Help:Viewing Pathways

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== Contents of the Pathway Page ==
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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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=== Graphical representation ===
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== Graphical representation ==
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==== Interactive pathway viewer ====
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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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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, scroll to zoom and click on a gene box to see the backpage.
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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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* 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)
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* Click on any pathway element to display its annotations in a pop-up annotations panel.
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* Selecting an element in the pathway displays its backpage in the left side 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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* The back page is organized into sections for each system 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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* 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.  
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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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* You can specify elements that should be highlighted in a url with the following syntax:
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[http://www.google.com/url?sa=D&q=http://test.wikipathways.org/index.php%3Ftitle%3DPathway:WP4%26label%3DCRH%26xref%3D8525,Entrez%2520Gene&usg=AFQjCNEH0y66C17ypUnEoftni-SpTWoPWA http://www.google.com/url?sa=D&q=http://test.wikipathways.org/index.php%3Ftitle%3DPathway:WP4%26label%3DCRH%26xref%3D8525,Entrez%2520Gene&usg=AFQjCNEH0y66C17ypUnEoftni-SpTWoPWA]
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* 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.
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=== Data formats ===
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* The url parameters for highlighting can be "label" (to match by text label) or "xref" (to match by xref, format: id,datasource).
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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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* You can specify multiple parameters to highlight multiple items. You can also specify an array of highlight colors using the color parameter:
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* PNG, PDF and SVG image formats
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[http://www.google.com/url?sa=D&q=http://wikipathways.org/index.php%3Ftitle%3DPathway:WP4%26label%3DCRH%26xref%3D8525,Entrez%2520Gene%26label%3Dinvalid%26label%3DDAG%26colors%3Dred,orange,greenusg=AFQjCNEGjvUaWX_Xd2EfGJzM_X5xG6Prng http://www.google.com/url?sa=D&q=http://wikipathways.org/index.php%3Ftitle%3DPathway:WP4%26label%3DCRH%26xref%3D8525,Entrez%2520Gene%26label%3Dinvalid%26label%3DDAG%26colors%3Dred,orange,greenusg=AFQjCNEGjvUaWX_Xd2EfGJzM_X5xG6Prng]
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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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* 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.  
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== Quality Tags ==
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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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==== Data formats ====
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== Description ==
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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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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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* PNG and PDF 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, for use in [[www.pathvisio.org|PathVisio]].
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* MAPP format, compatible with the GenMAPP program. ''Note:'' This export only works on PCs.
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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, pdf, pwf, svg, png and txt formats is available here: [[Download_Pathways |Batch Download]]. A flat file of all pathways is also available on the batch download page in both html and txt format.
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<br>Too edit the pathway, click the ''Edit pathway'' link under the pathway image to start [[:Help:Editing Pathways|editing]] the pathway. You can also use the ''Download'' button to open the pathway in [http://www.cytoscape.org Cytoscape].
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=== Curation Tags ===
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== Ontology Tags ==
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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.
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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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=== Description ===
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== Bibliography ==
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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 to the right of the ''Description'' section.
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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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=== Ontology Tags ===
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== History ==
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The ''Ontology Tags'' section contains any ontology tags added to the pathway, and an interface for adding ontology tags. To add ontology tags, click the ''Add Ontology tags!'' link, which will open two tools for finding and adding ontology tags: a search interface and browsable trees for the supported ontologies. To search for a term, simply begin typing in the ''Search'' field. Pick a term from the results and click the ''Add'' button (green check mark) to add the term. Alternatively, find a term from the browsable ontology trees, select it and click the ''Add'' button. You can delete any ontology term from the pathway by selecting it and clicking the ''Remove'' button (red x). To learn more about a particular term, click the ''View more info on BioPortal!'' button (blue i).
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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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=== Bibliography ===
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== External references ==
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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. 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''.
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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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=== Categories ===
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{{Help:XrefPanel}}
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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.
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=== History ===
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== Highlighting data nodes on pathways ==
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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.<br>
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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.
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=== External references ===
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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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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.
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{{Help:XrefPanel}}
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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]].
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Editing Pathways|Continue to Editing Pathways]]</p>
<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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