Help:Viewing Pathways
From WikiPathways
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* PNG and PDF image formats | * PNG and PDF image formats | ||
* Gene list (.txt) format | * Gene list (.txt) format | ||
| - | * GPML format (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content, for use in [ | + | * GPML format (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content, for use in [http://www.pathvisio.org PathVisio]. |
* MAPP format, compatible with the GenMAPP program. ''Note:'' This export only works on PCs. | * MAPP format, compatible with the GenMAPP program. ''Note:'' This export only works on PCs. | ||
* PWF format, for use in the [http://www.ducciocavalieri.org/dct.htm| Eu.Gene ] application. | * PWF format, for use in the [http://www.ducciocavalieri.org/dct.htm| Eu.Gene ] application. | ||
Revision as of 02:58, 17 July 2013
Contents |
Contents of the Pathway Page
Graphical representation
Interactive pathway viewer
The graphical representation of the pathway is located at the top of the Pathway Page, as an interactive viewer:
- You can drag the pathway to pan, scroll to zoom and click on a gene box to see the backpage.
- Use the search box to find elements in the pathway. Search hits are highlighted in yellow while typing and clicking enter will focus the view on the relevant element and highlight it (The search box can be hidden by clicking the magnifier icon next to it)
- Selecting an element in the pathway displays its backpage in the left side panel.
- The back page is organized into sections for each system and contains link-outs to all cross-references for the xref
- To find other pathways with the selected element, click the "Find pathways with..." link at the top of the back page. This initializes a search at WikiPathways for the element.
- You can specify elements that should be highlighted in a url with the following syntax:
- Highlights are organized into a box on the left with an entry for each highlight. Clicking one of the highlights focuses the viewer on the corresponding element on the pathway.
- The url parameters for highlighting can be "label" (to match by text label) or "xref" (to match by xref, format: id,datasource).
- You can specify multiple parameters to highlight multiple items. You can also specify an array of highlight colors using the color parameter:
- Labels or xrefs that can't be located on the pathway are shown in gray ("label=invalid" in the example above). Id mapping is not performed for xrefs, only exact matches are highlighted.
Data formats
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 Curation Tags page.
Description
The Description section contains a description the pathway, entered by the author. The Description can be edited by clicking the Edit link to the right of the Description section.
Ontology Tags
The Ontology Tags section contains any ontology tags added to the pathway, and an interface for adding ontology tags. Ontology tags can be located through a search interface and browsable trees for the supported ontologies.
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. Clicking on any highlighted part will bring up details of the difference between the two versions.
External references
The External references section contain a list of annotated genes, proteins, metabolite and pathway nodes that are on the pathway. You can click the info icon (see screenshot below) to show a dialog containing links to many different resources that provide detailed information.
