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RE: blog: semantic dissonance in uniprot

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Tue, 24 Mar 2009 09:52:19 -0700
Message-ID: <C9EDB84D403E654CB78E37A506E406AF022CB8B2@ussemx1101.merck.com>
To: <samwald@gmx.at>, "Bijan Parsia" <bparsia@cs.man.ac.uk>, <public-semweb-lifesci@w3.org>
hi all,

samwald@gmx.at wrote:
>>   Can any one name a real world example of where confusion between an
>> entity and its record was issue?
>>     
>
> I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web are examples. They are just so ill-designed that nobody wants to use them, and nobody CAN use them. The creators of these ontologies were unknowingly meandering between thinking describing things-in-reality, concepts, and abstract database records while creating these ontologies; a no-mans-land where almost any statement is somehow valid, and where there are thousand different ways to talk about a thing, because you are not really sure WHAT you are talking about.  
> Design processes like these lead to the kinds of difficulties described in the classic paper "Are the current ontologies in biology good ontologies?" [1]. I have worked with such ontologies, but they are bordering on being completely unusable -- at least for me.
>
> [1] http://dx.doi.org/10.1038/nbt0905-1095

as a member of the MGED board i can say we took this article that appeared four years ago quite seriously in that it focused on the MGED Ontology.  to be one of the ground breakers, as the MGED Ontology was, is wonderful in the sense that it showed that people could use ontologies to annotate their experiments but, as an early attempt, the design suffered from lack of experience, as was pointed out. 

the effort soon shifted to the Ontology for Biomedical Investigations (OBI)[2] which reached out to a broader participation than MGED.

cheers,
michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com

[2] http://obi-ontology.org/


 

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> samwald@gmx.at
> Sent: Tuesday, March 24, 2009 5:43 AM
> To: Bijan Parsia; public-semweb-lifesci@w3.org
> Subject: Re: blog: semantic dissonance in uniprot
> 
> 
> > On 24 Mar 2009, at 12:20, samwald@gmx.at wrote:
> > 
> > >
> > >>   Can any one name a real world example of where 
> confusion between an
> > >> entity and its record was issue?
> > >
> > > I would say that 80% of the RDF/OWL ontologies lingering 
> somewhere  
> > > on the web are examples.
> > 
> > Such a violation of Sturgeon's Law[1] would be cause for 
> much rejoicing!
> 
> Yes, I was actually thinking about 90% first, but then the 
> OBO Foundry ontologies are becoming more widespread (and do 
> not have this issue), and DBpedia shows some awareness of 
> these issues, too...
> 
> > I'd be interested in doing a survey on this to determine how  
> > widespread the problem really is. Is there a reasonable 
> corpus that  
> > approximates your experience?
> 
> That was my experience when using the entire web as a corpus, 
> i.e., searching for existing ontologies for a certain 
> use-case via Swoogle, Sindice etc.
> 
>  -- Matthias
> -- 
> Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s 
> mit allen: http://www.gmx.net/de/go/multimessenger01
> 
> 
Received on Tuesday, 24 March 2009 16:53:01 UTC

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