
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"

{"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 organism entities. 

PubMedBERT fine-tuned on the following datasets:
- CellFinder: entity type "species"
- CRAFT: entity type "NCBITaxon"
- MLEE:entity type "organism"
- LINNAEUS (train and dev sets):
- Species-800
- BioNLP11ID: entity type "Organism"
- BioNLP13CG: entity types "Organism", "Organism subdivision"
- miRNA-Test-Corpus: entity type "species"
- Mantra:entity type "DISO"

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 
