Bio::Ontology::OntologyI(3pm)

NAME
Bio::Ontology::OntologyI - Interface for an ontology implementation

SYNOPSIS
    # see method documentation

DESCRIPTION
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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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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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:

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AUTHOR - Hilmar Lapp
Email hlapp at gmx.net

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Methods defined in this interface.

  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

Methods inherited from Bio::Ontology::OntologyEngineI
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

Factory for relationships and terms

  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    :