GBrowse2 REST API
From GMOD
This article describes the GBrowse2 REST API.
For the main GBrowse 2.0 HOWTO article, see: GBrowse 2.0 HOWTO.
Contents
The GBrowse2 REST API
Getting Information from the Server
You can get a list of public data sources from the GBrowse server, and interrogate each one for a list and description of the tracks it supports.
Getting a List of Sources
Invoke gbrowse with "action=list":
http://somewhere.com/gb2/gbrowse/?action=list
This will return a plain text tab-delimited document like the following:
# Name Description Species TaxID CoordinateType BuildAuthority BuildVersion BuildURL elegans C. elegans genes Caenorhabditis elegans 6239 Chromosome WS 180 http://www.dasregistry.org/coordsys/CS_DS109 yeast Yeast chromosomes 1+2 Saccharomyces cerevisiae 4932 Chromosome SGD 1 http://www.dasregistry.org/coordsys/CS_DS69 bamtest BAM/SAM Test homo_36 Human NCI 36i coordinates volvox Volvox Tutorial Database
Each row is a data source. The fields are:
- Name
- Data source name to use in subsequent calls to gbrowse.
- Description
- Human readable text describing the data source
- Species (optional)
- Human readable species name.
- TaxID (optional)
- NCBI taxon ID.
- CoordinateType (optional)
- Description of the type of coordinate, such as "Chromosome" or "Contig"
- BuildAuthority (optional)
- The group that maintains the coordinate system. See http://www.dasregistry.org/help_coordsys.jsp for a list of codes.
- BuildVersion (optional)
- Version of the build.
- BuildURL (optional)
- URL that will provide information about the build (can also be used as a unique ID for the build).
These fields are derived from GBrowse.conf and the "metadata" option in the configuration file for the data source.
Generating Static Images
To generate static images of a region in PNG, SVG or PDF format, invoke gbrowse_img:
$HOST/gb2/gbrowse_img/SOURCE/?ARGS
- SOURCE
- The data source, such as