@oshw/linkml-schema

name: meta description: 'The metamodel for schemas defined using the Linked Data Modeling Language framework. For more information on LinkML: * [linkml.io](https://linkml.io) main website * [specification](https://w3id.org/linkml/docs/specification/) LinkML is self-describing. Every LinkML schema consists of elements that instantiate classes in this metamodel. Core metaclasses: * [SchemaDefinition](https://w3id.org/linkml/SchemaDefinition) * [ClassDefinition](https://w3id.org/linkml/ClassDefinition) * [SlotDefinition](https://w3id.org/linkml/SlotDefinition) * [TypeDefinition](https://w3id.org/linkml/TypeDefinition) There are many subsets of *profiles* of the metamodel, for different purposes: * [MinimalSubset](https://w3id.org/linkml/MinimalSubset) * [BasicSubset](https://w3id.org/linkml/BasicSubset) For canonical reference documentation on any metamodel construct, refer to the official URI for each construct, e.g. [https://w3id.org/linkml/is_a](https://w3id.org/linkml/is_a)' title: LinkML Schema Metamodel id: https://w3id.org/linkml/meta license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ skos: prefix_prefix: skos prefix_reference: http://www.w3.org/2004/02/skos/core# skosxl: prefix_prefix: skosxl prefix_reference: http://www.w3.org/2008/05/skos-xl# OIO: prefix_prefix: OIO prefix_reference: http://www.geneontology.org/formats/oboInOwl# NCIT: prefix_prefix: NCIT prefix_reference: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# pav: prefix_prefix: pav prefix_reference: http://purl.org/pav/ oslc: prefix_prefix: oslc prefix_reference: http://open-services.net/ns/core# schema: prefix_prefix: schema prefix_reference: http://schema.org/ bibo: prefix_prefix: bibo prefix_reference: http://purl.org/ontology/bibo/ swrl: prefix_prefix: swrl prefix_reference: http://www.w3.org/2003/11/swrl# sh: prefix_prefix: sh prefix_reference: http://www.w3.org/ns/shacl# owl: prefix_prefix: owl prefix_reference: http://www.w3.org/2002/07/owl# qb: prefix_prefix: qb prefix_reference: http://purl.org/linked-data/cube# prov: prefix_prefix: prov prefix_reference: http://www.w3.org/ns/prov# vann: prefix_prefix: vann prefix_reference: https://vocab.org/vann/ qudt: prefix_prefix: qudt prefix_reference: http://qudt.org/schema/qudt/ cdisc: prefix_prefix: cdisc prefix_reference: http://rdf.cdisc.org/mms# SIO: prefix_prefix: SIO prefix_reference: http://semanticscience.org/resource/SIO_ emit_prefixes: - linkml - rdf - rdfs - xsd - skos - dcterms - OIO - owl - pav - IAO default_curi_maps: - semweb_context default_prefix: linkml default_range: string subsets: MinimalSubset: name: MinimalSubset definition_uri: https://w3id.org/linkml/MinimalSubset description: 'The absolute minimal set of elements necessary for defining any schema. schemas conforming to the minimal subset consist of classes, with all slots inlined as attributes. There are no enums.' title: minimal subset from_schema: https://w3id.org/linkml/meta rank: 0 BasicSubset: name: BasicSubset definition_uri: https://w3id.org/linkml/BasicSubset description: 'An extension of MinimalSubset that avoids advanced constructs and can be implemented by a broad variety of tools. This subset roughly corresponds to the union of most standard constructs used in relational datamodel modeling, object oriented modeling, and simple JSON-style modeling, while avoiding more advanced constructs from these languages. It is often possible to translate from a more expressive schema to a BasicSubset schema, through a schema derivation process' title: basic subset from_schema: https://w3id.org/linkml/meta rank: 1 SpecificationSubset: name: SpecificationSubset definition_uri: https://w3id.org/linkml/SpecificationSubset description: 'A subset that includes all the metamodel elements that form part of the normative LinkML specification. The complete LinkML specification can be found at [linkml:specification](https://w3id.org/linkml/specification)' title: specification subset from_schema: https://w3id.org/linkml/meta rank: 2 RelationalModelProfile: name: RelationalModelProfile definition_uri: https://w3id.org/linkml/RelationalModelProfile description: 'A profile that includes all the metamodel elements whose semantics can be expressed using the classic Relational Model. The Relational Model excludes collections (multivalued slots) as first class entities. Instead, these must be mapped to backreferences The classic Relational Model excludes inheritance and polymorphism -- these must be rolled down to concrete classes or otherwise transformed.' title: relational model profile from_schema: https://w3id.org/linkml/meta rank: 3 ObjectOrientedProfile: name: ObjectOrientedProfile definition_uri: https://w3id.org/linkml/ObjectOrientedProfile description: 'A profile that includes all the metamodel elements whose semantics can be expressed using a minimal implementation of the object oriented metamodel as employed by languages such as Java and Python, or in modeling frameworks like UML' title: object oriented profile from_schema: https://w3id.org/linkml/meta rank: 4 OwlProfile: name: OwlProfile definition_uri: https://w3id.org/linkml/OwlProfile description: A profile that includes all the metamodel elements whose semantics can be expressed in OWL title: owl profile from_schema: https://w3id.org/linkml/meta types: string: name: string definition_uri: https://w3id.org/linkml/String description: A character string notes: - In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "string". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Text base: str uri: xsd:string integer: name: integer definition_uri: https://w3id.org/linkml/Integer description: An integer notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "integer". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Integer base: int uri: xsd:integer boolean: name: boolean definition_uri: https://w3id.org/linkml/Boolean description: A binary (true or false) value notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "boolean". