---
language:
- en
pipeline_tag: token-classification
license: apache-2.0
---

Named Entity Recognition (NER) model to recognize variant entities. Here variant entity is a DNA-level or protein-level mutation as defined by the [Human Genome Variation Society nomenclature](http://varnomen.hgvs.org/). 

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:
- [tmVar](https://www.ncbi.nlm.nih.gov/research/bionlp/Data/): entity types "DNAMutation", "ProteinMutation", "SNP"
- [PGxCorpus](https://www.nature.com/articles/s41597-019-0342-9): entity type "Limited_variation"
- [SNPPhenA](https://figshare.com/s/f19191317056d6835b38): entity type "SNP"