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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