Difference between revisions of "DAS1.6"

From BioDAS
Jump to: navigation, search
(added draft 6)
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
'''Note: this is NOT the official version of the [http://biodas.org/documents/spec.html DAS specification].'''
+
DAS 1.6 is, as of 19th October 2010, the latest official version of DAS. The specification document is found here:
 +
[http://www.biodas.org/documents/spec-1.6.html DAS 1.6 specification]
  
−
=Distributed Annotation System (DAS) 1.6=
+
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.
  
−
This is a working document and a proposal for a reworked DAS specification which hopes to:
+
==Purpose==
−
* clarify the existing DAS spec
+
 
 +
It is the first official version published in several years, and aims to:
 +
* clarify ambiguities in the previous DAS specification
 
* better reflect how DAS is being used in the community today
 
* 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)
 
* better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures)
−
* ratify commands from the [http://www.dasregistry.org/spec_1.53E.jsp 1.53E spec]  
+
* ratify commands from the [http://www.dasregistry.org/spec_1.53E.jsp 1.53E extended spec]  
 
* introduce some ideas inspired by DAS/2
 
* introduce some ideas inspired by DAS/2
 
* formally introduce the DAS registry
 
* formally introduce the DAS registry
 
* migrate from the use of DTDs for describing the XML formats to RelaxNG
 
* 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 list of changes is listed here: [[DAS 1.6 Changes]].
  
−
The specification has been written as a number of drafts:
+
==Compatibility==
 +
 
 +
Software developers wanting to know more about supporting or migrating between different versions of the specification may wish to consult the [[DAS 1.6 Migration]] page.
 +
 
 +
==Extensions==
 +
 
 +
Several extensions to the 1.6 are proposed by community members. See the [[DAS1.6E]] page for more details.
 +
 
 +
==Development==
 +
 
 +
The specification was developed as a community collaboration via progression through a number of drafts:
 
* [http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html Draft 1]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html Draft 1]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft2/documents/spec.html Draft 2]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft2/documents/spec.html Draft 2]
Line 21: Line 34:
 
* [http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html Draft 5]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html Draft 5]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft6/documents/spec.html Draft 6]
 
* [http://www.ebi.ac.uk/~aj/1.6_draft6/documents/spec.html Draft 6]
−
Last modified: 23rd June 2010
+
* [http://www.ebi.ac.uk/~aj/1.6_draft7/documents/spec.html Draft 7]
−
 
 
−
=(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.
 
−
<pre>
 
−
<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>
 
−
</pre>
 
−
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.
+
==Links==
  
−
The das registry also now responds to these requests e.g. http://www.dasregistry.org/das/DS_109
+
[[DAS 1.6 in Dazzle]]

Latest revision as of 17:26, 1 November 2010

DAS 1.6 is, as of 19th October 2010, the latest official version of DAS. The specification document is found here: DAS 1.6 specification

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.

Purpose

It is the first official version published in several years, and aims to:

  • clarify ambiguities in the previous DAS specification
  • 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 extended 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

The list of changes is listed here: DAS 1.6 Changes.

Compatibility

Software developers wanting to know more about supporting or migrating between different versions of the specification may wish to consult the DAS 1.6 Migration page.

Extensions

Several extensions to the 1.6 are proposed by community members. See the DAS1.6E page for more details.

Development

The specification was developed as a community collaboration via progression through a number of drafts:

Links

DAS 1.6 in Dazzle

Retrieved from "http://biodas.open-bio.org/w/index.php?title=DAS1.6&oldid=718"