| Feature |
Description |
| Name |
BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1_onnx |
| 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" |
0.94 |
0.92 |
0.93 |
41 |
| "chemical" |
0.86 |
0.92 |
0.89 |
589 |
| "complex_assembly" |
0.85 |
0.89 |
0.87 |
185 |
| "evidence" |
0.83 |
0.89 |
0.86 |
392 |
| "experimental_method" |
0.86 |
0.85 |
0.86 |
310 |
| "gene" |
0.73 |
0.86 |
0.79 |
26 |
| "mutant" |
0.88 |
0.94 |
0.91 |
216 |
| "oligomeric_state" |
0.92 |
0.96 |
0.94 |
116 |
| "protein" |
0.91 |
0.95 |
0.93 |
755 |
| "protein_state" |
0.78 |
0.88 |
0.82 |
577 |
| "protein_type" |
0.87 |
0.85 |
0.86 |
265 |
| "ptm" |
0.67 |
0.69 |
0.68 |
33 |
| "residue_name" |
0.88 |
0.95 |
0.91 |
76 |
| "residue_name_number" |
0.94 |
0.96 |
0.95 |
262 |
| "residue_number" |
0.62 |
0.88 |
0.73 |
45 |
| "residue_range" |
0.87 |
0.79 |
0.83 |
31 |
| "site" |
0.88 |
0.90 |
0.89 |
245 |
| "species" |
0.95 |
0.97 |
0.96 |
76 |
| "structure_element" |
0.90 |
0.93 |
0.92 |
751 |
| "taxonomy_domain" |
0.99 |
0.99 |
0.99 |
83 |
Citation
Vollmar, M., Tirunagari, S., Harrus, D. et al.
Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature.
Sci Data 11, 1032
2024
https://doi.org/10.1038/s41597-024-03841-9
