Modelpublic

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

sourceHugging Facemitupdated 2y agoView on Hugging Face

4likes28downloads

Model Card

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

<summary>View label scheme (19 labels for 1 components)</summary>

Component	Labels
`ner`	"chemical", "complexassembly", "evidence", "experimentalmethod", "gene", "mutant", "oligomericstate", "protein", "proteinstate", "proteintype", "ptm", "residuename", "residuenamenumber", "residuenumber", "residuerange", "site", "species", "structureelement", "taxonomydomain"

</details>

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
"residuenamenumber"	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/proteinstructureNERmodelv1.2

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