Perl Conference Handout

Steve A. Chervitz
Fri, 8 Aug 1997 18:00:31 -0700 (PDT)

>   I guess the question is does a sequence "hava a" structure or does a 3D
> structure "have a" sequence.   I guess, really it is a molecule which "has
> a" sequence, and (2d and 3d) structure.  

That is a nice way to frame it. Biological objects are multi-faceted and 
can be examined through various semantic filters. We encounter difficulty 
when we try to model a single real biological object using multiple
conceptual objects which embody different aspects of the real object. The 
problem is to figure out how to link all of the conceptual objects into a 
coherent whole.

>   Basically, I think that the objects should model biology as practically
> used, rather than biology as it presumably exists.  Therefore, knowing 1D
> sequence does not imply knowledge of 3D structure (even though
> biologically, it does).

This is a no less daunting task (well, maybe slightly less daunting :)