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BioRat specifications


Unique identifier OMICS_01175
Name BioRat
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


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  • person_outline David P. A. Corney <>

Publication for BioRat

BioRat in publications

PMCID: 5838116
PMID: 29527072
DOI: 10.1007/s11192-018-2661-6

[…] example, medical entity recognition (cf. abacha et al. ) seeks to extract instances from classes such as “disease”, “symptom” or “drug” to enrich the retrieval process. research assistants such as biorat (cf. corney et al. ) or facta (cf. tsuruoka et al. ) then can offer an added value employing this type of semantic information. liakata et al. () departed from a mere content-level enrichment […]

PMCID: 5133940
PMID: 27879651
DOI: 10.3390/ijms17111946

[…] (ypd) [], database of interacting proteins (dip) [], biogrid and hprd. in addition, there are some tm-based methods/tools that provide multiple-perspective evidence for ppi extraction, such as biorat (biological research assistant for text mining) [], efip (extracting functional impact of phosphorylation) [], facta (finding associated concepts with text analysis) [] and hit predict []., […]

PMCID: 5047355
PMID: 27548315
DOI: 10.1038/ng.3644

[…] pasteur, france. although by the 1960s, salmonella-based rodenticides had been banned in the us, germany and the uk, s. enteritidis is still produced as a rodenticide in cuba, under the name biorat®., serovars of salmonella that cause enterocolitis in industrialised settings are strongly associated with life-threatening invasive nontyphoidal salmonella (ints) disease in sub-saharan […]

PMCID: 4381107
PMID: 25833953
DOI: 10.1093/database/bav020

[…] of ppi events, we acknowledge the systems described by papanikolaou et al. (), as well as the akanere system () and suiseki (). four of these systems are currently available as stand-alone [biorat (), opendmap (), ppiextractor () and pplook ()], with two of them available when we started creating the efip system. however, we could not easily integrate them into our pipeline to address […]

PMCID: 4176459
PMID: 25309356
DOI: 10.3389/fnsys.2014.00182

[…] visualtext (meyers, ; alfred et al., )., biomedical tm rule-based approaches using fully automated stages in text processing: anote2 (lourenco et al., ) and biological research assistant for tm (biorat) (corney et al., )., gray scale qualitatively codes their weights in tm (the darker, the higher the importance). each subgroup (1–4) includes kernels of tm-tools (circled red) and “targeted […]

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BioRat institution(s)
Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, UK

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