# WikiPathways

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Database of biological pathways

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WikiPathways: an open resource for biological pathways. 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 https://sparql.wikipathways.org/sparql Miscellaneous License Creative Commons 0 Data release frequency monthly

**WikiPathways**[1][2] is a community resource for contributing and maintaining content dedicated to [biological pathways](/source/Biological_pathway). Any 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](/source/Peer_review), editorial curation, and maintenance is the responsibility of the user community. WikiPathways is originally built using [MediaWiki](/source/MediaWiki) software,[4] a custom graphical pathway editing tool ([PathVisio](/source/PathVisio)[5]) and integrated BridgeDb[6] databases covering major [gene](/source/Gene), [protein](/source/Protein), and [metabolite](/source/Metabolite) systems. WikiPathways was founded in 2008 by Thomas Kelder, Alex Pico, Martijn Van Iersel, Kristina Hanspers, Bruce Conklin and Chris Evelo. Current architects are Martina Summer-Kutmon and Egon Willighagen.[7]

## Pathway content

Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including [metabolic](/source/Metabolic_pathway),[8] [signaling](/source/Signal_transduction), [regulatory](/source/Regulation_of_gene_expression), etc. and the supported[9] [species](/source/Species) include [human](/source/Human), [mouse](/source/Mouse), [zebrafish](/source/Zebrafish), [fruit fly](/source/Drosophila_melanogaster), [C. elegans](/source/Caenorhabditis_elegans), [yeast](/source/Yeast), [rice](/source/Rice) and [arabidopsis](/source/Arabidopsis),[10] as well as [bacteria](/source/Bacteria) and [plant](/source/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](/source/Open_Biomedical_Ontologies) 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](/source/Open_access_(publishing)) and [open source](/source/Open-source_license). All content is available under [Creative Commons 0](https://www.wikipathways.org/index.php/WikiPathways:License_Terms). All source code for WikiPathways and the [PathVisio](/source/PathVisio) editor is available under the [Apache License, Version 2.0](https://www.apache.org/licenses/).

## Access and integration

In addition to various primary [data formats](/source/File_format) (e.g. GPML, [BioPAX](/source/BioPAX), [Reactome](/source/Reactome),[11] [KEGG](/source/KEGG), and RDF[12]), WikiPathways supports a variety of ways to integrate and interact with pathway content. These include directed link-outs, [image maps](/source/Image_maps), [RSS feeds](/source/RSS_feeds) and deep [web services](/source/Web_services).[13] This enables reuse in projects like COVID19 Disease Map.[14]

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](/source/Citric_acid_cycle#Interactive_pathway_map)

- [Articles that link to Citric acid cycle template](https://en.wikipedia.org/wiki/Special:WhatLinksHere/Template:TCACycle_WP78)

- [Category:WikiPathways templates](https://en.wikipedia.org/wiki/Category:WikiPathways_templates)

## See also

[Scholia](https://www.wikidata.org/wiki/Wikidata:Scholia) has a *topic* profile for ***[WikiPathways](https://iw.toolforge.org/scholia/topic/Q7999828)***.

- [Reactome](/source/Reactome)

- [Pathway Commons](/source/Pathway_Commons)

- [KEGG](/source/KEGG)

- [GenMAPP](/source/GenMAPP)

- [PathVisio](/source/PathVisio)

- [Genenetwork](/source/Genenetwork)

- [Cytoscape](/source/Cytoscape)

- [BioPAX](/source/BioPAX)

## References

*As of [this edit](https://en.wikipedia.org/wiki/Special:PermanentLink/378296515), this article uses content from*["WikiPathWays:About"](https://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](https://en.wikipedia.org/wiki/Wikipedia:Text_of_Creative_Commons_Attribution-ShareAlike_3.0_Unported_License), but not under the [GFDL](https://en.wikipedia.org/wiki/Wikipedia:Text_of_the_GNU_Free_Documentation_License). All relevant terms must be followed.*

1. **[^](#cite_ref-pmid18651794_1-0)** 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.ncbi.nlm.nih.gov/pmc/articles/PMC2475545). *[PLOS Biology](/source/PLOS_Biology)*. **6** (7): e184. [doi](/source/Doi_(identifier)):[10.1371/JOURNAL.PBIO.0060184](https://doi.org/10.1371%2FJOURNAL.PBIO.0060184). [ISSN](/source/ISSN_(identifier)) [1544-9173](https://search.worldcat.org/issn/1544-9173). [PMC](/source/PMC_(identifier)) [2475545](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475545). [PMID](/source/PMID_(identifier)) [18651794](https://pubmed.ncbi.nlm.nih.gov/18651794). [Wikidata](/source/WDQ_(identifier)) [Q21092742](https://www.wikidata.org/wiki/Q21092742).

1. **[^](#cite_ref-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.gov/pmc/articles/PMC4702772). *[Nucleic Acids Research](/source/Nucleic_Acids_Research)*. **44** (D1): D488-94. [doi](/source/Doi_(identifier)):[10.1093/NAR/GKV1024](https://doi.org/10.1093%2FNAR%2FGKV1024). [ISSN](/source/ISSN_(identifier)) [0305-1048](https://search.worldcat.org/issn/0305-1048). [PMC](/source/PMC_(identifier)) [4702772](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702772). [PMID](/source/PMID_(identifier)) [26481357](https://pubmed.ncbi.nlm.nih.gov/26481357). [Wikidata](/source/WDQ_(identifier)) [Q24082733](https://www.wikidata.org/wiki/Q24082733).

1. **[^](#cite_ref-3)** Marvin Martens; Ammar Ammar; Anders Riutta; et al. (8 January 2021). ["WikiPathways: connecting communities"](https://academic.oup.com/nar/article/49/D1/D613/5992285). *[Nucleic Acids Research](/source/Nucleic_Acids_Research)*. **49** (D1): D613–D621. [doi](/source/Doi_(identifier)):[10.1093/NAR/GKAA1024](https://doi.org/10.1093%2FNAR%2FGKAA1024). [ISSN](/source/ISSN_(identifier)) [0305-1048](https://search.worldcat.org/issn/0305-1048). [PMC](/source/PMC_(identifier)) [7779061](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779061). [PMID](/source/PMID_(identifier)) [33211851](https://pubmed.ncbi.nlm.nih.gov/33211851). [Wikidata](/source/WDQ_(identifier)) [Q102205677](https://www.wikidata.org/wiki/Q102205677).

1. **[^](#cite_ref-4)** Agrawal, Ayushi; Balcı, Hasan; Hanspers, Kristina; Coort, Susan L; Martens, Marvin; Slenter, Denise N; Ehrhart, Friederike; Digles, Daniela; Waagmeester, Andra; Wassink, Isabel; Abbassi-Daloii, Tooba; Lopes, Elisson N; Iyer, Aishwarya; Acosta, Javier Millán; Willighagen, Lars G; Nishida, Kozo; Riutta, Anders; Basaric, Helena; Evelo, Chris T; Willighagen, Egon L; Kutmon, Martina; Pico, Alexander R (6 November 2023). ["WikiPathways 2024: next generation pathway database"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10767877). *Nucleic Acids Research*. **52** (D1): D679–D689. [doi](/source/Doi_(identifier)):[10.1093/nar/gkad960](https://doi.org/10.1093%2Fnar%2Fgkad960). [PMC](/source/PMC_(identifier)) [10767877](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10767877). [PMID](/source/PMID_(identifier)) [37941138](https://pubmed.ncbi.nlm.nih.gov/37941138).

1. **[^](#cite_ref-pmid18817533_5-0)** Martijn P van Iersel; Thomas Kelder; Alexander R Pico; Kristina Hanspers; Susan Coort; Bruce R Conklin; Chris Evelo (2008). ["Presenting and exploring biological pathways with PathVisio"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2569944). *[BMC Bioinformatics](/source/BMC_Bioinformatics)*. **9** (1): 399. [doi](/source/Doi_(identifier)):[10.1186/1471-2105-9-399](https://doi.org/10.1186%2F1471-2105-9-399). [ISSN](/source/ISSN_(identifier)) [1471-2105](https://search.worldcat.org/issn/1471-2105). [PMC](/source/PMC_(identifier)) [2569944](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2569944). [PMID](/source/PMID_(identifier)) [18817533](https://pubmed.ncbi.nlm.nih.gov/18817533). [Wikidata](/source/WDQ_(identifier)) [Q21284199](https://www.wikidata.org/wiki/Q21284199).

1. **[^](#cite_ref-pmid20047655_6-0)** 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824678). *[BMC Bioinformatics](/source/BMC_Bioinformatics)*. **11** (1): 5. [doi](/source/Doi_(identifier)):[10.1186/1471-2105-11-5](https://doi.org/10.1186%2F1471-2105-11-5). [ISSN](/source/ISSN_(identifier)) [1471-2105](https://search.worldcat.org/issn/1471-2105). [PMC](/source/PMC_(identifier)) [2824678](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824678). [PMID](/source/PMID_(identifier)) [20047655](https://pubmed.ncbi.nlm.nih.gov/20047655). [Wikidata](/source/WDQ_(identifier)) [Q28842753](https://www.wikidata.org/wiki/Q28842753).

1. **[^](#cite_ref-7)** ["About | WikiPathways"](https://www.wikipathways.org/about.html). *www.wikipathways.org*. Retrieved 22 February 2026.

1. **[^](#cite_ref-8)** 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 pathway database bridging metabolomics to other omics research"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753270). *Nucleic Acids Research*. **46** (D1): D661–D667. [doi](/source/Doi_(identifier)):[10.1093/NAR/GKX1064](https://doi.org/10.1093%2FNAR%2FGKX1064). [PMC](/source/PMC_(identifier)) [5753270](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753270). [PMID](/source/PMID_(identifier)) [29136241](https://pubmed.ncbi.nlm.nih.gov/29136241).

1. **[^](#cite_ref-9)** ["Browse pathways - WikiPathways"](https://www.wikipathways.org//index.php?title=Special:BrowsePathwaysPage).

1. **[^](#cite_ref-10)** Hanumappa, Mamatha; Preece, Justin; Elser, Justin; Nemeth, Denise; Bono, Gina; Wu, Kenny; Jaiswal, Pankaj (2013). ["WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883732). *Rice*. **6** (1): 14. [Bibcode](/source/Bibcode_(identifier)):[2013Rice....6...14H](https://ui.adsabs.harvard.edu/abs/2013Rice....6...14H). [doi](/source/Doi_(identifier)):[10.1186/1939-8433-6-14](https://doi.org/10.1186%2F1939-8433-6-14). [PMC](/source/PMC_(identifier)) [4883732](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883732). [PMID](/source/PMID_(identifier)) [24280312](https://pubmed.ncbi.nlm.nih.gov/24280312).

1. **[^](#cite_ref-11)** 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/articles/PMC4874630). *PLOS Computational Biology*. **12** (5) e1004941. [Bibcode](/source/Bibcode_(identifier)):[2016PLSCB..12E4941B](https://ui.adsabs.harvard.edu/abs/2016PLSCB..12E4941B). [doi](/source/Doi_(identifier)):[10.1371/journal.pcbi.1004941](https://doi.org/10.1371%2Fjournal.pcbi.1004941). [PMC](/source/PMC_(identifier)) [4874630](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874630). [PMID](/source/PMID_(identifier)) [27203685](https://pubmed.ncbi.nlm.nih.gov/27203685).

1. **[^](#cite_ref-12)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918977). *PLOS Computational Biology*. **12** (6) e1004989. [Bibcode](/source/Bibcode_(identifier)):[2016PLSCB..12E4989W](https://ui.adsabs.harvard.edu/abs/2016PLSCB..12E4989W). [doi](/source/Doi_(identifier)):[10.1371/journal.pcbi.1004989](https://doi.org/10.1371%2Fjournal.pcbi.1004989). [PMC](/source/PMC_(identifier)) [4918977](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918977). [PMID](/source/PMID_(identifier)) [27336457](https://pubmed.ncbi.nlm.nih.gov/27336457).

1. **[^](#cite_ref-pmid19649250_13-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714472). *PLOS ONE*. **4** (7) e6447. [Bibcode](/source/Bibcode_(identifier)):[2009PLoSO...4.6447K](https://ui.adsabs.harvard.edu/abs/2009PLoSO...4.6447K). [doi](/source/Doi_(identifier)):[10.1371/journal.pone.0006447](https://doi.org/10.1371%2Fjournal.pone.0006447). [PMC](/source/PMC_(identifier)) [2714472](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714472). [PMID](/source/PMID_(identifier)) [19649250](https://pubmed.ncbi.nlm.nih.gov/19649250).

1. **[^](#cite_ref-14)** Ostaszewski, M.; et al. (1 October 2021). ["COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8524328). *Molecular Systems Biology*. **17** (10) e10387. [doi](/source/Doi_(identifier)):[10.15252/msb.202110387](https://doi.org/10.15252%2Fmsb.202110387). [PMC](/source/PMC_(identifier)) [8524328](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8524328). [PMID](/source/PMID_(identifier)) [34664389](https://pubmed.ncbi.nlm.nih.gov/34664389).

## External links

- [Official website](http://www.wikipathways.org)

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Adapted from the Wikipedia article [WikiPathways](https://en.wikipedia.org/wiki/WikiPathways) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/WikiPathways?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.