[DAS2] Why use URIs for feature IDs?

Andrew Dalke dalke at dalkescientific.com
Thu Feb 9 11:48:02 UTC 2006

Churn factor:

The only part of the spec that changes is the query interface
for types.  The type feature filter must take a full URL and
not a partial URL nor a non-existant 'short id'.

Allen's server does not support queries given the full URL.

Here's what the spec says -- note that it quotes the previous
draft and I added some comments.

> Query parameter "type"
>   type=type_url
> Example:
>   $FQ?type=http%3A%2F%2Fwww.biodas.org%2FtypeA
> Match features with the given feature type.
> XXX the previous version of this document says
> Match features of the given type. A type is one of:
>   1. a typeid returned by the feature type document described
>   earlier. Only features exactly matching the type are returned.
>   2. a sequence ontology term, such as "exon". Features matching the
>   term or *any of its ISA descendents* are returned.
>   3. a sequence ontology accession number, such as SO:12345. Features
>   matching the accession number or *any of its ISA descendents* are
>   returned.
>   4. a reserved type beginning with the namespace "das:". The only such
>   reserved type is currently "das:feature-lock", used for feature
>   updating.
> XXX I think we should only have it do 1.  For 2 and 3 use the query
> parameter 'ontology'.  For 4, use a different query term, or don't use
> locks as features.

Based on the discussion yesterday, this changes to:
   1. we support this one, with fully resolved URLs
   2. the searching is done in the client so this option is removed
   3. the searching is done in the client so this option is removed
   4. we can always define "http://www.biodas.org/spec/special-type"
as a URL to send to the server if we want to define a special query.

					dalke at dalkescientific.com

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