/ 
bioperl-1.2
/ Bio::Ontology::SimpleGOEngine

NAME

SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI

SYNOPSIS

  use Bio::Ontology::simpleGOparser;

  my $parser = Bio::Ontology::simpleGOparser->new
	( -go_defs_file_name    => "/home/czmasek/GO/GO.defs",
	  -components_file_name => "/home/czmasek/GO/component.ontology",
	  -functions_file_name  => "/home/czmasek/GO/function.ontology",
	  -processes_file_name  => "/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( $GOterm_obj );
Function: Adds a Bio::Ontology::GOterm to this engine
Returns : true
Args    : Bio::Ontology::GOterm

has_term

Title   : has_term
Usage   : $engine->has_term( $term );
Function: Checks whether this engine contains a particular GO term
Returns : true or false
Args    : Bio::Ontology::GOterm
          or
          GO term identifier (e.g. "GO:0012345")

add_relationship

Title   : add_relationship
Usage   : $engine->add_relationship( $relationship );
          $engine->add_relatioship( $parent_obj, $child_obj, $relationship_type );
          $engine->add_relatioship( $parent_id, $child_id, $relationship_type);
Function: Adds a relationship to this engine
Returns : true if successfully added, false otherwise
Args    : GO id, GO id, Bio::Ontology::RelationshipType
          or
          Bio::Ontology::GOterm, Bio::Ontology::GOterm, Bio::Ontology::RelationshipType
          or
          Bio::Ontology::RelationshipI

get_relationships

Title   : get_relationships
Usage   : $engine->get_relationships( $term );
Function: Returns all relationships of a term
Returns : Relationship[]
Args    : GO id
          or
          Bio::Ontology::GOterm

get_relationship_types

Title   : get_relationship_types
Usage   : $engine->get_relationship_types();
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::GOterm[]
Args    : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
          or
          GO 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::GOterm[]
Args    : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
          or
          GO 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::GOterm[]
Args    : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
          or
          GO 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::GOterm[]
Args    : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
          or
          GO 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::GOterm[]
Args    :

get_root_terms()

Title   : get_root_terms
Usage   : $engine->get_root_terms();
Function: Returns the root terms
Returns : Bio::Ontology::GOterm[]
Args    :

get_term

Title   : get_term
Usage   : $engine->get_term( "GO:1234567" );
Function: Returns a GO term with a given identifier
Returns : Bio::Ontology::GOterm is present, false otherwise
Args    : GO id

get_terms

Title   : get_terms
Usage   : $engine->get_term( "GO:1234567", "GO:2234567" );
Function: Returns a GO terms with given identifiers
Returns : Bio::Ontology::GOterm[]
Args    : GO id[]

each_term

Title   : each_term
Usage   : $engine->each_term();
Function: Returns all terms in this engine
Returns : Bio::Ontology::GOterm[]
Args    :

graph

Title   : graph()
Usage   : $engine->graph();
Function: Returns the Graph this engine is based on
Returns : Graph
Args    :