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Drug Discov Today. 2008 Oct;13(19-20):856-62. doi: 10.1016/j.drudis.2008.06.013. Epub 2008 Aug 27.

The public road to high-quality curated biological pathways.

Author information

  • 1Department of Bioinformatics-BiGCaT, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, The Netherlands. michiel.adriaens@bigcat.unimaas.nl

Abstract

Biological pathways are abstract and functional visual representations of existing biological knowledge. By mapping high-throughput data on these representations, changes and patterns in biological systems on the genetic, metabolic and protein level are instantly assessable. Many public domain repositories exist for storing biological pathways, each applying its own conventions and storage format. A pathway-based content review of these repositories reveals that none of them are comprehensive. To address this issue, we apply a general workflow to create curated biological pathways, in which we combine three content sources: public domain databases, literature and experts. In this workflow all content of a particular biological pathway is manually retrieved from biological pathway databases and literature, after which this content is compared, combined and subsequently curated by experts. From the curated content, new biological pathways can be created for a pathway analysis tool of choice and distributed among its user base. We applied this procedure to construct high-quality curated biological pathways involved in human fatty acid metabolism.

PMID:
18652912
[PubMed - indexed for MEDLINE]
PMCID:
PMC3646620
Free PMC Article

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