";
-  Recptor is "R";
-  Forming is "Forming  DR";
-  reaction_1 is "DR binding with G_GDP produc DRG_GDP";
-  reaction_2 is "GDP releasing";
-  reaction_3 is "GTP binding with DRG";
-  reaction_4 is "DRG_GTP dissociates(G protein activation)";
-  reaction_5 is "G protein inactivated";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005623"
-  agonist hypernym "http://identifiers.org/chebi/CHEBI:35569"
-  DR part "http://identifiers.org/chebi/CHEBI:35569",
-          "http://identifiers.org/uniprot/P18825"
-  DR part "http://identifiers.org/chebi/CHEBI:35569",
-          "http://identifiers.org/uniprot/P08913"
-  DR part "http://identifiers.org/chebi/CHEBI:35569",
-          "http://identifiers.org/uniprot/P18089"
-  DRG_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/uniprot/P08913",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/uniprot/P18089",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/uniprot/P18825",
-               "http://identifiers.org/go/GO:0005834"
-  DRG part "http://identifiers.org/chebi/CHEBI:35569",
-           "http://identifiers.org/uniprot/P18089",
-           "http://identifiers.org/go/GO:0005834"
-  DRG part "http://identifiers.org/chebi/CHEBI:35569",
-           "http://identifiers.org/uniprot/P08913",
-           "http://identifiers.org/go/GO:0005834"
-  DRG part "http://identifiers.org/chebi/CHEBI:35569",
-           "http://identifiers.org/uniprot/P18825",
-           "http://identifiers.org/go/GO:0005834"
-  GDP identity "http://identifiers.org/chebi/CHEBI:17552"
-  DRG_GTP part "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/uniprot/P08913",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GTP part "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/uniprot/P18089",
-               "http://identifiers.org/go/GO:0005834"
-  DRG_GTP part "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/chebi/CHEBI:35569",
-               "http://identifiers.org/uniprot/P18825",
-               "http://identifiers.org/go/GO:0005834"
-  GTP identity "http://identifiers.org/chebi/CHEBI:15996"
-  Recptor version "http://identifiers.org/uniprot/P08913",
-                  "http://identifiers.org/uniprot/P18089",
-                  "http://identifiers.org/uniprot/P18825"
-  G_GDP part "http://identifiers.org/chebi/CHEBI:17552",
-             "http://identifiers.org/go/GO:0005834"
-  G_GTP part "http://identifiers.org/chebi/CHEBI:15996",
-             "http://identifiers.org/go/GO:0005834"
-  Forming hypernym "http://identifiers.org/go/GO:0031690"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0001664"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0005525",
-                      "http://identifiers.org/go/GO:0032403"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0003924"
-end
-
-Model_1 is "Thomsen1988_AdenylateCyclase_Inhibition"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL1166069080"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000082"
-Model_1 description "http://identifiers.org/pubmed/2904647"
-Model_1 origin "http://identifiers.org/pubmed/6248546",
-               "http://identifiers.org/pubmed/6277164"
-Model_1 hypernym "http://identifiers.org/go/GO:0031684",
-                 "http://identifiers.org/go/GO:0007194"
-Model_1 taxon "http://identifiers.org/taxonomy/9606"
diff --git a/BioModelsRAG/data/BIOMD0000000083.txt b/BioModelsRAG/data/BIOMD0000000083.txt
deleted file mode 100644
index ce683feb6771c2be70b1d21f5890b808808c792c..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000083.txt
+++ /dev/null
@@ -1,356 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Leloup2003_CircClock_LD_REV_ERBalpha()
-
-  // Compartments and Species:
-  compartment cell;
-  species Mb in cell, Bc in cell, Bcp in cell, Bn in cell, Cc in cell, Mc in cell;
-  species Ccp in cell, Mp in cell, Pc in cell, Pcp in cell, PCc in cell, PCcp in cell;
-  species PCn in cell, Bnp in cell, PCnp in cell, In in cell, Mr in cell;
-  species Rc in cell, Rn in cell;
-
-  // Assignment Rules:
-  parameter_0000096 := ceil(sin(pi*time/12 + 0.001)/2);
-  parameter_0000097 := 2.4 + (3 - 2.4)*parameter_0000096;
-
-  // Reactions:
-  reaction_0:  => Mb; cell*(vsB*reaction_0_K^m/(reaction_0_K^m + Rn^m));
-  reaction_1:  => Bc; cell*ksB*Mb;
-  reaction_2: Mb => ; cell*kdmb*Mb;
-  reaction_3: Bc => Bcp; cell*(V1B*Bc/(Kp + Bc));
-  reaction_4: Bc -> Bn; cell*(k5*Bc - k6*Bn);
-  reaction_5:  => Cc; cell*ksC*Mc;
-  reaction_6: Mc => ; cell*kdmc*Mc;
-  reaction_7: Cc => Ccp; cell*(V1C*Cc/(Kp + Cc));
-  reaction_8: Ccp => ; cell*(vdCC*Ccp/(Kd + Ccp));
-  reaction_9:  => Mp; cell*(parameter_0000097*Bn^n/(KAP^n + Bn^n));
-  reaction_10:  => Pc; cell*ksP*Mp;
-  reaction_11: Pcp => ; cell*(VdPC*Pcp/(Kd + Pcp));
-  reaction_12: Pc => Pcp; cell*(V1P*Pc/(Kp + Pc));
-  reaction_13: Cc + Pc -> PCc; cell*(k3*Cc*Pc - k4*PCc);
-  reaction_14: PCc => PCcp; cell*(V1PC*PCc/(Kp + PCc));
-  reaction_15: PCcp => ; cell*(vdPCC*PCcp/(Kd + PCcp));
-  reaction_16: PCc -> PCn; cell*(k1*PCc - k2*PCn);
-  reaction_17: PCnp => ; cell*kdn*PCnp;
-  reaction_18: Bcp => ; cell*kdn*Bcp;
-  reaction_19: Bnp => ; cell*kdn*Bnp;
-  reaction_20:  => Mc; cell*(vsC*Bn^n/(KAC^n + Bn^n));
-  reaction_21: PCn => PCnp; cell*(V3PC*PCn/(Kp + PCn));
-  reaction_22: Mp => ; cell*kdmp*Mp;
-  reaction_23: PCn + Bn -> In; cell*(k7*PCn*Bn - k8*In);
-  reaction_24: Mb => ; cell*(vmB*Mb/(KmB + Mb));
-  reaction_25: Mc => ; cell*(vmC*Mc/(KmC + Mc));
-  reaction_26: Mp => ; cell*(vmP*Mp/(KmP + Mp));
-  reaction_27: Pc => ; cell*kdn*Pc;
-  reaction_28: Cc => ; cell*kdnC*Cc;
-  reaction_29: Pcp => ; cell*kdn*Pcp;
-  reaction_30: Ccp => ; cell*kdn*Ccp;
-  reaction_31: PCcp => ; cell*kdn*PCcp;
-  reaction_32: PCc => ; cell*kdn*PCc;
-  reaction_33: PCnp => ; cell*(vdPCN*PCnp/(Kd + PCnp));
-  reaction_34: Bc => ; cell*kdn*Bc;
-  reaction_35: Bcp => ; cell*(vdBC*Bcp/(Kd + Bcp));
-  reaction_36: Bn => Bnp; cell*(V3B*Bn/(Kp + Bn));
-  reaction_37: Bnp => ; cell*(vdBN*Bnp/(Kd + Bnp));
-  reaction_38: In => ; cell*kdn*In;
-  reaction_39: In => ; cell*(vdIN*In/(Kd + In));
-  reaction_40: Bn => ; cell*kdn*Bn;
-  reaction_41: Bcp => Bc; cell*(V2B*Bcp/(Kdp + Bcp));
-  reaction_42: Bnp => Bn; cell*(V4B*Bnp/(Kdp + Bnp));
-  reaction_43: Ccp => Cc; cell*(V2C*Ccp/(Kdp + Ccp));
-  reaction_44: Pcp => Pc; cell*(V2P*Pcp/(Kdp + Pcp));
-  reaction_45: PCnp => PCn; cell*(V4PC*PCnp/(Kdp + PCnp));
-  reaction_46: PCn => ; cell*kdn*PCn;
-  reaction_47: PCcp => PCc; cell*(V2PC*PCcp/(Kdp + PCcp));
-  reaction_48:  => Mr; cell*(vsR*Bn^h/(KAR^h + Bn^h));
-  reaction_49: Mr => ; cell*kdmr*Mr;
-  reaction_50: Mr => ; cell*(vmR*Mr/(kmR + Mr));
-  reaction_51:  => Rc; cell*ksR*Mr;
-  reaction_52: Rc -> Rn; cell*(k9*Rc - k10*Rn);
-  reaction_53: Rc => ; cell*(vdRC*Rc/(Kd + Rc));
-  reaction_54: Rc => ; cell*kdn*Rc;
-  reaction_55: Rn => ; cell*(vdRN*Rn/(Kd + Rn));
-  reaction_56: Rn => ; cell*kdn*Rn;
-
-  // Species initializations:
-  Mb = 0;
-  Bc = 0;
-  Bcp = 0;
-  Bn = 0;
-  Cc = 0;
-  Mc = 0;
-  Ccp = 0;
-  Mp = 0;
-  Pc = 0;
-  Pcp = 0;
-  PCc = 0;
-  PCcp = 0;
-  PCn = 0;
-  Bnp = 0;
-  PCnp = 0;
-  In = 0;
-  Mr = 0;
-  Rc = 0;
-  Rn = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  vmP = 2.2;
-  kdmp = 0.02;
-  vsC = 2.2;
-  vmC = 2;
-  kdmc = 0.02;
-  vsB = 1.8;
-  vmB = 1.3;
-  kdmb = 0.02;
-  ksP = 1.2;
-  V1P = 9.6;
-  V2P = 0.6;
-  k4 = 0.4;
-  k3 = 0.8;
-  kdn = 0.02;
-  ksC = 3.2;
-  V1C = 1.2;
-  V2C = 0.2;
-  kdnC = 0.02;
-  KmB = 0.4;
-  Kp = 1.006;
-  Kdp = 0.1;
-  VdPC = 3.4;
-  vdCC = 1.4;
-  Kd = 0.3;
-  V1PC = 2.4;
-  V2PC = 0.2;
-  k2 = 0.4;
-  k1 = 0.8;
-  V3PC = 2.4;
-  V4PC = 0.2;
-  k7 = 1;
-  k8 = 0.2;
-  vdPCC = 1.4;
-  vdPCN = 1.4;
-  ksB = 0.32;
-  V1B = 1.4;
-  V2B = 0.2;
-  k5 = 0.8;
-  k6 = 0.4;
-  vdBC = 3;
-  V3B = 1.4;
-  V4B = 0.4;
-  vdBN = 3;
-  vdIN = 1.6;
-  vsR = 1.6;
-  KAR = 0.6;
-  vmR = 1.6;
-  kmR = 0.4;
-  kdmr = 0.02;
-  ksR = 1.7;
-  k9 = 0.8;
-  k10 = 0.4;
-  vdRC = 4.4;
-  vdRN = 0.8;
-  KAP = 0.6;
-  KAC = 0.6;
-  KmP = 0.3;
-  KmC = 0.4;
-  h = 2;
-  m = 2;
-  n = 2;
-  reaction_0_K = 1;
-
-  // Other declarations:
-  var parameter_0000096, parameter_0000097;
-  const cell, vmP, kdmp, vsC, vmC, kdmc, vsB, vmB, kdmb, ksP, V1P, V2P, k4;
-  const k3, kdn, ksC, V1C, V2C, kdnC, KmB, Kp, Kdp, VdPC, vdCC, Kd, V1PC;
-  const V2PC, k2, k1, V3PC, V4PC, k7, k8, vdPCC, vdPCN, ksB, V1B, V2B, k5;
-  const k6, vdBC, V3B, V4B, vdBN, vdIN, vsR, KAR, vmR, kmR, kdmr, ksR, k9;
-  const k10, vdRC, vdRN, KAP, KAC, KmP, KmC, h, m, n;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  time_unit is "time";
-  parameter_0000096 is "LD";
-  parameter_0000097 is "vsp";
-  reaction_0 is "Mb synthesized";
-  reaction_1 is "Mb translated into protein";
-  reaction_2 is "Mb nonspecific degradation";
-  reaction_3 is "Bc phosphorylation";
-  reaction_4 is "Bc transfered from cytosolic to nuclear";
-  reaction_5 is "Mc translated into protein";
-  reaction_6 is "Mc nonspecific degradation";
-  reaction_7 is "Cc phosphorylation";
-  reaction_8 is "Ccp specific degradation";
-  reaction_9 is "Mp synthesis";
-  reaction_10 is "Mp translated into protein";
-  reaction_11 is "Pcp specific degradation";
-  reaction_12 is "Pc phospholation";
-  reaction_13 is "Cc and Pc produce PCc";
-  reaction_14 is "PCc phospholation";
-  reaction_15 is "PCcp specific degradation";
-  reaction_16 is "PCc transfered into nuclear";
-  reaction_17 is "PCnp nonspecific degradation";
-  reaction_18 is "Bcp nonspecific degradation";
-  reaction_19 is "Bnp nonspecific degradation";
-  reaction_20 is "Mc synthesis";
-  reaction_21 is "PCn phospholation";
-  reaction_22 is "Mp nonspecific degradation";
-  reaction_23 is "Per_Cry and Clock_Bmal form inactive complex";
-  reaction_24 is "Mb specific degradation";
-  reaction_25 is "Mc specific degradation";
-  reaction_26 is "Mp specific degradation";
-  reaction_27 is "Pc nonspecific degradation";
-  reaction_28 is "Cc nonspecific degradation";
-  reaction_29 is "Pcp nonspecific degradation";
-  reaction_30 is "Ccp nonspecific degradation";
-  reaction_31 is "PCcp nonspecific degradation";
-  reaction_32 is "PCc nonspecific degradation";
-  reaction_33 is "PCnp specific degradation";
-  reaction_34 is "Bc nonspecific degradation";
-  reaction_35 is "Bcp specific degradation";
-  reaction_36 is "Bn phospholation";
-  reaction_37 is "Bnp specific degradation";
-  reaction_38 is "In nonspecific degration";
-  reaction_39 is "In specific degradation";
-  reaction_40 is "Bn nonspecific degradation";
-  reaction_41 is "Bcp dephospholation";
-  reaction_42 is "Bnp dephospholation";
-  reaction_43 is "Ccp dephospholation";
-  reaction_44 is "Pcp dephospholation";
-  reaction_45 is "PCnp dephospholation";
-  reaction_46 is "PCn nonspecific degradation";
-  reaction_47 is "PCcp dephospholation";
-  reaction_48 is "Mr synthesized";
-  reaction_49 is "Mr nonspecific degradation";
-  reaction_50 is "Mr specific degradation";
-  reaction_51 is "Mr translated into protein";
-  reaction_52 is "Rc transfered into nuclear";
-  reaction_53 is "Rc specific degradation";
-  reaction_54 is "Rc nonspecific degradation";
-  reaction_55 is "Rn specific degradation";
-  reaction_56 is "Rn nonspecific degradation";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005623"
-  Mb encodement "http://identifiers.org/uniprot/O00327"
-  Mb hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  Bc version "http://identifiers.org/uniprot/O00327"
-  Bcp version "http://identifiers.org/uniprot/O00327"
-  Bn version "http://identifiers.org/uniprot/O00327"
-  Cc version "http://identifiers.org/uniprot/Q8IV71"
-  Cc version "http://identifiers.org/uniprot/Q16526"
-  Mc encodement "http://identifiers.org/uniprot/Q16526"
-  Mc encodement "http://identifiers.org/uniprot/Q8IV71"
-  Mc hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  Ccp version "http://identifiers.org/uniprot/Q8IV71"
-  Ccp version "http://identifiers.org/uniprot/Q16526"
-  Mp encodement "http://identifiers.org/uniprot/P56645"
-  Mp encodement "http://identifiers.org/uniprot/O15055"
-  Mp encodement "http://identifiers.org/uniprot/O15534"
-  Mp hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  Pc version "http://identifiers.org/uniprot/O15055"
-  Pc version "http://identifiers.org/uniprot/O15534"
-  Pc version "http://identifiers.org/uniprot/P56645"
-  Pcp version "http://identifiers.org/uniprot/O15534"
-  Pcp version "http://identifiers.org/uniprot/O15055"
-  Pcp version "http://identifiers.org/uniprot/P56645"
-  PCc part "http://identifiers.org/uniprot/Q16526"
-  PCc part "http://identifiers.org/uniprot/O15534"
-  PCc part "http://identifiers.org/uniprot/Q8IV71"
-  PCc part "http://identifiers.org/uniprot/P56645"
-  PCcp part "http://identifiers.org/uniprot/P56645"
-  PCcp part "http://identifiers.org/uniprot/O15534"
-  PCcp part "http://identifiers.org/uniprot/Q16526"
-  PCcp part "http://identifiers.org/uniprot/Q8IV71"
-  PCn part "http://identifiers.org/uniprot/Q8IV71"
-  PCn part "http://identifiers.org/uniprot/Q16526"
-  PCn part "http://identifiers.org/uniprot/P56645"
-  PCn part "http://identifiers.org/uniprot/O15534"
-  Bnp version "http://identifiers.org/uniprot/O00327"
-  PCnp part "http://identifiers.org/uniprot/P56645"
-  PCnp part "http://identifiers.org/uniprot/Q8IV71"
-  PCnp part "http://identifiers.org/uniprot/Q16526"
-  PCnp part "http://identifiers.org/uniprot/O15534"
-  Mr encodement "http://identifiers.org/uniprot/Q6EEZ7"
-  Mr hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  Rc version "http://identifiers.org/uniprot/Q6EEZ7"
-  Rn version "http://identifiers.org/uniprot/Q6EEZ7"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0045892"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_6 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_7 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_8 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_9 hypernym "http://identifiers.org/go/GO:0045893"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_11 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_12 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_13 hypernym "http://identifiers.org/go/GO:0043623"
-  reaction_14 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_15 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_16 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_17 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_18 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_19 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_20 parthood "http://identifiers.org/go/GO:0045893"
-  reaction_21 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_22 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_23 hypernym "http://identifiers.org/go/GO:0043623"
-  reaction_24 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_25 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_26 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_27 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_28 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_29 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_30 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_31 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_32 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_33 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_34 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_35 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_36 hypernym "http://identifiers.org/go/GO:0006468"
-  reaction_37 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_38 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_39 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_40 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_41 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_42 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_43 parthood "http://identifiers.org/go/GO:0006470"
-  reaction_44 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_45 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_46 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_47 hypernym "http://identifiers.org/go/GO:0006470"
-  reaction_48 parthood "http://identifiers.org/go/GO:0045893"
-  reaction_49 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_50 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_51 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_52 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_53 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_54 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction_55 hypernym "http://identifiers.org/go/GO:0008233"
-  reaction_56 hypernym "http://identifiers.org/go/GO:0044257"
-end
-
-Leloup2003_CircClock_LD_REV_ERBalpha is "Leloup2003_CircClock_LD_REV-ERBalpha"
-
-Leloup2003_CircClock_LD_REV_ERBalpha origin "http://identifiers.org/kegg.pathway/hsa04710",
-                                            "http://identifiers.org/biomodels.db/BIOMD0000000083",
-                                            "http://identifiers.org/biomodels.db/MODEL4710748444",
-                                            "http://identifiers.org/go/GO:0042752",
-                                            "http://identifiers.org/taxonomy/40674",
-                                            "http://identifiers.org/biomodels.db/BIOMD0000000021"
-Leloup2003_CircClock_LD_REV_ERBalpha model_entity_is "http://identifiers.org/biomodels.db/MODEL4710748444",
-                                                     "http://identifiers.org/biomodels.db/BIOMD0000000083"
-Leloup2003_CircClock_LD_REV_ERBalpha version "http://identifiers.org/kegg.pathway/hsa04710"
-Leloup2003_CircClock_LD_REV_ERBalpha identity "http://identifiers.org/biomodels.db/BIOMD0000000083"
-Leloup2003_CircClock_LD_REV_ERBalpha identity "http://identifiers.org/biomodels.db/MODEL4710748444"
-Leloup2003_CircClock_LD_REV_ERBalpha hypernym "http://identifiers.org/go/GO:0042752"
-Leloup2003_CircClock_LD_REV_ERBalpha taxon "http://identifiers.org/taxonomy/40674"
-Leloup2003_CircClock_LD_REV_ERBalpha description "http://identifiers.org/biomodels.db/BIOMD0000000021",
-                                                 "http://identifiers.org/pubmed/12775757"
diff --git a/BioModelsRAG/data/BIOMD0000000084.txt b/BioModelsRAG/data/BIOMD0000000084.txt
deleted file mode 100644
index 5eeca632778c0ec3e0f86f2c0d4c56a1c6d69159..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000084.txt
+++ /dev/null
@@ -1,103 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Hornberg2005_ERKcascade()
-
-  // Compartments and Species:
-  compartment compartment_;
-  substanceOnly species R in compartment_, Rin in compartment_, x1 in compartment_;
-  substanceOnly species x1p in compartment_, x2 in compartment_, x2p in compartment_;
-  substanceOnly species x3 in compartment_, x3p in compartment_;
-
-  // Reactions:
-  v1: R -> Rin; v1_Vm1*R/(v1_Km1 + R);
-  v2: Rin -> R; v2_Vm2*Rin/(v2_Km2 + Rin);
-  v3: x1 -> x1p; v3_k3*R*x1/(v3_Km3 + x1);
-  v4: x1p -> x1; v4_Vm4*x1p/(v4_Km4 + x1p);
-  v5: x2 -> x2p; v5_k5*x1p*x2/(v5_Km5 + x2);
-  v6: x2p -> x2; v6_Vm6*x2p/(v6_Km6 + x2p);
-  v7: x3 -> x3p; v7_k7*x2p*x3/(v7_Km7 + x3);
-  v8: x3p -> x3; v8_Vm8*x3p/v8_Km8/(1 + x3p/v8_Km8 + v8_Inh/v8_Ki8);
-
-  // Species initializations:
-  R = 0.5/compartment_;
-  Rin = 0;
-  x1 = 1/compartment_;
-  x1p = 0;
-  x2 = 1/compartment_;
-  x2p = 0;
-  x3 = 1/compartment_;
-  x3p = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_Vm1 = 1;
-  v1_Km1 = 0.1;
-  v2_Vm2 = 0.01;
-  v2_Km2 = 0.1;
-  v3_k3 = 1;
-  v3_Km3 = 0.1;
-  v4_Vm4 = 0.3;
-  v4_Km4 = 1;
-  v5_k5 = 1;
-  v5_Km5 = 0.1;
-  v6_Vm6 = 0.3;
-  v6_Km6 = 1;
-  v7_k7 = 1;
-  v7_Km7 = 0.1;
-  v8_Vm8 = 0.3;
-  v8_Km8 = 1;
-  v8_Inh = 0;
-  v8_Ki8 = 1;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = item;
-
-  // Display Names:
-  substance is "dimensionless";
-  compartment_ is "Cytosol";
-  v1 is "Receptor inactivation";
-  v2 is "Receptor activation";
-  v3 is "Kinase-1 activation";
-  v4 is "Kinase-1 inactivation";
-  v5 is "Kinase-2 activation";
-  v6 is "Kinase-2 inactivation";
-  v7 is "Kinase-3 activation";
-  v8 is "Kinase-3 inactivation";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005829"
-  R hypernym "http://identifiers.org/uniprot/Q9QX70"
-  Rin hypernym "http://identifiers.org/uniprot/Q9QX70"
-  x1 hypernym "http://identifiers.org/uniprot/P04049"
-  x1p hypernym "http://identifiers.org/uniprot/P04049"
-  x2 hypernym "http://identifiers.org/uniprot/Q02750"
-  x2p hypernym "http://identifiers.org/uniprot/Q02750"
-  x3 hypernym "http://identifiers.org/uniprot/P28482"
-  x3p hypernym "http://identifiers.org/uniprot/P28482"
-  v1 hypernym "http://identifiers.org/obo.go/GO:0007175"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0045741"
-  v3 identity "http://identifiers.org/obo.go/GO:0000185"
-  v4 identity "http://identifiers.org/obo.go/GO:0051390"
-  v5 identity "http://identifiers.org/ec-code/2.7.11.1",
-              "http://identifiers.org/obo.go/GO:0000186",
-              "http://identifiers.org/obo.go/GO:0004709"
-  v6 identity "http://identifiers.org/obo.go/GO:0051389"
-  v7 identity "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0000187",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v8 hypernym "http://identifiers.org/obo.go/GO:0043407"
-end
-
-Hornberg2005_ERKcascade is "Hornberg2005_ERKcascade"
-
-Hornberg2005_ERKcascade model_entity_is "http://identifiers.org/biomodels.db/MODEL6623610941"
-Hornberg2005_ERKcascade model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000084"
-Hornberg2005_ERKcascade description "http://identifiers.org/pubmed/15634347"
-Hornberg2005_ERKcascade identity "http://identifiers.org/obo.go/GO:0000165",
-                                 "http://identifiers.org/obo.go/GO:0007173"
-Hornberg2005_ERKcascade part "http://identifiers.org/kegg.pathway/rno04010"
-Hornberg2005_ERKcascade taxon "http://identifiers.org/taxonomy/40674"
diff --git a/BioModelsRAG/data/BIOMD0000000085.txt b/BioModelsRAG/data/BIOMD0000000085.txt
deleted file mode 100644
index 8915847cbacf5399656038712d25259e673a6876..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000085.txt
+++ /dev/null
@@ -1,216 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Maurya2005()
-
-  // Compartments and Species:
-  compartment compartment_0;
-  species species_0 in compartment_0, species_1 in compartment_0, species_2 in compartment_0;
-  species species_3 in compartment_0, species_4 in compartment_0, species_5 in compartment_0;
-  species species_6 in compartment_0, species_7 in compartment_0, species_8 in compartment_0;
-  species species_9 in compartment_0, species_10 in compartment_0, species_11 in compartment_0;
-  species species_12 in compartment_0, species_13 in compartment_0, species_14 in compartment_0;
-  species species_15 in compartment_0, species_16 in compartment_0;
-
-  // Assignment Rules:
-  parameter_0 := (species_5 + species_10 + species_15 + species_11)/1e-8;
-  parameter_1 := (25*species_15 + 25*species_11 + 0.013*species_10 + 0.013*species_5)/10e-9;
-
-  // Reactions:
-  reaction_1: species_1 + species_3 -> species_5; compartment_0*(reaction_1_k1*species_1*species_3 - reaction_1_k2*species_5);
-  reaction_3: species_5 -> species_6 + species_7; compartment_0*(reaction_3_k1*species_5 - reaction_3_k2*species_6*species_7);
-  reaction_4: species_6 -> species_1 + species_8; compartment_0*(reaction_4_k1*species_6 - reaction_4_k2*species_1*species_8);
-  reaction_5: species_9 + species_3 -> species_10; compartment_0*(reaction_5_k1*species_9*species_3 - reaction_5_k2*species_10);
-  reaction_6: species_5 + species_4 -> species_10; compartment_0*(reaction_6_k1*species_5*species_4 - reaction_6_k2*species_10);
-  reaction_7: species_5 + species_0 -> species_11; compartment_0*(reaction_7_k1*species_5*species_0 - reaction_7_k2*species_11);
-  reaction_8: species_6 + species_0 -> species_12; compartment_0*(reaction_8_k1*species_6*species_0 - reaction_8_k2*species_12);
-  reaction_9: species_6 + species_4 -> species_13; compartment_0*(reaction_9_k1*species_6*species_4 - reaction_9_k2*species_13);
-  reaction_10: species_10 -> species_13 + species_7; compartment_0*(reaction_10_k1*species_10 - reaction_10_k2*species_13*species_7);
-  reaction_11: species_13 -> species_9 + species_8; compartment_0*(reaction_11_k1*species_13 - reaction_11_k2*species_9*species_8);
-  reaction_13: species_11 -> species_12 + species_7; compartment_0*(reaction_13_k1*species_11 - reaction_13_k2*species_12*species_7);
-  reaction_14: species_12 -> species_2 + species_8; compartment_0*(reaction_14_k1*species_12 - reaction_14_k2*species_2*species_8);
-  reaction_16: species_2 + species_4 -> species_14; compartment_0*(reaction_16_k1*species_2*species_4 - reaction_16_k2*species_14);
-  reaction_17: species_14 + species_3 -> species_15; compartment_0*(reaction_17_k1*species_14*species_3 - reaction_17_k2*species_15);
-  reaction_19: species_10 + species_0 -> species_15; compartment_0*(reaction_19_k1*species_10*species_0 - reaction_19_k2*species_15);
-  reaction_20: species_15 -> species_16 + species_7; compartment_0*(reaction_20_k1*species_15 - reaction_20_k2*species_16*species_7);
-  reaction_23: species_16 -> species_14 + species_8; compartment_0*(reaction_23_k1*species_16 - reaction_23_k2*species_14*species_8);
-
-  // Species initializations:
-  species_0 = 0;
-  species_1 = 1e-08;
-  species_2 = 0;
-  species_3 = 0.000468;
-  species_4 = 1e-05;
-  species_5 = 0;
-  species_6 = 0;
-  species_7 = 0.0044;
-  species_8 = 0.000149;
-  species_9 = 0;
-  species_10 = 0;
-  species_11 = 0;
-  species_12 = 0;
-  species_13 = 0;
-  species_14 = 0;
-  species_15 = 0;
-  species_16 = 0;
-
-  // Compartment initializations:
-  compartment_0 = 1;
-
-  // Variable initializations:
-  reaction_1_k1 = 529000;
-  reaction_1_k2 = 8.38e-06;
-  reaction_3_k1 = 0.013;
-  reaction_3_k2 = 9.03e-07;
-  reaction_4_k1 = 0.0001;
-  reaction_4_k2 = 62.3;
-  reaction_5_k1 = 853000;
-  reaction_5_k2 = 0.00468;
-  reaction_6_k1 = 132000000;
-  reaction_6_k2 = 1.28;
-  reaction_7_k1 = 386000;
-  reaction_7_k2 = 0.0408;
-  reaction_8_k1 = 64100;
-  reaction_8_k2 = 0.95;
-  reaction_9_k1 = 94700000;
-  reaction_9_k2 = 0.00227;
-  reaction_10_k1 = 0.013;
-  reaction_10_k2 = 2.22e-09;
-  reaction_11_k1 = 2;
-  reaction_11_k2 = 1470000;
-  reaction_13_k1 = 25;
-  reaction_13_k2 = 0.244;
-  reaction_14_k1 = 0.0001;
-  reaction_14_k2 = 3.83;
-  reaction_16_k1 = 3960000000;
-  reaction_16_k2 = 5.43e-05;
-  reaction_17_k1 = 1620000;
-  reaction_17_k2 = 0.00875;
-  reaction_19_k1 = 6300000;
-  reaction_19_k2 = 0.478;
-  reaction_20_k1 = 25;
-  reaction_20_k2 = 0.00297;
-  reaction_23_k1 = 2.75;
-  reaction_23_k2 = 2940;
-
-  // Other declarations:
-  var parameter_0, parameter_1;
-  const compartment_0;
-
-  // Display Names:
-  compartment_0 is "cell";
-  species_0 is "A";
-  species_1 is "G";
-  species_2 is "GA";
-  species_3 is "T";
-  species_4 is "R";
-  species_5 is "G*T";
-  species_6 is "GD";
-  species_7 is "Pi";
-  species_8 is "D";
-  species_9 is "RG";
-  species_10 is "RG*T";
-  species_11 is "G*AT";
-  species_12 is "GAD";
-  species_13 is "RGD";
-  species_14 is "RGA";
-  species_15 is "RG*AT";
-  species_16 is "RGAD";
-  parameter_0 is "Z";
-  parameter_1 is "v";
-  reaction_1 is "G protein binding GTP";
-  reaction_3 is "G*T  hydrolysis";
-  reaction_4 is "GD dissociation";
-  reaction_5 is "RG binding GTP";
-  reaction_6 is "G*T binding Receptor";
-  reaction_7 is "G*T binding GAP";
-  reaction_8 is "GD binding GAP";
-  reaction_9 is "GD binding Receptor";
-  reaction_10 is "RG*T hydrolysis";
-  reaction_11 is "RGD dissociation";
-  reaction_13 is "G*AT hydrolysis";
-  reaction_14 is "GAD dissociation";
-  reaction_16 is "GA binding Receptor";
-  reaction_17 is "RGA binding  GTP";
-  reaction_19 is "RG*T binding GAP";
-  reaction_20 is "RG*AT hydrolysis";
-  reaction_23 is "RGAD dissociation";
-
-  // CV terms:
-  compartment_0 hypernym "http://identifiers.org/go/GO:0005623"
-  species_0 hypernym "http://identifiers.org/interpro/IPR000342"
-  species_1 hypernym "http://identifiers.org/go/GO:0005834"
-  species_2 part "http://identifiers.org/interpro/IPR000342",
-                 "http://identifiers.org/go/GO:0005834"
-  species_3 identity "http://identifiers.org/chebi/CHEBI:15996",
-                     "http://identifiers.org/kegg.compound/C00044"
-  species_4 hypernym "http://identifiers.org/go/GO:0043235"
-  species_4 version "http://identifiers.org/interpro/IPR000337"
-  species_5 part "http://identifiers.org/chebi/CHEBI:15996",
-                 "http://identifiers.org/go/GO:0005834"
-  species_6 identity "http://identifiers.org/chebi/CHEBI:17552",
-                     "http://identifiers.org/go/GO:0005834"
-  species_7 identity "http://identifiers.org/chebi/CHEBI:18367"
-  species_8 identity "http://identifiers.org/chebi/CHEBI:17552",
-                     "http://identifiers.org/kegg.compound/C00035"
-  species_9 part "http://identifiers.org/go/GO:0005834",
-                 "http://identifiers.org/go/GO:0043235"
-  species_10 part "http://identifiers.org/chebi/CHEBI:15996",
-                  "http://identifiers.org/go/GO:0005834",
-                  "http://identifiers.org/go/GO:0043235"
-  species_11 part "http://identifiers.org/chebi/CHEBI:15996",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/go/GO:0005834"
-  species_12 part "http://identifiers.org/chebi/CHEBI:17552",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/go/GO:0005834"
-  species_13 part "http://identifiers.org/chebi/CHEBI:17552",
-                  "http://identifiers.org/go/GO:0005834",
-                  "http://identifiers.org/go/GO:0043235"
-  species_14 part "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/go/GO:0005834",
-                  "http://identifiers.org/go/GO:0043235"
-  species_15 part "http://identifiers.org/chebi/CHEBI:15996",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/go/GO:0005834",
-                  "http://identifiers.org/go/GO:0043235"
-  species_16 part "http://identifiers.org/chebi/CHEBI:17552",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/go/GO:0005834",
-                  "http://identifiers.org/go/GO:0043235"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0005525",
-                      "http://identifiers.org/go/GO:0005515"
