| Feature |
Description |
| Name |
BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1 |
| Default Pipeline |
transformer, ner |
| Components |
transformer, ner |
| Vectors |
0 keys, 0 unique vectors (0 dimensions) |
| Sources |
n/a |
| License |
n/a |
| Author |
Melanie Vollmar |
Label Scheme
View label scheme (20 labels for 1 components)
| Component |
Labels |
ner |
"bond_interaction", "chemical", "complex_assembly", "evidence", "experimental_method", "gene", "mutant", "oligomeric_state", "protein", "protein_state", "protein_type", "ptm", "residue_name", "residue_name_number", "residue_number", "residue_range", "site", "species", "structure_element", "taxonomy_domain" |
Scores for entity types
| entity type |
precision |
recall |
F1 |
sample number |
| "bond_interaction" |
0.93 |
0.88 |
0.90 |
43 |
| "chemical" |
0.89 |
0.91 |
0.90 |
761 |
| "complex_assembly" |
0.91 |
0.93 |
0.92 |
288 |
| "evidence" |
0.84 |
0.88 |
0.86 |
390 |
| "experimental_method" |
0.85 |
0.85 |
0.85 |
357 |
| "gene" |
0.79 |
0.86 |
0.82 |
43 |
| "mutant" |
0.91 |
0.97 |
0.94 |
463 |
| "oligomeric_state" |
0.93 |
0.99 |
0.96 |
142 |
| "protein" |
0.94 |
0.97 |
0.95 |
1411 |
| "protein_state" |
0.83 |
0.88 |
0.85 |
546 |
| "protein_type" |
0.85 |
0.85 |
0.85 |
414 |
| "ptm" |
0.70 |
0.70 |
0.70 |
50 |
| "residue_name" |
0.92 |
0.97 |
0.94 |
90 |
| "residue_name_number" |
0.95 |
0.96 |
0.96 |
561 |
| "residue_number" |
0.80 |
0.97 |
0.88 |
33 |
| "residue_range" |
0.81 |
0.70 |
0.75 |
43 |
| "site" |
0.85 |
0.87 |
0.86 |
270 |
| "species" |
0.94 |
0.96 |
0.95 |
84 |
| "structure_element" |
0.91 |
0.92 |
0.92 |
992 |
| "taxonomy_domain" |
0.99 |
0.98 |
0.98 |
88 |
Data and annotations
The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v2.1
