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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',

http://semanticscience.org/resource/SIO_000628

 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?

m


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 GMT

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