| Bio::Ontology::OBOEngine(3pm) | User Contributed Perl Documentation | Bio::Ontology::OBOEngine(3pm) |
Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
use Bio::Ontology::OBOEngine;
my $parser = Bio::Ontology::OBOEngine->new
( -file => "gene_ontology.obo" );
my $engine = $parser->parse();
Needs Graph.pm from CPAN.
This module replaces SimpleGOEngine.pm, which is deprecated.
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
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.
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
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
Hilmar Lapp, hlapp at gmx.net Chris Mungall, cjm at fruitfly.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $engine = Bio::Ontology::OBOEngine->new() Function: Creates a new OBOEngine Returns : A new OBOEngine 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 : 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 :
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 :
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 :
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 :
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, $ont );
Function: Adds a new relationship type to the engine. Use
get_relationship_type($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
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 : 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
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) = $oe->find_terms(-identifier => "SO:0000263");
Function: Find term instances matching queries for their attributes.
This implementation can efficiently resolve queries by
identifier.
Example :
Returns : an array of zero or more Bio::Ontology::TermI objects
Args : Named parameters. The following parameters should be recognized
by any implementations:
-identifier query by the given identifier
-name query by the given name
Title : find_identically_named_terms
Usage : ($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
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
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
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 :
| 2021-08-15 | perl v5.32.1 |