Difference between revisions of "AmiGO Manual: Overview"

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Revision as of 18:37, 7 November 2007


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. 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

When you go to the URL of an AmiGO instantiation, you have the following options (roughly from top to bottom):

  • 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

The HTML page you view may vary slightly in details.