Bio::Ontology
TermI
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Summary
Bio::Ontology::TermI - interface for ontology terms
Package variables
No package variables defined.
Inherit
Synopsis
#get Bio::Ontology::TermI somehow.
print $term->identifier(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->comment(), "\n";
foreach my $synonym ( $term->get_synonyms() ) {
print $synonym, "\n";
}
Description
This is "dumb" interface for ontology terms providing basic methods
(it provides no functionality related to graphs).
Methods
Methods description
Title : identifier
Usage : $term->identifier( "0003947" );
or
print $term->identifier();
Function: Set/get for the identifier of this Term.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional). |
Title : name
Usage : $term->name( "N-acetylgalactosaminyltransferase" );
or
print $term->name();
Function: Set/get for the name of this Term.
Returns : The name [scalar].
Args : The name [scalar] (optional). |
Title : definition
Usage : $term->definition( "Catalysis of ..." );
or
print $term->definition();
Function: Set/get for the definition of this Term.
Returns : The definition [scalar].
Args : The definition [scalar] (optional). |
Title : ontology
Usage : $ont = $term->ontology();
or
$term->ontology( $ont );
Function: Get the ontology this term is in.
An implementation may not permit the value of this
attribute to be changed once it is set, since that may have
serious consequences (note that with the ontology in hand
you can query for all related terms etc).
Note for implementors: you will almost certainly have to
take special precaution in order not to create cyclical
references in memory.
Returns : The ontology of this Term as a Bio::Ontology::OntologyI
implementing object.
Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI
implementing object or a string representing its name.
See Bio::Ontology::OntologyI. |
Title : version
Usage : $term->version( "1.00" );
or
print $term->version();
Function: Set/get for version information.
Returns : The version [scalar].
Args : The version [scalar] (optional). |
Title : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the obsoleteness of this Term.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional). |
Title : comment
Usage : $term->comment( "Consider the term ..." );
or
print $term->comment();
Function: Set/get for an arbitrary comment about this Term.
Returns : A comment.
Args : A comment (optional). |
Title : get_synonyms
Usage : @aliases = $term->get_synonyms();
Function: Returns a list of aliases of this Term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_synonym() and remove_synonyms(), with obvious
functionality.
Returns : A list of aliases [array of [scalar]].
Args : |
Title : get_dblinks()
Usage : @ds = $term->get_dblinks();
Function: Returns a list of each dblink of this term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_dblink() and remove_dblinks(), with obvious
functionality.
Returns : A list of dblinks [array of [scalars]].
Args :
Note : This has been deprecated in favor of get_dbxrefs() |
Title : get_dbxrefs()
Usage : @ds = $term->get_dbxrefs();
Function: Returns a list of each link for this term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_dbxref() and remove_dbxrefs(), with obvious
functionality.
Returns : A list of dblinks. This can return a mixed 'bag' of scalars and
Bio::Annotation::DBLink instances, or specific subgroups
can be returned based on passed arguments
Args : implementation-specific |
Title : get_secondary_ids
Usage : @ids = $term->get_secondary_ids();
Function: Returns a list of secondary identifiers of this Term.
Secondary identifiers mostly originate from merging terms,
or possibly also from splitting terms.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_secondary_id() and remove_secondary_ids(), with
obvious functionality.
Returns : A list of secondary identifiers [array of [scalar]]
Args : |
Title : category
Usage :
Function: This method is deprecated. Use ontology() instead. We provide
an implementation here that preserves backwards compatibility,
but if you do not have legacy code using it you should not be
calling this method.
Example :
Returns :
Args : |
Methods code
sub identifier
{ shift->throw_not_implemented();
}
} | sub name
{ shift->throw_not_implemented();
}
} | sub definition
{ shift->throw_not_implemented();
}
} | sub ontology
{ shift->throw_not_implemented();
}
} | sub version
{ shift->throw_not_implemented();
}
} | sub is_obsolete
{ shift->throw_not_implemented();
}
} | sub comment
{ shift->throw_not_implemented();
}
} | sub get_synonyms
{ shift->throw_not_implemented();
}
} | sub get_dblinks
{ shift->throw('get_dblinks() is deprecated, use get_dbxrefs() instead');
}
} | sub get_dbxrefs
{ shift->throw_not_implemented();
}
} | sub get_secondary_ids
{ shift->throw_not_implemented();
}
} | sub category
{ my $self = shift;
$self->warn("TermI::category is deprecated and being phased out. ".
"Use TermI::ontology instead.");
if(@_) {
my $arg = shift;
$arg = $arg->name() if ref($arg) && $arg->isa("Bio::Ontology::TermI");
return $self->ontology($arg,@_);
} else {
my $ont = $self->ontology();
my $term;
if(defined($ont)) {
$term = Bio::Ontology::Term->new(-name => $ont->name(),
-identifier =>$ont->identifier());
}
return $term;
}
}
1;} | General documentation
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The rest of the documentation details each of the object
methods.
Used for looking up the methods that supercedes them.