[Bioperl-l] Bio::Ontology overhaul

[Aaron J Mackey]

Fantastic, code examples ... examining in more detail:

I. obtain an ontology term (and its parent ontology) from a seqfeature:

>   my $seqin = Bio::SeqIO->new( -format => 'embl');
>   while (my $seq = $seqin->next_seq()) ) {
>     foreach my $sf ( $seq->get_all_SeqFeatures() ) {
>       # unclear whether OntologyTermI's have an as_string method
>       print "Ooooh. It has ontology term ",$sf->type->as_string," from
> ontology ",$sf->type->ontology->name,"\n";
>     }
>   }

Great.  From this perspective, clearly an OntologyTermI has to somehow be
able to get to their parent OntologyI; Lincoln, how would a
OntologyHandleI help get around a "backref" to OntologyI from
OntologyTermI in this case?

II. Determine the "inheritance" of a term from another term (both obtained
via seqfeatures)

>   if( $sf->type->is_child_of($anothersf->type) ) {
>      # do something
>   }

Presumably, this gets passed off to the OntologyEngineI:
sub OntologyTermI::is_child_of {
   my $self = shift;
   return $self->ontology->engine->is_child_of($self, @_)
}

Q. Does is_child_of do path traversal?

Q. Can is_child_of be given the "predicate" type [ i.e.
$termA->is_child_of($termB, "isa") ]

Q. If "predicate" isn't given, what is assumed?

Q. What about two terms that are related through differing "predicates"
(i.e A isa B, B partof C, what is the relationship between A and C?)

III. Same as II, but with an "anonymous" term:

>   # this might not be the right class for this
>   # Hilmar and Chris to agree
>   $ontology = Bio::Ontology::Factory->new( -ontology => 'SO');

  $gene = $ontology->get_term("gene");

  # ...

  if($sf->type->is_child_of($gene)) {
    # do something
  }

BTW, why didn't this start as:

$ontology = new Bio::Ontology 'SO';

or, if necessary:

$ontology = new Bio::Ontology -name => 'SO',
                              -factory => "MyFunkyOntologyFactory";



Q. Should "is_child_of" be better as "is_subject_of" to reflect the
subject/object/predicate ontology term paradigm?

Q. Does is_subject_of need to know ontology namespace as well as
applicable predicate term(s)?

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu