Help:Viewing Pathways

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<div class="frontPagePanel yellowBg" style="width:90%;margin:1em;width=100%">
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Each pathway at WikiPathways has its own dedicated '''Pathway Page'''. In addition to the graphical representation of the pathway, they pathway page also includes other information about the pathway.
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<h2 class="frontPagePanel yellowFg">Viewing Pathways</h2>
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<h4>Contents of the ''Pathway Page''</h4>
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<font size=2>Each ''Pathway Page'' in WikiPathays has a defined structure:</font>
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<h5>Graphical representation</h5>
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<font size=2>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 [[:Help:Download|download]] in SVG and PNG formats. You can also click the ''Edit pathway'' link under the pathway image to start [[:Help:Editing Pathways|editing]] the pathway.</font>
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<h5>Description</h5>
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== Graphical representation ==
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<font size=2>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.</font>
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=== Interactive pathway viewer ===
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The graphical representation of the pathway is located at the top of the '''Pathway Page''', as an interactive viewer:
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* You can drag the pathway to pan and scroll to zoom. To reset pan or zoom, click the '''Reset''' button in the lower right corner.
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* Click on any pathway element to display its annotations in a pop-up annotations panel.
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* The annotations panel is organized as a list of data sources and contains link-outs to all cross-references for the xref.
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* To find other pathways with the selected element, click the '''Find other pathways containing...''' link at the bottom of the annotation panel. This initializes a search at WikiPathways for the particular element.
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* Move the annotations panel by click-and-drag on the '''move''' icon in the upper left corner, and use the '''close''' icon in the upper right corner to close the panel.
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<h5>Bibliography</h5>
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=== Data formats ===
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<font size=2>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.</font>
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The pathway data can be downloaded in several formats using the '''Download''' button under the pathway image:
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* PNG, PDF and SVG image formats
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* Gene list (.txt) format
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* GPML format (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. GPML-formatted files can be used in [http://www.pathvisio.org PathVisio] and [http://www.cytoscape.org Cytoscape].
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* PWF format, for use in the [http://www.ducciocavalieri.org/dct.htm| Eu.Gene ] application.
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Batch download of pathways in gpml, svg, and rdf formats is available here: [[Download_Pathways |Batch Download]]. Additional formats are available as [[Daily_Download|Daily Downloads]]. A flat file of all pathways is also available on the batch download page in both html and txt format.
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* BioPAX level 3 format (OWL)
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<h5>Categories</h5>
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== Quality Tags ==
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<font size=2>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.</font>
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'''Quality 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 Quality tags and how to add them, please see the [[:Help:QualityTags|Quality Tags]] page.
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<h5>Download files</h5>
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== Description ==
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<font size=2>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.
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The '''Description''' section contains a description the pathway, entered by the author. The description can be edited by clicking the '''Edit''' link on the right side of the '''Description''' section.
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Batch download of pathways in either gpml or svg format is available here: [http://www.wikipathways.org/index.php/Download_Pathways Batch Download]</font>
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<h5>History</h5>
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== Ontology Tags ==
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<font size=2>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.</font>
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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.
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<h5>Pathway Info</h5>
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<font size=2>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).</font>
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<p><font size=2>[[:Help:Contents|Return to Help Contents]]</font></p>
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== Bibliography ==
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<p><font size=2>[[:Help:Editing Pathways|Continue to Editing Pathways]]</font></p>
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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, PathVisio. In PathVisio, right-click anywhere on the pathway drawing board, or on a pathway element, and choose '''Literature -> Add literature reference'''.
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</div>
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== History ==
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The '''History''' section provides detailed information about the changes made to the pathway. The pathway history is formatted as a table, with information on 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.<br>
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== External references ==
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The '''External references''' section contains lists of annotated genes, proteins, metabolite and pathway nodes, and interactions, that are on the pathway. Annotation on nodes and interactions are displayed in separate tables, titled '''DataNodes''' and '''Annotated Interactions'''. You can click the info icon (see screenshot below) to show a dialog containing links to many different resources that provide detailed information.
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{{Help:XrefPanel}}
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== Highlighting data nodes on pathways ==
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You can specify elements that you want to highlight on a pathway using a url with the following syntax:
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http://www.wikipathways.org/wpi/PathwayWidget.php?id=WP528&label=PEMT&colors=green
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For more information on highlighting of specific nodes on pathways, see the [[PathwayWidget|PathwayWidget]].
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<p>[[:Help:Contents|Return to Help Contents]]</p>
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<p>[[:Help:Editing Pathways|Continue to Editing Pathways]]</p>

Current revision


Each pathway at WikiPathways has its own dedicated Pathway Page. In addition to the graphical representation of the pathway, they pathway page also includes other information about the pathway.

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 and scroll to zoom. To reset pan or zoom, click the Reset button in the lower right corner.
  • Click on any pathway element to display its annotations in a pop-up annotations panel.
  • The annotations panel is organized as a list of data sources and contains link-outs to all cross-references for the xref.
  • To find other pathways with the selected element, click the Find other pathways containing... link at the bottom of the annotation panel. This initializes a search at WikiPathways for the particular element.
  • Move the annotations panel by click-and-drag on the move icon in the upper left corner, and use the close icon in the upper right corner to close the panel.

Data formats

The pathway data can be downloaded in several formats using the Download button under the pathway image:

  • PNG, PDF and SVG image formats
  • Gene list (.txt) format
  • GPML format (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. GPML-formatted files can be used in PathVisio and Cytoscape.
  • PWF format, for use in the Eu.Gene application.

Batch download of pathways in gpml, svg, and rdf formats is available here: Batch Download. Additional formats are available as Daily Downloads. A flat file of all pathways is also available on the batch download page in both html and txt format.

  • BioPAX level 3 format (OWL)

Quality Tags

Quality 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 Quality tags and how to add them, please see the Quality 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 on the right side 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, PathVisio. In PathVisio, right-click anywhere on the pathway drawing board, or on a pathway element, and choose Literature -> Add literature reference.

History

The History section provides detailed information about the changes made to the pathway. The pathway history is formatted as a table, with information on 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.

External references

The External references section contains lists of annotated genes, proteins, metabolite and pathway nodes, and interactions, that are on the pathway. Annotation on nodes and interactions are displayed in separate tables, titled DataNodes and Annotated Interactions. You can click the info icon (see screenshot below) to show a dialog containing links to many different resources that provide detailed information.

Click on the info icon in the external references table to see links to detailed information about the gene, protein or metabolite.
Click on the info icon in the external references table to see links to detailed information about the gene, protein or metabolite.

Highlighting data nodes on pathways

You can specify elements that you want to highlight on a pathway using a url with the following syntax:

http://www.wikipathways.org/wpi/PathwayWidget.php?id=WP528&label=PEMT&colors=green

For more information on highlighting of specific nodes on pathways, see the PathwayWidget.

Return to Help Contents

Continue to Editing Pathways

Retrieved from "https://classic.wikipathways.org/index.php/Help:Viewing_Pathways"
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