Bio::Annotation::OntologyTerm(3pm) User Contributed Perl Documentation 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(),"
";
$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 :
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 :
perl v5.14.2 2012-03-02 Bio::Annotation::OntologyTerm(3pm)