biosyn-sapbert-regel-mondo

biosyn-sapbert-regel-bto

Biomedical Entity Mention Linking for DISEASE with MONDO Disease Ontology

• Model: dmis-lab/biosyn-sapbert-bc5cdr-disease
• Dictionary: Brenda Tissue Ontology

Demo: How to use in Flair

Requires:

• Flair>=0.14.0 (pip install flair or pip install git+https://github.com/flairNLP/flair.git)

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}")