[Owl-devel] New package owl.connections

Henning Stehr stehr at molgen.mpg.de
Tue Mar 16 10:07:21 EDT 2010

Dear developers,

I have just commited a new package owl.connections which is supposed
to contain connector classes to online databases and services.

The first such classes are

PhosphoSitePlusConnection - for accessing a popular database of
posttranslational modifications and
PDomainsConnection - for accessing a very useful webservice which
calculates structural domains using a variety of methods including
Scop, Cath, DomainParser, ProteinDomainParser and others

The results of such queries are implemented using the feature
interface (see owl.features):

PhosphoSitePlusFeature - for protein modifications from PhosphoSitePlus
StructuralDomainFeature - for structural domains from pDomains

Such features can be added to any structure or sequence object
implementing the owl.features.HasFeatures interface.

Two more classes that will probably be added to the package later are:

PrositeScanner - currently in owl.proteinstructure
UniprotConnector - already working for me but need to sort out some
things with dependencies before commiting


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