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WikiPathways

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WikiPathways: an open resource for biological pathways.
WikiPathways logo
Content
DescriptionA wiki-based resource for collection, maintenance and distribution of biological pathways
Contact
Primary citationPMID 18651794
Access
Data formatGPML
BioPAX
Eu.gene
Websitehttp://www.wikipathways.org
Download URLhttp://www.wikipathways.org/index.php/Download_Pathways
Web service URLhttp://www.wikipathways.org/index.php/Help:WikiPathways_Webservice

WikiPathways[1] 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[2]) and integrated BridgeDb[3] databases covering major gene, protein, and metabolite systems.

Pathway Content

Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and a total of 19 species are covered, including 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 license terms. 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, KEGG), 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.[4] 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


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. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 18651794, please use {{cite journal}} with |pmid=18651794 instead.
  2. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 18817533, please use {{cite journal}} with |pmid=18817533 instead.
  3. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 20047655, please use {{cite journal}} with |pmid=20047655 instead.
  4. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 19649250, please use {{cite journal}} with |pmid=19649250 instead.
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