[DAS2] DAS intro

[Andrew Dalke]

The front of the DAS doc starts

   DAS 2.0 is designed to address the shortcomings of DAS 1.0, including:

That kinda assumes people know what DAS 1.0 is to understand DAS 2.0.

How about this instead, as an overview/introduction.

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DAS/2 describes a data model for genome annotations.  An annotation
server provides 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.  Portions of
the assembly may have higher relative accuracy than the assembly as a
whole.  A reference server may supply these portions as an alternate
reference frame.

Annotations are located on the genome 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