Difference between revisions of "AmiGO 2 Manual: Linking"

From GO Wiki
Jump to: navigation, search
(Defining incoming searches)
(Defining incoming searches)
Line 42: Line 42:
 
== Defining incoming searches ==
 
== Defining incoming searches ==
  
The initial search may be changed by using the following query string parameters
+
The initial search may be changed by using various parameters. For example:
 +
 
 +
http://amigo.geneontology.org/search/bioentity?fq=annotation_class_list_label:%22Notch%20signaling%20pathway%22
  
 
=== Query (q) ===
 
=== Query (q) ===

Revision as of 17:46, 16 October 2013

Warning: This is a proposal and should not be treated like documentation.

AmiGO 2 now offers a stable set of URLs for linking. This page contains the supported methods for linking into AmiGO 2.

Users may also be interested in some of the more RESTy aspects of AmiGO 2 or the possibility of incorporating the widgets and interfaces used in AmiGO 2 into their own applications.

Terms

The supported format for linking to a GO term is:

http://amigo.geneontology.org/term/GO:XXXXXXX

For example:

http://amigo.geneontology.org/term/GO:0022008

This will resolve to an HTML page. Users may also manipulate the default search of the embedded search pane on a term details page by using the parameters described in the Searches section below.

Gene Products

The supported format for linking to a GO gene product is:

http://amigo.geneontology.org/gene_product/AAA:ZZZZZZZ

For example:

http://amigo.geneontology.org/gene_product/MGI:MGI:2177178

This will resolve to an HTML page. Users may also manipulate the default search of the embedded search pane on a gene product details page by using the parameters described in the Searches section below.

Searches

Base search pages

There are three base search pages. In order, they let you search for ontology terms, gene products and other bioentities, and annotations:

Defining incoming searches

The initial search may be changed by using various parameters. For example:

http://amigo.geneontology.org/search/bioentity?fq=annotation_class_list_label:%22Notch%20signaling%20pathway%22

Query (q)

The string to search for. It should contain no GOlr secrets, wildcards, or any kind of metadata.

Removable filters (fq)

By defining this parameter, you can set an additional initial filter to the search.

Usable fields are any defined in the schema. A partial listing can be found here. This parameter may be defined multiple times.

Sticky filters/pins (sfq)

By defining this parameter, you can set an additional initial filter to the search that cannot be undone within the interface.

Usable fields are any defined in the schema. A partial listing can be found here. This parameter may be defined multiple times.

Other pages

While one can link to other pages in AmiGO 2, they are not formally considered resources and have no publicly defined variations or variables that can be passed through the URL.

These URLs may change at short notice.