Help:Frequently Asked Questions
From WikiPathways
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See [[:WikiPathways:About|About WikiPathways]]. | See [[:WikiPathways:About|About WikiPathways]]. | ||
==== Where does the pathway content at WikiPathways come from? ==== | ==== Where does the pathway content at WikiPathways come from? ==== | ||
| - | + | The WikiPathways content is contributed by individual users and groups from the general scientific community. Any registered user at WikiPathways can contribute. | |
==== How do I cite pathways from WikiPathways? ==== | ==== How do I cite pathways from WikiPathways? ==== | ||
| - | See [ | + | See [https://www.wikipathways.org/index.php/How_to_cite_WikiPathways our How to Cite page] |
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==== Does WikiPathways check the content of contributed pathways for quality and accuracy? ==== | ==== Does WikiPathways check the content of contributed pathways for quality and accuracy? ==== | ||
| - | + | Of course! We perform ongoing [https://wikipathways.github.io/academy/qaprotocol.html quality assurance] on all pathways to look for vandalism and to ensure that the content meets our quality standards. In addition, indivdidual users and groups provide an extra layer of vigilence by adding pathways to their Watchlists. | |
==== How is WikiPathways different from KEGG, Reactome, BioCarta, Pathway Commons and other online pathway resources? ==== | ==== How is WikiPathways different from KEGG, Reactome, BioCarta, Pathway Commons and other online pathway resources? ==== | ||
In addition to viewing and distributing pathways, WikiPathways content is also fully editable directly on the website. This is possible since WikiPathways is based on a wiki platform, similar to Wikipedia. For a complete list of pathway resources, see [http://www.pathguide.org/ Pathguide]. | In addition to viewing and distributing pathways, WikiPathways content is also fully editable directly on the website. This is possible since WikiPathways is based on a wiki platform, similar to Wikipedia. For a complete list of pathway resources, see [http://www.pathguide.org/ Pathguide]. | ||
==== What is GPML? ==== | ==== What is GPML? ==== | ||
| - | GPML is the file format used to store pathway content at WikiPathways. GPML is short for | + | GPML is the file format used to store pathway content at WikiPathways. GPML is short for Graphical Pathway Markup Language and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio. |
== Using WikiPathways == | == Using WikiPathways == | ||
==== How can I use the pathway content from WikiPathways? ==== | ==== How can I use the pathway content from WikiPathways? ==== | ||
In addition to browsing and editing the content online, WikiPathways content can be downloaded in multiple formats for a variety of purposes: | In addition to browsing and editing the content online, WikiPathways content can be downloaded in multiple formats for a variety of purposes: | ||
| - | * Pathways in GPML format can be used in the [http://www.pathvisio.org PathVisio program] for editing. | + | * Pathways in GPML format can be used in the [http://www.pathvisio.org PathVisio program] for editing and [http://www.pathvisio.org/documentation/tutorials/tutorial-2/ data analysis]. |
| - | * Pathways at WikiPathways can be opened in | + | * Pathways at WikiPathways can be opened in [http://www.cytoscape.org Cytoscape] for [[Help:DataVisualizationInCytoscape|Data Visualization]], for [[Help:PathwayStyling|Pathway Styling]] and for general network biology workflows. The [http://apps.cytoscape.org/apps/wikipathways WikiPathways App] provides a direct link between WikiPathways and Cytoscape. |
* Pathways in SVG, PNG and PDF graphical formats can be directly incorporated into presentations and publications. | * Pathways in SVG, PNG and PDF graphical formats can be directly incorporated into presentations and publications. | ||
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* Pathways can be downloaded in PWF format for use with the [http://www.ducciocavalieri.org/bio.htm Eu.Gene tool]. | * Pathways can be downloaded in PWF format for use with the [http://www.ducciocavalieri.org/bio.htm Eu.Gene tool]. | ||
==== How can I download all pathways at WikiPathways? ==== | ==== How can I download all pathways at WikiPathways? ==== | ||
| - | + | We make available monthly versioned releases of our content, in gpml pdf, pwf, svg, png and txt formats. Downloads are available here: [[:Download_Pathways|Batch Download]]. A flat file of all pathways is also available on the batch download page in both html and txt format. | |
==== I created a pathway and made a mistake in it, how can I correct it? ==== | ==== I created a pathway and made a mistake in it, how can I correct it? ==== | ||
| - | You can revert the changes to your pathways under the ''History'' section of the ''Pathway page''. | + | You can revert the changes to your pathways under the '''History''' section of the '''Pathway page'''. |
==== I want to delete a pathway, but there is no option for deleting. ==== | ==== I want to delete a pathway, but there is no option for deleting. ==== | ||
