[BioSQL-l] Re: [Bioperl-l] parent <-> subject etc

[Matthew Pocock]

> One should note that
> "commutativity" in grammar is written with a "pair"
> as the subject: "These
> two things are the same".  But in our data models
> all we get to do is "A
> is the same as B; B is the same as A".  Is there
> some ontology-savvy
> solution to this small conundrum?

One way to model this is to have some declaration
that:

(A is_the_same_as B) identity (B is_the_same_as A)

which is the same as declaring:

identity is_a symetrical_relation

The other way is to use sets:

A member_of anonymous_set_X
B member_of anonymous_set_X

anonymous_set_X set_property synonymns

Goodness knows. Far to many ways to represent this.
IMHO the two ways out are a) extremely small number of
'ways we do things' or b) allow flexibility but rely
on predicates on relations to let things be
introspected e.g. discover that synonyms is
symetrical.

A is the quickest if you need to get something working
in a time-frame, but very constraining. Effectively,
you will need more special-case handlers for each
predicate. B is more work (you basicaly need a full
reasoning engine) but is infinitely extensible. In
practice, most interesting questions may well need the
full functionality of B - e.g. validate feature
locations and types relative to rules about feature
containment and SO terms where the features are
actualy labelled by EMBL feature types.

Which way should we jump? I think BioJava will go
route B. But, it's a little scarey making the full set
of predicates just another pot of data you can reason
over.

Matthew

> 
> Great discussion; I do wish we had it earlier. 
> There's now at least 4
> ontology implementations floating about, all with
> strengths and
> weaknesses.
> 
> -Aaron
> 
> -- 
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey at virginia.edu
> 
> 
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> BioSQL-l at open-bio.org
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