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Re: magetab2magerdf

From: mdmiller <mdmiller53@comcast.net>
Date: Wed, 9 Dec 2009 06:44:18 -0800
Message-ID: <2DCEAC0592B44D8A8D1035EA6C63CD31@mmPC>
To: "Jim McCusker" <james.mccusker@yale.edu>
Cc: "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
hi jim,

looks like you're making great progress.  i have a few comments in-line 


----- Original Message ----- 
From: "Jim McCusker" <james.mccusker@yale.edu>
To: "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
Sent: Tuesday, December 08, 2009 6:05 AM
Subject: magetab2magerdf

> 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.

as you probably noticed, 
http://mged.sourceforge.net/ontologies/MGEDontology.php allows appending 
"#{class name}" to go directly to the definition of the term, so in a sense 
it is indeed a valid URI, that is a URL.  it also came before the owl 
format.  can th epowl format be reached into over he net to extract simply 
the class definition or does it need to be downloaded and processed locally? 
my understanding is that a site would have to have some sort of query, 
hopefully sparql, mechanism on top to enable this.

> 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.

think of it as same as

> 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.

yes, and it does support a query mechinism, albeit a one off for that site. 
i believe they plan on adding support for a sparql endpoint but aren't sure 
if or when.

> 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.

i ran into this also, the implementation assumes 
"Comment[type]\ttext\ttext..." to coresspond to the format of the other 
fields in the IDF.  the MAGE-TAB 1.0 spec doesn't address, my assumption was 
that it was simply "Comment[type]text" but that's not what the parser 
expects.  we'll be discussing this for the MAGE-TAB 1.1 spec to clarify it 
one way or another, possibly updating the parser before that.

> 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, 9 December 2009 14:44:52 UTC

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