SimpleOntologyEngine - Implementation of OntologyEngineI interface my $soe = Bio::Ontology::SimpleOntologyEngine->new; This is a "simple" implementation of Bio::Ontology::OntologyEngineI.

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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 email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Email dimitrov@gnf.org Hilmar Lapp, hlapp at gmx.net The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $soe = Bio::Ontology::SimpleOntologyEngine->new; Function: Initializes the ontology engine. Example : $soe = Bio::Ontology::SimpleOntologyEngine->new; Returns : Object of class SimpleOntologyEngine. Args :

_instantiated_terms_store
Title : _instantiated_terms_store Usage : $obj->_instantiated_terms_store($newval) Function: Example : Returns : hash Args : empty hash

mark_instantiated
Title : mark_instantiated Usage : $self->mark_instantiated(TermI[] terms): TermI[] Function: Marks TermI objects as fully instantiated, allowing for proper counting of the number of terms in the term store. The TermI objects has to be already stored in the term store in order to be marked. Example : $self->mark_instantiated($term); Returns : its argument or throws an exception if a term is not in the term store. Args : array of objects of class TermI.

mark_uninstantiated
Title : mark_uninstantiated Usage : $self->mark_uninstantiated(TermI[] terms): TermI[] Function: Marks TermI objects as not fully instantiated, Example : $self->mark_uninstantiated($term); Returns : its argument or throws an exception if a term is not in the term store(if the term is not marked it does nothing). Args : array of objects of class TermI.

_term_store
Title : term_store Usage : $obj->_term_store($newval) Function: Example : Returns : reference to an array of Bio::Ontology::TermI objects Args : reference to an array of Bio::Ontology::TermI objects

add_term
Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store. Marks the term fully instantiated by default. Example : $soe->add_term($term) Returns : its argument. Args : object of class TermI.

get_term_by_identifier
Title : get_term_by_identifier Usage : get_term_by_identifier(String[] id): TermI[] Function: Retrieves terms from the term store by their identifier field, or undef if not there. Example : $term = $soe->get_term_by_identifier("IPR000001"); Returns : An array of zero or more Bio::Ontology::TermI objects. Args : An array of identifier strings

_get_number_rels
Title : get_number_rels Usage : Function: Example : Returns : Args :

_get_number_terms
Title : _get_number_terms Usage : Function: Example : Returns : Args :

_relationship_store
Title : _storerelationship_store Usage : $obj->relationship_store($newval) Function: Example : Returns : reference to an array of Bio::Ontology::TermI objects Args : reference to an array of Bio::Ontology::TermI objects

_inverted_relationship_store
Title : _inverted_relationship_store Usage : Function: Example : Returns : reference to an array of Bio::Ontology::TermI objects Args : reference to an array of Bio::Ontology::TermI objects

_relationship_type_store
Title : _relationship_type_store Usage : $obj->_relationship_type_store($newval) Function: Example : Returns : reference to an array of Bio::Ontology::RelationshipType objects Args : reference to an array of Bio::Ontology::RelationshipType objects

_add_relationship_simple
Title : _add_relationship_simple Usage : Function: Example : Returns : Args :

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(): RelationshipI[] Function: Retrieves all relationship objects. Example : Returns : Array of RelationshipI objects Args :

get_all_relationships
Title : get_all_relationships Usage : get_all_relationships(): RelationshipI[] Function: Retrieves all relationship objects. Example : Returns : Array of RelationshipI objects Args :

get_predicate_terms
Title : get_predicate_terms Usage : get_predicate_terms(): TermI[] Function: Retrives all relationship types stored in the engine Example : Returns : reference to an array of Bio::Ontology::RelationshipType objects Args :

_is_rel_type
Title : _is_rel_type Usage : Function: Example : Returns : Args :

_typed_traversal
Title : _typed_traversal Usage : Function: Example : Returns : Args :

get_child_terms
Title : get_child_terms Usage : get_child_terms(TermI term, TermI[] predicate_terms): TermI[] get_child_terms(TermI term, RelationshipType[] 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[] get_child_terms(TermI term, RelationshipType[] predicate_terms): 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. Uses _typed_traversal to find all descendants. 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[] get_child_terms(TermI term, RelationshipType[] 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[] get_child_terms(TermI term, RelationshipType[] 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. Uses _typed_traversal to find all ancestors. 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 :

_filter_repeated
Title : _filter_repeated Usage : @lst = $self->_filter_repeated(@old_lst); Function: Removes repeated terms Example : Returns : List of unique TermI objects Args : List of TermI objects

get_all_terms
Title : get_all_terms Usage : get_all_terms(): TermI[] Function: Retrieves all terms currently stored in the ontology. Example : @all_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. This implementation can efficiently resolve queries by identifier. 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/set 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 : on set, a Bio::Factory::ObjectFactoryI compliant object

term_factory
Title : term_factory Usage : $fact = $obj->term_factory() Function: Get/set the object factory to be used when term objects are created by the implementation on-the-fly. Note that this ontology engine implementation does not create term objects on the fly, and therefore setting this attribute is meaningless. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object

_filter_unmarked
Title : _filter_unmarked Usage : _filter_unmarked(TermI[] terms): TermI[] Function: Removes the uninstantiated terms from the list of terms Example : Returns : array of fully instantiated TermI objects Args : array of TermI objects

remove_term_by_id
Title : remove_term_by_id Usage : remove_term_by_id(String id): TermI Function: Removes TermI object from the ontology engine using the string id as an identifier. Current implementation does not enforce consistency of the relationships using that term. Example : $term = $soe->remove_term_by_id($id); Returns : Object of class TermI or undef if not found. Args : The string identifier of a term.

to_string
Title : to_string Usage : print $sv->to_string(); Function: Currently returns formatted string containing the number of terms and number of relationships from the ontology engine. Example : print $sv->to_string(); Returns : Args :

_unique_termid
Title : _unique_termid Usage : Function: Returns a string that can be used as ID using fail-over approaches. If the identifier attribute is not set, it uses the combination of name and ontology name, provided both are set. If they aren't, it returns the name alone. Note that this is a private method. Call from inheriting classes but not from outside. Example : Returns : a string Args : a Bio::Ontology::TermI compliant object