WikiPathways: building research communities on biological pathways

By Thomas Kelder, M. V. Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. A. Evelo, Alexander R. Pico. Nucleic Acids Res., 2011

541 citations recorded by the source corpus.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/5ef2d1e9cb2017c0161eaa2cc2351a2447f2b1ce

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Citations in the corpus

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “Wikipathways Pathways (90) CORUM Protein Complexes (91, 92)”
The ConsensusPathDB interaction database: 2013 update (2012, background): “The newly integrated resources are BIND (protein–protein interactions) (10), DrugBank (drug–target interactions) (11), InnateDB (protein–protein, biochemical and gene regulatory interactions) (12), MatrixDB (protein–protein interactions) (13), PDZBase (protein–protein interactions) (14), PhosphoPOIN”
Pathview Web: user friendly pathway visualization and data integration (2017, background): “A wide range of databases and resources have been built (KEGG (1), Reactome (2), Wikipathways (3), MetaCyc (4), PANTHER (5), Pathway Commons (6) etc.”
WikiPathways: capturing the full diversity of pathway knowledge (2015, methodology): “Overall, we report tremendous growth in content and features since the last update (3), and a continued commitment to capture every pathway of interest and disseminate it in as many useful ways as possible.”
The Reactome pathway knowledgebase (2013, unknown): “Community relationships and data exchange Reactome continues to collaborate with other data resources, such as GO, NCBI, EBI and WikiPathways (22).”
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, background): “0 [16], WikiPathways [17], Biographer [18], and the BioCyc pathway viewer [19].”
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees (2012, background): “PANTHER Pathway supports BioPAX, and therefore is able to import pathways from any pathway resources that support this standard, such as WikiPathways (28), Reactome (29), Pathway Interaction Database (30) and BioCyc (31).”
The UCSC Genome Browser database: 2018 update (2017, unknown): “1 (21,22), WikiPathways (23,24), the OpenBEL large corpus (https://github.”
PathVisio 3: An Extendable Pathway Analysis Toolbox (2015, methodology): “The applet version is integrated in WikiPathways as an online pathway editor.”