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README.md
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---
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license: mit
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---
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---
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license: mit
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language:
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- en
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tags:
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- biology
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- protein structure
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- token classification
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model-index:
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- name: BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.2
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results:
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- task:
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name: NER
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type: token-classification
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metrics:
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- name: NER Precision
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type: precision
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value: 0.87
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- name: NER Recall
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type: recall
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value: 0.89
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- name: NER F Score
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type: f_score
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value: 0.88
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---
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| Feature | Description |
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| --- | --- |
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| **Name** | `BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.2` |
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| **Default Pipeline** | `transformer`, `ner` |
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| **Components** | `transformer`, `ner` |
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| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
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| **Sources** | n/a |
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| **License** | n/a |
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| **Author** | [Melanie Vollmar]() |
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### Label Scheme
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<details>
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<summary>View label scheme (19 labels for 1 components)</summary>
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| Component | Labels |
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| --- | --- |
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| **`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" |
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</details>
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### Scores for entity types
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| entity type | precision | recall | F1 | sample number|
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| --- | --- | --- | --- | --- |
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| "chemical" | 0.84 | 0.90 | 0.87 | 194 |
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| "complex_assembly" | 0.85 | 0.76 | 0.80 | 51 |
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| "evidence" | 0.74 | 0.76 | 0.75 | 106 |
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| "experimental_method" | 0.77 | 0.75 | 0.76 | 116 |
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| "gene" | 0.86 | 0.92 | 0.89 | 74 |
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| "mutant" | 0.83 | 0.92 | 0.88 | 258 |
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| "oligomeric_state" | 0.94 | 1.00 | 0.97 | 15 |
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| "protein" | 0.91 | 0.93 | 0.92 | 463 |
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| "protein_state" | 0.80 | 0.83 | 0.81 | 191 |
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| "protein_type" | 0.85 | 0.84 | 0.84 | 166 |
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| "ptm" | 0.88 | 0.76 | 0.81 | 29 |
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| "residue_name" | 0.86 | 0.95 | 0.91 | 22 |
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| "residue_name_number" | 0.99 | 0.99 | 0.99 | 341 |
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| "residue_number" | 1.00 | 1.00 | 1.00 | 13 |
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| "residue_range" | 1.00 | 0.80 | 0.89 | 10 |
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| "site" | 0.83 | 0.82 | 0.82 | 99 |
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| "species" | 0.96 | 0.98 | 0.97 | 44 |
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| "structure_element" | 0.88 | 0.86 | 0.87 | 319 |
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| "taxonomy_domain" | 0.95 | 0.97 | 0.96 | 79 |
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### Data and annotations
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The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v1.2
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