Bio::Ontology::OntologyI - Interface for an ontology implementation # see method documentation This describes the minimal interface an ontology implementation must provide. In essence, it represents a namespace with description on top of the query interface OntologyEngineI. This interface inherits from Bio::Ontology::OntologyEngineI.

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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 email or 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 _

name
Title : name Usage : $obj->name($newval) Function: Get/set the name of this ontology. Example : Returns : value of name (a scalar) Args :

authority
Title : authority Usage : $auth = $obj->authority() 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 :

identifier
Title : identifier Usage : $id = $obj->identifier() Function: Get an identifier for this ontology. This is primarily intended for look-up purposes. Clients should not expect the value to be modifiable, and it may not be allowed to set its value from outside. Also, the identifier's uniqueness may only hold within the scope of a particular application's run time, i.e., it may be a memory location. Example : Returns : value of identifier (a scalar) Args :

definition
Title : definition Usage : $def = $obj->definition() Function: Get a descriptive definition for this ontology. Example : Returns : value of definition (a scalar) Args :

close
Title : close Usage : Function: Release any resources this ontology may occupy. In order to efficiently release used 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 Their documentations are copied here for completeness. In most use cases, you will want to access the query methods of an ontology, not just the name and description ...

add_term
Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store. For ease of use, if the ontology property of the term object was not set, an implementation is encouraged to 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 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 from this ontology engine, or all relationships of a term if a term is supplied. Example : Returns : Array of Bio::Ontology::RelationshipI objects Args : None, or a Bio::Ontology::TermI compliant object for which to retrieve the relationships.

get_predicate_terms
Title : get_predicate_terms Usage : get_predicate_terms(): TermI[] Function: Example : Returns : 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. 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. 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. 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. 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 implementation: -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 implementation 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 implementation 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 :