pruas/BENT-PubMedBERT-NER-Anatomical

Named Entity Recognition (NER) model to recognize anatomical 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 fine-tuned on the following datasets:

• MANTRA: entity type "ANAT"
• CellFinder: entity type "Anatomical parts"
• CRAFT: entity type "UBERON"
• MLEE: entity types "Anatomical_system", "Organ", "Multi-tissue structure", "Tissue", "Immaterial_anatomical_entity"
• AnatEM
• BioNLP13CG: entity types "Multi-tissue structure", "Tissue", "Organ", "Immaterial anatomical entity", "Anatomical system"
• GREC: entity type "Tissue"