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Project Summary

GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web service (suitable for more limited processing or testing). A combination of local and remote processing is also available, where CPU-heavy operations are performed locally and memory-intensive operations are performed remotely (this is suitable for large-scale processing where a large amount of memory is not available). GNAT uses LINNAEUS (Gerner et al., 2010) for species detection and BANNER (Leaman et al., 2008) in one part of its false positive filtering process.

Tags

academic article articles bioinformatics classification contextualprofiles database entrez eutils gazeteers gazetteer gene genes java library mesh namedentityrecognition ncbi ner nlp normalization protein proteins publication pubmed species webservice webservices web_services

In a Nutshell, GNAT NER...

 No recognizable code

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 No recognizable code

Open Hub computes statistics on FOSS projects by examining source code and commit history in source code management systems. This project has code locations but that location contains no recognizable source code for Open Hub to analyze.

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