GBrowse2 REST API

This article describes the GBrowse2 REST API.

For the main GBrowse 2.0 HOWTO article, see: GBrowse 2.0 HOWTO.

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":

$HOST/gb2/gbrowse/?action=list

This will return a plain text tab-delimited document like the following:

 # Name   Description        Species	TaxID	CoordinateType	BuildAuthority	BuildVersion	BuildURL
 bamtest  BAM/SAM Test
 elegans  C. elegans genes           Caenorhabditis elegans  6239  Chromosome  WS  180  http://www.dasregistry.org/coordsys/CS_DS109
 homo_36  Human NCI 36i coordinates
 volvox  Volvox Tutorial Database
 yeast   Yeast chromosomes 1+2       Saccharomyces cerevisiae	4932	Chromosome	SGD	1	http://www.dasregistry.org/coordsys/CS_DS69

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