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PLoS Comput Biol. 2016 May 20;12(5):e1004941. doi: 10.1371/journal.pcbi.1004941. eCollection 2016 May.

Reactome from a WikiPathways Perspective.

Author information

1
Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.
2
Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.
3
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
4
Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore.
5
Gladstone Institutes, San Francisco, California, United States of America.

Abstract

Reactome and WikiPathways are two of the most popular freely available databases for biological pathways. Reactome pathways are centrally curated with periodic input from selected domain experts. WikiPathways is a community-based platform where pathways are created and continually curated by any interested party. The nascent collaboration between WikiPathways and Reactome illustrates the mutual benefits of combining these two approaches. We created a format converter that converts Reactome pathways to the GPML format used in WikiPathways. In addition, we developed the ComplexViz plugin for PathVisio which simplifies looking up complex components. The plugin can also score the complexes on a pathway based on a user defined criterion. This score can then be visualized on the complex nodes using the visualization options provided by the plugin. Using the merged collection of curated and converted Reactome pathways, we demonstrate improved pathway coverage of relevant biological processes for the analysis of a previously described polycystic ovary syndrome gene expression dataset. Additionally, this conversion allows researchers to visualize their data on Reactome pathways using PathVisio's advanced data visualization functionalities. WikiPathways benefits from the dedicated focus and attention provided to the content converted from Reactome and the wealth of semantic information about interactions. Reactome in turn benefits from the continuous community curation available on WikiPathways. The research community at large benefits from the availability of a larger set of pathways for analysis in PathVisio and Cytoscape. The pathway statistics results obtained from PathVisio are significantly better when using a larger set of candidate pathways for analysis. The conversion serves as a general model for integration of multiple pathway resources developed using different approaches.

PMID:
27203685
PMCID:
PMC4874630
DOI:
10.1371/journal.pcbi.1004941
[Indexed for MEDLINE]
Free PMC Article
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