[Bioperl-l] InterPro parser

Hilmar Lapp hlapp at gnf.org
Thu Feb 6 01:00:56 EST 2003

I committed the InterPro parser written by Peter Dimitrov to the main 
trunk only. See Bio::OntologyIO::InterProParser. The format parsed is 
the XML format. There is no support for writing yet.

Note that there is no Bio::OntologyIO.pm module yet that would work in 
the same way as e.g. SeqIO or SearchIO. I.e., right now you have to 
instantiate the parser yourself. At some point soon I'm going to add 
that wrapper factory.

We chose to create artificial root nodes for the different InterPro 
'types', like Domain or Family. Whether this is the Right Thing to do 
or not is up for debate if people disagree, it has pluses and minuses.

Some additional modules come with it, among which is a 
Ontology::InterProTerm implementing Ontology::TermI, and 
Ontology::SimpleOntologyEngine, which is an implementation of 
Ontology::OntologyEngineI that does not use the Graph.pm module from 
CPAN. The latter is in no way tied to the InterPro parser, but is what 
the parser instantiates and populates.

Enjoy, -hilmar

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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