/ 
bioperl-1.2.2
/ Bio::Ontology::SimpleGOEngine

NAME

SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI

SYNOPSIS

  use Bio::Ontology::SimpleGOEngine;

  my $parser = Bio::Ontology::SimpleGOEngine->new
	( -defs_file => "/home/czmasek/GO/GO.defs",
	  -files     => ["/home/czmasek/GO/component.ontology",
	                 "/home/czmasek/GO/function.ontology",
	                 "/home/czmasek/GO/process.ontology"] );

  my $engine = $parser->parse();

  my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );

DESCRIPTION

Needs Graph.pm from CPAN.

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR

Christian M. Zmasek

Email: czmasek@gnf.org or cmzmasek@yahoo.com

WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/

Address:

Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121

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::SimpleGOEngine->new()
Function: Creates a new SimpleGOEngine
Returns : A new SimpleGOEngine 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    :

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
          erm identifier (e.g. "GO:0012345")

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    : term id, Bio::Ontology::TermI (rel.type), term id, ontology 
          or
          Bio::Ontology::TermI, Bio::Ontology::TermI (rel.type), Bio::Ontology::TermI, ontology
          or
          Bio::Ontology::RelationshipI

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

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    :