readme: ---
  language:
  - en
  pipeline_tag: token-classification
  ---
  
  Named Entity Recognition (NER) model to recognize gene and protein entities. 
  
  [PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:
  
  - [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html): entity type "Genes/Proteins"
  - [CellFinder](https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/resources/cellfinder/): entity type "GeneProtein"
  - [CoMAGC](http://biopathway.org/CoMAGC/): entity "Gene"
  - [CRAFT](https://github.com/UCDenver-ccp/CRAFT/tree/master/concept-annotation): entity type "PR"
  - [GREC Corpus](http://www.nactem.ac.uk/GREC/standoff.php): entity types "Gene", "Protein", "Protein_Complex", "Enzyme" 
  - [JNLPBA](http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004): entity types "protein", "DNA", "RNA"
  - [PGxCorpus](https://www.nature.com/articles/s41597-019-0342-9): entity type "Gene_or_protein"
  - [FSU_PRGE](https://julielab.de/Resources/FSU_PRGE.html): entity types "protein", "protein_complex", "protein_familiy_or_group"
  - [BC2GM corpus](https://github.com/spyysalo/bc2gm-corpus)- [](): entity type
  - [CHEMPROT](https://biocreative.bioinformatics.udel.edu/resources/corpora/chemprot-corpus-biocreative-vi/): entity types "GENE-Y", "GENE-N"
  - [mTOR pathway event corpus](https://github.com/openbiocorpora/mtor-pathway/tree/master/original-data): entity type "Protein"
  - [DNA Methylation](https://github.com/openbiocorpora/dna-methylation/tree/master/original-data)
  - [BioNLP11ID](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11ID-ggp-IOB): entity type "Gene/protein"
  - [BioNLP09](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP09-IOB)
  - [BioNLP11EPI](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11EPI-IOB)
  - [BioNLP13CG](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13CG-ggp-IOB): entity type "gene_or_gene_product"
  - [BioNLP13GE](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13GE-IOB): entity type "Protein"
  - [BioNLP13PC](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13PC-ggp-IOB): entity type "Gene_or_gene_product"
  - [MLEE](http://nactem.ac.uk/MLEE/): entity type "Gene_or_gene_product"