Difference between revisions of "AmiGO 2 Manual: Overview"

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AmiGO 2 is a project to create the next 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 is a project to create the next 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.


It can be accessed online at the main installation or deployed locally.
The most current installation of this software is at the [http://amigo.geneontology.org public] site.


The current installations of this software are :
While we are getting the new documentation sorted out, plase take a look at the pages in [[:Category:AmiGO_2_Manual]].


* [http://amigo.berkeleybop.org Public beta]
More technical information about AmiGO 2 can be found [[AmiGO_2 | here]].
* [http://nakama.berkeleybop.org Public development]


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


While we are getting the new documentation sorted out, plase take a look at the pages in the [[:Category:AmiGO_2_Manual]].
The current installation docs can be found [[AmiGO_2_Manual:_Installation | here]].
 
= Components =
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== Home ==
 
[[AmiGO_2_Manual:_Home | Home]] allows simple quick searches using autocomplete and the new [[GOlr]] backend.
 
== Search ==
 
[[AmiGO_2_Manual:_Search | Search]] interactively searches and filters the GO data as you type. Also allows you to use a powerful search syntax (including boolean operators).
 
[[AmiGO_2_Manual:_Search_Examples | Examples workflows]] are also documented.
 
== Term Page ==
 
[[AmiGO_2_Manual:_Term_Page | Term]] pages contain common information about GO terms and their annotations.
 
== Gene Product Page ==
 
[[AmiGO_2_Manual:_Gene_Product_Page | Gene product]] pages contain common information about gene product and their annotations.
 
== Grebe ==
 
The [[AmiGO_2_Manual:_Grebe | Grebe]] search wizard can be used to quickly answer common questions using a fill-in-the-blank approach.
 
== Visualize ==
 
[[AmiGO_2_Manual:_Visualize | Visualize]]s the GO graph. Freely make your own ontology graph, including label and color changes. Please see the documentation for more details.
 
== GOOSE ==
 
[[AmiGO_2_Manual:_GOOSE | GOOSE]] is the GO Online SQL Environment. Using this, users may query the GO database directly using SQL, or edit one of the already made templates.  





Latest revision as of 17:07, 27 July 2016

Introduction

AmiGO 2 is a project to create the next 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.

The most current installation of this software is at the public site.

While we are getting the new documentation sorted out, plase take a look at the pages in Category:AmiGO_2_Manual.

More technical information about AmiGO 2 can be found here.

Installation

The current installation docs can be found here.

Components

Home

Home allows simple quick searches using autocomplete and the new GOlr backend.

Search

Search interactively searches and filters the GO data as you type. Also allows you to use a powerful search syntax (including boolean operators).

Examples workflows are also documented.

Term Page

Term pages contain common information about GO terms and their annotations.

Gene Product Page

Gene product pages contain common information about gene product and their annotations.

Grebe

The Grebe search wizard can be used to quickly answer common questions using a fill-in-the-blank approach.

Visualize

Visualizes the GO graph. Freely make your own ontology graph, including label and color changes. Please see the documentation for more details.

GOOSE

GOOSE is the GO Online SQL Environment. Using this, users may query the GO database directly using SQL, or edit one of the already made templates.