- From: Michel Dumontier <michel.dumontier@gmail.com>
- Date: Thu, 26 Apr 2012 17:30:41 -0400
- To: "M. Scott Marshall" <mscottmarshall@gmail.com>
- Cc: Mark <markw@illuminae.com>, Jim McCusker <james.mccusker@yale.edu>, HCLS <public-semweb-lifesci@w3.org>
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 UTC