Bio::Ontology::Ontology - standard implementation of an Ontology use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf = Bio::Ontology::Term->new(-name => "OBF"); my $partof = Bio::Ontology::RelationshipType->get_instance("PART_OF"); $ont->add_term($bp); $ont->add_term($obf); $ont->add_relationship($bp, $obf, $partof); # then query my @terms = $ont->get_root_terms(); # "OBF" my @desc = $ont->get_descendant_terms($terms[0], $partof); # "Bioperl" # ... see methods for other ways to query # for advanced users, you can re-use the query engine outside of an # ontology to let one instance manage multiple ontologies my $ont2 = Bio::Ontology::Ontology->new(-name => "Foundations", -engine => $ont->engine()); This is a no-frills implementation of Bio::Ontology::OntologyI. The query functions are implemented by delegation to an OntologyEngineI implementation.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email hlapp at gmx.net Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Ontology::Ontology(); Function: Builds a new Bio::Ontology::Ontology object Returns : an instance of Bio::Ontology::Ontology Args :

name
Title : name Usage : $obj->name($newval) Function: Get/set the name of the ontology. Example : Returns : value of name (a scalar) Args : on set, new value (a scalar or undef, optional)

authority
Title : authority Usage : $obj->authority($newval) Function: Get/set the authority for this ontology, for instance the DNS base for the organization granting the name of the ontology and identifiers for the terms. This attribute is optional and should not generally expected by applications to have been set. It is here to follow the rules for namespaces, which ontologies serve as for terms. Example : Returns : value of authority (a scalar) Args : on set, new value (a scalar or undef, optional)

definition
Title : definition Usage : $obj->definition($newval) Function: Get/set a descriptive definition of the ontology. Example : Returns : value of definition (a scalar) Args : on set, new value (a scalar or undef, optional)

identifier
Title : identifier Usage : $id = $obj->identifier() Function: Get an identifier for this ontology. This is primarily intended for look-up purposes. The value is not modifiable and is determined automatically by the implementation. Also, the identifier's uniqueness will only hold within the scope of a particular application's run time since it is derived from a memory location. Example : Returns : value of identifier (a scalar) Args :

close
Title : close Usage : Function: Release any resources this ontology may occupy. In order to efficiently release unused memory or file handles, you should call this method once you are finished with an ontology. Example : Returns : TRUE on success and FALSE otherwise Args : none

engine
Title : engine Usage : $engine = $obj->engine() Function: Get/set the ontology engine to which all the query methods delegate. Example : Returns : an object implementing L<Bio::Ontology::OntologyEngineI> Args : on set, new value (an object implementing L<Bio::Ontology::OntologyEngineI>, or undef)

add_term
Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store If the ontology property of the term object was not set, this implementation will set it to itself upon adding the term. Example : $oe->add_term($term) Returns : its argument. Args : object of class TermI.

add_relationship
Title : add_relationship Usage : add_relationship(RelationshipI relationship): RelationshipI add_relatioship(TermI subject, TermI predicate, TermI object) Function: Adds a relationship object to the ontology engine. Example : Returns : Its argument. Args : A RelationshipI object.

get_relationships
Title : get_relationships Usage : get_relationships(TermI term): RelationshipI[] Function: Retrieves all relationship objects in the ontology, or all relationships of a given term. Example : Returns : Array of Bio::Ontology::RelationshipI objects Args : Optionally, a Bio::Ontology::TermI compliant object

get_predicate_terms
Title : get_predicate_terms Usage : get_predicate_terms(): TermI[] Function: Retrieves all relationship types. Example : Returns : Array of TermI objects Args :

get_child_terms
Title : get_child_terms Usage : get_child_terms(TermI term, TermI[] predicate_terms): TermI[] Function: Retrieves all child terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_child_terms is a special case of get_descendant_terms, limiting the search to the direct descendants. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.

get_descendant_terms
Title : get_descendant_terms Usage : get_descendant_terms(TermI term, TermI[] rel_types): TermI[] Function: Retrieves all descendant terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.

get_parent_terms
Title : get_parent_terms Usage : get_parent_terms(TermI term, TermI[] predicate_terms): TermI[] Function: Retrieves all parent terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_parent_terms is a special case of get_ancestor_terms, limiting the search to the direct ancestors. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.

get_ancestor_terms
Title : get_ancestor_terms Usage : get_ancestor_terms(TermI term, TermI[] predicate_terms): TermI[] Function: Retrieves all ancestor terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.

get_leaf_terms
Title : get_leaf_terms Usage : get_leaf_terms(): TermI[] Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants. Example : @leaf_terms = $obj->get_leaf_terms() Returns : Array of TermI objects. Args :

get_root_terms()
Title : get_root_terms Usage : get_root_terms(): TermI[] Function: Retrieves all root terms from the ontology. Root term is a term w/o descendants. Example : @root_terms = $obj->get_root_terms() Returns : Array of TermI objects. Args :

get_all_terms
Title : get_all_terms Usage : get_all_terms: TermI[] Function: Retrieves all terms from the ontology. We do not mandate an order here in which the terms are returned. In fact, the default implementation will return them in unpredictable order. Example : @terms = $obj->get_all_terms() Returns : Array of TermI objects. Args :

find_terms
Title : find_terms Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263"); Function: Find term instances matching queries for their attributes. An implementation may not support querying for arbitrary attributes, but can generally be expected to accept -identifier and -name as queries. If both are provided, they are implicitly intersected. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : Named parameters. The following parameters should be recognized by any implementations: -identifier query by the given identifier -name query by the given name

relationship_factory
Title : relationship_factory Usage : $fact = $obj->relationship_factory() Function: Get (and set, if the engine supports it) the object factory to be used when relationship objects are created by the implementation on-the-fly. Example : Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI compliant object) Args :

term_factory
Title : term_factory Usage : $fact = $obj->term_factory() Function: Get (and set, if the engine supports it) the object factory to be used when term objects are created by the implementation on-the-fly. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI compliant object) Args :