DAS1.6

Note: this is NOT the official version of the DAS specification.

Distributed Annotation System (DAS) 1.6

This is a working document and a proposal for a reworked DAS specification which hopes to:

• clarify the existing DAS spec
• better reflect how DAS is being used in the community today
• better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures)
• ratify commands from the 1.53E spec
• introduce some ideas inspired by DAS/2
• formally introduce the DAS registry
• migrate from the use of DTDs for describing the XML formats to RelaxNG

Note: the DAS specification is a technical document but with some effort should hopefully be readable and understandable by people without a deep understanding of broader technical issues and other system architectures. That is, it makes only basic assumptions.

The specification has been written as a number of drafts:

• Draft 1
• Draft 2
• Draft 3
• Draft 4
• Draft 5
• Draft 6
• Draft 7

Last modified: 22nd September 2010

(DAS) 1.6 Development and Tutorials

Dazzle Example Adaptor for 1.6 spec source compliant with the registry

Subversion develpment repository http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle See class org.biojava.servlets.dazzle.datasource.SimpleFile16ExampleSource for a datasource that conforms to the new 1.6 Spec.

<datasource id="test16genes" jclass="org.biojava.servlets.dazzle.datasource">
     <string name="name" value="16 File Test" />
     <string name="description" value="Data source for testing 1.6 heirachy structure" />
     <string name="version" value="1.0" /> 
     
     <string name="fileName" value="test16genes.txt" />

     <string name="stylesheet" value="test16.style" />
   </datasource>

Note: Older style adapters/datasources can be used in the new 16Dazzle and will be converted to the new 1.6 specification (you may need to add a allTypes method). However you will miss out on some of the advantages of the new spec if you update your source by this method rather than extending one of the new 16 classes.

The new Dazzle implements the single Data Source sources.xml request: blah/das/myDataSourceName. The current implementation relies on on a valid sources.xml document being available and then parses the appropriate section from this document in response to a request.

The das registry also now responds to these requests e.g. http://www.dasregistry.org/das/DS_109