title: CoPub update: CoPub 5.0 a text mining system to answer biological questions.
abstract: In this article, we present CoPub 5.0, a publicly available text mining system, which uses Medline abstracts to calculate robust statistics for keyword co-occurrences. CoPub was initially developed for the analysis of microarray data, but we broadened the scope by implementing new technology and new thesauri. In CoPub 5.0, we integrated existing CoPub technology with new features, and provided a new advanced interface, which can be used to answer a variety of biological questions. CoPub 5.0 allows searching for keywords of interest and its relations to curated thesauri and provides highlighting and sorting mechanisms, using its statistics, to retrieve the most important abstracts in which the terms co-occur. It also provides a way to search for indirect relations between genes, drugs, pathways and diseases, following an ABC principle, in which A and C have no direct connection but are connected via shared B intermediates. With CoPub 5.0, it is possible to create, annotate and analyze networks using the layout and highlight options of Cytoscape web, allowing for literature based systems biology. Finally, operations of the CoPub 5.0 Web service enable to implement the CoPub technology in bioinformatics workflows. CoPub 5.0 can be accessed through the CoPub portal http://www.copub.org.
authors.affiliation: Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands. w.fleuren@cmbi.ru.nl
authors.forename: Wilco W M
authors.initials: WW
authors.lastname: Fleuren
authors.forename: Stefan
authors.initials: S
authors.lastname: Verhoeven
authors.forename: Raoul
authors.initials: R
authors.lastname: Frijters
authors.forename: Bart
authors.initials: B
authors.lastname: Heupers
authors.forename: Jan
authors.initials: J
authors.lastname: Polman
authors.forename: René
authors.initials: R
authors.lastname: van Schaik
authors.forename: Jacob
authors.initials: J
authors.lastname: de Vlieg
authors.forename: Wynand
authors.initials: W
authors.lastname: Alkema
mesh_terms: D057225:Data Mining / Q000379:methods*; D053263:Gene Regulatory Networks; D020407:Internet; D039781:PubMed; D012984:Software