[DAS] querying for nonpositional annotations

Andy Jenkinson andy.jenkinson at ebi.ac.uk
Mon Aug 2 09:36:07 UTC 2010

I guess if being unable to filter out nonpositional features proves to be a problem, we can introduce a specific boolean or type-based filter in the next version of the specification.

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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