[MOBY-l] 2 ontologies

[Bruskiewich, Richard (IRRI)]

If by "biological logic" you mean *real* semantics, then I would hazard to
say that the domain modeling activity of the Generation Challenge Programme
is going in that direction, at least, for crop/plant science (though some of
the semantics is generic to all biology, of necessity).

It is interesting to note that human beings construct domain models, not
machines. Domain models cannot be autogenerated.  Real semantics is what
sets human beings apart from (practically) the rest of the animal kingdom,
let alone, the stupid (but ultra fast) machines that we've created in this
era.

Richard

"Daisy, daaaissy, ...."

-----Original Message-----
From: Benjamin Good [mailto:bmg at sfu.ca] 
Sent: Saturday, 2005 May 28 4:42 AM
To: mobydev; mobyl
Subject: [MOBY-l] 2 ontologies

 From Yan:
  "There is another solution instead which I think is more elegant: 
Associate biological objects with computer data types.
For Example: a DNA Sequence is the biological object but FASTA, EMBL 
and all the fancy bioinformatic formats are its computer 
representation? ."

-Ben -> I agree with this thinking and in fact that was what I was 
trying to suggest.  However, I think that you have things reversed in 
the following statement.

Yan: "So as I see things, we have two ontologies representing two 
logics:
-The biologocial logic represented by the bioMoby ontology
-A data type logic which should be represented by a separated ontology 
with of course our "primitives String/Float/Bytes etc.."

-> Ben
As I understand it, the BioMOBY object ontology is meant to describe 
data-types, not biological logic.  It does a nice job of the former but 
I would say not the latter.  My suggestion is to introduce a separate 
ontology that does describe the biology of the things represented by 
the data-types (that would NOT include things like "FASTA formatted 
sequence"!).   I think this may happen by default when moby-central 
merges with Grimoire/Feta, but this list needs to pay attention!

I think that it is very important to rectify this confusion between 
syntax and semantics as soon as we can.  What happens when the tools 
are written that create bioMoby services automatically from websites 
get going?  I think you will quickly see that the moby object ontology 
loses any notion of "biological logic" as it rapidly becomes populated 
by perfectly syntactically valid machine produced Objects - and this is 
GOOD.  We WANT thousands of services in there and they may require 
thousands of new objects!

Its important to keep in mind the underlying goals of these things.  
The Object ontology exists to ensure interoperability - not 
integration.  To me, that means that I can easily consume any service 
that uses objects from this ontology and it ensures (only helps 
actually) that the data types produced by service providers are 
sensible.  These SYNTACTIC problems are solved quite nicely by the 
Object ontology - regardless of the specific serialization you end up 
choosing and regardless of the name you give to your objects.

The SEMANTIC problems associated with INTEGRATION are different, large 
and growing and will need different solutions.

rant over.

-Ben


http://bioinfo.icapture.ubc.ca/bgood

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