WikiPathways:About

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== What is WikiPathways ==
== What is WikiPathways ==
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In the “tradition” of Wikipedia and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways to facilitate pathway contributions and maintenance from the scientific community. Each WikiPathways page is focused on a single pathway, displaying the current version and references. A pathway can be edited by activating a webstart version of the pathway editing tool, PathVisio. PathVisio provides a basic palette of objects and annotation needed to represent biological processes, including gene objects which are directly mapped to biological annotations from any source through an extensible identifier synonym database. PathVisio is actively being developed by members of Chris Evelo’s group (BiGCaT, University of Maastricht, The Netherlands) in collaboration with GenMAPP (Gladstone Institutes, UCSF). After editing is complete, the new version of the pathway is displayed on the wiki page along with an updated version of the underlying biological information in various pathway file formats. Pathway information downloaded in these formats can be used in applications such as GenMAPP, to analyze for example gene expression data.  While in beta, we are supporting the GenMAPP Pathway Markup Language (GPML) file format native to PathVisioGPML is an XML file format that is being developed to bridge the annotation-rich, curated style of GenMAPP pathways and the more structured, robust BioPAX format which is emerging as the community standard.
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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as [http://www.genome.jp/kegg/ KEGG], [http://www.reactome.org/ Reactome] and [http://www.pathwaycommons.org/pc/ Pathway Commons]. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each fieldThis approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
== Why Pathways ==
== Why Pathways ==
Biological pathways provide intuitive views of the myriad of interactions underlying biological processes. A typical signaling pathway, for example, can represent receptor-binding events, protein complexes, phosphorylation reactions, translocations and transcriptional regulation, with only a minimal set of symbols, lines and arrows. These powerful representations are essential tools, common among the textbooks and review articles that document any given field of biology.  Making these tools available for computational methods of analysis will allow researchers to connect pathways to databases of biological annotations and experimental data, creating effective products of systems biology. Collecting and maintaining pathway information in a robust database, however, is an ongoing challenge.
Biological pathways provide intuitive views of the myriad of interactions underlying biological processes. A typical signaling pathway, for example, can represent receptor-binding events, protein complexes, phosphorylation reactions, translocations and transcriptional regulation, with only a minimal set of symbols, lines and arrows. These powerful representations are essential tools, common among the textbooks and review articles that document any given field of biology.  Making these tools available for computational methods of analysis will allow researchers to connect pathways to databases of biological annotations and experimental data, creating effective products of systems biology. Collecting and maintaining pathway information in a robust database, however, is an ongoing challenge.
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== What's Next ==
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== How Does it Work ==
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As WikiPathways evolves, we plan to produce an embedded version of PathVisio directly into the wiki pages, eliminating the need for a webstart application altogether. Analogous to Wikipedia, modifications to pathways will be recorded, thereby creating a revision history for each pathway and allowing visual comparison between different versions of a pathway.  We will also support additional pathway file formats to encourage exchange across current applications and research preferences. We also recognize that the success of WikiPathways will depend heavily on clear and fair standards with regards to handling competing opinions and controversial findings. During beta, we will be gaining critical experience on managing style guides, versions and disputes. We are confident that WikiPathways will be a useful resource to the research community and provide a much needed forum for pathway curation.
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Each pathway at WikiPathways has a dedicated wiki page, displaying the current diagram, description, references, download options, version history, and component gene and protein lists. Any pathway can be edited from within its wiki page by activating an embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate particular pathways by name, by the genes and proteins they contain, or by the text displayed in their descriptions and comments. One can also browse the collection of pathways with combinations of species names and ontology-based categories. The pathway content at WikiPathways is freely available for download in a variety of data and image formats, including GPML, which is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio. <i>We are adding new features all the time. Visit the [[Help:Contents|Help pages]] to learn how to use the latest features.</i>
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== Who is Involved ==
== Who is Involved ==
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WikiPathways is maintained by [http://www.bigcat.nl BiGCaT Bioinformatics] ([http://www.unimaas.nl University of Maastricht]) and the [http://www.ConklinLab.org Conklin Lab] at the [http://www.gladstone.ucsf.edu/ Gladstone Institutes] ([http://www.ucsf.edu/ University of California, San Francisco])
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{{:Contact Us}}
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The current WikiPathway team includes Thomas Kelder, Alex Pico, Martijn van Iersel, Kristina Hanspers, Bruce Conklin and Chris Evelo.
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For questions, comments or suggestions, please contact:
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* Thomas Kelder: Thomas.Kelder[AT]BIGCAT.unimaas.nl
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Note that though WikiPathways is inspired by the open philosophy of Wikipedia and other wiki's, it is an independent project and not directly related to [[wikipedia:Main_Page|Wikipedia]] or other projects of the [[wikipedia:Wikimedia_foundation|Wikimedia foundation]]
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* Alex Pico: apico[AT]gladstone.ucsf.edu
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== How to cite WikiPathways ==
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{{:How to cite WikiPathways}}
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== WikiPathways Publications and Presentation ==
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* [http://highwire.stanford.edu/cgi/searchresults?andorexactfulltext=and&resourcetype=1&src=ml&author1=&fulltext=wikipathways Publications using or citing WikiPathways]
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* [http://wikipathways.tumblr.com/ Highlighted publications using WikiPathways]
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* [http://precedings.nature.com/collections/wikipathways Nature Precedings: WikiPathways Collection]
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* [http://figshare.com/articles/search?q=wikipathways&quick=1&x=0&y=0 WikiPathways at FigShare.com]
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* [http://www.slideshare.net/search/slideshow?searchfrom=header&q=wikipathways WikiPathways at SlideShare.net]
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* [http://nrnb.org/showcase-wikipathways-intro.html Introductory Slides]
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* [[Image:WikiPathways_Flyer.pdf|General purpose flyer]]
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* [http://developers.pathvisio.org/wiki/PresentationMaterial Archive of older ppt and pdf files]
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== Open Access and Open Source ==
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We are committed to [[wikipedia:open access|open access]] and [[wikipedia:open source|open source]]. All content is available under our [[WikiPathways:License_Terms|license terms]]. All source code for WikiPathways is available under the [http://www.apache.org/licenses/ Apache License, Version 2.0].
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* http://svn.bigcat.unimaas.nl/wikipathways/trunk/
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* http://svn.bigcat.unimaas.nl/pathvisio/trunk/src/wikipathways/
== Funding and Support ==
== Funding and Support ==
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* Google Summer of Code 2007 is supporting 2 students working on WikiPathways under the mentorship of GenMAPP
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* BiGCaT Bioinformatics
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An overview of projects that has financially support WikiPathways is provided on the [[WikiPathways:Funding and Support]] page.
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* GenMAPP.org is founded by a grant from the [http://www.nigms.nih.gov/ National Institute for General Medical Sciences] (R01-GM080223), as well as the [http://www.gladstone.ucsf.edu/gladstone/ Gladstone Institutes]
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Revision as of 20:22, 1 September 2017

