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

💖 Bio::Ontology::OBOterm 💖

okay so bestie, welcome to the Bio::Ontology::OBOterm page — it lives in the User Contributed Perl Documentation section of the manual, and it's literally a little data holder for OBO terms. Let's get into it 🫶

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✨ NAME ✨

Bio::Ontology::OBOterm — representation of OBO terms 🌸

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✨ SYNOPSIS ✨

no cap, here's how you actually use it:

  $term = Bio::Ontology::OBOterm->new
    ( -identifier       => "GO:0005623",
      -name        => "Cell",
      -definition  => "The basic structural and functional unit ...",
      -is_obsolete => 0,
      -comment     => "" );

  $term->add_reference( @refs );
  $term->add_secondary_id( @ids );
  $term->add_synonym( @synonym );

  # etc.

like... # etc. bestie, you get the vibe 💅

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✨ DESCRIPTION ✨

This is a data holder class for OBO terms. It's currently a dummy class — not because it's being shady, but because we anticipate that the OBO term will become more richer with more features being added to the OBO flat-file format. So it's giving "placeholder main character, waiting for its glow-up" 🌈✨

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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. fr fr, they want to hear from you 🫶

  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. the more detail the better, bestie — don't just say "it's broken" and dip 😭

🐛 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 ✨

Sohel Merchant 👑

Email: s-merchant@northwestern.edu

Address:

Northwestern University
Center for Genetic Medicine (CGM), dictyBase
Suite 1206,
676 St. Clair st
Chicago IL 60611

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. grab a snack, we're going through them all 🍓

🌟 new

Title   : new
Usage   :   $term = Bio::Ontology::OBOterm->new
    ( -identifier       => "GO:0005623",
     -name        => "Cell",
     -definition  => "The basic structural and functional unit ...",
     -is_obsolete => 0,
     -comment     => "" );

Function: Creates a new Bio::Ontology::OBOterm.
Returns : A new Bio::Ontology::OBOterm object.
Args    : -identifier    => the id of this OBO term [GO:nnnnnnn]
                            integer of seven digits)
          -name          => the name of this OBO term [scalar]
          -definition    => the definition of this OBO term [scalar]
          -ontology      => the ontology for this term (a
                            Bio::Ontology::OntologyI compliant object)
          -version       => version information [scalar]
          -is_obsolete   => the obsoleteness of this OBO term [0 or 1]
          -comment       => a comment [scalar]

okay so let's break the args down, one by one, because every single one matters 💖

• -identifier — the id of this OBO term, formatted as GO:nnnnnnn (an integer of seven digits). iconic naming convention, we love to see it ✨
• -name — the name of this OBO term [scalar]
• -definition — the definition of this OBO term [scalar]
• -ontology — the ontology for this term, and it's gotta be a Bio::Ontology::OntologyI compliant object 👑
• -version — version information [scalar]
• -is_obsolete — the obsoleteness of this OBO term, so like 0 or 1, yes/no, slay/not slay 💅
• -comment — a comment [scalar]

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💀 quick vibe check: this page is perl v5.32.1, dated 2021-08-15, from the Bio::O...BOterm(3pm) manual. periodt. 🎀

hope that helped bestie, go build something iconic 🦋