LinkML is a linked data modeling language following object-oriented and ontological principles. LinkML models are typically authored in YAML, and can be converted to other schema representation formats such as JSON or RDF.
LinkML is bundled with a number of generators which will take LinkML YAML schemas as input and output schemas in one of the following formats:
- ShEx
- JSON Schema
- OWL
- Python dataclasses
- Java
- SPARQL
- SQL DDL
- Markdown (for deployment in a GitHub pages site)
...and more.
More details about the the usage of different types of Generators can be viewed on the docs site.
You can browse the metamodel component documentation here. LinkML is self-describing, but a few important vocabulary terms to keep in mind are:
- ClassDefinition: Component for defining Classes
- SlotDefinition: Component for defining Class Properties (or Slots)
- TypeDefinition: Component for defining Data Types
- SchemaDefinition: Component for defining Schemas (combination of subset, type, slot, class)
As an example, LinkML has been used for the development of the Biolink Model, but the framework itself is general purpose and can be used for any kind of modeling. For an example Biolink metamodel, see this Jupyter Notebook.
This project uses pipenv for installation. Some IDE's like PyCharm also have direct support for pipenv.
> pipenv install linkmlAdditional installation instructions can be found on the LinkML docs site.
In the following sections we will use the Person example schema, which consists of a single class Person with a number of slots, to demonstrate the usage of various generators:
JSON Schema is a schema language for JSON documents.
To autogenerate JSON Schema output for the Person schema, run the following command:
pipenv run gen-json-schema examples/PersonSchema/personinfo.yamlJSON Schema output for Person schema
{
"$id": "https://w3id.org/linkml/examples/personinfo",
"$schema": "http://json-schema.org/draft-07/schema#",
"additionalProperties": true,
"definitions": {
"Address": {
"additionalProperties": false,
"description": "",
"properties": {
"city": {
"type": "string"
},
"postal_code": {
"type": "string"
},
"street": {
"type": "string"
}
},
"required": [],
"title": "Address",
"type": "object"
},
"Concept": {
"additionalProperties": false,
"description": "",
"properties": {
"description": {
"type": "string"
},
"id": {
"type": "string"
},
"image": {
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"id"
],
"title": "Concept",
"type": "object"
},
"Container": {
"additionalProperties": false,
"description": "",
"properties": {
"organizations": {
"items": {
"$ref": "#/definitions/Organization"
},
"type": "array"
},
"persons": {
"items": {
"$ref": "#/definitions/Person"
},
"type": "array"
}
},
"required": [],
"title": "Container",
"type": "object"
},
"DiagnosisConcept": {
"additionalProperties": false,
"description": "",
"properties": {
"description": {
"type": "string"
},
"id": {
"type": "string"
},
"image": {
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"id"
],
"title": "DiagnosisConcept",
"type": "object"
},
"DiagnosisType": {
"description": "",
"enum": [],
"title": "DiagnosisType",
"type": "string"
},
"EmploymentEvent": {
"additionalProperties": false,
"description": "",
"properties": {
"duration": {
"type": "number"
},
"employed_at": {
"type": "string"
},
"ended_at_time": {
"format": "date",
"type": "string"
},
"is_current": {
"type": "boolean"
},
"started_at_time": {
"format": "date",
"type": "string"
}
},
"required": [],
"title": "EmploymentEvent",
"type": "object"
},
"Event": {
"additionalProperties": false,
"description": "",
"properties": {
"duration": {
"type": "number"
},
"ended_at_time": {
"format": "date",
"type": "string"
},
"is_current": {
"type": "boolean"
},
"started_at_time": {
"format": "date",
"type": "string"
}
},
"required": [],
"title": "Event",
"type": "object"
},
"FamilialRelationship": {
"additionalProperties": false,
"description": "",
"properties": {
"ended_at_time": {
"format": "date",