-  reaction_3 version "http://identifiers.org/reactome/REACT_348"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0003924"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0005525",
-                      "http://identifiers.org/go/GO:0032403"
-  reaction_6 hypernym "http://identifiers.org/go/GO:0005102",
-                      "http://identifiers.org/go/GO:0001664"
-  reaction_7 hypernym "http://identifiers.org/go/GO:0032403"
-  reaction_8 hypernym "http://identifiers.org/go/GO:0032403"
-  reaction_9 hypernym "http://identifiers.org/go/GO:0005102",
-                      "http://identifiers.org/go/GO:0001664"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0003924"
-  reaction_10 version "http://identifiers.org/reactome/REACT_348"
-  reaction_11 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction_13 hypernym "http://identifiers.org/go/GO:0003924"
-  reaction_13 version "http://identifiers.org/reactome/REACT_348"
-  reaction_14 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction_16 hypernym "http://identifiers.org/go/GO:0005102",
-                       "http://identifiers.org/go/GO:0001664"
-  reaction_17 hypernym "http://identifiers.org/go/GO:0005525",
-                       "http://identifiers.org/go/GO:0032403"
-  reaction_19 hypernym "http://identifiers.org/go/GO:0032403",
-                       "http://identifiers.org/go/GO:0005102"
-  reaction_20 hypernym "http://identifiers.org/go/GO:0003924"
-  reaction_20 version "http://identifiers.org/reactome/REACT_348"
-  reaction_23 hypernym "http://identifiers.org/go/GO:0043241"
-end
-
-Maurya2005 is "Maurya2005_GTPaseCycle_reducedOrder"
-
-Maurya2005 model_entity_is "http://identifiers.org/biomodels.db/MODEL5317679037"
-Maurya2005 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000085"
-Maurya2005 description "http://identifiers.org/pubmed/16986265"
-Maurya2005 origin "http://identifiers.org/biomodels.db/BIOMD0000000086"
-Maurya2005 taxon "http://identifiers.org/taxonomy/131567"
-Maurya2005 hypernym "http://identifiers.org/go/GO:0008277"
diff --git a/BioModelsRAG/data/BIOMD0000000086.txt b/BioModelsRAG/data/BIOMD0000000086.txt
deleted file mode 100644
index e11aac710866afbeffc8770925e18ea203924137..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000086.txt
+++ /dev/null
@@ -1,252 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Model_0()
-
-  // Compartments and Species:
-  compartment compartment_0;
-  species species_0 in compartment_0, species_1 in compartment_0, species_2 in compartment_0;
-  species species_3 in compartment_0, species_4 in compartment_0, species_5 in compartment_0;
-  species species_6 in compartment_0, species_7 in compartment_0, species_8 in compartment_0;
-  species species_9 in compartment_0, species_10 in compartment_0, species_11 in compartment_0;
-  species species_12 in compartment_0, species_13 in compartment_0, species_14 in compartment_0;
-  species species_15 in compartment_0, species_16 in compartment_0;
-
-  // Assignment Rules:
-  parameter_0 := (species_5 + species_10 + species_15 + species_11)/1e-8;
-  parameter_1 := (25*species_15 + 25*species_11 + 0.013*species_10 + 0.013*species_5)/1e-8;
-
-  // Reactions:
-  reaction_0: species_1 + species_0 -> species_2; compartment_0*(reaction_0_k1*species_1*species_0 - reaction_0_k2*species_2);
-  reaction_1: species_1 + species_3 -> species_5; compartment_0*(reaction_1_k1*species_1*species_3 - reaction_1_k2*species_5);
-  reaction_2: species_1 + species_4 -> species_9; compartment_0*(reaction_2_k1*species_1*species_4 - reaction_2_k2*species_9);
-  reaction_3: species_5 -> species_6 + species_7; compartment_0*(reaction_3_k1*species_5 - reaction_3_k2*species_6*species_7);
-  reaction_4: species_6 -> species_1 + species_8; compartment_0*(reaction_4_k1*species_6 - reaction_4_k2*species_1*species_8);
-  reaction_5: species_9 + species_3 -> species_10; compartment_0*(reaction_5_k1*species_9*species_3 - reaction_5_k2*species_10);
-  reaction_6: species_5 + species_4 -> species_10; compartment_0*(reaction_6_k1*species_5*species_4 - reaction_6_k2*species_10);
-  reaction_7: species_5 + species_0 -> species_11; compartment_0*(reaction_7_k1*species_5*species_0 - reaction_7_k2*species_11);
-  reaction_8: species_6 + species_0 -> species_12; compartment_0*(reaction_8_k1*species_6*species_0 - reaction_8_k2*species_12);
-  reaction_9: species_6 + species_4 -> species_13; compartment_0*(reaction_9_k1*species_6*species_4 - reaction_9_k2*species_13);
-  reaction_10: species_10 -> species_13 + species_7; compartment_0*(reaction_10_k1*species_10 - reaction_10_k2*species_13*species_7);
-  reaction_11: species_13 -> species_9 + species_8; compartment_0*(reaction_11_k1*species_13 - reaction_11_k2*species_9*species_8);
-  reaction_12: species_2 + species_3 -> species_11; compartment_0*(reaction_12_k1*species_2*species_3 - reaction_12_k2*species_11);
-  reaction_13: species_11 -> species_12 + species_7; compartment_0*(reaction_13_k1*species_11 - reaction_13_k2*species_12*species_7);
-  reaction_14: species_12 -> species_2 + species_8; compartment_0*(reaction_14_k1*species_12 - reaction_14_k2*species_2*species_8);
-  reaction_15: species_9 + species_0 -> species_14; compartment_0*(reaction_15_k1*species_9*species_0 - reaction_15_k2*species_14);
-  reaction_16: species_2 + species_4 -> species_14; compartment_0*(reaction_16_k1*species_2*species_4 - reaction_16_k2*species_14);
-  reaction_17: species_14 + species_3 -> species_15; compartment_0*(reaction_17_k1*species_14*species_3 - reaction_17_k2*species_15);
-  reaction_18: species_11 + species_4 -> species_15; compartment_0*(reaction_18_k1*species_11*species_4 - reaction_18_k2*species_15);
-  reaction_19: species_10 + species_0 -> species_15; compartment_0*(reaction_19_k1*species_10*species_0 - reaction_19_k2*species_15);
-  reaction_20: species_15 -> species_16 + species_7; compartment_0*(reaction_20_k1*species_15 - reaction_20_k2*species_16*species_7);
-  reaction_21: species_13 + species_0 -> species_16; compartment_0*(reaction_21_k1*species_13*species_0 - reaction_21_k2*species_16);
-  reaction_22: species_12 + species_4 -> species_16; compartment_0*(reaction_22_k1*species_12*species_4 - reaction_22_k2*species_16);
-  reaction_23: species_16 -> species_14 + species_8; compartment_0*(reaction_23_k1*species_16 - reaction_23_k2*species_14*species_8);
-
-  // Species initializations:
-  species_0 = 0;
-  species_1 = 1e-08;
-  species_2 = 0;
-  species_3 = 0.000468;
-  species_4 = 1e-06;
-  species_5 = 0;
-  species_6 = 0;
-  species_7 = 0.0044;
-  species_8 = 0.000149;
-  species_9 = 0;
-  species_10 = 0;
-  species_11 = 0;
-  species_12 = 0;
-  species_13 = 0;
-  species_14 = 0;
-  species_15 = 0;
-  species_16 = 0;
-
-  // Compartment initializations:
-  compartment_0 = 1;
-
-  // Variable initializations:
-  reaction_0_k1 = 8780000;
-  reaction_0_k2 = 8;
-  reaction_1_k1 = 529000;
-  reaction_1_k2 = 8.38e-06;
-  reaction_2_k1 = 636000000;
-  reaction_2_k2 = 0.0179;
-  reaction_3_k1 = 0.013;
-  reaction_3_k2 = 9.03e-07;
-  reaction_4_k1 = 0.0001;
-  reaction_4_k2 = 62.3;
-  reaction_5_k1 = 853000;
-  reaction_5_k2 = 0.00468;
-  reaction_6_k1 = 132000000;
-  reaction_6_k2 = 1.28;
-  reaction_7_k1 = 386000;
-  reaction_7_k2 = 0.0408;
-  reaction_8_k1 = 64100;
-  reaction_8_k2 = 0.95;
-  reaction_9_k1 = 94700000;
-  reaction_9_k2 = 0.00227;
-  reaction_10_k1 = 0.013;
-  reaction_10_k2 = 2.22e-09;
-  reaction_11_k1 = 2;
-  reaction_11_k2 = 1470000;
-  reaction_12_k1 = 44700;
-  reaction_12_k2 = 8.32e-08;
-  reaction_13_k1 = 25;
-  reaction_13_k2 = 0.244;
-  reaction_14_k1 = 0.0001;
-  reaction_14_k2 = 3.83;
-  reaction_15_k1 = 74300;
-  reaction_15_k2 = 0.00572;
-  reaction_16_k1 = 22800000;
-  reaction_16_k2 = 5.43e-05;
-  reaction_17_k1 = 1620000;
-  reaction_17_k2 = 0.00875;
-  reaction_18_k1 = 6200000;
-  reaction_18_k2 = 0.0433;
-  reaction_19_k1 = 6300000;
-  reaction_19_k2 = 0.478;
-  reaction_20_k1 = 25;
-  reaction_20_k2 = 0.00297;
-  reaction_21_k1 = 13000;
-  reaction_21_k2 = 0.685;
-  reaction_22_k1 = 49400000;
-  reaction_22_k2 = 0.00421;
-  reaction_23_k1 = 2.75;
-  reaction_23_k2 = 2940;
-
-  // Other declarations:
-  var parameter_0, parameter_1;
-  const compartment_0;
-
-  // Display Names:
-  compartment_0 is "cell";
-  species_0 is "A";
-  species_1 is "G";
-  species_2 is "GA";
-  species_3 is "T";
-  species_4 is "R";
-  species_5 is "G*T";
-  species_6 is "GD";
-  species_7 is "Pi";
-  species_8 is "D";
-  species_9 is "RG";
-  species_10 is "RG*T";
-  species_11 is "G*AT";
-  species_12 is "GAD";
-  species_13 is "RGD";
-  species_14 is "RGA";
-  species_15 is "RG*AT";
-  species_16 is "RGAD";
-  parameter_0 is "Z";
-  parameter_1 is "v";
-  reaction_0 is "G protein binding GAP";
-  reaction_1 is "G protein binding GTP";
-  reaction_2 is "G binding Receptor";
-  reaction_3 is "G*T  hydrolysis";
-  reaction_4 is "GD dissociation";
-  reaction_5 is "RG binding GTP";
-  reaction_6 is "G*T binding Receptor";
-  reaction_7 is "G*T binding GAP";
-  reaction_8 is "GD binding GAP";
-  reaction_9 is "GD binding Receptor";
-  reaction_10 is "RG*T hydrolysis";
-  reaction_11 is "RGD dissociation";
-  reaction_12 is "GA binding GTP";
-  reaction_13 is "G*AT hydrolysis";
-  reaction_14 is "GAD dissociation";
-  reaction_15 is "RG binding  GAP";
-  reaction_16 is "GA binding Receptor";
-  reaction_17 is "RGA binding  GTP";
-  reaction_18 is "G*AT binding Receptor";
-  reaction_19 is "RG*T binding GAP";
-  reaction_20 is "RG*AT hydrolysis";
-  reaction_21 is "RGD binding GAP";
-  reaction_22 is "GAD binding Receptor";
-  reaction_23 is "RGAD dissociation";
-
-  // CV terms:
-  compartment_0 hypernym "http://identifiers.org/obo.go/GO:0005623"
-  species_0 hypernym "http://identifiers.org/interpro/IPR000342"
-  species_1 identity "http://identifiers.org/obo.go/GO:0005834"
-  species_2 part "http://identifiers.org/interpro/IPR000342",
-                 "http://identifiers.org/obo.go/GO:0005834"
-  species_3 identity "http://identifiers.org/obo.chebi/CHEBI:15996",
-                     "http://identifiers.org/kegg.compound/C00044"
-  species_4 version "http://identifiers.org/interpro/IPR000337"
-  species_4 hypernym "http://identifiers.org/obo.go/GO:0043235"
-  species_5 part "http://identifiers.org/obo.chebi/CHEBI:15996",
-                 "http://identifiers.org/obo.go/GO:0005834"
-  species_6 part "http://identifiers.org/obo.chebi/CHEBI:17552",
-                 "http://identifiers.org/obo.go/GO:0005834"
-  species_7 identity "http://identifiers.org/obo.chebi/CHEBI:18367"
-  species_8 identity "http://identifiers.org/obo.chebi/CHEBI:17552",
-                     "http://identifiers.org/kegg.compound/C00035"
-  species_9 part "http://identifiers.org/obo.go/GO:0043235",
-                 "http://identifiers.org/obo.go/GO:0005834"
-  species_10 part "http://identifiers.org/obo.chebi/CHEBI:15996",
-                  "http://identifiers.org/obo.go/GO:0043235",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  species_11 part "http://identifiers.org/obo.chebi/CHEBI:15996",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  species_12 part "http://identifiers.org/obo.chebi/CHEBI:17552",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  species_13 part "http://identifiers.org/obo.chebi/CHEBI:17552",
-                  "http://identifiers.org/obo.go/GO:0043235",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  species_14 part "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/obo.go/GO:0043235",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  species_15 part "http://identifiers.org/obo.chebi/CHEBI:15996",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/obo.go/GO:0043235",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  species_16 part "http://identifiers.org/obo.chebi/CHEBI:17552",
-                  "http://identifiers.org/interpro/IPR000342",
-                  "http://identifiers.org/obo.go/GO:0043235",
-                  "http://identifiers.org/obo.go/GO:0005834"
-  reaction_0 hypernym "http://identifiers.org/obo.go/GO:0005515"
-  reaction_1 hypernym "http://identifiers.org/obo.go/GO:0005515",
-                      "http://identifiers.org/obo.go/GO:0005525"
-  reaction_2 hypernym "http://identifiers.org/obo.go/GO:0001664"
-  reaction_3 version "http://identifiers.org/reactome/REACT_348"
-  reaction_3 hypernym "http://identifiers.org/obo.go/GO:0003924"
-  reaction_4 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_5 hypernym "http://identifiers.org/obo.go/GO:0032403",
-                      "http://identifiers.org/obo.go/GO:0005525"
-  reaction_6 hypernym "http://identifiers.org/obo.go/GO:0005102",
-                      "http://identifiers.org/obo.go/GO:0001664"
-  reaction_7 hypernym "http://identifiers.org/obo.go/GO:0032403"
-  reaction_8 hypernym "http://identifiers.org/obo.go/GO:0032403"
-  reaction_9 hypernym "http://identifiers.org/obo.go/GO:0005102",
-                      "http://identifiers.org/obo.go/GO:0001664"
-  reaction_10 version "http://identifiers.org/reactome/REACT_348"
-  reaction_10 hypernym "http://identifiers.org/obo.go/GO:0003924"
-  reaction_11 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_12 hypernym "http://identifiers.org/obo.go/GO:0005525",
-                       "http://identifiers.org/obo.go/GO:0005515"
-  reaction_13 version "http://identifiers.org/reactome/REACT_348"
-  reaction_13 hypernym "http://identifiers.org/obo.go/GO:0003924"
-  reaction_14 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_15 hypernym "http://identifiers.org/obo.go/GO:0032403"
-  reaction_16 hypernym "http://identifiers.org/obo.go/GO:0005102",
-                       "http://identifiers.org/obo.go/GO:0001664"
-  reaction_17 hypernym "http://identifiers.org/obo.go/GO:0032403",
-                       "http://identifiers.org/obo.go/GO:0005525"
-  reaction_18 hypernym "http://identifiers.org/obo.go/GO:0001664",
-                       "http://identifiers.org/obo.go/GO:0005102"
-  reaction_19 hypernym "http://identifiers.org/obo.go/GO:0032403"
-  reaction_20 hypernym "http://identifiers.org/obo.go/GO:0003924"
-  reaction_20 version "http://identifiers.org/reactome/REACT_348"
-  reaction_21 hypernym "http://identifiers.org/obo.go/GO:0032403"
-  reaction_22 hypernym "http://identifiers.org/obo.go/GO:0001664",
-                       "http://identifiers.org/obo.go/GO:0005102"
-  reaction_23 hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-Model_0 is "Bornheimer2004_GTPaseCycle"
-
-Model_0 model_entity_is "http://identifiers.org/biomodels.db/MODEL4822989369"
-Model_0 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000086"
-Model_0 description "http://identifiers.org/pubmed/15520372"
-Model_0 taxon "http://identifiers.org/taxonomy/131567"
-Model_0 hypernym "http://identifiers.org/obo.go/GO:0008277"
diff --git a/BioModelsRAG/data/BIOMD0000000087.txt b/BioModelsRAG/data/BIOMD0000000087.txt
deleted file mode 100644
index d11cf8e208c1a95c7848459f7f35f408c525b331..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000087.txt
+++ /dev/null
@@ -1,328 +0,0 @@
-// Created by libAntimony v2.13.0
-model *YeastWTmodel2()
-
-  // Compartments and Species:
-  compartment cellMembrane, nucleus;
-  substanceOnly species Ctelo in nucleus, Utelo in nucleus, Cdc13 in nucleus;
-  substanceOnly species Rad17Utelo in nucleus, Rad17 in nucleus, Rad24 in nucleus;
-  substanceOnly species RPA in nucleus, Mec1 in nucleus, ssDNA in nucleus;
-  substanceOnly species RPAssDNA in nucleus, RPAssDNA1 in nucleus, RPAssDNA2 in nucleus;
-  substanceOnly species Mec1RPAssDNA in nucleus, ExoXI in nucleus, ExoXA in nucleus;
-  substanceOnly species Exo1I in nucleus, Exo1A in nucleus, Rad9I in nucleus;
-  substanceOnly species Rad9A in nucleus, Rad53I in nucleus, Rad53A in nucleus;
-  substanceOnly species Chk1I in nucleus, Chk1A in nucleus, Dun1I in nucleus;
-  substanceOnly species Dun1A in nucleus, ATP in nucleus, ADP in nucleus;
-  substanceOnly species Rad9Kin in nucleus, recovery in nucleus, G1 in nucleus;
-  substanceOnly species S in nucleus, G2 in nucleus, M in nucleus, G1cyclin in nucleus;
-  substanceOnly species Scyclin in nucleus, G2cyclin in nucleus, Mcyclin in nucleus;
-  substanceOnly species G1CdkI in nucleus, G1CdkA in nucleus, SCdkI in nucleus;
-  substanceOnly species SCdkA in nucleus, G2CdkI in nucleus, G2CdkA in nucleus;
-  substanceOnly species MCdkI in nucleus, MCdkA in nucleus, G1Soff in nucleus;
-  substanceOnly species G1Son in nucleus, SG2off in nucleus, SG2on in nucleus;
-  substanceOnly species G2Moff in nucleus, G2Mon in nucleus, MG1off in nucleus;
-  substanceOnly species MG1on in nucleus, $sink in nucleus, budscar in cellMembrane;
-
-  // Reactions:
-  Capping: Cdc13 + Utelo => Ctelo; Capping_k1*Cdc13*Utelo*kalive;
-  Uncapping: Ctelo => Cdc13 + Utelo; Uncapping_k2*Ctelo*kalive;
-  Rad17binding: Utelo + Rad17 + Rad24 + ATP => Rad17Utelo + Rad24 + ADP; Rad17binding_k3*Utelo*Rad17*Rad24*ATP*kalive/(5000 + ATP);
-  ExoXactivation: ExoXI + Rad17Utelo => ExoXA + Rad17Utelo; ExoXactivation_k4*ExoXI*Rad17Utelo*kalive;
-  ExoXactivity: ExoXA + Rad17Utelo => ExoXA + Rad17Utelo + ssDNA; ExoXactivity_k5*ExoXA*Rad17Utelo*kalive;
-  Exo1activation: Exo1I => Exo1A; Exo1activation_k6a*Exo1I*kalive;
-  Exo1Rad24dependentActivation: Exo1I + Rad24 => Exo1A + Rad24; Exo1Rad24dependentActivation_k6b*Exo1I*Rad24*kalive;
-  Exo1Rad17independentActivity: Utelo + Exo1A => Utelo + Exo1A + ssDNA; Exo1Rad17independentActivity_k7a*Utelo*Exo1A*kalive;
-  Exo1Rad17dependentActivity: Rad17Utelo + Exo1A => Rad17Utelo + Exo1A + ssDNA; Exo1Rad17dependentActivity_k7b*Rad17Utelo*Exo1A*kalive;
-  RPAbinding1: ssDNA + RPA => RPAssDNA1; RPAbinding1_k8a*RPA*ssDNA*kalive;
-  RPAbinding2: ssDNA + RPAssDNA1 => RPAssDNA2; RPAbinding2_k8b*RPAssDNA1*ssDNA*kalive;
-  RPAbinding: ssDNA + RPAssDNA2 => RPAssDNA; RPAbinding_k8c*RPAssDNA2*ssDNA*kalive;
-  Mec1binding: RPAssDNA + Mec1 => Mec1RPAssDNA; Mec1binding_k8d*RPAssDNA*Mec1*kalive;
-  Rad9activation: Rad9Kin + Rad9I => Rad9Kin + Rad9A; Rad9activation_k9*Rad9Kin*Rad9I*kalive;
-  ExoXinhibition: ExoXA + Rad9A => ExoXI + Rad9A; ExoXA*ExoXinhibition_k10a*Rad9A*kalive;
-  ExoXinhibition2: ExoXA + Rad9I => ExoXI + Rad9I; ExoXA*ExoXinhibition2_k10b*Rad9I*kalive;
-  Rad53activation: Rad53I + Rad9A => Rad53A + Rad9A; Rad53activation_k11*Rad53I*Rad9A*kalive;
-  Chk1Activation: Chk1I + Rad9A => Chk1A + Rad9A; Chk1I*Chk1Activation_k12*Rad9A*kalive;
-  Exo1inhibition: Exo1A + Rad53A => Exo1I + Rad53A; Exo1A*Exo1inhibition_k13*Rad53A*kalive;
-  Dun1activation: Dun1I + Rad53A => Dun1A + Rad53A; Dun1I*Dun1activation_k14*Rad53A*kalive;
-  Chk1cellArrest: Chk1A + G2Mon => Chk1A + G2Moff; Chk1A*G2Mon*Chk1cellArrest_k15*kalive;
-  Dun1cellArrest: Dun1A + G2Mon => Dun1A + G2Moff; Dun1A*G2Mon*Dun1cellArrest_k16*kalive;
-  SDNArepair1: Mec1RPAssDNA + S => Mec1 + RPA + S + 3 ssDNA; SDNArepair1_k17a*Mec1RPAssDNA*S*kalive;
-  G2DNArepair1: G2 + G2Moff + Mec1RPAssDNA => G2 + G2Moff + Mec1 + RPA + 3 ssDNA; G2*G2Moff*G2DNArepair1_k17b*Mec1RPAssDNA*kalive;
-  SDNArepair2: S + ssDNA => S; SDNArepair2_k18a*S*ssDNA*kalive;
-  G2DNArepair2: G2 + G2Moff + ssDNA => G2 + G2Moff; G2*G2Moff*G2DNArepair2_k18b*ssDNA*kalive;
-  Recovery: Cdc13 + Rad17Utelo + recovery => Ctelo + Rad17 + recovery; Cdc13*Recovery_k19*Rad17Utelo*recovery*kalive;
-  G1cyclinSynthesis: G1 => G1cyclin + G1; G1*G1cyclinSynthesis_kc1*kalive;
-  ScyclinSynthesis: S => Scyclin + S; ScyclinSynthesis_kc1*S*kalive;
-  G2cyclinSynthesis: G2 => G2cyclin + G2; G2*G2cyclinSynthesis_kc1*kalive;
-  McyclinSynthesis: M => Mcyclin + M; McyclinSynthesis_kc1*M*kalive;
-  G1toSGenesOn: G1Soff + G1 + G1CdkA => G1Son + G1 + G1CdkA; G1*G1CdkA*G1Soff*G1toSGenesOn_kc2*kalive;
-  StoG2GenesOn: SG2off + S + SCdkA => SG2on + S + SCdkA; StoG2GenesOn_kc2*S*SCdkA*SG2off*kalive;
-  G2toMGenesOn: G2Moff + G2 + G2CdkA => G2Mon + G2 + G2CdkA; G2*G2CdkA*G2Moff*G2toMGenesOn_kc2*kalive;
-  MtoG1GenesOn: MG1off + M + MCdkA => MG1on + M + MCdkA; MtoG1GenesOn_kc2*M*MCdkA*MG1off*kalive;
-  G1cyclinDegradation: G1cyclin => $sink; G1cyclin*G1cyclinDegradation_kc3*kalive;
-  ScyclinDegradation: Scyclin => $sink; ScyclinDegradation_kc3*Scyclin*kalive;
-  G2cyclinDegradation: G2cyclin => $sink; G2cyclin*G2cyclinDegradation_kc3*kalive;
-  McyclinDegradation: Mcyclin => $sink; McyclinDegradation_kc3*Mcyclin*kalive;
-  G1toSProgession: G1 + G1CdkA + G1Son => G1CdkI + G1Soff + S; G1*G1CdkA*G1Son*G1toSProgession_kc4*kalive;
-  StoG2Progession: S + SCdkA + SG2on => G2 + SCdkI + SG2off; StoG2Progession_kc4*S*SCdkA*SG2on*kalive;
-  G2toMProgession: G2 + G2CdkA + G2Mon => G2CdkI + G2Moff + M; G2*G2CdkA*G2Mon*G2toMProgession_kc4*kalive;
-  MtoG1Progession: M + MCdkA + MG1on => budscar + G1 + MCdkI + MG1off; MtoG1Progession_kc4*M*MCdkA*MG1on*kalive;
-
-  // Events:
-  Rad9KinaseActivation: at Mec1RPAssDNA >= 800: Rad9Kin = 1;
-  ssDNAremoval: at (Mec1RPAssDNA + RPAssDNA + ssDNA) <= 1: ssDNA = 0, RPAssDNA = 0, Mec1RPAssDNA = 0, recovery = 1;
-  G2MRecoveryCompleted: at (G2 == 1) && (Rad17Utelo == 0): Rad53A = 0, Rad53I = 6900, ExoXI = 70, ExoXA = 0, Exo1I = 670, Exo1A = 0, Dun1I = 3000, Dun1A = 0, Chk1I = 60, Chk1A = 0, Rad9I = 20, Rad9A = 0, recovery = 0, G2Moff = 0, G2Mon = 1;
-  SphaseRecoveryCompleted: at Rad17Utelo == 0: recovery = 0;
-  G1CdkActivation: at G1cyclin > 100: G1CdkI = 0, G1CdkA = 1;
-  SCdkActivation: at Scyclin > 100: SCdkI = 0, SCdkA = 1;
-  G2CdkActivation: at G2cyclin > 100: G2CdkI = 0, G2CdkA = 1;
-  MCdkActivation: at Mcyclin > 100: MCdkI = 0, MCdkA = 1;
-  CellDeath: at (Mec1RPAssDNA + RPAssDNA + ssDNA) >= 2000: kalive = 0;
-
-  // Species initializations:
-  Ctelo = 64/nucleus;
-  Utelo = 0;
-  Cdc13 = 300/nucleus;
-  Rad17Utelo = 0;
-  Rad17 = 70/nucleus;
-  Rad24 = 70/nucleus;
-  RPA = 4000/nucleus;
-  Mec1 = 4000/nucleus;
-  ssDNA = 0;
-  RPAssDNA = 0;
-  RPAssDNA1 = 0;
-  RPAssDNA2 = 0;
-  Mec1RPAssDNA = 0;
-  ExoXI = 70/nucleus;
-  ExoXA = 0;
-  Exo1I = 670/nucleus;
-  Exo1A = 0;
-  Rad9I = 20/nucleus;
-  Rad9A = 0;
-  Rad53I = 6900/nucleus;
-  Rad53A = 0;
-  Chk1I = 60/nucleus;
-  Chk1A = 0;
-  Dun1I = 3000/nucleus;
-  Dun1A = 0;
-  ATP = 10000/nucleus;
-  ADP = 1000/nucleus;
-  Rad9Kin = 0;
-  recovery = 0;
-  G1 = 1/nucleus;
-  S = 0;
-  G2 = 0;
-  M = 0;
-  G1cyclin = 0;
-  Scyclin = 0;
-  G2cyclin = 0;
-  Mcyclin = 0;
-  G1CdkI = 1/nucleus;
-  G1CdkA = 0;
-  SCdkI = 1/nucleus;
-  SCdkA = 0;
-  G2CdkI = 1/nucleus;
-  G2CdkA = 0;
-  MCdkI = 1/nucleus;
-  MCdkA = 0;
-  G1Soff = 1/nucleus;
-  G1Son = 0;
-  SG2off = 1/nucleus;
-  SG2on = 0;
-  G2Moff = 1/nucleus;
-  G2Mon = 0;
-  MG1off = 1/nucleus;
-  MG1on = 0;
-  sink = 0;
-  budscar = 0;
-
-  // Compartment initializations:
-  cellMembrane = 1;
-  nucleus = 1;
-
-  // Variable initializations:
-  kalive = 1;
-  Capping_k1 = 0.0005;
-  Uncapping_k2 = 0.000385;
-  Rad17binding_k3 = 1.5e-08;
-  ExoXactivation_k4 = 0.01;
-  ExoXactivity_k5 = 0.0003;
-  Exo1activation_k6a = 5e-05;
-  Exo1Rad24dependentActivation_k6b = 0.0005;
-  Exo1Rad17independentActivity_k7a = 3e-05;
-  Exo1Rad17dependentActivity_k7b = 3e-05;
-  RPAbinding1_k8a = 0.001;
-  RPAbinding2_k8b = 100;
-  RPAbinding_k8c = 100;
-  Mec1binding_k8d = 0.004;
-  Rad9activation_k9 = 100;
-  ExoXinhibition_k10a = 0.05;
-  ExoXinhibition2_k10b = 0.05;
-  Rad53activation_k11 = 1e-05;
-  Chk1Activation_k12 = 0.00017;
-  Exo1inhibition_k13 = 1;
-  Dun1activation_k14 = 3.3e-06;
-  Chk1cellArrest_k15 = 0.2;
-  Dun1cellArrest_k16 = 0.1;
-  SDNArepair1_k17a = 0.05;
-  G2DNArepair1_k17b = 0.05;
-  SDNArepair2_k18a = 0.001;
-  G2DNArepair2_k18b = 1e-05;
-  Recovery_k19 = 0.001;
-  G1cyclinSynthesis_kc1 = 0.16;
-  ScyclinSynthesis_kc1 = 0.16;
-  G2cyclinSynthesis_kc1 = 0.16;
-  McyclinSynthesis_kc1 = 0.16;
-  G1toSGenesOn_kc2 = 0.01;
-  StoG2GenesOn_kc2 = 0.01;
-  G2toMGenesOn_kc2 = 0.01;
-  MtoG1GenesOn_kc2 = 0.01;
-  G1cyclinDegradation_kc3 = 0.0012;
-  ScyclinDegradation_kc3 = 0.0012;
-  G2cyclinDegradation_kc3 = 0.0012;
-  McyclinDegradation_kc3 = 0.0012;
-  G1toSProgession_kc4 = 0.01;
-  StoG2Progession_kc4 = 0.01;
-  G2toMProgession_kc4 = 0.01;
-  MtoG1Progession_kc4 = 0.01;
-
-  // Other declarations:
-  var kalive;
-  const cellMembrane, nucleus;
-
-  // Unit definitions:
-  unit substance = item;
-
-  // Display Names:
-  Exo1activation is "Rad24independentExo1Activation";
-  Exo1Rad24dependentActivation is "Rad24dependentExo1Activation";
-  Exo1Rad17independentActivity is "Rad17independentExo1Activity";
-  Exo1Rad17dependentActivity is "Rad17dependentExo1Activity";
-  RPAbinding1 is "RPAbinding-stage1";
-  RPAbinding2 is "RPAbinding-stage2";
-  RPAbinding is "RPAbinding-completed";
-
-  // CV terms:
-  cellMembrane hypernym "http://identifiers.org/obo.go/GO:0016020"
-  nucleus hypernym "http://identifiers.org/obo.go/GO:0005634"
-  Ctelo part "http://identifiers.org/obo.go/GO:0000782"
-  Ctelo hypernym "http://identifiers.org/obo.go/GO:0000781"
-  Utelo hypernym "http://identifiers.org/obo.go/GO:0000781"
-  Cdc13 identity "http://identifiers.org/uniprot/P32797"
-  Rad17Utelo part "http://identifiers.org/uniprot/P48581",
-                  "http://identifiers.org/obo.go/GO:0000781"
-  Rad17 identity "http://identifiers.org/uniprot/P48581"
-  Rad24 identity "http://identifiers.org/uniprot/P32641"
-  RPA hypernym "http://identifiers.org/pirsf/PIRSF002091"
-  Mec1 identity "http://identifiers.org/uniprot/P38111"
-  ssDNA hypernym "http://identifiers.org/obo.chebi/CHEBI:09160",
-                 "http://identifiers.org/kegg.compound/C00271"
-  RPAssDNA part "http://identifiers.org/kegg.compound/C00271",
-                "http://identifiers.org/pirsf/PIRSF002091",
-                "http://identifiers.org/chebi/CHEBI:9160"
-  RPAssDNA1 part "http://identifiers.org/kegg.compound/C00271",
-                 "http://identifiers.org/pirsf/PIRSF002091",
-                 "http://identifiers.org/chebi/CHEBI:9160"
-  RPAssDNA2 part "http://identifiers.org/kegg.compound/C00271",
-                 "http://identifiers.org/pirsf/PIRSF002091",
-                 "http://identifiers.org/chebi/CHEBI:9160"
-  Mec1RPAssDNA part "http://identifiers.org/uniprot/P38111",
-                    "http://identifiers.org/kegg.compound/C00271",
-                    "http://identifiers.org/pirsf/PIRSF002091",
-                    "http://identifiers.org/chebi/CHEBI:9160"
-  ExoXI homolog "http://identifiers.org/uniprot/P0AEK1"
-  ExoXA homolog "http://identifiers.org/uniprot/P0AEK1"
-  Exo1I identity "http://identifiers.org/uniprot/P39875"
-  Exo1A hypernym "http://identifiers.org/uniprot/P39875"
-  Rad9I hypernym "http://identifiers.org/uniprot/P14737"
-  Rad9A identity "http://identifiers.org/uniprot/P14737"
-  Rad53I identity "http://identifiers.org/uniprot/P22216"
-  Rad53A hypernym "http://identifiers.org/uniprot/P22216"
-  Chk1I identity "http://identifiers.org/uniprot/P38147"
-  Chk1A identity "http://identifiers.org/uniprot/P38147"
-  Dun1I identity "http://identifiers.org/uniprot/P39009"
-  Dun1A identity "http://identifiers.org/uniprot/P39009"
-  ATP identity "http://identifiers.org/obo.chebi/CHEBI:15422"
-  ADP identity "http://identifiers.org/obo.chebi/CHEBI:16761"
-  G1 hypernym "http://identifiers.org/obo.go/GO:0051318"
-  S hypernym "http://identifiers.org/obo.go/GO:0000084"
-  G2 hypernym "http://identifiers.org/obo.go/GO:0051319"
-  M hypernym "http://identifiers.org/obo.go/GO:0000279"
-  G1cyclin version "http://identifiers.org/uniprot/P20437"
-  Scyclin version "http://identifiers.org/uniprot/P30283"
-  G2cyclin version "http://identifiers.org/uniprot/P24868"
-  Mcyclin homolog "http://identifiers.org/uniprot/O14332"
-  G1CdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
-  G1CdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
-  SCdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
-  SCdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
-  G2CdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
-  G2CdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
-  MCdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
-  MCdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
-  G1Soff hypernym "http://identifiers.org/obo.go/GO:0031575"
-  G1Son hypernym "http://identifiers.org/obo.go/GO:0000082"
-  SG2off hypernym "http://identifiers.org/obo.go/GO:0000115"
-  SG2on hypernym "http://identifiers.org/obo.go/GO:0000115"
-  G2Moff hypernym "http://identifiers.org/obo.go/GO:0031572"
-  G2Mon hypernym "http://identifiers.org/obo.go/GO:0000086"
-  MG1on hypernym "http://identifiers.org/obo.go/GO:0000087"
-  budscar hypernym "http://identifiers.org/obo.go/GO:0005621"
-  Capping hypernym "http://identifiers.org/obo.go/GO:0016233"
-  Uncapping hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Rad17binding hypernym "http://identifiers.org/obo.go/GO:0005515",
-                        "http://identifiers.org/obo.go/GO:0016887"
-  ExoXactivation hypernym "http://identifiers.org/obo.go/GO:0032075"
-  ExoXactivity hypernym "http://identifiers.org/obo.go/GO:0008856"
-  ExoXactivity hypernym "http://identifiers.org/ec-code/3.1.11.1"
-  Exo1activation hypernym "http://identifiers.org/obo.go/GO:0032075"
-  Exo1Rad24dependentActivation hypernym "http://identifiers.org/obo.go/GO:0032075"
-  Exo1Rad17independentActivity hypernym "http://identifiers.org/obo.go/GO:0008856"
-  Exo1Rad17dependentActivity hypernym "http://identifiers.org/obo.go/GO:0008856"
-  RPAbinding1 hypernym "http://identifiers.org/obo.go/GO:0003676",
-                       "http://identifiers.org/obo.go/GO:0005515"
-  RPAbinding2 hypernym "http://identifiers.org/obo.go/GO:0003676",
-                       "http://identifiers.org/obo.go/GO:0032403"
-  RPAbinding hypernym "http://identifiers.org/obo.go/GO:0003676",
-                      "http://identifiers.org/obo.go/GO:0032403"
-  Mec1binding hypernym "http://identifiers.org/obo.go/GO:0005515"
-  Mec1binding hypernym "http://identifiers.org/obo.go/GO:0006461"
-  Rad9activation hypernym "http://identifiers.org/obo.go/GO:0030295"
-  ExoXinhibition hypernym "http://identifiers.org/obo.go/GO:0004860"
-  ExoXinhibition2 hypernym "http://identifiers.org/obo.go/GO:0004860"
-  Rad53activation hypernym "http://identifiers.org/obo.go/GO:0030295"
-  Chk1Activation hypernym "http://identifiers.org/obo.go/GO:0030295"
-  Exo1inhibition hypernym "http://identifiers.org/obo.go/GO:0004860"
-  Dun1activation hypernym "http://identifiers.org/obo.go/GO:0030295"
