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

💖 NAME 💖

Bio::Ontology::DocumentRegistry — bestie, this is the little address book that keeps track of where all the ontologies live, and it lets you look them up by name. That's the whole vibe. ✨

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🌸 SYNOPSIS 🌸

okay so here's how you'd actually use it:

my $registry = Bio::Ontology::DocumentRegistry->get_instance();
my($ont,$def,$fmt) = $registry->documents('Sequence Ontology');

my $io = Bio::OntologyIO->new(-url => $ont,
                              -defs_url => $def,
                              -format => $fmt);
my $so = $io->next_ontology();
#...

no cap, that's it. 💅

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🦋 DESCRIPTION 🦋

Do not use this directly, use Bio::Ontology::OntologyStore instead. fr fr, I'm so serious.

Here's the tea: Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to load and cache ontologies as object graphs, so you can literally just ask it for whatever you want by name and it handles the rest. Go read Bio::Ontology::OntologyStore for the details, bestie. 🫶

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules — like, you are the main character of this module's glow-up, honestly. Send your comments and suggestions preferably to the Bioperl mailing list. 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. 👑

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

not me begging you to file your bugs properly, but yes. 💀

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🌈 AUTHOR - Allen Day 🌈

Email allenday@ucla.edu

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. iykyk. 🧚

🌟 get_instance 🌟

Title   : get_instance
Usage   : my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
Function: constructor
Returns : The Bio::Ontology::DocumentRegistry singleton.
Args    : None

Usage

get_instance is your constructor, and it hands you back the Bio::Ontology::DocumentRegistry singleton. No args, no drama. It's giving one-and-only-one. 💖

🌟 documents 🌟

Title   : documents
Usage   : my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
Function: Maps an ontology name to a list of (local or) remote URIs where the
          files can be located.
Returns : A 3-item list:
          (1) URI for the ontology file
          (2) URI for the ontology definitions file
          (3) format of the files (dagedit, obo, etc)
Args    : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
          (Gene Ontology)'

so like, documents maps an ontology name to a list of (local or) remote URIs where the files can be located. 🔥

What you get back is a 3-item list:

1. URI for the ontology file
2. URI for the ontology definitions file
3. format of the files (dagedit, obo, etc)

And the arg? Just the name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component (Gene Ontology)'. Slay. ✨

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and that's the whole page, bestie — go forth and ontology 💅

this page is perl v5.32.1, dated 2021-08-15. mwah. 🎀