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Re: magetab2magerdf

From: Jim McCusker <james.mccusker@yale.edu>
Date: Wed, 9 Dec 2009 09:59:22 -0500
Message-ID: <68084f3e0912090659y25f55554ma215ecb242b06e97@mail.gmail.com>
To: mdmiller <mdmiller53@comcast.net>
Cc: w3c semweb HCLS <public-semweb-lifesci@w3.org>
On Wed, Dec 9, 2009 at 9:44 AM, mdmiller <mdmiller53@comcast.net> wrote:
> ----- Original Message ----- From: "Jim McCusker" <james.mccusker@yale.edu>

>> 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.

No need for a SPARQL endpoint for these, the ontology is enough. It is
possible to link OWL files together using the owl:Import feature
(which I use in the example file). If you load this into Protege or an
API, the imported ontologies will be automatically be loaded.

>> 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

Maybe I should build a map of common website -> ontology conversions...


>> 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.

I'll leave that alone then. I was worried that something more
technical had gone wrong somewhere.

Thanks,
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 14:59:56 UTC

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