-  Chk1cellArrest hypernym "http://identifiers.org/obo.go/GO:0007050"
-  Dun1cellArrest hypernym "http://identifiers.org/obo.go/GO:0007050"
-  SDNArepair1 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  SDNArepair1 hypernym "http://identifiers.org/obo.go/GO:0006281"
-  G2DNArepair1 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  G2DNArepair1 hypernym "http://identifiers.org/obo.go/GO:0006281"
-  SDNArepair2 hypernym "http://identifiers.org/obo.go/GO:0006308"
-  G2DNArepair2 hypernym "http://identifiers.org/obo.go/GO:0006308"
-  Recovery hypernym "http://identifiers.org/obo.go/GO:0005515",
-                    "http://identifiers.org/obo.go/GO:0016233"
-  G1cyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  ScyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  G2cyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  McyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
-  G1toSGenesOn hypernym "http://identifiers.org/obo.go/GO:0007089"
-  G2toMGenesOn hypernym "http://identifiers.org/obo.go/GO:0031572"
-  G1cyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
-  ScyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
-  G2cyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
-  McyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
-  G1toSProgession hypernym "http://identifiers.org/obo.go/GO:0000082"
-  G2toMProgession hypernym "http://identifiers.org/obo.go/GO:0000086"
-  MtoG1Progession hypernym "http://identifiers.org/obo.go/GO:0000216"
-end
-
-YeastWTmodel2 is "Proctor2006_telomere"
-
-YeastWTmodel2 model_entity_is "http://identifiers.org/biomodels.db/MODEL8679489165"
-YeastWTmodel2 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000087"
-YeastWTmodel2 description "http://identifiers.org/pubmed/17015293"
-YeastWTmodel2 taxon "http://identifiers.org/taxonomy/4932"
-YeastWTmodel2 parthood "http://identifiers.org/kegg.pathway/sce04111"
-YeastWTmodel2 hypernym "http://identifiers.org/obo.go/GO:0000075"
diff --git a/BioModelsRAG/data/BIOMD0000000088.txt b/BioModelsRAG/data/BIOMD0000000088.txt
deleted file mode 100644
index 17b6bdeaa7dae68b9b5c387225d84776ea798f46..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000088.txt
+++ /dev/null
@@ -1,1373 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Maeda2006_MyosinPhosphorylation()
-
-  // Compartments and Species:
-  compartment c0, c1, c2;
-  species $s2 in c0, s174 in c1, s130 in c1, s4 in c0, s57 in c1, s93 in c1;
-  species s165 in c1, s183 in c1, s55 in c1, s184 in c1, $s48 in c1, s187 in c1;
-  species $s50 in c1, s171 in c1, s173 in c1, s98 in c1, s124 in c1, s118 in c1;
-  species s153 in c1, s152 in c1, s213 in c1, s214 in c1, $s151 in c1, s164 in c1;
-  species s231 in c1, s233 in c1, s245 in c1, s252 in c1, s277 in c1, s278 in c1;
-  species s279 in c1, s280 in c1, s289 in c1, s292 in c1, s293 in c1, s294 in c1;
-  species s295 in c1, s309 in c1, s310 in c1, s311 in c1, s314 in c1, s324 in c1;
-  species s329 in c1, s330 in c1, s331 in c1, s332 in c1, s335 in c1, s338 in c1;
-  species s352 in c1, s355 in c1, s349 in c1, s360 in c1, s358 in c1, s361 in c1;
-  species s362 in c1, s350 in c1, s135 in c1, s276 in c1, s172 in c2, s410 in c1;
-  species s421 in c1, s424 in c1, s430 in c1, s432 in c1, s435 in c1, s436 in c1;
-  species s437 in c1, s438 in c1, s439 in c1, s440 in c1, s441 in c1, s442 in c1;
-  species s443 in c1, s444 in c1, s446 in c1, s449 in c1, s456 in c1, s359 in c1;
-  species s463 in c1, s467 in c1, s470 in c1, s477 in c1, s480 in c1, s491 in c1;
-  species s487 in c1, s496 in c1, s506 in c1, s512 in c1, s513 in c1, s520 in c1;
-  species s526 in c1, s539 in c1, s546 in c1, s551 in c1, $s556 in c1, $s267 in c0;
-  species $s557 in c1, s564 in c1, s565 in c1, s566 in c1, s567 in c1, s568 in c1;
-  species s569 in c1, s351 in c1, s570 in c1;
-
-  // Reactions:
-  re1: $s2 + s130 -> s174; c1*((1 + re1_ratio)*re1_Vmax*s130*s2/re1_Km - re1_Vmax*re1_ratio*s174);
-  re12: $s48 + s435 => s439 + s410 + $s50 + s55; c1*re12_kf*s48*s435;
-  re14: s55 => s183; c1*re14_kf*s55;
-  re15: s442 + s57 -> s441; c1*(re15_kf*s442*s57 - re15_kb*s441);
-  re16: s441 + $s48 => s187 + s55 + $s50 + s421; c1*re16_kf*s48*s441;
-  re17: s439 => s438; c1*re17_kf*s439;
-  re19: s410 + s438 => s437; c1*re19_kf*s410*s438;
-  re20: s93 + s187 -> s184; c1*((1 + re20_ratio)*re20_Vmax*s187*s93/re20_Km - re20_ratio*re20_Vmax*s184);
-  re22: s421 + s440 => s442; c1*re22_kf*s421*s440;
-  re23: s439 + s98 -> s436; c1*(re23_kf*s439*s98 - re23_kb*s436);
-  re24: s231 => s214; c1*(re24_Vmax*s231*s436/(re24_Km + s214));
-  re26: s98 + s231 -> s233; c1*((1 + re26_ratio)*re26_Vmax*s98*s231/re26_Km - re26_Vmax*re26_ratio*s233);
-  re28: s118 + s214 -> s213; c1*((1 + re28_ratio)*re28_Vmax*s118*s214/re28_Km - re28_Vmax*re28_ratio*s213);
-  re32: s233 => s214 + s98; c1*re32_Vmax*s233;
-  re33: s213 => s231 + s118; c1*re33_Vmax*s213;
-  re34: s184 => s440 + s93; c1*re34_Vmax*s184;
-  re37: s436 => s438 + s98; c1*re37_kf*s436;
-  re38: s214 => s231; c1*re38_kf*s214;
-  re39: s124 + s214 -> s252; c1*(re39_kf*s124*s214 - re39_kb*s252);
-  re40: s174 => s57 + s4 + $s2; c1*re40_Vmax*s174;
-  re43: s437 + s57 -> s435; c1*(re43_kf*s437*s57 - re43_kb*s435);
-  re44: s187 => s440; c1*re44_kf*s187;
-  re45: s57 => s183; c1*re45_kf*s57;
-  re47: s187 + s569 -> s564; c1*(re47_kf*s187*s569 - re47_kb*s564);
-  re48: s424 + s187 -> s443; c1*(re48_kf*s424*s187 - re48_kb*s443);
-  re51: s135 + s443 -> s564; c1*(re51_kf*s135*s443 - re51_kb*s564);
-  re52: s424 + s135 -> s569; c1*(re52_kf*s424*s135 - re52_kb*s569);
-  re54: s564 => s569 + s440; c1*re54_kf*s564;
-  re55: s569 + $s151 -> s568; c1*((1 + re55_ratio)*re55_Vmax*s569*s151/re55_Km - re55_ratio*re55_Vmax*s568);
-  re56: s564 + $s151 -> s567; c1*((1 + re56_ratio)*re56_Vmax*s564*s151/re56_Km - re56_ratio*re56_Vmax*s567);
-  re57: s568 => s152 + s153 + s569; c1*re57_Vmax*s568;
-  re58: s567 => s153 + s152 + s564; c1*re58_Vmax*s567;
-  re59: s153 => s164; c1*re59_kf*s153;
-  re60: s152 => s165; c1*re60_kf*s152;
-  re68: s171 + 3 s152 -> s173; c1*(re68_kf*s152*s152*s152*s171 - re68_kb*s173);
-  re73: s172 -> s135; c1*re73_g*s173*(s172 - s135);
-  re85: s444 => 2 s172 + s430; c1*re85_kf*s444;
-  re86: s276 + s135 -> s277; c1*(re86_kf*s276*s135 - re86_kb*s277);
-  re87: s277 + s135 -> s278; c1*(re87_kf*s277*s135 - re87_kb*s278);
-  re88: s279 + s135 -> s280; c1*(re88_kf*s279*s135 - re88_kb*s280);
-  re89: s278 + s135 -> s279; c1*(re89_kf*s278*s135 - re89_kb*s279);
-  re90: s280 + s289 -> s295; c1*(re90_kf*s280*s289 - re90_kb*s295);
-  re91: s279 + s289 -> s294; c1*(re91_kf*s279*s289 - re91_kb*s294);
-  re92: s278 + s289 -> s293; c1*(re92_kf*s278*s289 - re92_kb*s293);
-  re93: s277 + s289 -> s292; c1*(re93_kf*s277*s289 - re93_kb*s292);
-  re94: s309 -> s310; c1*(re94_kf*s309 - re94_kb*s310);
-  re95: s309 + s153 -> s311; c1*(re95_kf*s309*s153 - re95_kb*s311);
-  re96: s566 -> s314; c1*(re96_kf*s566 - re96_kb*s314);
-  re97: s309 + s135 -> s566; c1*(re97_kf*s309*s135 - re97_kb*s566);
-  re98: s446 => s432 + $s267; c1*re98_Vmax*s446;
-  re100: s430 + 2 s135 -> s444; c1*(re100_kf*s135*s135*s430 - re100_kb*s444);
-  re101: s566 + s153 -> s565; c1*(re101_kf*s566*s153 - re101_kb*s565);
-  re102: s565 -> s324; c1*(re102_kf*s565 - re102_kb*s324);
-  re106: s324 => s329; c1*re106_kf*s324;
-  re107: s314 => s330; c1*re107_kf*s314;
-  re108: s310 => s331; c1*re108_kf*s310;
-  re109: s432 + s135 -> s446; c1*((1 + re109_ratio)*re109_Vmax*s432*s135/re109_Km - re109_Vmax*re109_ratio*s446);
-  re110: s324 + s349 -> s338; c1*((1 + re110_ratio)*re110_Vmax*s324*s349/re110_Km - re110_Vmax*re110_ratio*s338);
-  re111: s314 + s349 -> s335; c1*((1 + re111_ratio)*re111_Vmax*s314*s349/re111_Km - re111_ratio*re111_Vmax*s335);
-  re112: s310 + s349 -> s332; c1*((1 + re112_ratio)*re112_Vmax*s310*s349/re112_Km - re112_Vmax*re112_ratio*s332);
-  re113: s338 => s324 + s350; c1*re113_Vmax*s338;
-  re114: s335 => s314 + s350; c1*re114_Vmax*s335;
-  re115: s332 => s310 + s350; c1*re115_Vmax*s332;
-  re116: s350 => s349; c1*re116_kf*s350;
-  re117: s351 + s350 -> s352; c1*(re117_kf*s351*s350 - re117_kb*s352);
-  re118: s351 + s349 -> s355; c1*(re118_kf*s351*s349 - re118_kb*s355);
-  re119: s352 => s355; c1*re119_kf*s352;
-  re120: s124 + s358 -> s361; c1*((1 + re120_ratio)*re120_Vmax*s124*s358/re120_Km - re120_Vmax*re120_ratio*s361);
-  re121: s124 + s359 -> s362; c1*((1 + re121_ratio)*re121_Vmax*s124*s359/re121_Km - re121_Vmax*re121_ratio*s362);
-  re123: s361 => s359 + s124; c1*re123_Vmax*s361;
-  re124: s362 => s360 + s124; c1*re124_Vmax*s362;
-  re125: s252 + s358 -> s456; c1*((1 + re125_ratio)*re125_Vmax*s252*s358/re125_Km - re125_Vmax*re125_ratio*s456);
-  re126: s252 + s359 => s449; c1*((1 + re126_ratio)*re126_Vmax*s252*s359/re126_Km - re126_Vmax*re126_ratio*s449);
-  re127: s456 => s252 + s359; c1*re127_Vmax*s456;
-  re128: s449 => s252 + s360; c1*re128_Vmax*s449;
-  re129: s124 + s351 -> s463; c1*((1 + re129_ratio)*re129_Vmax*s124*s351/re129_Km - re129_Vmax*re129_ratio*s463);
-  re130: s463 => s124 + s570; c1*re130_Vmax*s463;
-  re131: s252 + s351 -> s496; c1*((1 + re131_ratio)*re131_Vmax*s252*s351/re131_Km - re131_Vmax*re131_ratio*s496);
-  re132: s496 => s252 + s570; c1*re132_Vmax*s496;
-  re133: s360 + s570 -> s467; c1*((1 + re133_ratio)*re133_Vmax*s360*s570/re133_Km - re133_Vmax*re133_ratio*s467);
-  re134: s360 + s351 -> s470; c1*((1 + re134_ratio)*re134_Vmax*s360*s351/re134_Km - re134_Vmax*re134_ratio*s470);
-  re135: s359 + s570 -> s477; c1*((1 + re135_ratio)*re135_Vmax*s359*s570/re135_Km - re135_Vmax*re135_ratio*s477);
-  re136: s359 + s351 -> s480; c1*((1 + re136_ratio)*re136_Vmax*s351*s359/re136_Km - re136_Vmax*re136_ratio*s480);
-  re137: s467 => s359 + s570; c1*re137_Vmax*s467;
-  re138: s470 => s359 + s351; c1*re138_Vmax*s470;
-  re139: s477 => s358 + s570; c1*re139_Vmax*s477;
-  re140: s480 => s358 + s351; c1*re140_Vmax*s480;
-  re141: s570 => s351; c1*re141_kf*s570;
-  re154: s358 + s289 -> s487; c1*((1 + re154_ratio)*re154_Vmax*s289*s358/re154_Km - re154_Vmax*re154_ratio*s487);
-  re155: s359 + s289 -> s491; c1*((1 + re155_ratio)*re155_Vmax*s289*s359/re155_Km - re155_Vmax*re155_ratio*s491);
-  re156: s487 => s359 + s289; c1*re156_Vmax*s487;
-  re157: s491 => s360 + s289; c1*re157_Vmax*s491;
-  re158: s358 + s292 -> s551; c1*((1 + re158_ratio)*re158_Vmax*s292*s358/re158_Km - re158_Vmax*re158_ratio*s551);
-  re159: s358 + s293 -> s539; c1*((1 + re159_ratio)*re159_Vmax*s293*s358/re159_Km - re159_Vmax*re159_ratio*s539);
-  re160: s358 + s294 -> s520; c1*((1 + re160_ratio)*re160_Vmax*s294*s358/re160_Km - re160_Vmax*re160_ratio*s520);
-  re161: s358 + s295 -> s513; c1*((1 + re161_ratio)*re161_Vmax*s295*s358/re161_Km - re161_Vmax*re161_ratio*s513);
-  re162: s359 + s292 -> s546; c1*((1 + re162_ratio)*re162_Vmax*s292*s359/re162_Km - re162_Vmax*re162_ratio*s546);
-  re163: s359 + s293 -> s526; c1*((1 + re163_ratio)*re163_Vmax*s293*s359/re163_Km - re163_Vmax*re163_ratio*s526);
-  re164: s359 + s294 -> s512; c1*((1 + re164_ratio)*re164_Vmax*s294*s359/re164_Km - re164_Vmax*re164_ratio*s512);
-  re165: s359 + s295 -> s506; c1*((1 + re165_ratio)*re165_Vmax*s295*s359/re165_Km - re165_Vmax*re165_ratio*s506);
-  re166: s506 => s360 + s295; c1*re166_Vmax*s506;
-  re167: s513 => s359 + s295; c1*re167_Vmax*s513;
-  re168: s512 => s360 + s294; c1*re168_Vmax*s512;
-  re169: s520 => s359 + s294; c1*re169_Vmax*s520;
-  re170: s526 => s360 + s293; c1*re170_Vmax*s526;
-  re171: s539 => s359 + s293; c1*re171_Vmax*s539;
-  re172: s546 => s360 + s292; c1*re172_Vmax*s546;
-  re173: s551 => s359 + s292; c1*re173_Vmax*s551;
-  re174: $s267 -> s135; c1*re174_g*s556*(s267 - s135);
-  re175: s172 -> s135; c1*re175_g*s557*(s172 - s135);
-
-  // Events:
-  event_0000001: at time >= 300: s2 = 0.01;
-
-  // Species initializations:
-  s2 = 0;
-  s174 = 0;
-  s130 = 0.42;
-  s4 = 0;
-  s57 = 0;
-  s93 = 0.2;
-  s165 = 0;
-  s183 = 0;
-  s55 = 0;
-  s184 = 0;
-  s48 = 50;
-  s187 = 0;
-  s50 = 5;
-  s171 = 0.008333;
-  s173 = 0;
-  s98 = 0.1;
-  s124 = 0.042;
-  s118 = 0.1;
-  s153 = 0;
-  s152 = 0.3;
-  s213 = 0;
-  s214 = 0.005;
-  s151 = 10;
-  s164 = 0;
-  s231 = 0.09;
-  s233 = 0;
-  s245 = 0;
-  s252 = 0.005;
-  s277 = 0.3;
-  s278 = 0;
-  s279 = 0;
-  s280 = 0;
-  s289 = 0.69;
-  s292 = 0.05;
-  s293 = 0;
-  s294 = 0;
-  s295 = 0;
-  s309 = 2;
-  s310 = 0.039823;
-  s311 = 0;
-  s314 = 0.68193;
-  s324 = 0;
-  s329 = 0;
-  s330 = 0;
-  s331 = 0;
-  s332 = 0;
-  s335 = 0;
-  s338 = 0;
-  s352 = 0;
-  s355 = 0;
-  s349 = 0.059;
-  s360 = 0.1;
-  s358 = 4.3;
-  s361 = 0;
-  s362 = 0;
-  s350 = 0;
-  s135 = 0.0833;
-  s276 = 19.65;
-  s172 = 155;
-  s410 = 0;
-  s421 = 0;
-  s424 = 0.57;
-  s430 = 0.5;
-  s432 = 0.1;
-  s435 = 0;
-  s436 = 0;
-  s437 = 0.5;
-  s438 = 0;
-  s439 = 0;
-  s440 = 0;
-  s441 = 0;
-  s442 = 0.5;
-  s443 = 0;
-  s444 = 0;
-  s446 = 0;
-  s449 = 0;
-  s456 = 0;
-  s359 = 0.6;
-  s463 = 0;
-  s467 = 0;
-  s470 = 0;
-  s477 = 0;
-  s480 = 0;
-  s491 = 0;
-  s487 = 0;
-  s496 = 0;
-  s506 = 0;
-  s512 = 0;
-  s513 = 0;
-  s520 = 0;
-  s526 = 0;
-  s539 = 0;
-  s546 = 0;
-  s551 = 0;
-  s556 = 0.00833;
-  s267 = 4000;
-  s557 = 0.001;
-  s564 = 0;
-  s565 = 0;
-  s566 = 0.094;
-  s567 = 0;
-  s568 = 0.08;
-  s569 = 0.15;
-  s351 = 0.7;
-  s570 = 0.4941;
-
-  // Compartment initializations:
-  c0 = 1;
-  c1 = 1;
-  c2 = 0.1;
-
-  // Variable initializations:
-  re1_Km = 5;
-  re1_Km has microMolar;
-  re1_ratio = 4;
-  re1_ratio has dimensionless;
-  re1_Vmax = 15;
-  re1_Vmax has per_sec;
-  re12_kf = 0.01;
-  re12_kf has per_uM_per_sec;
-  re14_kf = 0.00224;
-  re14_kf has per_sec;
-  re15_kf = 1;
-  re15_kf has per_uM_per_sec;
-  re15_kb = 0.006;
-  re15_kb has per_sec;
-  re16_kf = 0.01;
-  re16_kf has per_uM_per_sec;
-  re17_kf = 0.0133;
-  re17_kf has per_sec;
-  re19_kf = 0.01;
-  re19_kf has per_uM_per_sec;
-  re20_Km = 0.05;
-  re20_Km has microMolar;
-  re20_ratio = 23.51;
-  re20_ratio has dimensionless;
-  re20_Vmax = 0.0102;
-  re20_Vmax has per_sec;
-  re22_kf = 0.01;
-  re22_kf has per_uM_per_sec;
-  re23_kf = 20;
-  re23_kf has per_uM_per_sec;
-  re23_kb = 0.1;
-  re23_kb has per_sec;
-  re24_Km = 0.015;
-  re24_Km has microMolar;
-  re24_Vmax = 0.052;
-  re24_Vmax has per_sec;
-  re26_Km = 2;
-  re26_Km has microMolar;
-  re26_ratio = 4;
-  re26_ratio has dimensionless;
-  re26_Vmax = 0.04;
-  re26_Vmax has per_sec;
-  re28_Km = 2.83;
-  re28_Km has microMolar;
-  re28_ratio = 13.246;
-  re28_ratio has dimensionless;
-  re28_Vmax = 0.993;
-  re28_Vmax has per_sec;
-  re32_Vmax = 0.04;
-  re32_Vmax has per_sec;
-  re33_Vmax = 0.9933;
-  re33_Vmax has per_sec;
-  re34_Vmax = 0.0102;
-  re34_Vmax has per_sec;
-  re37_kf = 0.0117;
-  re37_kf has per_sec;
-  re38_kf = 0.0003667;
-  re38_kf has per_sec;
-  re39_kf = 10;
-  re39_kf has per_uM_per_sec;
-  re39_kb = 0.5;
-  re39_kb has per_sec;
-  re40_Vmax = 15;
-  re40_Vmax has per_sec;
-  re43_kf = 1;
-  re43_kf has per_uM_per_sec;
-  re43_kb = 0.006;
-  re43_kb has per_sec;
-  re44_kf = 0.0133;
-  re44_kf has per_sec;
-  re45_kf = 0.00224;
-  re45_kf has per_sec;
-  re47_kf = 25.201;
-  re47_kf has per_uM_per_sec;
-  re47_kb = 1;
-  re47_kb has per_sec;
-  re48_kf = 2.5201;
-  re48_kf has per_uM_per_sec;
-  re48_kb = 1;
-  re48_kb has per_sec;
-  re51_kf = 30;
-  re51_kf has per_uM_per_sec;
-  re51_kb = 1;
-  re51_kb has per_sec;
-  re52_kf = 3;
-  re52_kf has per_uM_per_sec;
-  re52_kb = 1;
-  re52_kb has per_sec;
-  re54_kf = 0.0133;
-  re54_kf has per_sec;
-  re55_Km = 19.841;
-  re55_Km has microMolar;
-  re55_ratio = 4;
-  re55_ratio has dimensionless;
-  re55_Vmax = 10;
-  re55_Vmax has per_sec;
-  re56_Km = 5;
-  re56_Km has microMolar;
-  re56_ratio = 4;
-  re56_ratio has dimensionless;
-  re56_Vmax = 48;
-  re56_Vmax has per_sec;
-  re57_Vmax = 10;
-  re57_Vmax has per_sec;
-  re58_Vmax = 48;
-  re58_Vmax has per_sec;
-  re59_kf = 0.15;
-  re59_kf has per_sec;
-  re60_kf = 2.5;
-  re60_kf has per_sec;
-  re68_kf = 0.1;
-  re68_kf has per_uM3_per_sec;
-  re68_kb = 10;
-  re68_kb has per_sec;
-  re73_g = 150;
-  re73_g has per_uM_per_sec;
-  re85_kf = 1;
-  re85_kf has per_sec;
-  re86_kf = 10;
-  re86_kf has per_uM_per_sec;
-  re86_kb = 50;
-  re86_kb has per_sec;
-  re87_kf = 10;
-  re87_kf has per_uM_per_sec;
-  re87_kb = 45;
-  re87_kb has per_sec;
-  re88_kf = 10;
-  re88_kf has per_uM_per_sec;
-  re88_kb = 500;
-  re88_kb has per_sec;
-  re89_kf = 10;
-  re89_kf has per_uM_per_sec;
-  re89_kb = 170;
-  re89_kb has per_sec;
-  re90_kf = 10;
-  re90_kf has per_uM_per_sec;
-  re90_kb = 0.01;
-  re90_kb has per_sec;
-  re91_kf = 10;
-  re91_kf has per_uM_per_sec;
-  re91_kb = 0.01;
-  re91_kb has per_sec;
-  re92_kf = 0.1;
-  re92_kf has per_uM_per_sec;
-  re92_kb = 0.45;
-  re92_kb has per_sec;
-  re93_kf = 0.1;
-  re93_kf has per_uM_per_sec;
-  re93_kb = 0.5;
-  re93_kb has per_sec;
-  re94_kf = 1;
-  re94_kf has per_sec;
-  re94_kb = 50;
-  re94_kb has per_sec;
-  re95_kf = 0.0003;
-  re95_kf has per_uM_per_sec;
-  re95_kb = 0.1;
-  re95_kb has per_sec;
-  re96_kf = 1.2705;
-  re96_kf has per_sec;
-  re96_kb = 3.5026;
-  re96_kb has per_sec;
-  re97_kf = 0.3;
-  re97_kf has per_uM_per_sec;
-  re97_kb = 0.5;
-  re97_kb has per_sec;
-  re98_Vmax = 4.9;
-  re98_Vmax has per_sec;
-  re100_kf = 30;
-  re100_kf has per_uM2_per_sec;
-  re100_kb = 3;
-  re100_kb has per_sec;
-  re101_kf = 0.004;
-  re101_kf has per_uM_per_sec;
-  re101_kb = 8.6348;
-  re101_kb has per_sec;
-  re102_kf = 1;
-  re102_kf has per_sec;
-  re102_kb = 0.1;
-  re102_kb has per_sec;
-  re106_kf = 4.63e-05;
-  re106_kf has per_sec;
-  re107_kf = 4.63e-05;
-  re107_kf has per_sec;
-  re108_kf = 4.63e-05;
-  re108_kf has per_sec;
-  re109_Km = 0.04;
-  re109_Km has microMolar;
-  re109_ratio = 4;
-  re109_ratio has dimensionless;
-  re109_Vmax = 4.9;
-  re109_Vmax has per_sec;
-  re110_Km = 0.0014;
-  re110_Km has microMolar;
-  re110_ratio = 4;
-  re110_ratio has dimensionless;
-  re110_Vmax = 3.94;
-  re110_Vmax has per_sec;
-  re111_Km = 0.0014;
-  re111_Km has microMolar;
-  re111_ratio = 4;
-  re111_ratio has dimensionless;
-  re111_Vmax = 3.94;
-  re111_Vmax has per_sec;
-  re112_Km = 0.0014;
-  re112_Km has microMolar;
-  re112_ratio = 4;
-  re112_ratio has dimensionless;
-  re112_Vmax = 3.94;
-  re112_Vmax has per_sec;
-  re113_Vmax = 3.94;
-  re113_Vmax has per_sec;
-  re114_Vmax = 3.94;
-  re114_Vmax has per_sec;
-  re115_Vmax = 3.94;
-  re115_Vmax has per_sec;
-  re116_kf = 0.5;
-  re116_kf has per_sec;
-  re117_kf = 100;
-  re117_kf has per_uM_per_sec;
-  re117_kb = 0.62;
-  re117_kb has per_sec;
-  re118_kf = 0.01;
-  re118_kf has per_uM_per_sec;
-  re118_kb = 0.1;
-  re118_kb has per_sec;
-  re119_kf = 0.5;
-  re119_kf has per_sec;
-  re120_Km = 4.5099;
-  re120_Km has microMolar;
-  re120_ratio = 16.617;
-  re120_ratio has dimensionless;
-  re120_Vmax = 1.28;
-  re120_Vmax has per_sec;
-  re121_Km = 4.5099;
-  re121_Km has microMolar;
-  re121_ratio = 16.617;
-  re121_ratio has dimensionless;
-  re121_Vmax = 1.28;
-  re121_Vmax has per_sec;
-  re123_Vmax = 1.28;
-  re123_Vmax has per_sec;
-  re124_Vmax = 1.28;
-  re124_Vmax has per_sec;
-  re125_Km = 2.47;
-  re125_Km has microMolar;
-  re125_ratio = 0.4261;
-  re125_ratio has dimensionless;
-  re125_Vmax = 8.66;
-  re125_Vmax has per_sec;
-  re126_Km = 2.47;
-  re126_Km has microMolar;
-  re126_ratio = 0.4261;
-  re126_ratio has dimensionless;
-  re126_Vmax = 8.66;
-  re126_Vmax has per_sec;
-  re127_Vmax = 8.66;
-  re127_Vmax has per_sec;
-  re128_Vmax = 8.66;
-  re128_Vmax has per_sec;
-  re129_Km = 0.18;
-  re129_Km has microMolar;
-  re129_ratio = 0.23288;
-  re129_ratio has dimensionless;
-  re129_Vmax = 1.46;
-  re129_Vmax has per_sec;
-  re130_Vmax = 1.46;
-  re130_Vmax has per_sec;
-  re131_Km = 0.1;
-  re131_Km has microMolar;
-  re131_ratio = 0.028278;
-  re131_ratio has dimensionless;
-  re131_Vmax = 17.505;
-  re131_Vmax has per_sec;
-  re132_Vmax = 17.505;
-  re132_Vmax has per_sec;
-  re133_Km = 58.099;
-  re133_Km has microMolar;
-  re133_ratio = 28.795;
-  re133_ratio has dimensionless;
-  re133_Vmax = 1.95;
-  re133_Vmax has per_sec;
-  re134_Km = 16;
-  re134_Km has microMolar;
-  re134_ratio = 7.5865;
-  re134_ratio has dimensionless;
-  re134_Vmax = 9.317;
-  re134_Vmax has per_sec;
-  re135_Km = 58.099;
-  re135_Km has microMolar;
-  re135_ratio = 28.795;
-  re135_ratio has dimensionless;
-  re135_Vmax = 1.95;
-  re135_Vmax has per_sec;
-  re136_Km = 16;
-  re136_Km has microMolar;
-  re136_ratio = 7.5865;
-  re136_ratio has dimensionless;
-  re136_Vmax = 9.317;
-  re136_Vmax has per_sec;
-  re137_Vmax = 1.95;
-  re137_Vmax has per_sec;
-  re138_Vmax = 9.317;
-  re138_Vmax has per_sec;
-  re139_Vmax = 1.95;
-  re139_Vmax has per_sec;
-  re140_Vmax = 9.317;
-  re140_Vmax has per_sec;
-  re141_kf = 0.2;
-  re141_kf has per_sec;
-  re154_Km = 148.08;
-  re154_Km has microMolar;
-  re154_ratio = 39.349;
-  re154_ratio has dimensionless;
-  re154_Vmax = 3.67;
-  re154_Vmax has per_sec;
-  re155_Km = 148.08;
-  re155_Km has microMolar;
-  re155_ratio = 39.349;
-  re155_ratio has dimensionless;
-  re155_Vmax = 3.67;
-  re155_Vmax has per_sec;
-  re156_Vmax = 3.67;
-  re156_Vmax has per_sec;
-  re157_Vmax = 3.67;
-  re157_Vmax has per_sec;
-  re158_Km = 10.019;
-  re158_Km has microMolar;
-  re158_ratio = 1.7299;
-  re158_ratio has dimensionless;
-  re158_Vmax = 3.67;
-  re158_Vmax has per_sec;
-  re159_Km = 10.019;
-  re159_Km has microMolar;
-  re159_ratio = 1.7299;
-  re159_ratio has dimensionless;
-  re159_Vmax = 3.67;
-  re159_Vmax has per_sec;
-  re160_Km = 10.019;
-  re160_Km has microMolar;
-  re160_ratio = 1.7299;
-  re160_ratio has dimensionless;
-  re160_Vmax = 3.67;
-  re160_Vmax has per_sec;
-  re161_Km = 10.019;
-  re161_Km has microMolar;
-  re161_ratio = 1.7299;
-  re161_ratio has dimensionless;
-  re161_Vmax = 3.67;
-  re161_Vmax has per_sec;
-  re162_Km = 10.019;
-  re162_Km has microMolar;
-  re162_ratio = 1.7299;
-  re162_ratio has dimensionless;
-  re162_Vmax = 3.67;
-  re162_Vmax has per_sec;
-  re163_Km = 10.019;
-  re163_Km has microMolar;
-  re163_ratio = 1.7299;
-  re163_ratio has dimensionless;
-  re163_Vmax = 3.67;
-  re163_Vmax has per_sec;
-  re164_Km = 10.019;
-  re164_Km has microMolar;
-  re164_ratio = 1.7299;
-  re164_ratio has dimensionless;
-  re164_Vmax = 3.67;
-  re164_Vmax has per_sec;
-  re165_Km = 10.019;
-  re165_Km has microMolar;
-  re165_ratio = 1.7299;
-  re165_ratio has dimensionless;
-  re165_Vmax = 3.67;
-  re165_Vmax has per_sec;
-  re166_Vmax = 3.67;
-  re166_Vmax has per_sec;
-  re167_Vmax = 3.67;
-  re167_Vmax has per_sec;
-  re168_Vmax = 3.67;
-  re168_Vmax has per_sec;
-  re169_Vmax = 3.67;
-  re169_Vmax has per_sec;
-  re170_Vmax = 3.67;
-  re170_Vmax has per_sec;
-  re171_Vmax = 3.67;
-  re171_Vmax has per_sec;
-  re172_Vmax = 3.67;
-  re172_Vmax has per_sec;
-  re173_Vmax = 3.67;
-  re173_Vmax has per_sec;
-  re174_g = 0.01;
-  re174_g has per_uM_per_sec;
-  re175_g = 0.01;
-  re175_g has per_uM_per_sec;
-
-  // Other declarations:
-  const c0, c1, c2;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit microMolar = 1e-6 mole / litre;
-  unit per_uM_per_sec = litre / (1e-6 mole * second);
-  unit per_sec = 1 / second;
-  unit per_uM2_per_sec = litre^2 / ((1e-6 mole)^2 * second);
-  unit per_uM3_per_sec = litre^3 / ((1e-6 mole)^3 * second);
-
-  // Display Names:
-  substance is "micromoles";
-  c0 is "Default";
-  c1 is "cytosol";
-  c2 is "ER";
-  s2 is "thrombin";
-  s174 is "thrombin_R";
-  s130 is "pro_thrombinR";
-  s4 is "thrombin_ligand";
-  s57 is "thrombinR active";
-  s93 is "RGS";
-  s165 is "Inositol";
-  s183 is "sa40_degraded";
-  s55 is "thrombinR";
-  s184 is "RGS";
-  s48 is "GTP";
-  s187 is "G_sub_q_endsub__alpha_.GTP";
-  s50 is "GDP";
-  s171 is "IP3R";
-  s173 is "3IP3.IP3R";
-  s98 is "p115RhoGEF";
-  s124 is "Rho-kinase";
-  s118 is "RhoGAP";
-  s153 is "DAG";
-  s152 is "IP3";
-  s213 is "Rho_GAP";
-  s214 is "Rho.GTP";
-  s151 is "PIP2";
-  s164 is "PC";
-  s231 is "Rho.GDP";
-  s233 is "Rho_GEF";
-  s245 is "Rho_GEF_active";
-  s252 is "Rho.GTP.Rho-kinase";
-  s277 is "Ca_super_2_plus__endsuper_.CaM";
-  s278 is "2Ca_super_2_plus__endsuper_.CaM";
-  s279 is "3Ca_super_2_plus__endsuper_.CaM";
-  s280 is "4Ca_super_2_plus__endsuper_.CaM";
-  s289 is "MLCK";
-  s292 is "MLCK.Ca_super_2_plus__endsuper_.CaM";
-  s293 is "MLCK.2Ca_super_2_plus__endsuper_.CaM";
-  s294 is "MLCK.3Ca_super_2_plus__endsuper_.CaM";
-  s295 is "MLCK.4Ca_super_2_plus__endsuper_.CaM";
-  s309 is "PKC";
-  s310 is "PKC active1";
-  s311 is "PKC.DAG";
-  s314 is "PKC active_2";
-  s324 is "PKC active_3";
-  s329 is "csa39_degraded";
-  s330 is "csa36_degraded";
-  s331 is "csa35_degraded";
-  s332 is "PKC active_1.CPI";
-  s335 is "PKC active_2.CPI";
-  s338 is "PKC active_3.CPI";
-  s352 is "CPI-17.MYPT1_PPase";
-  s355 is "CPI-17.MYPT1_PPase";
-  s349 is "CPI-17";
-  s360 is "MLC";
-  s358 is "MLC";
-  s361 is "Rho-kinase.MLC";
-  s362 is "Rho-kinase.MLC";
-  s350 is "CPI-17";
-  s135 is "Ca_super_2_plus__endsuper_";
-  s276 is "CaM";
-  s172 is "Ca_super_2_plus__endsuper_ store";
-  s410 is "G_beta__gamma__1";
-  s421 is "G_beta__gamma__2";
-  s424 is "PLC_beta_";
-  s430 is "Ca_super_2_plus__endsuper_ trunsp";
-  s432 is "Ca_super_2_plus__endsuper_ pump";
-  s435 is "G_sub_12_endsub__alpha__beta__gamma__thrombinR active";
-  s436 is "p115RhoGEF.GTP_alpha_";
-  s437 is "G_sub_12_endsub__alpha__beta__gamma_";
-  s438 is "G_sub_12_endsub__alpha_.GDP";
-  s439 is "G_sub_12_endsub__alpha_.GTP";
-  s440 is "G_sub_q_endsub__alpha_.GDP";
-  s441 is "G_sub_q_endsub__alpha__beta__gamma__thrombinR active";
-  s442 is "G_sub_q_endsub__alpha__beta__gamma_";
-  s443 is "PLC_beta_.G_sub_q_endsub__alpha_.GTP";
-  s444 is "2Ca_super_2_plus__endsuper_ .Ca_super_2_plus__endsuper_ trunsp";
-  s446 is "Ca_super_2_plus__endsuper_  pump.Ca_super_2_plus__endsuper_";
-  s449 is "Rho.GTP.Rho-kinase.MLC";
-  s456 is "Rho.GTP.Rho-kinase.MLC";
-  s359 is "MLC";
-  s463 is "MYPT1.Rho-kinase";
-  s467 is "MYPT1.MLC";
-  s470 is "MYPT1.MLC";
-  s477 is "MYPT1.MLC";
-  s480 is "MYPT1.MLC";
-  s491 is "MLCK.MLC";
-  s487 is "MLCK.MLC";
-  s496 is "MYPT1.Rho-kinase";
-  s506 is "MLCK.4Ca_super_2_plus__endsuper_.CaM.MLC";
-  s512 is "MLCK.3Ca_super_2_plus__endsuper_.CaM.MLC";
-  s513 is "MLCK.4Ca_super_2_plus__endsuper_.CaM.MLC";
-  s520 is "MLCK.3Ca_super_2_plus__endsuper_.CaM.MLC";
-  s526 is "MLCK.2Ca_super_2_plus__endsuper_.CaM.MLC";
-  s539 is "MLCK.2Ca_super_2_plus__endsuper_.CaM.MLC";
-  s546 is "MLCK.Ca_super_2_plus__endsuper_.CaM.MLC";
-  s551 is "MLCK.Ca_super_2_plus__endsuper_.CaM.MLC";
-  s556 is "Ca_super_2_plus__endsuper_ ext leak";
-  s267 is "Ca_super_2_plus__endsuper_ ext";
-  s557 is "Ca_super_2_plus__endsuper_ int leak";
-  s564 is "PLC_beta_.G_sub_q_endsub__alpha_.GTP.Ca_super_2_plus__endsuper_";
-  s565 is "PKC.Ca_super_2_plus__endsuper_.DAG";
-  s566 is "PKC.Ca_super_2_plus__endsuper_";
-  s567 is "PLC_beta_.G_sub_q_endsub_.GTP.Ca.PIP2";
-  s568 is "PLC_beta_.Ca.PIP2";
-  s569 is "PLC_beta_.Ca_super_2_plus__endsuper_";
-  s351 is "MYPT1_PPase";
-  s570 is "MYPT1_PPase";
-  re1 is "A2-1.1";
-  re12 is "A1-2";
-  re14 is "A1-5.1";
-  re15 is "A1-3";
-  re16 is "A1-4";
-  re17 is "A1-6";
-  re19 is "A1-7";
-  re20 is "A2-2.1";
-  re22 is "A1-9";
-  re23 is "B1-1";
-  re24 is "B2-1.1";
-  re26 is "B2-2.1";
-  re28 is "B2-3.1";
-  re32 is "B2-1.2";
-  re33 is "B2-3.2";
-  re34 is "A2-2.2";
-  re37 is "B1-2";
-  re38 is "B1-3";
-  re39 is "B1-4";
-  re40 is "A2-1.2";
-  re43 is "A1-1";
-  re44 is "A1-8";
-  re45 is "A1-5.2";
-  re47 is "C1-2";
-  re48 is "C1-3";
-  re51 is "C1-4";
-  re52 is "C1-1";
-  re54 is "C1-5";
-  re55 is "C2-1.1";
-  re56 is "C2-2.1";
-  re57 is "C2-1.2";
-  re58 is "C2-2.2";
-  re59 is "C1-6";
-  re60 is "C1-7";
-  re68 is "C1-8";
-  re73 is "D3-1";
-  re85 is "D1-2";
-  re86 is "D1-3";
-  re87 is "D1-4";
-  re88 is "D1-6";
-  re89 is "D1-5";
-  re90 is "D1-10";
-  re91 is "D1-9";
-  re92 is "D1-8";
-  re93 is "D1-7";
-  re94 is "E1-1";
-  re95 is "E1-3";
-  re96 is "E1-5";
-  re97 is "E1-4";
-  re98 is "D2-1.2";
-  re100 is "D1-1";
-  re101 is "E1-7";
-  re102 is "E1-8";
-  re106 is "E1-9";
-  re107 is "E1-6";
-  re108 is "E1-2";
-  re109 is "D2-1.1";
-  re110 is "E2-1.1.3";
-  re111 is "E2-1.1.2";
-  re112 is "E2-1.1.1";
-  re113 is "E2-1.2.3";
-  re114 is "E2-1.2.2";
-  re115 is "E2-1.2.1";
-  re116 is "E1-10";
-  re117 is "E1-11";
-  re118 is "E1-12";
-  re119 is "E1-13";
-  re120 is "F2-1.1";
-  re121 is "F2-2.1";
-  re123 is "F2-1.2";
-  re124 is "F2-2.2";
-  re125 is "F2-3.1";
-  re126 is "F2-4.1";
-  re127 is "F2-3.2";
-  re128 is "F2-4.2";
-  re129 is "F2-14.1";
-  re130 is "F2-14.2";
-  re131 is "F2-13.1";
-  re132 is "F2-13.2";
-  re133 is "F2-11.1";
-  re134 is "F2-9.1";
-  re135 is "F2-12.1";
-  re136 is "F2-10.1";
-  re137 is "F2-11.2";
-  re138 is "F2-9.2";
-  re139 is "F2-12.2";
-  re140 is "F2-10.2";
-  re141 is "F1-1";
-  re154 is "F2-7.1";
-  re155 is "F2-8.1";
-  re156 is "F2-7.2";
-  re157 is "F2-8.2";
-  re158 is "F2-5.1.1";
-  re159 is "F2-5.2.1";
-  re160 is "F2-5.3.1";
-  re161 is "F2-5.4.1";
-  re162 is "F2-6.1.1";
-  re163 is "F2-6.2.1";
-  re164 is "F2-6.3.1";
-  re165 is "F2-6.4.1";
-  re166 is "F2-6.4.2";
-  re167 is "F2-5.4.2";
-  re168 is "F2-6.3.2";
-  re169 is "F2-5.3.2";
-  re170 is "F2-6.2.2";
-  re171 is "F2-5.2.2";
-  re172 is "F2-6.1.2";
-  re173 is "F2-5.1.2";
-  re174 is "D3-3";
-  re175 is "D3-2";
-
-  // CV terms:
-  c1 identity "http://identifiers.org/go/GO:0005829"
-  c2 identity "http://identifiers.org/go/GO:0005783"
-  s2 identity "http://identifiers.org/uniprot/P00734"
-  s174 identity "http://identifiers.org/uniprot/P25116",
-                "http://identifiers.org/interpro/IPR000935"
-  s130 identity "http://identifiers.org/uniprot/P25116",
-                "http://identifiers.org/interpro/IPR000935"
-  s4 identity "http://identifiers.org/uniprot/P00734"
-  s57 identity "http://identifiers.org/uniprot/P25116",
-               "http://identifiers.org/interpro/IPR000935"
-  s93 hypernym "http://identifiers.org/uniprot/O94810"
-  s93 identity "http://identifiers.org/interpro/IPR000342"
-  s165 identity "http://identifiers.org/chebi/CHEBI:17268",
-                "http://identifiers.org/kegg.compound/C00137"
-  s55 identity "http://identifiers.org/uniprot/P25116",
-               "http://identifiers.org/interpro/IPR000935"
