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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?

Thanks!
Lena

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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