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---
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" |