Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should
       satisfy

SYNOPSIS

           # see documentation of methods

DESCRIPTION

       This describes the minimal interface an ontology query engine should provide.  It
       intentionally does not 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 are not, 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.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

       bioperl-l@bioperl.org

       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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Peter Dimitrov

       Email dimitrov@gnf.org

APPENDIX

       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    :

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::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    :

Decorator Methods

        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

Experimental API method proposals

        Ontologies are a very new domain in bioperl, and we are not 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.