DAS sources command

This page is part of the DAS 1.53E specification

Documentation DAS - sources command

The DAS 1.53 specification provides a DSN command that returns the list of available data sources. Unfortunately this command did not scale well with the wide acceptance of DAS and it has become necessary to provide more meta-information for a DAS server.

In particular the following information for a DAS server is important:

The email address of the maintainer of a DAS source
The coordiante system(namespace) of the provided data
different properties that allow to describe a server closer

Obtain the meta descripton of DAS sources on a server

Version: May 11th, 2006
Reference:

Integrating sequence and structural biology with DAS
Andreas Prlic, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kahari, Tim JP Hubbard
BMC Bioinformatics 2007, 8:333 (12 September 2007)
[abstract] [pdf] [pubmed] [related articles]

Scope: all DAS servers
Command: sources
Format:


PREFIX/das[1]/sources

The PREFIX can be either das or das1 in order to refer to the major version 1 of the DAS protocol and in order to provide support for the future das2 protocol.

Description: This query returns the meta information for a DAS server
Arguments: none

Response:

The response to the sources command is the "DASSSOURCE" XML-formatted document:

<?xml version='1.0' encoding='UTF-8' ?>
<?xml-stylesheet type="text/xsl" href="das.xsl"?>
<SOURCES>
 <SOURCE uri="URI" title="title" doc_href="URL" description="description">
    <MAINTAINER email="email address" />
    <VERSION uri="URI" created="date">
      <COORDINATES uri="uri" source="data type" authority="authority" test_range="ID">coordinate string</COORDINATES>      
      <CAPABILITY type="das1:command" query_uri="URL" />
      <PROP name="key" value="value" />     
     </VERSION>
   </SOURCE>
</SOURCES>

Format:

xml-stylesheet	optional	an XSL stylesheet that e.g. allows a browser to nicely display the XML response
SOURCES	mandatory	the main container for several DAS sources
SOURCE	mandatory, one or many	the description for a DAS datasource
uri	mandatory	a unique URI for the DAS source
title, description	mandatory	the nickname under which a DAS server shall be known and displayed in a view. The description is a free text description of the provided data
doc_href	optional	points to a web site where more information about a DAS source can get obtained.
MAINTAINER, email	mandatory	the email address of the maintainer of this DAS source.
VERSION	mandatory	in principle this would allow hosting several versions of a DAS sources (with unque uris) on a server, but in practise most people provide only the server with the latest data. the created attribute provides the date on which a DAS server has been set up initially. For a DAS registation server this is the date at which a DAS server has been pulished.
COORDINATES	mandatory, one or many	The description of the namespace of a DAS source. uri - the unique URI for a DAS source. For a DAS registration server these should be resolvable and allow to access more information about this. e.g. http://www.dasregistry.org/dasregistry/coordsys/CS_DS6 for the UniProt,Protein Sequence coordinate system. source - the data type. This refers to the "physical dimension" of the data. Currently the following categories are available: Chromosome, Clone, Contig, Gene_ID, Super_Contig, Protein Sequence, Protein Structure authority - the authority, or institution that assigns the accession code for this namespace. In case of genome assemblies the authority that builds the assembly. version - (optional) for genome assemblies the version of the build. To learn more about coordinate systems, please see here.
CAPABILTIY	mandatory, one or many	The supported DAS commmand type - the type of the DAS command. to distinguish DAS/1 from DAS/2 servers das1: is used before the name of the command. query_urithe URL of the server location, with the command attached. e.g. http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features Note: For some DAS commands this will not resolve, since e.g. for the features command the extension /features?segment=ID needs to be attached.
PROP	optional, one or many	a free key- value style property that allows to add more tags to a server

Example Responses

http://www.dasregistry.org/das1/sources - the listing of DAS/1 sources at the DAS registration server
http://www.ensembl.org/das/sources - the DAS sources provided by Ensembl. The DAS registration server uses this listing to automatically update the registration for these DAS servers.
http://vega.sanger.ac.uk/das/sources - the VEGA DAS sources