PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.2

Feature	Description
Name	BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.2
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 (19 labels for 1 components)

Component	Labels
ner	"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
"chemical"	0.84	0.90	0.87	194
"complex_assembly"	0.85	0.76	0.80	51
"evidence"	0.74	0.76	0.75	106
"experimental_method"	0.77	0.75	0.76	116
"gene"	0.86	0.92	0.89	74
"mutant"	0.83	0.92	0.88	258
"oligomeric_state"	0.94	1.00	0.97	15
"protein"	0.91	0.93	0.92	463
"protein_state"	0.80	0.83	0.81	191
"protein_type"	0.85	0.84	0.84	166
"ptm"	0.88	0.76	0.81	29
"residue_name"	0.86	0.95	0.91	22
"residue_name_number"	0.99	0.99	0.99	341
"residue_number"	1.00	1.00	1.00	13
"residue_range"	1.00	0.80	0.89	10
"site"	0.83	0.82	0.82	99
"species"	0.96	0.98	0.97	44
"structure_element"	0.88	0.86	0.87	319
"taxonomy_domain"	0.95	0.97	0.96	79

Data and annotations

The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v1.2