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Bio::Annotation::OntologyTerm.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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    :
 
 

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    :