"type": "string"
},
"related_to": {
"type": "string"
},
"started_at_time": {
"format": "date",
"type": "string"
},
"type": {
"$ref": "#/definitions/FamilialRelationshipType"
}
},
"required": [
"type",
"related_to"
],
"title": "FamilialRelationship",
"type": "object"
},
"FamilialRelationshipType": {
"description": "",
"enum": [
"SIBLING_OF",
"PARENT_OF",
"CHILD_OF"
],
"title": "FamilialRelationshipType",
"type": "string"
},
"GenderType": {
"description": "",
"enum": [
"nonbinary man",
"nonbinary woman",
"transgender woman",
"transgender man",
"cisgender man",
"cisgender woman"
],
"title": "GenderType",
"type": "string"
},
"MedicalEvent": {
"additionalProperties": false,
"description": "",
"properties": {
"diagnosis": {
"$ref": "#/definitions/DiagnosisConcept"
},
"duration": {
"type": "number"
},
"ended_at_time": {
"format": "date",
"type": "string"
},
"in_location": {
"type": "string"
},
"is_current": {
"type": "boolean"
},
"procedure": {
"$ref": "#/definitions/ProcedureConcept"
},
"started_at_time": {
"format": "date",
"type": "string"
}
},
"required": [],
"title": "MedicalEvent",
"type": "object"
},
"NamedThing": {
"additionalProperties": false,
"description": "A generic grouping for any identifiable entity",
"properties": {
"description": {
"type": "string"
},
"id": {
"type": "string"
},
"image": {
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"id"
],
"title": "NamedThing",
"type": "object"
},
"Organization": {
"additionalProperties": false,
"description": "An organization such as a company or university",
"properties": {
"aliases": {
"items": {
"type": "string"
},
"type": "array"
},
"description": {
"type": "string"
},
"founding_date": {
"type": "string"
},
"founding_location": {
"type": "string"
},
"id": {
"type": "string"
},
"image": {
"type": "string"
},
"mission_statement": {
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"id"
],
"title": "Organization",
"type": "object"
},
"Person": {
"additionalProperties": false,
"description": "A person (alive, dead, undead, or fictional).",
"properties": {
"age_in_years": {
"type": "integer"
},
"aliases": {
"items": {
"type": "string"
},
"type": "array"
},
"birth_date": {
"type": "string"
},
"current_address": {
"$ref": "#/definitions/Address",
"description": "The address at which a person currently lives"
},
"description": {
"type": "string"
},
"gender": {
"$ref": "#/definitions/GenderType"
},
"has_employment_history": {
"items": {
"$ref": "#/definitions/EmploymentEvent"
},
"type": "array"
},
"has_familial_relationships": {
"items": {
"$ref": "#/definitions/FamilialRelationship"
},
"type": "array"
},
"has_medical_history": {
"items": {
"$ref": "#/definitions/MedicalEvent"
},
"type": "array"
},
"id": {
"type": "string"
},
"image": {
"type": "string"
},
"name": {
"type": "string"
},
"primary_email": {
"pattern": "^\\S+@[\\S+\\.]+\\S+",
"type": "string"
}
},
"required": [
"id"
],
"title": "Person",
"type": "object"
},
"Place": {
"additionalProperties": false,
"description": "",
"properties": {
"aliases": {
"items": {
"type": "string"
},
"type": "array"
},
"id": {
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"id"
],
"title": "Place",
"type": "object"
},
"ProcedureConcept": {
"additionalProperties": false,
"description": "",
"properties": {
"description": {
"type": "string"
},
"id": {
"type": "string"
},
"image": {
"type": "string"
},
"name": {
"type": "string"
}
},
"required": [
"id"
],
"title": "ProcedureConcept",
"type": "object"
},
"Relationship": {
"additionalProperties": false,
"description": "",
"properties": {
"ended_at_time": {
"format": "date",
"type": "string"
},
"related_to": {
"type": "string"
},
"started_at_time": {
"format": "date",
"type": "string"
},
"type": {
"type": "string"
}
},
"required": [],
"title": "Relationship",
"type": "object"
}
},
"properties": {},
"title": "personinfo",
"type": "object"
}
Note that any JSON that conforms to the derived JSON Schema can be converted to RDF using the derived JSON-LD context.
JSON-LD context provides mapping from JSON to RDF.
