Adriaens Michiel E, Jaillard Magali, Waagmeester Andra, Coort Susan L M, Pico Alex R, Evelo Chris T A
Department of Bioinformatics-BiGCaT, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, The Netherlands.
Drug Discov Today. 2008 Oct;13(19-20):856-62. doi: 10.1016/j.drudis.2008.06.013. Epub 2008 Aug 27.
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.
生物途径是现有生物学知识的抽象且功能性的可视化表示。通过将高通量数据映射到这些表示上，可以立即评估生物系统在基因、代谢和蛋白质水平上的变化和模式。存在许多用于存储生物途径的公共领域存储库，每个存储库都应用自己的约定和存储格式。对这些存储库进行基于途径的内容审查发现，没有一个是全面的。为了解决这个问题，我们应用一个通用工作流程来创建经过整理的生物途径，在这个流程中，我们结合了三个内容来源：公共领域数据库、文献和专家。在这个工作流程中，特定生物途径的所有内容都从生物途径数据库和文献中手动检索，然后由专家对这些内容进行比较、合并并随后进行整理。从整理后的内容中，可以为所选的途径分析工具创建新的生物途径，并在其用户群体中分发。我们应用这个程序构建了涉及人类脂肪酸代谢的高质量整理生物途径。
