Help:Guidelines
From WikiPathways
When creating or editing pathway information at WikiPathways, please keep the following guidelines in mind. These guidelines aim to promote consistency, accuracy and stability for the pathway content. By following these guidelines, you will help to maintain the highest possible quality of pathway information and to promote the success of community-based curation.
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Editing Pathways
Pathway annotation
Properly annotating pathways is essential to maintaining a high quality of curation and content at WikiPathways. Annotation includes assigning the pathway to one or more categories, defining each node with a database ID and adding a description for each pathway.
References to literature
Citing peer-reviewed publications is a quality standard in the scientific community and WikiPathways is no exception. We strongly encourage including relevant literature references both at the pathway level (Bibliography) and for individual interactions in pathways.
References to other sources
For all evidence from sources other than the scientific literature, please cite the source in the Bibliography section.
Representing complexes
Representing molecular complexes can be done in a variety of styles. We recommend using a stacked representation whenever possible, which can easily be accomplished with the “Stack genes” feature in the editor Toolbar.
Representing pathway flow
To represent a flow of cascading events or direction in a pathway, arrange the cascade top to bottom whenever possible.
Pathway boundaries
The scope of a pathway can vary depending on the process it describes. WikiPathways does not define a minimum or maximum number of entities or reactions required for each pathway. However, very large pathways may adversely impact the readability. Please keep this in mind when editing pathways. If there are uncertainties about the boundaries of the particular pathway you are editing please browse related pathways at WikiPathways to get an idea of appropriate pathway boundaries.
Making major edits
When making major edits (deletions in particular) to an existing pathway not created by you, first suggest the changes on the pathway discussion page, as a courtesy to the original author. Starting a discussion about the proposed changes is a productive way of community editing.
Content forking
If you plan to add tissue- or state-specific information to a pathway describing a general process, please create a new pathway and copy the relevant content from the original pathway, rather than making edits directly to the original pathway. When naming the new related pathway, it is appropriate to use the name of the original pathway, with a suffix or addition explaining the edits. This will ensure that pathway names are not duplicated and will help in organizing related pathway content.
Creating Pathways
Pathway naming
Pathways should have a descriptive name, like “Cholesterol Biosynthesis”. Do not name your pathway after your favorite pet or something else that is not descriptive of the process represented in the pathway. Do not include your name or username in the pathway name. If your pathway is specific to a particular state or tissue, this may be included in the name. If the pathway is based on content from an external source, the name of the source may be included in the name.
Adding author information
When creating a new pathway, add your name and contact email to the pathway. This will ensure that your information will be linked to the pathway even if it is downloaded and used in external applications.
References to other sources
For all evidence from sources other than the scientific literature, please cite the source in the Bibliography section.
Enforceable Policies
- See policies page for list of rules regarding conduct, content and contributions at WikiPathways.
