Re: Rules

>>>>> "CM" == Chris Mungall <cjm@fruitfly.org> writes:

  CM> Definitely - although I don't think OWL/SWRL is quite the right tool for
  CM> this job yet

  CM> although perhaps getting closer:

  CM> Putting OWL in Order: Patterns for Sequences in OWL Nick Drummond1, Alan
  CM> Rector1, Robert Stevens1, Georgina M2Matthew Horridge1, Hai H. Wang1,
  CM> Julian Seidenberg1
  CM> http://owl-workshop.man.ac.uk/acceptedLong/submission_12.pdf

  CM> (I'm not a big fan of the modeling biological sequences as lists
  CM> approach, but I think the results could be replicated using a realist
  CM> representation)


There is a much more relevant paper by some of the same authors.

  author =       {Wolstencroft, K. and Lord, P. and Tabernero, L. and
                  Brass, A. and Stevens, R.},
  title =        {{Protein classification using ontology
                  classification}},
  journal =      {Bioinformatics},
  volume =       22,
  number =       14,
  pages =        {e530-538},
  doi =          {10.1093/bioinformatics/btl208},
  year =         2006,

We can define proteins and classes of proteins in OWL and in some
circumstances this can be useful. 

I think, though, that it's a danger for us to say that because we can define
things, we should. At times, it's better to allow things to be self-standing
kinds, and leave the details of the definition to authors. 

Uniprots rules for distinguishing between one protein and another are complex,
and I can't see the point of codifying them in OWL (even if you could). 

Of course, there may be times when you need to make separations that uniprot
doesn't -- two isoforms may have the same uniprot ID -- but you could still
make this distinction with reference to uniprot. 

Phil