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Boolean base: Bool uri: xsd:boolean repr: bool float: name: float definition_uri: https://w3id.org/linkml/Float description: A real number that conforms to the xsd:float specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "float". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Float base: float uri: xsd:float double: name: double definition_uri: https://w3id.org/linkml/Double description: A real number that conforms to the xsd:double specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "double". from_schema: https://w3id.org/linkml/types imported_from: linkml:types close_mappings: - schema:Float base: float uri: xsd:double decimal: name: decimal definition_uri: https://w3id.org/linkml/Decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "decimal". from_schema: https://w3id.org/linkml/types imported_from: linkml:types broad_mappings: - schema:Number base: Decimal uri: xsd:decimal time: name: time definition_uri: https://w3id.org/linkml/Time description: A time object represents a (local) time of day, independent of any particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "time". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Time base: XSDTime uri: xsd:time repr: str date: name: date definition_uri: https://w3id.org/linkml/Date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Date base: XSDDate uri: xsd:date repr: str datetime: name: datetime definition_uri: https://w3id.org/linkml/Datetime description: The combination of a date and time notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "datetime". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:DateTime base: XSDDateTime uri: xsd:dateTime repr: str date_or_datetime: name: date_or_datetime definition_uri: https://w3id.org/linkml/DateOrDatetime description: Either a date or a datetime notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date_or_datetime". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: linkml:DateOrDatetime repr: str uriorcurie: name: uriorcurie definition_uri: https://w3id.org/linkml/Uriorcurie description: a URI or a CURIE notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uriorcurie". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: URIorCURIE uri: xsd:anyURI repr: str curie: name: curie definition_uri: https://w3id.org/linkml/Curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: Curie uri: xsd:string repr: str uri: name: uri definition_uri: https://w3id.org/linkml/Uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node from_schema: https://w3id.org/linkml/types imported_from: linkml:types close_mappings: - schema:URL base: URI uri: xsd:anyURI repr: str ncname: name: ncname definition_uri: https://w3id.org/linkml/Ncname description: Prefix part of CURIE notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "ncname". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: NCName uri: xsd:string repr: str objectidentifier: name: objectidentifier definition_uri: https://w3id.org/linkml/Objectidentifier description: A URI or CURIE that represents an object in the model. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "objectidentifier". comments: - Used for inheritance and type checking from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: ElementIdentifier uri: shex:iri repr: str nodeidentifier: name: nodeidentifier definition_uri: https://w3id.org/linkml/Nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "nodeidentifier". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: NodeIdentifier uri: shex:nonLiteral repr: str jsonpointer: name: jsonpointer definition_uri: https://w3id.org/linkml/Jsonpointer conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 description: A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpointer". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: xsd:string repr: str jsonpath: name: jsonpath definition_uri: https://w3id.org/linkml/Jsonpath conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html description: A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpath". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: xsd:string repr: str sparqlpath: name: sparqlpath definition_uri: https://w3id.org/linkml/Sparqlpath conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths description: A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "sparqlpath". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: xsd:string repr: str enums: pv_formula_options: name: pv_formula_options definition_uri: https://w3id.org/linkml/PvFormulaOptions description: The formula used to generate the set of permissible values from the code_set values in_subset: - SpecificationSubset - BasicSubset from_schema: https://w3id.org/linkml/meta rank: 1 permissible_values: CODE: text: CODE description: The permissible values are the set of possible codes in the code set CURIE: text: CURIE description: The permissible values are the set of CURIES in the code set URI: text: URI description: The permissible values are the set of code URIs in the code set FHIR_CODING: text: FHIR_CODING description: The permissible values are the set of FHIR coding elements derived from the code set LABEL: text: LABEL description: The permissible values are the set of human readable labels in the code set presence_enum: name: presence_enum definition_uri: https://w3id.org/linkml/PresenceEnum description: enumeration of conditions by which a slot value should be set from_schema: https://w3id.org/linkml/meta status: testing rank: 11 permissible_values: UNCOMMITTED: text: UNCOMMITTED PRESENT: text: PRESENT ABSENT: text: ABSENT relational_role_enum: name: relational_role_enum definition_uri: https://w3id.org/linkml/RelationalRoleEnum description: enumeration of roles a slot on a relationship class can play from_schema: https://w3id.org/linkml/meta rank: 3 permissible_values: SUBJECT: text: SUBJECT description: a slot with this role connects a relationship to its subject/source node meaning: rdf:subject exact_mappings: - owl:annotatedSource OBJECT: text: