LinkML <-> Apache Ossie ontology mapping

How the ossie generator and importer map between LinkML and Apache Ossie ontologies (ontology/ontology.json, version 0.2.0.dev0).

Document

From LinkML	Ossie field	To LinkML
Hardcoded 0.2.0.dev0	version	Not read.
name	name	Inverse.
description	description	Inverse.
One component per class, enum, and named type.	ontology	Inverse.
extensions.ai_context	ai_context	Inverse.
The root schema’s prefixes that iris use.	prefixes	Inverse, declared after linkml.
Not emitted.	requires	Not read.
Not emitted.	ontology_mappings	Not read.

See IRIs for how prefixes and iri are handled.

By default, the importer invents an identifier for the LinkML schema as https://example.org/ + name in snake_case, unless the caller supplies it.

Concept (OntologyComponent)

From LinkML	Ossie field	To LinkML
Element name in PascalCase.	concept	Inverse. Original spelling kept in alias.
EntityType for classes, ValueType for enums and types.	type	Inverse.
class_uri, enum_uri, or the type’s uri. See IRIs.	iri	Inverse.
Element description, in --metadata-language.	description	Inverse.
Classes: is_a + mixins. Enums and types: the built-in value type for their base.	extends	Last entry is is_a, the rest are mixins. For a value type it is typeof, or string if the base is unknown.
identifier, key, or unique_keys	identify_by	One entry, OneToOne, or scalar range → identifier. Otherwise unique_keys.
Required slots: Concept.relationship. Enums and named types: see Expressions.	requires	Inverse. Any other restriction is ignored.
The class’ derived slots, minus the ones stated identically in a supertype.	relationships	One attribute each.
Not emitted.	derived_by	Not read.

Abstract classes and mixins become ordinary concepts – Ossie has no abstract elements.

A subtype only declares what it does not inherit unchanged. If it narrows a slot (a tighter range or required where the supertype had it optional), the relationship is declared again on the subtype.

Relationship

One per derived slot of the class. Identified as Concept.name, so names only need to be unique within their concept.

From LinkML	Ossie field	To LinkML
Slot alias, else slot name in snake_case.	name	Slot name in snake_case, original spelling in alias.
slot_uri. See IRIs.	iri	slot_uri.
{Concept} <title or space-case name> {Range}	verbalizes	The phrase becomes the slot title, unless it is just the space-cased name. Only the first is read.
Slot description, in --metadata-language.	description	Inverse.
Always exactly one, played by the slot’s range concept. A union (any_of) uses the slot’s own range, otherwise Any.	roles	The first role’s concept is the range. Any others are dropped.
Single-valued identifier/key slot or maximum_cardinality: 1 → OneToOne. Others → ManyToOne.	multiplicity	Absent → multivalued: true.
Slot minimum_value / maximum_value / pattern, as expressions over the role.	requires	Inverse.
Not emitted.	derived_by	Not read.
rank of the slot	(relationship order)	Inverse.

Roles

A role’s name is only emitted when the player would otherwise be ambiguous – i.e. a slot whose range is its own class. Person.parent_of becomes roles: [{concept: Person, name: parent_of}] and verbalizes as {Person} parent of {Person:parent_of}, per the spec’s disambiguation rule.

Ranges

Primitive LinkML types map straight onto Ossie’s built-in concepts:

From LinkML	Ossie	To LinkML
string, uri, uriorcurie, curie, ncname	String	string
integer	Integer	integer
float, double	Float	float
decimal	Decimal	decimal
boolean	Boolean	boolean
date	Date	date
datetime	DateTime	datetime
time	String	string
localized text	String	string
linkml:Any, unknown base	Any	A class with class_uri: linkml:Any

Several LinkML types share one Ossie concept, so the last column is not the inverse of the first: a uri comes back as a string, and a double as a float.

A non-primitive LinkML type becomes its own ValueType concept extending a built-in.

An enum becomes a ValueType extending String, with its permissible values as a requires expression. Enum inheritance and dynamic enums are not mapped.

Expressions

From LinkML	Ossie	To LinkML
required: true	Concept.relationship	Inverse.
permissible_values	Ref IN ('a', 'b')	Inverse.
minimum_value, maximum_value	Ref >= v, Ref <= v	Inverse.
pattern	REGEXP_LIKE(Ref, 'p')	Inverse.

IRIs

The LinkML → Ossie generator gives every class, slot, enum and named type an iri: its class_uri, slot_uri, enum_uri or uri, or the URI LinkML derives when there is none. An IRI is written as a QName (basically, same thing as short IRIs in Turtle) when one of the root schema’s prefixes covers it, and as a full IRI otherwise. A full IRI that would be read back as a QName, such as the IRI ex:Person when ex is a declared prefix or a prefix of the LinkML metamodel, can’t be written, so the generator fails with an error. Only the prefixes that some iri uses go into the ontology’s prefixes.

The Ossie → LinkML importer copies the ontology’s prefixes into the schema, and expands each iri that is a QName, as a LinkML schema is read. The schema then writes the URI as a CURIE again, so iri: foaf:Agent becomes class_uri: foaf:Agent. The one exception is a linkml prefix that points anywhere other than https://w3id.org/linkml/. The schema needs linkml for its own imports, so that prefix is not copied, and any iri using it is written out as a full IRI instead.

A QName whose prefix the ontology doesn’t declare is expanded with the prefixes of the LinkML metamodel, so iri: skos:Concept is http://www.w3.org/2004/02/skos/core#Concept. Any other iri must be a full IRI, such as acme:Thing when acme isn’t a prefix. The import stops with an error for an iri, a schema id or a prefix namespace that isn’t a valid IRI, such as Person or John Doe.

Not mapped from LinkML

Ossie does not support arbitrary extensions, so the following LinkML features are not mapped:

• Permissible value meaning, and the *_mappings metaslots
• deprecated, annotations, extensions, subsets, see_also and other metadata
• unit, default / ifabsent, recommended
• Cardinality counts (minimum_cardinality, maximum_cardinality)
• rules, any_of / all_of / none_of / exactly_one_of
• Type designators, arrays