-  s184 hypernym "http://identifiers.org/uniprot/O94810"
-  s184 identity "http://identifiers.org/interpro/IPR000342"
-  s48 identity "http://identifiers.org/chebi/CHEBI:15996",
-               "http://identifiers.org/kegg.compound/C00044"
-  s187 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/P29992",
-            "http://identifiers.org/kegg.compound/C00044"
-  s50 identity "http://identifiers.org/chebi/CHEBI:17552",
-               "http://identifiers.org/kegg.compound/C00035"
-  s171 identity "http://identifiers.org/uniprot/Q14643"
-  s173 part "http://identifiers.org/chebi/CHEBI:16595",
-            "http://identifiers.org/uniprot/Q14643",
-            "http://identifiers.org/kegg.compound/C01245"
-  s98 identity "http://identifiers.org/uniprot/Q92888",
-               "http://identifiers.org/interpro/IPR000219"
-  s124 identity "http://identifiers.org/uniprot/Q13464"
-  s118 identity "http://identifiers.org/uniprot/Q9NRY4",
-                "http://identifiers.org/interpro/IPR008936"
-  s153 identity "http://identifiers.org/chebi/CHEBI:18035",
-                "http://identifiers.org/kegg.compound/C00165"
-  s152 identity "http://identifiers.org/chebi/CHEBI:16595",
-                "http://identifiers.org/kegg.compound/C01245"
-  s213 identity "http://identifiers.org/uniprot/Q9NRY4"
-  s214 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/P61586",
-            "http://identifiers.org/kegg.compound/C00044"
-  s151 identity "http://identifiers.org/chebi/CHEBI:18348",
-                "http://identifiers.org/kegg.compound/C04637"
-  s231 part "http://identifiers.org/chebi/CHEBI:17552",
-            "http://identifiers.org/uniprot/P61586",
-            "http://identifiers.org/kegg.compound/C00035"
-  s233 part "http://identifiers.org/uniprot/Q92888"
-  s252 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/P61586",
-            "http://identifiers.org/kegg.compound/C00044"
-  s277 version "http://identifiers.org/chebi/CHEBI:29108",
-               "http://identifiers.org/uniprot/P62158",
-               "http://identifiers.org/kegg.compound/C00391",
-               "http://identifiers.org/kegg.compound/C00076"
-  s278 version "http://identifiers.org/chebi/CHEBI:29108",
-               "http://identifiers.org/uniprot/P62158",
-               "http://identifiers.org/kegg.compound/C00391",
-               "http://identifiers.org/kegg.compound/C00076"
-  s279 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/uniprot/P62158",
-                "http://identifiers.org/kegg.compound/C00391",
-                "http://identifiers.org/kegg.compound/C00076"
-  s280 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/uniprot/P62158",
-                "http://identifiers.org/kegg.compound/C00391",
-                "http://identifiers.org/kegg.compound/C00076"
-  s289 hypernym "http://identifiers.org/uniprot/Q9H1R3"
-  s292 version "http://identifiers.org/chebi/CHEBI:29108",
-               "http://identifiers.org/uniprot/P62158",
-               "http://identifiers.org/uniprot/Q9H1R3",
-               "http://identifiers.org/kegg.compound/C00391",
-               "http://identifiers.org/kegg.compound/C00076"
-  s293 version "http://identifiers.org/chebi/CHEBI:29108",
-               "http://identifiers.org/uniprot/P62158",
-               "http://identifiers.org/uniprot/Q9H1R3",
-               "http://identifiers.org/kegg.compound/C00391",
-               "http://identifiers.org/kegg.compound/C00076"
-  s294 version "http://identifiers.org/chebi/CHEBI:29108",
-               "http://identifiers.org/uniprot/P62158",
-               "http://identifiers.org/uniprot/Q9H1R3",
-               "http://identifiers.org/kegg.compound/C00391",
-               "http://identifiers.org/kegg.compound/C00076"
-  s295 version "http://identifiers.org/chebi/CHEBI:29108",
-               "http://identifiers.org/uniprot/P62158",
-               "http://identifiers.org/uniprot/Q9H1R3",
-               "http://identifiers.org/kegg.compound/C00391",
-               "http://identifiers.org/kegg.compound/C00076"
-  s309 identity "http://identifiers.org/uniprot/P17252"
-  s310 identity "http://identifiers.org/uniprot/P17252"
-  s311 part "http://identifiers.org/chebi/CHEBI:18035",
-            "http://identifiers.org/uniprot/P17252",
-            "http://identifiers.org/kegg.compound/C00165"
-  s314 identity "http://identifiers.org/uniprot/P17252"
-  s324 identity "http://identifiers.org/uniprot/P17252"
-  s332 part "http://identifiers.org/uniprot/Q96A00",
-            "http://identifiers.org/uniprot/P17252"
-  s335 part "http://identifiers.org/uniprot/Q96A00",
-            "http://identifiers.org/uniprot/P17252"
-  s338 part "http://identifiers.org/uniprot/Q96A00",
-            "http://identifiers.org/uniprot/P17252"
-  s352 part "http://identifiers.org/uniprot/O14974",
-            "http://identifiers.org/uniprot/Q96A00"
-  s355 part "http://identifiers.org/uniprot/O14974",
-            "http://identifiers.org/uniprot/Q96A00"
-  s349 hypernym "http://identifiers.org/uniprot/Q96A00"
-  s360 identity "http://identifiers.org/kegg.compound/C01003"
-  s360 hypernym "http://identifiers.org/uniprot/P05976"
-  s358 identity "http://identifiers.org/kegg.compound/C03875"
-  s358 hypernym "http://identifiers.org/uniprot/P05976"
-  s361 part "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/P05976"
-  s362 part "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/P05976"
-  s350 hypernym "http://identifiers.org/uniprot/Q96A00"
-  s135 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s276 identity "http://identifiers.org/uniprot/P62158",
-                "http://identifiers.org/kegg.compound/C00391"
-  s172 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s410 part "http://identifiers.org/uniprot/P63211",
-            "http://identifiers.org/uniprot/P62873"
-  s421 identity "http://identifiers.org/uniprot/P63211",
-                "http://identifiers.org/uniprot/P62873"
-  s424 identity "http://identifiers.org/uniprot/Q9NQ66"
-  s430 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s432 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s435 part "http://identifiers.org/uniprot/P25116",
-            "http://identifiers.org/uniprot/P63211",
-            "http://identifiers.org/uniprot/P62873",
-            "http://identifiers.org/uniprot/Q03113",
-            "http://identifiers.org/interpro/IPR000935"
-  s436 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/Q03113",
-            "http://identifiers.org/uniprot/Q92888",
-            "http://identifiers.org/kegg.compound/C00044"
-  s437 part "http://identifiers.org/uniprot/P63211",
-            "http://identifiers.org/uniprot/P62873",
-            "http://identifiers.org/uniprot/Q03113"
-  s438 part "http://identifiers.org/chebi/CHEBI:17552",
-            "http://identifiers.org/uniprot/Q03113",
-            "http://identifiers.org/kegg.compound/C00035"
-  s439 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/Q03113",
-            "http://identifiers.org/kegg.compound/C00044"
-  s440 part "http://identifiers.org/chebi/CHEBI:17552",
-            "http://identifiers.org/uniprot/P29992",
-            "http://identifiers.org/kegg.compound/C00035"
-  s441 part "http://identifiers.org/uniprot/P25116",
-            "http://identifiers.org/uniprot/P63211",
-            "http://identifiers.org/uniprot/P62873",
-            "http://identifiers.org/uniprot/P29992"
-  s442 part "http://identifiers.org/uniprot/P63211",
-            "http://identifiers.org/uniprot/P62873",
-            "http://identifiers.org/uniprot/P29992"
-  s443 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/Q9NQ66",
-            "http://identifiers.org/uniprot/P63211",
-            "http://identifiers.org/uniprot/P62873",
-            "http://identifiers.org/uniprot/P29992",
-            "http://identifiers.org/kegg.compound/C00044"
-  s444 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s446 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s449 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/P61586",
-            "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00044"
-  s456 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/uniprot/P61586",
-            "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00044"
-  s359 identity "http://identifiers.org/kegg.compound/C03875"
-  s359 part "http://identifiers.org/uniprot/P05976"
-  s463 part "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/O14974"
-  s467 part "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/uniprot/O14974"
-  s470 part "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/uniprot/O14974"
-  s477 part "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/uniprot/O14974"
-  s480 part "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/uniprot/O14974"
-  s491 part "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P05976"
-  s487 part "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P05976"
-  s496 part "http://identifiers.org/uniprot/Q13464",
-            "http://identifiers.org/uniprot/O14974"
-  s506 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s512 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s513 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s520 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s526 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s539 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s546 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s551 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9H1R3",
-            "http://identifiers.org/uniprot/P62158",
-            "http://identifiers.org/uniprot/P05976",
-            "http://identifiers.org/kegg.compound/C00391",
-            "http://identifiers.org/kegg.compound/C00076"
-  s556 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s267 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s557 identity "http://identifiers.org/chebi/CHEBI:29108",
-                "http://identifiers.org/kegg.compound/C00076"
-  s564 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9NQ66",
-            "http://identifiers.org/uniprot/P29992",
-            "http://identifiers.org/kegg.compound/C00044",
-            "http://identifiers.org/kegg.compound/C00076"
-  s565 part "http://identifiers.org/chebi/CHEBI:18035",
-            "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/P17252",
-            "http://identifiers.org/kegg.compound/C00165",
-            "http://identifiers.org/kegg.compound/C00076"
-  s566 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/P17252",
-            "http://identifiers.org/kegg.compound/C00076"
-  s567 part "http://identifiers.org/chebi/CHEBI:15996",
-            "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9NQ66",
-            "http://identifiers.org/uniprot/P29992",
-            "http://identifiers.org/kegg.compound/C00044",
-            "http://identifiers.org/kegg.compound/C00076"
-  s568 part "http://identifiers.org/chebi/CHEBI:18348",
-            "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9NQ66",
-            "http://identifiers.org/kegg.compound/C04637",
-            "http://identifiers.org/kegg.compound/C00076"
-  s569 part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/uniprot/Q9NQ66",
-            "http://identifiers.org/kegg.compound/C00076"
-  s351 hypernym "http://identifiers.org/uniprot/O14974"
-  s570 hypernym "http://identifiers.org/uniprot/O14974"
-  re1 identity "http://identifiers.org/ec-code/3.4.21.5",
-               "http://identifiers.org/go/GO:0015057",
-               "http://identifiers.org/go/GO:0005102"
-  re12 identity "http://identifiers.org/go/GO:0015057",
-                "http://identifiers.org/go/GO:0031684",
-                "http://identifiers.org/go/GO:0003924"
-  re14 identity "http://identifiers.org/go/GO:0030163"
-  re15 identity "http://identifiers.org/go/GO:0015057",
-                "http://identifiers.org/go/GO:0004930"
-  re16 identity "http://identifiers.org/go/GO:0031684",
-                "http://identifiers.org/go/GO:0003924"
-  re17 identity "http://identifiers.org/go/GO:0003924"
-  re19 identity "http://identifiers.org/go/GO:0031684"
-  re20 identity "http://identifiers.org/go/GO:0016299"
-  re22 identity "http://identifiers.org/go/GO:0031684"
-  re23 identity "http://identifiers.org/go/GO:0005515"
-  re24 identity "http://identifiers.org/go/GO:0005089"
-  re26 identity "http://identifiers.org/go/GO:0005089"
-  re28 identity "http://identifiers.org/go/GO:0035024"
-  re32 identity "http://identifiers.org/go/GO:0005089"
-  re33 identity "http://identifiers.org/go/GO:0035024"
-  re34 identity "http://identifiers.org/go/GO:0016299"
-  re37 identity "http://identifiers.org/go/GO:0005089"
-  re38 identity "http://identifiers.org/go/GO:0003924"
-  re39 identity "http://identifiers.org/intact/EBI-876651",
-                "http://identifiers.org/go/GO:0035025"
-  re40 identity "http://identifiers.org/ec-code/3.4.21.5",
-                "http://identifiers.org/go/GO:0015057"
-  re43 identity "http://identifiers.org/go/GO:0015057",
-                "http://identifiers.org/go/GO:0004930"
-  re44 identity "http://identifiers.org/go/GO:0003924"
-  re45 identity "http://identifiers.org/go/GO:0030163"
-  re47 parthood "http://identifiers.org/go/GO:0007200"
-  re47 identity "http://identifiers.org/go/GO:0001965"
-  re48 identity "http://identifiers.org/go/GO:0001965"
-  re48 parthood "http://identifiers.org/go/GO:0007200"
-  re51 parthood "http://identifiers.org/go/GO:0007200"
-  re52 parthood "http://identifiers.org/go/GO:0007202"
-  re52 identity "http://identifiers.org/go/GO:0005509"
-  re54 identity "http://identifiers.org/go/GO:0003924"
-  re55 parthood "http://identifiers.org/kegg.reaction/R03435",
-                "http://identifiers.org/go/GO:0007202"
-  re55 identity "http://identifiers.org/go/GO:0005546"
-  re56 parthood "http://identifiers.org/kegg.reaction/R03435",
-                "http://identifiers.org/go/GO:0004435"
-  re56 identity "http://identifiers.org/go/GO:0005546"
-  re57 identity "http://identifiers.org/ec-code/3.1.4.11",
-                "http://identifiers.org/kegg.reaction/R03435",
-                "http://identifiers.org/go/GO:0004435"
-  re58 identity "http://identifiers.org/ec-code/3.1.4.11",
-                "http://identifiers.org/kegg.reaction/R03435",
-                "http://identifiers.org/go/GO:0004435"
-  re59 identity "http://identifiers.org/go/GO:0046340"
-  re60 identity "http://identifiers.org/go/GO:0032957"
-  re68 identity "http://identifiers.org/go/GO:0005220"
-  re73 identity "http://identifiers.org/go/GO:0005220",
-                "http://identifiers.org/go/GO:0015085"
-  re85 identity "http://identifiers.org/go/GO:0006816"
-  re86 identity "http://identifiers.org/go/GO:0005516",
-                "http://identifiers.org/go/GO:0005509"
-  re87 identity "http://identifiers.org/go/GO:0005509"
-  re88 identity "http://identifiers.org/go/GO:0005509"
-  re89 identity "http://identifiers.org/go/GO:0005509"
-  re90 identity "http://identifiers.org/go/GO:0019901"
-  re91 identity "http://identifiers.org/go/GO:0019901"
-  re92 identity "http://identifiers.org/go/GO:0019901"
-  re93 identity "http://identifiers.org/go/GO:0019901"
-  re94 identity "http://identifiers.org/go/GO:0007205"
-  re95 identity "http://identifiers.org/go/GO:0005080",
-                "http://identifiers.org/go/GO:0019992",
-                "http://identifiers.org/go/GO:0008426"
-  re96 identity "http://identifiers.org/go/GO:0007205"
-  re97 identity "http://identifiers.org/go/GO:0005509",
-                "http://identifiers.org/go/GO:0005080"
-  re98 identity "http://identifiers.org/go/GO:0051928"
-  re100 identity "http://identifiers.org/go/GO:0051928"
-  re101 parthood "http://identifiers.org/go/GO:0007205"
-  re101 identity "http://identifiers.org/go/GO:0019992"
-  re102 parthood "http://identifiers.org/go/GO:0007205"
-  re106 identity "http://identifiers.org/go/GO:0030163"
-  re107 identity "http://identifiers.org/go/GO:0030163"
-  re108 identity "http://identifiers.org/go/GO:0030163"
-  re109 identity "http://identifiers.org/go/GO:0051928"
-  re110 identity "http://identifiers.org/ec-code/2.7.11.13",
-                 "http://identifiers.org/go/GO:0005080",
-                 "http://identifiers.org/go/GO:0004697"
-  re111 identity "http://identifiers.org/ec-code/2.7.11.13",
-                 "http://identifiers.org/go/GO:0005080",
-                 "http://identifiers.org/go/GO:0004698"
-  re112 identity "http://identifiers.org/ec-code/2.7.11.13",
-                 "http://identifiers.org/go/GO:0005080",
-                 "http://identifiers.org/go/GO:0004699"
-  re113 identity "http://identifiers.org/ec-code/2.7.11.13",
-                 "http://identifiers.org/go/GO:0004697"
-  re114 identity "http://identifiers.org/ec-code/2.7.11.13",
-                 "http://identifiers.org/go/GO:0004698"
-  re115 identity "http://identifiers.org/ec-code/2.7.11.13",
-                 "http://identifiers.org/go/GO:0004699"
-  re116 identity "http://identifiers.org/go/GO:0006470"
-  re117 identity "http://identifiers.org/go/GO:0017020"
-  re118 identity "http://identifiers.org/go/GO:0017020"
-  re119 identity "http://identifiers.org/go/GO:0006470"
-  re120 identity "http://identifiers.org/go/GO:0032027"
-  re121 identity "http://identifiers.org/go/GO:0032027"
-  re123 identity "http://identifiers.org/ec-code/2.7.11.1",
-                 "http://identifiers.org/go/GO:0004674"
-  re124 identity "http://identifiers.org/ec-code/2.7.11.1",
-                 "http://identifiers.org/go/GO:0004674"
-  re125 identity "http://identifiers.org/go/GO:0017049",
-                 "http://identifiers.org/go/GO:0032027"
-  re126 identity "http://identifiers.org/go/GO:0032027",
-                 "http://identifiers.org/go/GO:0017049"
-  re127 identity "http://identifiers.org/ec-code/2.7.11.1",
-                 "http://identifiers.org/go/GO:0004674"
-  re128 identity "http://identifiers.org/ec-code/2.7.11.1",
-                 "http://identifiers.org/go/GO:0004674"
-  re129 identity "http://identifiers.org/go/GO:0019901",
-                 "http://identifiers.org/go/GO:0017020"
-  re130 identity "http://identifiers.org/ec-code/2.7.11.1",
-                 "http://identifiers.org/go/GO:0004674",
-                 "http://identifiers.org/go/GO:0017020"
-  re131 identity "http://identifiers.org/go/GO:0019901",
-                 "http://identifiers.org/go/GO:0017049",
-                 "http://identifiers.org/go/GO:0017020"
-  re132 identity "http://identifiers.org/ec-code/2.7.11.1",
-                 "http://identifiers.org/go/GO:0004674",
-                 "http://identifiers.org/go/GO:0017020"
-  re133 identity "http://identifiers.org/go/GO:0017018",
-                 "http://identifiers.org/go/GO:0032027"
-  re134 identity "http://identifiers.org/go/GO:0017018",
-                 "http://identifiers.org/go/GO:0032027"
-  re135 identity "http://identifiers.org/go/GO:0017018",
-                 "http://identifiers.org/go/GO:0032027"
-  re136 identity "http://identifiers.org/go/GO:0017018",
-                 "http://identifiers.org/go/GO:0032027"
-  re137 identity "http://identifiers.org/ec-code/3.1.3.53",
-                 "http://identifiers.org/kegg.reaction/R03151",
-                 "http://identifiers.org/go/GO:0050115"
-  re138 identity "http://identifiers.org/ec-code/3.1.3.53",
-                 "http://identifiers.org/kegg.reaction/R03151",
-                 "http://identifiers.org/go/GO:0050115"
-  re139 identity "http://identifiers.org/ec-code/3.1.3.53",
-                 "http://identifiers.org/kegg.reaction/R03151",
-                 "http://identifiers.org/go/GO:0050115"
-  re140 identity "http://identifiers.org/ec-code/3.1.3.53",
-                 "http://identifiers.org/kegg.reaction/R03151",
-                 "http://identifiers.org/go/GO:0050115"
-  re141 identity "http://identifiers.org/go/GO:0017020",
-                 "http://identifiers.org/go/GO:0006470"
-  re154 identity "http://identifiers.org/go/GO:0032027",
-                 "http://identifiers.org/go/GO:0019901"
-  re155 identity "http://identifiers.org/go/GO:0032027",
-                 "http://identifiers.org/go/GO:0019901"
-  re156 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re157 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re158 identity "http://identifiers.org/go/GO:0032027"
-  re158 parthood "http://identifiers.org/kegg.reaction/R03150"
-  re159 identity "http://identifiers.org/go/GO:0032027"
-  re159 parthood "http://identifiers.org/kegg.reaction/R03150"
-  re160 identity "http://identifiers.org/go/GO:0032027"
-  re160 parthood "http://identifiers.org/kegg.reaction/R03150"
-  re161 identity "http://identifiers.org/go/GO:0032027"
-  re161 parthood "http://identifiers.org/kegg.reaction/R03150"
-  re162 identity "http://identifiers.org/go/GO:0032027"
-  re162 parthood "http://identifiers.org/kegg.reaction/R03150"
-  re163 identity "http://identifiers.org/go/GO:0032027"
-  re163 identity "http://identifiers.org/kegg.reaction/R03150"
-  re164 identity "http://identifiers.org/go/GO:0032027"
-  re164 parthood "http://identifiers.org/kegg.reaction/R03150"
-  re165 identity "http://identifiers.org/go/GO:0032027"
-  re165 identity "http://identifiers.org/kegg.reaction/R03150"
-  re166 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re167 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re168 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re169 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re170 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re171 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re172 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re173 identity "http://identifiers.org/ec-code/2.7.11.18",
-                 "http://identifiers.org/kegg.reaction/R03150",
-                 "http://identifiers.org/go/GO:0004687"
-  re174 identity "http://identifiers.org/go/GO:0006816"
-  re175 identity "http://identifiers.org/go/GO:0006816"
-end
-
-Maeda2006_MyosinPhosphorylation is "Maeda2006_MyosinPhosphorylation"
-
-Maeda2006_MyosinPhosphorylation model_entity_is "http://identifiers.org/biomodels.db/MODEL7944007619"
-Maeda2006_MyosinPhosphorylation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000088"
-Maeda2006_MyosinPhosphorylation description "http://identifiers.org/pubmed/16923126"
-Maeda2006_MyosinPhosphorylation taxon "http://identifiers.org/taxonomy/9606"
-Maeda2006_MyosinPhosphorylation parthood "http://identifiers.org/kegg.pathway/hsa04810"
-Maeda2006_MyosinPhosphorylation identity "http://identifiers.org/go/GO:0035023",
-                                         "http://identifiers.org/go/GO:0030036"
diff --git a/BioModelsRAG/data/BIOMD0000000089.txt b/BioModelsRAG/data/BIOMD0000000089.txt
deleted file mode 100644
index 22b41ccd91a7f5eeabfd9a4e6cd25cc43178df6d..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000089.txt
+++ /dev/null
@@ -1,424 +0,0 @@
-// Created by libAntimony v2.13.0
-function function_1(V, substrate, Km)
-  V*substrate/(Km + substrate);
-end
-
-function_1.sboTerm = 29
-
-function_1 is "degradation (Michaelis_Menten_Equation)"
-
-
-model *Locke2006_CircClock_LL()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species cLm in compartment_, cLc in compartment_, cLn in compartment_, cTm in compartment_;
-  species cTc in compartment_, cTn in compartment_, cXm in compartment_, cXc in compartment_;
-  species cXn in compartment_, cYm in compartment_, cYc in compartment_, cYn in compartment_;
-  species cPn in compartment_, cAm in compartment_, cAc in compartment_, cAn in compartment_;
-
-  // Reactions:
-  reaction_1:  => cLm; (compartment_*g0^alpha/(g0^alpha + cAn^alpha))*(light*(q1*cPn + n0) + n1*cXn^a/(g1^a + cXn^a));
-  reaction_0: cLm => ; compartment_*function_1(m1, cLm, k1);
-  reaction_2:  => cLc; compartment_*p1*cLm;
-  reaction_3: cLc -> cLn; compartment_*(r1*cLc - r2*cLn);
-  reaction_4: cLc => ; compartment_*function_1(m2, cLc, k2);
-  reaction_5: cLn => ; compartment_*function_1(m3, cLn, k3);
-  reaction_6:  => cTm; (compartment_*n2*cYn^b/(g2^b + cYn^b))*(g3^c/(g3^c + cLn^c));
-  reaction_7: cTm => ; compartment_*function_1(m4, cTm, k4);
-  reaction_9: cYc -> cYn; compartment_*(r7*cYc - r8*cYn);
-  reaction_10: cYn => ; compartment_*function_1(m14, cYn, k12);
-  reaction_11:  => cYc; compartment_*p4*cYm;
-  reaction_12: cYc => ; compartment_*function_1(m13, cYc, k11);
-  reaction_13: cXc -> cXn; compartment_*(r5*cXc - r6*cXn);
-  reaction_14: cXc => ; compartment_*function_1(m10, cXc, k8);
-  reaction_15:  => cXc; compartment_*p3*cXm;
-  reaction_16: cXn => ; compartment_*function_1(m11, cXn, k9);
-  reaction_17:  => cAc; compartment_*p6*cAm;
-  reaction_18: cAc -> cAn; compartment_*(r9*cAc - r10*cAn);
-  reaction_19: cAc => ; compartment_*function_1(m17, cAc, k15);
-  reaction_20: cAn => ; compartment_*function_1(m18, cAn, k16);
-  reaction_21:  => cPn; (1 - light)*p5*compartment_;
-  reaction_22: cPn => ; q3*light*cPn*compartment_;
-  reaction_23: cPn => ; compartment_*m15*cPn/(k13 + cPn);
-  reaction_25:  => cAm; light*q4*cPn*compartment_;
-  reaction_26:  => cAm; compartment_*n6*cLn^g/(g7^g + cLn^g);
-  reaction_27: cAm => ; compartment_*m16*cAm/(k14 + cAm);
-  reaction_28:  => cXm; compartment_*n3*cTn^d/(g4^d + cTn^d);
-  reaction_29: cXm => ; compartment_*m9*cXm/(k7 + cXm);
-  reaction_30:  => cTc; p2*compartment_*cTm;
-  reaction_31: cTc -> cTn; compartment_*(-r4*cTn + r3*cTc);
-  reaction_32: cTc => ; compartment_*(1 - light)*m5*cTc/(k5 + cTc);
-  reaction_33: cTc => ; m6*compartment_*cTc/(k5 + cTc);
-  reaction_34: cTn => ; compartment_*(1 - light)*m7*cTn/(k6 + cTn);
-  reaction_38: cTn => ; m8*compartment_*cTn/(k6 + cTn);
-  reaction_39:  => cYm; compartment_*(light*q2*cPn + (light*n4 + n5)*g5^e/(g5^e + cTn^e))*(g6^f/(g6^f + cLn^f));
-  reaction_40: cYm => ; compartment_*m12*cYm/(k10 + cYm);
-
-  // Species initializations:
-  cLm = 0.4625;
-  cLc = 0.0132;
-  cLn = 0.0699;
-  cTm = 0.4303;
-  cTc = 10.2965;
-  cTn = 0.5402;
-  cXm = 0.0957;
-  cXc = 1.5413;
-  cXn = 0.4585;
-  cYm = 0.0303;
-  cYc = 0.0041;
-  cYn = 0.0122;
-  cPn = 0.8476;
-  cAm = 14.6921;
-  cAc = 0.7027;
-  cAn = 0.8648;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  q1 = 4.1954;
-  n0 = 0.05;
-  g0 = 1;
-  alpha = 4;
-  n1 = 7.8142;
-  a = 1.2479;
-  g1 = 3.1383;
-  m1 = 1.999;
-  k1 = 2.392;
-  p1 = 0.8295;
-  r1 = 16.8363;
-  r2 = 0.1687;
-  m2 = 20.44;
-  k2 = 1.5644;
-  m3 = 3.6888;
-  k3 = 1.2765;
-  n2 = 3.0087;
-  b = 1.0258;
-  g2 = 0.0368;
-  g3 = 0.2658;
-  c = 1.0258;
-  m4 = 3.8231;
-  k4 = 2.5734;
-  p2 = 4.324;
-  r3 = 0.3166;
-  r4 = 2.1509;
-  m5 = 0.0013;
-  m6 = 3.1741;
-  k5 = 2.7454;
-  m7 = 0.0492;
-  m8 = 4.0424;
-  k6 = 0.4033;
-  n3 = 0.2431;
-  d = 1.4422;
-  g4 = 0.5388;
-  m9 = 10.1132;
-  k7 = 6.5585;
-  p3 = 2.147;
-  r5 = 1.0352;
-  r6 = 3.3017;
-  m10 = 0.2179;
-  k8 = 0.6632;
-  m11 = 3.3442;
-  k9 = 17.1111;
-  q2 = 2.4017;
-  n4 = 0.0857;
-  n5 = 0.1649;
-  g5 = 1.178;
-  g6 = 0.0645;
-  e = 3.6064;
-  f = 1.0237;
-  m12 = 4.297;
-  k10 = 1.7303;
-  p4 = 0.2485;
-  r7 = 2.2123;
-  r8 = 0.2002;
-  m13 = 0.1347;
-  k11 = 1.8258;
-  m14 = 0.6114;
-  k12 = 1.8066;
-  p5 = 0.5;
-  k13 = 1.2;
-  m15 = 1.2;
-  q3 = 1;
-  q4 = 2.4514;
-  g = 1.0258;
-  n6 = 8.0706;
-  g7 = 0.0004;
-  m16 = 12.2398;
-  k14 = 10.3617;
-  p6 = 0.2907;
-  r9 = 0.2528;
-  r10 = 0.2212;
-  m17 = 4.4505;
-  k15 = 0.0703;
-  m18 = 0.0156;
-  k16 = 0.6104;
-  light = 1;
-
-  // Other declarations:
-  const compartment_, q1, n0, g0, alpha, n1, a, g1, m1, k1, p1, r1, r2, m2;
-  const k2, m3, k3, n2, b, g2, g3, c, m4, k4, p2, r3, r4, m5, m6, k5, m7;
-  const m8, k6, n3, d, g4, m9, k7, p3, r5, r6, m10, k8, m11, k9, q2, n4, n5;
-  const g5, g6, e, f, m12, k10, p4, r7, r8, m13, k11, m14, k12, p5, k13, m15;
-  const q3, q4, g, n6, g7, m16, k14, p6, r9, r10, m17, k15, m18, k16, light;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nM";
-  compartment_ is "cell";
-  cLm is "LHY mRNA";
-  cLc is "LHY protein in cytoplasm";
-  cLn is "LHY protein in nucleus";
-  cTm is "TOC1 mRNA";
-  cTc is "TOC1 protein  in cytoplasm";
-  cTn is "TOC1 protein in nucleus";
-  cXm is "X mRNA";
-  cXc is "X protein in cytoplasm";
-  cXn is "X protein in nucleus";
-  cYm is "Y mRNA";
-  cYc is "Y protein in the cytoplasm";
-  cYn is "Y protein in nucleus";
-  cPn is "light sensitive protein P";
-  cAm is "PPR7/9 mRNA";
-  cAc is "PPR7/9 protein in cytoplasm";
-  cAn is "PPR7/9 protein in nucleus";
-  reaction_1 is "cLm transcription";
-  reaction_0 is "cLm degradation";
-  reaction_2 is "cLc translation";
-  reaction_3 is "LHY protein translocation";
-  reaction_4 is "cLc degradation";
-  reaction_5 is "cLn degradation";
-  reaction_6 is "cTm  transcription";
-  reaction_7 is "cTm degradation";
-  reaction_9 is "Y protein translocation";
-  reaction_10 is "cYn degradation";
-  reaction_11 is "cYc translation";
-  reaction_12 is "cYc degradation";
-  reaction_13 is "X protein translocation";
-  reaction_14 is "cXc degradation";
-  reaction_15 is "cXc translation";
-  reaction_16 is "cXn degradation";
-  reaction_17 is "cAc translation";
-  reaction_18 is "PPR7/9 protein translocation";
-  reaction_19 is "cAc degradation";
-  reaction_20 is "cAn degradation";
-  reaction_21 is "light dependent production of protein P";
-  reaction_22 is "light activation protein P degradation";
-  reaction_23 is "cPn degradation";
-  reaction_25 is "light activation of cAm transcription";
-  reaction_26 is "light independent cAm transcription";
-  reaction_27 is "cAm degradation";
-  reaction_28 is "cXm transcription";
-  reaction_29 is "cXm degradation";
-  reaction_30 is "cTc translation";
-  reaction_31 is "TOC1 protein translocation";
-  reaction_32 is "light activation degradation of cTc";
-  reaction_33 is "light independent degradation of cTc";
-  reaction_34 is "light activation degradation of cTn";
-  reaction_38 is "light independent degradation cTn";
-  reaction_39 is "cYm transcription";
-  reaction_40 is "cYm degradation";
-
-  // SBO terms:
-  compartment_.sboTerm = 290
-  cLm.sboTerm = 278
-  cLc.sboTerm = 245
-  cLn.sboTerm = 245
-  cTm.sboTerm = 278
-  cTc.sboTerm = 245
-  cTn.sboTerm = 245
-  cXm.sboTerm = 278
-  cXc.sboTerm = 245
-  cXn.sboTerm = 245
