SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI use Bio::Ontology::SimpleGOEngine; my $parser = Bio::Ontology::SimpleGOEngine->new ( -defs_file => "/home/czmasek/GO/GO.defs", -files => ["/home/czmasek/GO/component.ontology", "/home/czmasek/GO/function.ontology", "/home/czmasek/GO/process.ontology"] ); my $engine = $parser->parse(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); Needs Graph.pm from CPAN.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 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::SimpleGOEngine->new() Function: Creates a new SimpleGOEngine Returns : A new SimpleGOEngine 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 :

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, $ont ); Function: Adds a new relationship type to the engine. User get_relationship_type($type_name) to retrieve. Returns : true if successfully added, false otherwise Args : relationship type name to add (scalar)

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 : term id, Bio::Ontology::TermI (rel.type), term id, ontology or Bio::Ontology::TermI, Bio::Ontology::TermI (rel.type), Bio::Ontology::TermI, ontology or Bio::Ontology::RelationshipI

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

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 :