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.

FEEDBACK

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       Please direct usage questions or support issues to the mailing list:

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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.

   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:

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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    :