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

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Thu, 26 Apr 2012 17:30:41 -0400
Message-Id: <25E9ED0E-D58F-463C-B909-3083E15F5C74@gmail.com>
Cc: Mark <markw@illuminae.com>, Jim McCusker <james.mccusker@yale.edu>, HCLS <public-semweb-lifesci@w3.org>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
Hi from a rest stop in Vermont with tasty coffee and wifi :) 

  So SIO features a few information relations of interest.  The most basic is 'refers to',


 which is to say that an entity is mentioned.  If there is an actual description, then we can use 'describes' otherwise, it might only be a reference without further elaboration - 'references'.
Does that help?


On 2012-04-26, at 4:03 PM, "M. Scott Marshall" <mscottmarshall@gmail.com> wrote:

> Hmm. Michel suggested that "set" of relations in November:
> Michel wrote: " there are some basic relations that we can look at,
> for instance, i have defined a wider set of relations as part of my
> SIO ontology: "
> What we were looking for was a way to describe that a given dataset
> might have to do with a number of specific subjects, such as the
> taxonomic identifier of the model organism from which the data was
> collected, but possibly also, the disease or phenotype that was being
> modelled. So, we needed a predicate that was vague enough to express
> such things, yet still be useful in other domains.
> -Scott
> On Thu, Apr 26, 2012 at 9:52 PM, Mark <markw@illuminae.com> wrote:
>> 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
>> "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 .
>>> -Scott
>>> 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 21:31:15 UTC

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