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  language:
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  - en
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  pipeline_tag: token-classification
 
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  ---
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- Named Entity Recognition (NER) model to recognize organism entities.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  [PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:
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  - [CellFinder](http://cellfinder.org/about/annotation/): entity type "species"
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  - [BioNLP11ID](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11ID-species-IOB): entity type "Organism"
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  - [BioNLP13CG](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13CG-species-IOB): entity types "Organism", "Organism subdivision"
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  - [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html): entity type "species"
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- - [Mantra](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986661/pdf/ocv037.pdf):entity type "DISO"
 
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  language:
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  - en
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  pipeline_tag: token-classification
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+ license: apache-2.0
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  ---
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+ Named Entity Recognition (NER) model to recognize organism entities.
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+
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+ Please cite our work:
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+
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+ ```
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+ @article{NILNKER2022,
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+ title = {NILINKER: Attention-based approach to NIL Entity Linking},
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+ journal = {Journal of Biomedical Informatics},
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+ volume = {132},
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+ pages = {104137},
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+ year = {2022},
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+ issn = {1532-0464},
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+ doi = {https://doi.org/10.1016/j.jbi.2022.104137},
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+ url = {https://www.sciencedirect.com/science/article/pii/S1532046422001526},
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+ author = {Pedro Ruas and Francisco M. Couto},
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+ }
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+ ```
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  [PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets:
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  - [CellFinder](http://cellfinder.org/about/annotation/): entity type "species"
 
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  - [BioNLP11ID](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP11ID-species-IOB): entity type "Organism"
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  - [BioNLP13CG](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/BioNLP13CG-species-IOB): entity types "Organism", "Organism subdivision"
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  - [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html): entity type "species"
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+ - [Mantra](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986661/pdf/ocv037.pdf):entity type "DISO"