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Re: magetab2magerdf

From: Helena Deus <helenadeus@gmail.com>
Date: Wed, 6 Jan 2010 10:08:53 -0600
Message-ID: <6bd01db91001060808m57e3b7b6m8fd981f8f08c7516@mail.gmail.com>
To: Jim McCusker <james.mccusker@yale.edu>
Cc: w3c semweb HCLS <public-semweb-lifesci@w3.org>
Hi Jim,

This is great! I noticed you already add the links both to the raw data
files and the processed data files, am I right in assuming this data comes
from the SDRF?
I see you intergrated the MGED ontology with the data nicelly, have you
attempted a few SPARQL queries, for example, retrieve all raw data files
from "mged:arabidopsis_thaliana"?

Also, I noticed that in your ontology you don't separate each sample
hydridization raw file, probably because they are all distributed in the ftp
as a compressed folder. For example, I see that inside raw data file archive
"E-MEXP-986.raw.1.zip" there are 4 text files:
1d1S15.txt.txt, 2d1S15.txt.txt, 2d1S22.txt.txt and 4d1S22.txt.txt. Since
it's possible to add a link from a Sample to each of these .txt files, do
you think it would be useful to add this information in the raw rdf file?


On Tue, Dec 8, 2009 at 8:05 AM, Jim McCusker <james.mccusker@yale.edu>wrote:

> 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 Wednesday, 6 January 2010 16:09:42 UTC

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