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

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

💖 NAME 💖

Bio::Ontology::GOterm — bestie, this is the representation of GO terms ✨

(also hi, welcome to the Bio::O...:GOterm(3pm) page, you found it, you're doing amazing 🫶)

🌸 SYNOPSIS 🌸

okay so here's the whole vibe in one code block, no notes:

$term = Bio::Ontology::GOterm->new
  ( -go_id       => "GO:0016847",
    -name        => "1-aminocyclopropane-1-carboxylate synthase",
    -definition  => "Catalysis of ...",
    -is_obsolete => 0,
    -comment     => "" );

$term->add_definition_references( @refs );
$term->add_secondary_GO_ids( @ids );
$term->add_aliases( @aliases );

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

# etc.

the # etc. is doing so much heavy lifting and honestly? iconic. 👑

🦋 DESCRIPTION 🦋

So this is a "dumb" class for GO terms — and before you come for it, that's the official word, it literally means it provides no functionality related to graphs. It just sits there being a term. No graph drama. It's giving low-maintenance.

It implements Bio::Ontology::TermI. That's the whole thing. Periodt. 💅

💌 FEEDBACK 💌

🎀 Mailing Lists 🎀

User feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, they want to hear from 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 the reason is good: many experienced and reponsive experts will be able look at the problem and quickly address it. So like, don't DM the maintainer, post in the group chat. 🫶

Please include a thorough description of the problem with code and data examples if at all possible. the more detail the better, we love a thorough queen.

🔥 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

go off, tell them everything. 📝

👑 AUTHOR 👑

Christian M. Zmasek

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

🌈 APPENDIX 🌈

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

⭐ new ⭐

  • Title: new
  • Usage:
$term = Bio::Ontology::GOterm->new(
      -go_id       => "GO:0016847",
      -name        => "1-aminocyclopropane-1-carboxylate synthase",
      -definition  => "Catalysis of ...",
      -is_obsolete => 0,
      -comment     => "" );
  • Function: Creates a new Bio::Ontology::GOterm.
  • Returns: A new Bio::Ontology::GOterm object.
  • Args:
    • -go_id => the goid of this GO term [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a zero-padded integer of seven digits)
    • -name => the name of this GO term [scalar]
    • -definition => the definition of this GO term [scalar]
    • -ontology => the ontology for this term (a Bio::Ontology::OntologyI compliant object)
    • -version => version information [scalar]
    • -is_obsolete => the obsoleteness of this GO term [0 or 1]
    • -comment => a comment [scalar]

✨ init ✨

  • Title: init()
  • Usage: $term->init();
  • Function: Initializes this GOterm to all "" and empty lists.
  • Returns: (nothing, it's a fresh start bestie)
  • Args: (none)

💖 GO_id 💖

  • Title: GO_id
  • Usage:
$term->GO_id( "GO:0003947" );
or
print $term->GO_id();
  • Function: Set/get for the goid of this GO term.

This is essentially an alias to identifier(), with added format checking. 👀

  • Returns: The goid [GO:nnnnnnn].
  • Args: The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a zero-padded integer of seven digits) (optional).

🧚 get_secondary_GO_ids 🧚

  • Title: get_secondary_GO_ids
  • Usage: @ids = $term->get_secondary_GO_ids();
  • Function: Returns a list of secondary goids of this Term.

This is aliased to remove_secondary_ids().

  • Returns: A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits).
  • Args: (none)

🌸 add_secondary_GO_id 🌸

  • Title: add_secondary_GO_id
  • Usage:
$term->add_secondary_GO_id( @ids );
or
$term->add_secondary_GO_id( $id );
  • Function: Pushes one or more secondary goids into the list of secondary goids.

This is aliased to remove_secondary_ids().

  • Returns: (nothing)
  • Args: One secondary goid [GO:nnnnnnn or nnnnnnn] or a list of secondary goids [array of [GO:nnnnnnn or nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits).

💜 remove_secondary_GO_ids 💜

  • Title: remove_secondary_GO_ids()
  • Usage: $term->remove_secondary_GO_ids();
  • Function: Deletes (and returns) the secondary goids of this Term.

This is aliased to remove_secondary_ids().

  • Returns: A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits).
  • Args: (none)

🎀 to_string 🎀

  • Title: to_string()
  • Usage: print $term->to_string();
  • Function: to_string method for GO terms.
  • Returns: A string representation of this GOterm.
  • Args: (none)

and that's the whole page bestie, you ate that 💅✨

this lil legend was brought to you by perl v5.32.1, dated 2021-08-15, under the Bio::O...:GOterm(3pm) name — user contributed perl documentation, no cap. 🦋 go forth and annotate some GO terms, mwah 💖

📦 where this page comes from