[Bioperl-l] GO parser

[Allen Day]

is anyone working on a script that will load GO terms into chado, or chado
via the godb views?  i seem to remember something along these lines being
mentioned, but i don't remember by whom or where.

sorry to those receiving this multiple times from the crosspost.

-Allen


On Thu, 14 Nov 2002, Chris Mungall wrote:

> Cool, thanks Chris
> 
> is this just for go ontology files, or for the other stuff too (defs,
> xrefs, associations)
> 
> On Thu, 14 Nov 2002, Chris Zmasek wrote:
> 
> > All:
> >
> > I just submitted all the necessary classes for my "simpleGOparser" (this parser returns a "simpleGOengine").
> > In particular, these are:
> > - Ontology/OntologyEngineI.pm (by Peter Dimitrov)
> > - Ontology/Relationship.pm
> > - Ontology/RelationshipI.pm (by Peter Dimitrov)
> > - Ontology/RelationshipType.pm
> > - Ontology/simpleGOengine.pm
> > - Ontology/simpleGOparser.pm
> >
> > Tests and data:
> > - t/simpleGOparser.t
> > - t/data/component.ontology.test
> > - t/data/GO.defs.test
> >
> > Example script:
> > - examples/ontology/simpleGOparser_example.pl
> >
> >
> > Please note that this parser (or to be more precise, "simpleGOengine") requires the Graph.pm module from CPAN.
> >
> > Christian [czmasek@gnf.org]
> >
> > PS:
> > Here's an example on how to use the parser:
> >
> > use Bio::Ontology::simpleGOparser;
> >
> >
> > my $parser = Bio::Ontology::simpleGOparser->new( -go_defs_file_name    => "GO.defs",
> >                                                  -components_file_name => "component.ontology",
> >                                                  -functions_file_name  => "function.ontology",
> >                                                  -processes_file_name  => "process.ontology" );
> >
> > my $engine = $parser->parse();
> >
> > my $IS_A    = $engine->is_a_relationship();
> > my $PART_OF = $engine->part_of_relationship();
> >
> >
> > # root terms
> > # ----------
> >
> > print scalar( $engine->get_root_terms() ), "\n";
> >
> > print( ( $engine->get_root_terms() )[ 0 ]->to_string(), "\n" );
> >
> > print "\n\n";
> >
> >
> > # parent terms
> > # ------------
> >
> > my @parents1 = $engine->get_parent_terms( "GO:0045474", $IS_A );
> >
> > my @parents2 = $engine->get_parent_terms( $parents1[ 0 ] );
> >
> > foreach my $p ( @parents2 ) {
> >     print $p->to_string(), "\n";
> > }
> >
> > print "\n\n";
> >
> >
> >
> > # child terms
> > # -----------
> >
> >
> > my @child0 = $engine->get_child_terms( ( $engine->get_root_terms() )[ 0 ] );
> >
> > foreach my $c ( @child0 ) {
> >     print $c->to_string(), "\n";
> > }
> >
> > print "\n\n";
> >
> > my @child1 = $engine->get_child_terms( "GO:0008044", $IS_A );
> >
> > foreach my $cc ( @child1 ) {
> >     print $cc->to_string(), "\n";
> > }
> >
> > print "\n\n";
> >
> >
> > # ancestor terms
> > # --------------
> >
> > my @ancestor1 = $engine->get_ancestor_terms( "GO:0007323", $PART_OF );
> >
> >
> >
> > # descendant terms
> > # ----------------
> >
> > my @descendant1 = $engine->get_descendant_terms( "GO:0007323", $PART_OF );
> >
> >
> >
> > # relationships
> > # -------------
> >
> > my @rel1 = $engine->get_relationships( "GO:0007323", $PART_OF, $IS_A );
> >
> >
> > # leaf terms
> > # ----------
> >
> > my @l1 = $engine->get_leaf_terms();
> >
> >
> > # get term with id
> > # ----------------
> >
> > my $term = $engine->get_term( "GO:0001661" );
> >
> >
> > # all terms
> > # ---------
> >
> > my @terms = $engine->each_term();
> >
> >
> > exit( 1 );
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
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