Bio::O...:TermI(3pm)

💖 Bio::Ontology::TermI — the vibe ✨

okay so bestie, welcome to the Bio::Ontology::TermI manual page 💅 this is the interface for ontology terms, and ngl it's giving "simple but iconic" — it's literally just a "dumb" interface, so don't come here looking for graph stuff, that's a whole other page, iykyk.

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🌸 NAME 🌸

Bio::Ontology::TermI — interface for ontology terms 🧚

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✨ SYNOPSIS ✨

okay so first you gotta get yourself a Bio::Ontology::TermI somehow, and then:

#get Bio::Ontology::TermI somehow.

print $term->identifier(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->comment(), "\n";

foreach my $synonym ( $term->get_synonyms() ) {
    print $synonym, "\n";
}

no cap, that's the whole vibe. 🦋

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🎀 DESCRIPTION 🎀

This is a "dumb" interface for ontology terms that serves up the basic methods — and that's it, periodt. It provides no functionality related to graphs, so if you came here for graph energy you are in the wrong group chat, bestie 😭.

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💌 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. (that means: show your work, bestie, receipts and all 🙈)

🐛 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

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👑 AUTHOR 👑

Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

WWW: http://monochrome-effect.net/

Address:

Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. lowkey this is the main character section, so let's get into it 💅

⭐ 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   : $ont = $term->ontology();
          or
          $term->ontology( $ont );
Function: Get the ontology this term is in.

          An implementation may not permit the value of this
          attribute to be changed once it is set, since that may have
          serious consequences (note that with the ontology in hand
          you can query for all related terms etc).

          Note for implementors: you will almost certainly have to
          take special precaution in order not to create cyclical
          references in memory.

Returns : The ontology of this Term as a Bio::Ontology::OntologyI
          implementing object.
Args    : On set, the  ontology of this Term as a Bio::Ontology::OntologyI
          implementing object or a string representing its name.

See Bio::Ontology::OntologyI.

⚠️ heads up bestie — an implementation may not let you change this once it's set, because that can have serious consequences (you can query for all related terms with the ontology in hand, so yeah, it matters). And implementors: you will almost certainly have to take special precaution not to create cyclical references in memory. that's the drama 🫠

⭐ version

Title   : version
Usage   : $term->version( "1.00" );
          or
          print $term->version();
Function: Set/get for version information.
Returns : The version [scalar].
Args    : The version [scalar] (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.

          If an implementor of this interface permits modification of
          this array property, the class should define at least
          methods add_synonym() and remove_synonyms(), with obvious
          functionality.

Returns : A list of aliases [array of [scalar]].
Args    :

⭐ get_dblinks

Title   : get_dblinks()
Usage   : @ds = $term->get_dblinks();
Function: Returns a list of each dblink of this term.

          If an implementor of this interface permits modification of
          this array property, the class should define at least
          methods add_dblink() and remove_dblinks(), with obvious
          functionality.

Returns : A list of dblinks [array of [scalars]].
Args    :
Note    : This has been deprecated in favor of get_dbxrefs()

💀 deprecated, bestie — use get_dbxrefs() instead.

⭐ get_dbxrefs

Title   : get_dbxrefs()
Usage   : @ds = $term->get_dbxrefs();
Function: Returns a list of each link for this term.

          If an implementor of this interface permits modification of
          this array property, the class should define at least
          methods add_dbxref() and remove_dbxrefs(), with obvious
          functionality.

Returns : A list of dblinks.  This can return a mixed 'bag' of scalars and
          L<Bio::Annotation::DBLink> instances, or specific subgroups
          can be returned based on passed arguments
Args    : implementation-specific

⭐ 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.

          If an implementor of this interface permits modification of
          this array property, the class should define at least
          methods add_secondary_id() and remove_secondary_ids(), with
          obvious functionality.

Returns : A list of secondary identifiers [array of [scalar]]
Args    :

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🙈 Deprecated methods 🙈

Used for looking up the methods that supersedes them. yes bestie, we keep the legacy lore for the historians 💜

🕰️ category

Title   : category
Usage   :
Function: This method is deprecated. Use ontology() instead. We provide
          an implementation here that preserves backwards compatibility,
          but if you do not have legacy code using it you should not be
          calling this method.
Example :
Returns :
Args    :

🚨 it's deprecated fr fr. Use ontology() instead. There's an implementation here that preserves backwards compatibility, but if you do not have legacy code using it, you should not be calling this method. periodt.

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that's the whole page, bestie 💖 this was Bio::O...:TermI(3pm), documented under perl v5.32.1, dated 2021-08-15 — go forth and annotate those terms, you absolute icon 👑✨