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

💖 Bio::Ontology::PathI — the vibe ✨

okay bestie, welcome to Bio::O...:PathI(3pm), which is literally the manual page for this interface. Settle in, it's short but it's iconic 🎀

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🌸 NAME 🌸

Bio::Ontology::PathI — the interface for a path between ontology terms, fr fr. That's it. That's the whole name. Periodt 💅

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✨ SYNOPSIS ✨

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

so like, there's no big dramatic example here, the original is just pointing you at the method docs and at an actual implementation like Bio::Ontology::Path. Go look at those, iykyk 🦋

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💜 DESCRIPTION 💜

Bestie. Listen. This is the minimal interface for a path between two terms in an ontology. That's the whole assignment. Ontology engines are allowed to use it, and honestly? slay 👑

Here's the tea: it's basically a very thin extension of the Bio::Ontology::RelationshipI interface. Like, thin thin. The one (1) thing it adds is an attribute: distance().

And the way to think about distance() for a RelationshipI? It's equal to zero when subject == object, or 1 when subject != object. That's the lore 🔥

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is, no exaggeration, an integral part of the evolution of this and every other Bioperl module. So send your comments and suggestions, preferably to the Bioperl mailing list. Your participation is so appreciated, genuinely 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🌈 Support

okay real talk — please send usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

...and not directly to the module maintainer. Why? Because there are many experienced and responsive experts who can look at your problem and quickly address it 🙌 And please, for the love of everything, include a thorough description of the problem with code and data examples if at all possible. It helps so much, no cap.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system — it helps them 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 - Hilmar Lapp 👑

Email: hlapp at gmx.net

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📖 APPENDIX 📖

The rest of the documentation goes into detail on each of the object methods. Internal methods are usually preceded with a _ (so if you see one, that's the heads-up, bestie 🫡).

⭐ distance

• Title — distance
• Usage — $obj->distance($newval)
• Function — Get (and set, if the implementation allows it) the distance between the two terms connected by this path.
• Example —
• Returns — value of distance (a scalar)
• Args — on set, new value (a scalar or undef, optional)

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🧚 Bio::Ontology::RelationshipI Methods 🧚

🌸 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 predicate of this relationship.

For a path, the predicate (relationship type) is defined as the greatest common denominator of all predicates (relationship types) encountered along the path. I.e., if predicate A is-a predicate B, the greatest common denominator for a path containing both predicates A and B is B

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

🌸 ontology

• Title — ontology
• Usage — $ont = $obj->ontology()
• Function — Get the ontology that defined 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 perl v5.32.1, dated 2021-08-15, and the module is Bio::O...:PathI(3pm) — go forth and slay your ontology paths ✨🎀🦋