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RE: "factoring out" in the construction of FuGO = the search for "universals"

From: Xiaoshu Wang <wangxiao@musc.edu>
Date: Sat, 8 Jul 2006 08:06:11 -0400
To: <public-semweb-lifesci@w3.org>
Message-ID: <001201c6a286$e7872930$03241780@bioxiao>

> To use the example you have chosen, for an anatomist to want 
> to use FuGO and be ontological compatible, they need only use 
> an ontology founded on the same definition of continuants & 
> occurents.  How does this differ from what I think you are 
> claiming.  An anatomist need not necessarily care about the 
> details of FuGO entities bearing no relation to data they 
> intend to semantically integrate with (such as 
> 'LC_instrument') to remain fundamentally compatible with 
> FuGO.  They only need agree on the definition and use of the 
> foundational levels of the ontology they share in common - in 
> this case 'Continuant', 'Independent_ continuant', and 
> 'Object'.  In fact, this would be encouraged by the OBO 
> Foundry participants - use FuGO for formal semantic 
> descriptions of assay/instrument/reagent provenance and use 
> the Foundational Model of Anatomy to deal with anatomy (right 
> now, just human anatomy, but that is being worked on) - both 
> of which are founded on BFO.

I think we have discussed the problem of "web closure", see Chimezie's wiki
here http://esw.w3.org/topic/HCLS/WebClosureSocialConvention.  We have to
realize that you cannot selectively import a subgraph from an RDF model.
And using owl:import, in effect, tightly bind one ontology to another.  If
ontological terms are not carefully grouped under different namespaces, we
will eventually end up a one-for-all schema, which is neither practical nor
useful.  

> The "modularization" you refer to via namespaces relates to a 
> conceptually different issue, as I see it.  Even though the 
> use of namespace - especially in XML & RDF - has advanced to 
> something considerably beyond its original application of 
> simply avoiding tag/term/name "collisions", the 
> "modularization" namespaces can support in XML space is 
> distinctly different from the "factoring out" of universals 
> to which Trish referred.

When I think of "factoring out", I thought of software engineer's term of
"refactoring" to decouple the hard-coded dependency.  Yes, when I replied to
Trish, I want to state explicitly what I mean by "factoring out".

> Using the namespace facility inherent in XML formalisms might 
> be a useful way of enabling people to exchange different 
> world views for sub-regions of the graph, that's true.  But 
> it is by no means a requirement.  One should still expect 
> whether or not you are using namespaces to chop up or 
> modularize different portions of the ontological graph, you 
> are still following the same principle of extrapolating to 
> universals, even if the universals for "namespace_a"'s 
> coverage of the cardinal parts of a liquid chromatographic 
> apparatus differed from the universals defined for 
> "namespace_b"s coverage of the cardinal parts of a liquid 
> chromatographic apparatus .

I think you misunderstood the topic.  The factoring out to "universals" etc.
is semantic issue.  For instance, what makes a "is_a" relationship, or
Guiono's OntoClean Methodology.  The factoring out that I mean, a.k.a.,
modulization is an engineer issue.  The task is not difficult to envision,
imaging that you are writing an RDF reasoner, and given one assertion from
say ":foo a fugo:continuant", try to play around it and see how many
assertions you will be end up with.  For human beings, there is no such
"engineer" issue.  When we speak one word, we never intend to pull out the
entire dictionary.  But semantic web is dealling with machines.  

> If namespaces were used as the primary means of "factoring 
> out" universals, you could end up with quite a proliferation 
> of namespaces for FuGO - in the extreme - one for every node 
> in the graph.

Yes, of course. It is a price we have to pay in order to maximize the
sharing and reuse of an ontology.  Nothing comes for free.

Of course, how to modulize is more of an art than science.  But there are
certain principles that we can follow.  One is Gruber's "Principle of
minimal ontological commitment" (Gruber, Toward Principles for the Design of
Ontologies Used for Knowledge Sharing, Knowledge Systems Laboratory.
Stanford University., 1993).  The other that I proposed the Principles of
Orthogonal Domain in my manuscripts.   

> I wish I could understand what you describe at 
> http://www.charlestoncore.org/ont/2005/08/o3.htm a little 
> better.  I found your Nature Biotech. paper very clear and 
> extremely helpful in several discussions I've been having on 
> the issue of XML vs. RDF, but I really am having a hard time 
> with your description of O3 on that web page.  Is there a 
> publication where you go into this in more detail?

Yes, I did have a manuscript written and send to Journal of Applied
Ontologies recently.  I tried to keep the informaiton on the web to be
minimal because I don't want to incur any potential conflict.  But I will
send you my manuscript in private.

Xiaoshu
Received on Saturday, 8 July 2006 12:38:35 GMT

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