Bio::A...ogyTerm(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

👑 NAME 💅

Bio::Annotation::OntologyTerm — an ontology term that's been adapted to play nice with AnnotationI. bestie it's literally a glow-up for ontology terms ✨

🎀 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 🦋

okay so. it's an ontology term annotation object. that's the whole vibe. short, sweet, iconic 🌸

💌 FEEDBACK 💌

🌈 Mailing Lists 🌈

user feedback is so integral to the evolution of this and other Bioperl modules — like genuinely, the glow-up doesn't happen without you 🫶 send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, fr fr.

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. bestie, there are so many experienced and reponsive experts who 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.

like, it makes you a whole new OntologyTerm object. no cap. 🎀

🧚 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    :
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
🚨 heads up bestie: that Note is real — get_dblinks() is deprecated in favor of get_dbxrefs(). use the new one, she ate 💅

🍓 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
🚨 yeah, add_dblink is deprecated too — add_dbxref() is the moment now ✨

🍓 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
🚨 and yes, remove_dblinks is deprecated as well — remove_dbxrefs() is the one you want 🫶

🍓 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    :

okay that's the whole page bestie, you understood all of it, main character energy fr 💅✨

this was Bio::A...ogyTerm(3pm) from the User Contributed Perl Documentation, perl v5.32.1, dated 2021-08-15 — love that for us 🎀 bye! 🦋

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