| biodas.org | $Id: das2_protocol.html,v 1.26 2006/08/17 23:58:48 dalke Exp $ |
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 biodas.org 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 protocolLast modified: Fri Aug 18 01:54:29 SAST 2006