On 02/08/2010 16:17, Jonathan Warren wrote:
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
I think I am confused about the annotation type filter.
Why do you need type=annotation to retrieve non-positional features when
no range is specified? -->
/das/source/features?segment=P99999;type=annotation
If I am not mistaken, no range will retrieve both positional and
non-positional features.
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?
So far, non-positional features will be always retrieve, with or without
range. The idea behind using a type filter (type=annotation) is to
specify whether or not non-positional features should be retrieve (or
any other type). So the last query should actually retrieve the
"annotation" type features, or not?
Leyla
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
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Jonathan Warren
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[email protected]
Ext: 2314
Telephone: 01223 492314
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