Jim
Stanford are now using the limpopo parser as well, the cannonical one
has been replaced by this. Limpopo is used by at least 3 groups EBI,
SMD, and MeV and is tested, I'd go with this,
thanks
Helen
Jim McCusker wrote:
Hi all, I have a quick bit of input about MAGE-TAB->RDF (which is
something that I'm rather interested in).
On Tue, Oct 13, 2009 at 1:00 AM, Helen Parkinson <parkin...@ebi.ac.uk
<mailto:parkin...@ebi.ac.uk>> wrote:
here are my action items from the call today
1. MAGE-TAB->RDF, Lena requested details.
Code here: https://sourceforge.net/projects/limpopo/
Java Parser for MAGE-TAB developed by EBI, used by several groups.
Contact Tony Burdett tburd...@ebi.ac.uk
<mailto:tburd...@ebi.ac.uk> for details. Tony estimates for a
simple RDF dump a few days work. Lena if you are interested in
working on this java code please contact Tony as he's already
designed with rdf export in mind
I have been experimenting with
ftp://smd-ftp.stanford.edu/smd/transfers/magetab/, which is the
"canonical" magetab parser, and includes an object model. I have been
attempting to annotate the data model with Sesame Elmo annotations to
produce a useful RDF graph from the parsed object graph. I have only
made some progress on this, as the its use of custom collection
subclasses confuses the Elmo mapping code.
If Limpopo is separate from the parser that I'm working on, and has an
easier-to-work-with object model, I can possibly make some good
progress on this in a short period of time. Glancing at the code from
Limpopo, the object model seems very different, and can possibly be
used by Elmo to generate RDF.
If I use this route, is this something that would be interesting to
the group?
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu <mailto:james.mccus...@yale.edu> | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu <mailto:mcc...@cs.rpi.edu>
http://tw.rpi.edu
