[DAS] next "feature" for 1.6 spec

[Lincoln Stein]

The NEXTLEFT and NEXTRIGHT pseudo-features should appear even if there are
no conventional features in the <SEGMENT>.

There is an ambiguity here. It is completely possible for a DAS server to
return multiple distinct feature types per segment. However, a type
"NEXTLEFT" does not distinguish which feature type can be found to the left.
Is the intent here to say that "any" feature can be found to the left or the
right?

Lincoln

On Mon, Jun 29, 2009 at 5:31 AM, Jonathan Warren <jw12 at sanger.ac.uk> wrote:

> Another feature we would like to add to the current 1.6 spec is the ability
> for a server to return the next feature both left and right of the current
> region if they exist but are out the currently selected range.
> This would not need a new command, but will be specified in the spec as a
> valid response to the features cmd.
>
> so if a user specifies chr1:1000,2000 the server can return something like
> this:
> <SEGMENT id="id" start="start" stop="stop" version="X.XX" label="label">
> //minimal information about the next feature in a minimal feature element
> to include location so the client knows where the next region of interest
> for this das source is.
> //if the current region has no features showing then these features can be
> returned, but as they are outside the asked for range of the client they
> will not be displayed (but can be used to have a next left or next right
> button on the client.
> <FEATURE id="id">
> //NEXTLEFT as the type id rather than what the type id would be if in the
> normal region.
>         <TYPE id="NEXTLEFT" >type label</TYPE>
>         <START> 20 </START>
>         <END> 30</END>
>      </FEATURE>
> <FEATURE id="id">
>         <TYPE id="NEXTRIGHT" >type label</TYPE>
>         <START> 3000</START>
>         <END> 3050 </END>
>      </FEATURE>
> //the rest of the response as normal if features for this region exist
>      <FEATURE id="id" label="label">
>         <TYPE id="id" category="category" reference="yes|no"
> cvId="SO:1234">type label</TYPE>
>         <METHOD id="id" cvId="ECO:5678"> method label </METHOD>
>         <START> start </START>
>         <END> end </END>
>         <SCORE> [X.XX|-] </SCORE>
>         <ORIENTATION> [0|-|+] </ORIENTATION>
>         <PHASE> [0|1|2|-]</PHASE>
>         <NOTE> note text </NOTE>
>         <LINK href="url"> link text </LINK>
>         <TARGET id="id" start="x" stop="y"> target name </TARGET>
>         <PART id="child id1" />
>         <PART id="child id2" />
>      </FEATURE>
>      <FEATURE id="child id1" label="child label">
>         ...
>      </FEATURE>
>      <FEATURE id="child id2" label="child label">
>         ...
>      </FEATURE>
>      ...
>  </SEGMENT>
>
>
>
> This ability would be an optional one, but we at the sanger, EBI  and
> Lincoln are very keen on this and see a great need and demand for it. It's
> especially useful for when there are no features returned for a region, for
> sparse data sources and for testing DAS sources in clients. There maybe a
> performance hit to implement this by the server and this is another reason
> why this response would be optional.
>
> What do other people think?
>
> Cheers
>
> Jonathan.
>
>
> Jonathan Warren
> Senior Developer and DAS coordinator for the Sanger
> jw12 at sanger.ac.uk
>
>
>
>
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited,
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>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>