WikiPathways: capturing the full diversity of pathway knowledge

By Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon Willighagen, Anwesha Bohler, Jonathan Mélius, A. Waagmeester, Sravanthi R. Sinha, Ryan A Miller and 5 more. Nucleic Acids Res., 2015

435 citations recorded by the source corpus.

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.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e3274b05a5ee3bd708c5cd818a401fd1a8ef3e04

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Citations in the corpus

The UCSC Genome Browser database: 2018 update (2017, neutral): “1 (21,22), WikiPathways (23,24), the OpenBEL large corpus (https://github.”
Functional mapping and annotation of genetic associations with FUMA (2017, methodology): “To test for overrepresentation of biological functions, the prioritized genes (or a list of genes of interest) are tested against gene sets obtained from MsigDB (i.e., hallmark gene sets, positional gene sets, curated gene sets, motif gene sets, computational gene sets, GO gene sets, oncogenic signa”
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants (2016, methodology): “Representative queries linking the data to other re-Nucleic sources such as Wikipathways (27), ChEMBL (28) and the Gene Expression Atlas (29) are available at the RDF page in the website (http://www.disgenet.org/web/DisGeNET/ menu/rdf#sparql-queries).”
Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression (2017, positive): “Pathway representation was based on interferon type I signaling (Homo sapiens) from Wikipathways (WP585) and edited for size and clarity and to include type II interferon pathway components (Kutmon et al., 2016).”
Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, methodology): “Pathways were extracted by combining human pathways from WikiPathways ( Kutmon et al., 2016 ; Pico et al., 2008 ), Reactome ( Fabregat et al., 2016 ), and the Pathway Interaction Database ( Schaefer et al., 2009 ).”
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research (2017, background): “Our previous update reported over 2300 pathways for 25 different species (13) and over the last two years this number has increased by 14% to 2614 pathways, as of September 2017.”