[Bioperl-l] common ancestor for ontology terms

[Matthew Pocock]

The way we're tying to do this, Ontology is pure-data.
OntologyOps is an interface that has
limited-namespace-aware versions of common optimizable
operations. This includes transient closure. Multiple
namespaces that shair some backing data (like in
biosql) can return the same OntologyOps.

OntoTools has the real methods that users invoke for
checking inheritance and transient closures and
things. This tools class is responsible for waling
between the different ops domains.

Our first attempt made Ontology 'clever', but that
realy sucks because you never know what extra external
info you should be dealing with to answer a lookup.
For example, if it is provable that _my_inherits_from_
inherits from _isa_, then in the ontology object, a
call to something like 'a _isa_ b' on an Ontology will
fail if they are infact linked by _my_inherits_from_,
will fail if invoked via an OntologyOps that doesn't
directly contain both _my_inherits_from_ and _isa_,
but will succeed if you go via OntoTools.

Particularly if we start to use a implies b, where a
and/or b are relations themselves (e.g. X has_a Y, x
is_a X => x has_a Y), it becomes nearly impossible to
mix up the things we know (have defined as being true)
and the things we have proven (using some
graph-walking strategy) without serious brain melt.

YMMV

Matthew

 --- Chris Mungall <cjm at fruitfly.org> wrote: > 

> Maybe its
> better to keep *all*
> these methods (including common_ancestor_path) out
> of the classes, and
> keep the object model focused on modeling the data.
> I'm not really sure
> what encapsulation buys you here. The only use I can
> think of is if you
> wanted to hide an in-memory/on-disk closure and use
> that in your
> calculation behind the scenes. But I don't think
> that's such a good idea.
> I guess what I'm suggesting is contrary to the
> spirit of bioperl and OO in
> general, but I would like to see more seperation of
> data from behaviour.
> 
> 

__________________________________________________
Yahoo! Plus
For a better Internet experience
http://www.yahoo.co.uk/btoffer