[Biodevelopers] RDBMS vers new data model

Michel Dumontier micheld at mshri.on.ca
Thu Apr 22 15:05:07 EDT 2004


> IMHO, I think no one datamodel can / should / would or could be set in
> place, rather every biologist makes their own data model either from
> scratch, by combining other datamodels in to larger models and/or with
> available ontologies.

Your statement hardly helps the state of things... which is a disaster from
an integrative and service perspective.  Aside from issues of data quality,
it is current very difficult to make full and accurate database cross
references, nevermind doing proper updates where everybody has their own
accession space.  If each person has their own data model, then it makes it
extremely difficult to share information without having to write additional
code to map your object model to mine.  However, given a standard way of
representing a gene and all associated annotation,  then I could use your
annotation immediately without having to do the tedious mapping  If you only
need a particular aspect of a grander data model for your purposes, then
just use that part.  If you need to extend a data model, for whatever
reason, then there should be a process (and XML/ASN.1 based data models are
fully extensible).  However, experience says that once you start building a
'new'/'better suited' model, you'll end up re-inventing a well-thought-out
model.  Having standardized, even peer-reviewed, data models promotes a
better computing environment and makes it easier to make advances in
science.  For most of us, Science, not technology or programming, is the
ultimate pursuit.


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