Help:Viewing Pathways
From WikiPathways
Contents |
Contents of the Pathway Page
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 and download the SVG version of the image.
The pathway data can be downloaded in several formats using the Download button under the pathway image:
- PNG and PDF image formats
- Gene list (.txt) format
- GPML format (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content, for use in PathVisio.
- MAPP format, compatible with the GenMAPP program. Note: This export only works on PCs.
- PWF format, for use in the Eu.Gene application.
Batch download of pathways in gpml, pdf, pwf, svg, png and txt formats is available here: Batch Download. A flat file of all pathways is also available on the batch download page in both html and txt format.
Too edit the pathway, click the Edit pathway link under the pathway image to start editing the pathway. You can also use the Download button to open the pathway in Cytoscape.
Curation Tags
Curation tags are a set of tags that can be added to a pathway to notify the author and community about the state of the pathway. For example, you could tag a pathway that isn't annotated properly or tag your own pathway as work in progress. For more information on Curation tags and how to add them, please see the [:Help:CurationTags|Curation Tags] page.
Description
The Description section contains a description the pathway, entered by the auhtor. 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 in the pathway editor. Click on the Edit pathway button below the pathway image to start the editor. Right-click anywhere on the pathway drawing board and choose Literature>Add literature reference.
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.
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. A revert link is also available for reverting the pathway to a previous version.
Any two versions of a pathway can be compared visually in the Pathway Difference Viewer. To do this, select two versions of the pathway in the History table by clicking the radio buttons in the Compare column, then click the Compare selected versions button. In the difference viewer, both versions of the pathway will open with the differing parts highlighted in yellow.
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).
