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Bio::Ontology::OBOEngine.3pm

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:

   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    :