diff --git a/BioModelsRAG/2data/BIOMD0000000001.txt b/BioModelsRAG/2data/BIOMD0000000001.txt new file mode 100644 index 0000000000000000000000000000000000000000..a372fc16aae623ce4435e2d867fd11e3de0ceef6 --- /dev/null +++ b/BioModelsRAG/2data/BIOMD0000000001.txt @@ -0,0 +1,224 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..74ca525c2c72610f83ecffde4008ccd00b4f84f8 --- /dev/null +++ b/BioModelsRAG/__init__.py @@ -0,0 +1,19 @@ +__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 new file mode 100644 index 0000000000000000000000000000000000000000..510b1f11d02cbeeeb0361863633ef98990ab7b63 Binary files /dev/null and b/BioModelsRAG/__pycache__/__init__.cpython-311.pyc differ diff --git a/BioModelsRAG/data/BIOMD0000000001.txt b/BioModelsRAG/data/BIOMD0000000001.txt new file mode 100644 index 0000000000000000000000000000000000000000..a372fc16aae623ce4435e2d867fd11e3de0ceef6 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000001.txt @@ -0,0 +1,224 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..809ba11be2fab031cc9eb60920ae91b22b9399d3 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000002.txt @@ -0,0 +1,155 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..c2a1caa4dba162fb4c168d3db7350b320ad7adc2 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000003.txt @@ -0,0 +1,124 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..37c23d2a08c2593df3e83659070f3122ccf30277 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000004.txt @@ -0,0 +1,102 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..aa5f21eb247e58aa3e0949fb1264b07461f8c069 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000005.txt @@ -0,0 +1,114 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..830a1c7ecd9646eb55fea96c460b0806ec3b6b71 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000006.txt @@ -0,0 +1,66 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..d22e00febb2aff7e36fcca72f726f7a1309b7398 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000007.txt @@ -0,0 +1,266 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..b8f93c665b31f708fcccf06658aced8f106aaa23 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000008.txt @@ -0,0 +1,121 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..f4960d986770bba9a9967a579c6af419173e7a4b --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000009.txt @@ -0,0 +1,250 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..f0f5bc9197738de17664c6570d17e07feed098fd --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000010.txt @@ -0,0 +1,140 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..b11b2a260f9b44c2dce717b1ecffd22f2601b090 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000011.txt @@ -0,0 +1,272 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..985a9d8b9c8d0c7b5514d47422df2bc5b3f8e634 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000012.txt @@ -0,0 +1,161 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..aa0b5329c530fd283e752a287e406d949769143a --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000013.txt @@ -0,0 +1,264 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..271ba48bdd7b4ce3cf3b726f2bb4c7eed9ab4bf7 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000014.txt @@ -0,0 +1,1635 @@ +// 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 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"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 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"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 new file mode 100644 index 0000000000000000000000000000000000000000..94e954d0c1f4b7cf796ce124a010e1a73e42a462 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000015.txt @@ -0,0 +1,411 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..28c3c4881dcfb4cfe6b37684ef2ed8976b4b95d8 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000016.txt @@ -0,0 +1,119 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..ac421146043a333f3259eed0ad754b68398f0b8c --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000017.txt @@ -0,0 +1,218 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..89c91df43f414cb8bc50b1a205de067855020bb6 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000018.txt @@ -0,0 +1,341 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..f53a7be43ac759da86a50cffba44bf63bfeeea59 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000019.txt @@ -0,0 +1,652 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..37187972eb4970fc81a6d1e85ace4bc22a2abf0a --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000020.txt @@ -0,0 +1,101 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..0c51ff8c820da6e8e25ee7d2e5bee68b7367f264 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000021.txt @@ -0,0 +1,214 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..1668b0861844e56953eb512308ec2b3a655391c1 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000022.txt @@ -0,0 +1,257 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..6e6226959a5bbe96576779a23f7c303427301bc2 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000023.txt @@ -0,0 +1,175 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..49fe4559947c21a4f811e2f5ba4cb38c7a120c09 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000024.txt @@ -0,0 +1,67 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..c171b0b3c461b4771546ff6398e25bd084d6393b --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000025.txt @@ -0,0 +1,87 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..5bda92c6f7f4178f847255bebb767a0de7a25abb --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000026.txt @@ -0,0 +1,135 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..9612e64794de2e48342af42dd590704be8d4cfb4 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000027.txt @@ -0,0 +1,78 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..6582c32fcd822279d26f31f4407eaf9791884ab6 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000028.txt @@ -0,0 +1,208 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..552a07b398318971b864f2e56438462436f2b7a3 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000029.txt @@ -0,0 +1,112 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..8f46aee8dd8080bff5cc71c52c35429b2e914ab7 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000030.txt @@ -0,0 +1,233 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..e63907a1b2de689eb72a6b5b875c68c12bec99ad --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000031.txt @@ -0,0 +1,80 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..d996ed31fc558a75779bf895fd88b3957367f8f8 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000032.txt @@ -0,0 +1,423 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..dc54ef5491023c0f1e64497854ed9bfc37537cf9 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000033.txt @@ -0,0 +1,278 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..820d14a610278a1c8d740cff3a3c46ed791a1bf8 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000034.txt @@ -0,0 +1,259 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..edc7981451e91509fa042f155f32e04ecabee62a --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000035.txt @@ -0,0 +1,103 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..9236435635a85bc2c2da148838c1eb0cb790437c --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000036.txt @@ -0,0 +1,72 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..26a37d840ee424fc6173f9141add713a3888d195 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000037.txt @@ -0,0 +1,89 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..7d74487ccf6364e016ee1f950a3126fb6fb1850d --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000038.txt @@ -0,0 +1,158 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..490f122b72b13fc46fe79b8f8bd6792548b6f7fb --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000039.txt @@ -0,0 +1,95 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..6eb433a1e3e28d842399fb2265041b233e86c51b --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000040.txt @@ -0,0 +1,61 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..4460529e5a9c3b76a17fb5ade2c79958b9307a13 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000041.txt @@ -0,0 +1,127 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..a070201a42fcc3a9ef2840f6c972544ba8a96ff9 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000042.txt @@ -0,0 +1,189 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..487ce8eb29ea2838cf5687693547e4971df59e4c --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000043.txt @@ -0,0 +1,88 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..80162dbe39ebba50cbe5d6dc9562bd99e7603774 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000044.txt @@ -0,0 +1,129 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..db8d00c66254dd15cee0befebdc7cda34a353163 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000045.txt @@ -0,0 +1,97 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..616db6882572302b4aef724feae359dd2516aff0 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000046.txt @@ -0,0 +1,127 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..07cf65ea7c3f1c16a5eff6c7ae93b91b57af48ac --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000047.txt @@ -0,0 +1,80 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..9a087375fef45816260c504492e90b2a58073938 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000048.txt @@ -0,0 +1,277 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..04cfa50ae8f2d36fdbfb470421d713d0f6733363 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000049.txt @@ -0,0 +1,1102 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..00c41f48fb8ec458fc06445bb3fc1f488ac68fb4 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000050.txt @@ -0,0 +1,101 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..afeb2e15833d3a6887008b79e7611339edb0faad --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000051.txt @@ -0,0 +1,601 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..fc265ecb3be00727a2a62b84279ca26fd84c090c --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000052.txt @@ -0,0 +1,85 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..63be9c8ae31598c91716c5190425135231ee1f93 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000053.txt @@ -0,0 +1,96 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..0d3e7de6e618667eb31032bb15f37baf9ff1a8ba --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000054.txt @@ -0,0 +1,106 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..d18756abec1f33d03df7df9576c5d4f44ca958cf --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000055.txt @@ -0,0 +1,362 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..0999d83633432af1880ae12ceec56bfc1f9ea177 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000056.txt @@ -0,0 +1,817 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..646f6989c97221e9276ec84889ec5f5d575bd46b --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000057.txt @@ -0,0 +1,110 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..23df4745d84a8d51e5e63a42d055990d3c2088cc --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000058.txt @@ -0,0 +1,124 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..bef3829ca86287a54a73735caa3b3a597418479e --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000059.txt @@ -0,0 +1,348 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..bab99ae6c925c256bc68c8c9deb0a58d35908083 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000060.txt @@ -0,0 +1,87 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..8841eb4a4aeff0b8a0785fdeb3ec7814f970b348 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000061.txt @@ -0,0 +1,384 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..2d9b124a9e1e8e67f3f0394d266f30585835822f --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000062.txt @@ -0,0 +1,111 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..da82a5791cc403bb6b65d86bcf5f0f49ddc28e5b --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000063.txt @@ -0,0 +1,267 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..ac7e5c3e0afc5bf1749bf4ec5bb0d86c006c54fe --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000064.txt @@ -0,0 +1,434 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..5ad7aba7124712dce476693bc25dab288d85d2ae --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000065.txt @@ -0,0 +1,140 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..6d69a7df2a6b0652f302891f1c898542cab990a4 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000066.txt @@ -0,0 +1,217 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..36e49c7f7f3c68b7dacf067f610bb6e9861bf9e8 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000067.txt @@ -0,0 +1,131 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..dc450fed86b1bab6b61d25160232711440a42a26 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000068.txt @@ -0,0 +1,104 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..bde99e43d205b32509545c8b02c7a5ecf69e977b --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000069.txt @@ -0,0 +1,99 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..0a0c289cf10585b668f29ef12081f9d22737518a --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000070.txt @@ -0,0 +1,754 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..fbe16c62d7b5ecca2ec2d28d1f2130df73f6ca7e --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000071.txt @@ -0,0 +1,376 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..1bd28ae80ad6624b3b3bbad22aad6317a7da3786 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000072.txt @@ -0,0 +1,102 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..949d653f1bff3ee88f6518a6d51895026221ff7f --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000073.txt @@ -0,0 +1,364 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..23c41b7421dbae25dc28076ef262660ed06c3570 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000074.txt @@ -0,0 +1,411 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..2cac405edf083b801c56a30a6c519e3b316afdc8 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000075.txt @@ -0,0 +1,250 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..5cef2d80124aaaa19830781a37f7814b80356884 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000076.txt @@ -0,0 +1,97 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..496497d7d6c03be5e57b33bc55101e0b6bcc42f1 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000077.txt @@ -0,0 +1,96 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..750ad3b07bbfdbe215a921d9018314111998313f --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000078.txt @@ -0,0 +1,374 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..ca5b2d9e2e57dec1e1fa2cf02f6481e2f63a4ade --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000079.txt @@ -0,0 +1,91 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..13e775ef0953016700a1caaa339dca9055cf9da9 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000080.txt @@ -0,0 +1,123 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..fa07279649acb166698857fe720ea1814f5a4d5e --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000081.txt @@ -0,0 +1,373 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..78e3b5b7e521dc17e03724ae74b15c3c5d8866df --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000082.txt @@ -0,0 +1,126 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..ce683feb6771c2be70b1d21f5890b808808c792c --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000083.txt @@ -0,0 +1,356 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..5eeca632778c0ec3e0f86f2c0d4c56a1c6d69159 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000084.txt @@ -0,0 +1,103 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..8915847cbacf5399656038712d25259e673a6876 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000085.txt @@ -0,0 +1,216 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..e11aac710866afbeffc8770925e18ea203924137 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000086.txt @@ -0,0 +1,252 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..d11cf8e208c1a95c7848459f7f35f408c525b331 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000087.txt @@ -0,0 +1,328 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..17b6bdeaa7dae68b9b5c387225d84776ea798f46 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000088.txt @@ -0,0 +1,1373 @@ +// 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", + 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"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 new file mode 100644 index 0000000000000000000000000000000000000000..22b41ccd91a7f5eeabfd9a4e6cd25cc43178df6d --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000089.txt @@ -0,0 +1,424 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..c0ef63c2f114081cd89aacffb62642b5ea4b1148 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000090.txt @@ -0,0 +1,217 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..d3ed48f239d81265088ee70ce40e12133c1606de --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000091.txt @@ -0,0 +1,144 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..2cae152a944a654bad7df4fc8e8c90df0ad3e60f --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000092.txt @@ -0,0 +1,65 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..952286ae72ec0f141315d935572e10fecc90cbeb --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000093.txt @@ -0,0 +1,458 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..8bd3f41f1632803523ac3fe9ce19c38d6c16e003 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000094.txt @@ -0,0 +1,450 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..ff1de9c54d7deaf716744c41b6a1b4463e62c96a --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000095.txt @@ -0,0 +1,426 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..7f37680cb663dbac0c077ef8d38492df5a453dcf --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000096.txt @@ -0,0 +1,434 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..d3611e516a82791b2838d7d51597ef9d9e211a36 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000097.txt @@ -0,0 +1,431 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..126e6f793ffbba3e9beb8b9e15e8cc3c64db5066 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000098.txt @@ -0,0 +1,96 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..c83d2bcf46bcc033e6cedc9ff6a83ee37b3828f0 --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000099.txt @@ -0,0 +1,146 @@ +// 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 new file mode 100644 index 0000000000000000000000000000000000000000..2e0f804b98ae520aa50510362221fa7d24eaec0c --- /dev/null +++ b/BioModelsRAG/data/BIOMD0000000100.txt @@ -0,0 +1,164 @@ +// 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"