[Bioperl-l] Bio::Ontology overhaul

[Ewan Birney]

On Thu, 27 Feb 2003, Aaron J Mackey wrote:

>
> On Wed, 26 Feb 2003, Hilmar Lapp wrote:
>
> > Guys/gals on the list, please vote: ontology accessible from a term, or
> > the plain name of the ontology suffices?
>

<snip>

>
> Or do I (the lowly biologist trying to program with BioPerl), need to
> instantiate my own OntologyEngineI (and/or OntologyI) before getting at
> OntologyTermI's?
>

My suspicion/hope is that when you are working against Bioperl in a client
mode, the OntologyEngineI and Ontology is magically sorted out for you by
which every implmentation; for example

  Bio::SeqIO - will probably use an in-memory, hard-coded SO-Lite
ontology, which comes with Bioperl

  BioSQL - will use database loaded ontology


The client will be doing these sorts of things:


  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";
    }
  }


One presumable will be able to do things like:

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

and also

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



etc etc...






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