[DAS] querying for nonpositional annotations

Jonathan Warren jw12 at sanger.ac.uk
Mon Aug 2 09:45:50 UTC 2010

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.

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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