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2016 ; 12
(5
): e1004941
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English Wikipedia
Reactome from a WikiPathways Perspective
#MMPMID27203685
Bohler A
; Wu G
; Kutmon M
; Pradhana LA
; Coort SL
; Hanspers K
; Haw R
; Pico AR
; Evelo CT
PLoS Comput Biol
2016[May]; 12
(5
): e1004941
PMID27203685
show ga
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.
free
free
free
