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://github.com/bioperl/bioperl-live/issues

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 category 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    :

get_dblinks

 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    :

add_dblink

 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    :

remove_dblinks

 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    :