| | --- |
| | 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" |
