WikiPathways

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WikiPathways: an open resource for biological pathways.
WikiPathways logo
Content
Description A wiki-based resource for collection, maintenance and distribution of biological pathways
Contact
Primary citation PMID 18651794
Access
Data format GPML
BioPAX
Website http://www.wikipathways.org
Download URL Pathways
Web service URL REST
Sparql endpoint http://sparql.wikipathways.org/
Miscellaneous
License Creative Commons Attribution 3.0 Unported

WikiPathways[1][2] is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is built using MediaWiki software, a custom graphical pathway editing tool (PathVisio[3]) and integrated BridgeDb[4] databases covering major gene, protein, and metabolite systems.

Pathway content[edit]

Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and the supported[5] species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, as well as bacteria and plant species. Using a search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or by the text displayed in its description. The pathway collection can also be browsed with combinations of species names and ontology-based categories.

In addition to the pathway diagram, each pathway page also includes a description, bibliography, pathway version history and list of component genes and proteins with linkouts to public resources. For individual pathway nodes, users can access a list of other pathways with that node. Pathway changes can be monitored by displaying previous revisions or by viewing differences between specific revisions. Using the pathway history one can also revert to a previous revision of a pathway. Pathways can also be tagged with ontology terms from three major BioPortal ontologies (Pathway, Disease and Cell Type).

The pathway content at WikiPathways is freely available for download in a several data and image formats. WikiPathways is completely open access and open source. All content is available under Creative Commons-Attribution 3.0 license terms. All source code for WikiPathways and the PathVisio editor is available under the Apache License, Version 2.0.

Access and integration[edit]

In addition to various primary data formats (e.g. GPML, BioPAX, Reactome,[6] KEGG, and RDF[7]), WikiPathways supports a variety of ways to integrate and interact with pathway content. These include directed link-outs, image maps, RSS feeds and deep web services.[8] WikiPathways webservices can be used by bioinformaticians, e.g., to perform enrichment analysis on WikiPathways in R and web developers, e.g. to link to relevant pathways.

WikiPathways content is used to annotate and cross-link Wikipedia articles covering various genes, proteins, metabolites and pathways. Here are a few examples:

See also[edit]

References[edit]

As of this edit, this article uses content from "WikiPathWays:About", which is licensed in a way that permits reuse under the Creative Commons Attribution-ShareAlike 3.0 Unported License, but not under the GFDL. All relevant terms must be followed.

  1. ^ Pico, A. R.; Kelder, T.; Van Iersel, M. P.; Hanspers, K.; Conklin, B. R.; Evelo, C. (2008). "WikiPathways: Pathway Editing for the People". PLoS Biology. 6 (7): e184. doi:10.1371/journal.pbio.0060184. PMC 2475545Freely accessible. PMID 18651794. 
  2. ^ Kutmon, M.; Riutta, A.; Nunes, N.; Haspers, K.; Willighagen, E.L.; Bohler, A.; Mélius, J.; Waagmeester, A.; Sinha, S.R.; Miller, R.; Coort, S.L.; Cirillo, M.; Smeets, B.; Evelo, C.T.; Pico, A. (2015). "WikiPathways: capturing the full diversity of pathway knowledge". Nucleic Acids Research. doi:10.1093/nar/gkv1024. PMID 26481357. 
  3. ^ Van Iersel, M. P.; Kelder, T.; Pico, A. R.; Hanspers, K.; Coort, S.; Conklin, B. R.; Evelo, C. (2008). "Presenting and exploring biological pathways with PathVisio". BMC Bioinformatics. 9: 399. doi:10.1186/1471-2105-9-399. PMC 2569944Freely accessible. PMID 18817533. 
  4. ^ Van Iersel, M. P.; Pico, A. R.; Kelder, T.; Gao, J.; Ho, I.; Hanspers, K.; Conklin, B. R.; Evelo, C. T. (2010). "The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services". BMC Bioinformatics. 11: 5. doi:10.1186/1471-2105-11-5. PMC 2824678Freely accessible. PMID 20047655. 
  5. ^ http://www.wikipathways.org//index.php?title=Special:BrowsePathwaysPage
  6. ^ Bohler, Anwesha; Wu, Guanming; Kutmon, Martina; Pradhana, Leontius Adhika; Coort, Susan L.; Hanspers, Kristina; Haw, Robin; Pico, Alexander R.; Evelo, Chris T. (20 May 2016). "Reactome from a WikiPathways Perspective". PLOS Computational Biology. 12 (5): e1004941. doi:10.1371/journal.pcbi.1004941. 
  7. ^ Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L.; Evelo, Chris T.; Pico, Alexander R. (23 June 2016). "Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources". PLOS Computational Biology. 12 (6): e1004989. doi:10.1371/journal.pcbi.1004989. 
  8. ^ Kelder, T.; Pico, A. R.; Hanspers, K.; Van Iersel, M. P.; Evelo, C.; Conklin, B. R.; Hide, W. (2009). Hide, Winston, ed. "Mining Biological Pathways Using WikiPathways Web Services". PLoS ONE. 4 (7): e6447. Bibcode:2009PLoSO...4.6447K. doi:10.1371/journal.pone.0006447. PMC 2714472Freely accessible. PMID 19649250. 

External links[edit]