Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology

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

   new
        Title   : new
        Usage   : $engine = Bio::Ontology::OBOEngine->new()
        Function: Creates a new OBOEngine
        Returns : A new OBOEngine object
        Args    :

   init
        Title   : init()
        Usage   : $engine->init();
        Function: Initializes this Engine.
        Returns :
        Args    :

   is_a_relationship
        Title   : is_a_relationship()
        Usage   : $IS_A = $engine->is_a_relationship();
        Function: Returns a Bio::Ontology::RelationshipType object for "is-a"
                  relationships
        Returns : Bio::Ontology::RelationshipType set to "IS_A"
        Args    :

   part_of_relationship
        Title   : part_of_relationship()
        Usage   : $PART_OF = $engine->part_of_relationship();
        Function: Returns a Bio::Ontology::RelationshipType object for "part-of"
                  relationships
        Returns : Bio::Ontology::RelationshipType set to "PART_OF"
        Args    :

   related_to_relationship
        Title   : related_to_relationship()
        Usage   : $RELATED_TO = $engine->related_to_relationship();
        Function: Returns a Bio::Ontology::RelationshipType object for "related-to"
                  relationships
        Returns : Bio::Ontology::RelationshipType set to "RELATED_TO"
        Args    :

   regulates_relationship
        Title   : regulates_relationship()
        Usage   : $REGULATES = $engine->regulates_relationship();
        Function: Returns a Bio::Ontology::RelationshipType object for "regulates"
                  relationships
        Returns : Bio::Ontology::RelationshipType set to "REGULATES"
        Args    :

   positively_regulates_relationship
        Title   : positively_regulates_relationship()
        Usage   : $REGULATES = $engine->positively_regulates_relationship();
        Function: Returns a Bio::Ontology::RelationshipType object for "positively_regulates"
                  relationships
        Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES"
        Args    :

   negatively_regulates_relationship
        Title   : negatively_regulates_relationship()
        Usage   : $REGULATES = $engine->negatively_regulates_relationship();
        Function: Returns a Bio::Ontology::RelationshipType object for "negatively_regulates"
                  relationships
        Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES"
        Args    :

   add_term
        Title   : add_term
        Usage   : $engine->add_term( $term_obj );
        Function: Adds a Bio::Ontology::TermI to this engine
        Returns : true if the term was added and false otherwise (e.g., if the
                  term already existed in the ontology engine)
        Args    : Bio::Ontology::TermI`

   has_term
        Title   : has_term
        Usage   : $engine->has_term( $term );
        Function: Checks whether this engine contains a particular term
        Returns : true or false
        Args    : Bio::Ontology::TermI
                  or
                  Term identifier (e.g. "GO:0012345")

   add_relationship_type
        Title   : add_relationship_type
        Usage   : $engine->add_relationship_type( $type_name, $ont );
        Function: Adds a new relationship type to the engine.  Use
                  get_relationship_type($type_name) to retrieve.
        Returns : true if successfully added, false otherwise
        Args    : relationship type name to add (scalar)
                  ontology to which to assign the relationship type

   get_relationship_type
        Title   : get_relationship_type
        Usage   : $engine->get_relationship_type( $type_name );
        Function: Gets a Bio::Ontology::RelationshipI object corresponding
                  to $type_name
        Returns : a Bio::Ontology::RelationshipI object
        Args    :

   add_relationship
        Title   : add_relationship
        Usage   : $engine->add_relationship( $relationship );
                  $engine->add_relatioship( $subject_term, $predicate_term,
                                            $object_term, $ontology );
                  $engine->add_relatioship( $subject_id, $predicate_id,
                                            $object_id, $ontology);
        Function: Adds a relationship to this engine
        Returns : true if successfully added, false otherwise
        Args    : The relationship in one of three ways:

                    a) subject (or child) term id, Bio::Ontology::TermI
                       (rel.type), object (or parent) term id, ontology

                  or

                    b) subject Bio::Ontology::TermI, predicate
                       Bio::Ontology::TermI (rel.type), object
                       Bio::Ontology::TermI, ontology

                  or

                    c) Bio::Ontology::RelationshipI-compliant object

   get_relationships
        Title   : get_relationships
        Usage   : $engine->get_relationships( $term );
        Function: Returns all relationships of a term, or all relationships in
                  the graph if no term is specified.
        Returns : Relationship
        Args    : term id
                  or
                  Bio::Ontology::TermI

   get_all_relationships
        Title   : get_all_relationships
        Usage   : @rels = $engine->get_all_relationships();
        Function: Returns all relationships in the graph.
        Returns : Relationship
        Args    :

   get_predicate_terms
        Title   : get_predicate_terms
        Usage   : $engine->get_predicate_terms();
        Function: Returns the types of relationships this engine contains
        Returns : Bio::Ontology::RelationshipType
        Args    :

