Apache Ossie

Read an Apache Ossie ontology, as YAML or JSON, and produce the LinkML schema it describes. The opposite of ossie.

Usage

CLI

ohi get w3c/prov-o --format ossie-yaml
ohi linkml from ossie --schema-id https://example.org/prov \
  --to prov.yaml prov-o.ossie.yaml

Python

from pathlib import Path

import ohi_linkml

result = ohi_linkml.from_ossie(
    Path("prov-o.ossie.yaml").read_text(),
    schema_id="https://example.org/prov",
)

JavaScript

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

const result = LinkML.fromOssie(
  readFileSync("prov-o.ossie.yaml", "utf8"),
  { schema_id: "https://example.org/prov" },
);

Scala

import eu.neverblink.linkml.generator.options.OssieImporterOptions
import eu.neverblink.linkml.generator.ossie.OssieImporter

import java.nio.file.{Files, Path}

val schema = OssieImporter().serializeFromString(
  Files.readString(Path.of("prov-o.ossie.yaml")),
  OssieImporterOptions(schemaId = Some("https://example.org/prov")),
)

C

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

/* document is the text of prov-o.ossie.yaml. */
/* The result is an ImportResult in JSON. */
linkml_init_threads();
char *error = NULL;
char *result = linkml_from_ossie(
    document,
    "{\"schema_id\": \"https://example.org/prov\"}",
    &error
);
linkml_free(result);
linkml_free(error);

Try it in the playground, with PROV-O

Options

formatJsonOutputFormatdefault yaml

CLI --format

The serialization of the schema.

• yaml YAML.
• json JSON.

full_urisbooleandefault false

CLI --full-urisScala fullUris

Whether to write URIs in full, instead of compacting them to CURIEs with the schema's prefixes.

schema_idstring

CLI --schema-idScala schemaId

The id of the schema to produce. An Ossie ontology has none of its own, so by default it is a placeholder built from the ontology's name.

Mapping Ossie to LinkML

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

Document

Ossie field	LinkML
name	name
description	description
ontology	A class, enum, or type per component.
ai_context	extensions.ai_context
prefixes	prefixes, declared after linkml.

version, requires and ontology_mappings are 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 schema_id.

Concept (OntologyComponent)

Ossie field	LinkML
concept	Element name, with the original spelling in alias.
type	A class for EntityType, an enum or a type for ValueType.
iri	class_uri, enum_uri, or the type’s uri. See IRIs.
description	description
extends	Last entry is is_a, the rest are mixins. For a value type it is typeof, or string if the base is unknown.
identify_by	One entry, OneToOne, or scalar range → identifier. Otherwise unique_keys.
requires	Concept.relationship makes the slot required. For enums and types, see Expressions. Any other restriction is ignored.
relationships	One attribute each.

derived_by is not read.

Relationship

Ossie field	LinkML
name	Slot name in snake_case, original spelling in alias.
iri	slot_uri. See IRIs.
verbalizes	The phrase becomes the slot title, unless it is just the space-cased name. Only the first is read.
description	description
roles	The first role’s concept is the range. Any others are dropped.
multiplicity	Absent → multivalued: true.
requires	minimum_value, maximum_value and pattern, from expressions over the role.
(relationship order)	rank

derived_by is not read.

Ranges

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

Ossie	LinkML
String	string
Integer	integer
Float	float
Decimal	decimal
Boolean	boolean
Date	date
DateTime	datetime
Any	A class with class_uri: linkml:Any

The generator maps several LinkML types to one Ossie concept, so a round trip changes them: a uri comes back as a string, and a double as a float.

Expressions

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

IRIs

The 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.