readme: ---
  language:
  - en
  pipeline_tag: token-classification
  ---
  
  Named Entity Recognition (NER) model to recognize disease entities. 
  
  [PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:
  
  - [NCBI Disease Corpus](https://www.ncbi.nlm.nih.gov/research/bionlp/Data/disease/) (train and dev sets)
  - [PHAEDRA](http://www.nactem.ac.uk/PHAEDRA/) (train, dev, test sets): entity type "Disorder"
  - [Corpus for Disease Names and Adverse Effects](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/corpus-for-disease-names-and-adverse-effects.html) (train, dev, test sets): entity types "DISEASE", "ADVERSE"
  - [RareDis corpus](https://github.com/isegura/NLP4RARE-CM-UC3M/tree/main/corpus) (train, dev, test sets): entity types "DISEASE", "RAREDISEASE", "SYMPTOM"
  - [CoMAGC](https://github.com/isegura/NLP4RARE-CM-UC3M/tree/main/corpus) (train, dev, test sets): entity type "cancer_term"
  - [PGxCorpus](https://www.nature.com/articles/s41597-019-0342-9) (train, dev, test sets):
  - [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html) (train, dev, test sets): entity type "Diseases"
  - [BC5CDR]() (train and dev sets): entity type "Disease"
  - [Mantra](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986661/pdf/ocv037.pdf) (train, dev, test sets): entity type "DISO"