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Feature Description
Name BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1
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" 0.93 0.88 0.90 43
"chemical" 0.89 0.91 0.90 761
"complex_assembly" 0.91 0.93 0.92 288
"evidence" 0.84 0.88 0.86 390
"experimental_method" 0.85 0.85 0.85 357
"gene" 0.79 0.86 0.82 43
"mutant" 0.91 0.97 0.94 463
"oligomeric_state" 0.93 0.99 0.96 142
"protein" 0.94 0.97 0.95 1411
"protein_state" 0.83 0.88 0.85 546
"protein_type" 0.85 0.85 0.85 414
"ptm" 0.70 0.70 0.70 50
"residue_name" 0.92 0.97 0.94 90
"residue_name_number" 0.95 0.96 0.96 561
"residue_number" 0.80 0.97 0.88 33
"residue_range" 0.81 0.70 0.75 43
"site" 0.85 0.87 0.86 270
"species" 0.94 0.96 0.95 84
"structure_element" 0.91 0.92 0.92 992
"taxonomy_domain" 0.99 0.98 0.98 88

Data and annotations

The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v2.1

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Evaluation results