title: Reactome from a WikiPathways Perspective.
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.
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.
authors.forename: Anwesha
authors.initials: A
authors.lastname: Bohler
authors.affiliation: Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.
authors.forename: Guanming
authors.initials: G
authors.lastname: Wu
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.|Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
authors.forename: Martina
authors.identifier: 0000-0002-7699-8191
authors.initials: M
authors.lastname: Kutmon
authors.affiliation: Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore.
authors.forename: Leontius Adhika
authors.initials: LA
authors.lastname: Pradhana
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.
authors.forename: Susan L
authors.identifier: 0000-0003-1224-9690
authors.initials: SL
authors.lastname: Coort
authors.affiliation: Gladstone Institutes, San Francisco, California, United States of America.
authors.forename: Kristina
authors.initials: K
authors.lastname: Hanspers
authors.affiliation: Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.
authors.forename: Robin
authors.initials: R
authors.lastname: Haw
authors.affiliation: Gladstone Institutes, San Francisco, California, United States of America.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
authors.affiliation: Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.|Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
authors.forename: Chris T
authors.identifier: 0000-0002-5301-3142
authors.initials: CT
authors.lastname: Evelo
mesh_terms: D019295:Computational Biology; D003196:Computer Graphics; D016208:Databases, Factual; D063990:Gene Ontology; D006801:Humans; D020407:Internet; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software