To autogenerate JSON LD context output for the Person schema, run the following command:
pipenv run gen-jsonld-context examples/PersonSchema/personinfo.yamlJSON LD Context output for Person schema
{
"_comments": "Auto generated from personinfo.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-09-13 12:01\n Schema: personinfo\n \n id: https://w3id.org/linkml/examples/personinfo\n description: Information about people, based on [schema.org](http://schema.org)\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
"@context": {
"GSSO": {
"@id": "http://purl.obolibrary.org/obo/GSSO_",
"@prefix": true
},
"famrel": "https://example.org/FamilialRelations#",
"linkml": "https://w3id.org/linkml/",
"personinfo": "https://w3id.org/linkml/examples/personinfo/",
"prov": "http://www.w3.org/ns/prov#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"schema": "http://schema.org/",
"skos": "http://example.org/UNKNOWN/skos/",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"@vocab": "https://w3id.org/linkml/examples/personinfo/",
"age_in_years": {
"@type": "xsd:integer"
},
"birth_date": {
"@id": "schema:birthDate"
},
"current_address": {
"@type": "@id"
},
"description": {
"@id": "schema:description"
},
"diagnosis": {
"@type": "@id"
},
"duration": {
"@type": "xsd:float"
},
"employed_at": {
"@type": "@id"
},
"ended_at_time": {
"@type": "xsd:date",
"@id": "prov:endedAtTime"
},
"founding_location": {
"@type": "@id"
},
"gender": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "schema:gender"
},
"has_employment_history": {
"@type": "@id"
},
"has_familial_relationships": {
"@type": "@id"
},
"has_medical_history": {
"@type": "@id"
},
"id": "@id",
"image": {
"@id": "schema:image"
},
"in_location": {
"@type": "@id"
},
"is_current": {
"@type": "xsd:boolean"
},
"name": {
"@id": "schema:name"
},
"organizations": {
"@type": "@id"
},
"persons": {
"@type": "@id"
},
"primary_email": {
"@id": "schema:email"
},
"procedure": {
"@type": "@id"
},
"related_to": {
"@type": "@id"
},
"started_at_time": {
"@type": "xsd:date",
"@id": "prov:startedAtTime"
},
"Address": {
"@id": "schema:PostalAddress"
},
"Organization": {
"@id": "schema:Organization"
},
"Person": {
"@id": "schema:Person"
}
}
}
You can control the output via prefixes declarations and default_curi_maps.
Any JSON that conforms to the derived JSON Schema (see above) can be converted to RDF using this context.
To autogenerate Python dataclasses output for the Person schema, run the following command:
pipenv run gen-py-classes examples/PersonSchema/personinfo.yaml > examples/PersonSchema/personinfo.pyPython dataclass output for Person schema
@dataclass
class NamedThing(YAMLRoot):
"""
A generic grouping for any identifiable entity
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = PERSONINFO.NamedThing
class_class_curie: ClassVar[str] = "personinfo:NamedThing"
class_name: ClassVar[str] = "NamedThing"
class_model_uri: ClassVar[URIRef] = PERSONINFO.NamedThing
id: Union[str, NamedThingId] = None
name: Optional[str] = None
description: Optional[str] = None
image: Optional[str] = None
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.id):
self.MissingRequiredField("id")
if not isinstance(self.id, NamedThingId):
self.id = NamedThingId(self.id)
if self.name is not None and not isinstance(self.name, str):
self.name = str(self.name)
if self.description is not None and not isinstance(self.description, str):
self.description = str(self.description)
if self.image is not None and not isinstance(self.image, str):
self.image = str(self.image)
super().__post_init__(**kwargs)For more details see PythonGenNotes.
The python object can be directly serialized as RDF.
ShEx, short for Shape Expressions Language is a modeling language for RDF files.
