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+

README.md

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

pytorch_model.bin

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