[DAS2] DAS/2 progress report - CSHL

[Lincoln Stein]

Hi Gregg,

Here is some material for the progress report:

DAS/2 Specification (CSHL)

The work on the DAS/2 specification has centered on two major 
categories: enhancement of the retrieval protocol to support more 
flexible queries, and development of a new writeback protocol to 
support creation of new biological data objects and editing of 
existing ones.

The changes to the retrieval protocol are finished.  It has been 
enhanced to provide for retrieval of biological objects using 
multiple combinations of attributes.  In DAS/1, objects could only be 
retrieved using combinations of genomic position, object name, and 
object type.  In DAS/2, objects can be retrieved using any 
combination of arbitrary attribute: for example, genes can be 
retrieved using GO terms or the presence of an orthologue in another 
species.

The writeback protocol is roughly 75% complete. We have developed a 
locking protocol, a scheme for requesting new identifiers, and a 
scheme for addressing objects that are not yet created.  We have also 
specified the protocol for writing new objects into the database.  
However there is still ambiguity in the protocol for updating 
existing objects, primarily decisions relating to the granularity of 
updates. On the one hand, it might be desirable to be able to address 
and update an individual field in an object. On the other hand, this 
type of granularity significantly complicates the implementation of 
the protocol and introduces issues relating to locking and atomicity 
of updates.

Work on the protocol is continuing, however, and we anticipate that it 
will be ready for public comment by the end of spring 2005.

Lincoln


-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
all emails regarding scheduling and other time-critical topics.
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