-  cYm.sboTerm = 278
-  cYc.sboTerm = 245
-  cYn.sboTerm = 245
-  cPn.sboTerm = 245
-  cAm.sboTerm = 278
-  cAc.sboTerm = 245
-  cAn.sboTerm = 245
-  q1.sboTerm = 337
-  n0.sboTerm = 186
-  g0.sboTerm = 186
-  alpha.sboTerm = 261
-  n1.sboTerm = 186
-  a.sboTerm = 190
-  g1.sboTerm = 363
-  m1.sboTerm = 324
-  k1.sboTerm = 27
-  p1.sboTerm = 153
-  r1.sboTerm = 153
-  r2.sboTerm = 156
-  m2.sboTerm = 324
-  k2.sboTerm = 27
-  m3.sboTerm = 324
-  k3.sboTerm = 27
-  n2.sboTerm = 186
-  b.sboTerm = 190
-  g2.sboTerm = 363
-  g3.sboTerm = 261
-  c.sboTerm = 190
-  m4.sboTerm = 324
-  k4.sboTerm = 27
-  p2.sboTerm = 153
-  r3.sboTerm = 153
-  r4.sboTerm = 156
-  m5.sboTerm = 324
-  m6.sboTerm = 324
-  k5.sboTerm = 27
-  m7.sboTerm = 324
-  m8.sboTerm = 324
-  k6.sboTerm = 27
-  n3.sboTerm = 186
-  d.sboTerm = 190
-  g4.sboTerm = 363
-  m9.sboTerm = 324
-  k7.sboTerm = 27
-  p3.sboTerm = 153
-  r5.sboTerm = 153
-  r6.sboTerm = 156
-  m10.sboTerm = 324
-  k8.sboTerm = 27
-  m11.sboTerm = 324
-  k9.sboTerm = 27
-  q2.sboTerm = 337
-  n4.sboTerm = 186
-  n5.sboTerm = 186
-  g5.sboTerm = 261
-  g6.sboTerm = 261
-  e.sboTerm = 190
-  f.sboTerm = 190
-  m12.sboTerm = 324
-  k10.sboTerm = 27
-  p4.sboTerm = 153
-  r7.sboTerm = 153
-  r8.sboTerm = 156
-  m13.sboTerm = 324
-  k11.sboTerm = 27
-  m14.sboTerm = 324
-  k12.sboTerm = 27
-  p5.sboTerm = 153
-  k13.sboTerm = 27
-  m15.sboTerm = 324
-  q3.sboTerm = 337
-  q4.sboTerm = 337
-  g.sboTerm = 190
-  n6.sboTerm = 186
-  g7.sboTerm = 363
-  m16.sboTerm = 324
-  k14.sboTerm = 27
-  p6.sboTerm = 153
-  r9.sboTerm = 153
-  r10.sboTerm = 156
-  m17.sboTerm = 324
-  k15.sboTerm = 27
-  m18.sboTerm = 324
-  k16.sboTerm = 27
-  light.sboTerm = 492
-  reaction_1.sboTerm = 183
-  reaction_0.sboTerm = 179
-  reaction_2.sboTerm = 184
-  reaction_3.sboTerm = 185
-  reaction_4.sboTerm = 179
-  reaction_5.sboTerm = 179
-  reaction_6.sboTerm = 183
-  reaction_7.sboTerm = 179
-  reaction_9.sboTerm = 185
-  reaction_10.sboTerm = 179
-  reaction_11.sboTerm = 184
-  reaction_12.sboTerm = 179
-  reaction_13.sboTerm = 185
-  reaction_14.sboTerm = 179
-  reaction_15.sboTerm = 184
-  reaction_16.sboTerm = 179
-  reaction_17.sboTerm = 184
-  reaction_18.sboTerm = 185
-  reaction_19.sboTerm = 179
-  reaction_20.sboTerm = 179
-  reaction_21.sboTerm = 393
-  reaction_22.sboTerm = 179
-  reaction_23.sboTerm = 179
-  reaction_25.sboTerm = 183
-  reaction_26.sboTerm = 183
-  reaction_27.sboTerm = 179
-  reaction_28.sboTerm = 183
-  reaction_29.sboTerm = 179
-  reaction_30.sboTerm = 184
-  reaction_31.sboTerm = 185
-  reaction_32.sboTerm = 179
-  reaction_33.sboTerm = 179
-  reaction_34.sboTerm = 179
-  reaction_38.sboTerm = 179
-  reaction_39.sboTerm = 183
-  reaction_40.sboTerm = 179
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  cLm hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  cLc version "http://identifiers.org/uniprot/O81713",
-              "http://identifiers.org/uniprot/P92973"
-  cLn version "http://identifiers.org/uniprot/P92973",
-              "http://identifiers.org/uniprot/O81713"
-  cTm hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  cTc identity "http://identifiers.org/uniprot/Q9LKL2"
-  cTn identity "http://identifiers.org/uniprot/Q9LKL2"
-  cXm hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  cYm hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  cYc version "http://identifiers.org/uniprot/Q9SQI2"
-  cYn version "http://identifiers.org/uniprot/Q9SQI2"
-  cAm hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  cAc part "http://identifiers.org/uniprot/Q93WK5",
-           "http://identifiers.org/uniprot/Q8L500"
-  cAn part "http://identifiers.org/uniprot/Q93WK5",
-           "http://identifiers.org/uniprot/Q8L500"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0006351"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0006402"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_6 hypernym "http://identifiers.org/go/GO:0006351"
-  reaction_7 hypernym "http://identifiers.org/go/GO:0006402"
-  reaction_9 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_11 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_12 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_13 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_14 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_15 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_16 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_17 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_18 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_19 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_20 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_21 hypernym "http://identifiers.org/go/GO:0045727"
-  reaction_22 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_23 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_25 hypernym "http://identifiers.org/go/GO:0006351"
-  reaction_26 hypernym "http://identifiers.org/go/GO:0006351"
-  reaction_27 hypernym "http://identifiers.org/go/GO:0006402"
-  reaction_28 hypernym "http://identifiers.org/go/GO:0006351"
-  reaction_29 hypernym "http://identifiers.org/go/GO:0006402"
-  reaction_30 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction_31 hypernym "http://identifiers.org/go/GO:0000060"
-  reaction_32 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_32 hypernym "http://identifiers.org/go/GO:0045732"
-  reaction_33 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_34 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_38 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_39 hypernym "http://identifiers.org/go/GO:0006351"
-  reaction_40 hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-Locke2006_CircClock_LL is "Locke2006_CircClock_LL"
-
-Locke2006_CircClock_LL model_entity_is "http://identifiers.org/biomodels.db/MODEL4025803561"
-Locke2006_CircClock_LL model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000089"
-Locke2006_CircClock_LL description "http://identifiers.org/pubmed/17102804"
-Locke2006_CircClock_LL origin "http://identifiers.org/biomodels.db/BIOMD0000000055"
-Locke2006_CircClock_LL taxon "http://identifiers.org/taxonomy/3702"
-Locke2006_CircClock_LL hypernym "http://identifiers.org/go/GO:0042752"
diff --git a/BioModelsRAG/data/BIOMD0000000090.txt b/BioModelsRAG/data/BIOMD0000000090.txt
deleted file mode 100644
index c0ef63c2f114081cd89aacffb62642b5ea4b1148..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000090.txt
+++ /dev/null
@@ -1,217 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Wolf2001_Respiratory_Oscillations()
-
-  // Compartments and Species:
-  compartment c0, c1, c2;
-  species $sul_ex in c0, $eth_ex in c0, $oxy_ex in c0, oxy in c2, $H2O in c2;
-  species A3c in c1, aps in c1, $PPi in c1, pap in c1, sul in c1, eth in c1;
-  species $A2c in c1, hyd in c1, cys in c1, N2 in c1, $N1 in c1, aco in c1;
-  species oah in c1, S1 in c2, $S2 in c2, $C1 in c2, $C2 in c2, $A2m in c2;
-  species A3m in c2, $Ho in c1, $Hm in c2;
-
-  // Assignment Rules:
-  A2c := Ac - A3c;
-  N1 := N - N2;
-  S2 := S - S1;
-  A2m := Am - A3m;
-
-  // Reactions:
-  v1: $sul_ex => sul; c0*k_v0/(1 + (cys/Kc)^n);
-  v13: $eth_ex => eth; c0*k_v13;
-  v2: sul + A3c => aps + $PPi; c1*k2*sul*A3c;
-  v10: $oxy_ex => oxy; c0*k_v10;
-  v14: oxy => $oxy_ex; c2*k14*oxy;
-  v3: aps + A3c => pap + $A2c; c1*k3*aps*A3c;
-  v4: pap + 3 N2 => hyd + 3 $N1; c1*k4*pap*N2;
-  v5: hyd + oah => cys; c1*k5*hyd*oah;
-  v6: cys => ; c1*k6*cys;
-  v7: eth + 2 $N1 => aco + 2 N2; c1*k7*eth*N1;
-  v15: aco => oah; c1*k15*aco;
-  v17: hyd => ; c1*k17*hyd;
-  v18: oah => ; c1*k18*oah;
-  v8: $S2 + aco => S1; c2*k8*aco*S2;
-  v9: S1 + 4 $N1 => $S2 + 4 N2; c2*k9*S1*N1;
-  v11a: $C1 + $Hm + N2 => $C2 + $Ho + $N1; c2*k11*N2*oxy/((a*N2 + oxy)*(1 + (hyd/Kh)^m));
-  v11a2: $C2 + oxy => $C1 + $H2O; c2*k11*N2*oxy/((a*N2 + oxy)*(1 + (hyd/Kh)^m));
-  v16: $A2c + A3m => $A2m + A3c; c2*k16*A3m*A2c;
-  v11b: $Ho + $A2m => $Hm + A3m; (c2*3*k11*N2*oxy/((a*N2 + oxy)*(1 + (hyd/Kh)^m)))*A2m/(Ka + A2m);
-  vLEAK: $Ho => $Hm; 0;
-  v12: A3c => $A2c; c1*k12*A3c;
-
-  // Species initializations:
-  sul_ex = 0;
-  eth_ex = 0;
-  oxy_ex = 0;
-  oxy = 7;
-  oxy has substance_per_volume;
-  H2O = 0;
-  A3c = 1.5;
-  A3c has substance_per_volume;
-  aps = 0.5;
-  aps has substance_per_volume;
-  PPi = 0;
-  pap = 0.4;
-  pap has substance_per_volume;
-  sul = 0.4;
-  sul has substance_per_volume;
-  eth = 4;
-  eth has substance_per_volume;
-  A2c has substance_per_volume;
-  hyd = 0.5;
-  hyd has substance_per_volume;
-  cys = 0.3;
-  cys has substance_per_volume;
-  N2 = 2;
-  N2 has substance_per_volume;
-  N1 has substance_per_volume;
-  aco = 0.3;
-  aco has substance_per_volume;
-  oah = 1.5;
-  oah has substance_per_volume;
-  S1 = 1.5;
-  S1 has substance_per_volume;
-  S2 has substance_per_volume;
-  C1 = 0;
-  C2 = 0;
-  A2m has substance_per_volume;
-  A3m = 1.5;
-  A3m has substance_per_volume;
-  Ho = 0;
-  Hm = 0;
-
-  // Compartment initializations:
-  c0 = 1;
-  c1 = 1;
-  c2 = 1;
-
-  // Variable initializations:
-  Ac = 2;
-  N = 2;
-  S = 2;
-  Am = 2;
-  k_v0 = 1.6;
-  k2 = 0.2;
-  k3 = 0.2;
-  k4 = 0.2;
-  k5 = 0.1;
-  k6 = 0.12;
-  k7 = 10;
-  k8 = 10;
-  k9 = 10;
-  k_v10 = 80;
-  k11 = 10;
-  k12 = 5;
-  k_v13 = 4;
-  k14 = 10;
-  k15 = 5;
-  k16 = 10;
-  k17 = 0.02;
-  k18 = 1;
-  n = 4;
-  m = 4;
-  Ka = 1;
-  Kc = 0.1;
-  a = 0.1;
-  Kh = 0.5;
-
-  // Other declarations:
-  const c0, c1, c2, Ac, N, S, Am, k_v0, k2, k3, k4, k5, k6, k7, k8, k9, k_v10;
-  const k11, k12, k_v13, k14, k15, k16, k17, k18, n, m, Ka, Kc, a, Kh;
-
-  // Unit definitions:
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  c0 is "external";
-  c1 is "cytosol";
-  c2 is "mitochondria";
-  sul_ex is "SO4_ex";
-  eth_ex is "EtOH_ex";
-  oxy_ex is "O2_ex";
-  oxy is "O2";
-  A3c is "ATP";
-  aps is "APS";
-  pap is "PAPS";
-  sul is "SO4";
-  eth is "EtOH";
-  A2c is "ADP";
-  hyd is "H2S";
-  cys is "CYS";
-  N2 is "NADH";
-  N1 is "NAD";
-  aco is "AcCoA";
-  oah is "OAH";
-  A2m is "ADP_mit";
-  A3m is "ATP_mit";
-  v11a is "vET1";
-  v11a2 is "vET2";
-  v11b is "vSYNT";
-
-  // CV terms:
-  c0 hypernym "http://identifiers.org/obo.go/GO:0005576"
-  c1 hypernym "http://identifiers.org/obo.go/GO:0005829"
-  c2 hypernym "http://identifiers.org/obo.go/GO:0005739"
-  sul_ex identity "http://identifiers.org/obo.chebi/CHEBI:16189"
-  eth_ex identity "http://identifiers.org/obo.chebi/CHEBI:16236"
-  oxy_ex identity "http://identifiers.org/obo.chebi/CHEBI:15379"
-  oxy identity "http://identifiers.org/obo.chebi/CHEBI:15379"
-  H2O identity "http://identifiers.org/obo.chebi/CHEBI:15377"
-  A3c identity "http://identifiers.org/obo.chebi/CHEBI:15422"
-  aps identity "http://identifiers.org/obo.chebi/CHEBI:17709"
-  PPi identity "http://identifiers.org/obo.chebi/CHEBI:18361"
-  pap identity "http://identifiers.org/obo.chebi/CHEBI:17980"
-  sul identity "http://identifiers.org/obo.chebi/CHEBI:16189"
-  eth identity "http://identifiers.org/obo.chebi/CHEBI:16236"
-  A2c identity "http://identifiers.org/obo.chebi/CHEBI:16761"
-  hyd identity "http://identifiers.org/obo.chebi/CHEBI:16136"
-  cys identity "http://identifiers.org/obo.chebi/CHEBI:17561"
-  N2 identity "http://identifiers.org/obo.chebi/CHEBI:16908"
-  N1 identity "http://identifiers.org/obo.chebi/CHEBI:15846"
-  aco identity "http://identifiers.org/obo.chebi/CHEBI:15351"
-  oah identity "http://identifiers.org/obo.chebi/CHEBI:16288"
-  S1 parthood "http://identifiers.org/obo.go/GO:0030062"
-  S2 parthood "http://identifiers.org/obo.go/GO:0030062"
-  C1 hypernym "http://identifiers.org/obo.go/GO:0005746"
-  C2 hypernym "http://identifiers.org/obo.go/GO:0005746"
-  A2m identity "http://identifiers.org/obo.chebi/CHEBI:16761"
-  A3m identity "http://identifiers.org/obo.chebi/CHEBI:15422"
-  Ho identity "http://identifiers.org/obo.chebi/CHEBI:24636"
-  Hm identity "http://identifiers.org/obo.chebi/CHEBI:24636"
-  v1 hypernym "http://identifiers.org/obo.go/GO:0015381"
-  v13 hypernym "http://identifiers.org/obo.go/GO:0015850"
-  v2 identity "http://identifiers.org/ec-code/2.7.7.4"
-  v3 identity "http://identifiers.org/ec-code/2.7.1.25"
-  v3 hypernym "http://identifiers.org/obo.go/GO:0004020"
-  v4 version "http://identifiers.org/ec-code/1.8.4.8",
-             "http://identifiers.org/ec-code/1.8.1.2"
-  v5 version "http://identifiers.org/ec-code/4.4.1.1",
-             "http://identifiers.org/ec-code/4.2.1.22",
-             "http://identifiers.org/ec-code/2.5.1.49"
-  v7 version "http://identifiers.org/ec-code/6.2.1.1",
-             "http://identifiers.org/ec-code/1.2.1.3",
-             "http://identifiers.org/ec-code/1.1.1.1"
-  v15 identity "http://identifiers.org/ec-code/2.3.1.31"
-  v8 parthood "http://identifiers.org/obo.go/GO:0006099"
-  v9 parthood "http://identifiers.org/obo.go/GO:0006099"
-  v11a identity "http://identifiers.org/obo.go/GO:0015990"
-  v11a parthood "http://identifiers.org/obo.go/GO:0042775"
-  v11a version "http://identifiers.org/obo.go/GO:0002082"
-  v11a2 parthood "http://identifiers.org/obo.go/GO:0042775"
-  v11a2 version "http://identifiers.org/obo.go/GO:0002082"
-  v11a2 identity "http://identifiers.org/obo.go/GO:0006123"
-  v16 identity "http://identifiers.org/obo.go/GO:0005471"
-  v11b parthood "http://identifiers.org/obo.go/GO:0042775"
-  v11b hypernym "http://identifiers.org/obo.go/GO:0006119"
-  v11b version "http://identifiers.org/obo.go/GO:0002082"
-  vLEAK hypernym "http://identifiers.org/obo.go/GO:0006810"
-  v12 hypernym "http://identifiers.org/obo.go/GO:0006200"
-end
-
-Wolf2001_Respiratory_Oscillations is "Wolf2001_Respiratory_Oscillations"
-
-Wolf2001_Respiratory_Oscillations model_entity_is "http://identifiers.org/biomodels.db/MODEL9728951048"
-Wolf2001_Respiratory_Oscillations model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000090"
-Wolf2001_Respiratory_Oscillations description "http://identifiers.org/pubmed/11423122"
-Wolf2001_Respiratory_Oscillations taxon "http://identifiers.org/taxonomy/4932"
-Wolf2001_Respiratory_Oscillations hypernym "http://identifiers.org/obo.go/GO:0019379"
diff --git a/BioModelsRAG/data/BIOMD0000000091.txt b/BioModelsRAG/data/BIOMD0000000091.txt
deleted file mode 100644
index d3ed48f239d81265088ee70ce40e12133c1606de..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000091.txt
+++ /dev/null
@@ -1,144 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Proctor2005_Hsp90()
-
-  // Compartments and Species:
-  compartment compartment_;
-  substanceOnly species Hsp90 in compartment_, HCom in compartment_, HSF1 in compartment_;
-  substanceOnly species MisP in compartment_, MCom in compartment_, TriH in compartment_;
-  substanceOnly species DiH in compartment_, NatP in compartment_, AggP in compartment_;
-  substanceOnly species HSE in compartment_, HSETriH in compartment_, X in compartment_;
-  substanceOnly species ROS in compartment_, ATP in compartment_, ADP in compartment_;
-  substanceOnly species $source in compartment_;
-
-  // Reactions:
-  proteinSynthesis: 0 $source => NatP; k1;
-  misfolding: NatP + ROS => MisP + ROS; k2*NatP*ROS;
-  Hsp90MisPBinding: MisP + Hsp90 => MCom; k3*MisP*Hsp90;
-  unsuccessulRefolding: MCom => MisP + Hsp90; k4*MCom;
-  refolding: MCom + ATP => Hsp90 + NatP + ADP; k5*MCom*ATP;
-  proteinDegradation: MisP + ATP => ADP; k6*MisP*ATP;
-  proteinAggregation1: 2 MisP => AggP; (MisP - 1)*k7*MisP/2;
-  proteinAggregation2: MisP + AggP => 2 AggP; k7*MisP*AggP;
-  Hsp90HSF1Binding: Hsp90 + HSF1 => HCom; k8*Hsp90*HSF1;
-  Hsp90HSF1Release: HCom => Hsp90 + HSF1; k9*HCom;
-  dimerisation: 2 HSF1 => DiH; (HSF1 - 1)*k10*HSF1/2;
-  trimerisation: HSF1 + DiH => TriH; k11*HSF1*DiH;
-  deTrimerisation: TriH => HSF1 + DiH; k12*TriH;
-  deDimerisation: DiH => 2 HSF1; k13*DiH;
-  HSETriHBinding: TriH + HSE => HSETriH; k14*HSE*TriH;
-  HSETriHRelease: HSETriH => HSE + TriH; k15*HSETriH;
-  Hsp90Transcription: HSETriH => HSETriH + Hsp90; k16*HSETriH;
-  Hsp90Degradation: Hsp90 + ATP => ADP; k17*Hsp90*ATP;
-  countTime: 0 $source => X; 1;
-  ATPformation: ADP => ATP; k18*ADP;
-  ATPconsumption: ATP => ADP; k19*ATP;
-  radicalFormation: 0 $source => ROS; k20;
-  radicalScavenging: ROS => ; k21*ROS;
-
-  // Species initializations:
-  Hsp90 = 300000/compartment_;
-  HCom = 5900/compartment_;
-  HSF1 = 100/compartment_;
-  MisP = 0;
-  MCom = 0;
-  TriH = 0;
-  DiH = 0;
-  NatP = 6000000/compartment_;
-  AggP = 0;
-  HSE = 1/compartment_;
-  HSETriH = 0;
-  X = 0;
-  ROS = 100/compartment_;
-  ATP = 10000/compartment_;
-  ADP = 1000/compartment_;
-  source = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  k1 = 10;
-  k2 = 2e-05;
-  k3 = 50;
-  k4 = 1e-05;
-  k5 = 4e-06;
-  k6 = 6e-07;
-  k7 = 1e-07;
-  k8 = 500;
-  k9 = 1;
-  k10 = 0.01;
-  k11 = 100;
-  k12 = 0.5;
-  k13 = 0.5;
-  k14 = 0.05;
-  k15 = 0.08;
-  k16 = 1000;
-  k17 = 8.02e-09;
-  k18 = 12;
-  k19 = 0.02;
-  k20 = 0.1;
-  k21 = 0.001;
-
-  // Other declarations:
-  const compartment_, k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13;
-  const k14, k15, k16, k17, k18, k19, k20, k21;
-
-  // Unit definitions:
-  unit substance = item;
-
-  // Display Names:
-  unsuccessulRefolding is "unsuccessfulRefolding";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  Hsp90 identity "http://identifiers.org/interpro/IPR001404"
-  HCom hypernym "http://identifiers.org/go/GO:0043234"
-  HSF1 hypernym "http://identifiers.org/interpro/IPR000232"
-  MCom hypernym "http://identifiers.org/go/GO:0043234"
-  TriH hypernym "http://identifiers.org/go/GO:0043234"
-  TriH part "http://identifiers.org/interpro/IPR000232"
-  DiH hypernym "http://identifiers.org/go/GO:0043234"
-  DiH part "http://identifiers.org/interpro/IPR000232"
-  ROS hypernym "http://identifiers.org/chebi/CHEBI:26523"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  proteinSynthesis hypernym "http://identifiers.org/go/GO:0009059"
-  misfolding version "http://identifiers.org/go/GO:0022417"
-  Hsp90MisPBinding hypernym "http://identifiers.org/go/GO:0051879"
-  unsuccessulRefolding hypernym "http://identifiers.org/go/GO:0043624"
-  refolding hypernym "http://identifiers.org/go/GO:0042026",
-                     "http://identifiers.org/go/GO:0016887"
-  proteinDegradation hypernym "http://identifiers.org/go/GO:0016887"
-  proteinAggregation1 hypernym "http://identifiers.org/go/GO:0043623"
-  proteinAggregation2 hypernym "http://identifiers.org/go/GO:0043623"
-  Hsp90HSF1Binding hypernym "http://identifiers.org/go/GO:0051879"
-  Hsp90HSF1Release hypernym "http://identifiers.org/go/GO:0043624"
-  dimerisation hypernym "http://identifiers.org/go/GO:0043623"
-  trimerisation hypernym "http://identifiers.org/go/GO:0043623"
-  deTrimerisation hypernym "http://identifiers.org/go/GO:0043624"
-  deDimerisation hypernym "http://identifiers.org/go/GO:0043624"
-  HSETriHBinding hypernym "http://identifiers.org/go/GO:0043623"
-  HSETriHRelease hypernym "http://identifiers.org/go/GO:0043624"
-  Hsp90Transcription hypernym "http://identifiers.org/go/GO:0006351"
-  Hsp90Degradation hypernym "http://identifiers.org/go/GO:0044257",
-                            "http://identifiers.org/go/GO:0016887"
-  ATPformation hypernym "http://identifiers.org/go/GO:0006757"
-  ATPconsumption hypernym "http://identifiers.org/go/GO:0016887"
-  radicalFormation parthood "http://identifiers.org/go/GO:0006800"
-  radicalScavenging hypernym "http://identifiers.org/go/GO:0016209"
-end
-
-Proctor2005_Hsp90 is "Proctor2005 - Actions of chaperones and their role in ageing"
-
-Proctor2005_Hsp90 model_entity_is "http://identifiers.org/biomodels.db/MODEL2223638385"
-Proctor2005_Hsp90 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000091"
-Proctor2005_Hsp90 description "http://identifiers.org/pubmed/15610770"
-Proctor2005_Hsp90 hypernym "http://identifiers.org/go/GO:0051085",
-                           "http://identifiers.org/go/GO:0007569",
-                           "http://identifiers.org/go/GO:0009408"
-Proctor2005_Hsp90 taxon "http://identifiers.org/taxonomy/131567"
-Proctor2005_Hsp90 version "http://identifiers.org/doid/DOID:10652",
-                          "http://identifiers.org/doid/DOID:14330",
-                          "http://identifiers.org/doid/DOID:83"
diff --git a/BioModelsRAG/data/BIOMD0000000092.txt b/BioModelsRAG/data/BIOMD0000000092.txt
deleted file mode 100644
index 2cae152a944a654bad7df4fc8e8c90df0ad3e60f..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000092.txt
+++ /dev/null
@@ -1,65 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Fuentes2005_ZymogenActivation()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species z in compartment_, e in compartment_, w in compartment_, ez in compartment_;
-
-  // Reactions:
-  v1: z -> w + e; compartment_*v1_k1*z;
-  v2: z + e -> ez; compartment_*(v2_k21*e*z - v2_k22*ez);
-  v3: ez -> w + 2 e; compartment_*v3_k3*ez;
-
-  // Species initializations:
-  z = 2.4e-05;
-  e = 0;
-  w = 0;
-  ez = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1 = 0.004;
-  v1_k1 has sec_inv;
-  v2_k21 = 1000;
-  v2_k21 has M_inv_sec_inv;
-  v2_k22 = 0.00021;
-  v2_k22 has sec_inv;
-  v3_k3 = 0.00054;
-  v3_k3 has sec_inv;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit M_inv_sec_inv = litre / (mole * second);
-  unit sec_inv = 1 / second;
-
-  // Display Names:
-  compartment_ is "compartment";
-  z is "Zymogen";
-  e is "Enzyme";
-  w is "Peptide";
-  ez is "Enzyme-Substrate complex";
-  v1 is "Intramolecular autoactivation";
-  v2 is "Intermolecular autoactivation-Complex formation";
-  v3 is "Intermolecular autoactivation-Enzyme release";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/go/GO:0005623"
-  z parthood "http://identifiers.org/go/GO:0042588"
-  ez hypernym "http://identifiers.org/go/GO:0043234"
-  v1 hypernym "http://identifiers.org/go/GO:0043085"
-  v2 hypernym "http://identifiers.org/go/GO:0019899"
-  v3 hypernym "http://identifiers.org/go/GO:0043085"
-end
-
-Fuentes2005_ZymogenActivation is "Fuentes2005_ZymogenActivation"
-
-Fuentes2005_ZymogenActivation model_entity_is "http://identifiers.org/biomodels.db/MODEL6623597435"
-Fuentes2005_ZymogenActivation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000092"
-Fuentes2005_ZymogenActivation description "http://identifiers.org/pubmed/15634334"
-Fuentes2005_ZymogenActivation origin "http://identifiers.org/pubmed/7558"
-Fuentes2005_ZymogenActivation identity "http://identifiers.org/go/GO:0031638"
-Fuentes2005_ZymogenActivation taxon "http://identifiers.org/taxonomy/131567"
diff --git a/BioModelsRAG/data/BIOMD0000000093.txt b/BioModelsRAG/data/BIOMD0000000093.txt
deleted file mode 100644
index 952286ae72ec0f141315d935572e10fecc90cbeb..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000093.txt
+++ /dev/null
@@ -1,458 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Yamada2003_JAK_STAT_Pathway()
-
-  // Compartments and Species:
-  compartment cytoplasm, nucleus;
-  species R in cytoplasm, JAK in cytoplasm, RJ in cytoplasm, IFNRJ in cytoplasm;
-  species IFNRJ2 in cytoplasm, IFNRJ2_star in cytoplasm, STAT1c in cytoplasm;
-  species IFNRJ2_star_STAT1c in cytoplasm, STAT1c_star in cytoplasm, IFNRJ2_star_STAT1c_star in cytoplasm;
-  species STAT1c_star_STAT1c_star in cytoplasm, SHP2 in cytoplasm, IFNRJ2_star_SHP2 in cytoplasm;
-  species PPX in cytoplasm, STAT1c_star_PPX in cytoplasm, STAT1c_STAT1c_star in cytoplasm;
-  species STAT1n_star_STAT1n_star in nucleus, STAT1n_star in nucleus, PPN in nucleus;
-  species STAT1n_star_PPN in nucleus, STAT1n in nucleus, STAT1n_STAT1n_star in nucleus;
-  species mRNAn in nucleus, mRNAc in cytoplasm, SOCS1 in cytoplasm, IFNRJ2_star_SOCS1 in cytoplasm;
-  species IFNRJ2_star_SHP2_SOCS1_STAT1c in cytoplasm, STAT1c_star_STAT1c_star_PPX in cytoplasm;
-  species STAT1n_star_STAT1n_star_PPN in nucleus, IFNRJ2_star_SOCS1_STAT1c in cytoplasm;
-  species $IFN in cytoplasm, IFNRJ2_star_SHP2_STAT1c in cytoplasm, IFNRJ2_star_SHP2_SOCS1 in cytoplasm;
-  species IFNR in cytoplasm;
-
-  // Reactions:
-  v1: JAK + R => RJ; cytoplasm*(v1_kf*R*JAK - v1_kb*RJ);
-  v2: RJ + $IFN => IFNRJ; cytoplasm*(v2_kf*IFN*RJ - v2_kb*IFNRJ);
-  v3: 2 IFNRJ => IFNRJ2; cytoplasm*(v3_kf*IFNRJ*IFNRJ - v3_kb*IFNRJ2);
-  v4: IFNRJ2 => IFNRJ2_star; cytoplasm*v4_kf*IFNRJ2;
-  v5: IFNRJ2_star + STAT1c => IFNRJ2_star_STAT1c; cytoplasm*(v5_kf*STAT1c*IFNRJ2_star - v5_kb*IFNRJ2_star_STAT1c);
-  v6: IFNRJ2_star_STAT1c => STAT1c_star + IFNRJ2_star; cytoplasm*v6_kf*IFNRJ2_star_STAT1c;
-  v7: STAT1c_star + IFNRJ2_star => IFNRJ2_star_STAT1c_star; cytoplasm*(v7_kf*IFNRJ2_star*STAT1c_star - v7_kb*IFNRJ2_star_STAT1c_star);
-  v8: 2 STAT1c_star => STAT1c_star_STAT1c_star; cytoplasm*(v8_kf*STAT1c_star*STAT1c_star - v8_kb*STAT1c_star_STAT1c_star);
-  v9: SHP2 + IFNRJ2_star => IFNRJ2_star_SHP2; cytoplasm*(v9_kf*IFNRJ2_star*SHP2 - v9_kb*IFNRJ2_star_SHP2);
-  v10: IFNRJ2_star_SHP2 => SHP2 + IFNRJ2; cytoplasm*v10_kf*IFNRJ2_star_SHP2;
-  v11: STAT1c_star + PPX => STAT1c_star_PPX; cytoplasm*(v11_kf*PPX*STAT1c_star - v11_kb*STAT1c_star_PPX);
-  v12: STAT1c_star_PPX => STAT1c + PPX; cytoplasm*v12_kf*STAT1c_star_PPX;
-  v13: STAT1c_star_STAT1c_star + PPX => STAT1c_star_STAT1c_star_PPX; cytoplasm*(v13_kf*PPX*STAT1c_star_STAT1c_star - v13_kb*STAT1c_star_STAT1c_star_PPX);
-  v14: STAT1c_star_STAT1c_star_PPX => STAT1c_STAT1c_star + PPX; cytoplasm*v14_kf*STAT1c_star_STAT1c_star_PPX;
-  v15: STAT1c_star + STAT1c => STAT1c_STAT1c_star; cytoplasm*(v15_kf*STAT1c*STAT1c_star - v15_kb*STAT1c_STAT1c_star);
-  v16: STAT1c_star_STAT1c_star => STAT1n_star_STAT1n_star; cytoplasm*v16_kf*STAT1c_star_STAT1c_star;
-  v17: 2 STAT1n_star => STAT1n_star_STAT1n_star; nucleus*(v17_kf*STAT1n_star*STAT1n_star - v17_kb*STAT1n_star_STAT1n_star);
-  v18: STAT1n_star + PPN => STAT1n_star_PPN; nucleus*(v18_kf*PPN*STAT1n_star - v18_kb*STAT1n_star_PPN);
-  v19: STAT1n_star_PPN => STAT1n + PPN; nucleus*v19_kf*STAT1n_star_PPN;
-  v20: STAT1n_star_STAT1n_star + PPN => STAT1n_star_STAT1n_star_PPN; nucleus*(v20_kf*PPN*STAT1n_star_STAT1n_star - v20_kb*STAT1n_star_STAT1n_star_PPN);
-  v21: STAT1n_star_STAT1n_star_PPN => STAT1n_STAT1n_star + PPN; nucleus*v21_kf*STAT1n_star_STAT1n_star_PPN;
-  v22: STAT1n_star + STAT1n => STAT1n_STAT1n_star; nucleus*(v22_kf*STAT1n*STAT1n_star - v22_kb*STAT1n_STAT1n_star);
-  v23: STAT1n => STAT1c; nucleus*v23_kf*STAT1n;
-  v24:  => mRNAn; nucleus*v24_ka*STAT1n_star_STAT1n_star/(v24_kb + STAT1n_star_STAT1n_star);
-  v25: mRNAn => mRNAc; nucleus*v25_kf*mRNAn;
-  v26:  => SOCS1; cytoplasm*v26_kf*mRNAc;
-  v27: mRNAc => ; cytoplasm*v27_kf*mRNAc;
-  v28: SOCS1 => ; cytoplasm*v28_kf*SOCS1;
-  v29: IFNRJ2_star + SOCS1 => IFNRJ2_star_SOCS1; cytoplasm*(v29_kf*SOCS1*IFNRJ2_star - v29_kb*IFNRJ2_star_SOCS1);
-  v30: IFNRJ2_star_SOCS1 + STAT1c => IFNRJ2_star_SOCS1_STAT1c; cytoplasm*(v30_kf*STAT1c*IFNRJ2_star_SOCS1 - v30_kb*IFNRJ2_star_SOCS1_STAT1c);
-  v31: IFNRJ2_star_SOCS1_STAT1c + SHP2 => IFNRJ2_star_SHP2_SOCS1_STAT1c; cytoplasm*(v31_kf*SHP2*IFNRJ2_star_SOCS1_STAT1c - v31_kb*IFNRJ2_star_SHP2_SOCS1_STAT1c);
-  v32: IFNRJ2_star_SHP2_SOCS1_STAT1c => IFNRJ2 + SOCS1 + STAT1c + SHP2; cytoplasm*v32_kf*IFNRJ2_star_SHP2_SOCS1_STAT1c;
-  v33: IFNRJ2_star_SHP2_SOCS1_STAT1c => IFNRJ2_star_SHP2_STAT1c; cytoplasm*v33_kf*IFNRJ2_star_SHP2_SOCS1_STAT1c;
-  v34: IFNRJ2_star_SOCS1 + SHP2 => IFNRJ2_star_SHP2_SOCS1; cytoplasm*(v34_kf*SHP2*IFNRJ2_star_SOCS1 - v34_kb*IFNRJ2_star_SHP2_SOCS1);
-  v35: IFNRJ2_star_SHP2_SOCS1 + STAT1c => IFNRJ2_star_SHP2_SOCS1_STAT1c; cytoplasm*(v35_kf*STAT1c*IFNRJ2_star_SHP2_SOCS1 - v35_kb*IFNRJ2_star_SHP2_SOCS1_STAT1c);
-  v36: IFNRJ2_star_STAT1c + SHP2 => IFNRJ2_star_SHP2_STAT1c; cytoplasm*(v36_kf*SHP2*IFNRJ2_star_STAT1c - v36_kb*IFNRJ2_star_SHP2_STAT1c);
-  v37: IFNRJ2_star_SHP2_STAT1c => STAT1c + SHP2 + IFNRJ2; cytoplasm*v37_kf*IFNRJ2_star_SHP2_STAT1c;
-  v38: IFNRJ2_star_SOCS1_STAT1c => IFNRJ2_star_STAT1c; cytoplasm*v38_kf*IFNRJ2_star_SOCS1_STAT1c;
-  v39: IFNRJ2_star_SHP2_SOCS1 => IFNRJ2_star_SHP2; cytoplasm*v39_kf*IFNRJ2_star_SHP2_SOCS1;
-  v40: IFNRJ2_star_SHP2_SOCS1 => SHP2 + IFNRJ2 + SOCS1; cytoplasm*v40_kf*IFNRJ2_star_SHP2_SOCS1;
-  v41: IFNRJ2_star_SOCS1 => IFNRJ2_star; cytoplasm*v41_kf*IFNRJ2_star_SOCS1;
-  v42: IFNRJ2_star_STAT1c + SOCS1 => IFNRJ2_star_SOCS1_STAT1c; cytoplasm*(v42_kf*SOCS1*IFNRJ2_star_STAT1c - v42_kb*IFNRJ2_star_SOCS1_STAT1c);
-  v43: IFNRJ2_star_SHP2 + SOCS1 => IFNRJ2_star_SHP2_SOCS1; cytoplasm*(v43_kf*SOCS1*IFNRJ2_star_SHP2 - v43_kb*IFNRJ2_star_SHP2_SOCS1);
-  v44: IFNRJ2_star_SHP2_STAT1c + SOCS1 => IFNRJ2_star_SHP2_SOCS1_STAT1c; cytoplasm*(v44_kf*SOCS1*IFNRJ2_star_SHP2_STAT1c - v44_kb*IFNRJ2_star_SHP2_SOCS1_STAT1c);
-  v45: R + $IFN => IFNR; cytoplasm*(v45_kf*IFN*R - v45_kb*IFNR);
-  v46: JAK + IFNR => IFNRJ; cytoplasm*(v46_kf*IFNR*JAK - v46_kb*IFNRJ);
-
-  // Species initializations:
-  R = 10;
-  JAK = 10;
-  RJ = 0;
-  IFNRJ = 0;
-  IFNRJ2 = 0;
-  IFNRJ2_star = 0;
-  STAT1c = 1000;
-  IFNRJ2_star_STAT1c = 0;
-  STAT1c_star = 0;
-  IFNRJ2_star_STAT1c_star = 0;
-  STAT1c_star_STAT1c_star = 0;
-  SHP2 = 100;
-  IFNRJ2_star_SHP2 = 0;
-  PPX = 50;
-  STAT1c_star_PPX = 0;
-  STAT1c_STAT1c_star = 0;
-  STAT1n_star_STAT1n_star = 0;
-  STAT1n_star = 0;
-  PPN = 60;
-  STAT1n_star_PPN = 0;
-  STAT1n = 0;
-  STAT1n_STAT1n_star = 0;
-  mRNAn = 0;
-  mRNAc = 0;
-  SOCS1 = 0;
-  IFNRJ2_star_SOCS1 = 0;
-  IFNRJ2_star_SHP2_SOCS1_STAT1c = 0;
-  STAT1c_star_STAT1c_star_PPX = 0;
-  STAT1n_star_STAT1n_star_PPN = 0;
-  IFNRJ2_star_SOCS1_STAT1c = 0;
-  IFN = 10;
-  IFNRJ2_star_SHP2_STAT1c = 0;
-  IFNRJ2_star_SHP2_SOCS1 = 0;
-  IFNR = 0;
-
-  // Compartment initializations:
-  cytoplasm = 1;
-  nucleus = 1;
-
-  // Variable initializations:
-  v1_kf = 0.1;
-  v1_kf has nM_inv_sec_inv;
-  v1_kb = 0.05;
-  v1_kb has sec_inv;
-  v2_kf = 0.02;
-  v2_kf has nM_inv_sec_inv;
-  v2_kb = 0.02;
-  v2_kb has sec_inv;
-  v3_kf = 0.04;
-  v3_kf has nM_inv_sec_inv;
-  v3_kb = 0.2;
-  v3_kb has sec_inv;
-  v4_kf = 0.005;
-  v4_kf has sec_inv;
-  v5_kf = 0.008;
-  v5_kf has nM_inv_sec_inv;
-  v5_kb = 0.8;
-  v5_kb has sec_inv;
-  v6_kf = 0.4;
-  v6_kf has sec_inv;
-  v7_kf = 0.005;
-  v7_kf has nM_inv_sec_inv;
-  v7_kb = 0.5;
-  v7_kb has sec_inv;
-  v8_kf = 0.02;
-  v8_kf has nM_inv_sec_inv;
-  v8_kb = 0.1;
-  v8_kb has sec_inv;
-  v9_kf = 0.001;
-  v9_kf has nM_inv_sec_inv;
-  v9_kb = 0.2;
-  v9_kb has sec_inv;
-  v10_kf = 0.003;
-  v10_kf has sec_inv;
-  v11_kf = 0.001;
-  v11_kf has nM_inv_sec_inv;
-  v11_kb = 0.2;
