Re: Action Items from call today

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 <parkinson@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 tburdett@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.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