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README.md ADDED
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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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+
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+ ## biosyn-sapbert-regel-bto
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+
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+ Biomedical Entity Mention Linking for DISEASE with MONDO Disease Ontology
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+
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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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+
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+ ### Demo: How to use in Flair
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+
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+ Requires:
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+
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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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+
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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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+
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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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+
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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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+
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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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