You can delete a pathway only if you are the sole author of the pathway. For details on deleting a pathway, see [[:Help:Deleting_Pathways|Deleting Pathways]]. | You can delete a pathway only if you are the sole author of the pathway. For details on deleting a pathway, see [[:Help:Deleting_Pathways|Deleting Pathways]]. | ||
==== I am working on a pathway for a publication, and I don't want to share it with the rest of the community just yet. Can I still author my pathway at WikiPathways? ==== | ==== I am working on a pathway for a publication, and I don't want to share it with the rest of the community just yet. Can I still author my pathway at WikiPathways? ==== | ||
| - | Yes! WikiPathways supports the notion of private pathways that are visible only to the author and hidden for the rest of the community. You can designate a pathway as private when you first create it. For details on this topic, see the section on [[:Help:Private Pathways| | + | Yes! WikiPathways supports the notion of private pathways that are visible only to the author and hidden for the rest of the community. You can designate a pathway as private when you first create it. For details on this topic, see the section on [[:Help:Private Pathways|'''Private Pathways''']]. |
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==== Where can I report bugs? ==== | ==== Where can I report bugs? ==== | ||
| - | Please report any bugs you encounter and submit any general comments to our | + | Please report any bugs you encounter and submit any general comments directly to our [https://github.com/wikipathways/wikipathways.org/issues issue tracker]. You can also report bugs to our |
| + | [http://groups.google.com/group/wikipathways-dev Google group]. Also check our [[Help:Known problems|known problems]] to see if your problem is a known issue. | ||
<p>[[:Help:Contents|Return to Help Contents]]</p> | <p>[[:Help:Contents|Return to Help Contents]]</p> | ||
<p>[[:Help:Known_problems|Continue to Known Problems]]</p> | <p>[[:Help:Known_problems|Continue to Known Problems]]</p> | ||
Current revision
General
Who, What and Why is WikiPathways?
See About WikiPathways.
Where does the pathway content at WikiPathways come from?
The WikiPathways content is contributed by individual users and groups from the general scientific community. Any registered user at WikiPathways can contribute.
How do I cite pathways from WikiPathways?
Does WikiPathways check the content of contributed pathways for quality and accuracy?
Of course! We perform ongoing quality assurance on all pathways to look for vandalism and to ensure that the content meets our quality standards. In addition, indivdidual users and groups provide an extra layer of vigilence by adding pathways to their Watchlists.
How is WikiPathways different from KEGG, Reactome, BioCarta, Pathway Commons and other online pathway resources?
In addition to viewing and distributing pathways, WikiPathways content is also fully editable directly on the website. This is possible since WikiPathways is based on a wiki platform, similar to Wikipedia. For a complete list of pathway resources, see Pathguide.
What is GPML?
GPML is the file format used to store pathway content at WikiPathways. GPML is short for Graphical Pathway Markup Language and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio.
Using WikiPathways
How can I use the pathway content from WikiPathways?
In addition to browsing and editing the content online, WikiPathways content can be downloaded in multiple formats for a variety of purposes:
- Pathways in GPML format can be used in the PathVisio program for editing and data analysis.
- Pathways at WikiPathways can be opened in Cytoscape for Data Visualization, for Pathway Styling and for general network biology workflows. The WikiPathways App provides a direct link between WikiPathways and Cytoscape.
- Pathways in SVG, PNG and PDF graphical formats can be directly incorporated into presentations and publications.
- Pathways can be downloaded in PWF format for use with the Eu.Gene tool.
How can I download all pathways at WikiPathways?
We make available monthly versioned releases of our content, in gpml pdf, pwf, svg, png and txt formats. Downloads are available here: Batch Download. A flat file of all pathways is also available on the batch download page in both html and txt format.
I created a pathway and made a mistake in it, how can I correct it?
You can revert the changes to your pathways under the History section of the Pathway page.
I want to delete a pathway, but there is no option for deleting.
You can delete a pathway only if you are the sole author of the pathway. For details on deleting a pathway, see Deleting Pathways.
I am working on a pathway for a publication, and I don't want to share it with the rest of the community just yet. Can I still author my pathway at WikiPathways?
Yes! WikiPathways supports the notion of private pathways that are visible only to the author and hidden for the rest of the community. You can designate a pathway as private when you first create it. For details on this topic, see the section on Private Pathways.
Where can I report bugs?
Please report any bugs you encounter and submit any general comments directly to our issue tracker. You can also report bugs to our Google group. Also check our known problems to see if your problem is a known issue.
