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Number of citations per year for the bioinformatics software tool BioRat

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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


No version available


  • person_outline David P. A. Corney

Publication for BioRat

BioRat citations


Construction of phosphorylation interaction networks by text mining of full length articles using the eFIP system

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

[…] detection 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 ou […]


Nanoinformatics: Emerging Databases and Available Tools

Int J Mol Sci
PMCID: 4057665
PMID: 24776761
DOI: 10.3390/ijms15057158

[…] stage, some recent studies have been published [–]. The few available text-mining tools are as follows: (1) the Google Scholar search engine []; (2) the GoPubMed engine []; (3) Textpresso []; and (4) BioRAT []. When literature is available for analysis, it is possible to predict interactions via text mining, for example, using iHOP [], which is an online service through which the names of genes an […]


Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges

Adv Bioinformatics
PMCID: 3388278
PMID: 22778730
DOI: 10.1155/2012/573846

[…] es to relate medical concepts. The authors include also domain-specific knowledge, as they use information in the form of chromosome location and gene expression localization.Corney et al. [] propose BioRAT ( (Biological Research Assistant for Text mining), an information extraction tool specifically tailored for biomedical tasks. Able to acces […]


BioEve Search: A Novel Framework to Facilitate Interactive Literature Search

Adv Bioinformatics
PMCID: 3368157
PMID: 22693501
DOI: 10.1155/2012/509126

[…] (NLP) engine for information extraction. Recently, it has been extended as GeneWays [], which also provides a Web interface that allows users to search and submit papers of interest for analysis. The BioRAT system [] uses manually engineered templates that combine lexical and semantic information to identify protein interactions. The GeneScene system [] extracts interactions using frequent preposi […]


Semantic text mining support for lignocellulose research

BMC Med Inform Decis Mak
PMCID: 3339392
PMID: 22595090
DOI: 10.1186/1472-6947-12-S1-S5

[…] gement of the abstracts returned from a PubMed query. iHOP [] converts the information in PubMed into one navigable resource by using genes and proteins as hyperlinks between sentences and abstracts. BioRAT [] extracts biological information from full-length papers. Bio-Jigsaw [] is a visual analytics system highlighting connections between biological entities or concepts grounded in the biomedica […]


MimoSA: a system for minimotif annotation

BMC Bioinformatics
PMCID: 2905367
PMID: 20565705
DOI: 10.1186/1471-2105-11-328

[…] scientific literature, no tool existed that met the requirements we required for accurately annotating minimotif data. For example, each of the existing annotation tools such as MIMAS, Textpresso and Biorat only addresses a subset of the above requirements [-].In this paper, we describe MimoSA, a Minimotif System for Annotation designed for managing and facilitating minimotif annotation. MimoSA al […]

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

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