dan.bolser at gmail.com
Thu Mar 18 13:36:46 EDT 2010
On 18 March 2010 16:36, Jose M. Duarte <jose.m.duarte at gmail.com> wrote:
> 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?
I used to know all about this... IIRC the SwissProt format READMEs are
the best place to go to work out what is what. Also the module
documentation for the SwissKnife parser was good.
> - 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.
I know BioPerl has a lot of modules for handling generic 'sequence
features'. You may try looking at BioJava to see if there is something
All the best,
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