[DAS] querying for nonpositional annotations

[Dave Messina]

I too agree with Eugene.

No magic numbers.

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.


Dave

* It might be nice, though, to add 'positional' and 'non-positional' types, which would be a way to grab all of the existing positional or non-positional types in one go. (currently it's necessary to specify multiple types to get the same functionality.)