W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2011

Re: Relations in RDF

From: Chris Mungall <cjmungall@lbl.gov>
Date: Wed, 4 May 2011 14:27:30 -0700
Cc: HCLS <public-semweb-lifesci@w3.org>, "James Malone" <malone@ebi.ac.uk>, "M. Scott Marshall" <mscottmarshall@gmail.com>
Message-Id: <150935B4-9EFE-45A9-BFF0-D0F84ADFB0C3@lbl.gov>
To: "Mark Wilkinson" <markw@illuminae.com>
A number of ontologies are starting to use "shortcut" relations. These are expanded to more complex class expressions prior to OWL reasoning:

http://precedings.nature.com/documents/5292/version/1
http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html#7

On May 4, 2011, at 9:00 AM, Mark Wilkinson wrote:

> Heya,
> 
> My personal take on this is that it becomes a trade-off.  More granular predicates generally means that you are creating less descriptive Classes (i.e. that the Class does not have a lot of class-defining properties).  So while more descriptive predicates are good for SPARQL querying, they are less good for DL reasoning (class reasoning is ~more powerful than predicate reasoning)
> 
> That's a superficial view, but it's something that we have also been struggling with.  We've tended to try bridging the two approaches by defining elaborate classes with "basic" predicates, and then minting new, more descriptive predicates that join these classes as well.
> 
> Don't know if I am explaining myself clearly :-/
> 
> M
> 
> 
> 
> On Wed, 04 May 2011 08:42:21 -0700, James Malone <malone@ebi.ac.uk> wrote:
> 
>> Hi Scott, All,
>> 
>> I was wondering what the general take is on predicates in RDF representations used by the HCLS group. I've been looking at our RDF model for Gene Expression Atlas at EBI and presently I'm using the same "is_about" relation for a lot of the predicates as this is the lowest level of constraint from the OBO Foundry folks for some of these information relations. Alan Ruttenberg tells me that empirical evidence suggests that using a larger number of relationships correlates to poorer ontologies. However, I've also been told from various RDF advocates that having more granular level predicates is useful for querying. Are there any thoughts from the group on this? I have no preconceptions here (I have no reason to disbelieve Alan or the RDF folks) so open to thoughts and suggestions.
>> 
>> Cheers,
>> 
>> James
>> 
> 
> 
> -- 
> Dr. Mark Wilkinson
> Assistant Professor, Medical Genetics
> PI Bioinformatics, Institute for Heart and Lung Health
> St. Paul's Hospital/UBC
> Vancouver, BC, Canada
> 
Received on Wednesday, 4 May 2011 21:30:50 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:01 GMT