- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Thu, 29 Oct 2009 21:54:12 -0400
- To: Helen Parkinson <parkinson@ebi.ac.uk>
- CC: Jim McCusker <mccusker@gmail.com>, HCLS <public-semweb-lifesci@w3.org>, Tony Burdett <tburdett@ebi.ac.uk>
Hi Jim, Helen, et al, If Limpopo has been used by multiple microarray data providers, it should be more robust and useful to the microarray use case. -Kei Helen Parkinson wrote: > 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 has been replaced by this.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 Friday, 30 October 2009 01:54:56 UTC