[Owl-devel] Uniprot entries and mapping to Pdb structures

Henning Stehr stehr at molgen.mpg.de
Tue Apr 27 11:50:41 EDT 2010

Hi Jose,

I saw your latest commits to OWL. Nice stuff. I have a few minor questions:

- For the classes that implement some interface, you had @Override
annotations for all implemented methods (I guess your Eclipse is doing
that automatically). For some reason, my Eclipse is giving me
compilation errors (not even warning) and asks me to remove the
annotations. Do you have an idea why that could be happening? Do you
get warnings for missing annotations when you check out my latest
changes? (I have seen something like this happening)

- Your UniprotHomolog is using a local standalone blast database,
right? So you will have to use formatdb and make sure that you use a
current Uniprot DB. Apart from the effort to create that DB, that is
actually nice, because the results will be reproducable. I had been
using the Uniprot Java API which can also do blasting against the
online Uniprot (mutanom.UniprotConnection). This is nice but the
results change with every Uniprot update, which is sometimes not
optimal.The reason why I havn't moved UniprotConnection to OWL yet was
that it requies lots of external jars to function properly and I was
hesitating whether it's worth it. Eventuelly we should probably move
it there. What are you using currently to retrieve the actual Uniprot
entries identified with blast? The perfect solution would be a class
which can use both online and offline Uniprot versions so you can
switch depending on the purpose. Maybe even parsing Uniprot text
format would do. Any success on that?

- The SiftsFeature for mapping Pdbs to Uniprot sequences is really
nice. How do you get the mapping then? Shall we move my SiftsMapping
class to OWL (maybe calling it SiftsConnection)?

- Once you have selected the appropriate protein from your
UniprotHomologs, do you have a UniprotEntry class which owns the
SiftsFeatures? Otherwise shall we create one in owl.core.sequence?


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