readme: ---
  language:
  - en
  pipeline_tag: token-classification
  ---
  
  Named Entity Recognition (NER) model to recognize organism entities. 
  
  [PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:
  - [CellFinder](http://cellfinder.org/about/annotation/): entity type "species"
  - [CRAFT](https://github.com/UCDenver-ccp/CRAFT/tree/master/concept-annotation): entity type "NCBITaxon"
  - [MLEE](http://nactem.ac.uk/MLEE/):entity type "organism"
  - [LINNAEUS](http://linnaeus.sourceforge.net/) (train and dev sets):
  - [Species-800](https://species.jensenlab.org/)
  - [BioNLP11ID](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11ID-species-IOB): entity type "Organism"
  - [BioNLP13CG](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13CG-species-IOB): entity types "Organism", "Organism subdivision"
  - [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html): entity type "species"
  - [Mantra](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986661/pdf/ocv037.pdf):entity type "DISO"
  