Apache Ossie

Generate an Apache Ossie ontology, serialized as YAML or JSON. Classes become entity types, enums and named types become value types, and slots become relationships.

Usage

CLI

ohi get w3c/prov-o
ohi linkml to ossie --format json \
  --to prov-o.ossie.json prov-o.linkml.yaml

Python

import ohi_linkml

with ohi_linkml.load_file("prov-o.linkml.yaml") as schema:
    output = schema.ossie(format="json")

JavaScript

import { readFileSync } from "node:fs";
import { LinkML } from "@neverblink/linkml";

const yaml = readFileSync("prov-o.linkml.yaml", "utf8");
const { view, report } = LinkML.loadFromString(yaml, {});
if (!view) throw new Error(JSON.stringify(report));
const output = view.ossie({ format: "json" });

Scala

import eu.neverblink.linkml.generator.options.*
import eu.neverblink.linkml.generator.ossie.OssieGenerator
import eu.neverblink.linkml.schemaview.{SchemaIssues, SchemaView}

val loaded = SchemaView.loadSchemaViewFromUri("prov-o.linkml.yaml")
given SchemaView = SchemaIssues.orThrow(loaded)
val output = OssieGenerator().serialize(
  OssieGeneratorOptions(format = JsonOutputFormat.Json),
)

C

#include <stddef.h>
#include "ohi_linkml.h"

linkml_init_threads();
char *report = NULL, *error = NULL;
long long schema =
    linkml_load_file("prov-o.linkml.yaml", NULL, &report, &error);
char *output = linkml_ossie(schema, "{\"format\": \"json\"}", &error);
linkml_free(output);
linkml_free(report);
linkml_free(error);
linkml_close(schema);

Try it in the playground, with PROV-O

Options

formatJsonOutputFormatdefault yaml

CLI --format

The serialization of the output.

• yaml YAML.
• json JSON.

metadata_languagestringdefault en

CLI --metadata-languageScala metadataLanguage

The language of the titles and descriptions in the output, for schemas with text in more than one language.

pruning_modePruningModedefault skip

CLI --pruning-modeScala pruningMode

Which elements become concepts.

• tree_root The elements reachable from the tree root class. Without a tree root, the same as schema.
• schema Everything defined in the root schema, and every element reachable from it. This leaves out the unused parts of imported schemas, such as most of linkml:types.
• skip Every element of the root schema and of all its imports.

tree_rootstring

CLI --tree-rootScala treeRoot

The class to use as the tree root, instead of the class with tree_root: true in the schema. Only for the tree_root pruning mode.

Mapping LinkML to Ossie

The generator writes Apache Ossie ontologies (ontology/ontology.json, version 0.2.0.dev0). The Ossie importer does the reverse.

Document

LinkML	Ossie field
Always 0.2.0.dev0	version
name	name
description	description
One component per class, enum, and named type.	ontology
extensions.ai_context	ai_context
The root schema’s prefixes that iris use.	prefixes

requires and ontology_mappings are not written. See IRIs for how prefixes and iri are handled.

Concept (OntologyComponent)

LinkML	Ossie field
Element name in PascalCase.	concept
EntityType for classes, ValueType for enums and types.	type
class_uri, enum_uri, or the type’s uri. See IRIs.	iri
Element description, in metadata_language.	description
Classes: is_a + mixins. Enums and types: the built-in value type for their base.	extends
identifier, key, or unique_keys	identify_by
Required slots: Concept.relationship. Enums and named types: see Expressions.	requires
The class’ derived slots, minus the ones stated identically in a supertype.	relationships

derived_by is not written.

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.

LinkML	Ossie field
Slot alias, else slot name in snake_case.	name
slot_uri. See IRIs.	iri
{Concept} <title or space-case name> {Range}	verbalizes
Slot description, in metadata_language.	description
Always exactly one, played by the slot’s range concept. A union (any_of) uses the slot’s own range, otherwise Any.	roles
Single-valued identifier/key slot or maximum_cardinality: 1 → OneToOne. Others → ManyToOne.	multiplicity
Slot minimum_value / maximum_value / pattern, as expressions over the role.	requires
rank of the slot	(relationship order)

derived_by is not written.

A role’s name is only written 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:

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

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

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

IRIs

The 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.

Not mapped

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