WikiPathways: Pathway Editing for the People

By Alexander R. Pico, Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo. PLoS Biology, 2008

726 citations recorded by the source corpus.

WikiPathways provides a collaborative platform for creating, updating, and sharing pathway diagrams and serves as an example of content curation by the biology community.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/00536b014eb7ac7e248ff23ccbc67bdff02b84fe

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Citations in the corpus

WikiPathways: connecting communities (2020, background): “The WikiPathways project was founded in 2007 upon the idea that everyone should be able to participate in the collection and curation of scientific knowledge (1).”
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 (2013, background): “In contrast to centrally curated databases, open, collaborative platforms that allow for broader participation by the entire biology community, such as WikiPathways (9), have become a new model for community-based curation of biological data.”
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources (2009, background): “Recent examples include the Gene Wiki [14], WikiProteins [21], WikiGenes [22], and WikiPathways [23].”
Database resources of the National Center for Biotechnology Information (2014, methodology): “Currently Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (49–51), BioCyc (52), Reactome (53), the Pathway Interaction Database (54), WikiPathways (55,56) and Gene Ontology (57).”
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database (2013, background): “As a result, there is now a plethora of very popular, very high-quality web-accessible pathway databases such as KEGG (1), the ‘Cyc’ databases (2,3), the Reactome database (4), WikiPathways (5) and PharmGKB (6).”
Presenting and exploring biological pathways with PathVisio (2008, methodology): “An applet version of PathVisio is used for the WikiPathways [18,19] resource, where the research community can collaborate in the task of curating and updating pathway content.”
Reactome: a database of reactions, pathways and biological processes (2010, methodology): “Reactome participated in this year’s Google Summer of Code program, collaborating with WikiPathways (31).”
SMPDB: The Small Molecule Pathway Database (2009, background): “Over the past decade, a number of superb, web-accessible molecular pathway resources have emerged, including Kyoto Encyclopedia of Genes and Genomes (KEGG) (5), the ‘Cyc’ databases (6,7), the Reactome database (8), WikiPathways/GeneMAPP (9), the Edinburgh Human Metabolic Network (EHMN) (10), PharmGK”
Single-cell RNA-seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis (2015, methodology): “We used GO (Ashburner et al., 2000), KEGG (Kanehisa and Goto, 2000), and wikipathway (Pico et al., 2008) for functional GO analyses, along with the R bioconductor package (Gentleman et al., 2004) or Cytoscape software (Shannon et al., 2003).”
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data (2010, methodology): “Furthermore, overrepresentation analyses can be performed for pathways annotated by WikiPathways (22) and Gene Ontology (23), using the integrated program GO-Elite (24).”
BioPAX – A community standard for pathway data sharing (2010, positive): “Ideally, appropriate software would allow authors to enter data directly in standard formats during the publication process, to facilitate annotation and normalization by curators before incorporation into databases for use by researchers 53 . p e r s p e c t i v e”
EnrichNet: network-based gene set enrichment analysis (2012, methodology): “…gene/protein set and different reference datasets, the target set is first mapped onto a molecular network (here a connected human interactome graph extracted from the STRING 9.0 database (Snel et al., 2000; Von Mering et al., 2003), with edges weighted by the STRING combined confidence score…”
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool (2013, methodology): “Finally, to demonstrate how Enrichr can be applied globally to obtain a regulatory picture of cancer cell lines and their corresponding normal tissues, we used nine gene sets from the CCLE gene-set library and matching nine gene sets from the Human Gene Atlas library to perform enrichment analysis u”
NetPath: a public resource of curated signal transduction pathways (2010, background): “Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C: WikiPathways: pathway editing for the people.”
Database resources of the National Center for Biotechnology Information (2006, methodology): “Currently, Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (35–37), BioCyc (38), Reactome (39), the Pathway Interaction Database (40), WikiPathways (41,42) and Gene Ontology (43).”
WikiPathways: capturing the full diversity of pathway knowledge (2015, methodology): “Launched in 2008 as an experiment to see if crowdsourcing could work for a pathway archive, WikiPathways started out with 500 pathways across six species maintained by four individuals (1).”