CoPub update: CoPub 5.0 a text mining system to answer biological questions

Wilco W M Fleuren, Stefan Verhoeven, Raoul Frijters, Bart Heupers, Jan Polman, René van Schaik, Jacob de Vlieg, Wynand Alkema

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
JournalNucleic acids research
Volume39
Issue numberWeb Server issue
DOIs
Publication statusPublished - 1 Jul 2011

Keywords

  • data mining
  • gene regulatory networks
  • internet
  • software

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    Fleuren, W. W. M., Verhoeven, S., Frijters, R., Heupers, B., Polman, J., van Schaik, R., de Vlieg, J., & Alkema, W. (2011). CoPub update: CoPub 5.0 a text mining system to answer biological questions. Nucleic acids research, 39(Web Server issue). https://doi.org/10.1093/nar/gkr310