Help:Viewing Pathways

Viewing Pathways

Contents of the Pathway Page

Each Pathway Page in WikiPathays has a defined structure:

Graphical representation

The graphical representation of the pathway is located at the top of the Pathway Page. You can click on the image of the pathway to view the SVG version of the image. The pathway image is available for download in SVG and PNG formats. You can also click the Edit pathway link under the pathway image to start editing the pathway.

Description

Directly under the image of the pathway is the Description section, which contains information about the biological process described in the pathway. The Description can be edited by clicking the Edit link to the right of the Description section.

Bibliography

The Bibliography section contains relevant references for the pathway, from literature, textbooks, the web and other sources. The Bibliography can be edited by clicking the Edit link to the right of the Bibliography section.

Categories

Each pathway is categorized into one or several categories, listed under Categories. Clicking on any of the listed categories will open the page listing all pathways in that category. The category assignment can be edited or new categories added by clicking the Edit link to the right of the Categories section.

Download files

The Download files section provides direct downloads of pathway data. The pathway image can be downloaded in svg or png format. The pathway data can be downloaded in GPML format (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. Batch download of pathways in either gpml or svg format is available here: Batch Download

History

The History section provides detailed information about the changes done to the pathway. The History is formatted as a table, showing all changes done to the pathway. The information includes when the change was made, who made the change, and any comments entered by the user. A direct link to the pathway change is available by clicking the view link for each change.

Pathway Info

The Pathway Info contains any information about the pathway from the gpml source, such as Comments and DataNodes. Comments typically include references and relevant links from the gpml. The DataNodes section lists all gene and gene product objects (data nodes) on the pathway in a table format. For each data node, the table includes the name and type of the node, as well as the backpage header (short description) and database reference (gene ID).

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