[DAS] querying for nonpositional annotations

[Andy Jenkinson]

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
>> 
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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
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