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Bio::Ontology::OBOEngiUser)Contributed Perl DocumenBio::Ontology::OBOEngine(3)

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	:

perl v5.32.0			  2019-12-07	   Bio::Ontology::OBOEngine(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

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