Difference between revisions of "AmiGO Manual: Overview"

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= Introduction =
 
= Introduction =
  
AmiGO is a web based application which allows the user to browse, query, and visualize data from the Gene Ontology, or any ontology in OBO format. AmiGO can be accessed [http://amigo.geneontology.org online]. AmiGO is open source software and can be downloaded and installed as part of the go-dev CVS repository from the Gene Ontology SourceForge.net page.
+
AmiGO is a web based application which allows the user to browse, query, and visualize data from the Gene Ontology, or any ontology in OBO format. AmiGO can be accessed [http://amigo.geneontology.org online] or deployed locally.
 +
 
 +
= Availability =
 +
 
 +
AmiGO is open source software and can be downloaded and installed as part of the go-dev CVS repository from the Gene Ontology SourceForge.net page.
  
 
= Browser Compatibility =
 
= Browser Compatibility =
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The Main Window
 
The Main Window
  
= Layout =
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The HTML page you view may vary slightly in details.
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= Database Filtering =
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The form on the lower left hand side of the screen labeled "Gene Product Filters" allows you to set filters for which gene products you'd like to see.
 +
 
 +
You can choose to view only gene products from a given species, annotated by a specific organization, or associated by a specific evidence code. In any given field, you may select more than one value by selecting one, then holding down your control key and selecting others. To instate the filters that you have selected, click the "Set Filters" button.
 +
 
 +
When filters are turned on, this will be reflected in the gene product counts in the treeview.
 +
 
 +
Filters will also change the gene product associations that are displayed in the detailed term view.
 +
 
 +
To reset the filters to their original state, click the "Reset Filters" button below the "Set Filters" button.
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= File Formats =
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Clicking the "XML" or "Flat File" links will bring you to an XML or GO Flat File representation of the tree that is currently selected.
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Clicking the "Permalink" link will bring you to a URL that you can bookmark to save the currently selected tree. AmiGO keeps track of the tree you build with user sessions. If your session is inactive for more than two hours, your session will be lost along with a tree you've built. The permalink can save the tree indefinitely. Just add it to your bookmarks.
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== XML ==
  
When you go to the URL of an AmiGO instantiation, you have the following options (roughly from top to bottom):
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== Flat ==
  
* Returning to the initial tree state (go to the top level of the ontology)
 
* Viewing the current tree as a graph
 
* Browsing the ontology using the tree browser
 
* Searching the ontology or associated gene products by keywords and phrases, going to the advanced query page, or querying by sequence using GOst (the Gene Ontology Blast server)
 
* Filtering which gene products will be displayed
 
* Getting the current page in a different format
 
* Going to a related site
 
  
 
[[Category:AmiGO]]
 
[[Category:AmiGO]]
 
[[Category:AmiGO_Manual]]
 
[[Category:AmiGO_Manual]]

Revision as of 19:19, 7 November 2007

Introduction

AmiGO is a web based application which allows the user to browse, query, and visualize data from the Gene Ontology, or any ontology in OBO format. AmiGO can be accessed online or deployed locally.

Availability

AmiGO is open source software and can be downloaded and installed as part of the go-dev CVS repository from the Gene Ontology SourceForge.net page.

Browser Compatibility

AmiGO is compatible with most modern operating system/browser combinations with good CSS support, including:

  • Firefox on Linux, Windows, and Mac OS X.
  • Mozilla/Netscape 6 on Linux, Windows, and Mac OS X.
  • IE on Windows, but NOT on Mac OS X. IE on Mac OS X does support CSS standards.
  • Safari on Mac OS X.
  • Konqueror on Linux.
  • Opera on Linux, Windows, and Mac OS X.

In order to use all of the functionality available in this version of AmiGO, we recommend that cookies are allowed and JavaScript is turned on. The Main Window

The HTML page you view may vary slightly in details.

Database Filtering

The form on the lower left hand side of the screen labeled "Gene Product Filters" allows you to set filters for which gene products you'd like to see.

You can choose to view only gene products from a given species, annotated by a specific organization, or associated by a specific evidence code. In any given field, you may select more than one value by selecting one, then holding down your control key and selecting others. To instate the filters that you have selected, click the "Set Filters" button.

When filters are turned on, this will be reflected in the gene product counts in the treeview.

Filters will also change the gene product associations that are displayed in the detailed term view.

To reset the filters to their original state, click the "Reset Filters" button below the "Set Filters" button.

File Formats

Clicking the "XML" or "Flat File" links will bring you to an XML or GO Flat File representation of the tree that is currently selected.

Clicking the "Permalink" link will bring you to a URL that you can bookmark to save the currently selected tree. AmiGO keeps track of the tree you build with user sessions. If your session is inactive for more than two hours, your session will be lost along with a tree you've built. The permalink can save the tree indefinitely. Just add it to your bookmarks.

XML

Flat