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BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Ontology::OBOEngine

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    :
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    :