[DAS] next "feature" for 1.6 spec

Mon Jun 29 16:59:48 UTC 2009

How about if the server is simply allowed to return features that  
don't overlap the queried segment range, if they declare the  
appropriate capability? They would then carry the correct type etc.  
The only question is whether a client is significantly helped by an  
explicit marking of some sort. My personal view is that it's OK  
without it.

Andy

On 29 Jun 2009, at 15:34, Jonathan Warren wrote:

> Yes that was the intent. I guess if a client is filtering on feature  
> type then the way we have suggested is not going to be very useful -  
> the client would have to walk along the source until it found a  
> feature of the type it wants ( using the nextleft every time and  
> looking at the region).
>
> Perhaps a better way is not have any "next" flag at all as the  
> segments location will show it's out of range and to the left so  
> this should be obvious. This way a client can filter on type of  
> feature in the normal features command and the server can return a  
> type appropriate to that filter?
>
> On 29 Jun 2009, at 14:44, Lincoln Stein wrote:
>
>> 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, a charity registered in England with number  
>> 1021457 and acompany registered in England with number 2742969,  
>> whose registeredoffice is 215 Euston Road, London, NW1  
>> 2BE._______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>>
>>
>>
>> -- 
>> 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>
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
>
>
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome  
> ResearchLimited, a charity registered in England with number 1021457  
> and acompany registered in England with number 2742969, whose  
> registeredoffice is 215 Euston Road, London, NW1  
> 2BE._______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das