Bio::Ontology TermI
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Summary
Bio::Ontology::TermI - interface for ontology terms
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
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
identifierDescriptionCode
nameDescriptionCode
definitionDescriptionCode
ontologyDescriptionCode
versionDescriptionCode
is_obsoleteDescriptionCode
commentDescriptionCode
get_synonymsDescriptionCode
get_dblinksDescriptionCode
get_dbxrefsDescriptionCode
get_secondary_idsDescriptionCode
categoryDescriptionCode
Methods description
identifiercode    nextTop
 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).
namecodeprevnextTop
 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).
definitioncodeprevnextTop
 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).
ontologycodeprevnextTop
 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.
versioncodeprevnextTop
 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).
is_obsoletecodeprevnextTop
 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).
commentcodeprevnextTop
 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).
get_synonymscodeprevnextTop
 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 :
get_dblinkscodeprevnextTop
 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()
get_dbxrefscodeprevnextTop
 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
get_secondary_idscodeprevnextTop
 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 :
categorycodeprevnextTop
 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
identifierdescriptionprevnextTop
sub identifier {
    shift->throw_not_implemented();
} # identifier
}
namedescriptionprevnextTop
sub name {
    shift->throw_not_implemented();
} # name
}
definitiondescriptionprevnextTop
sub definition {
    shift->throw_not_implemented();
} # definition
}
ontologydescriptionprevnextTop
sub ontology {
    shift->throw_not_implemented();
} # ontology
}
versiondescriptionprevnextTop
sub version {
    shift->throw_not_implemented();
} # version
}
is_obsoletedescriptionprevnextTop
sub is_obsolete {
    shift->throw_not_implemented();
} # is_obsolete
}
commentdescriptionprevnextTop
sub comment {
    shift->throw_not_implemented();
} # comment
}
get_synonymsdescriptionprevnextTop
sub get_synonyms {
    shift->throw_not_implemented();
} # get_synonyms
}
get_dblinksdescriptionprevnextTop
sub get_dblinks {
    shift->throw('get_dblinks() is deprecated, use get_dbxrefs() instead');
} # get_dblinks
}
get_dbxrefsdescriptionprevnextTop
sub get_dbxrefs {
    shift->throw_not_implemented();
} # get_dblinks
}
get_secondary_idsdescriptionprevnextTop
sub get_secondary_ids {
    shift->throw_not_implemented();
} # get_secondary_ids
}
categorydescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHORTop
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
APPENDIXTop
The rest of the documentation details each of the object
methods.
Deprecated methodsTop
Used for looking up the methods that supercedes them.