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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Annotation::OntologyTerm

NAME

Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI

SYNOPSIS

use Bio::Annotation::OntologyTerm;
use Bio::Annotation::Collection;
use Bio::Ontology::Term;

my $coll = Bio::Annotation::Collection->new();

# this also implements a tag/value pair, where tag _and_ value are treated
# as ontology terms
my $annterm = Bio::Annotation::OntologyTerm->new(-label => 'ABC1',
                                                -tagname => 'Gene Name');
# ontology terms can be added directly - they implicitly have a tag
$coll->add_Annotation($annterm);

# implementation is by composition - you can get/set the term object
# e.g.
my $term = $annterm->term(); # term is-a Bio::Ontology::TermI
print "ontology term ",$term->name()," (ID ",$term->identifier(),
      "), ontology ",$term->ontology()->name(),"\n";
$term = Bio::Ontology::Term->new(-name => 'ABC2',
                                 -ontology => 'Gene Name');
$annterm->term($term);

DESCRIPTION

Ontology term annotation object

FEEDBACK

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

Support

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 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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $sv = Bio::Annotation::OntologyTerm->new();
Function: Instantiate a new OntologyTerm object
Returns : Bio::Annotation::OntologyTerm object
Args    : -term => $term to initialize the term data field [optional]
          Most named arguments that Bio::Ontology::Term accepts will work
          here too. -label is a synonym for -name, -tagname is a synonym for
          -ontology.

AnnotationI implementing functions

as_text

Title   : as_text
Usage   : my $text = $obj->as_text
Function: Returns a textual representation of the annotation that
          this object holds. Presently, it is tag name, name of the
          term, and the is_obsolete attribute concatenated togather
          with a delimiter (|).

Returns : string
Args    : none

display_text

Title   : display_text
Usage   : my $str = $ann->display_text();
Function: returns a string. Unlike as_text(), this method returns a string
          formatted as would be expected for te specific implementation.

          One can pass a callback as an argument which allows custom text
          generation; the callback is passed the current instance and any text
          returned
Example :
Returns : a string
Args    : [optional] callback

hash_tree

Title   : hash_tree
Usage   : my $hashtree = $value->hash_tree
Function: For supporting the AnnotationI interface just returns the value
          as a hashref with the key 'value' pointing to the value
Returns : hashrf
Args    : none

tagname

Title   : tagname
Usage   : $obj->tagname($newval)
Function: Get/set the tagname for this annotation value.

          Setting this is optional. If set, it obviates the need to provide
          a tag to AnnotationCollection when adding this object.

          This is aliased to ontology() here.
Example :
Returns : value of tagname (a scalar)
Args    : new value (a scalar, optional)

Methods for Bio::Ontology::TermI compliance

term

Title   : term
Usage   : $obj->term($newval)
Function: Get/set the Bio::Ontology::TermI implementing object.

          We implement TermI by composition, and this method sets/gets the
          object we delegate to.
Example :
Returns : value of term (a Bio::Ontology::TermI compliant object)
Args    : new value (a Bio::Ontology::TermI compliant object, optional)

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).

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).

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).

ontology

Title   : ontology
Usage   : $term->ontology( $top );
          or
          $top = $term->ontology();
Function: Set/get for a relationship between this Term and
          another Term (e.g. the top level of the ontology).
Returns : The ontology of this Term [TermI].
Args    : The ontology of this Term [TermI or scalar -- which
          becomes the name of the catagory term] (optional).

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).

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).

get_synonyms

Title   : get_synonyms()
Usage   : @aliases = $term->get_synonyms();
Function: Returns a list of aliases of this Term.
Returns : A list of aliases [array of [scalar]].
Args    :

add_synonym

Title   : add_synonym
Usage   : $term->add_synonym( @asynonyms );
          or
          $term->add_synonym( $synonym );
Function: Pushes one or more synonyms into the list of synonyms.
Returns :
Args    : One synonym [scalar] or a list of synonyms [array of [scalar]].

remove_synonyms

Title   : remove_synonyms()
Usage   : $term->remove_synonyms();
Function: Deletes (and returns) the synonyms of this Term.
Returns : A list of synonyms [array of [scalar]].
Args    :
Title   : get_dblinks()
Usage   : @ds = $term->get_dblinks();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args    :
Note    : this is deprecated in favor of get_dbxrefs(), which works with strings
          or L<Bio::Annotation::DBLink> instances

get_dbxrefs

Title   : get_dbxrefs()
Usage   : @ds = $term->get_dbxrefs();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars] or Bio::Annotation::DBLink instances].
Args    :
Title   : add_dblink
Usage   : $term->add_dblink( @dbls );
          or
          $term->add_dblink( $dbl );
Function: Pushes one or more dblinks
          into the list of dblinks.
Returns :
Args    : One  dblink [scalar] or a list of
           dblinks [array of [scalars]].
Note    : this is deprecated in favor of add_dbxref(), which works with strings
          or L<Bio::Annotation::DBLink> instances

add_dbxref

Title   : add_dbxref
Usage   : $term->add_dbxref( @dbls );
          or
          $term->add_dbxref( $dbl );
Function: Pushes one or more dblinks
          into the list of dblinks.
Returns :
Args    : 
Title   : remove_dblinks()
Usage   : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args    :
Note    : this is deprecated in favor of remove_dbxrefs(), which works with strings
          or L<Bio::Annotation::DBLink> instances

remove_dbxrefs

Title   : remove_dbxrefs()
Usage   : $term->remove_dbxrefs();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args    :

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.

Returns : A list of secondary identifiers [array of [scalar]]
Args    :

add_secondary_id

Title   : add_secondary_id
Usage   : $term->add_secondary_id( @ids );
          or
          $term->add_secondary_id( $id );
Function: Adds one or more secondary identifiers to this term.
Returns :
Args    : One or more secondary identifiers [scalars]

remove_secondary_ids

Title   : remove_secondary_ids
Usage   : $term->remove_secondary_ids();
Function: Deletes (and returns) the secondary identifiers of this Term.
Returns : The previous list of secondary identifiers [array of [scalars]]
Args    :