[Owl-devel] Features

Jose M. Duarte jose.m.duarte at gmail.com
Thu Mar 18 12:36:23 EDT 2010

Hi Henning

I'm trying to get Uniprot mapping from the data file provided by the SIFTS
project (http://www.ebi.ac.uk/msd/sifts/), so now I need to use the
UniprotFeature class.

I have a few questions about this (no need to reply all of them!):

- I'm not sure what the fields in the UniprotFeature are. What's the
uniprotTypeName and what's the description?

- How are you doing the mapping between Uniprot and pdb? Maybe this is
provided by the Uniprot API and you don't need to be doing that kind of
thing? The thing is the SIFTS file has the mapping so now I'm trying to see
how to design the flow of things: where and how to store the mapping and so

- 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.

By the way I've created now the owl.runners package and put some new runner
classes there that I extracted from the Pdb class (e.g. dssp runner). Also
I've added some new stuff to the owl.connections package, again things
extracted from the Pdb class. When I have some time I will move more stuff
into owl.runners.

While doing that I also realised that the tests we have are hard-coded to
work only over there. So I've created a "owl_tests_path.dat" file that
contains the paths for external programs needed to run the tests, at the
moment only tests.proteinstructure.PdbTest uses it. I'm already thinking in
redoing that and have something that is more general for the whole OWL
library, some sort of global config file.

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