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/PDBEurope/protein_structure_NER_model_v3.1

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

PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1

Label Scheme

Scores for entity types

Data and annotations

Citation

PDBEurope/
BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1