To autogenerate ShEx output for the Person schema, run the following command:
pipenv run gen-shex examples/PersonSchema/personinfo.yaml > examples/PersonSchema/personinfo.shexjShEx output for Person schema
BASE <https://w3id.org/linkml/examples/personinfo/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX linkml: <https://w3id.org/linkml/>
PREFIX schema: <http://schema.org/>
PREFIX prov: <http://www.w3.org/ns/prov#>
linkml:String xsd:string
linkml:Integer xsd:integer
linkml:Boolean xsd:boolean
linkml:Float xsd:float
linkml:Double xsd:double
linkml:Decimal xsd:decimal
linkml:Time xsd:dateTime
linkml:Date xsd:date
linkml:Datetime xsd:dateTime
linkml:Uriorcurie IRI
linkml:Uri IRI
linkml:Ncname xsd:string
linkml:Objectidentifier IRI
linkml:Nodeidentifier NONLITERAL
<Address> CLOSED {
( $<Address_tes> ( <street> @linkml:String ? ;
<city> @linkml:String ? ;
<postal_code> @linkml:String ?
) ;
rdf:type [ schema:PostalAddress ] ?
)
}
<Concept> (
CLOSED {
( $<Concept_tes> ( &<NamedThing_tes> ;
rdf:type [ <NamedThing> ] ?
) ;
rdf:type [ <Concept> ]
)
} OR @<DiagnosisConcept> OR @<ProcedureConcept>
)
<Container> CLOSED {
( $<Container_tes> ( <persons> @<Person> * ;
<organizations> @<Organization> *
) ;
rdf:type [ <Container> ] ?
)
}
<DiagnosisConcept> CLOSED {
( $<DiagnosisConcept_tes> ( &<Concept_tes> ;
rdf:type [ <Concept> ] ?
) ;
rdf:type [ <DiagnosisConcept> ]
)
}
<EmploymentEvent> CLOSED {
( $<EmploymentEvent_tes> ( &<Event_tes> ;
rdf:type [ <Event> ] ? ;
<employed_at> @<Organization> ?
) ;
rdf:type [ <EmploymentEvent> ] ?
)
}
<Event> (
CLOSED {
( $<Event_tes> ( prov:startedAtTime @linkml:Date ? ;
prov:endedAtTime @linkml:Date ? ;
<duration> @linkml:Float ? ;
<is_current> @linkml:Boolean ?
) ;
rdf:type [ <Event> ] ?
)
} OR @<EmploymentEvent> OR @<MedicalEvent>
)
<FamilialRelationship> CLOSED {
( $<FamilialRelationship_tes> ( &<Relationship_tes> ;
rdf:type [ <Relationship> ] ? ;
<type> @<FamilialRelationshipType> ;
<related_to> @<Person>
) ;
rdf:type [ <FamilialRelationship> ] ?
)
}
<HasAliases> {
( $<HasAliases_tes> <aliases> @linkml:String * ;
rdf:type [ <HasAliases> ] ?
)
}
<MedicalEvent> CLOSED {
( $<MedicalEvent_tes> ( &<Event_tes> ;
rdf:type [ <Event> ] ? ;
<in_location> @<Place> ? ;
<diagnosis> @<DiagnosisConcept> ? ;
<procedure> @<ProcedureConcept> ?
) ;
rdf:type [ <MedicalEvent> ] ?
)
}
<NamedThing> (
CLOSED {
( $<NamedThing_tes> ( schema:name @linkml:String ? ;
schema:description @linkml:String ? ;
schema:image @linkml:String ?
) ;
rdf:type [ <NamedThing> ]
)
} OR @<Concept> OR @<Organization> OR @<Person>
)
<Organization> CLOSED {
( $<Organization_tes> ( &<NamedThing_tes> ;
rdf:type [ <NamedThing> ] ? ;
&<HasAliases_tes> ;
rdf:type [ <HasAliases> ] ? ;
<mission_statement> @linkml:String ? ;
<founding_date> @linkml:String ? ;
<founding_location> @<Place> ? ;
<aliases> @linkml:String *
) ;
rdf:type [ schema:Organization ]
)
}
<Person> CLOSED {
( $<Person_tes> ( &<NamedThing_tes> ;
rdf:type [ <NamedThing> ] ? ;
&<HasAliases_tes> ;
rdf:type [ <HasAliases> ] ? ;
<primary_email> @linkml:String ? ;
schema:birthDate @linkml:String ? ;
<age_in_years> @linkml:Integer ? ;
schema:gender @<GenderType> ? ;
<current_address> @<Address> ? ;
<has_employment_history> @<EmploymentEvent> * ;
<has_familial_relationships> @<FamilialRelationship> * ;
<has_medical_history> @<MedicalEvent> * ;
<aliases> @linkml:String *
) ;
rdf:type [ schema:Person ]
)
}
<Place> CLOSED {
( $<Place_tes> ( &<HasAliases_tes> ;
rdf:type [ <HasAliases> ] ? ;
schema:name @linkml:String ? ;
<aliases> @linkml:String *
) ;
rdf:type [ <Place> ]
)
}
<ProcedureConcept> CLOSED {
( $<ProcedureConcept_tes> ( &<Concept_tes> ;
rdf:type [ <Concept> ] ?
