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Re: [ontac-forum] lattice of ontology

To: "ONTAC-WG General Discussion" <ontac-forum@xxxxxxxxxxxxxx>
From: "Azamat" <abdoul@xxxxxxxxxxxxxx>
Date: Thu, 22 Dec 2005 17:14:28 +0200
Message-id: <006d01c6070a$6999c3b0$f802960a@az00evbfog6nhh>
Paul wrote:
''I see the OWL projects fail because what is attempted might not be doable 
using RDF plus logic organized as "theories".  ...''But OWL seems mandated 
by government work, and many of us simply cannot understand why the 
continued support.''    (01)

It must be acknowledge that much intelligence, effort and logical skill were 
put up in the project proposed to be a standard SW language. But appears in 
vain. This language is fundamentally defective for several reasons:
I. Its subject matter is not representing the basic kinds of entities and 
relationships with their properties and instances, but rather ''the meaning 
of terms in vocabularies and the relationships between those terms'';
II. It also repeated a common confusion of viewing ontologies as the content 
theory of classes partitioned from their vital part, the mechanism theories 
of rules prescribing general reasoning strategies about things ( and now 
trying to patch the 'black hole' with the SW Rule Langauge);
III. It is mainly constructed as an extension of formal logical constructs: 
classes, attributes, relationships, individuals, and values.    (02)

As expected results, there are at least two fundamental obstacles which the 
developers of the SW are striving to overcome, understandibility and 
interoperability. Namely:
1. Negotiation of the meanings of the real world, scientific and business 
terms with the significance of the machine-oriented notations of RDF-classes 
and OWL constructs;
2. Unreliability and distrust of RDF/OWL-based rule systems which semantics 
are not supported  neither with world knowledge models nor with natural 
language; the errors may come from the RDF/OWL data, rules, context or 
reasoning engines themselves.    (03)

Here is an example how a simple question "Find genes
 associated with human diseases" is manually RDF coded:    (04)

> rulebase trans{ infer {[rdfs:subClassOf] ?a ?c} from
> {[rdfs:subClassOf] ?a ?b} and {[rdfs:subClassOf] ?b ?c}; infer
> {[uni:organism] ?p ?o} from {[rdfs:subClassOf] ?x ?o} and
> {[uni:organism] ?p ?x}; } SELECT TOP 10 ?gene, ?name, ?text USING
> uniprot RULEBASE trans WHERE {[uni:organism] ?protein
> [urn:lsid:uniprot.org:taxonomy:9606]} and {[rdf:type] ?protein
> [uni:Protein]} and {[uni:annotation] ?protein ?annotation} and
> {[rdf:type] ?annotation [uni:Disease_Annotation]} and
> {[uni:encodedBy] ?protein ?gene} and {[uni:name] ?gene ?name} and
> {[rdfs:comment] ?annotation 
> ?text}http://labs.intellidimension.com/uniprot/    (05)


Paul said:
''The government goes its merry way listening to high priests like Hendler 
and Berners-Lee...and yet
the real work is done elsewhere.  If it where not for peer review, the 
community might actually get on to talking about real work''.    (06)

These are rather more ethical and political issues. Science looks no more 
the quest for the truth for its own sake. It is more a degenerate sort of 
business enterprise with all ugly features typical for this sort of human 
activity, a shameful and ruthless competition for all sorts  of financial 
aids [government subsidies, subventions, grants, fellowships, etc.] acquired 
as the public gifts usually without any real compensation. Just ride the 
wave of public inability to understand all the complexities of modern 
Science and Technology, collect like(mean)-minded teams, declare yourself 
'World Consortium' or, at least, 'KW excellence', and waste money on 
conferences, simposia, workshops, and other pleasing but useless gatherings. 
As the deliverables, if you are asked for this at all, just put some 
quasi-academic rubish published by the assemblages you organized on the 
public money just to dump your trash in the proceedings printed again for 
the public funds..    (07)



----- Original Message ----- 
From: "Paul S Prueitt" <psp@xxxxxxxxxxxxxxxxxx>
To: "ONTAC-WG General Discussion" <ontac-forum@xxxxxxxxxxxxxx>
Sent: Thursday, December 22, 2005 2:04 AM
Subject: RE: [ontac-forum] lattice of ontology    (08)


>
>
>
> well, this discussion on lattice of theories seems to be missing a lot.
> Perhaps we would see why it became part of the ONTAC discussion only if we
> know about things happening behind the scenes.  Micro-theories was 
> something
> that came up with Doug system, can all micro-theories by usefully mapped 
> to
> a single lattice?  But somehow I feel that there is no fire behind this
> smoke.
>
> John, the comparison to the integers seems very weak.  As a historical 
> fact,
> the integers placed a key role in the development of modern civilizations.
> (It is not clear that counting was universally recognized - not by Toltec
> (indigenous Mexican) or by some indigenous peoples in Australia.)
>
> Lev Goldfarb develops a wonderful new approach on non-numeric models of
> ontological realities - particularily relational models that do not borrow
> heavily from the notion of quantification.
>
> He asks: "Is there a different mathematics, a mathematics of generatively
> structured entities,  that would explain the biological, or structural,
> "measurement" processes?"
>
> http://www.cs.unb.ca/profs/goldfarb/
>
>
>
> Ring theory is a Platonic form, why not suggest that we standardize around
> ontological theories that form rings?  Or perhaps we should talk about 
> fiber
> bundles of inferences.  These are Platonic also.
>
> You said:
>
> "The reason why a lattice is better than the
> integers is that the integers are linearly ordered,
> but a lattice has a partial order, which allows more
> options in the way one theory is related to any other."
>
> <end quote>
>
>
> But in both cases, the ordering relationship is a single formally defined
> relationship.  This is contrasted with the "classes" of relationships
> between natural occuring concepts when experienced and communicated within
> human communities.
>
> oh well, I give up on this discussion regarding a lattice of theories - it
> just does not make sense and no one - John in particular - gives a reason
> for talking about it.  The hand waving just become a habit after a while.
>
>
> I am not sure what I want to suggest.  The government goes its merry way
> listening to high priests like Hendler and Berners-Lee (and John) and yet
> the real work is done elsewhere.  If it where not for peer review, the
> community might actually get on to talking about real work.
>
>
> For those who might like to have serious discussions, please send me a
> separate email.
>
> psp@xxxxxxxxxxxxxxxxxx
>
>
>
>
>
>
>
>
>
>
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