| Feature |
Description |
| Name |
BiomedNLP-PubMedBERT-ProteinStructure-NER-3.1 |
| 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" |
0.82 |
0.91 |
0.86 |
66 |
| "chemical" |
0.92 |
0.91 |
0.92 |
1046 |
| "complex_assembly" |
0.89 |
0.90 |
0.90 |
320 |
| "evidence" |
0.89 |
0.88 |
0.89 |
513 |
| "experimental_method" |
0.80 |
0.82 |
0.81 |
451 |
| "gene" |
0.79 |
0.65 |
0.71 |
63 |
| "mutant" |
0.92 |
0.94 |
0.93 |
548 |
| "oligomeric_state" |
0.96 |
1.00 |
0.98 |
149 |
| "protein" |
0.96 |
0.96 |
0.96 |
1769 |
| "protein_state" |
0.86 |
0.88 |
0.87 |
727 |
| "protein_type" |
0.85 |
0.88 |
0.87 |
585 |
| "ptm" |
0.85 |
0.79 |
0.82 |
77 |
| "residue_name" |
0.74 |
0.96 |
0.84 |
108 |
| "residue_name_number" |
0.96 |
0.98 |
0.97 |
689 |
| "residue_number" |
0.70 |
0.73 |
0.71 |
22 |
| "residue_range" |
0.89 |
0.86 |
0.87 |
93 |
| "site" |
0.88 |
0.90 |
0.89 |
336 |
| "species" |
0.95 |
0.95 |
0.95 |
152 |
| "structure_element" |
0.91 |
0.92 |
0.91 |
1278 |
| "taxonomy_domain" |
0.98 |
0.98 |
0.98 |
117 |
Data and annotations
The dataset can be found here: https://huggingface.co/datasets/mevol/protein_structure_NER_model_v3.1
