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

💖 NAME 💖

Bio::Ontology::Relationship — bestie, it's a relationship for an ontology. Yes, literally, that's the whole vibe. It's the Bio::O...ionship page from the 3pm manual, part of the User Contributed Perl Documentation situation.

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✨ SYNOPSIS ✨

okay so here's how you summon one, no cap:

$rel = Bio::Ontology::Relationship->new( -identifier     => "16847",
                                         -subject_term   => $subj,
                                         -object_term    => $obj,
                                         -predicate_term => $pred );

that's it. that's the whole entrance. 🦋

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🌸 DESCRIPTION 🌸

This is a basic implementation of Bio::Ontology::RelationshipI. Iconic behavior honestly.

So the terminology we use here is the one that's commonly used for ontologies, and it's the triple of (subject, predicate, object) — which, plot twist, is also scoped in a namespace (the ontology). We call it a triple because it's a tuple of three ontology terms. Three terms, one vibe. 💅

Now listen, there are other terminologies floating around for expressing relationships. And for anyone who finds it easier to get the concept that way: the triple of (child, relationship type, parent) would be equivalent to the terminology we chose here — disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. So like, we're not judging, we're just saying.

BUT. Especially when you have 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

and are therefore strongly discouraged. Like, don't do it. That's the rule. 🚫

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So like, send your comments and suggestions, preferably to 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. The way that this works is that many experienced and reponsive experts will be able look at the problem and quickly address it. So like, the group chat is faster than the DM, iykyk. 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 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 👑

Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

WWW: http://monochrome-effect.net/

Address:

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

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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 _. (secret little underscore, you know how it is 💀)

🧚 new

Creates a new Bio::Ontology::Relationship. Fresh out the box, main character energy.

Title   : new
Usage   : $rel = Bio::Ontology::Relationship->new(-identifier   => "16847",
                                                  -subject_term => $subject,
                                                  -object_term  => $object,
                                                  -predicate_term => $type );
Function: Creates a new Bio::Ontology::Relationship.
Returns : A new Bio::Ontology::Relationship object.
Args    : -identifier     => the identifier of this relationship [scalar]
          -subject_term   => the subject term [Bio::Ontology::TermI]
          -object_term    => the object term [Bio::Ontology::TermI]
          -predicate_term => the predicate term [Bio::Ontology::TermI]

🦋 init

Initializes this Relationship to all undef. Everything is nothing, very existential, very slay.

Title   : init()
Usage   : $rel->init();
Function: Initializes this Relationship to all undef.
Returns :
Args    :

💜 identifier

Set/get for the identifier of this Relationship. It's a scalar, bestie, it's not that deep.

Title   : identifier
Usage   : $rel->identifier( "100050" );
          or
          print $rel->identifier();
Function: Set/get for the identifier of this Relationship.
Returns : The identifier [scalar].
Args    : The identifier [scalar] (optional).

🌸 subject_term

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). You know the one.

Title   : subject_term
Usage   : $rel->subject_term( $subject );
          or
          $subject = $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    : The subject term [Bio::Ontology::TermI] (optional).

🎀 object_term

Set/get for the object term of this Relationship.

Again with the convention: ontologies express relationships between terms as triples (subject, predicate, object). Same triple, different slot. 💖

Title   : object_term
Usage   : $rel->object_term( $object );
          or
          $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    : The object term [Bio::Ontology::TermI] (optional).

🔥 predicate_term

Set/get for the predicate (relationship type) of this relationship. This is the one that says how the two terms are linked, and honestly? It's the moment.

And yes: the common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Third time's the charm.

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

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

Returns : The predicate term [Bio::Ontology::TermI].
Args    : The predicate term [Bio::Ontology::TermI] (optional).

🌈 ontology

Get/set the ontology that defined this relationship. It returns an object implementing Bio::Ontology::OntologyI, and on set you can hand it undef or an object implementing Bio::Ontology::OntologyI (optional).

Title   : ontology
Usage   : $ont = $obj->ontology()
Function: Get/set the ontology that defined this relationship.
Example :
Returns : an object implementing L<Bio::Ontology::OntologyI>
Args    : on set, undef or an object implementing
          Bio::Ontology::OntologyI (optional)

See Bio::Ontology::OntologyI.

💅 to_string

to_string method for Relationship. It hands you back a string representation of this Relationship, so you can print it and feel something. 🫶

Title   : to_string()
Usage   : print $rel->to_string();
Function: to_string method for Relationship.
Returns : A string representation of this Relationship.
Args    :

💀 Deprecated Methods

These methods are deprecated and defined here solely to preserve backwards compatibility.

So like, they're still here, they're just here for the nostalgia. Don't build anything new on them, bestie. 🙈

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and that's the whole page!! 🌟 this was Bio::O...ionship(3pm) from perl v5.32.1, dated 2021-08-15, brought to you by User Contributed Perl Documentation. mwah, take care of yourselves, hydrate, and go write some ontologies. 💖✨🎀