
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"
{"language": ["en"], "pipeline_tag": "token-classification"}
transformers pytorch bert token-classification en autotrain_compatible endpoints_compatible has_space region:us
TAGS
#transformers #pytorch #bert #token-classification #en #autotrain_compatible #endpoints_compatible #has_space #region-us 


Named Entity Recognition (NER) model to recognize gene and protein entities. 

PubMedBERT fine-tuned on the following datasets:

- miRNA-Test-Corpus: entity type "Genes/Proteins"
- CellFinder: entity type "GeneProtein"
- CoMAGC: entity "Gene"
- CRAFT: entity type "PR"
- GREC Corpus: entity types "Gene", "Protein", "Protein_Complex", "Enzyme" 
- JNLPBA: entity types "protein", "DNA", "RNA"
- PGxCorpus: entity type "Gene_or_protein"
- FSU_PRGE: entity types "protein", "protein_complex", "protein_familiy_or_group"
- BC2GM corpus- [](): entity type
- CHEMPROT: entity types "GENE-Y", "GENE-N"
- mTOR pathway event corpus: entity type "Protein"
- DNA Methylation
- BioNLP11ID: entity type "Gene/protein"
- BioNLP09
- BioNLP11EPI
- BioNLP13CG: entity type "gene_or_gene_product"
- BioNLP13GE: entity type "Protein"
- BioNLP13PC: entity type "Gene_or_gene_product"
- MLEE: entity type "Gene_or_gene_product"
TAGS
#transformers #pytorch #bert #token-classification #en #autotrain_compatible #endpoints_compatible #has_space #region-us 

TAGS
#transformers #pytorch #bert #token-classification #en #autotrain_compatible #endpoints_compatible #has_space #region-us 
