Bio::Ontology::OBOEngiUser)Contributed Perl DocumenBio::Ontology::OBOEngine(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Ontology::OBOEngine(3)
