transformers pytorch bert token-classification en license:apache-2.0 autotrain_compatible endpoints_compatible region:us
---
language:
- en
license: apache-2.0
pipeline_tag: token-classification
---

Named Entity Recognition (NER) model to recognize gene and protein entities. 

Please cite our work:

```
@article{NILNKER2022,
  title = {NILINKER: Attention-based approach to NIL Entity Linking},
  journal = {Journal of Biomedical Informatics},
  volume = {132},
  pages = {104137},
  year = {2022},
  issn = {1532-0464},
  doi = {https://doi.org/10.1016/j.jbi.2022.104137},
  url = {https://www.sciencedirect.com/science/article/pii/S1532046422001526},
  author = {Pedro Ruas and Francisco M. Couto},
}
```

[PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:

- [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html): entity type "Genes/Proteins"
- [CellFinder](https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/resources/cellfinder/): entity type "GeneProtein"
- [CoMAGC](http://biopathway.org/CoMAGC/): entity "Gene"
- [CRAFT](https://github.com/UCDenver-ccp/CRAFT/tree/master/concept-annotation): entity type "PR"
- [GREC Corpus](http://www.nactem.ac.uk/GREC/standoff.php): entity types "Gene", "Protein", "Protein_Complex", "Enzyme" 
- [JNLPBA](http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004): entity types "protein", "DNA", "RNA"
- [PGxCorpus](https://www.nature.com/articles/s41597-019-0342-9): entity type "Gene_or_protein"
- [FSU_PRGE](https://julielab.de/Resources/FSU_PRGE.html): entity types "protein", "protein_complex", "protein_familiy_or_group"
- [BC2GM corpus](https://github.com/spyysalo/bc2gm-corpus)- [](): entity type
- [CHEMPROT](https://biocreative.bioinformatics.udel.edu/resources/corpora/chemprot-corpus-biocreative-vi/): entity types "GENE-Y", "GENE-N"
- [mTOR pathway event corpus](https://github.com/openbiocorpora/mtor-pathway/tree/master/original-data): entity type "Protein"
- [DNA Methylation](https://github.com/openbiocorpora/dna-methylation/tree/master/original-data)
- [BioNLP11ID](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11ID-ggp-IOB): entity type "Gene/protein"
- [BioNLP09](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP09-IOB)
- [BioNLP11EPI](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11EPI-IOB)
- [BioNLP13CG](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13CG-ggp-IOB): entity type "gene_or_gene_product"
- [BioNLP13GE](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13GE-IOB): entity type "Protein"
- [BioNLP13PC](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13PC-ggp-IOB): entity type "Gene_or_gene_product"
- [MLEE](http://nactem.ac.uk/MLEE/): entity type "Gene_or_gene_product"