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] or deployed locally.
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AmiGO is the official web-based set of 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.
 +
 
 +
[[AmiGO 2]] information can be found [[AmiGO_2 | here]].
 +
 
 +
It can be accessed [http://amigo.geneontology.org online] at the main installation or [[AmiGO_Manual:_Installation | deployed locally]].
 +
 
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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].
 +
 
 +
There is also a [[AmiGO_Manual:_FAQ | FAQ]] for questions that are commonly asked, but might not have a home somewhere else.
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== What can I do using AmiGO? ==
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* [[AmiGO_Manual:_Gene_Product_Search | search for a gene or gene product]], or a list of gene or gene products, and view the GO term associations
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* perform a [[AmiGO_Manual:_BLAST | sequence identity BLAST search]] and view the GO term associations for the genes or proteins returned
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* [[AmiGO_Manual:_Term_Search | search for GO terms]] and view the genes or gene products they are annotated to
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* [[AmiGO_Manual:_Browse | browse the GO ontology]] and view terms
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* the [[AmiGO_Manual:_Slimmer | slimmer tool]] can be used to map the granular annotations of the query set of genes to one or more high-level
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* [[AmiGO_Manual:_Term_Enrichment | term enrichment tool]] is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
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* [[AmiGO_Manual:_GOOSE | GOOSE]] is for advanced users who want to run custom SQL queries against the GO database.
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== What data does AmiGO use? ==
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Unless otherwise noted, the public installation of AmiGO (http://amigo.geneontology.org) uses the "seqdb" version of the database, which includes all manual gene product annotations and electronic annotations (IEA) from all databases other than UniProtKB.
 +
 
 +
For more detail on this subject, please see the GO database documentation [http://geneontology.org/GO.database.shtml#dbtypes here].
  
 
= Availability =
 
= 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.
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AmiGO is an open source software project and can be downloaded and installed as part of the [http://geneontology.cvs.sourceforge.net/geneontology/ go-dev] CVS repository from the Gene Ontology  
 +
[https://sourceforge.net/projects/geneontology SourceForge.net page].
 +
 
 +
For full installation instructions, please see the [[AmiGO_Manual:_Installation | installation]] wiki pages.
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For information on maintenance and upkeep, please see the [[AmiGO_Manual:_Maintenance | maintenance]] wiki pages.
  
 
= Browser Compatibility =
 
= Browser Compatibility =
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= Components =
 
= Components =
  
== Major Components ==
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AmiGO is made up of several interacting programs that work together to create a coherent whole.
  
*[[AmiGO_Manual:_Main_Page | MainPage]]
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== Main components ==
 +
 
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The most used components
 +
 
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AmiGO's major components are the ones that are listed at the top of every page; these are the ones where your work will usually begin.
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 +
*[[AmiGO_Manual:_Main_Page | Main Page]]
 
*[[AmiGO_Manual:_Browse | Browse]]
 
*[[AmiGO_Manual:_Browse | Browse]]
*[[AmiGO_Manual:_BLAST | BLAST]]
 
 
*[[AmiGO_Manual:_Search | Search]]
 
*[[AmiGO_Manual:_Search | Search]]
*[[AmiGO_Manual:_Slimmer | Slimmer]]
 
*[[AmiGO_Manual:_Term_Enrichment | Term Enrichment]]
 
  
== Minor Components ==
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=== Pages from the main components ===
  
 
*[[AmiGO_Manual:_Term_Details | Term Details]]
 
*[[AmiGO_Manual:_Term_Details | Term Details]]
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*[[AmiGO_Manual:_Bar_Chart | Bar Chart]]
 
*[[AmiGO_Manual:_Bar_Chart | Bar Chart]]
 
*[[AmiGO_Manual:_GraphViz | GraphViz]]
 
*[[AmiGO_Manual:_GraphViz | GraphViz]]
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*[[AmiGO_Manual:_RG_Graphical_View | Reference Genome Graphical View]]
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== Other Components ==
 +
 +
AmiGO's other components are those that have specialized output in result of some kind of action.
 +
 +
*[[AmiGO_Manual:_BLAST | BLAST]]
 +
*[[AmiGO_Manual:_Slimmer | Slimmer]]
 +
*[[AmiGO_Manual:_Term_Enrichment | Term Enrichment]]
 +
*[[AmiGO_Manual:_GOOSE | GOOSE]]
  
= Database Filtering =
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=Versions=
  
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.
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The [[AmiGO_1_8 | current]] stable version is [[AmiGO_1_8 | 1.8]] (tagged amigo_1_8). It is available for direct download at [http://sourceforge.net/project/showfiles.php?group_id=36855 SourceForge.net ].
  
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.
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Information on the [[AmiGO_2 | upcoming]] version is at the [[AmiGO_2 | 2.0]] site.
  
When filters are turned on, this will be reflected in the gene product counts in the treeview.
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Version numbers are as follows:
  
Filters will also change the gene product associations that are displayed in the detailed term view.
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A.B.C.D
  
To reset the filters to their original state, click the "Reset Filters" button below the "Set Filters" button.
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A = Major release
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B = Standard release (general testing)
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C = Bugfix release (test of fixes)
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D = Text fix release (minor changes that don't need testing)
  
= File Formats =
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The last two numbers are mostly for internal use.
  
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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= Articles =
  
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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[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2639003 Application note] in Bioinformatics.
  
== XML ==
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= Working Group Information =
  
== Flat ==
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[[AmiGO_Hub | AmiGO Hub Working Group]]
  
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[[Web_Presence_Working_Group | Web Presence Working Group]]
  
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[[Category:AmiGO_Manual]]
 
[[Category:AmiGO]]
 
[[Category:AmiGO]]
[[Category:AmiGO_Manual]]
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[[Category:Software]]

Latest revision as of 10:59, 16 May 2014

Introduction

AmiGO is the official web-based set of 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.

AmiGO 2 information can be found here.

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.

There is also a FAQ for questions that are commonly asked, but might not have a home somewhere else.

What can I do using AmiGO?

What data does AmiGO use?

Unless otherwise noted, the public installation of AmiGO (http://amigo.geneontology.org) uses the "seqdb" version of the database, which includes all manual gene product annotations and electronic annotations (IEA) from all databases other than UniProtKB.

For more detail on this subject, please see the GO database documentation here.

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 installation wiki pages.

For information on maintenance and upkeep, please see the maintenance 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 programs that work together to create a coherent whole.

Main components

The most used components

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

Pages from the main components

Other Components

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

Versions

The current stable version is 1.8 (tagged amigo_1_8). It is available for direct download at SourceForge.net .

Information on the upcoming version is at the 2.0 site.

Version numbers are as follows:

A.B.C.D
A = Major release
B = Standard release (general testing)
C = Bugfix release (test of fixes)
D = Text fix release (minor changes that don't need testing)

The last two numbers are mostly for internal use.

Articles

Application note in Bioinformatics.

Working Group Information

AmiGO Hub Working Group

Web Presence Working Group