[DAS2] Re: Apollo and DAS/2 priorities

Andrew Dalke dalke at dalkescientific.com
Mon Jan 30 15:31:11 UTC 2006

> Is the spec going to be in a stable state for the code sprint?  I'd 
> like
> to use this time to sync the server implementation with a stable 
> version
> of the spec.  It looks like there have been many substantial changes.

I have just (within the last few minutes) completed the first draft
of the update of the spec.

It's not in HTML - that calls for too much work for this stage.
It's text, in CVS under das/das2/new_spec.txt

There are many parts which need clarification.  These are marked
with a "XXX" along with my comments.

The RNC files are in

along with some test XML files.  These XML files are not meant
to be realistic.  They are meant more to check edge cases.

I do no think there are major changes to the spec.  Most of the
changes have actually trimmed things down, like getting rid of
the "properties" subtree and merging the different "sources" requests
into a single document.

Here are the major interfaces

$PREFIX/sequence - a "sources" request
   This is the top-level entry point to a DAS 2 server.  It returns a
   list of the available genomic sequence and their versions.

$PREFIX/sequence/$SOURCE - a "source" request
   Returns the available versions of the given genomic sequence.

$PREFIX/sequence/$SOURCE/$VERSION - a "versioned source" request
   Returns information about a given version of a genomic sequence.
   Clients may assume that the sequence and assembly are constant for a
   given version of a source. Note that annotation data on a server
   with curational write-back support may change without changing the

For a given version here are the sub-parts.  Note that I've gone ahead
and split the query urls (segment, features and types each have query
interfaces) from the base directory used as containers for the segments,
features and types.

  $VERSION/segments - the segments query URL; summarizes the top-level
     segments in the data source

  $VERSION/segment/$SEGMENT_ID - a segment query; used to get detailed
     information about the identified segment

  $VERSION/features - the feature filter query URL.  Features are
    locatable annotations or experimental results.  The feature filter
    URL supports query parameters to select a subset of the features
    based on position, feature type and other properties.

  $VERSION/feature/$FEATURE_ID - a feature query; used to get detailed
     information about the identified feature

  $VERSION/types - the types query URL which returns a list of all
    feature types.  Feature types include ontology and depiction
    details for all features of the given type.

  $VERSION/type/$TYPE_ID - details about the specified feature type

Oh, and there are internal conflicts which will be straightened
out in the next draft.  These shouldn't be big.

					dalke at dalkescientific.com

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