Difference between revisions of "AmiGO 2 Manual: Linking"

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There are three base search pages. In order, they let you search for ontology terms, gene products and other bioentities, and annotations:
 
There are three base search pages. In order, they let you search for ontology terms, gene products and other bioentities, and annotations:
  
* http://amigo.geneontology.org/search/ontology
+
* http://amigo.geneontology.org/amigo/search/ontology
* http://amigo.geneontology.org/search/bioentity
+
* http://amigo.geneontology.org/amigo/search/bioentity
* http://amigo.geneontology.org/search/annotation
+
* http://amigo.geneontology.org/amigo/search/annotation
  
 
== Embedded search ==
 
== Embedded search ==
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Adding a negative to an item (e.g. term=-GO:0060579) will add a negative filter.
 
Adding a negative to an item (e.g. term=-GO:0060579) will add a negative filter.
 +
 +
/amigo/search/annotation?bioentity=FOO:0000001&-term=GO:0060579&term=GO:0008150
  
 
== BETA Expert API ==
 
== BETA Expert API ==
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The initial search may be changed by using various parameters. For example,
 
The initial search may be changed by using various parameters. For example,
  
<pre>http://amigo.geneontology.org/search/bioentity?fq=annotation_class_list_label:%22Notch%20signaling%20pathway%22</pre>
+
<pre>http://amigo.geneontology.org/amigo/search/bioentity?fq=annotation_class_list_label:%22Notch%20signaling%20pathway%22</pre>
  
 
is a bioentity search that returns only bioentities that have "Notch signalling pathway" in its term association ancestors.
 
is a bioentity search that returns only bioentities that have "Notch signalling pathway" in its term association ancestors.
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Or
 
Or
  
<pre>http://amigo.geneontology.org/search/annotation?q=nucleus&fq=assigned_by:%22MGI%22</pre>
+
<pre>http://amigo.geneontology.org/amigo/search/annotation?q=nucleus&fq=assigned_by:%22MGI%22</pre>
  
 
which searches for annotations that were assigned by MGI that are somehow are connected to the string "nucleus".
 
which searches for annotations that were assigned by MGI that are somehow are connected to the string "nucleus".

Latest revision as of 15:27, 3 April 2017

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/amigo/term/GO:XXXXXXX

For example:

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

This will resolve to an HTML page.

Embedded search

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/amigo/gene_product/AAA:ZZZZZZZ

For example:

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

This will resolve to an HTML page.

Embedded search

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:

Embedded search

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.

Defining incoming searches

Public API

You can add one or more of these to the URL:

  • term (as DB:INTERNAL)
  • taxon (as NCBI taxon ID)
  • bioentity (as DB:INTERNAL)
  • aspect (P, F, or C)
  • evidence (ECO:ID)

These will add filters to the embedded search pane on the given pages (pretty much the whole page in the case of searches).

For example:

/amigo/bioentity/FOO:0000001?term=GO:0060579

would add a positive filter for GO:0060579 in annotation_Class for the embedded search on the page for bioentity FOO:0000001.

Adding a negative to an item (e.g. term=-GO:0060579) will add a negative filter.

/amigo/search/annotation?bioentity=FOO:0000001&-term=GO:0060579&term=GO:0008150

BETA Expert API

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

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

is a bioentity search that returns only bioentities that have "Notch signalling pathway" in its term association ancestors.

Or

http://amigo.geneontology.org/amigo/search/annotation?q=nucleus&fq=assigned_by:%22MGI%22

which searches for annotations that were assigned by MGI that are somehow are connected to the string "nucleus".

The exact nature and use of the parameters are explained below.

q

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

An example of this argument could be:

q=pigment

fq

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

An example of this argument could be:

fq=assigned_by:%22MGI%22

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

sfq

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

An example of this argument could be:

sfq=assigned_by:%22MGI%22

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

Other pages (not necessarily stable)

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.