Re: [ontolog-forum] [Obi-devel] FYI: Fwd: Interesting observation about

[Michel Dumontier <michel.dumontier@xxxxxxxxx>]

John,

 You're making some pretty bold statements without appropriate analysis:

1) there are ontologies listed in the NCBO bioportal with more than subclass axioms, but it may be the case that the NCBO web service only provides subclasses from the original ontologies - so.... if you look at the source files, you'll see that they are much richer than this

e.g. http://semanticsciencie.org/ontology/sio.owl

or http://purl.obolibrary.org/obo/obi.owl

also note that the bioportal service consumes many formats (OBO, RRF, OWL, LEXGRID) and generates a common representation

2) it certainly is the case that many terminologies were never designed with formal methods in mind, and that the formalization to OWL leads to an erroneous representation. We have made some effort to accurately translate OBO ontologies that make use of the Relation Ontology with appropriate OWL constructs:

http://www.biomedcentral.com/1471-2105/11/441

3) is entirely speculative and creates no opportunity for meaningful discourse.

4) not true - particularly of biomedical ontologies where the terminology sources have many uses - they have value as common terminology for annotation purposes, data integration, and statistical analysis.  More sophisticated uses include consistency checking and classification, and I would agree that that feature is under-utilized, but that doesn't invalidate the efforts thusfar.

m.

-------- Original Message --------

Subject:	[ontolog-forum] Interesting observation about OWL ontologies
Date:	Thu, 13 Jan 2011 09:17:49 -0500
From:	John F. Sowa <sowa@xxxxxxxxxxx>
Reply-To:	[ontolog-forum] <ontolog-forum@xxxxxxxxxxxxxxxx>
To:	[ontolog-forum] <ontolog-forum@xxxxxxxxxxxxxxxx>

At the end of this note is a comment that was sent to a mailing list
concerning metadata standards by SC32WG2.

I have previously made the observation that many people who use OWL
don't use anything that goes beyond Aristotle's syllogisms.  I cited
the BFO ontology as an example, but I had never done a thorough
analysis of any large collection of OWL ontologies.

But the following observation shows that of the 202 registered
ontologies in the NCBO BioPortal, the *only* relation used in
their triples is rdfs:subClassOf -- i.e., those "ontologies"
are just trivial hierarchies of undefined terms.

This leads to several observations:

  1. Many so-called ontologies written in OWL are nothing more than
     lists of terms organized in a simple hierarchy -- i.e., they
     should be called *terminologies* rather than ontologies.

  2. The people who have been writing those ontologies never saw any
     use for any of the formal methods supported by OWL for defining
     terms and reasoning about them.

  3. They were probably pushed into using OWL by some higher level
     executives who were sold on OWL by hype encoded in glossy slides
     with no supporting evidence.

  4. But the resulting so-called ontologies *cannot* be used for any
     kind of reasoning that goes beyond what could have been done
     with the original terminologies written in ordinary English.

And by the way, I realize that there are useful applications of OWL
when implemented by people who know what they're doing.  But large
numbers of people who have no idea what they should be doing have
been pushed into using a technology they don't understand.

As a result, huge amounts of time, money, and the expertise of
highly-paid professionals have been flushed down the drain for
no useful purpose.

John Sowa

--- Additional Comments From kdkeck@xxxxxxx  2011-01-12 11:49 ET ---

I've used SPARQL to query the NCBO BioPortal for any statements
of the form (?x ?p ?x).  The only statements of that form found,
out of 202 registered ontologies, had p=rdfs:subClassOf.  Such
assertions are strictly redundant--ALL classes are subclasses
of themselves, by definition.

 
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