   get_child_terms
        Title   : get_child_terms
        Usage   : $engine->get_child_terms( $term_obj, @rel_types );
                  $engine->get_child_terms( $term_id, @rel_types );
        Function: Returns the children of this term
        Returns : Bio::Ontology::TermI
        Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
                  or
                  term id, Bio::Ontology::RelationshipType

                  if NO Bio::Ontology::RelationshipType is indicated: children
                  of ALL types are returned

   get_descendant_terms
        Title   : get_descendant_terms
        Usage   : $engine->get_descendant_terms( $term_obj, @rel_types );
                  $engine->get_descendant_terms( $term_id, @rel_types );
        Function: Returns the descendants of this term
        Returns : Bio::Ontology::TermI
        Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
                  or
                  term id, Bio::Ontology::RelationshipType

                  if NO Bio::Ontology::RelationshipType is indicated:
                  descendants of ALL types are returned

   get_parent_terms
        Title   : get_parent_terms
        Usage   : $engine->get_parent_terms( $term_obj, @rel_types );
                  $engine->get_parent_terms( $term_id, @rel_types );
        Function: Returns the parents of this term
        Returns : Bio::Ontology::TermI
        Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
                  or
                  term id, Bio::Ontology::RelationshipType

                  if NO Bio::Ontology::RelationshipType is indicated:
                  parents of ALL types are returned

   get_ancestor_terms
        Title   : get_ancestor_terms
        Usage   : $engine->get_ancestor_terms( $term_obj, @rel_types );
                  $engine->get_ancestor_terms( $term_id, @rel_types );
        Function: Returns the ancestors of this term
        Returns : Bio::Ontology::TermI
        Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
                  or
                  term id, Bio::Ontology::RelationshipType

                  if NO Bio::Ontology::RelationshipType is indicated:
                  ancestors of ALL types are returned

   get_leaf_terms
        Title   : get_leaf_terms
        Usage   : $engine->get_leaf_terms();
        Function: Returns the leaf terms
        Returns : Bio::Ontology::TermI
        Args    :

   get_root_terms()
        Title   : get_root_terms
        Usage   : $engine->get_root_terms();
        Function: Returns the root terms
        Returns : Bio::Ontology::TermI
        Args    :

   get_terms
        Title   : get_terms
        Usage   : @terms = $engine->get_terms( "GO:1234567", "GO:2234567" );
        Function: Returns term objects with given identifiers
        Returns : Bio::Ontology::TermI, or the term corresponding to the
                  first identifier if called in scalar context
        Args    : term ids

   get_all_terms
        Title   : get_all_terms
        Usage   : $engine->get_all_terms();
        Function: Returns all terms in this engine
        Returns : Bio::Ontology::TermI
        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

   find_identically_named_terms
        Title   : find_identically_named_terms
        Usage   : ($term) = $oe->find_identically_named_terms($term0);
        Function: Find term instances where names match the query term
                  name exactly
        Example :
        Returns : an array of zero or more Bio::Ontology::TermI objects
        Args    : a Bio::Ontology::TermI object

   find_identical_terms
        Title   : find_identical_terms
        Usage   : ($term) = $oe->find_identical_terms($term0);
        Function: Find term instances where name or synonym
                  matches the query exactly
        Example :
        Returns : an array of zero or more Bio::Ontology::TermI objects
        Args    : a Bio::Ontology::TermI object

   find_similar_terms
        Title   : find_similar_terms
        Usage   : ($term) = $oe->find_similar_terms($term0);
        Function: Find term instances where name or synonym, or part of one,
                  matches the query.
        Example :
        Returns : an array of zero or more Bio::Ontology::TermI objects
        Args    : a Bio::Ontology::TermI object

   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

   graph
        Title   : graph()
        Usage   : $engine->graph();
        Function: Returns the Graph this engine is based on
        Returns : Graph
        Args    :

perl v5.32.1                                       2021-08-15                      Bio::Ontology::OBOEngine(3pm)

       Sohel Merchant

       Email: s-merchant@northwestern.edu

       Address:

         Northwestern University
         Center for Genetic Medicine (CGM), dictyBase
         Suite 1206,
         676 St. Clair st
         Chicago IL 60611

   CONTRIBUTOR
        Hilmar Lapp, hlapp at gmx.net
        Chris Mungall,   cjm at fruitfly.org

       Needs Graph.pm from CPAN.

       This module replaces SimpleGOEngine.pm, which is deprecated.

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       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 lists  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
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   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.

   ReportingBugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug
       reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

       Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology
       Consortium

         use Bio::Ontology::OBOEngine;

         my $parser = Bio::Ontology::OBOEngine->new
               ( -file => "gene_ontology.obo" );

         my $engine = $parser->parse();