--- name: "Bio::Ontology::OBOEngine" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Ontology::OBOEngine" --- # Bio::Ontology::OBOEngine(3pm) An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium ## NAME Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium ## SYNOPSIS ``` use Bio::Ontology::OBOEngine; my $parser = Bio::Ontology::OBOEngine->new ( -file => "gene_ontology.obo" ); my $engine = $parser->parse(); ``` ## DESCRIPTION Needs Graph.pm from CPAN. This module replaces SimpleGOEngine.pm, which is deprecated. ## 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 lists 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 the bugs and their resolution. Bug reports can be submitted via the web: ``` https://github.com/bioperl/bioperl-live/issues ``` ## AUTHOR 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 ``` ## APPENDIX 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 : ```