Bio::Ontology
SimpleGOEngine
Summary
SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
Title : new
Usage : $engine = Bio::Ontology::SimpleGOEngine->new()
Function: Creates a new SimpleGOEngine
Returns : A new SimpleGOEngine 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 : add_term
Usage : $engine->add_term( $GOterm_obj );
Function: Adds a Bio::Ontology::GOterm to this engine
Returns : true
Args : Bio::Ontology::GOterm |
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") |
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 |
Title : get_relationships
Usage : $engine->get_relationships( $term );
Function: Returns all relationships of a term
Returns : Relationship[]
Args : GO id
or
Bio::Ontology::GOterm |
Title : get_relationship_types
Usage : $engine->get_relationship_types();
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::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 |
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 |
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 |
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 |
Title : get_leaf_terms
Usage : $engine->get_leaf_terms();
Function: Returns the leaf terms
Returns : Bio::Ontology::GOterm[]
Args : |
Title : get_root_terms
Usage : $engine->get_root_terms();
Function: Returns the root terms
Returns : Bio::Ontology::GOterm[]
Args : |
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 |
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[] |
Title : each_term
Usage : $engine->each_term();
Function: Returns all terms in this engine
Returns : Bio::Ontology::GOterm[]
Args : |
Title : graph()
Usage : $engine->graph();
Function: Returns the Graph this engine is based on
Returns : Graph
Args : |
Methods code
sub new
{ my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
$self->init();
return $self;
}
} | sub is_a_relationship
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_is_a_relationship" };
}
} | sub part_of_relationship
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "Attempted to change immutable field" );
}
return $self->{ "_part_of_relationship" };
}
} | sub add_term
{ my ( $self, $term ) = @_;
$self->_check_class( $term, "Bio::Ontology::GOterm" );
my $goid = $term->GO_id();
if ( $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology already contains a GO term with an identifier of\" $goid\"" );
}
$self->graph()->add_vertex( $goid );
$self->graph()->set_attribute( TERM, $goid, $term );
return TRUE;
}
} | sub has_term
{ my ( $self, $term ) = @_;
$term = $self->_get_id( $term );
if ( $self->graph()->has_vertex( $term ) ) {
return TRUE;
}
else {
return FALSE;
}
}
} | sub add_relationship
{ my ( $self, $parent, $child, $type ) = @_;
if ( scalar( @_ ) == 2 ) {
$self->_check_class( $parent, "Bio::Ontology::RelationshipI" );
$child = $parent->child_term();
$type = $parent->relationship_type();
$parent = $parent->parent_term();
}
$self->_check_class( $type, "Bio::Ontology::RelationshipType" );
$parent = $self->_get_id( $parent );
$child = $self->_get_id( $child );
if ( ! $self->graph()->has_vertex( $child ) ) {
$self->throw( "Ontology does not contain a GO term with an identifier of\" $child\"" );
}
if ( ! $self->graph()->has_vertex( $parent ) ) {
$self->throw( "Ontology does not contain a GO term with an identifier of\" $parent\"" );
}
if ( $self->graph()->has_edge( $parent, $child ) ) {
return FALSE;
}
$self->graph()->add_edge( $parent, $child );
$self->graph()->set_attribute( TYPE, $parent, $child, $type );
return TRUE;
}
} | sub get_relationships
{ my ( $self, $term ) = @_;
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a GO term with an identifier of\" $term\"" );
}
my @childs = $self->get_child_terms( $term );
my @parents = $self->get_parent_terms( $term );
my @rels = ();
foreach my $child ( @childs ) {
my $rel = Bio::Ontology::Relationship->new();
$rel->parent_term( $self->get_terms( $term ) );
$rel->child_term( $child );
$rel->relationship_type( $self->graph()->get_attribute( TYPE, $term, $child->GO_id() ) );
push( @rels, $rel );
}
foreach my $parent ( @parents ) {
my $rel = Bio::Ontology::Relationship->new();
$rel->parent_term( $parent );
$rel->child_term( $self->get_terms( $term ) );
$rel->relationship_type( $self->graph()->get_attribute( TYPE, $parent->GO_id(), $term ) );
push( @rels, $rel );
}
return @rels;
}
} | sub get_relationship_types
{ my ( $self ) = @_;
my @a = ( $self->is_a_relationship(),
$self->part_of_relationship() );
return @a;
}
} | sub get_child_terms
{ my ( $self, $term, @types ) = @_;
return $self->_get_child_parent_terms_helper( $term, TRUE, @types );
}
} | sub get_descendant_terms
{ my ( $self, $term, @types ) = @_;
my %ids = ();
my @ids = ();
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a GO term with an identifier of\" $term\"" );
}
$self->_get_descendant_terms_helper( $term,\% ids,\@ types );
while( ( my $id ) = each ( %ids ) ) {
push( @ids, $id );
}
return $self->get_terms( @ids );
}
} | sub get_parent_terms
{ my ( $self, $term, @types ) = @_;
return $self->_get_child_parent_terms_helper( $term, FALSE, @types );
}
} | sub get_ancestor_terms
{ my ( $self, $term, @types ) = @_;
my %ids = ();
my @ids = ();
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a GO term with an identifier of\" $term\"" );
}
$self->_get_ancestor_terms_helper( $term,\% ids,\@ types );
while( ( my $id ) = each ( %ids ) ) {
push( @ids, $id );
}
return $self->get_terms( @ids );
}
} | sub get_leaf_terms
{ my ( $self ) = @_;
my @a = $self->graph()->sink_vertices();
return $self->get_terms( @a );} | sub get_root_terms
{ my ( $self ) = @_;
my @a = $self->graph()->source_vertices();
return $self->get_terms( @a );} | sub get_term
{ my ( $self, $id ) = @_;
if ( $self->graph()->has_vertex( $id ) ) {
return( $self->graph()->get_attribute( TERM, $id ) );
}
}
} | sub get_terms
{ my ( $self, @ids ) = @_;
my @terms = ();
foreach my $id ( @ids ) {
if ( $self->graph()->has_vertex( $id ) ) {
push( @terms, $self->graph()->get_attribute( TERM, $id ) );
}
}
return @terms;
}
} | sub each_term
{ my ( $self ) = @_;
return( $self->get_terms( $self->graph()->vertices() ) );
}
} | sub graph
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_check_class( $value, "Graph::Directed" );
$self->{ "_graph" } = $value;
}
return $self->{ "_graph" };
}
} | sub _get_id
{ my ( $self, $term ) = @_;
if ( ref( $term ) ) {
if ( $term->isa( "Bio::Ontology::GOterm" ) ) {
return $term->GO_id();
}
else {
$self->throw( "Found [" . ref( $term ) . "] where [Bio::Ontology::GOterm] expected" );
}
}
else {
if ( $term =~ /^GO:\d{7}$/ ) {
return $term;
}
elsif ( $term =~ /^\d{7}$/ ) {
return "GO:" . $term;
}
else {
$self->throw( "Illegal format for GO identifier [$term]" );
}
}
}
} | sub _get_child_parent_terms_helper
{ my ( $self, $term, $do_get_child_terms, @types ) = @_;
foreach my $type ( @types ) {
$self->_check_class( $type, "Bio::Ontology::RelationshipType" );
}
my @relative_terms = ();
$term = $self->_get_id( $term );
if ( ! $self->graph()->has_vertex( $term ) ) {
$self->throw( "Ontology does not contain a GO term with an identifier of\" $term\"" );
}
my @all_relative_terms = ();
if ( $do_get_child_terms ) {
@all_relative_terms = $self->graph()->successors( $term );
}
else {
@all_relative_terms = $self->graph()->predecessors( $term );
}
foreach my $relative ( @all_relative_terms ) {
if ( scalar( @types ) > 0 ) {
foreach my $type ( @types ) {
my $relative_type;
if ( $do_get_child_terms ) {
$relative_type = $self->graph()->get_attribute( TYPE, $term, $relative );
}
else {
$relative_type = $self->graph()->get_attribute( TYPE, $relative, $term );
}
if ( $relative_type->equals( $type ) ) {
push( @relative_terms, $relative );
}
}
}
else {
push( @relative_terms, $relative );
}
}
return $self->get_terms( @relative_terms );
}
} | sub _get_descendant_terms_helper
{ my ( $self, $term, $ids_ref, $types_ref ) = @_;
my @child_terms = $self->get_child_terms( $term, @$types_ref );
if ( scalar( @child_terms ) < 1 ) {
return;
}
foreach my $child_term ( @child_terms ) {
my $child_term_id = $child_term->GO_id();
$ids_ref->{ $child_term_id } = 0;
$self->_get_descendant_terms_helper( $child_term_id, $ids_ref, $types_ref );
}
}
} | sub _get_ancestor_terms_helper
{ my ( $self, $term, $ids_ref, $types_ref ) = @_;
my @parent_terms = $self->get_parent_terms( $term, @$types_ref );
if ( scalar( @parent_terms ) < 1 ) {
return;
}
foreach my $parent_term ( @parent_terms ) {
my $parent_term_id = $parent_term->GO_id();
$ids_ref->{ $parent_term_id } = 0;
$self->_get_ancestor_terms_helper( $parent_term_id, $ids_ref, $types_ref );
}
}
} | sub _check_class
{ my ( $self, $value, $expected_class ) = @_;
if ( ! defined( $value ) ) {
$self->throw( "Found [undef] where [$expected_class] expected" );
}
elsif ( ! ref( $value ) ) {
$self->throw( "Found [scalar] where [$expected_class] expected" );
}
elsif ( ! $value->isa( $expected_class ) ) {
$self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" );
}
}
} | General documentation
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
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/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _