[Owl-devel] Features

[Jose M. Duarte]

>
>
> UniprotFeature is currently only for sequence features annotated in
> Uniprot such as active sites, posttranslational modifications etc.
> These are parsed by my UniprotConnection class (using the uniprotjapi)
> and returned as UniprotFeatures. For Pdb structures associated with a
> Uniprot entry, I don't use the UniprotFeature class, but now thinking
> about it, it would also make sense to implement this as a feature.
> Instead, I'm using a very simple SiftsConnection class, which parses
> SIFTS (either locally or from the ftp site). The thing is that after
> taking the data from SIFTS (which gives you start and end residues in
> Uniprot and Pdb entry) you still need to do an alignment to get the
> actual residue mapping because there may still be gaps and/or
> mutations.
>

Ok I didn't realise that, of course one would need both: uniprot annotation
and pdb to uniprot mapping.



> > - I'm not sure what the fields in the UniprotFeature are. What's the
> > uniprotTypeName and what's the description?
>
> As mentioned, UniprotFeature stores sequence annotations as described
> in http://www.uniprot.org/manual/sequence_annotation.
> uniprotTypeName is the category of annotation, e.g. Modified residue
> (actually the abbreviation returned by the uniprotjapi, i.e. MOD_RES)
> and description is the actual annotation, e.g. Phosphorylation.
>
>
Cool thanks, I was thinking always in uniprot mapping so that's why I
couldn't make any sense of this uniprotTypeName.

> - How do you go about storing the Collection of features belonging to a
> > certain structure/sequence. I can see that the HasFeatures interface
> intends
> > to help there. Have you already implemented something with it? That'd be
> > nice to have as an example.
>
> I'm using a class 'Gene' which implements HasFeatures. I guess we
> could make the classes
> Pdb and/or Sequence to implement the HasFeatures interface as examples.
> For the moment, I'll send you my Gene class for reference.
>
>
Yes that's tricky. The problem is that Pdb or Sequence could have more than
one annotation attached to it, for instance Pdb can have uniprot annotation
+ catalytic sites annotation + structural domains +....... you name it. So
how to use all of those together? If I understand it well the implementation
of HasFeatures would only be for one type of Feature. Of course Pdb/Sequence
could be subclassed case by case or something similar.... At some point we
should really look for inspiration in other projects as Dan said :-)

Now I've just had new idea. Could one use generics for the HasFeatures
interface and then implement several of them, something like
HasFeatures<UniprotFeature>, HasFeatures<StructuralDomainFeature> and so on.
Can one do that kind of thing?

Alright that's it for now

Nice weekend to all!

Jose
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