OntologyEngineI - Interface a minimal Ontology implementation should satisfy # see documentation of methods This describes the minimal interface an ontology query engine should provide. It intentionally doesn't make explicit references to the ontology being a DAG, nor does it mandate that the ontology be a vocabulary. Rather, it tries to generically express what should be accessible (queriable) about an ontology. The idea is to allow for different implementations for different purposes, which may then differ as to which operations are efficient and which aren't, and how much richer the functionality is on top of this minimalistic set of methods. Check modules in the Bio::Ontology namespace to find out which implementations exist. At the time of writing, there is a SimpleOntologyEngine (which does not use Graph.pm), and a Graph.pm-based implementation in SimpleGOEngine. Ontology parsers in Bio::OntologyIO are required to return an implementation of this interface.

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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://bugzilla.bioperl.org/ Email dimitrov@gnf.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

add_term
Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store 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.

add_relationship_type
Title : add_relationship_type Usage : add_relationship_type(scalar,OntologyI ontology) Function: Adds a relationshiptype object to the ontology engine. Example : Returns : 1 on success, undef on failure Args : The name(scalar) of the relationshiptype, and the OntologyI it is to be added to.

get_relationship_type
Title : get_relationship_type Usage : get_relationship_type(scalar): RelationshipTypeI Function: Get a relationshiptype object from the ontology engine. Example : Returns : A RelationshipTypeI object. Args : The name (scalar) of the RelationshipTypeI object desired.

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 ancestors. Example : @root_terms = $obj->get_root_terms() Returns : Array of TermI objects. Args :

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::ObjectFactory 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::ObjectFactory compliant object) Args : These methods come with a default implementation that uses the abstract methods defined for this interface. This may not be very efficient, and hence implementors are encouraged to override these methods if they can provide more efficient implementations.

get_all_terms
Title : get_all_terms Usage : get_all_terms: TermI[] Function: Retrieves all terms from the ontology. This is more a decorator method. We provide a default implementation here that loops over all root terms and gets all descendants for each root term. The overall union of terms is then made unique by name and 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. Engine implementations that can provide a more efficient method for obtaining all terms should definitely override this. 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 Ontologies are a very new domain in bioperl, and we aren't sure yet what we will want to do on and with ontologies in which situation. The methods from here on downwards are solely API descriptions to solicit comment and feedback; the chance of any of those being actually implemented already is very slim. Disclaimer: As long as an API method stays in this section, it is subject to change, possibly even radical change or complete deletion. If it's not implemented yet (most likely it isn't), implement yourself at your own risk. So far for the disclaimer. The reason the API description is here, however, is to solicit feedback. Please feel encouraged to share your opinion, regardless of what it is (a notable difference of this API method to others is that there is actually no working code behind it - so the defense line is non-existent for practical purposes).

common_ancestor_path
Title : common_ancestor_path Usage : Function: Get the paths from two terms A and B to term C, such that there is no other term D to which A and B would have a shorter path, provided there is a term C to which both A and B are connected by a path. Note that the path to the common ancestor between A and A exists, has distance zero, and predicate "identity". The search for the common ancestor C can be further constrained by supplying a predicate term. If supplied, the predicates of the two paths (A,C) and (B,C) must have a common ancestor identical to the predicate, or that has a path to the predicate. Example : Returns : The path of the first term to the common ancestor in scalar context, and both paths in list context. Paths are Bio::Ontology::PathI compliant objects. Args : The two terms (Bio::Ontology::TermI objects), and optionally a constraining common predicate (Bio::Ontology::TermI object). The latter may also be given as a scalar, in which case it is treated as a boolean that, if TRUE, means that the two paths must have identical predicates in order to be returned.