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BioNLP is an initiative by the University of Colorado Denver Health Sciences Center to create and distribute code, software, and data for applying natural language processing techniques to biomedical texts
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID.
March 2017: We started to upload GNAT output on Medline.
The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.
...Double Layered Learning for Biological Event Extraction from Text. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistic