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
http://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. 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, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is originally built using MediaWiki software,[4] a custom graphical pathway editing tool (PathVisio[5]) and integrated BridgeDb[6] databases covering major gene, protein, and 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 Alex Pico and Martina Summer-Kutmon.
^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". PLOS Biology. 6 (7): e184. doi:10.1371/JOURNAL.PBIO.0060184. ISSN 1544-9173. PMC 2475545. PMID 18651794. Wikidata Q21092742.
^Martina Summer-Kutmon; Anders Riutta; Nuno Nunes; et al. (4 January 2016). "WikiPathways: capturing the full diversity of pathway knowledge". Nucleic Acids Research. 44 (D1): D488-94. doi:10.1093/NAR/GKV1024. ISSN 0305-1048. PMC 4702772. PMID 26481357. Wikidata Q24082733.
^Marvin Martens; Ammar Ammar; Anders Riutta; et al. (8 January 2021). "WikiPathways: connecting communities". Nucleic Acids Research. 49 (D1): D613–D621. doi:10.1093/NAR/GKAA1024. ISSN 0305-1048. PMC 7779061. PMID 33211851. Wikidata Q102205677.
^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". Nucleic Acids Research. doi:10.1093/nar/gkad960. PMC 10767877. PMID 37941138.
^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". BMC Bioinformatics. 9 (1): 399. doi:10.1186/1471-2105-9-399. ISSN 1471-2105. PMC 2569944. PMID 18817533. Wikidata Q21284199.
^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". BMC Bioinformatics. 11 (1): 5. doi:10.1186/1471-2105-11-5. ISSN 1471-2105. PMC 2824678. PMID 20047655. Wikidata Q28842753.
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute...
|alt=Glycolysis and Gluconeogenesis edit]] The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". Some of the metabolites...
transduction pathway KEGG Pathway database is a popular pathway search database highly used by biologists. WikiPathways is a community curated pathway database...
|alt=Glycolysis and Gluconeogenesis edit]] The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". Acids in wine Citrate–malate...
rat has been described in literature, and is part of the WikiPathways machine readable pathway collection. Vanillin 2-Hydroxy-5-methoxybenzaldehyde ortho-Vanillin...
|alt=Glycolysis and Gluconeogenesis edit]] The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". PEP may be used for...
such as KEGG, WikiPathways, or Reactome. Also exist proprietary pathways collections used by e.g. Pathway Studio and Ingenuity Pathway Analysis tools...
Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory) WikiPathways BioCyc Database Collection: includes EcoCyc and MetaCyc BRENDA: the comprehensive...
caspase-7 pathway; and by external signals (FAS and TNF), along the caspase 8 pathway. Accessed 25 March 2007. WikiPathways – Apoptosis pathway Archived...
|alt=Glycolysis and Gluconeogenesis edit]] The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". In the Calvin cycle...
also a potent inhibitor of complex II. Gluconeogenesis is a metabolic pathway consisting of a series of eleven enzyme-catalyzed reactions, resulting...
Localization database (PathLocdb) DAVID: Visualize genes on pathway maps Wikipathways: pathways for the people ConsensusPathDB metpath: Integrated interactive metabolic...
|alt=Fluorouracil (5-FU) Activity edit]] The interactive pathway map can be edited at WikiPathways: "FluoropyrimidineActivity_WP1601". DCMP deaminase Uridine...
|alt=Glycolysis and Gluconeogenesis edit]] The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". Pyruvate decarboxylation...
[[ ]] [[ ]] |alt=TCACycle_WP78 edit]] The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78". The metabolic role of lactate is well...
|alt=Fluorouracil (5-FU) Activity edit]] The interactive pathway map can be edited at WikiPathways: "FluoropyrimidineActivity_WP1601". Gangjee, Aleem; Jain...
]] [[ ]] |alt=Vitamin D Synthesis Pathway (view / edit)]] The interactive pathway map can be edited at WikiPathways: "VitaminDSynthesis_WP1531". 7-Dehydrocholesterol...
[[ ]] [[ ]] |alt=TCACycle_WP78 edit]] The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78". Fumaric acid has been used as a food...
]] [[ ]] |alt=Vitamin D Synthesis Pathway (view / edit)]] The interactive pathway map can be edited at WikiPathways: "VitaminDSynthesis_WP1531". The transformation...
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