Difference between revisions of "AmiGO Manual: Overview"

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It can be accessed [http://amigo.geneontology.org online] at the main installation or deployed locally.
 
It can be accessed [http://amigo.geneontology.org online] at the main installation or deployed locally.
  
To learn more about what the Gene Ontology is and what it does, please <a href="http://geneontology.org/GO.doc.shtml" title="GO introductory documentation">read the introductory documentation</a>.
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To learn more about what the Gene Ontology is and what it does, please read the [http://geneontology.org/GO.doc.shtml introductory documentation].
  
 
== What can I do using AmiGO? ==
 
== What can I do using AmiGO? ==

Revision as of 11:13, 9 February 2009

Introduction

AmiGO is the official web-based set tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms.

It can be accessed online at the main installation or deployed locally.

To learn more about what the Gene Ontology is and what it does, please read the introductory documentation.

What can I do using AmiGO?

  • <a href="help-gp_search.shtml" title="search for a gene or gene product">search for a gene or gene product</a>, or a list of gene or gene products, and view the GO term associations
  • perform a <a href="help-gost_query.shtml" title="search by sequence using BLAST">sequence identity BLAST search</a> and view the GO term associations for the genes or proteins returned
  • <a href="help-term_search.shtml" title="search for a GO terms">search for GO terms</a> and view the genes or gene products they are annotated to
  • <a href="help-browse.shtml" title="browse the ontology">browse the GO ontology</a> and view terms
  • slimmer: TODO
  • term enrichment: TODO
  • GOOSE: TODO

Availability

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

For full installation instructions, please see the AmiGO_Manual:_Installation wiki pages.

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.

Components

AmiGO is made up of several interacting CGI scripts that work together to create a coherent whole.

Major Components

AmiGO's major components are the ones that are listed at the top of ever page; these are the ones where your work will usually begin.

Minor Components

AmiGO's minor components are those that have specialized output in result of some kind of action.

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