Bio::Ontology::GOterm - representation of GO terms
$term = Bio::Ontology::GOterm->new
( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
$term->add_definition_references( @refs );
$term->add_secondary_GO_ids( @ids );
$term->add_aliases( @aliases );
foreach my $dr ( $term->each_definition_reference() ) {
print $dr, "\n";
}
# etc.
This is "dumb" class for GO terms (it provides no functionality
related to graphs). Implements Bio::Ontology::TermI.
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at all possible.
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Christian M. Zmasek
Email: czmasek-at-burnham.org or
[email protected]
WWW:
http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
The rest of the documentation details each of the object methods.
Title : new
Usage : $term = Bio::Ontology::GOterm->new(
-go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::GOterm.
Returns : A new Bio::Ontology::GOterm object.
Args : -go_id => the goid of this GO term [GO:nnnnnnn]
or [nnnnnnn] (nnnnnnn is a zero-padded
integer of seven digits)
-name => the name of this GO term [scalar]
-definition => the definition of this GO term [scalar]
-ontology => the ontology for this term (a
Bio::Ontology::OntologyI compliant object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this GO term [0 or 1]
-comment => a comment [scalar]
Title : init()
Usage : $term->init();
Function: Initializes this GOterm to all "" and empty lists.
Returns :
Args :
Title : GO_id
Usage : $term->GO_id( "GO:0003947" );
or
print $term->GO_id();
Function: Set/get for the goid of this GO term.
This is essentially an alias to identifier(), with added
format checking.
Returns : The goid [GO:nnnnnnn].
Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a
zero-padded integer of seven digits) (optional).
Title : get_secondary_GO_ids
Usage : @ids = $term->get_secondary_GO_ids();
Function: Returns a list of secondary goids of this Term.
This is aliased to remove_secondary_ids().
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args :
Title : add_secondary_GO_id
Usage : $term->add_secondary_GO_id( @ids );
or
$term->add_secondary_GO_id( $id );
Function: Pushes one or more secondary goids into
the list of secondary goids.
This is aliased to remove_secondary_ids().
Returns :
Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list
of secondary goids [array of [GO:nnnnnnn or nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Title : remove_secondary_GO_ids()
Usage : $term->remove_secondary_GO_ids();
Function: Deletes (and returns) the secondary goids of this Term.
This is aliased to remove_secondary_ids().
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args :
Title : to_string()
Usage : print $term->to_string();
Function: to_string method for GO terms.
Returns : A string representation of this GOterm.
Args :