[Top] [All Lists]

Re: [ontac-forum] taxonomy of relationships

To: ONTAC-WG General Discussion <ontac-forum@xxxxxxxxxxxxxx>
From: "I.N. Sarkar" <sarkar@xxxxxxxx>
Date: Sat, 26 Nov 2005 14:14:38 -0500
Message-id: <4258AE2C-C282-46CC-9EEF-434A55E5E4D6@xxxxxxxx>
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
--    (06)

Message Archives: http://colab.cim3.net/forum/ontac-forum/
To Post: mailto:ontac-forum@xxxxxxxxxxxxxx
Shared Files: http://colab.cim3.net/file/work/SICoP/ontac/
Community Wiki: 
http://colab.cim3.net/cgi-bin/wiki.pl?SICoP/OntologyTaxonomyCoordinatingWG    (07)
<Prev in Thread] Current Thread [Next in Thread>