-  v11_kb has sec_inv;
-  v12_kf = 0.003;
-  v12_kf has sec_inv;
-  v13_kf = 0.001;
-  v13_kf has nM_inv_sec_inv;
-  v13_kb = 0.2;
-  v13_kb has sec_inv;
-  v14_kf = 0.003;
-  v14_kf has sec_inv;
-  v15_kf = 2e-07;
-  v15_kf has nM_inv_sec_inv;
-  v15_kb = 0.2;
-  v15_kb has sec_inv;
-  v16_kf = 0.005;
-  v16_kf has sec_inv;
-  v17_kf = 0.02;
-  v17_kf has nM_inv_sec_inv;
-  v17_kb = 0.1;
-  v17_kb has sec_inv;
-  v18_kf = 0.001;
-  v18_kf has nM_inv_sec_inv;
-  v18_kb = 0.2;
-  v18_kb has sec_inv;
-  v19_kf = 0.005;
-  v19_kf has sec_inv;
-  v20_kf = 0.001;
-  v20_kf has nM_inv_sec_inv;
-  v20_kb = 0.2;
-  v20_kb has sec_inv;
-  v21_kf = 0.005;
-  v21_kf has sec_inv;
-  v22_kf = 2e-07;
-  v22_kf has nM_inv_sec_inv;
-  v22_kb = 0.2;
-  v22_kb has sec_inv;
-  v23_kf = 0.05;
-  v23_kf has sec_inv;
-  v24_ka = 0.01;
-  v24_ka has nM_per_second;
-  v24_kb = 400;
-  v24_kb has nM;
-  v25_kf = 0.001;
-  v25_kf has sec_inv;
-  v26_kf = 0.01;
-  v26_kf has sec_inv;
-  v27_kf = 0.0005;
-  v27_kf has sec_inv;
-  v28_kf = 0.0005;
-  v28_kf has sec_inv;
-  v29_kf = 0.02;
-  v29_kf has nM_inv_sec_inv;
-  v29_kb = 0.1;
-  v29_kb has sec_inv;
-  v30_kf = 0.008;
-  v30_kf has nM_inv_sec_inv;
-  v30_kb = 0.8;
-  v30_kb has sec_inv;
-  v31_kf = 0.001;
-  v31_kf has nM_inv_sec_inv;
-  v31_kb = 0.2;
-  v31_kb has sec_inv;
-  v32_kf = 0.003;
-  v32_kf has sec_inv;
-  v33_kf = 0.0005;
-  v33_kf has sec_inv;
-  v34_kf = 0.001;
-  v34_kf has nM_inv_sec_inv;
-  v34_kb = 0.2;
-  v34_kb has sec_inv;
-  v35_kf = 0.008;
-  v35_kf has nM_inv_sec_inv;
-  v35_kb = 0.8;
-  v35_kb has sec_inv;
-  v36_kf = 0.001;
-  v36_kf has nM_inv_sec_inv;
-  v36_kb = 0.2;
-  v36_kb has sec_inv;
-  v37_kf = 0.003;
-  v37_kf has sec_inv;
-  v38_kf = 0.0005;
-  v38_kf has sec_inv;
-  v39_kf = 0.0005;
-  v39_kf has sec_inv;
-  v40_kf = 0.003;
-  v40_kf has sec_inv;
-  v41_kf = 0.0005;
-  v41_kf has sec_inv;
-  v42_kf = 0.02;
-  v42_kf has nM_inv_sec_inv;
-  v42_kb = 0.1;
-  v42_kb has sec_inv;
-  v43_kf = 0.02;
-  v43_kf has nM_inv_sec_inv;
-  v43_kb = 0.1;
-  v43_kb has sec_inv;
-  v44_kf = 0.02;
-  v44_kf has nM_inv_sec_inv;
-  v44_kb = 0.1;
-  v44_kb has sec_inv;
-  v45_kf = 0.02;
-  v45_kf has nM_inv_sec_inv;
-  v45_kb = 0.02;
-  v45_kb has sec_inv;
-  v46_kf = 0.1;
-  v46_kf has nM_inv_sec_inv;
-  v46_kb = 0.05;
-  v46_kb has sec_inv;
-
-  // Other declarations:
-  const cytoplasm, nucleus;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit nM_per_second = 1e-9 mole / (litre * second);
-  unit sec_inv = 1 / second;
-  unit nM_inv_sec_inv = litre / (1e-9 mole * second);
-  unit nM = 1e-9 mole / litre;
-
-  // Display Names:
-  substance is "nanomoles";
-  R is "Receptor";
-  RJ is "Receptor JAK complex";
-  IFNRJ is "Interferon-Receptor-JAK complex";
-  IFNRJ2 is "IFNRJ dimer";
-  IFNRJ2_star is "Activated IFNRJ complex";
-  v1 is "Receptor-JAK Binding";
-  v2 is "Interferon-Receptor Binding";
-  v3 is "IFN-Receptor complex dimerization";
-  v4 is "INF-Receptor complex activation";
-  v5 is "Activated INFRJ2-STAT1c binding";
-  v6 is "STAT1c activation";
-  v7 is "Activated IFNRJ2-STAT1c binding";
-  v8 is "Activated STAT1c dimerization";
-  v9 is "SHP2 binding";
-  v10 is "IFNJR2 dephosphorylation";
-  v11 is "Phosphorylated STAT1c-PPX binding";
-  v12 is "STAT1c dephosphorylation";
-  v13 is "PPX binding";
-  v14 is "STAT1c dimer dephosphorylation";
-  v15 is "STAT1c-phosphorylated STAT1c binding";
-  v16 is "STAT1c-nuclear transport";
-  v17 is "Phosphorylated STAT1n dimerization";
-  v18 is "PPN binding";
-  v19 is "STAT1n dephosphorylation";
-  v20 is "PPN binding";
-  v21 is "STAT1n dephosphorylation";
-  v22 is "STAT1n-phosphorylated STAT1n dimerization";
-  v23 is "STAT1n transport to cytoplasm";
-  v24 is "Transcription";
-  v25 is "mRNA transport to cytoplasm";
-  v26 is "SOCS1 synthesis";
-  v27 is "mRNAc degradation";
-  v28 is "SOCS1 degradation";
-  v29 is "phosphorylated IFNRJ2-SOCS1 binding";
-  v30 is "STAT1c binding";
-  v31 is "SHP2 binding";
-  v32 is "IFNRJ2 dephosphorylation";
-  v33 is "SOCS1 unbinding";
-  v34 is "SHP2 binding";
-  v35 is "STAT1c binding";
-  v36 is "SHP2 binding";
-  v38 is "SOCS1 unbinding";
-  v39 is "SOCS1 unbinding";
-  v40 is "IFNRJ2 dephosphorylation";
-  v41 is "SOCS1 unbinding";
-  v42 is "SOCS1 binding";
-  v43 is "SOCS1 binding";
-  v44 is "SOCS1 binding";
-  v45 is "Interferon-receptor binding";
-  v46 is "IFNR-JAK binding";
-
-  // CV terms:
-  cytoplasm identity "http://identifiers.org/obo.go/GO:0005737"
-  nucleus identity "http://identifiers.org/obo.go/GO:0005634"
-  R identity "http://identifiers.org/uniprot/O88507"
-  JAK identity "http://identifiers.org/uniprot/P52332",
-               "http://identifiers.org/interpro/IPR009127"
-  RJ part "http://identifiers.org/uniprot/P52332",
-          "http://identifiers.org/uniprot/O88507"
-  IFNRJ part "http://identifiers.org/uniprot/P52332",
-             "http://identifiers.org/uniprot/O88507",
-             "http://identifiers.org/uniprot/P01572"
-  IFNRJ2 part "http://identifiers.org/uniprot/P52332",
-              "http://identifiers.org/uniprot/O88507",
-              "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star part "http://identifiers.org/uniprot/P52332",
-                   "http://identifiers.org/uniprot/O88507",
-                   "http://identifiers.org/uniprot/P01572"
-  STAT1c identity "http://identifiers.org/uniprot/P42225",
-                  "http://identifiers.org/interpro/IPR001217"
-  IFNRJ2_star_STAT1c part "http://identifiers.org/uniprot/P42225",
-                          "http://identifiers.org/uniprot/P52332",
-                          "http://identifiers.org/uniprot/O88507",
-                          "http://identifiers.org/uniprot/P01572"
-  STAT1c_star identity "http://identifiers.org/uniprot/P42225"
-  IFNRJ2_star_STAT1c_star part "http://identifiers.org/uniprot/P42225",
-                               "http://identifiers.org/uniprot/P52332",
-                               "http://identifiers.org/uniprot/O88507",
-                               "http://identifiers.org/uniprot/P01572"
-  STAT1c_star_STAT1c_star identity "http://identifiers.org/uniprot/P42225"
-  SHP2 identity "http://identifiers.org/uniprot/P35235",
-                "http://identifiers.org/interpro/IPR000980"
-  IFNRJ2_star_SHP2 part "http://identifiers.org/uniprot/P35235",
-                        "http://identifiers.org/uniprot/P52332",
-                        "http://identifiers.org/uniprot/O88507",
-                        "http://identifiers.org/uniprot/P01572"
-  STAT1c_star_PPX part "http://identifiers.org/uniprot/P42225"
-  STAT1c_STAT1c_star identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_star_STAT1n_star identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_star identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_star_PPN part "http://identifiers.org/uniprot/P42225"
-  STAT1n identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_STAT1n_star identity "http://identifiers.org/uniprot/P42225"
-  mRNAn identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-                 "http://identifiers.org/kegg.compound/C00046"
-  mRNAc identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-                 "http://identifiers.org/kegg.compound/C00046"
-  SOCS1 identity "http://identifiers.org/uniprot/O35716",
-                 "http://identifiers.org/interpro/IPR001496"
-  IFNRJ2_star_SOCS1 part "http://identifiers.org/uniprot/O35716",
-                         "http://identifiers.org/uniprot/P52332",
-                         "http://identifiers.org/uniprot/O88507",
-                         "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star_SHP2_SOCS1_STAT1c part "http://identifiers.org/uniprot/P42225",
-                                     "http://identifiers.org/uniprot/O35716",
-                                     "http://identifiers.org/uniprot/P35235",
-                                     "http://identifiers.org/uniprot/P52332",
-                                     "http://identifiers.org/uniprot/O88507",
-                                     "http://identifiers.org/uniprot/P01572"
-  STAT1c_star_STAT1c_star_PPX part "http://identifiers.org/uniprot/P42225"
-  STAT1n_star_STAT1n_star_PPN part "http://identifiers.org/uniprot/P42225"
-  IFNRJ2_star_SOCS1_STAT1c part "http://identifiers.org/uniprot/P42225",
-                                "http://identifiers.org/uniprot/O35716",
-                                "http://identifiers.org/uniprot/P52332",
-                                "http://identifiers.org/uniprot/O88507",
-                                "http://identifiers.org/uniprot/P01572"
-  IFN identity "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star_SHP2_STAT1c part "http://identifiers.org/uniprot/P42225",
-                               "http://identifiers.org/uniprot/P35235",
-                               "http://identifiers.org/uniprot/P52332",
-                               "http://identifiers.org/uniprot/O88507",
-                               "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star_SHP2_SOCS1 part "http://identifiers.org/uniprot/O35716",
-                              "http://identifiers.org/uniprot/P35235",
-                              "http://identifiers.org/uniprot/P52332",
-                              "http://identifiers.org/uniprot/O88507",
-                              "http://identifiers.org/uniprot/P01572"
-  IFNR identity "http://identifiers.org/uniprot/O88507",
-                "http://identifiers.org/uniprot/P01572"
-  v1 identity "http://identifiers.org/obo.go/GO:0005133",
-              "http://identifiers.org/obo.go/GO:0005515"
-  v2 identity "http://identifiers.org/obo.go/GO:0004906",
-              "http://identifiers.org/obo.go/GO:0019964"
-  v3 identity "http://identifiers.org/obo.go/GO:0007171"
-  v4 identity "http://identifiers.org/ec-code/2.7.10.2",
-              "http://identifiers.org/kegg.reaction/R02584",
-              "http://identifiers.org/obo.go/GO:0004713"
-  v5 identity "http://identifiers.org/obo.go/GO:0005515"
-  v6 identity "http://identifiers.org/ec-code/2.7.10.2",
-              "http://identifiers.org/obo.go/GO:0007260"
-  v7 identity "http://identifiers.org/obo.go/GO:0005515"
-  v8 identity "http://identifiers.org/obo.go/GO:0007261"
-  v9 identity "http://identifiers.org/obo.go/GO:0019902",
-              "http://identifiers.org/obo.go/GO:0005515"
-  v10 identity "http://identifiers.org/ec-code/3.1.3.48",
-               "http://identifiers.org/kegg.reaction/R02585",
-               "http://identifiers.org/obo.go/GO:0005001"
-  v11 identity "http://identifiers.org/obo.go/GO:0019902",
-               "http://identifiers.org/obo.go/GO:0005515"
-  v12 identity "http://identifiers.org/obo.go/GO:0042512"
-  v13 identity "http://identifiers.org/obo.go/GO:0019902"
-  v14 identity "http://identifiers.org/obo.go/GO:0042512"
-  v15 identity "http://identifiers.org/obo.go/GO:0005515"
-  v16 identity "http://identifiers.org/obo.go/GO:0007262"
-  v17 identity "http://identifiers.org/obo.go/GO:0007261"
-  v18 identity "http://identifiers.org/obo.go/GO:0019902"
-  v19 identity "http://identifiers.org/obo.go/GO:0042512"
-  v20 identity "http://identifiers.org/obo.go/GO:0019902"
-  v21 identity "http://identifiers.org/obo.go/GO:0042512"
-  v22 identity "http://identifiers.org/obo.go/GO:0007261"
-  v23 identity "http://identifiers.org/obo.go/GO:0065002"
-  v24 identity "http://identifiers.org/obo.go/GO:0006351"
-  v25 identity "http://identifiers.org/obo.go/GO:0006406"
-  v26 identity "http://identifiers.org/obo.go/GO:0006412"
-  v27 identity "http://identifiers.org/obo.go/GO:0006402"
-  v28 identity "http://identifiers.org/obo.go/GO:0044257"
-  v29 identity "http://identifiers.org/obo.go/GO:0005515"
-  v30 identity "http://identifiers.org/obo.go/GO:0005515"
-  v31 identity "http://identifiers.org/obo.go/GO:0005515",
-               "http://identifiers.org/obo.go/GO:0019902"
-  v32 identity "http://identifiers.org/obo.go/GO:0005001"
-  v34 identity "http://identifiers.org/obo.go/GO:0019902"
-  v35 identity "http://identifiers.org/obo.go/GO:0005515"
-  v36 identity "http://identifiers.org/obo.go/GO:0019902"
-  v37 identity "http://identifiers.org/obo.go/GO:0043624"
-  v40 identity "http://identifiers.org/obo.go/GO:0005001",
-               "http://identifiers.org/obo.go/GO:0043624"
-  v42 identity "http://identifiers.org/obo.go/GO:0005515"
-  v43 identity "http://identifiers.org/obo.go/GO:0005515"
-  v44 identity "http://identifiers.org/obo.go/GO:0005515"
-  v45 identity "http://identifiers.org/obo.go/GO:0019964",
-               "http://identifiers.org/obo.go/GO:0004906"
-  v46 identity "http://identifiers.org/obo.go/GO:0005515",
-               "http://identifiers.org/obo.go/GO:0005133"
-end
-
-Yamada2003_JAK_STAT_Pathway is "Yamada2003_JAK_STAT_pathway"
-
-Yamada2003_JAK_STAT_Pathway model_entity_is "http://identifiers.org/biomodels.db/MODEL4879478021"
-Yamada2003_JAK_STAT_Pathway model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000093"
-Yamada2003_JAK_STAT_Pathway description "http://identifiers.org/pubmed/12527385"
-Yamada2003_JAK_STAT_Pathway identity "http://identifiers.org/kegg.pathway/mmu04630",
-                                     "http://identifiers.org/obo.go/GO:0007259"
-Yamada2003_JAK_STAT_Pathway taxon "http://identifiers.org/taxonomy/10090"
diff --git a/BioModelsRAG/data/BIOMD0000000094.txt b/BioModelsRAG/data/BIOMD0000000094.txt
deleted file mode 100644
index 8bd3f41f1632803523ac3fe9ce19c38d6c16e003..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000094.txt
+++ /dev/null
@@ -1,450 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Yamada2003_JAK_STAT_SOCS1_knockout()
-
-  // Compartments and Species:
-  compartment cytoplasm, nucleus;
-  species R in cytoplasm, JAK in cytoplasm, RJ in cytoplasm, IFNRJ in cytoplasm;
-  species IFNRJ2 in cytoplasm, IFNRJ2_star in cytoplasm, STAT1c in cytoplasm;
-  species IFNRJ2_star_STAT1c in cytoplasm, STAT1c_star in cytoplasm, IFNRJ2_star_STAT1c_star in cytoplasm;
-  species STAT1c_star_STAT1c_star in cytoplasm, SHP2 in cytoplasm, IFNRJ2_star_SHP2 in cytoplasm;
-  species PPX in cytoplasm, STAT1c_star_PPX in cytoplasm, STAT1c_STAT1c_star in cytoplasm;
-  species STAT1n_star_STAT1n_star in nucleus, STAT1n_star in nucleus, PPN in nucleus;
-  species STAT1n_star_PPN in nucleus, STAT1n in nucleus, STAT1n_STAT1n_star in nucleus;
-  species mRNAn in nucleus, mRNAc in cytoplasm, SOCS1 in cytoplasm, IFNRJ2_star_SOCS1 in cytoplasm;
-  species IFNRJ2_star_SHP2_SOCS1_STAT1c in cytoplasm, STAT1c_star_STAT1c_star_PPX in cytoplasm;
-  species STAT1n_star_STAT1n_star_PPN in nucleus, IFNRJ2_star_SOCS1_STAT1c in cytoplasm;
-  species $IFN in cytoplasm, IFNRJ2_star_SHP2_STAT1c in cytoplasm, IFNRJ2_star_SHP2_SOCS1 in cytoplasm;
-  species IFNR in cytoplasm;
-
-  // Reactions:
-  v1: JAK + R => RJ; cytoplasm*(v1_kf*R*JAK - v1_kb*RJ);
-  v2: RJ + $IFN => IFNRJ; cytoplasm*(v2_kf*IFN*RJ - v2_kb*IFNRJ);
-  v3: 2 IFNRJ => IFNRJ2; cytoplasm*(v3_kf*IFNRJ*IFNRJ - v3_kb*IFNRJ2);
-  v4: IFNRJ2 => IFNRJ2_star; cytoplasm*v4_kf*IFNRJ2;
-  v5: IFNRJ2_star + STAT1c => IFNRJ2_star_STAT1c; cytoplasm*(v5_kf*STAT1c*IFNRJ2_star - v5_kb*IFNRJ2_star_STAT1c);
-  v6: IFNRJ2_star_STAT1c => STAT1c_star + IFNRJ2_star; cytoplasm*v6_kf*IFNRJ2_star_STAT1c;
-  v7: STAT1c_star + IFNRJ2_star => IFNRJ2_star_STAT1c_star; cytoplasm*(v7_kf*IFNRJ2_star*STAT1c_star - v7_kb*IFNRJ2_star_STAT1c_star);
-  v8: 2 STAT1c_star => STAT1c_star_STAT1c_star; cytoplasm*(v8_kf*STAT1c_star*STAT1c_star - v8_kb*STAT1c_star_STAT1c_star);
-  v9: SHP2 + IFNRJ2_star => IFNRJ2_star_SHP2; cytoplasm*(v9_kf*IFNRJ2_star*SHP2 - v9_kb*IFNRJ2_star_SHP2);
-  v10: IFNRJ2_star_SHP2 => SHP2 + IFNRJ2; cytoplasm*v10_kf*IFNRJ2_star_SHP2;
-  v11: STAT1c_star + PPX => STAT1c_star_PPX; cytoplasm*(v11_kf*PPX*STAT1c_star - v11_kb*STAT1c_star_PPX);
-  v12: STAT1c_star_PPX => STAT1c + PPX; cytoplasm*v12_kf*STAT1c_star_PPX;
-  v13: STAT1c_star_STAT1c_star + PPX => STAT1c_star_STAT1c_star_PPX; cytoplasm*(v13_kf*PPX*STAT1c_star_STAT1c_star - v13_kb*STAT1c_star_STAT1c_star_PPX);
-  v14: STAT1c_star_STAT1c_star_PPX => STAT1c_STAT1c_star + PPX; cytoplasm*v14_kf*STAT1c_star_STAT1c_star_PPX;
-  v15: STAT1c_star + STAT1c => STAT1c_STAT1c_star; cytoplasm*(v15_kf*STAT1c*STAT1c_star - v15_kb*STAT1c_STAT1c_star);
-  v16: STAT1c_star_STAT1c_star => STAT1n_star_STAT1n_star; cytoplasm*v16_kf*STAT1c_star_STAT1c_star;
-  v17: 2 STAT1n_star => STAT1n_star_STAT1n_star; nucleus*(v17_kf*STAT1n_star*STAT1n_star - v17_kb*STAT1n_star_STAT1n_star);
-  v18: STAT1n_star + PPN => STAT1n_star_PPN; nucleus*(v18_kf*PPN*STAT1n_star - v18_kb*STAT1n_star_PPN);
-  v19: STAT1n_star_PPN => STAT1n + PPN; nucleus*v19_kf*STAT1n_star_PPN;
-  v20: STAT1n_star_STAT1n_star + PPN => STAT1n_star_STAT1n_star_PPN; nucleus*(v20_kf*PPN*STAT1n_star_STAT1n_star - v20_kb*STAT1n_star_STAT1n_star_PPN);
-  v21: STAT1n_star_STAT1n_star_PPN => STAT1n_STAT1n_star + PPN; nucleus*v21_kf*STAT1n_star_STAT1n_star_PPN;
-  v22: STAT1n_star + STAT1n => STAT1n_STAT1n_star; nucleus*(v22_kf*STAT1n*STAT1n_star - v22_kb*STAT1n_STAT1n_star);
-  v23: STAT1n => STAT1c; nucleus*v23_kf*STAT1n;
-  v25: mRNAn => mRNAc; nucleus*v25_kf*mRNAn;
-  v26:  => SOCS1; cytoplasm*v26_kf*mRNAc;
-  v27: mRNAc => ; cytoplasm*v27_kf*mRNAc;
-  v28: SOCS1 => ; cytoplasm*v28_kf*SOCS1;
-  v29: IFNRJ2_star + SOCS1 => IFNRJ2_star_SOCS1; cytoplasm*(v29_kf*SOCS1*IFNRJ2_star - v29_kb*IFNRJ2_star_SOCS1);
-  v30: IFNRJ2_star_SOCS1 + STAT1c => IFNRJ2_star_SOCS1_STAT1c; cytoplasm*(v30_kf*STAT1c*IFNRJ2_star_SOCS1 - v30_kb*IFNRJ2_star_SOCS1_STAT1c);
-  v31: IFNRJ2_star_SOCS1_STAT1c + SHP2 => IFNRJ2_star_SHP2_SOCS1_STAT1c; cytoplasm*(v31_kf*SHP2*IFNRJ2_star_SOCS1_STAT1c - v31_kb*IFNRJ2_star_SHP2_SOCS1_STAT1c);
-  v32: IFNRJ2_star_SHP2_SOCS1_STAT1c => IFNRJ2 + SOCS1 + STAT1c + SHP2; nucleus*v32_kf*IFNRJ2_star_SHP2_SOCS1_STAT1c;
-  v33: IFNRJ2_star_SHP2_SOCS1_STAT1c => IFNRJ2_star_SHP2_STAT1c; cytoplasm*v33_kf*IFNRJ2_star_SHP2_SOCS1_STAT1c;
-  v34: IFNRJ2_star_SOCS1 + SHP2 => IFNRJ2_star_SHP2_SOCS1; cytoplasm*(v34_kf*SHP2*IFNRJ2_star_SOCS1 - v34_kb*IFNRJ2_star_SHP2_SOCS1);
-  v35: IFNRJ2_star_SHP2_SOCS1 + STAT1c => IFNRJ2_star_SHP2_SOCS1_STAT1c; cytoplasm*(v35_kf*STAT1c*IFNRJ2_star_SHP2_SOCS1 - v35_kb*IFNRJ2_star_SHP2_SOCS1_STAT1c);
-  v36: IFNRJ2_star_STAT1c + SHP2 => IFNRJ2_star_SHP2_STAT1c; cytoplasm*(v36_kf*SHP2*IFNRJ2_star_STAT1c - v36_kb*IFNRJ2_star_SHP2_STAT1c);
-  v37: IFNRJ2_star_SHP2_STAT1c => STAT1c + SHP2 + IFNRJ2; cytoplasm*v37_kf*IFNRJ2_star_SHP2_STAT1c;
-  v38: IFNRJ2_star_SOCS1_STAT1c => IFNRJ2_star_STAT1c; cytoplasm*v38_kf*IFNRJ2_star_SOCS1_STAT1c;
-  v39: IFNRJ2_star_SHP2_SOCS1 => IFNRJ2_star_SHP2; cytoplasm*v39_kf*IFNRJ2_star_SHP2_SOCS1;
-  v40: IFNRJ2_star_SHP2_SOCS1 => SHP2 + IFNRJ2 + SOCS1; cytoplasm*v40_kf*IFNRJ2_star_SHP2_SOCS1;
-  v41: IFNRJ2_star_SOCS1 => IFNRJ2_star; cytoplasm*v41_kf*IFNRJ2_star_SOCS1;
-  v42: IFNRJ2_star_STAT1c + SOCS1 => IFNRJ2_star_SOCS1_STAT1c; cytoplasm*(v42_kf*SOCS1*IFNRJ2_star_STAT1c - v42_kb*IFNRJ2_star_SOCS1_STAT1c);
-  v43: IFNRJ2_star_SHP2 + SOCS1 => IFNRJ2_star_SHP2_SOCS1; cytoplasm*(v43_kf*SOCS1*IFNRJ2_star_SHP2 - v43_kb*IFNRJ2_star_SHP2_SOCS1);
-  v44: IFNRJ2_star_SHP2_STAT1c + SOCS1 => IFNRJ2_star_SHP2_SOCS1_STAT1c; cytoplasm*(v44_kf*SOCS1*IFNRJ2_star_SHP2_STAT1c - v44_kb*IFNRJ2_star_SHP2_SOCS1_STAT1c);
-  v45: R + $IFN => IFNR; cytoplasm*(v45_kf*IFN*R - v45_kb*IFNR);
-  v46: JAK + IFNR => IFNRJ; cytoplasm*(v46_kf*IFNR*JAK - v46_kb*IFNRJ);
-
-  // Species initializations:
-  R = 10;
-  JAK = 10;
-  RJ = 0;
-  IFNRJ = 0;
-  IFNRJ2 = 0;
-  IFNRJ2_star = 0;
-  STAT1c = 1000;
-  IFNRJ2_star_STAT1c = 0;
-  STAT1c_star = 0;
-  IFNRJ2_star_STAT1c_star = 0;
-  STAT1c_star_STAT1c_star = 0;
-  SHP2 = 100;
-  IFNRJ2_star_SHP2 = 0;
-  PPX = 50;
-  STAT1c_star_PPX = 0;
-  STAT1c_STAT1c_star = 0;
-  STAT1n_star_STAT1n_star = 0;
-  STAT1n_star = 0;
-  PPN = 60;
-  STAT1n_star_PPN = 0;
-  STAT1n = 0;
-  STAT1n_STAT1n_star = 0;
-  mRNAn = 0;
-  mRNAc = 0;
-  SOCS1 = 0;
-  IFNRJ2_star_SOCS1 = 0;
-  IFNRJ2_star_SHP2_SOCS1_STAT1c = 0;
-  STAT1c_star_STAT1c_star_PPX = 0;
-  STAT1n_star_STAT1n_star_PPN = 0;
-  IFNRJ2_star_SOCS1_STAT1c = 0;
-  IFN = 10;
-  IFNRJ2_star_SHP2_STAT1c = 0;
-  IFNRJ2_star_SHP2_SOCS1 = 0;
-  IFNR = 0;
-
-  // Compartment initializations:
-  cytoplasm = 1;
-  nucleus = 1;
-
-  // Variable initializations:
-  v1_kf = 0.1;
-  v1_kf has nM_inv_sec_inv;
-  v1_kb = 0.05;
-  v1_kb has sec_inv;
-  v2_kf = 0.02;
-  v2_kf has nM_inv_sec_inv;
-  v2_kb = 0.02;
-  v2_kb has sec_inv;
-  v3_kf = 0.04;
-  v3_kf has nM_inv_sec_inv;
-  v3_kb = 0.2;
-  v3_kb has sec_inv;
-  v4_kf = 0.005;
-  v4_kf has sec_inv;
-  v5_kf = 0.008;
-  v5_kf has nM_inv_sec_inv;
-  v5_kb = 0.8;
-  v5_kb has sec_inv;
-  v6_kf = 0.4;
-  v6_kf has sec_inv;
-  v7_kf = 0.005;
-  v7_kf has nM_inv_sec_inv;
-  v7_kb = 0.5;
-  v7_kb has sec_inv;
-  v8_kf = 0.02;
-  v8_kf has nM_inv_sec_inv;
-  v8_kb = 0.1;
-  v8_kb has sec_inv;
-  v9_kf = 0.001;
-  v9_kf has nM_inv_sec_inv;
-  v9_kb = 0.2;
-  v9_kb has sec_inv;
-  v10_kf = 0.003;
-  v10_kf has sec_inv;
-  v11_kf = 0.001;
-  v11_kf has nM_inv_sec_inv;
-  v11_kb = 0.2;
-  v11_kb has sec_inv;
-  v12_kf = 0.003;
-  v12_kf has sec_inv;
-  v13_kf = 0.001;
-  v13_kf has nM_inv_sec_inv;
-  v13_kb = 0.2;
-  v13_kb has sec_inv;
-  v14_kf = 0.003;
-  v14_kf has sec_inv;
-  v15_kf = 2e-07;
-  v15_kf has nM_inv_sec_inv;
-  v15_kb = 0.2;
-  v15_kb has sec_inv;
-  v16_kf = 0.005;
-  v16_kf has sec_inv;
-  v17_kf = 0.02;
-  v17_kf has nM_inv_sec_inv;
-  v17_kb = 0.1;
-  v17_kb has sec_inv;
-  v18_kf = 0.001;
-  v18_kf has nM_inv_sec_inv;
-  v18_kb = 0.2;
-  v18_kb has sec_inv;
-  v19_kf = 0.005;
-  v19_kf has sec_inv;
-  v20_kf = 0.001;
-  v20_kf has nM_inv_sec_inv;
-  v20_kb = 0.2;
-  v20_kb has sec_inv;
-  v21_kf = 0.005;
-  v21_kf has sec_inv;
-  v22_kf = 2e-07;
-  v22_kf has nM_inv_sec_inv;
-  v22_kb = 0.2;
-  v22_kb has sec_inv;
-  v23_kf = 0.05;
-  v23_kf has sec_inv;
-  v25_kf = 0.001;
-  v25_kf has sec_inv;
-  v26_kf = 0.01;
-  v26_kf has sec_inv;
-  v27_kf = 0.0005;
-  v27_kf has sec_inv;
-  v28_kf = 0.0005;
-  v28_kf has sec_inv;
-  v29_kf = 0.02;
-  v29_kf has nM_inv_sec_inv;
-  v29_kb = 0.1;
-  v29_kb has sec_inv;
-  v30_kf = 0.008;
-  v30_kf has nM_inv_sec_inv;
-  v30_kb = 0.8;
-  v30_kb has sec_inv;
-  v31_kf = 0.001;
-  v31_kf has nM_inv_sec_inv;
-  v31_kb = 0.2;
-  v31_kb has sec_inv;
-  v32_kf = 0.003;
-  v32_kf has sec_inv;
-  v33_kf = 0.0005;
-  v33_kf has sec_inv;
-  v34_kf = 0.001;
-  v34_kf has nM_inv_sec_inv;
-  v34_kb = 0.2;
-  v34_kb has sec_inv;
-  v35_kf = 0.008;
-  v35_kf has nM_inv_sec_inv;
-  v35_kb = 0.8;
-  v35_kb has sec_inv;
-  v36_kf = 0.001;
-  v36_kf has nM_inv_sec_inv;
-  v36_kb = 0.2;
-  v36_kb has sec_inv;
-  v37_kf = 0.003;
-  v37_kf has sec_inv;
-  v38_kf = 0.0005;
-  v38_kf has sec_inv;
-  v39_kf = 0.0005;
-  v39_kf has sec_inv;
-  v40_kf = 0.003;
-  v40_kf has sec_inv;
-  v41_kf = 0.0005;
-  v41_kf has sec_inv;
-  v42_kf = 0.02;
-  v42_kf has nM_inv_sec_inv;
-  v42_kb = 0.1;
-  v42_kb has sec_inv;
-  v43_kf = 0.02;
-  v43_kf has nM_inv_sec_inv;
-  v43_kb = 0.1;
-  v43_kb has sec_inv;
-  v44_kf = 0.02;
-  v44_kf has nM_inv_sec_inv;
-  v44_kb = 0.1;
-  v44_kb has sec_inv;
-  v45_kf = 0.02;
-  v45_kf has nM_inv_sec_inv;
-  v45_kb = 0.02;
-  v45_kb has sec_inv;
-  v46_kf = 0.1;
-  v46_kf has nM_inv_sec_inv;
-  v46_kb = 0.05;
-  v46_kb has sec_inv;
-
-  // Other declarations:
-  const cytoplasm, nucleus;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit nM_per_second = 1e-9 mole / (litre * second);
-  unit sec_inv = 1 / second;
-  unit nM_inv_sec_inv = litre / (1e-9 mole * second);
-  unit nM = 1e-9 mole / litre;
-
-  // Display Names:
-  substance is "nanomoles";
-  R is "Receptor";
-  RJ is "Receptor JAK complex";
-  IFNRJ is "Interferon-Receptor-JAK complex";
-  IFNRJ2 is "IFNRJ dimer";
-  IFNRJ2_star is "Activated IFNRJ complex";
-  v1 is "Receptor-JAK Binding";
-  v2 is "Interferon-Receptor Binding";
-  v3 is "IFN-Receptor complex dimerization";
-  v4 is "INF-Receptor complex activation";
-  v5 is "Activated INFRJ2-STAT1c binding";
-  v6 is "STAT1c activation";
-  v7 is "Activated IFNRJ2-STAT1c binding";
-  v8 is "Activated STAT1c dimerization";
-  v9 is "SHP2 binding";
-  v10 is "IFNJR2 dephosphorylation";
-  v11 is "Phosphorylated STAT1c-PPX binding";
-  v12 is "STAT1c dephosphorylation";
-  v13 is "PPX binding";
-  v14 is "STAT1c dimer dephosphorylation";
-  v15 is "STAT1c-phosphorylated STAT1c binding";
-  v16 is "STAT1c-nuclear transport";
-  v17 is "Phosphorylated STAT1n dimerization";
-  v18 is "PPN binding";
-  v19 is "STAT1n dephosphorylation";
-  v20 is "PPN binding";
-  v21 is "STAT1n dephosphorylation";
-  v22 is "STAT1n-phosphorylated STAT1n dimerization";
-  v23 is "STAT1n transport to cytoplasm";
-  v25 is "mRNA transport to cytoplasm";
-  v26 is "SOCS1 synthesis";
-  v27 is "mRNAc degradation";
-  v28 is "SOCS1 degradation";
-  v29 is "phosphorylated IFNRJ2-SOCS1 binding";
-  v30 is "STAT1c binding";
-  v31 is "SHP2 binding";
-  v32 is "IFNRJ2 dephosphorylation";
-  v33 is "SOCS1 unbinding";
-  v34 is "SHP2 binding";
-  v35 is "STAT1c binding";
-  v36 is "SHP2 binding";
-  v38 is "SOCS1 unbinding";
-  v39 is "SOCS1 unbinding";
-  v40 is "IFNRJ2 dephosphorylation";
-  v41 is "SOCS1 unbinding";
-  v42 is "SOCS1 binding";
-  v43 is "SOCS1 binding";
-  v44 is "SOCS1 binding";
-  v45 is "Interferon-receptor binding";
-  v46 is "IFNR-JAK binding";
-
-  // CV terms:
-  cytoplasm identity "http://identifiers.org/go/GO:0005737"
-  nucleus identity "http://identifiers.org/go/GO:0005634"
-  R identity "http://identifiers.org/uniprot/P15261",
-             "http://identifiers.org/interpro/IPR008355"
-  JAK identity "http://identifiers.org/uniprot/P52332",
-               "http://identifiers.org/interpro/IPR009127"
-  RJ part "http://identifiers.org/uniprot/P52332",
-          "http://identifiers.org/uniprot/P15261"
-  IFNRJ identity "http://identifiers.org/uniprot/P52332",
-                 "http://identifiers.org/uniprot/P15261",
-                 "http://identifiers.org/uniprot/P01572"
-  IFNRJ2 part "http://identifiers.org/uniprot/P52332",
-              "http://identifiers.org/uniprot/P15261",
-              "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star part "http://identifiers.org/uniprot/P52332",
-                   "http://identifiers.org/uniprot/P15261",
-                   "http://identifiers.org/uniprot/P01572"
-  STAT1c identity "http://identifiers.org/uniprot/P42225",
-                  "http://identifiers.org/interpro/IPR001217"
-  IFNRJ2_star_STAT1c part "http://identifiers.org/uniprot/P42225",
-                          "http://identifiers.org/uniprot/P52332",
-                          "http://identifiers.org/uniprot/P15261",
-                          "http://identifiers.org/uniprot/P01572"
-  STAT1c_star identity "http://identifiers.org/uniprot/P42225"
-  IFNRJ2_star_STAT1c_star part "http://identifiers.org/uniprot/P52332",
-                               "http://identifiers.org/uniprot/P42225",
-                               "http://identifiers.org/uniprot/P01572",
-                               "http://identifiers.org/uniprot/P15261"
-  STAT1c_star_STAT1c_star identity "http://identifiers.org/uniprot/P42225"
-  SHP2 identity "http://identifiers.org/uniprot/P35235"
-  IFNRJ2_star_SHP2 part "http://identifiers.org/uniprot/P35235",
-                        "http://identifiers.org/uniprot/P52332",
-                        "http://identifiers.org/uniprot/P15261",
-                        "http://identifiers.org/uniprot/P01572"
-  STAT1c_star_PPX part "http://identifiers.org/uniprot/P42225"
-  STAT1c_STAT1c_star identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_star_STAT1n_star identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_star identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_star_PPN part "http://identifiers.org/uniprot/P42225"
-  STAT1n identity "http://identifiers.org/uniprot/P42225"
-  STAT1n_STAT1n_star identity "http://identifiers.org/uniprot/P42225"
-  mRNAn identity "http://identifiers.org/chebi/CHEBI:33699",
-                 "http://identifiers.org/kegg.compound/C00046"
-  mRNAc identity "http://identifiers.org/chebi/CHEBI:33699",
-                 "http://identifiers.org/kegg.compound/C00046"
-  SOCS1 identity "http://identifiers.org/uniprot/O35716",
-                 "http://identifiers.org/interpro/IPR001496"
-  IFNRJ2_star_SOCS1 part "http://identifiers.org/uniprot/O35716",
-                         "http://identifiers.org/uniprot/P52332",
-                         "http://identifiers.org/uniprot/P15261",
-                         "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star_SHP2_SOCS1_STAT1c part "http://identifiers.org/uniprot/P35235",
-                                     "http://identifiers.org/uniprot/P42225",
-                                     "http://identifiers.org/uniprot/O35716",
-                                     "http://identifiers.org/uniprot/P52332",
-                                     "http://identifiers.org/uniprot/P15261",
-                                     "http://identifiers.org/uniprot/P01572"
-  STAT1c_star_STAT1c_star_PPX part "http://identifiers.org/uniprot/P42225"
-  STAT1n_star_STAT1n_star_PPN part "http://identifiers.org/uniprot/P42225"
-  IFNRJ2_star_SOCS1_STAT1c part "http://identifiers.org/uniprot/P42225",
-                                "http://identifiers.org/uniprot/O35716",
-                                "http://identifiers.org/uniprot/P52332",
-                                "http://identifiers.org/uniprot/P15261",
-                                "http://identifiers.org/uniprot/P01572"
-  IFN identity "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star_SHP2_STAT1c part "http://identifiers.org/uniprot/P35235",
-                               "http://identifiers.org/uniprot/P42225",
-                               "http://identifiers.org/uniprot/P52332",
-                               "http://identifiers.org/uniprot/P15261",
-                               "http://identifiers.org/uniprot/P01572"
-  IFNRJ2_star_SHP2_SOCS1 part "http://identifiers.org/uniprot/P35235",
-                              "http://identifiers.org/uniprot/O35716",
-                              "http://identifiers.org/uniprot/P52332",
