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

💖 Bio::O...ologyI(3pm) 💖

okay bestie, so this is a page from the User Contributed Perl Documentation section of the manual, and it's all about Bio::Ontology::OntologyI — the interface for an ontology implementation. it's giving "I'm the blueprint, not the building" energy and honestly? iconic. 🦋

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✨ NAME ✨

Bio::Ontology::OntologyI — Interface for an ontology implementation 👑

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✨ SYNOPSIS ✨

# see method documentation

yeah that's it, that's the synopsis. no cap, the docs are all down in the method sections. keep scrolling bestie 💅

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✨ DESCRIPTION ✨

so this is the minimal interface that any ontology implementation has to provide. like, the bare minimum. the vibe check every implementation must pass. 🎀

in essence? it represents a namespace with description sitting on top of the query interface OntologyEngineI.

and this interface inherits from Bio::Ontology::OntologyEngineI. so it's part of the family, it got the genes. 🧬

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✨ FEEDBACK ✨

💌 Mailing Lists

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. literally the glow-up depends on you. send your comments and suggestions (preferably) to the Bioperl mailing list — 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 and support issues to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, okay? not me DMing the maintainer, please. 🙈 there are many experienced and responsive experts who will be able to look at the problem and quickly address it. and if at all possible, include a thorough description of the problem with code and data examples — the more detail the better, we eat that up. 💖

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via email or the web:

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

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✨ AUTHOR - Hilmar Lapp ✨

Email hlapp at gmx.net — shoutout to the author, absolute main character energy 👑

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk 👀).

🌸 Methods defined in this interface.

name

• Title: name
• Usage: $obj->name($newval)
• Function: get/set the name of this ontology.
• Example:
• Returns: value of name (a scalar)
• Args:

authority

• Title: authority
• Usage: $auth = $obj->authority()
• Function: get/set the authority for this ontology — for instance the DNS base for the organization granting the name of the ontology and identifiers for the terms.

this attribute is optional and applications should not generally expect it to have been set. it's here to follow the rules for namespaces, which ontologies serve as for terms. lowkey a formality, highkey still in the docs. 💅

• Example:
• Returns: value of authority (a scalar)
• Args:

identifier

• Title: identifier
• Usage: $id = $obj->identifier()
• Function: get an identifier for this ontology.

this is primarily intended for look-up purposes. clients should not expect the value to be modifiable, and it may not be allowed to set its value from outside. also, the identifier's uniqueness may only hold within the scope of a particular application's run time — i.e., it may be a memory location. so like... it's unique-ish, bestie. don't build your whole personality on it. 💀

• Example:
• Returns: value of identifier (a scalar)
• Args:

definition

• Title: definition
• Usage: $def = $obj->definition()
• Function: get a descriptive definition for this ontology.
• Example:
• Returns: value of definition (a scalar)
• Args:

close

• Title: close
• Usage:
• Function: release any resources this ontology may occupy. in order to efficiently release used memory or file handles, you should call this method once you are finished with an ontology. like, clean up after yourself, it's called being a considerate queen ✨
• Example:
• Returns: TRUE on success and FALSE otherwise
• Args: none

🌈 Methods inherited from Bio::Ontology::OntologyEngineI

their documentations are copied here for completeness. in most use cases, you will want to access the query methods of an ontology, not just the name and description ... 👀

add_term

• Title: add_term
• Usage: add_term(TermI term): TermI
• Function: adds TermI object to the ontology engine term store.

for ease of use, if the ontology property of the term object was not set, an implementation is encouraged to set it to itself upon adding the term.

