#
# BioPerl module for Bio::Ontology::Term
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::TermI - interface for ontology terms
=head1 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";
}
=head1 DESCRIPTION
This is "dumb" interface for ontology terms providing basic methods
(it provides no functionality related to graphs).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 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
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
=head1 APPENDIX
The rest of the documentation details each of the object
methods.
=cut
# Let the code begin...
package Bio::Ontology::TermI;
use strict;
use base qw(Bio::Root::RootI);
=head2 identifier
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).
=cut
sub identifier {
shift->throw_not_implemented();
} # identifier
=head2 name
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).
=cut
sub name {
shift->throw_not_implemented();
} # name
=head2 definition
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).
=cut
sub definition {
shift->throw_not_implemented();
} # definition
=head2 ontology
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 L<Bio::Ontology::OntologyI>.
=cut
sub ontology {
shift->throw_not_implemented();
} # ontology
=head2 version
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).
=cut
sub version {
shift->throw_not_implemented();
} # version
=head2 is_obsolete
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).
=cut
sub is_obsolete {
shift->throw_not_implemented();
} # is_obsolete
=head2 comment
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).
=cut
sub comment {
shift->throw_not_implemented();
} # comment
=head2 get_synonyms
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 :
=cut
sub get_synonyms {
shift->throw_not_implemented();
} # get_synonyms
=head2 get_dblinks
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()
=cut
sub get_dblinks {
shift->throw('get_dblinks() is deprecated, use get_dbxrefs() instead');
} # get_dblinks
=head2 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
L<Bio::Annotation::DBLink> instances, or specific subgroups
can be returned based on passed arguments
Args : implementation-specific
=cut
sub get_dbxrefs {
shift->throw_not_implemented();
} # get_dblinks
=head2 get_secondary_ids
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 :
=cut
sub get_secondary_ids {
shift->throw_not_implemented();
} # get_secondary_ids
=head1 Deprecated methods
Used for looking up the methods that supercedes them.
=cut
=head2 category
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 :
=cut
sub category {
my $self = shift;
$self->warn("TermI::category is deprecated and being phased out. ".
"Use TermI::ontology instead.");
# called in set mode?
if(@_) {
# yes; what is incompatible with ontology() is if we were given
# a TermI object
my $arg = shift;
$arg = $arg->name() if ref($arg) && $arg->isa("Bio::Ontology::TermI");
return $self->ontology($arg,@_);
} else {
# No, called in get mode. This is always incompatible with ontology()
# since category is supposed to return a TermI.
my $ont = $self->ontology();
my $term;
if(defined($ont)) {
$term = Bio::Ontology::Term->new(-name => $ont->name(),
-identifier =>$ont->identifier());
}
return $term;
}
} # category
1;