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.
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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 _
Title : new Usage : $engine = Bio::Ontology::SimpleGOEngine->new() Function: Creates a new SimpleGOEngine Returns : A new SimpleGOEngine object Args :
Title : init() Usage : $engine->init(); Function: Initializes this Engine. Returns : Args :
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 :
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 :
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
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")
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)
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 :
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
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
Title : get_all_relationships Usage : @rels = $engine->get_all_relationships(); Function: Returns all relationships in the graph. Returns : Relationship[] Args :
Title : get_predicate_terms Usage : $engine->get_predicate_terms(); Function: Returns the types of relationships this engine contains Returns : Bio::Ontology::RelationshipType[] Args :
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
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
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
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
Title : get_leaf_terms Usage : $engine->get_leaf_terms(); Function: Returns the leaf terms Returns : Bio::Ontology::TermI[] Args :
Title : get_root_terms Usage : $engine->get_root_terms(); Function: Returns the root terms Returns : Bio::Ontology::TermI[] Args :
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[]
Title : get_all_terms Usage : $engine->get_all_terms(); Function: Returns all terms in this engine Returns : Bio::Ontology::TermI[] Args :
Title : find_terms Usage : ($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
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
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
Title : graph() Usage : $engine->graph(); Function: Returns the Graph this engine is based on Returns : Graph Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.