Well, maybe in some instances, yes- However, in many other instances
this is not the case. Some molecular structures may indeed act
independently, and there are numerous examples of genetic disorders
that can be associated with single genes, for example Mendelian
disease are often associated with just single genes. Environment
*may* play a factor in some diseases, but it is not the rule.
Biochemistry and immunobiology are very distinct fields, so in your
example, one would probably have separate ontological representations
depending on whether one is focused on immunobiological or
biochemical aspects of the molecule. What is important, and this
might be what you are getting at, is that relationships may be needed
between biochemical and immunobiological ontologies. But, if the
point is to make an upper level representation of all this, maybe the
best way is to not obfuscate the known relationships -- and the known
homologies -- with uncertainty. Or at minimum provide a means to
extract just the simple ontological representations that are at the
higher level-- and leave the nuances of biology or whatever specific
field to the domain expert ontologies being full aware that they will
always be in flux -- which is the whole point of this endeavor, I
believe. (01)
Best. (02)
-Neil. (03)
On 2005 Nov 26, at 13:53 EST, Paul S Prueitt wrote: (04)
> One MUST say that the environment co-caused the state s(3) of the
> macromolecule. How does this happen? An answer might be that
> there is a
> templating of environment to local protein reactions by the "needs"
> of the
> environment. So in each case, s(i) (where i is a ordering index) is a
> representation of the state of the macromolecule in a reaction
> chain which
> is produced (on a regular basis !) by cellular mechanisms. (05)
--
Indra Neil Sarkar, PhD
Bioinformatics Associate
Divisions of Invertebrate Zoology
& Library Services
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024 USA
+1 212 769 5571
--
sarkar@xxxxxxxx
www.genomeCurator.org/people/sarkar
-- (06)
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