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Nucleic Acids Res. 2016 Jan 4;44(D1):D488-94. doi: 10.1093/nar/gkv1024. Epub 2015 Oct 19.

WikiPathways: capturing the full diversity of pathway knowledge.

Author information

1
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands martina.kutmon@maastrichtuniversity.nl.
2
Gladstone Institutes, San Francisco, California, CA 94158, USA.
3
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
4
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Micelio, Antwerp, 2180 Antwerp, Belgium.
5
Keshav Memorial Institute of Technology, Hyderabad, Telangana 500029, India.
6
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
7
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands apico@gladstone.ucsf.edu.

Abstract

WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access.

PMID:
26481357
PMCID:
PMC4702772
DOI:
10.1093/nar/gkv1024
[Indexed for MEDLINE]
Free PMC Article

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