-                              "http://identifiers.org/uniprot/P15261",
-                              "http://identifiers.org/uniprot/P01572"
-  IFNR part "http://identifiers.org/uniprot/P15261",
-            "http://identifiers.org/uniprot/P01572"
-  v1 identity "http://identifiers.org/go/GO:0005515",
-              "http://identifiers.org/go/GO:0005133"
-  v2 identity "http://identifiers.org/go/GO:0004906",
-              "http://identifiers.org/go/GO:0019964"
-  v3 identity "http://identifiers.org/go/GO:0007171"
-  v4 identity "http://identifiers.org/ec-code/2.7.10.2",
-              "http://identifiers.org/kegg.reaction/R02584",
-              "http://identifiers.org/go/GO:0004713"
-  v5 identity "http://identifiers.org/go/GO:0005515"
-  v6 identity "http://identifiers.org/go/GO:0007260"
-  v7 identity "http://identifiers.org/go/GO:0005515"
-  v8 identity "http://identifiers.org/go/GO:0007261"
-  v9 identity "http://identifiers.org/go/GO:0019902"
-  v10 identity "http://identifiers.org/ec-code/3.1.3.48",
-               "http://identifiers.org/kegg.reaction/R02585",
-               "http://identifiers.org/go/GO:0005001"
-  v11 identity "http://identifiers.org/go/GO:0019902"
-  v13 identity "http://identifiers.org/go/GO:0019902"
-  v14 identity "http://identifiers.org/go/GO:0042512"
-  v15 identity "http://identifiers.org/go/GO:0005515"
-  v16 identity "http://identifiers.org/go/GO:0007262"
-  v17 identity "http://identifiers.org/go/GO:0007261"
-  v18 identity "http://identifiers.org/go/GO:0005515",
-               "http://identifiers.org/go/GO:0019902"
-  v19 identity "http://identifiers.org/go/GO:0042512"
-  v20 identity "http://identifiers.org/go/GO:0019902"
-  v21 identity "http://identifiers.org/go/GO:0042512"
-  v22 identity "http://identifiers.org/go/GO:0007261"
-  v23 identity "http://identifiers.org/go/GO:0065002"
-  v25 identity "http://identifiers.org/go/GO:0006406"
-  v26 identity "http://identifiers.org/go/GO:0006412"
-  v27 identity "http://identifiers.org/go/GO:0006402"
-  v28 identity "http://identifiers.org/go/GO:0044257"
-  v29 identity "http://identifiers.org/go/GO:0005515"
-  v30 identity "http://identifiers.org/go/GO:0005515"
-  v31 identity "http://identifiers.org/go/GO:0005515",
-               "http://identifiers.org/go/GO:0019902"
-  v32 identity "http://identifiers.org/go/GO:0005001"
-  v34 identity "http://identifiers.org/go/GO:0005515",
-               "http://identifiers.org/go/GO:0019902"
-  v35 identity "http://identifiers.org/go/GO:0005515"
-  v36 identity "http://identifiers.org/go/GO:0005515",
-               "http://identifiers.org/go/GO:0019902"
-  v37 identity "http://identifiers.org/go/GO:0043624",
-               "http://identifiers.org/go/GO:0005001"
-  v40 identity "http://identifiers.org/go/GO:0005001"
-  v42 identity "http://identifiers.org/go/GO:0005515"
-  v43 identity "http://identifiers.org/go/GO:0005515"
-  v44 identity "http://identifiers.org/go/GO:0005515"
-  v45 identity "http://identifiers.org/go/GO:0005133",
-               "http://identifiers.org/go/GO:0019964"
-  v46 identity "http://identifiers.org/go/GO:0019964"
-end
-
-Yamada2003_JAK_STAT_SOCS1_knockout is "Yamada2003_JAK_STAT_SOCS1_knockout"
-
-Yamada2003_JAK_STAT_SOCS1_knockout model_entity_is "http://identifiers.org/biomodels.db/MODEL4883413839"
-Yamada2003_JAK_STAT_SOCS1_knockout model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000094"
-Yamada2003_JAK_STAT_SOCS1_knockout description "http://identifiers.org/pubmed/12527385"
-Yamada2003_JAK_STAT_SOCS1_knockout origin "http://identifiers.org/biomodels.db/BIOMD0000000093"
-Yamada2003_JAK_STAT_SOCS1_knockout identity "http://identifiers.org/kegg.pathway/mmu04630",
-                                            "http://identifiers.org/go/GO:0007259"
-Yamada2003_JAK_STAT_SOCS1_knockout taxon "http://identifiers.org/taxonomy/10090"
diff --git a/BioModelsRAG/data/BIOMD0000000095.txt b/BioModelsRAG/data/BIOMD0000000095.txt
deleted file mode 100644
index ff1de9c54d7deaf716744c41b6a1b4463e62c96a..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000095.txt
+++ /dev/null
@@ -1,426 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Zeilinger2006_PRR7_PRR9_Y()
-
-  // Compartments and Species:
-  compartment cytoplasm, nucleus;
-  species cLc in cytoplasm, cLm in nucleus, cLn in nucleus, cP7c in cytoplasm;
-  species cP7m in nucleus, cP7n in nucleus, cP9c in cytoplasm, cP9m in nucleus;
-  species cP9n in nucleus, cPn in nucleus, cTc in cytoplasm, cTm in nucleus;
-  species cTn in nucleus, cXc in cytoplasm, cXm in nucleus, cXn in nucleus;
-  species cYc in cytoplasm, cYm in nucleus, cYn in nucleus;
-
-  // Reactions:
-  R1:  => cLm; nucleus*ld*q1*cPn;
-  R2:  => cLm; nucleus*(n1*cXn^a/(g1^a + cXn^a))*(g7^h/(g7^h + cP7n^h))*(g8^i/(g8^i + cP9n^i));
-  R3: cLm => ; nucleus*m1*cLm/(k1 + cLm);
-  R4:  => cLc; cytoplasm*p1*cLm;
-  R5: cLc => cLn; cytoplasm*r1*cLc;
-  R6: cLn => cLc; nucleus*r2*cLn;
-  R7: cLc => ; cytoplasm*m2*cLc/(k2 + cLc);
-  R8: cLn => ; nucleus*m3*cLn/(k3 + cLn);
-  R9:  => cTm; nucleus*(n2*cYn^b/(g2^b + cYn^b))*(g3^c/(g3^c + cLn^c));
-  R10: cTm => ; nucleus*m4*cTm/(k4 + cTm);
-  R11:  => cTc; cytoplasm*p2*cTm;
-  R12: cTc => cTn; cytoplasm*r3*cTc;
-  R13: cTn => cTc; nucleus*r4*cTn;
-  R14: cTc => ; cytoplasm*((lmax - ld)*m5 + m6)*(cTc/(k5 + cTc));
-  R15: cTn => ; nucleus*((lmax - ld)*m7 + m8)*(cTn/(k6 + cTn));
-  R16:  => cXm; nucleus*(n3*cTn^d/(g4^d + cTn^d));
-  R17: cXm => ; nucleus*(m9*cXm/(k7 + cXm));
-  R18:  => cXc; cytoplasm*p3*cXm;
-  R19: cXc => cXn; cytoplasm*r5*cXc;
-  R20: cXn => cXc; nucleus*r6*cXn;
-  R21: cXc => ; cytoplasm*m10*cXc/(k8 + cXc);
-  R22: cXn => ; nucleus*m11*cXn/(k9 + cXn);
-  R23:  => cYm; nucleus*(ld*q2*cPn + (ld*n4 + n5)*g5^e/(g5^e + cTn^e))*(g6^f/(g6^f + cLn^f));
-  R24: cYm => ; nucleus*m12*cYm/(k10 + cYm);
-  R25:  => cYc; cytoplasm*p4*cYm;
-  R26: cYc => cYn; cytoplasm*r7*cYc;
-  R27: cYn => cYc; nucleus*r8*cYn;
-  R28: cYc => ; cytoplasm*m13*cYc/(k11 + cYc);
-  R29: cYn => ; nucleus*m14*cYn/(k12 + cYn);
-  R30:  => cPn; nucleus*(lmax - ld)*p5;
-  R31a: cPn => ; nucleus*m15*cPn/(k13 + cPn);
-  R31b: cPn => ; nucleus*q3*ld*cPn;
-  R32:  => cP7m; nucleus*n6*cLn^j/(g9^j + cLn^j);
-  R33: cP7m => ; nucleus*m16*cP7m/(k14 + cP7m);
-  R34:  => cP7c; cytoplasm*p6*cP7m;
-  R35: cP7c => cP7n; cytoplasm*r9*cP7c;
-  R36: cP7n => cP7c; nucleus*r10*cP7n;
-  R37: cP7c => ; cytoplasm*m17*cP7c/(k15 + cP7c);
-  R38: cP7n => ; nucleus*m18*cP7n/(k16 + cP7n);
-  R39:  => cP9m; nucleus*n7*cLn^k/(g10^k + cLn^k);
-  R40: cP9m => ; nucleus*m19*cP9m/(k17 + cP9m);
-  R41:  => cP9c; cytoplasm*p7*cP9m;
-  R42: cP9c => cP9n; cytoplasm*r11*cP9c;
-  R43: cP9n => cP9c; nucleus*r12*cP9n;
-  R44: cP9c => ; cytoplasm*m20*cP9c/(k18 + cP9c);
-  R45: cP9n => ; nucleus*m21*cP9n/(k19 + cP9n);
-
-  // Events:
-  event_0000001: at time > 30: ld = 1;
-
-  // Species initializations:
-  cLc = 6.7846;
-  cLm = 0.8539;
-  cLn = 6.8104;
-  cP7c = 20.0554;
-  cP7m = 4.28;
-  cP7n = 2.091;
-  cP9c = 6.0091;
-  cP9m = 1.1006;
-  cP9n = 3.7528;
-  cPn = 0;
-  cTc = 0.1724;
-  cTm = 0.3717;
-  cTn = 8.0398;
-  cXc = 13.0372;
-  cXm = 8.487;
-  cXn = 31.8995;
-  cYc = 7.075;
-  cYm = 0.1937;
-  cYn = 1.07;
-
-  // Compartment initializations:
-  cytoplasm = 1;
-  nucleus = 1;
-
-  // Variable initializations:
-  ld = 0;
-  ld has dimensionless;
-  q1 = 13.1446;
-  q1 has Hr_inv;
-  n1 = 1.0988;
-  n1 has nM_per_hour;
-  g1 = 11.7992;
-  g1 has nM;
-  m1 = 3.7622;
-  m1 has nM_per_hour;
-  k1 = 4.1029;
-  k1 has nM;
-  p1 = 7.5408;
-  p1 has Hr_inv;
-  r1 = 9.9378;
-  r1 has Hr_inv;
-  r2 = 9.6442;
-  r2 has Hr_inv;
-  m2 = 22.5198;
-  m2 has nM_per_hour;
-  k2 = 29.5681;
-  k2 has nM;
-  m3 = 4.5545;
-  m3 has nM_per_hour;
-  k3 = 18.6335;
-  k3 has nM;
-  n2 = 13.5067;
-  n2 has nM_per_hour;
-  g2 = 8.733;
-  g2 has nM;
-  g3 = 17.9887;
-  g3 has nM;
-  m4 = 7.1601;
-  m4 has nM_per_hour;
-  k4 = 4.7728;
-  k4 has nM;
-  p2 = 1.4452;
-  p2 has Hr_inv;
-  p3 = 3.1473;
-  p3 has Hr_inv;
-  r5 = 31.0081;
-  r5 has Hr_inv;
-  r6 = 12.5039;
-  r6 has Hr_inv;
-  m10 = 35.1982;
-  m10 has nM_per_hour;
-  k8 = 9.5343;
-  k8 has nM;
-  m11 = 7.0274;
-  m11 has nM_per_hour;
-  k9 = 45.1336;
-  k9 has nM;
-  q2 = 12.7437;
-  q2 has Hr_inv;
-  n4 = 1.8828;
-  n4 has nM_per_hour;
-  n5 = 1.506;
-  n5 has nM_per_hour;
-  g5 = 1.5091;
-  g5 has nM;
-  g6 = 20.7577;
-  g6 has nM;
-  m12 = 3.4563;
-  m12 has nM_per_hour;
-  k10 = 16.4042;
-  k10 has nM;
-  r3 = 14.7607;
-  r3 has Hr_inv;
-  r4 = 0.2559;
-  r4 has Hr_inv;
-  m5 = 1.5511;
-  m5 has nM_per_hour;
-  m6 = 1.4189;
-  m6 has nM_per_hour;
-  k5 = 3.0204;
-  k5 has nM;
-  m7 = 1.6789;
-  m7 has nM_per_hour;
-  m8 = 11.3548;
-  m8 has nM_per_hour;
-  k6 = 55.3798;
-  k6 has nM;
-  n3 = 1.7236;
-  n3 has nM_per_hour;
-  g4 = 5.6552;
-  g4 has nM;
-  m9 = 5.7847;
-  m9 has nM_per_hour;
-  k7 = 29.3208;
-  k7 has nM;
-  p4 = 2.8599;
-  p4 has Hr_inv;
-  r7 = 5.735;
-  r7 has Hr_inv;
-  r8 = 37.3301;
-  r8 has Hr_inv;
-  m13 = 9.1535;
-  m13 has nM_per_hour;
-  k11 = 55.7326;
-  k11 has nM;
-  m14 = 7.5549;
-  m14 has nM_per_hour;
-  k12 = 9.0406;
-  k12 has nM;
-  p5 = 0.5;
-  p5 has nM_per_hour;
-  k13 = 1.2;
-  k13 has nM;
-  q3 = 1;
-  q3 has Hr_inv;
-  m15 = 1.2;
-  m15 has nM_per_hour;
-  g7 = 4.6434;
-  g7 has nM;
-  g8 = 4.7985;
-  g8 has nM;
-  n6 = 4.6039;
-  n6 has nM_per_hour;
-  g9 = 4.8052;
-  g9 has nM;
-  m16 = 10.1357;
-  m16 has nM_per_hour;
-  k14 = 14.0306;
-  k14 has nM;
-  p6 = 2.0248;
-  p6 has Hr_inv;
-  r9 = 3.2996;
-  r9 has Hr_inv;
-  r10 = 30.7684;
-  r10 has Hr_inv;
-  m17 = 7.2481;
-  m17 has nM_per_hour;
-  k15 = 19.799;
-  k15 has nM;
-  m18 = 7.8275;
-  m18 has nM_per_hour;
-  k16 = 8.7977;
-  k16 has nM;
-  n7 = 4.4383;
-  n7 has nM_per_hour;
-  g10 = 17.7951;
-  g10 has nM;
-  m19 = 10.1288;
-  m19 has nM_per_hour;
-  k17 = 16.0706;
-  k17 has nM;
-  p7 = 1.0929;
-  p7 has Hr_inv;
-  r11 = 9.7804;
-  r11 has Hr_inv;
-  r12 = 15.4577;
-  r12 has Hr_inv;
-  m20 = 0.5315;
-  m20 has nM_per_hour;
-  k18 = 48.4999;
-  k18 has nM;
-  m21 = 8.5942;
-  m21 has nM_per_hour;
-  k19 = 57.4671;
-  k19 has nM;
-  lmax = 1;
-  lmax has dimensionless;
-  a = 1.8775;
-  a has dimensionless;
-  b = 1.5408;
-  b has dimensionless;
-  c = 1.4723;
-  c has dimensionless;
-  d = 4.0627;
-  d has dimensionless;
-  e = 3.5723;
-  e has dimensionless;
-  f = 2.0127;
-  f has dimensionless;
-  h = 3.3286;
-  h has dimensionless;
-  i = 3.5898;
-  i has dimensionless;
-  j = 1.269;
-  j has dimensionless;
-  k = 1.5212;
-  k has dimensionless;
-
-  // Other declarations:
-  var ld;
-  const cytoplasm, nucleus, q1, n1, g1, m1, k1, p1, r1, r2, m2, k2, m3, k3;
-  const n2, g2, g3, m4, k4, p2, p3, r5, r6, m10, k8, m11, k9, q2, n4, n5;
-  const g5, g6, m12, k10, r3, r4, m5, m6, k5, m7, m8, k6, n3, g4, m9, k7;
-  const p4, r7, r8, m13, k11, m14, k12, p5, k13, q3, m15, g7, g8, n6, g9;
-  const m16, k14, p6, r9, r10, m17, k15, m18, k16, n7, g10, m19, k17, p7;
-  const r11, r12, m20, k18, m21, k19, lmax, a, b, c, d, e, f, h, i, j, k;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-  unit Hr_inv = 1 / 3600 second;
-  unit nM = 1e-9 mole / litre;
-  unit nM_per_hour = 1e-9 mole / (litre * 3600 second);
-
-  // Display Names:
-  substance is "nanomoles";
-  time_unit is "hour";
-  Hr_inv is "Hour_inv";
-  R1 is "Light dependent cLm transcription";
-  R2 is "Light independent cLm transcription";
-  R3 is "cLm degradation";
-  R4 is "cLc synthesis";
-  R5 is "cLc transport into nucleus";
-  R6 is "cLn transport into cytoplasm";
-  R7 is "cLc degradation";
-  R8 is "cLn degradation";
-  R9 is "cTm transcription";
-  R10 is "cTm degradation";
-  R11 is "cTc synthesis";
-  R12 is "cTc transport into nucleus";
-  R13 is "cTn transport into cytoplasm";
-  R14 is "cTc degradation";
-  R15 is "cTn degradation";
-  R16 is "cXm transcription";
-  R17 is "cXm degradation";
-  R18 is "cXc synthesis";
-  R19 is "cXc transport into nucleus";
-  R20 is "cXn transport into cytoplasm";
-  R21 is "cXc degradation";
-  R22 is "cXn degradation";
-  R23 is "cYm transcription";
-  R24 is "cYm degradation";
-  R25 is "cYc synthesis";
-  R26 is "cYc transport to nucleus";
-  R27 is "cYn transport to cytoplasm";
-  R28 is "cYc degradation";
-  R29 is "cYn degradation";
-  R30 is "cPn synthesis";
-  R31a is "cPn degradation";
-  R31b is "Light dependent cPn degradation";
-  R32 is "cP7m transcription";
-  R33 is "cP7m degradation";
-  R34 is "cP7c synthesis";
-  R35 is "cP7c transport to nucleus";
-  R36 is "cP7n transport to cytoplasm";
-  R37 is "cP7c degradation";
-  R38 is "cP7n degradation";
-  R39 is "cP9m transcription";
-  R40 is "cP9m degradation";
-  R41 is "cP9c synthesis";
-  R42 is "cP9c transport to nucleus";
-  R43 is "cP9n transport to cytoplasm";
-  R44 is "cP9c degradation";
-  R45 is "cP9n degradation";
-
-  // CV terms:
-  cytoplasm identity "http://identifiers.org/obo.go/GO:0005737"
-  nucleus identity "http://identifiers.org/obo.go/GO:0005634"
-  cLc identity "http://identifiers.org/uniprot/O81713"
-  cLm hypernym "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cLn identity "http://identifiers.org/uniprot/O81713"
-  cP7c identity "http://identifiers.org/uniprot/Q93WK5"
-  cP7m hypernym "http://identifiers.org/obo.chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  cP7n identity "http://identifiers.org/uniprot/Q93WK5"
-  cP9c identity "http://identifiers.org/uniprot/Q8L500"
-  cP9m hypernym "http://identifiers.org/obo.chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  cP9n identity "http://identifiers.org/uniprot/Q8L500"
-  cTc identity "http://identifiers.org/uniprot/Q9LKL2",
-               "http://identifiers.org/interpro/IPR010402"
-  cTm hypernym "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cTn identity "http://identifiers.org/uniprot/Q9LKL2",
-               "http://identifiers.org/interpro/IPR010402"
-  cXm hypernym "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cXn identity "http://identifiers.org/obo.go/GO:0005667"
-  cYm hypernym "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cYn identity "http://identifiers.org/obo.go/GO:0005667"
-  R1 identity "http://identifiers.org/obo.go/GO:0006351",
-              "http://identifiers.org/obo.go/GO:0009642"
-  R2 identity "http://identifiers.org/obo.go/GO:0006351"
-  R3 identity "http://identifiers.org/obo.go/GO:0006402"
-  R4 identity "http://identifiers.org/obo.go/GO:0006412"
-  R5 identity "http://identifiers.org/obo.go/GO:0000060"
-  R6 identity "http://identifiers.org/obo.go/GO:0065002"
-  R7 identity "http://identifiers.org/obo.go/GO:0044257"
-  R8 identity "http://identifiers.org/obo.go/GO:0044257"
-  R9 identity "http://identifiers.org/obo.go/GO:0006351"
-  R10 identity "http://identifiers.org/obo.go/GO:0006402"
-  R11 identity "http://identifiers.org/obo.go/GO:0006412"
-  R12 identity "http://identifiers.org/obo.go/GO:0000060"
-  R13 identity "http://identifiers.org/obo.go/GO:0065002"
-  R14 identity "http://identifiers.org/obo.go/GO:0044257"
-  R15 identity "http://identifiers.org/obo.go/GO:0044257"
-  R16 identity "http://identifiers.org/obo.go/GO:0006351"
-  R17 identity "http://identifiers.org/obo.go/GO:0006402"
-  R18 identity "http://identifiers.org/obo.go/GO:0006412"
-  R19 identity "http://identifiers.org/obo.go/GO:0000060"
-  R20 identity "http://identifiers.org/obo.go/GO:0065002"
-  R21 identity "http://identifiers.org/obo.go/GO:0044257"
-  R22 identity "http://identifiers.org/obo.go/GO:0044257"
-  R23 identity "http://identifiers.org/obo.go/GO:0006351"
-  R23 part "http://identifiers.org/obo.go/GO:0009642"
-  R24 identity "http://identifiers.org/obo.go/GO:0006402"
-  R25 identity "http://identifiers.org/obo.go/GO:0006412"
-  R26 identity "http://identifiers.org/obo.go/GO:0000060"
-  R27 identity "http://identifiers.org/obo.go/GO:0065002"
-  R28 identity "http://identifiers.org/obo.go/GO:0044257"
-  R29 identity "http://identifiers.org/obo.go/GO:0044257"
-  R30 identity "http://identifiers.org/obo.go/GO:0009642",
-               "http://identifiers.org/obo.go/GO:0006412"
-  R31a identity "http://identifiers.org/obo.go/GO:0044257"
-  R31b identity "http://identifiers.org/obo.go/GO:0045732",
-                "http://identifiers.org/obo.go/GO:0009642"
-  R32 identity "http://identifiers.org/obo.go/GO:0006351"
-  R33 identity "http://identifiers.org/obo.go/GO:0006402"
-  R34 identity "http://identifiers.org/obo.go/GO:0006412"
-  R35 identity "http://identifiers.org/obo.go/GO:0000060"
-  R36 identity "http://identifiers.org/obo.go/GO:0065002"
-  R37 identity "http://identifiers.org/obo.go/GO:0044257"
-  R38 identity "http://identifiers.org/obo.go/GO:0044257"
-  R39 identity "http://identifiers.org/obo.go/GO:0006351"
-  R40 identity "http://identifiers.org/obo.go/GO:0006402"
-  R41 identity "http://identifiers.org/obo.go/GO:0006412"
-  R42 identity "http://identifiers.org/obo.go/GO:0000060"
-  R43 identity "http://identifiers.org/obo.go/GO:0065002"
-  R44 identity "http://identifiers.org/obo.go/GO:0044257"
-  R45 identity "http://identifiers.org/obo.go/GO:0044257"
-end
-
-Zeilinger2006_PRR7_PRR9_Y is "Zeilinger2006_PRR7-PRR9-Y"
-
-Zeilinger2006_PRR7_PRR9_Y model_entity_is "http://identifiers.org/biomodels.db/MODEL4025663985"
-Zeilinger2006_PRR7_PRR9_Y model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000095"
-Zeilinger2006_PRR7_PRR9_Y description "http://identifiers.org/pubmed/17102803"
-Zeilinger2006_PRR7_PRR9_Y origin "http://identifiers.org/biomodels.db/BIOMD0000000055"
-Zeilinger2006_PRR7_PRR9_Y taxon "http://identifiers.org/taxonomy/3701"
-Zeilinger2006_PRR7_PRR9_Y identity "http://identifiers.org/kegg.pathway/ath04710",
-                                   "http://identifiers.org/obo.go/GO:0007623"
diff --git a/BioModelsRAG/data/BIOMD0000000096.txt b/BioModelsRAG/data/BIOMD0000000096.txt
deleted file mode 100644
index 7f37680cb663dbac0c077ef8d38492df5a453dcf..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000096.txt
+++ /dev/null
@@ -1,434 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Zeilinger2006_PRR7_PRR9light_Y()
-
-  // Compartments and Species:
-  compartment cytoplasm, nucleus;
-  species cLc in cytoplasm, cLm in nucleus, cLn in nucleus, cP7c in cytoplasm;
-  species cP7m in nucleus, cP7n in nucleus, cP9c in cytoplasm, cP9m in nucleus;
-  species cP9n in nucleus, cPn in nucleus, cTc in cytoplasm, cTm in nucleus;
-  species cTn in nucleus, cXc in cytoplasm, cXm in nucleus, cXn in nucleus;
-  species cYc in cytoplasm, cYm in nucleus, cYn in nucleus;
-
-  // Reactions:
-  R1:  => cLm; nucleus*ld*q1*cPn;
-  R2:  => cLm; nucleus*(n1*cXn^a/(g1^a + cXn^a))*(g7^h/(g7^h + cP7n^h))*(g8^i/(g8^i + cP9n^i));
-  R3: cLm => ; nucleus*m1*cLm/(k1 + cLm);
-  R4:  => cLc; cytoplasm*p1*cLm;
-  R5: cLc => cLn; cytoplasm*r1*cLc;
-  R6: cLn => cLc; nucleus*r2*cLn;
-  R7: cLc => ; cytoplasm*m2*cLc/(k2 + cLc);
-  R8: cLn => ; nucleus*m3*cLn/(k3 + cLn);
-  R9:  => cTm; nucleus*(n2*cYn^b/(g2^b + cYn^b))*(g3^c/(g3^c + cLn^c));
-  R10: cTm => ; nucleus*m4*cTm/(k4 + cTm);
-  R11:  => cTc; cytoplasm*p2*cTm;
-  R12: cTc => cTn; cytoplasm*r3*cTc;
-  R13: cTn => cTc; nucleus*r4*cTn;
-  R14: cTc => ; cytoplasm*((lmax - ld)*m5 + m6)*(cTc/(k5 + cTc));
-  R15: cTn => ; nucleus*((lmax - ld)*m7 + m8)*(cTn/(k6 + cTn));
-  R16:  => cXm; nucleus*(n3*cTn^d/(g4^d + cTn^d));
-  R17: cXm => ; nucleus*(m9*cXm/(k7 + cXm));
-  R18:  => cXc; cytoplasm*p3*cXm;
-  R19: cXc => cXn; cytoplasm*r5*cXc;
-  R20: cXn => cXc; nucleus*r6*cXn;
-  R21: cXc => ; cytoplasm*m10*cXc/(k8 + cXc);
-  R22: cXn => ; nucleus*m11*cXn/(k9 + cXn);
-  R23:  => cYm; nucleus*(ld*q2*cPn + (ld*n4 + n5)*g5^e/(g5^e + cTn^e))*(g6^f/(g6^f + cLn^f));
-  R24: cYm => ; nucleus*m12*cYm/(k10 + cYm);
-  R25:  => cYc; cytoplasm*p4*cYm;
-  R26: cYc => cYn; cytoplasm*r7*cYc;
-  R27: cYn => cYc; nucleus*r8*cYn;
-  R28: cYc => ; cytoplasm*m13*cYc/(k11 + cYc);
-  R29: cYn => ; nucleus*m14*cYn/(k12 + cYn);
-  R30:  => cPn; nucleus*(lmax - ld)*p5;
-  R31a: cPn => ; nucleus*m15*cPn/(k13 + cPn);
-  R31b: cPn => ; nucleus*q3*ld*cPn;
-  R32:  => cP7m; nucleus*n6*cLn^j/(g9^j + cLn^j);
-  R33: cP7m => ; nucleus*m16*cP7m/(k14 + cP7m);
-  R34:  => cP7c; cytoplasm*p6*cP7m;
-  R35: cP7c => cP7n; cytoplasm*r9*cP7c;
-  R36: cP7n => cP7c; nucleus*r10*cP7n;
-  R37: cP7c => ; cytoplasm*m17*cP7c/(k15 + cP7c);
-  R38: cP7n => ; nucleus*m18*cP7n/(k16 + cP7n);
-  R39:  => cP9m; (ld*q4*cPn + n7*ld + n8)*cLn^k/(g10^k + cLn^k);
-  R40: cP9m => ; nucleus*m19*cP9m/(k17 + cP9m);
-  R41:  => cP9c; cytoplasm*p7*cP9m;
-  R42: cP9c => cP9n; cytoplasm*r11*cP9c;
-  R43: cP9n => cP9c; nucleus*r12*cP9n;
-  R44: cP9c => ; cytoplasm*m20*cP9c/(k18 + cP9c);
-  R45: cP9n => ; nucleus*m21*cP9n/(k19 + cP9n);
-
-  // Events:
-  event_0000001: at (Day_in_hours - time) <= 0: ld = 1, Day_in_hours = Day_in_hours + 24;
-  event_0000002: at ((Day_in_hours - time) <= 12) && ((Day_in_hours - time) > 0): ld = 0;
-
-  // Species initializations:
-  cLc = 0.0731;
-  cLm = 0.1114;
-  cLn = 0.2366;
-  cP7c = 0.0266;
-  cP7m = 0.0204;
-  cP7n = 1.5103;
-  cP9c = 0.734;
-  cP9m = 0.002;
-  cP9n = 1.1162;
-  cPn = 0;
-  cTc = 5.2235;
-  cTm = 3.6732;
-  cTn = 4.5333;
-  cXc = 2.4188;
-  cXm = 0.652;
-  cXn = 14.7289;
-  cYc = 49.2611;
-  cYm = 0.2992;
-  cYn = 17.4355;
-
-  // Compartment initializations:
-  cytoplasm = 1;
-  nucleus = 1;
-
-  // Variable initializations:
-  Day_in_hours = 24;
-  Day_in_hours has time_unit;
-  ld = 1;
-  ld has dimensionless;
-  q1 = 7.9798;
-  q1 has Hr_inv;
-  n1 = 2.3023;
-  n1 has nM_per_hour;
-  g1 = 16.3389;
-  g1 has nM;
-  m1 = 8.0568;
-  m1 has nM_per_hour;
-  k1 = 22.3951;
-  k1 has nM;
-  p1 = 1.2294;
-  p1 has Hr_inv;
-  r1 = 31.5166;
-  r1 has Hr_inv;
-  r2 = 9.1138;
-  r2 has Hr_inv;
-  m2 = 10.4609;
-  m2 has nM_per_hour;
-  k2 = 32.7881;
-  k2 has nM;
-  m3 = 12.7853;
-  m3 has nM_per_hour;
-  k3 = 29.0823;
-  k3 has nM;
-  n2 = 7.5433;
-  n2 has nM_per_hour;
-  g2 = 16.7487;
-  g2 has nM;
-  g3 = 11.5922;
-  g3 has nM;
-  m4 = 8.5185;
-  m4 has nM_per_hour;
-  k4 = 4.0551;
-  k4 has nM;
-  p2 = 1.0494;
-  p2 has Hr_inv;
-  p3 = 8.583;
-  p3 has Hr_inv;
-  r5 = 27.818;
-  r5 has Hr_inv;
-  r6 = 4.2863;
-  r6 has Hr_inv;
-  m10 = 9.2511;
-  m10 has nM_per_hour;
-  k8 = 13.4324;
-  k8 has nM;
-  m11 = 7.9066;
-  m11 has nM_per_hour;
-  k9 = 14.605;
-  k9 has nM;
-  q2 = 2.5505;
-  q2 has Hr_inv;
-  n4 = 1.5293;
-  n4 has nM_per_hour;
-  n5 = 2.6296;
-  n5 has nM_per_hour;
-  g5 = 0.5061;
-  g5 has nM;
-  g6 = 7.8469;
-  g6 has nM;
-  m12 = 8.4753;
-  m12 has nM_per_hour;
-  k10 = 16.1162;
-  k10 has nM;
-  r3 = 29.4222;
-  r3 has Hr_inv;
-  r4 = 33.6178;
-  r4 has Hr_inv;
-  m5 = 9.3024;
-  m5 has nM_per_hour;
-  m6 = 10.899;
-  m6 has nM_per_hour;
-  k5 = 16.9133;
-  k5 has nM;
-  m7 = 0.7527;
-  m7 has nM_per_hour;
-  m8 = 13.7459;
-  m8 has nM_per_hour;
-  k6 = 43.7049;
-  k6 has nM;
-  n3 = 0.6703;
-  n3 has nM_per_hour;
-  g4 = 11.3625;
-  g4 has nM;
-  m9 = 2.6345;
-  m9 has nM_per_hour;
-  k7 = 8.6873;
-  k7 has nM;
-  p4 = 14.6828;
-  p4 has Hr_inv;
-  r7 = 9.1917;
-  r7 has Hr_inv;
-  r8 = 25.8963;
-  r8 has Hr_inv;
-  m13 = 6.8544;
-  m13 has nM_per_hour;
-  k11 = 48.5862;
-  k11 has nM;
-  m14 = 3.2581;
-  m14 has nM_per_hour;
-  k12 = 23.2876;
-  k12 has nM;
-  p5 = 0.5;
-  p5 has nM_per_hour;
-  k13 = 1.2;
-  k13 has nM;
-  q3 = 1;
-  q3 has Hr_inv;
-  m15 = 1.2;
-  m15 has nM_per_hour;
-  g7 = 0.4444;
-  g7 has nM;
-  g8 = 11.0459;
-  g8 has nM;
-  n6 = 11.3117;
-  n6 has nM_per_hour;
-  g9 = 14.5219;
-  g9 has nM;
-  m16 = 9.531;
-  m16 has nM_per_hour;
-  k14 = 50.9418;
-  k14 has nM;
-  p6 = 6.7738;
-  p6 has Hr_inv;
-  r9 = 31.0318;
-  r9 has Hr_inv;
-  r10 = 0.4557;
-  r10 has Hr_inv;
-  m17 = 5.4062;
-  m17 has nM_per_hour;
-  k15 = 49.4094;
-  k15 has nM;
-  m18 = 8.671;
-  m18 has nM_per_hour;
-  k16 = 42.4837;
-  k16 has nM;
-  n7 = 0.0833;
-  n7 has nM_per_hour;
-  g10 = 5.6855;
-  g10 has nM;
-  m19 = 6.1155;
-  m19 has nM_per_hour;
-  k17 = 18.6089;
-  k17 has nM;
-  p7 = 10.4532;
-  p7 has Hr_inv;
-  r11 = 34.6266;
-  r11 has Hr_inv;
-  r12 = 22.838;
-  r12 has Hr_inv;
-  m20 = 3.4152;
-  m20 has nM_per_hour;
-  k18 = 16.2407;
-  k18 has nM;
-  m21 = 0.028;
-  m21 has nM_per_hour;
-  k19 = 26.5795;
-  k19 has nM;
-  q4 = 7.4548;
-  q4 has Hr_inv;
-  n8 = 2.0738;
-  n8 has nM;
-  lmax = 1;
-  lmax has dimensionless;
-  a = 2.2802;
-  a has dimensionless;
-  b = 3.1075;
-  b has dimensionless;
-  c = 1.6808;
-  c has dimensionless;
-  d = 1.0164;
-  d has dimensionless;
-  e = 1.4943;
-  e has dimensionless;
-  f = 1.9491;
-  f has dimensionless;
-  h = 2.2116;
-  h has dimensionless;
-  i = 1.1065;
-  i has dimensionless;
-  j = 2.5579;
-  j has dimensionless;
-  k = 3.3953;
-  k has dimensionless;
-
-  // Other declarations:
-  var Day_in_hours, ld;
-  const cytoplasm, nucleus, q1, n1, g1, m1, k1, p1, r1, r2, m2, k2, m3, k3;
-  const n2, g2, g3, m4, k4, p2, p3, r5, r6, m10, k8, m11, k9, q2, n4, n5;
-  const g5, g6, m12, k10, r3, r4, m5, m6, k5, m7, m8, k6, n3, g4, m9, k7;
-  const p4, r7, r8, m13, k11, m14, k12, p5, k13, q3, m15, g7, g8, n6, g9;
-  const m16, k14, p6, r9, r10, m17, k15, m18, k16, n7, g10, m19, k17, p7;
-  const r11, r12, m20, k18, m21, k19, q4, n8, lmax, a, b, c, d, e, f, h, i;
-  const j, k;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-  unit Hr_inv = 1 / 3600 second;
-  unit nM = 1e-9 mole / litre;
-  unit nM_per_hour = 1e-9 mole / (litre * 3600 second);
-
-  // Display Names:
-  substance is "nanomoles";
-  time_unit is "hour";
-  Hr_inv is "Hour_inv";
-  R1 is "Light dependent cLm synthesis";
-  R2 is "Light independent cLm synthesis";
-  R3 is "cLm degradation";
-  R4 is "cLc synthesis";
-  R5 is "cLc transport into nucleus";
-  R6 is "cLn transport into cytoplasm";
-  R7 is "cLc degradation";
-  R8 is "cLn degradation";
-  R9 is "cTm transcription";
-  R10 is "cTm degradation";
-  R11 is "cTc synthesis";
-  R12 is "cTc transport into nucleus";
-  R13 is "cTn transport into cytoplasm";
-  R14 is "cTc degradation";
-  R15 is "cTn degradation";
-  R16 is "cXm transcription";
-  R17 is "cXm degradation";
-  R18 is "cXc transcription";
-  R19 is "cXc transport into nucleus";
-  R20 is "cXn transport into cytoplasm";
-  R21 is "cXc degradation";
-  R22 is "cXn degradation";
-  R23 is "cYm transcription";
-  R24 is "cYm degradation";
-  R25 is "cYc transcription";
-  R26 is "cYc transport to nucleus";
-  R27 is "cYn transport to cytoplasm";
-  R28 is "cYc degradation";
-  R29 is "cYn degradation";
-  R30 is "cPn synthesis";
-  R31a is "cPn degradation";
-  R31b is "Light dependent cPn degradation";
-  R32 is "cP7m transcription";
-  R33 is "cP7m degradation";
-  R34 is "cP7c synthesis";
-  R35 is "cP7c transport to nucleus";
-  R36 is "cP7n transport to cytoplasm";
-  R37 is "cP7c degradation";
-  R38 is "cP7n degradation";
-  R39 is "cP9m transcription";
-  R40 is "cP79m degradation";
-  R41 is "cP9c synthesis";
-  R42 is "cP9c transport to nucleus";
-  R43 is "cP9n transport to cytoplasm";
-  R44 is "cP9c degradation";
-  R45 is "cP9n degradation";
-
-  // CV terms:
-  cytoplasm identity "http://identifiers.org/obo.go/GO:0005737"
-  nucleus identity "http://identifiers.org/obo.go/GO:0005634"
-  cLc identity "http://identifiers.org/uniprot/O81713"
-  cLm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cLn identity "http://identifiers.org/uniprot/O81713"
-  cP7c identity "http://identifiers.org/uniprot/Q93WK5"
-  cP7m identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  cP7n identity "http://identifiers.org/uniprot/Q93WK5"
-  cP9c identity "http://identifiers.org/uniprot/Q8L500"
-  cP9m identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  cP9n identity "http://identifiers.org/uniprot/Q8L500"
-  cTc identity "http://identifiers.org/uniprot/Q9LKL2",
-               "http://identifiers.org/interpro/IPR010402"
-  cTm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cTn identity "http://identifiers.org/uniprot/Q9LKL2"
-  cXm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cXn identity "http://identifiers.org/obo.go/GO:0005667"
-  cYm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cYn identity "http://identifiers.org/obo.go/GO:0005667"
-  R1 identity "http://identifiers.org/obo.go/GO:0006351",
-              "http://identifiers.org/obo.go/GO:0009642"
-  R2 identity "http://identifiers.org/obo.go/GO:0006351"
-  R3 identity "http://identifiers.org/obo.go/GO:0006402"
-  R4 identity "http://identifiers.org/obo.go/GO:0006412"
-  R5 identity "http://identifiers.org/obo.go/GO:0000060"
-  R6 identity "http://identifiers.org/obo.go/GO:0065002"
-  R7 identity "http://identifiers.org/obo.go/GO:0044257"
-  R8 identity "http://identifiers.org/obo.go/GO:0044257"
-  R9 identity "http://identifiers.org/obo.go/GO:0006351"
-  R10 identity "http://identifiers.org/obo.go/GO:0006402"
-  R11 identity "http://identifiers.org/obo.go/GO:0006412"
-  R12 identity "http://identifiers.org/obo.go/GO:0000060"
-  R13 identity "http://identifiers.org/obo.go/GO:0065002"
-  R14 identity "http://identifiers.org/obo.go/GO:0044257"
-  R15 identity "http://identifiers.org/obo.go/GO:0044257"
-  R16 identity "http://identifiers.org/obo.go/GO:0006351"
-  R17 identity "http://identifiers.org/obo.go/GO:0006402"
-  R18 identity "http://identifiers.org/obo.go/GO:0006412"
-  R19 identity "http://identifiers.org/obo.go/GO:0000060"
-  R20 identity "http://identifiers.org/obo.go/GO:0065002"
-  R21 identity "http://identifiers.org/obo.go/GO:0044257"
-  R22 identity "http://identifiers.org/obo.go/GO:0044257"
-  R23 identity "http://identifiers.org/obo.go/GO:0006351",
-               "http://identifiers.org/obo.go/GO:0009642"
-  R24 identity "http://identifiers.org/obo.go/GO:0006402"
-  R25 identity "http://identifiers.org/obo.go/GO:0006412"
-  R26 identity "http://identifiers.org/obo.go/GO:0000060"
-  R27 identity "http://identifiers.org/obo.go/GO:0065002"
-  R28 identity "http://identifiers.org/obo.go/GO:0044257"
-  R29 identity "http://identifiers.org/obo.go/GO:0044257"
-  R30 identity "http://identifiers.org/obo.go/GO:0009642",
-               "http://identifiers.org/obo.go/GO:0006412"
-  R31a identity "http://identifiers.org/obo.go/GO:0044257"
-  R31b identity "http://identifiers.org/obo.go/GO:0045732",
-                "http://identifiers.org/obo.go/GO:0009642"
-  R32 identity "http://identifiers.org/obo.go/GO:0006351"
-  R33 identity "http://identifiers.org/obo.go/GO:0006402"
