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bgc-accession
Maaly/bgc-accession
bgc-accession is a token classification model from Maaly. Use it when you need labels on individual words, such as names. It is set up for transformers.
bgc-accession model is a Named Entity Recognition (NER) model that identifies and annotates the accession number of biosynthetic gene clusters in texts.
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At a glance
- Task
- Token Classification
- Library
- transformers
- Model type
- bert
- Access
- Public
- Created
- Mar 2, 2022
- Updated
- May 28, 2022
- SHA
- 971d9914
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Model card
From the Hugging Face model README
bgc-accession model is a Named Entity Recognition (NER) model that identifies and annotates the accession number of biosynthetic gene clusters in texts.
The model is a fine-tuned BioBERT model and the training dataset is available in https://gitlab.com/maaly7/emerald_bgcs_annotations
Testing examples:
- The genome sequences of Leptolyngbya sp. PCC 7375 (ALVN00000000) and G. sunshinyii YC6258 (NZ_CP007142.1) were obtained previously.36,59
- K311 was sequenced (NCBI accession number: JN852959) and analyzed with FramePlot and 18 genes were predicted to be involved in echinomycin biosynthesis (Figure 2).
- The mar cluster was sequenced and annotated and the complete sequence was deposited into Genbank (accession KF711829).
- Task
- Token Classification
- Library
- transformers
- Type
- bert
- Created
- Mar 2, 2022
- Updated
- May 28, 2022