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Bio::Annotation::OntologyTerm.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationISYNOPSIS
use Bio::Annotation::OntologyTerm; use Bio::Annotation::Collection; use Bio::Ontology::Term;
my $coll = new Bio::Annotation::Collection;
# this also implements a tag/value pair, where tag _and_ value are treated # as ontology terms my $annterm = new Bio::Annotation::OntologyTerm(-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 objectFEEDBACK
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
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.netAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : my $sv = new Bio::Annotation::OntologyTerm; 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
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 :
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]].
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 :
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 :
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