-  R34 identity "http://identifiers.org/obo.go/GO:0006412"
-  R35 identity "http://identifiers.org/obo.go/GO:0000060"
-  R36 identity "http://identifiers.org/obo.go/GO:0065002"
-  R37 identity "http://identifiers.org/obo.go/GO:0044257"
-  R38 identity "http://identifiers.org/obo.go/GO:0044257"
-  R39 identity "http://identifiers.org/obo.go/GO:0006351"
-  R39 part "http://identifiers.org/obo.go/GO:0009642"
-  R40 identity "http://identifiers.org/obo.go/GO:0006402"
-  R41 identity "http://identifiers.org/obo.go/GO:0006412"
-  R42 identity "http://identifiers.org/obo.go/GO:0000060"
-  R43 identity "http://identifiers.org/obo.go/GO:0065002"
-  R44 identity "http://identifiers.org/obo.go/GO:0044257"
-  R45 identity "http://identifiers.org/obo.go/GO:0044257"
-end
-
-Zeilinger2006_PRR7_PRR9light_Y is "Zeilinger2006_PRR7-PRR9light-Y"
-
-Zeilinger2006_PRR7_PRR9light_Y model_entity_is "http://identifiers.org/biomodels.db/MODEL4025634026"
-Zeilinger2006_PRR7_PRR9light_Y model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000096"
-Zeilinger2006_PRR7_PRR9light_Y description "http://identifiers.org/pubmed/17102803"
-Zeilinger2006_PRR7_PRR9light_Y origin "http://identifiers.org/biomodels.db/BIOMD0000000055"
-Zeilinger2006_PRR7_PRR9light_Y identity "http://identifiers.org/kegg.pathway/ath04710",
-                                        "http://identifiers.org/obo.go/GO:0007623"
-Zeilinger2006_PRR7_PRR9light_Y taxon "http://identifiers.org/taxonomy/3701"
diff --git a/BioModelsRAG/data/BIOMD0000000097.txt b/BioModelsRAG/data/BIOMD0000000097.txt
deleted file mode 100644
index d3611e516a82791b2838d7d51597ef9d9e211a36..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000097.txt
+++ /dev/null
@@ -1,431 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Zeilinger2006_PRR7_PRR9light_Yprime()
-
-  // Compartments and Species:
-  compartment cytoplasm, nucleus;
-  species cLc in cytoplasm, cLm in nucleus, cLn in nucleus, cP7c in cytoplasm;
-  species cP7m in nucleus, cP7n in nucleus, cP9c in cytoplasm, cP9m in nucleus;
-  species cP9n in nucleus, cPn in nucleus, cTc in cytoplasm, cTm in nucleus;
-  species cTn in nucleus, cXc in cytoplasm, cXm in nucleus, cXn in nucleus;
-  species cYc in cytoplasm, cYm in nucleus, cYn in nucleus;
-
-  // Reactions:
-  R1:  => cLm; nucleus*ld*q1*cPn;
-  R2:  => cLm; nucleus*(n1*cXn^a/(g1^a + cXn^a))*(g7^h/(g7^h + cP7n^h))*(g8^i/(g8^i + cP9n^i));
-  R3: cLm => ; nucleus*m1*cLm/(k1 + cLm);
-  R4:  => cLc; cytoplasm*p1*cLm;
-  R5: cLc => cLn; cytoplasm*r1*cLc;
-  R6: cLn => cLc; nucleus*r2*cLn;
-  R7: cLc => ; cytoplasm*m2*cLc/(k2 + cLc);
-  R8: cLn => ; nucleus*m3*cLn/(k3 + cLn);
-  R9:  => cTm; nucleus*(n2*cYn^b/(g2^b + cYn^b))*(g3^c/(g3^c + cLn^c));
-  R10: cTm => ; nucleus*m4*cTm/(k4 + cTm);
-  R11:  => cTc; cytoplasm*p2*cTm;
-  R12: cTc => cTn; cytoplasm*r3*cTc;
-  R13: cTn => cTc; nucleus*r4*cTn;
-  R14: cTc => ; cytoplasm*((lmax - ld)*m5 + m6)*(cTc/(k5 + cTc));
-  R15: cTn => ; nucleus*((lmax - ld)*m7 + m8)*(cTn/(k6 + cTn));
-  R16:  => cXm; nucleus*n3*cTn^d/(g4^d + cTn^d);
-  R17: cXm => ; nucleus*m9*cXm/(k7 + cXm);
-  R18:  => cXc; cytoplasm*p3*cXm;
-  R19: cXc => cXn; cytoplasm*r5*cXc;
-  R20: cXn => cXc; nucleus*r6*cXn;
-  R21: cXc => ; cytoplasm*m10*cXc/(k8 + cXc);
-  R22: cXn => ; nucleus*m11*cXn/(k9 + cXn);
-  R23:  => cYm; nucleus*((ld*n4 + n5)*g5^e/(g5^e + cTn^e))*(g6^f/(g6^f + cLn^f));
-  R24: cYm => ; nucleus*m12*cYm/(k10 + cYm);
-  R25:  => cYc; cytoplasm*p4*cYm;
-  R26: cYc => cYn; cytoplasm*r7*cYc;
-  R27: cYn => cYc; nucleus*r8*cYn;
-  R28: cYc => ; cytoplasm*m13*cYc/(k11 + cYc);
-  R29: cYn => ; nucleus*m14*cYn/(k12 + cYn);
-  R30:  => cPn; nucleus*(lmax - ld)*p5;
-  R31a: cPn => ; nucleus*m15*cPn/(k13 + cPn);
-  R31b: cPn => ; nucleus*q3*ld*cPn;
-  R32:  => cP7m; nucleus*n6*cLn^j/(g9^j + cLn^j);
-  R33: cP7m => ; nucleus*m16*cP7m/(k14 + cP7m);
-  R34:  => cP7c; cytoplasm*p6*cP7m;
-  R35: cP7c => cP7n; cytoplasm*r9*cP7c;
-  R36: cP7n => cP7c; nucleus*r10*cP7n;
-  R37: cP7c => ; cytoplasm*m17*cP7c/(k15 + cP7c);
-  R38: cP7n => ; nucleus*m18*cP7n/(k16 + cP7n);
-  R39:  => cP9m; nucleus*((ld*q4*cPn + n7*ld + n8)*cLn^k/(g10^k + cLn^k));
-  R40: cP9m => ; nucleus*m19*cP9m/(k17 + cP9m);
-  R41:  => cP9c; cytoplasm*p7*cP9m;
-  R42: cP9c => cP9n; cytoplasm*r11*cP9c;
-  R43: cP9n => cP9c; nucleus*r12*cP9n;
-  R44: cP9c => ; cytoplasm*m20*cP9c/(k18 + cP9c);
-  R45: cP9n => ; nucleus*m21*cP9n/(k19 + cP9n);
-
-  // Events:
-  event_0000001: at (Day_in_hours - time) <= 0: ld = 1, Day_in_hours = Day_in_hours + 24;
-  event_0000002: at ((Day_in_hours - time) <= 16) && ((Day_in_hours - time) > 0): ld = 0;
-
-  // Species initializations:
-  cLc = 0.0659;
-  cLm = 0.1951;
-  cLn = 0.3952;
-  cP7c = 0.0861;
-  cP7m = 0.0772;
-  cP7n = 2.7182;
-  cP9c = 0.0077;
-  cP9m = 0.0011;
-  cP9n = 0.0073;
-  cPn = 0;
-  cTc = 0.7852;
-  cTm = 0.1234;
-  cTn = 4.5209;
-  cXc = 2.5615;
-  cXm = 1.6104;
-  cXn = 14.5474;
-  cYc = 7.6795;
-  cYm = 1.1149;
-  cYn = 9.7016;
-
-  // Compartment initializations:
-  cytoplasm = 1;
-  nucleus = 1;
-
-  // Variable initializations:
-  Day_in_hours = 24;
-  Day_in_hours has time_unit;
-  ld = 1;
-  ld has dimensionless;
-  q1 = 13.4334;
-  q1 has Hr_inv;
-  n1 = 3.2016;
-  n1 has nM_per_hour;
-  g1 = 9.041;
-  g1 has nM;
-  m1 = 6.8248;
-  m1 has nM_per_hour;
-  k1 = 13.0594;
-  k1 has nM;
-  p1 = 0.6926;
-  p1 has Hr_inv;
-  r1 = 25.6818;
-  r1 has Hr_inv;
-  r2 = 3.9781;
-  r2 has Hr_inv;
-  m2 = 9.4099;
-  m2 has nM_per_hour;
-  k2 = 30.5639;
-  k2 has nM;
-  m3 = 13.7795;
-  m3 has nM_per_hour;
-  k3 = 33.514;
-  k3 has nM;
-  n2 = 11.6086;
-  n2 has nM_per_hour;
-  g2 = 16.6598;
-  g2 has nM;
-  g3 = 13.4112;
-  g3 has nM;
-  m4 = 12.1232;
-  m4 has nM_per_hour;
-  k4 = 1.3722;
-  k4 has nM;
-  p2 = 0.5403;
-  p2 has Hr_inv;
-  p3 = 6.9124;
-  p3 has Hr_inv;
-  r5 = 29.4607;
-  r5 has Hr_inv;
-  r6 = 4.5034;
-  r6 has Hr_inv;
-  m10 = 8.5523;
-  m10 has nM_per_hour;
-  k8 = 12.528;
-  k8 has nM;
-  m11 = 23.5996;
-  m11 has nM_per_hour;
-  k9 = 15.0626;
-  k9 has nM;
-  n4 = 1.7832;
-  n4 has nM_per_hour;
-  n5 = 7.4615;
-  n5 has nM_per_hour;
-  g5 = 1.5987;
-  g5 has nM;
-  g6 = 16.489;
-  g6 has nM;
-  m12 = 5.9504;
-  m12 has nM_per_hour;
-  k10 = 11.5688;
-  k10 has nM;
-  r3 = 51.1965;
-  r3 has Hr_inv;
-  r4 = 8.9147;
-  r4 has Hr_inv;
-  m5 = 7.2129;
-  m5 has nM_per_hour;
-  m6 = 9.5754;
-  m6 has nM_per_hour;
-  k5 = 34.2078;
-  k5 has nM;
-  m7 = 1.1032;
-  m7 has nM_per_hour;
-  m8 = 2.2006;
-  m8 has nM_per_hour;
-  k6 = 56.7596;
-  k6 has nM;
-  n3 = 2.4751;
-  n3 has nM_per_hour;
-  g4 = 20.5277;
-  g4 has nM;
-  m9 = 4.2193;
-  m9 has nM_per_hour;
-  k7 = 14.9114;
-  k7 has nM;
-  p4 = 6.0042;
-  p4 has Hr_inv;
-  r7 = 35.7842;
-  r7 has Hr_inv;
-  r8 = 27.9229;
-  r8 has Hr_inv;
-  m13 = 7.5959;
-  m13 has nM_per_hour;
-  k11 = 26.9638;
-  k11 has nM;
-  m14 = 8.1796;
-  m14 has nM_per_hour;
-  k12 = 21.8348;
-  k12 has nM;
-  p5 = 0.5;
-  p5 has nM_per_hour;
-  k13 = 1.2;
-  k13 has nM;
-  q3 = 1;
-  q3 has Hr_inv;
-  m15 = 1.2;
-  m15 has nM_per_hour;
-  g7 = 0.2778;
-  g7 has nM;
-  g8 = 0.9187;
-  g8 has nM;
-  n6 = 11.0924;
-  n6 has nM_per_hour;
-  g9 = 20.3795;
-  g9 has nM;
-  m16 = 9.3186;
-  m16 has nM_per_hour;
-  k14 = 51.261;
-  k14 has nM;
-  p6 = 9.8416;
-  p6 has Hr_inv;
-  r9 = 24.5689;
-  r9 has Hr_inv;
-  r10 = 0.5024;
-  r10 has Hr_inv;
-  m17 = 3.6143;
-  m17 has nM_per_hour;
-  k15 = 32.939;
-  k15 has nM;
-  m18 = 6.7455;
-  m18 has nM_per_hour;
-  k16 = 24.451;
-  k16 has nM;
-  n7 = 0.1031;
-  n7 has nM_per_hour;
-  g10 = 5.8418;
-  g10 has nM;
-  m19 = 1.9234;
-  m19 has nM_per_hour;
-  k17 = 9.8065;
-  k17 has nM;
-  p7 = 1.5323;
-  p7 has Hr_inv;
-  r11 = 25.7542;
-  r11 has Hr_inv;
-  r12 = 27.2451;
-  r12 has Hr_inv;
-  m20 = 3.7484;
-  m20 has nM_per_hour;
-  k18 = 25.9739;
-  k18 has nM;
-  m21 = 0.0193;
-  m21 has nM_per_hour;
-  k19 = 21.6441;
-  k19 has nM;
-  q4 = 6.274;
-  q4 has Hr_inv;
-  n8 = 3.5262;
-  n8 has nM;
-  a = 1.2497;
-  a has dimensionless;
-  b = 4.2126;
-  b has dimensionless;
-  c = 1.4509;
-  c has dimensionless;
-  d = 1.3058;
-  d has dimensionless;
-  e = 2.4146;
-  e has dimensionless;
-  f = 2.1349;
-  f has dimensionless;
-  h = 1.4176;
-  h has dimensionless;
-  i = 2.0074;
-  i has dimensionless;
-  j = 1.7615;
-  j has dimensionless;
-  k = 3.8877;
-  k has dimensionless;
-  lmax = 1;
-  lmax has dimensionless;
-
-  // Other declarations:
-  var Day_in_hours, ld;
-  const cytoplasm, nucleus, q1, n1, g1, m1, k1, p1, r1, r2, m2, k2, m3, k3;
-  const n2, g2, g3, m4, k4, p2, p3, r5, r6, m10, k8, m11, k9, n4, n5, g5;
-  const g6, m12, k10, r3, r4, m5, m6, k5, m7, m8, k6, n3, g4, m9, k7, p4;
-  const r7, r8, m13, k11, m14, k12, p5, k13, q3, m15, g7, g8, n6, g9, m16;
-  const k14, p6, r9, r10, m17, k15, m18, k16, n7, g10, m19, k17, p7, r11;
-  const r12, m20, k18, m21, k19, q4, n8, a, b, c, d, e, f, h, i, j, k, lmax;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-  unit Hr_inv = 1 / 3600 second;
-  unit nM = 1e-9 mole / litre;
-  unit nM_per_hour = 1e-9 mole / (litre * 3600 second);
-
-  // Display Names:
-  substance is "nanomoles";
-  time_unit is "hour";
-  Hr_inv is "Hour_inv";
-  R1 is "Light dependent cLm production";
-  R2 is "Light independent cLm production";
-  R3 is "cLm degradation";
-  R4 is "cLc synthesis";
-  R5 is "cLc transport to nucleus";
-  R6 is "cLn transport to cytoplasm";
-  R7 is "cLc degradation";
-  R8 is "cLn degradation";
-  R9 is "cTm transcription";
-  R10 is "cTm degradation";
-  R11 is "cTc synthesis";
-  R12 is "cTc transport to nucleus";
-  R13 is "cTn transport to cytoplasm";
-  R14 is "cTc degradation";
-  R15 is "cTn degradation";
-  R16 is "Species X transcription";
-  R17 is "Species X degradation";
-  R18 is "cXc synthesis";
-  R19 is "cXc transport to nucleus";
-  R20 is "cXn transport to cytoplasm";
-  R21 is "cXc degradation";
-  R22 is "cXn degradation";
-  R23 is "Species Y transcription";
-  R24 is "cYm degradation";
-  R25 is "cYc synthesis";
-  R26 is "cYc transport to nucleus";
-  R27 is "cYn transport to cytoplasm";
-  R28 is "cYc degradation";
-  R29 is "cYn degradation";
-  R30 is "cPn synthesis";
-  R31a is "cPn degradation";
-  R31b is "cPn light dependent degradation";
-  R32 is "cP7m transcription";
-  R33 is "cP7m degradation";
-  R34 is "cP7c synthesis";
-  R35 is "cP7c transport to nucleus";
-  R36 is "cP7n transport to cytoplasm";
-  R37 is "cP7c degradation";
-  R38 is "cP7n degradation";
-  R39 is "cP9m transcription";
-  R40 is "cP9m degradation";
-  R41 is "cP9c synthesis";
-  R42 is "cP9c transport to nucleus";
-  R43 is "cP9n transport to cytoplasm";
-  R44 is "cP9c degradation";
-  R45 is "cP9n degradation";
-
-  // CV terms:
-  cytoplasm identity "http://identifiers.org/obo.go/GO:0005737"
-  nucleus identity "http://identifiers.org/obo.go/GO:0005634"
-  cLc identity "http://identifiers.org/uniprot/O81713"
-  cLm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cLn identity "http://identifiers.org/uniprot/O81713"
-  cP7c identity "http://identifiers.org/uniprot/Q93WK5"
-  cP7m identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  cP7n identity "http://identifiers.org/uniprot/Q93WK5"
-  cP9c identity "http://identifiers.org/uniprot/Q8L500"
-  cP9m identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  cP9n identity "http://identifiers.org/uniprot/Q8L500"
-  cTc identity "http://identifiers.org/uniprot/Q9LKL2",
-               "http://identifiers.org/interpro/IPR010402"
-  cTm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cTn identity "http://identifiers.org/uniprot/Q9LKL2",
-               "http://identifiers.org/interpro/IPR010402"
-  cXm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cXn identity "http://identifiers.org/obo.go/GO:0005667"
-  cYm identity "http://identifiers.org/obo.chebi/CHEBI:33699",
-               "http://identifiers.org/kegg.compound/C00046"
-  cYn identity "http://identifiers.org/obo.go/GO:0005667"
-  R1 identity "http://identifiers.org/obo.go/GO:0006351",
-              "http://identifiers.org/obo.go/GO:0009642"
-  R2 identity "http://identifiers.org/obo.go/GO:0006351"
-  R3 identity "http://identifiers.org/obo.go/GO:0006402"
-  R4 identity "http://identifiers.org/obo.go/GO:0006412"
-  R5 identity "http://identifiers.org/obo.go/GO:0000060"
-  R6 identity "http://identifiers.org/obo.go/GO:0065002"
-  R7 identity "http://identifiers.org/obo.go/GO:0044257"
-  R8 identity "http://identifiers.org/obo.go/GO:0044257"
-  R9 identity "http://identifiers.org/obo.go/GO:0006351"
-  R10 identity "http://identifiers.org/obo.go/GO:0006402"
-  R11 identity "http://identifiers.org/obo.go/GO:0006412"
-  R12 identity "http://identifiers.org/obo.go/GO:0000060"
-  R13 identity "http://identifiers.org/obo.go/GO:0065002"
-  R14 identity "http://identifiers.org/obo.go/GO:0044257"
-  R15 identity "http://identifiers.org/obo.go/GO:0044257"
-  R16 identity "http://identifiers.org/obo.go/GO:0006351"
-  R17 identity "http://identifiers.org/obo.go/GO:0006402"
-  R18 identity "http://identifiers.org/obo.go/GO:0006412"
-  R19 identity "http://identifiers.org/obo.go/GO:0000060"
-  R20 identity "http://identifiers.org/obo.go/GO:0065002"
-  R21 identity "http://identifiers.org/obo.go/GO:0044257"
-  R22 identity "http://identifiers.org/obo.go/GO:0044257"
-  R23 identity "http://identifiers.org/obo.go/GO:0006351"
-  R23 part "http://identifiers.org/obo.go/GO:0009642"
-  R24 identity "http://identifiers.org/obo.go/GO:0006402"
-  R25 identity "http://identifiers.org/obo.go/GO:0006412"
-  R26 identity "http://identifiers.org/obo.go/GO:0000060"
-  R27 identity "http://identifiers.org/obo.go/GO:0065002"
-  R28 identity "http://identifiers.org/obo.go/GO:0044257"
-  R29 identity "http://identifiers.org/obo.go/GO:0044257"
-  R30 identity "http://identifiers.org/obo.go/GO:0009642",
-               "http://identifiers.org/obo.go/GO:0006412"
-  R31a identity "http://identifiers.org/obo.go/GO:0044257"
-  R31b identity "http://identifiers.org/obo.go/GO:0045732",
-                "http://identifiers.org/obo.go/GO:0009642"
-  R32 identity "http://identifiers.org/obo.go/GO:0006351"
-  R33 identity "http://identifiers.org/obo.go/GO:0006402"
-  R34 identity "http://identifiers.org/obo.go/GO:0006412"
-  R35 identity "http://identifiers.org/obo.go/GO:0000060"
-  R36 identity "http://identifiers.org/obo.go/GO:0065002"
-  R37 identity "http://identifiers.org/obo.go/GO:0044257"
-  R38 identity "http://identifiers.org/obo.go/GO:0044257"
-  R39 identity "http://identifiers.org/obo.go/GO:0006351"
-  R40 identity "http://identifiers.org/obo.go/GO:0006402"
-  R41 identity "http://identifiers.org/obo.go/GO:0006412"
-  R42 identity "http://identifiers.org/obo.go/GO:0000060"
-  R43 identity "http://identifiers.org/obo.go/GO:0065002"
-  R44 identity "http://identifiers.org/obo.go/GO:0044257"
-  R45 identity "http://identifiers.org/obo.go/GO:0044257"
-end
-
-Zeilinger2006_PRR7_PRR9light_Yprime is "Zeilinger2006_PRR7-PRR9light-Yprime"
-
-Zeilinger2006_PRR7_PRR9light_Yprime model_entity_is "http://identifiers.org/biomodels.db/MODEL4025650992"
-Zeilinger2006_PRR7_PRR9light_Yprime model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000097"
-Zeilinger2006_PRR7_PRR9light_Yprime description "http://identifiers.org/pubmed/17102803"
-Zeilinger2006_PRR7_PRR9light_Yprime origin "http://identifiers.org/biomodels.db/BIOMD0000000055"
-Zeilinger2006_PRR7_PRR9light_Yprime taxon "http://identifiers.org/taxonomy/3701"
-Zeilinger2006_PRR7_PRR9light_Yprime identity "http://identifiers.org/kegg.pathway/ath04710",
-                                             "http://identifiers.org/obo.go/GO:0007623"
diff --git a/BioModelsRAG/data/BIOMD0000000098.txt b/BioModelsRAG/data/BIOMD0000000098.txt
deleted file mode 100644
index 126e6f793ffbba3e9beb8b9e15e8cc3c64db5066..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000098.txt
+++ /dev/null
@@ -1,96 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter1990_CalciumSpike_CICR()
-
-  // Compartments and Species:
-  compartment cytosol, store;
-  species Z in cytosol, Y in store;
-
-  // Reactions:
-  R0:  => Z; cytosol*v0;
-  R1:  => Z; cytosol*v1*beta;
-  R2: Z => Y; cytosol*(Vm2*Z^n/(K2^n + Z^n));
-  R3: Y => Z; store*(Vm3*Y^m*Z^p/((Kr^m + Y^m)*(Ka^p + Z^p)));
-  Rf: Y => Z; store*kf*Y;
-  R_eff: Z => ; cytosol*k*Z;
-
-  // Species initializations:
-  Z = 0.15;
-  Y = 1.6;
-
-  // Compartment initializations:
-  cytosol = 1;
-  store = 1;
-
-  // Variable initializations:
-  v0 = 1;
-  v0 has uM_per_sec;
-  v1 = 7.3;
-  v1 has uM_per_sec;
-  beta = 0.301;
-  beta has dimensionless;
-  Vm2 = 65;
-  Vm2 has uM_per_sec;
-  n = 2;
-  n has dimensionless;
-  K2 = 1;
-  K2 has uM;
-  Vm3 = 500;
-  Vm3 has uM_per_sec;
-  m = 2;
-  m has dimensionless;
-  Kr = 2;
-  Kr has uM;
-  Ka = 0.9;
-  Ka has uM;
-  kf = 1;
-  kf has sec_inv;
-  k = 10;
-  k has sec_inv;
-  p = 4;
-  p has dimensionless;
-
-  // Other declarations:
-  const cytosol, store, v0, v1, beta, Vm2, n, K2, Vm3, m, Kr, Ka, kf, k, p;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit uM_per_sec = 1e-6 mole / (litre * second);
-  unit sec_inv = 1 / second;
-  unit uM = 1e-6 mole / litre;
-
-  // Display Names:
-  substance is "micromole";
-  R0 is "Ca influx";
-  R1 is "InsP3 dependent Ca influx";
-  R2 is "ATP driven Ca pumping into store";
-  R3 is "ATP driven pumping into cytosol";
-  Rf is "Ca leak";
-  R_eff is "Ca efflux";
-
-  // CV terms:
-  cytosol identity "http://identifiers.org/go/GO:0005829"
-  store identity "http://identifiers.org/go/GO:0005783"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  R0 identity "http://identifiers.org/go/GO:0006816"
-  R1 identity "http://identifiers.org/go/GO:0005220"
-  R2 identity "http://identifiers.org/go/GO:0032470"
-  R3 identity "http://identifiers.org/go/GO:0007204",
-              "http://identifiers.org/go/GO:0048763"
-  Rf identity "http://identifiers.org/go/GO:0007204"
-  R_eff identity "http://identifiers.org/go/GO:0006816"
-end
-
-Goldbeter1990_CalciumSpike_CICR is "Goldbeter1990_CalciumSpike_CICR"
-
-Goldbeter1990_CalciumSpike_CICR model_entity_is "http://identifiers.org/biomodels.db/MODEL4519937652"
-Goldbeter1990_CalciumSpike_CICR model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000098"
-Goldbeter1990_CalciumSpike_CICR description "http://identifiers.org/pubmed/2304911"
-Goldbeter1990_CalciumSpike_CICR origin "http://identifiers.org/pubmed/6281582"
-Goldbeter1990_CalciumSpike_CICR hypernym "http://identifiers.org/go/GO:0005220",
-                                         "http://identifiers.org/go/GO:0006816",
-                                         "http://identifiers.org/go/GO:0019722"
-Goldbeter1990_CalciumSpike_CICR taxon "http://identifiers.org/taxonomy/131567"
-Goldbeter1990_CalciumSpike_CICR property "http://identifiers.org/mamo/MAMO_0000046"
diff --git a/BioModelsRAG/data/BIOMD0000000099.txt b/BioModelsRAG/data/BIOMD0000000099.txt
deleted file mode 100644
index c83d2bcf46bcc033e6cedc9ff6a83ee37b3828f0..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000099.txt
+++ /dev/null
@@ -1,146 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Model_1()
-
-  // Compartments and Species:
-  compartment compartment_0, compartment_1;
-  species species_0 in compartment_0, species_1 in compartment_1, species_2 in compartment_1;
-  species species_3 in compartment_1, species_4 in compartment_1, species_5 in compartment_1;
-  species species_6 in compartment_1;
-
-  // Reactions:
-  reaction_0:  => species_4; compartment_1*parameter_0*species_6;
-  reaction_1: species_4 => ; compartment_1*parameter_1*species_4;
-  reaction_2:  => species_2; compartment_1*parameter_2*species_1;
-  reaction_3: species_2 => ; compartment_1*parameter_3*species_2;
-  reaction_4:  => species_6; compartment_1*parameter_4*species_5;
-  reaction_5: species_6 => ; compartment_1*parameter_5*species_6*species_2;
-  reaction_6:  => species_3; compartment_1*parameter_6;
-  reaction_7: species_3 => ; compartment_1*parameter_7*species_3*species_6;
-  reaction_8:  => species_1; compartment_1*parameter_8*species_4;
-  reaction_9: species_1 => ; compartment_1*parameter_9*species_1*species_3;
-  reaction_10:  => species_0; compartment_0*parameter_10*species_4;
-  reaction_11: species_0 => ; compartment_0*parameter_11*species_0;
-  reaction_12:  => species_5; compartment_1*parameter_12*species_0;
-  reaction_13: species_5 => ; compartment_1*parameter_13*species_5*species_2;
-
-  // Species initializations:
-  species_0 = 0;
-  species_1 = 1;
-  species_2 = 1;
-  species_3 = 2.5;
-  species_4 = 1.4;
-  species_5 = 1.5;
-  species_6 = 1.6;
-
-  // Compartment initializations:
-  compartment_0 = 1;
-  compartment_1 = 1;
-
-  // Variable initializations:
-  parameter_0 = 1.4;
-  parameter_1 = 0.9;
-  parameter_2 = 2.5;
-  parameter_3 = 1.5;
-  parameter_4 = 0.6;
-  parameter_5 = 0.8;
-  parameter_6 = 2;
-  parameter_7 = 1.3;
-  parameter_8 = 0.29;
-  parameter_9 = 1;
-  parameter_10 = 0.6;
-  parameter_11 = 3.1;
-  parameter_12 = 33;
-  parameter_13 = 4.5;
-
-  // Other declarations:
-  const compartment_0, compartment_1, parameter_0, parameter_1, parameter_2;
-  const parameter_3, parameter_4, parameter_5, parameter_6, parameter_7, parameter_8;
-  const parameter_9, parameter_10, parameter_11, parameter_12, parameter_13;
-
-  // Unit definitions:
-  unit time_unit = 60 second;
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  time_unit is "min";
-  substance is "micro_Mole";
-  compartment_0 is "Extracellular";
-  compartment_1 is "Intracellular";
-  species_0 is "Ex_cAMP";
-  species_1 is "In_cAMP";
-  species_2 is "PKA";
-  species_3 is "REGA";
-  species_4 is "ACA";
-  species_5 is "CAR1";
-  species_6 is "ERK2";
-  parameter_0 is "k1";
-  parameter_1 is "k2";
-  parameter_2 is "k3";
-  parameter_3 is "k4";
-  parameter_4 is "k5";
-  parameter_5 is "k6";
-  parameter_6 is "k7";
-  parameter_7 is "k8";
-  parameter_8 is "k9";
-  parameter_9 is "k10";
-  parameter_10 is "k11";
-  parameter_11 is "k12";
-  parameter_12 is "k13";
-  parameter_13 is "k14";
-  reaction_0 is "k1";
-  reaction_1 is "k2";
-  reaction_2 is "k3";
-  reaction_3 is "k4";
-  reaction_4 is "k5";
-  reaction_5 is "k6";
-  reaction_6 is "k7";
-  reaction_7 is "k8";
-  reaction_8 is "k9";
-  reaction_9 is "k10";
-  reaction_10 is "k11";
-  reaction_11 is "k12";
-  reaction_12 is "k13";
-  reaction_13 is "k14";
-
-  // CV terms:
-  compartment_0 hypernym "http://identifiers.org/go/GO:0005576"
-  compartment_1 hypernym "http://identifiers.org/go/GO:0005623"
-  species_0 identity "http://identifiers.org/chebi/CHEBI:17489",
-                     "http://identifiers.org/kegg.compound/C00575"
-  species_1 identity "http://identifiers.org/chebi/CHEBI:17489",
-                     "http://identifiers.org/kegg.compound/C00575"
-  species_2 identity "http://identifiers.org/uniprot/P34099"
-  species_2 hypernym "http://identifiers.org/interpro/IPR002373"
-  species_3 hypernym "http://identifiers.org/interpro/IPR000396"
-  species_4 hypernym "http://identifiers.org/interpro/IPR008172"
-  species_5 identity "http://identifiers.org/uniprot/P13773"
-  species_5 hypernym "http://identifiers.org/interpro/IPR000848"
-  species_6 hypernym "http://identifiers.org/interpro/IPR008349"
-  species_6 homolog "http://identifiers.org/uniprot/P28482"
-  reaction_0 hypernym "http://identifiers.org/go/GO:0004707",
-                      "http://identifiers.org/go/GO:0007190"
-  reaction_1 hypernym "http://identifiers.org/go/GO:0007194"
-  reaction_2 hypernym "http://identifiers.org/go/GO:0001646",
-                      "http://identifiers.org/go/GO:0032147"
-  reaction_3 hypernym "http://identifiers.org/go/GO:0006469"
-  reaction_4 hypernym "http://identifiers.org/go/GO:0045860"
-  reaction_5 hypernym "http://identifiers.org/go/GO:0004672"
-  reaction_7 hypernym "http://identifiers.org/go/GO:0004707"
-  reaction_8 hypernym "http://identifiers.org/go/GO:0004016",
-                      "http://identifiers.org/go/GO:0030819"
-  reaction_9 hypernym "http://identifiers.org/go/GO:0004115"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0004016"
-  reaction_11 hypernym "http://identifiers.org/go/GO:0006198"
-  reaction_12 hypernym "http://identifiers.org/go/GO:0001646"
-  reaction_13 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0004672"
-end
-
-Model_1 is "Laub1998_SpontaneousOscillations"
-
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL4515710981"
-Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000099"
-Model_1 description "http://identifiers.org/pubmed/9843585"
-Model_1 taxon "http://identifiers.org/taxonomy/5782"
-Model_1 property "http://identifiers.org/mamo/MAMO_0000046"
-Model_1 hypernym "http://identifiers.org/go/GO:0019933"
diff --git a/BioModelsRAG/data/BIOMD0000000100.txt b/BioModelsRAG/data/BIOMD0000000100.txt
deleted file mode 100644
index 2e0f804b98ae520aa50510362221fa7d24eaec0c..0000000000000000000000000000000000000000
--- a/BioModelsRAG/data/BIOMD0000000100.txt
+++ /dev/null
@@ -1,164 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Rozi2003_Glycogen_Phosphorylase_Activation()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular;
-  species $EC in extracellular, Z in cytosol, A in cytosol, Y in intravesicular;
-  species GP in cytosol;
-
-  // Reactions:
-  vin: $EC => Z; extracellular*(v0 + v1*beta);
-  R2: Z => Y; cytosol*(Vm2*Z^2/(K2^2 + Z^2));
-  R3: Y => Z; intravesicular*Vm3*A^4*Y^2*Z^m/((Ka^4 + A^4)*(Ky^2 + Y^2)*(Kz^m + Z^m));
-  Rkf: Y => Z; intravesicular*Kf*Y;
-  Rkz: Z => $EC; cytosol*K*Z;
-  R4:  => A; cytosol*beta*V4;
-  R5: A => ; cytosol*Vm5*A^p*Z^n/((K5^p + A^p)*(Kd^n + Z^n));
-  R6: A => ; cytosol*epsilon*A;
-  R7:  => GP; cytosol*(Vpm1*(1 + gamma_*Z^4/(Ka5^4 + Z^4))*(1 - GP)/(K1/(1 + Z^4/Ka6^4) + 1 - GP));
-  R8: GP => ; cytosol*(Vpm2*(1 + alpha*G/(Ka1 + G))*GP/(Kp2/(1 + G/Ka2) + GP));
-
-  // Species initializations:
-  EC = 1000;
-  Z = 0;
-  A = 0.45;
-  Y = 0.36;
-  GP = 1;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular = 1;
-
-  // Variable initializations:
-  v0 = 2;
-  v0 has uM_per_min;
-  v1 = 2;
-  v1 has uM_per_min;
-  beta = 0.5;
-  beta has dimensionless;
-  Vm2 = 6;
-  Vm2 has uM_per_min;
-  K2 = 0.1;
-  K2 has uM;
-  Vm3 = 20;
-  Vm3 has uM_per_min;
-  m = 2;
-  m has dimensionless;
-  Ka = 0.2;
-  Ka has uM;
-  Ky = 0.2;
-  Ky has uM;
-  Kz = 0.5;
-  Kz has uM;
-  Kf = 1;
-  Kf has min_inv;
-  K = 10;
-  K has min_inv;
-  V4 = 2;
-  V4 has uM_per_min;
-  Vm5 = 30;
-  Vm5 has uM_per_min;
-  n = 4;
-  n has dimensionless;
-  K5 = 1;
-  K5 has uM;
-  Kd = 0.4;
-  Kd has uM;
-  epsilon = 0.1;
-  epsilon has min_inv;
-  Vpm1 = 1.5;
-  Vpm1 has min_inv;
-  gamma_ = 9;
-  gamma_ has dimensionless;
-  Ka5 = 0.5;
-  Ka5 has uM;
-  K1 = 0.1;
-  Ka6 = 0.5;
-  Ka6 has uM;
-  Vpm2 = 0.6;
-  Vpm2 has min_inv;
-  alpha = 9;
-  alpha has dimensionless;
-  G = 10000;
-  G has uM;
-  Ka1 = 10000;
-  Ka1 has uM;
-  Kp2 = 0.2;
-  Ka2 = 10000;
-  Ka2 has uM;
-  p = 2;
-  p has dimensionless;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular, v0, v1, beta, Vm2, K2, Vm3;
-  const m, Ka, Ky, Kz, Kf, K, V4, Vm5, n, K5, Kd, epsilon, Vpm1, gamma_, Ka5;
-  const K1, Ka6, Vpm2, alpha, G, Ka1, Kp2, Ka2, p;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit uM = 1e-6 mole / litre;
-  unit uM_per_min = 1e-6 mole / (litre * 3600 second);
-  unit time_unit = 3600 second;
-  unit min_inv = 1 / 3600 second;
-
-  // Display Names:
-  substance is "micromole";
-  time_unit is "minutes";
-  EC is "Extracellular Calcium";
-  Z is "Cytosolic Calcium";
-  A is "IP3";
-  Y is "Intravesicular Calcium";
-  GP is "Glycogen Phosphorylase";
-  vin is "Calcium Influx";
-  R2 is "Calcium transport to internal store";
-  R3 is "Calcium transport to cytosol";
-  Rkf is "Calcium leak";
-  Rkz is "Calcium efflux";
-  R4 is "Agonist stimulated production of IP3";
-  R5 is "Ca-dependant IP3 degradation";
-  R6 is "Ca independent IP3 degradation";
-  R7 is "Phosphorylase kinase activity";
-  R8 is "Phosphatase activity";
-
-  // CV terms:
-  extracellular identity "http://identifiers.org/go/GO:0005615"
-  cytosol identity "http://identifiers.org/go/GO:0005829"
-  intravesicular hypernym "http://identifiers.org/go/GO:0005783"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  A identity "http://identifiers.org/chebi/CHEBI:16595",
-             "http://identifiers.org/kegg.compound/C01245"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  GP hypernym "http://identifiers.org/uniprot/P11216"
-  vin hypernym "http://identifiers.org/go/GO:0007204",
-               "http://identifiers.org/go/GO:0006816"
-  R2 hypernym "http://identifiers.org/go/GO:0032470",
-              "http://identifiers.org/go/GO:0051481"
-  R3 hypernym "http://identifiers.org/go/GO:0007204"
-  Rkf hypernym "http://identifiers.org/go/GO:0007204"
-  Rkz hypernym "http://identifiers.org/go/GO:0051481"
-  R4 hypernym "http://identifiers.org/go/GO:0032959"
-  R5 hypernym "http://identifiers.org/go/GO:0032961"
-  R6 hypernym "http://identifiers.org/go/GO:0032961"
-  R7 identity "http://identifiers.org/ec-code/2.7.11.19",
-              "http://identifiers.org/go/GO:0004689"
-  R8 identity "http://identifiers.org/ec-code/3.1.3.17",
-              "http://identifiers.org/go/GO:0050196"
-end
-
-Rozi2003_Glycogen_Phosphorylase_Activation is "Rozi2003_GlycogenPhosphorylase_Activation"
-
-Rozi2003_Glycogen_Phosphorylase_Activation model_entity_is "http://identifiers.org/biomodels.db/MODEL4589754842"
-Rozi2003_Glycogen_Phosphorylase_Activation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000100"
-Rozi2003_Glycogen_Phosphorylase_Activation description "http://identifiers.org/pubmed/14556891"
-Rozi2003_Glycogen_Phosphorylase_Activation origin "http://identifiers.org/pubmed/11093832",
-                                                  "http://identifiers.org/pubmed/17883229"
-Rozi2003_Glycogen_Phosphorylase_Activation taxon "http://identifiers.org/taxonomy/131567"
-Rozi2003_Glycogen_Phosphorylase_Activation part "http://identifiers.org/go/GO:0008607"
-Rozi2003_Glycogen_Phosphorylase_Activation part "http://identifiers.org/kegg.pathway/hsa04020"
-Rozi2003_Glycogen_Phosphorylase_Activation hypernym "http://identifiers.org/go/GO:0019722",
-                                                    "http://identifiers.org/go/GO:0048016"