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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}")
```
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