• Example: $oe->add_term($term)
• Returns: its argument.
• Args: object of class TermI.

add_relationship

• Title: add_relationship
• Usage: add_relationship(RelationshipI relationship): RelationshipI
• Function: adds a relationship object to the ontology engine.
• Example:
• Returns: its argument.
• Args: a RelationshipI object.

get_relationships

• Title: get_relationships
• Usage: get_relationships(TermI term): RelationshipI
• Function: retrieves all relationship objects from this ontology engine, or all relationships of a term if a term is supplied.
• Example:
• Returns: array of Bio::Ontology::RelationshipI objects
• Args: none, or a Bio::Ontology::TermI compliant object for which to retrieve the relationships.

get_predicate_terms

• Title: get_predicate_terms
• Usage: get_predicate_terms(): TermI[]
• Function:
• Example:
• Returns:
• Args:

(yes bestie, that one is literally blank in the original. it's giving mysterious. leave it alone. 🙈)

get_child_terms

• Title: get_child_terms
• Usage: get_child_terms(TermI term, TermI predicate_terms): TermI
• Function: retrieves all child terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_child_terms is a special case of get_descendant_terms, limiting the search to the direct descendants.
• Example:
• Returns: array of TermI objects.
• Args: first argument is the term of interest, second is the list of relationship type terms.

get_descendant_terms

• Title: get_descendant_terms
• Usage: get_descendant_terms(TermI term, TermI rel_types): TermI
• Function: retrieves all descendant terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise.
• Example:
• Returns: array of TermI objects.
• Args: first argument is the term of interest, second is the list of relationship type terms.

get_parent_terms

• Title: get_parent_terms
• Usage: get_parent_terms(TermI term, TermI predicate_terms): TermI
• Function: retrieves all parent terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_parent_terms is a special case of get_ancestor_terms, limiting the search to the direct ancestors.
• Example:
• Returns: array of TermI objects.
• Args: first argument is the term of interest, second is the list of relationship type terms.

get_ancestor_terms

• Title: get_ancestor_terms
• Usage: get_ancestor_terms(TermI term, TermI predicate_terms): TermI
• Function: retrieves all ancestor terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise.
• Example:
• Returns: array of TermI objects.
• Args: first argument is the term of interest, second is the list of relationship type terms.

get_leaf_terms

• Title: get_leaf_terms
• Usage: get_leaf_terms(): TermI
• Function: retrieves all leaf terms from the ontology. a leaf term is a term w/o descendants.
• Example: @leaf_terms = $obj->get_leaf_terms()
• Returns: array of TermI objects.
• Args:

get_root_terms()

• Title: get_root_terms
• Usage: get_root_terms(): TermI
• Function: retrieves all root terms from the ontology. a root term is a term w/o descendants.
• Example: @root_terms = $obj->get_root_terms()
• Returns: array of TermI objects.
• Args:

get_all_terms

• Title: get_all_terms
• Usage: get_all_terms: TermI
• Function: retrieves all terms from the ontology.

we do not mandate an order here in which the terms are returned. in fact, the default implementation will return them in unpredictable order. so like, don't count on it being sorted, bestie, it's chaotic on purpose. 💀

• Example: @terms = $obj->get_all_terms()
• Returns: array of TermI objects.
• Args:

find_terms

• Title: find_terms
• Usage: ($term) = $oe->find_terms(-identifier => "SO:0000263");
• Function: find term instances matching queries for their attributes.

an implementation may not support querying for arbitrary attributes, but can generally be expected to accept -identifier and -name as queries. if both are provided, they are implicitly intersected. ✨

• Example:
• Returns: an array of zero or more Bio::Ontology::TermI objects
• Args: named parameters. the following parameters should be recognized by any implementation:
  • -identifier — query by the given identifier
  • -name — query by the given name

🧚 Factory for relationships and terms

relationship_factory

• Title: relationship_factory
• Usage: $fact = $obj->relationship_factory()
• Function: get (and set, if the implementation supports it) the object factory to be used when relationship objects are created by the implementation on-the-fly.
• Example:
• Returns: value of relationship_factory (a Bio::Factory::ObjectFactoryI compliant object)
• Args:

term_factory

• Title: term_factory
• Usage: $fact = $obj->term_factory()
• Function: get (and set, if the implementation supports it) the object factory to be used when term objects are created by the implementation on-the-fly.
• Example:
• Returns: value of term_factory (a Bio::Factory::ObjectFactoryI compliant object)
• Args:

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and that's the whole page, bestie!! 💖 this one's from perl v5.32.1, dated 2021-08-15, and it lives in the manual as Bio::O...ologyI(3pm). periodt. 🎀✨🦋