Contents

What is WikiPathways

WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

Why Pathways

Biological pathways provide intuitive views of the myriad of interactions underlying biological processes. A typical signaling pathway, for example, can represent receptor-binding events, protein complexes, phosphorylation reactions, translocations and transcriptional regulation, with only a minimal set of symbols, lines and arrows. These powerful representations are essential tools, common among the textbooks and review articles that document any given field of biology. Making these tools available for computational methods of analysis will allow researchers to connect pathways to databases of biological annotations and experimental data, creating effective products of systems biology. Collecting and maintaining pathway information in a robust database, however, is an ongoing challenge.

How Does it Work

Each pathway at WikiPathways has a dedicated wiki page, displaying the current diagram, description, references, download options, version history, and component gene and protein lists. Any pathway can be edited from within its wiki page by activating an embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate particular pathways by name, by the genes and proteins they contain, or by the text displayed in their descriptions and comments. One can also browse the collection of pathways with combinations of species names and ontology-based categories. The pathway content at WikiPathways is freely available for download in a variety of data and image formats, including GPML, which is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio. We are adding new features all the time. Visit the Help pages to learn how to use the latest features.

Who is Involved

Find information about the WikiPathways team.

For questions, comments or suggestions, please post a message to the discussion mailinglist

Or join us at the help desk!

Additional contact:

  • Alex Pico: alex.pico[AT] gladstone.ucsf.edu
  • Martina Kutmon: mkutmon [AT] gmail.com


Note that though WikiPathways is inspired by the open philosophy of Wikipedia and other wiki's, it is an independent project and not directly related to Wikipedia or other projects of the Wikimedia foundation

How to cite WikiPathways

When referring to the latest website or content, please cite the most recent update paper:

  • Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research Nucleic Acids Research, (2017) doi.org/10.1093/nar/gkx1064 PMC5753270




When referring to specific issues described in previous update papers, please cite the respective paper:

  • Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, Bohler A, Mélius J, Waagmeester A, Sinha SR, Miller R, Coort SL, Cirillo E, Smeets B, Evelo CT, Pico AR. WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494 (2016) doi:10.1093/nar/gkv1024 PMC4702772
  • Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo C, Pico AR. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7 (link to article)




When referring to the web services, please cite:

  • Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS ONE 4(7): (link to article)




When referring to the origins of WikiPathways, please cite:

  • Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biol 6(7): (link to article)




When using or referencing WikiPathways in general, please cite the main page:




When using, referencing or redistributing particular pathways, please cite the specific pathway, for example: wikipathways.org/instance/WP254

  • When citing the live version of a pathway, attribution to individual contributors is not necessary. WikiPathways will track and display contributions from individual authors and curators to each pathway on each pathway page. So as long as hyperlinks are provided to WikiPathways, the evolving list of contributors will be indirectly referenced.
  • However, if you are referencing a specific version of a pathway (even including the current version), then it is important to include a URL of the form: wikipathways.org/instance/WP254_r93003. This approach is useful if you want to maintain a link to a snapshot of the pathway and not have future changes obscure your original points. Use the "r" argument in the URL to refer to particular revision ID numbers, which you can find in the History section of each pathway page.
  • Also, when referencing a specific version, it is appropriate to list the individual contributors, since future contributors are not an issue. Thus, the reference might look like this:

Salomonis N, Pico A, Hanspers K: SIDS Susceptibility Pathways (Homo sapiens). wikipathways.org/instance/WP706_r92921



When referring to the use of Adverse Outcome Pathways (AOPs) and WikiPathways, please cite the respective paper:

  • Martens M, Verbruggen T, Nymark P, Grafström R, Burgoon LD, Aladjov H, Torres Andón T, Evelo CT, Willighagen EL. Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials. Front. Genet. , (2018) doi:10.3389/fgene.2018.00661

WikiPathways Publications and Presentation

Open Access and Open Source

We are committed to open access and open source. All content is available under our license terms. All source code for WikiPathways is available under the Apache License, Version 2.0.

Funding and Support

An overview of projects that has financially support WikiPathways is provided on the WikiPathways:Funding and Support page.

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