WikiPathways

WikiPathways[1][2] is a community resource

WikiPathways: an open resource for
for contributing and maintaining content
dedicated to biological pathways. Any biological pathways.
registered WikiPathways user can contribute,
and anybody can become a registered user.[3]
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[4]) and Content
integrated BridgeDb[5] databases covering
Description A wiki-based resource for collection,
major gene, protein, and metabolite systems.
maintenance and distribution of
WikiPathways was founded in 2008 by
Thomas Kelder, Alex Pico, Martijn Van Iersel, biological pathways
Kristina Hanspers, Bruce Conklin and Chris Contact
Evelo. Current architects are Alex Pico and Primary citation PMID 18651794 (https://pubmed.nc
Martina Summer-Kutmon.
bi.nlm.nih.gov/18651794)
Access
Pathway content
Data format GPML (http://developers.pathvisio.o
Each article at WikiPathways is dedicated to a rg/wiki/EverythingGpml)
particular pathway. Many types of molecular BioPAX
pathways are covered, including metabolic,[6] Website http://www.wikipathways.org
signaling, regulatory, etc. and the supported[7] Download URL Pathways (https://www.wikipathway
species include human, mouse, zebrafish, fruit
s.org/index.php/Download_Pathway
fly, C. elegans, yeast, rice and arabidopsis,[8]
s)
as well as bacteria and plant species. Using a
search feature, one can locate a particular Web service URL REST (https://www.wikipathways.or
pathway by name, by the genes and proteins it g/index.php/Help:WikiPathways_We
contains, or by the text displayed in its bservice)
description. The pathway collection can also
Sparql endpoint http://sparql.wikipathways.org/sparql
be browsed with combinations of species
names and ontology-based categories. Miscellaneous
License Creative Commons 0
In addition to the pathway diagram, each
pathway page also includes a description, Data release monthly
bibliography, pathway version history and list frequency
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 several data and image formats.
WikiPathways is completely open access and open source. All content is available under Creative
Commons 0 (http://www.wikipathways.org/index.php/WikiPathways:License_Terms). All source code for
WikiPathways and the PathVisio editor is available under the Apache License, Version 2.0 (http://www.apa
che.org/licenses/).

Access and integration

In addition to various primary data formats (e.g. GPML, BioPAX, Reactome,[9] KEGG, and RDF[10]),
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.[11] This enables reuse in projects like
COVID19 Disease Map.[12]

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

Citric acid cycle § Interactive pathway map

Articles that link to Citric acid cycle template
Category:WikiPathways templates

See also
Reactome
KEGG
GenMAPP
PathVisio
Genenetwork
Cytoscape
BioPAX

References
As of this edit (https://en.wikipedia.org/w/index.php?title=WikiPathways&oldid=378296515), this article
uses content from "WikiPathWays:About" (http://wikipathways.org/index.php/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. Alexander R Pico; Thomas Kelder; Martijn P van Iersel; Kristina Hanspers; Bruce R Conklin;
Chris Evelo (22 July 2008). "WikiPathways: pathway editing for the people" (https://www.ncb
i.nlm.nih.gov/pmc/articles/PMC2475545). PLOS Biology. 6 (7): e184.
doi:10.1371/JOURNAL.PBIO.0060184 (https://doi.org/10.1371%2FJOURNAL.PBIO.006018
4). ISSN 1544-9173 (https://www.worldcat.org/issn/1544-9173). PMC 2475545 (https://www.
ncbi.nlm.nih.gov/pmc/articles/PMC2475545). PMID 18651794 (https://pubmed.ncbi.nlm.nih.
gov/18651794). Wikidata Q21092742.
2. Martina Summer-Kutmon; Anders Riutta; Nuno Nunes; et al. (4 January 2016).
"WikiPathways: capturing the full diversity of pathway knowledge" (https://www.ncbi.nlm.nih.
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10.1093%2FNAR%2FGKAA1024). ISSN 0305-1048 (https://www.worldcat.org/issn/0305-10
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PMID 33211851 (https://pubmed.ncbi.nlm.nih.gov/33211851). Wikidata Q102205677.
4. Martijn P van Iersel; Thomas Kelder; Alexander R Pico; Kristina Hanspers; Susan Coort;
Bruce R Conklin; Chris Evelo; Bruce R Conklin (2008). "Presenting and exploring biological
pathways with PathVisio" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2569944). BMC
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s://www.ncbi.nlm.nih.gov/pmc/articles/PMC2569944). PMID 18817533 (https://pubmed.ncbi.
nlm.nih.gov/18817533). Wikidata Q21284199.
5. Martijn P van Iersel; Alexander R. Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina
Hanspers; Bruce R Conklin; Chris T. Evelo (4 January 2010). "The BridgeDb framework:
standardized access to gene, protein and metabolite identifier mapping services" (https://ww
w.ncbi.nlm.nih.gov/pmc/articles/PMC2824678). BMC Bioinformatics. 11 (1): 5.
doi:10.1186/1471-2105-11-5 (https://doi.org/10.1186%2F1471-2105-11-5). ISSN 1471-2105
(https://www.worldcat.org/issn/1471-2105). PMC 2824678 (https://www.ncbi.nlm.nih.gov/pm
c/articles/PMC2824678). PMID 20047655 (https://pubmed.ncbi.nlm.nih.gov/20047655).
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6. Slenter, Denise N.; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob;
Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L.; Digles, Daniela; Ehrhart,
Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida,
Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M.T.; Evelo, Chris T.; Pico,
Alexander R.; Willighagen, Egon L. (10 November 2017). "WikiPathways: a multifaceted
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h.gov/pmc/articles/PMC5753270). Nucleic Acids Research. 46 (D1): D661–D667.
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Kenny; Jaiswal, Pankaj (2013). "WikiPathways for plants: a community pathway curation
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 9. 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" (https://www.ncbi.nlm.nih.gov/pmc/arti
cles/PMC4874630). PLOS Computational Biology. 12 (5): e1004941.
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(2009). Hide, Winston (ed.). "Mining Biological Pathways Using WikiPathways Web
Services" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714472). PLOS ONE. 4 (7):
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knowledge repository of virus–host interaction mechanisms" (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC8524328). Molecular Systems Biology. 17 (10): e10387.
doi:10.15252/msb.202110387 (https://doi.org/10.15252%2Fmsb.202110387). PMC 8524328
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8524328). PMID 34664389 (https://pubmed.
ncbi.nlm.nih.gov/34664389).

External links
Official website (http://www.wikipathways.org)

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