$Id: das2_protocol.html,v 1.26 2006/08/17 23:58:48 dalke Exp $

Table of Contents

DAS/2 Overview

DAS is a protocol for sharing biological data. This version of the specification, DAS 2.0, describes features located on the genomic sequence. Future versions will add support for sharing annotations of protein sequences, expression data, 3D structures and ontologies. The genomic DAS interface is deliberately designed so there will be a large core shared with the protein sequence DAS.

A DAS 2.0 annotation server provides feature information about one or more genome sources. Each source may have one or more versions. Different versions are usually based on different assemblies. As an implementation detail an assembly and corresponding sequence data may be distributed via a different machine, which is called the reference server.

Annotations are located on the genomic sequence with a start and end position. The range may be specified multiple times if there are alternate coordinate systems. An annotation may contain multiple non-continguous parts, making it the parent of those parts. Some parts may have more than one parent. Annotations have a type based on terms in SOFA (Sequence Ontology for Feature Annotation). Stylesheets contain a set of properties used to depict a given type.

Annotations can be searched by range, type, and a properties table associated with each annotation. These are called feature filters.

DAS 2.0 is implemented using a ReST architecture. Each document (also called an entity or object) has a name, which is a URL. Fetching the URL gets information about the document. The DAS-specific documents are all in XML. Other data types have existing widely used formats, and sometimes more than one for the same data. A DAS server may provide a distinct document for each of these formats, along with information about which formats are available.

DAS 2.0 addresses some shortcomings of the DAS 1.x protocol, including:

$Log: das2_protocol.html,v $
Revision 1.26  2006/08/17 23:58:48  dalke
Added emacs timestamp

Revision 1.25  2006/04/27 03:15:34  dalke
Added link to locks document

Revision 1.24  2006/04/24 16:08:55  dalke
Updated to spec 300

Revision 1.23  2005/11/29 22:20:16  dalke
Updated from template

Revision 1.6  2005/11/08 23:04:00  sac
Added link to at top left corner.

Revision 1.5  2005/10/18 20:14:16  sac
Added sentence on requirement of "das/" for all DAS/2 URLs.

Revision 1.4  2005/10/18 19:55:58  allenday
forgot to commit template

Revision 1.3  2005/09/22 21:01:45  allenday
link to assay document from main

Revision 1.2  2005/09/22 20:37:25  allenday
update to nomenclature of URL parts

Revision 1.1  2005/05/03 13:53:31  edgrif
make protocol doc. into a template file, now all html files are the same.

Revision 1.12  2005/04/29 19:36:13  edgrif
Add a table of suggested response codes for DAS/2

Revision 1.11  2005/03/15 23:15:39  dalke
changed "URN" to "URI"

Revision 1.10  2005/01/11 13:46:58  lstein
Described the PUT and POST requests for updating existing objects.

Revision 1.9  2005/01/07 01:37:36  lstein
a little more work on writeback protocol

Revision 1.8  2004/12/12 17:39:58  lstein
began reorganization of html pages

Revision 1.7  2004/11/13 20:01:52  lstein
committed changes that allen things i forgot

Revision 1.6  2004/11/12 01:12:08  lstein
Folded in changes discussed during Hinxton meeting; need to work on writeback description now

Revision 1.5  2004/09/26 10:49:59  lstein
very minor changes to correct xemacs regexp overflow bug

Revision 1.4  2004/09/26 10:06:25  lstein
gene das cleaned up

Revision 1.3  2004/09/26 09:57:54  lstein
gene das explained

Revision 1.2  2004/09/24 11:41:43  lstein
minor typographical changes

Revision 1.1  2004/09/17 20:02:49  lstein
added htmlized version of das2 protocol

Last modified: Fri Aug 18 01:54:29 SAST 2006