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Re: Minutes from Monday's Linked Life Data (BioRDF / LODD) teleconference

From: Mark <markw@illuminae.com>
Date: Thu, 26 Apr 2012 21:52:55 +0200
To: "M. Scott Marshall" <mscottmarshall@gmail.com>,Michel Dumontier <michel.dumontier@gmail.com>
CC: Jim McCusker <james.mccusker@yale.edu>,HCLS <public-semweb-lifesci@w3.org>
Message-ID: <bdfc8820-de02-431e-8b48-4140b52f4553@email.android.com>
I think Michel deprecated "is related to" DURING the Hackathon! (out of disgust, if I recall correctly...) "not enough semantics"! 

So... He's forcing us to be more clever :-)


"M. Scott Marshall" <mscottmarshall@gmail.com> wrote:

On Monday, Jim's description reminded me about a recent discussion in
the biohackathon dbcatalog group about the best predicate for
indicating that a dataset has 'something to do with', for example, mus
musculus (not unlike Mark's example). I remembered some is_about
predicate from SIO. The predicate that I couldn't quite remember at
that time but has remained the strongest contender for the job was
http://semanticscience.org/resource/is-related-to .


P.S. My sympathy goes out to you Mark as you wait for your WIFI
hookup. I guess that you are forced to go to the pub and have a drink
in order to get a bit of normal net speed (from their WIFI). :)

On Thu, Apr 26, 2012 at 9:04 PM, Jim McCusker <james.mccusker@yale.edu> wrote:
> Actually, we've switched over to generating subproperties of
> sio:has_predicate, so I'm glad you suggested the same thing.
> Jim
> On Thu, Apr 26, 2012 at 2:07 PM, Mark <markw@illuminae.com> wrote:
>> Hmmmm... what's the range of that predicate? It's a bit like the SIO "has
>> attribute", where you need to be sure to explicitly type what's at the other
>> end to do "useful" reasoning. We're just concluding a project where we use
>> species-of-origin to restrict the choices the SHARE query resolver can make
>> when it queries the SADI registry. (the query requires the discovery of a
>> BLAST service, and it will chose the right one based on the species that the
>> sequence is derived from...)
>> Similar problem? if so, let me know and I'll post the model we came-up with
>> a few weeks ago... Maybe we can converge on a common solution?
>> Cheers all!
>> M
>> "M. Scott Marshall" <mscottmarshall@gmail.com> wrote:
>>> We had an interesting discussion with Jim McCusker about Linked Data /
>>> RDF representations of MAGE-TAB and some issues, such as choices of
>>> predicates to make describe a human sample.
>>> how to encode "is a sample originating from human"
>>> closest now is "has characteristic"
>>> Jim showed us some linked data versions of MAGE-TAB containing
>>> descriptions and data of studies. Very nice!
>>> The minutes are here:
>>> http://www.w3.org/2012/04/23-HCLS-minutes.html
>>> Cheers,
>>> Scott
> --
> 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 Thursday, 26 April 2012 19:53:38 UTC

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