AmiGO 2 Web Services
This page has been deprecated.
Purpose
To provide the services required to drive a client application such as AmiGO 2.
The services include
- fetching gene / gene product metadata
- protein family
- annotations
- symbol, synonyms, etc
- fetching annotations for an ontology class (performing appropriate inference)
- Filtering by arbitrary facets
- species
- protein family
- co-annotated term
- source
- Filtering by arbitrary facets
- fetching annotations for a given publication (with similar facets)
- fetching gene counts for the above
The services may make use of or delegate to Ontology Web Services
Maintainers
- Seth
Implementation
At this time AmiGO 2 Web Services are provided primarily by a Solr server
Starting a server
TODO: see AmiGO 2 documentation.
Examples
Contacting the Solr backend to AmiGO is probably best illustrated through the wiki example queries page and the experimental GOOSE:
http://wiki.geneontology.org/index.php/Example_Solr_Queries http://amigo2.berkeleybop.org/cgi-bin/amigo2/goose
Also, simple tests and scripts are described in the AmiGO test directory:
http://geneontology.svn.sourceforge.net/viewvc/geneontology/AmiGO/trunk/perl/lib/t/
Or:
svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/AmiGO/trunk AmiGO
API Documentation
TODO: See AmiGO 2 API documentation.
Authentication
None--AmiGO 2 should be stateless. Offending queries should be taken care of by proxy filters.