[DAS] querying for nonpositional annotations

[Jonathan Warren]

Currently having read all points and thought about  it properly I  
agree with Eugenes summary of what the behavior should be.
I was thinking that types filtering is not implemented and understood  
well by many casual users of DAS. But as the types command and  
filtering is something we want to encourage using the non-positional  
type should encourage this and as long as it's documented well and  
splattered everywhere I think it should be fine. But using the logic  
below as far as I can see this means you have to do 2 requests if you  
want features and non-positional annotations for a range /das/source/ 
features?segment=P99999:1,150 and   /das/source/features? 
segment=P99999;type=annotation

But presumably doing /das/source/features? 
segment=P99999:1,150;type=gene;type=annotation would actually return  
genes if in region but no non-positional results which isn't really  
logical on its own?


On 2 Aug 2010, at 13:33, Andy Jenkinson wrote:

> On 2 Aug 2010, at 10:45, Jonathan Warren wrote:
>
>> I'm not sure I agree with returning all annotations for every tiny  
>> part of a sequence requested.
>> If you consider DAS to be used for visual display mainly  - then it  
>> seems a bit ridiculous to return all publications related to a  
>> segment (take a case where you have many publications related to a  
>> protein sequence). If publications aren't asked for i.e. non- 
>> positional annotations then I don't think they should be given. So  
>> I guess I'm agreeing with Jim here.
>>
>> Given the history of DAS I would propose a non-positional parameter  
>> as apposed to "positional".
>>
>> I think we have to remember that the 1.6 spec is supposed to mainly  
>> be a consolidation of the way DAS is being used and DAS is supposed  
>> to be simple (or not overly technical and difficult to pick up  
>> anyway). However- obviously we don't want to propagate practices  
>> that really don't make sense. The 0,0 thing is a hack like we had  
>> hacks for ontologies which now for 1.6 we have cvIds (I think are a  
>> big improvement). So we need something that is simple and obvious  
>> for a big all encompassing thing like positional vs non-positional.
>
> I'm not quite sure what you're suggesting we do in 1.6?
>
>>
>>
>>
>> On 2 Aug 2010, at 09:50, Leyla Garcia wrote:
>>
>>> *Hi list,
>>>
>>> *>No magic numbers.
>>>
>>> *According to discussions on this matter, I will change MyDas  
>>> behaviour so 0 will be no
>>> "magic number" any more,
>>>
>>> *>Types can be used for filtering, and actually you get more fine- 
>>> grained control than simply positional or non-positional. (I use  
>>> this technique now in DASher.) *
>>>> In my opinion, the current spec as written is correct. That is,  
>>>> non-positional features don't just apply to the whole sequence,  
>>>> they apply to any part of the sequence.
>>>> As an example, consider a journal reference --- a particular  
>>>> protein was isolated by a lab, they wrote a paper about it, and  
>>>> deposited the protein sequence in a database. If you look at a  
>>>> subsequence of the protein sequence, that subsequence still  
>>>> derives from the paper, right? So therefore the feature  
>>>> containing that journal reference should still be attached to the  
>>>> subsequence.
>>>> On that basis, I think the uniprot server is technically doing it  
>>>> wrong and should be changed, although I have to say that in  
>>>> practice it hasn't been an issue for me.
>>>
>>> *and non-positional features will be always returned.
>>> Since UniProt is built upon MyDas, its behaviour will change as  
>>> well.
>>>
>>> Thanks,
>>>
>>> Leyla
>>> *
>>>
>>>>
>>>> Dave
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> blog: http://biodasman.wordpress.com/
>> 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  
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>

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.