[DAS] querying for nonpositional annotations

Leyla Garcia ljgarcia at ebi.ac.uk
Mon Aug 2 10:29:53 UTC 2010

On 02/08/2010 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.

I think a specific boolean (positional or non-positional) is a better 
idea than a type-based filter

> 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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