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BioNLP specifications


Unique identifier OMICS_14736
Name BioNLP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Python
License Mozilla Public License version 2.0
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes




No version available



  • person_outline Lawrence Hunter

Publication for BioNLP

BioNLP citations


Using rule based natural language processing to improve disease normalization in biomedical text

PMCID: 3756254
PMID: 23043124
DOI: 10.1136/amiajnl-2012-001173

[…] is generally considered a more difficult task than concept recognition. this is reflected in the variety of named-entity recognition challenges in the biomedical domain, for example, biocreative and bionlp (recognition of proteins and genes in scientific literature), and trec and i2b2 (drugs, diseases, and treatments in electronic patient records), whereas normalization challenges have been few. […]


The structural and content aspects of abstracts versus bodies of full text journal articles are different

BMC Bioinformatics
PMCID: 3098079
PMID: 20920264
DOI: 10.1186/1471-2105-11-492

[…] is present in article bodies but not in article abstracts., two exciting developments in recent years have the potential to change the face of biomedical natural language processing or text mining (bionlp). one of these is the attention that the community has begun to turn to using full-text journal articles as inputs--previously (and continuing into the present), the majority of bionlp work […]

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BioNLP institution(s)
Center for Computational Pharmacology, University of Colorado School of Medicine, Denver, CO, USA
BioNLP funding source(s)
This work was supported by NIH grants R01-LM008111 and R01-LM009254.

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