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magetab2magerdf

From: Jim McCusker <james.mccusker@yale.edu>
Date: Tue, 8 Dec 2009 09:05:05 -0500
Message-ID: <68084f3e0912080605x781e6911ve934dd3f6e903af1@mail.gmail.com>
To: w3c semweb HCLS <public-semweb-lifesci@w3.org>
I'm distinguishing between magetab2rdf (raw conversion of magetab into
an RDF structure) and magetab2magerdf (conversion of magetab into an
RDF-based MAGE-OM structure) here. My purposes and goals require a
magetab2magerdf approach, so that's what I've been working on.

I have checked in code for magetab2magerdf at the googlecode project
http://magetab2rdf.googlecode.com. The code can be checked out from:

http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/

and example RDF is in:

http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986/

I currently load the IDF-related entities into the RDF. I'm beginning
work on SDRF next.

http://magetab2rdf.googlecode.com/svn/trunk/ontologies/mage-om.owl
contains the additional properties and classes needed to support an
RDF-based MAGE-OM on top of the MGED Ontology.

A few notes on E-MEXP-986:

The URI for the MGED Ontology is
http://mged.sourceforge.net/ontologies/MGEDontology.owl, but has been
set to http://mged.sourceforge.net/ontologies/MGEDontology.php in the
IDF. The actual Term Source name is "The MGED Ontology".
A common practice seems to be to refer to "MGED Ontology" without
reference to its URI.

Since I have to import the MGED ontology already for it's classes and
properties, I have already imported it under the correct URI. I have
added a kludge where if the term source name contains the string "MGED
Ontology", the code assumes you mean the MGED Ontology, and sets the
URI appropriately. However, this is a one-off solution.

I went back and forth about importing the Term Source ontologies.
However, this particular experiment has used the "ArrayExpress" term
source using the URI "http://www.ebi.ac.uk/arrayexpress/" which
doesn't correspond to an available ontology, but is technically a term
source.

I'm considering attempting to import the ontology if it's available
and validate if it is, but if it fails to resolve to a document the
validation will not happen against that term source.

A note on Limpopo:

The IDF Comment didn't seem to import on this experiment. I'm not sure
if it's a format problem or something else.

Thoughts and feedback are greatly appreciated.

Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Tuesday, 8 December 2009 14:06:46 UTC

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