) ;
rdf:type [ <ProcedureConcept> ]
)
}
<Relationship> (
CLOSED {
( $<Relationship_tes> ( prov:startedAtTime @linkml:Date ? ;
prov:endedAtTime @linkml:Date ? ;
<related_to> @linkml:String ? ;
<type> @linkml:String ?
) ;
rdf:type [ <Relationship> ] ?
)
} OR @<FamilialRelationship>
)
<WithLocation> {
( $<WithLocation_tes> <in_location> @<Place> ? ;
rdf:type [ <WithLocation> ] ?
)
}
Web Ontology Language OWL is modeling language used to author ontologies.
To autogenerate OWL output for the Person schema, run the following command:
pipenv run gen-owl examples/PersonSchema/personinfo.yaml > examples/PersonSchema/personinfo.owl.ttlOWL output for Person schema
<https://w3id.org/linkml/examples/personinfo/Person> a owl:Class,
linkml:ClassDefinition ;
rdfs:label "Person" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxQualifiedCardinality 1 ;
owl:onClass linkml:Integer ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/age_in_years> ],
[ a owl:Restriction ;
owl:allValuesFrom <https://w3id.org/linkml/examples/personinfo/EmploymentEvent> ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/has_employment_history> ],
[ a owl:Restriction ;
owl:maxQualifiedCardinality 1 ;
owl:onClass linkml:String ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/primary_email> ],
[ a owl:Restriction ;
owl:maxQualifiedCardinality 1 ;
owl:onClass linkml:String ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/birth_date> ],
[ a owl:Restriction ;
owl:maxQualifiedCardinality 1 ;
owl:onClass <http://UNKNOWN.org/GenderType> ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/gender> ],
[ a owl:Restriction ;
owl:allValuesFrom <https://w3id.org/linkml/examples/personinfo/MedicalEvent> ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/has_medical_history> ],
[ a owl:Restriction ;
owl:allValuesFrom <https://w3id.org/linkml/examples/personinfo/FamilialRelationship> ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/has_familial_relationships> ],
[ a owl:Restriction ;
owl:maxQualifiedCardinality 1 ;
owl:onClass <https://w3id.org/linkml/examples/personinfo/Address> ;
owl:onProperty <https://w3id.org/linkml/examples/personinfo/current_address> ],
[ a owl:Restriction ;
owl:allValuesFrom linkml:String ;
owl:onProperty linkml:aliases ],
<https://w3id.org/linkml/examples/personinfo/HasAliases>,
<https://w3id.org/linkml/examples/personinfo/NamedThing> ;
skos:definition "A person (alive, dead, undead, or fictional)." ;
skos:exactMatch <http://schema.org/Person> .The below command will generate a Markdown document for every class and slot in the model which can be used in a static site for ex., GitHub pages.
pipenv run gen-markdown examples/PersonSchema/personinfo.yaml -d examples/PersonSchema/personinfomdSee specification. Also see the semantics folder for an experimental specification in terms of FOL.
A Github action is set up to automatically release the package to PyPI. When it is ready for a new release, create a Github release. The version should be in the vX.X.X format following the semantic versioning specification.
After the release is created, the GitHub action will be triggered to publish to PyPI. The release version will be used to create the PyPI package.
If the PyPI release failed, make fixes, delete the GitHub release, and recreate a release with the same version again.
LinkML for environmental and omics metadata
This framework used to be called BiolinkML. LinkML replaces BiolinkML. For assistance in migration, see Migration.md.