WikiPathways

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WikiPathways: an open resource for biological pathways.
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Content
DescriptionA 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.

Contents

Pathway content

Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, [7] signaling, regulatory, etc. and the supported [8] species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, rice and arabidopsis, [9] 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 several data and image formats. WikiPathways is completely open access and open source. All content is available under Creative Commons 0. All source code for WikiPathways and the PathVisio editor is available under the Apache License, Version 2.0.

Access and integration

In addition to various primary data formats (e.g. GPML, BioPAX, Reactome, [10] KEGG, and RDF [11] ), 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. [12] This enables reuse in projects like COVID19 Disease Map. [13]

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

References

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. ↑ 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.
  2. ↑ 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.
  3. ↑ 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.
  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". Nucleic Acids Research. 52 (D1): D679 –D689. doi: 10.1093/nar/gkad960 . PMC   10767877 . PMID   37941138.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ 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". Nucleic Acids Research. 46 (D1): D661 –D667. doi:10.1093/NAR/GKX1064. PMC   5753270 . PMID   29136241.
  8. ↑ "Browse pathways - WikiPathways".
  9. ↑ 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". Rice. 6 (1): 14. Bibcode:2013Rice....6...14H. doi: 10.1186/1939-8433-6-14 . PMC   4883732 . PMID   24280312.
  10. ↑ 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. Bibcode:2016PLSCB..12E4941B. doi: 10.1371/journal.pcbi.1004941 . PMC   4874630 . PMID   27203685.
  11. ↑ 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. Bibcode:2016PLSCB..12E4989W. doi: 10.1371/journal.pcbi.1004989 . PMC   4918977 . PMID   27336457.
  12. ↑ 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   2714472 . PMID   19649250.
  13. ↑ Ostaszewski, M.; et al. (1 October 2021). "COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms". Molecular Systems Biology. 17 (10) e10387. doi:10.15252/msb.202110387. PMC   8524328 . PMID   34664389.
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