AmiGO 2 Web Services

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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
  • 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.

Clients

See also