[DAS2] DAS intro

[Andrew Dalke]

Ed:
> I definitely think of DAS as a protocol first, rather than a data 
> model first.

Mmm.  I see you all's point.  All protocols express a data model, though
neither side necessarily must implement it that way.

Here's the updated text.  This is what I just committed to CVS.  Note
that it's missing mention of the '/region' section.

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DAS/2 is a protocol for sharing biological data.  This version of the
specification describes features located on the genomic sequence.
Future extensions will add support for sharing annotations of expression
data, protein sequences, 3D structures, and ontologies.

A DAS/2 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 mutiple times if there are
alternate reference frames.  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 is implemented using a ReST architecture.  Each entity (also
called a document or object) has a name, which is a URL.  Fetching the
URL gets information about the entity.  The DAS-specific entities are
all XML documents.  Other entities contain data types with an existing
and frequently used file format.  Where possible, a DAS server returns
data using existing formats.  In some cases a server may describe how
to fetch a given entity in several different formats.

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					Andrew
					dalke at dalkescientific.com