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--- |
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tags: |
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- flair |
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- entity-mention-linker |
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--- |
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## biosyn-sapbert-regel-bto |
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Biomedical Entity Mention Linking for DISEASE with MONDO Disease Ontology |
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- Model: [dmis-lab/biosyn-sapbert-bc5cdr-disease](https://huggingface.co/dmis-lab/biosyn-sapbert-bc5cdr-disease) |
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- Dictionary: [Brenda Tissue Ontology](https://mondo.monarchinitiative.org/) |
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### Demo: How to use in Flair |
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Requires: |
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- **[Flair](https://github.com/flairNLP/flair/)>=0.14.0** (`pip install flair` or `pip install git+https://github.com/flairNLP/flair.git`) |
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```python |
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from flair.data import Sentence |
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from flair.models import Classifier, EntityMentionLinker |
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from flair.tokenization import SciSpacyTokenizer |
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sentence = Sentence( |
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"The mutation in the ABCD1 gene causes X-linked adrenoleukodystrophy, " |
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"a neurodegenerative disease, which is exacerbated by exposure to high " |
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"levels of mercury in dolphin populations.", |
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use_tokenizer=SciSpacyTokenizer() |
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) |
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# load hunflair to detect the entity mentions we want to link. |
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tagger = Classifier.load("hunflair2") |
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tagger.predict(sentence) |
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# load the linker and dictionary |
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linker = EntityMentionLinker.load("regel-corpus/biosyn-sapbert-regel-mondo") |
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linker.predict(sentence) |
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# print the results for each entity mention: |
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for span in sentence.get_spans(tagger.label_type): |
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for link in span.get_labels(linker.label_type): |
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print(f"{span.text} -> {link.value}") |
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``` |
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