Info

HunFlair2 (biomedical flair) for enhancer entity
pre-trained language model: michiyasunaga/BioLinkBERT-base
fine-tuned on RegEl corpus for Enhancer entity type

Predicts 1 tag:

tag	meaning
Enhancer	DNA enhancer region

Demo: How to use in Flair

Requires:

Flair>=0.15.1 (pip install flair or pip install git+https://github.com/flairNLP/flair.git)

from flair.data import Sentence
from flair.nn import Classifier
from flair.tokenization import SciSpacyTokenizer

text = "An upstream activator of the mitogen-activated protein (MAP) kinase pathways was used to isolate an enhancer element located between -89 and -50 bp in PAI-1 promoter that was activated by MEKK-1."
sentence = Sentence(text, use_tokenizer=SciSpacyTokenizer())

tagger = Classifier.load("regel-corpus/hunflair2-regel2-enhancer")
tagger.predict(sentence)

print('The following NER tags are found:')
# iterate over entities and print
for entity in sentence.get_spans('ner'):
    print(entity)

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