[DAS2] segments and coordinates

Andreas Prlic ap3 at sanger.ac.uk
Tue Mar 14 16:48:09 UTC 2006

On 14 Mar 2006, at 16:09, Andrew Dalke wrote:

> Summary:  I want to
>    - move the COORDINATE element inside of the
>          CAPABILITY[type="segments"] element

Is this really needed?

> The current spec has COORDINATES and the "segments" capability
> as different elements, like
> <COORDINATES source="Chromosome" authority="NCBI" version="v22"
>         taxid="9606" created="2006-03-14T07:27:49" />
> <CAPABILITY type="segments"
>      query_id="http://localhost/das2/h.sapiens/v22/segments" />

> With the current discussion on multiple coordinates, it
> looks like there is a 1-to-1 relationship between a COORDIANTES
> record and a CAPABILITY record.  As that's the case I want
> to merge them together, as in (note change from "_id" to "_uri")

I think hat this is a many to many relationship.
Do you still want to provide the link to the reference server from an 
annotation server?
This is not needed because the coordinates describe the reference 
server sufficiently.

Annotation servers do not need the segments capability - only the 
features capability.

> <CAPABILITY type="segments"
>       query_uri="http://localhost/das2/h.sapiens/v22/segments">
>    <COORDINATES source="Chromosome" authority="NCBI" version="v22"
>           taxid="9606" created="2006-03-14T07:27:49" />
> In talking with Andreas I think he agrees that this makes sense.

If you really *want* to have the link back from the annotation server 
to the reference then
I would propose to put capability under coordinates - i.e. the other 
way round.

> econd, there's a question of identity.  When are two coordinates
> the same?  Is it when they have the same
>    (authority, source, version)
> the same
>    (authority, source, version, taxid)


> Since taxid is optional, what if one server leaves it out;
> are the two still the same?

no - because if a taxid is specified that is a restriction for one 
organism. no taxid means that  this refers to multiple organisms.

> I decided to solve it with a unique identifier.

that might be good. this identifier could also be used to restrict 
searches on servers with many coordinate systems.

> Let's say that
>    http://das.sanger.ac.uk/registry/coordinates/ABC123
> is the identifier for:
>    authority=NCBI
>    version=v22
>    taxid=9606
>    source=Chromosome
>    created=2006-03-14T07:27:49


> Then the following are equivalent.  The only difference is the
> number of properties defined in the COORDINATES tag.
> <CAPABILITY type="segments"
>       query_uri="http://localhost/das2/h.sapiens/v22/segments">
> uri="http://das.sanger.ac.uk/registry/coordinates/ABC123" />
> <CAPABILITY type="segments"
>       query_uri="http://localhost/das2/h.sapiens/v22/segments">
> uri="http://das.sanger.ac.uk/registry/coordinates/ABC123"
>        source="Chromosome"/>
> <CAPABILITY type="segments"
>       query_uri="http://localhost/das2/h.sapiens/v22/segments">
> uri="http://das.sanger.ac.uk/registry/coordinates/ABC123"
>       source="Chromosome" authority="NCBI" version="v22" taxid="9606"
>       created="2006-03-14T07:27:49" />


This is a lot of change to the spec for us being already on the second 
code sprint,
but I think it makes things clearer



Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891

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