Jose M. Duarte
jose.m.duarte at gmail.com
Fri Mar 19 09:28:11 EDT 2010
> 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
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
> > 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!
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