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

💖 Bio::Ontology::RelationshipI — the vibe check 💖

okay so real quick, bestie: this is a page from the User Contributed Perl Documentation, and the module we're stanning today is Bio::Ontology::RelationshipI — like, it's a Perl module, so it lives in section 3pm of the manual. She's an interface, she's minimal, and she's so important. let's get into it ✨

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🌸 NAME 🌸

Bio::Ontology::RelationshipI — the interface for a relationship between ontology terms. that's it, that's her 🎀

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✨ SYNOPSIS ✨

# see documentation of methods and an implementation, e.g.,
# Bio::Ontology::Relationship

like, no cap, there's no big dramatic example here — go read the methods below, and go peek at an actual implementation such as Bio::Ontology::Relationship if you wanna see a real one doing its thing 💅

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🦋 DESCRIPTION 🦋

This is the minimal interface for a relationship between two terms in an ontology. Ontology engines will use this. lowkey that's the whole job and she does it flawlessly 👑

So the terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (the ontology). It's called a triple because it is a tuple of three ontology terms. three terms. a trio. the friend group 🫶

There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of (child, relationship type, parent) would be equivalent to the terminology chosen here — disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. And honestly? Especially in the case of ontologies with a wide variety of predicates, the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds B), or even conflicting (e.g., A is-parent-of B). so yeah — they are therefore strongly discouraged. not me warning you in advance 😭 it's giving "please don't do this"

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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 the Bioperl mailing list. Your participation is much appreciated. fr fr, they mean it, 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 responsive 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. like, give them the full tea, bestie, they can't debug a vibe 🍓

🐛 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

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👑 AUTHOR - Peter Dimitrov 👑

Email dimitrov@gnf.org

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🌟 CONTRIBUTORS 🌟

Hilmar Lapp, email: hlapp at gmx.net

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🧚 APPENDIX 🧚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. (so if you see an underscore, mind your business, that's internal 😌)

🌸 identifier 🌸

• Title: identifier
• Usage: print $rel->identifier();
• Function: Set/get for the identifier of this Relationship.

Note that this may not necessarily be used by a particular ontology. (so don't come for her if your ontology's like "never heard of her" 🙈)

• Returns: The identifier [scalar].
• Args:

🌸 subject_term 🌸

• Title: subject_term
• Usage: $subj = $rel->subject_term();
• Function: Set/get for the subject term of this Relationship.

The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object).

• Returns: The subject term [Bio::Ontology::TermI].
• Args:

🌸 object_term 🌸

• Title: object_term
• Usage: $object = $rel->object_term();
• Function: Set/get for the object term of this Relationship.

The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object).

• Returns: The object term [Bio::Ontology::TermI].
• Args:

🌸 predicate_term 🌸

• Title: predicate_term
• Usage: $type = $rel->predicate_term();
• Function: Set/get for the relationship type of this relationship.

The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object).

• Returns: The relationship type [Bio::Ontology::TermI].
• Args:

🌸 ontology 🌸

• Title: ontology
• Usage: $ont = $obj->ontology()
• Function: Get the ontology that defined (is the scope for) this relationship.
• Example:
• Returns: an object implementing Bio::Ontology::OntologyI
• Args:

See Bio::Ontology::OntologyI.

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and that's the whole page, bestie!! 💜 this was served up courtesy of perl v5.32.1, dated 2021-08-15, and it's literally the Bio::O...nshipI(3pm) page from the User Contributed Perl Documentation. slay, ate, no crumbs, periodt. 🎀✨