Re: Action Items from call today

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has been replaced by this.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 <parkinson@ebi.ac.uk 
> <mailto: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
>     <mailto: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 <mailto:james.mccusker@yale.edu> | (203) 785-6330
> http://krauthammerlab.med.yale.edu
>
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@cs.rpi.edu <mailto:mccusj@cs.rpi.edu>
> http://tw.rpi.edu

Received on Thursday, 29 October 2009 21:44:22 UTC