Difference between revisions of "AmiGO Manual: Overview"

From GO Wiki
Jump to: navigation, search
Line 24: Line 24:
  
 
= Components =
 
= Components =
 +
 +
AmiGO is made up of several interacting CGI scripts that work together to create a coherent whole.
  
 
== Major Components ==
 
== 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.
  
 
*[[AmiGO_Manual:_Main_Page | MainPage]]
 
*[[AmiGO_Manual:_Main_Page | MainPage]]
Line 35: Line 39:
  
 
== Minor Components ==
 
== Minor Components ==
 +
 +
AmiGO's minor components are those that have specialized output in result of some kind of action.
  
 
*[[AmiGO_Manual:_Term_Details | Term Details]]
 
*[[AmiGO_Manual:_Term_Details | Term Details]]

Revision as of 10:52, 18 December 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.

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