README.md

metadata

tags:
  - flair
  - hunflair
  - token-classification
  - sequence-tagger-model
language: en
widget:
  - text: It contains a functional GCGGCGGCG Egr-1-binding site

HunFlair2 model for TFBS

HunFlair (biomedical flair) for enhancer entity:

• pre-trained language model: michiyasunaga/BioLinkBERT-base
• fine-tuned on RegEl corpus for Tfbs entity type

Predicts 1 tag:

tag	meaning
Tfbs	DNA region bound by transcription factor

---

Info

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.nn import Classifier
from flair.tokenization import SciSpacyTokenizer

text = "We found that Egr-1 specifically binds to the PTEN 5' untranslated region, which contains a functional GCGGCGGCG Egr-1-binding site."
sentence = Sentence(text, use_tokenizer=SciSpacyTokenizer())

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

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