OBJECT description: a slot with this role connects a relationship to its object/target node meaning: rdf:object exact_mappings: - owl:annotatedTarget PREDICATE: text: PREDICATE description: a slot with this role connects a relationship to its predicate/property meaning: rdf:predicate exact_mappings: - owl:annotatedProperty NODE: text: NODE description: a slot with this role connects a symmetric relationship to a node that represents either subject or object node OTHER_ROLE: text: OTHER_ROLE description: a slot with this role connects a relationship to a node that is not subject/object/predicate alias_predicate_enum: name: alias_predicate_enum definition_uri: https://w3id.org/linkml/AliasPredicateEnum description: permissible values for the relationship between an element and an alias from_schema: https://w3id.org/linkml/meta rank: 5 permissible_values: EXACT_SYNONYM: text: EXACT_SYNONYM meaning: skos:exactMatch RELATED_SYNONYM: text: RELATED_SYNONYM meaning: skos:relatedMatch BROAD_SYNONYM: text: BROAD_SYNONYM meaning: skos:broaderMatch NARROW_SYNONYM: text: NARROW_SYNONYM meaning: skos:narrowerMatch obligation_level_enum: name: obligation_level_enum definition_uri: https://w3id.org/linkml/ObligationLevelEnum description: The level of obligation or recommendation strength for a metadata element in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta rank: 10 permissible_values: REQUIRED: text: REQUIRED description: The metadata element is required to be present in the model RECOMMENDED: text: RECOMMENDED description: The metadata element is recommended to be present in the model aliases: - ENCOURAGED OPTIONAL: text: OPTIONAL description: The metadata element is optional to be present in the model EXAMPLE: text: EXAMPLE description: The metadata element is an example of how to use the model DISCOURAGED: text: DISCOURAGED description: The metadata element is allowed but discouraged to be present in the model slots: name: name: name definition_uri: https://w3id.org/linkml/name description: the unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class. in_subset: - SpecificationSubset - OwlProfile - MinimalSubset - BasicSubset - RelationalModelProfile - ObjectOrientedProfile from_schema: https://w3id.org/linkml/meta see_also: - https://en.wikipedia.org/wiki/Data_element_name - https://linkml.io/linkml/faq/modeling.html#why-are-my-class-names-translated-to-camelcase aliases: - short name - unique name mappings: - rdfs:label exact_mappings: - schema:name rank: 1 domain: element slot_uri: rdfs:label identifier: true owner: element domain_of: - element range: string required: true title: name: title definition_uri: https://w3id.org/linkml/title description: A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation. in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - long name mappings: - dcterms:title rank: 3 domain: element slot_uri: dcterms:title owner: title domain_of: - common_metadata range: string conforms_to: name: conforms_to definition_uri: https://w3id.org/linkml/conforms_to description: An established standard to which the element conforms. in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta see_also: - linkml:implements mappings: - dcterms:conformsTo domain: element slot_uri: dcterms:conformsTo owner: element domain_of: - element range: string implements: name: implements definition_uri: https://w3id.org/linkml/implements description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element. from_schema: https://w3id.org/linkml/meta domain: element slot_uri: linkml:implements owner: permissible_value domain_of: - element - permissible_value range: uriorcurie multivalued: true instantiates: name: instantiates definition_uri: https://w3id.org/linkml/instantiates description: An element in another schema which this element instantiates. from_schema: https://w3id.org/linkml/meta domain: element slot_uri: linkml:instantiates owner: permissible_value domain_of: - element - permissible_value range: uriorcurie multivalued: true categories: name: categories definition_uri: https://w3id.org/linkml/categories description: Controlled terms used to categorize an element. comments: - if you wish to use uncontrolled terms or terms that lack identifiers then use the keywords element in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - dcterms:subject singular_name: category slot_uri: dcterms:subject owner: structured_alias domain_of: - common_metadata - structured_alias range: uriorcurie multivalued: true keywords: name: keywords definition_uri: https://w3id.org/linkml/keywords description: Keywords or tags used to describe the element in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - schema:keywords singular_name: keyword domain: element slot_uri: schema:keywords owner: keywords domain_of: - common_metadata range: string multivalued: true definition_uri: name: definition_uri definition_uri: https://w3id.org/linkml/definition_uri description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri comments: - Formed by combining the default_prefix with the normalized element name from_schema: https://w3id.org/linkml/meta see_also: - linkml:class_uri - linkml:slot_uri domain: element slot_uri: linkml:definition_uri readonly: filled in by the schema loader or schema view owner: element domain_of: - element range: uriorcurie id_prefixes: name: id_prefixes definition_uri: https://w3id.org/linkml/id_prefixes description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix comments: - Order of elements may be used to indicate priority order - If identifiers are treated as CURIEs, then the CURIE must start with one of the indicated prefixes followed by `:` (_should_ start if the list is open) - If identifiers are treated as URIs, then the URI string must start with the expanded for of the prefix (_should_ start if the list is open) in_subset: - SpecificationSubset - BasicSubset from_schema: https://w3id.org/linkml/meta see_also: - https://github.com/linkml/linkml-model/issues/28 domain: element slot_uri: linkml:id_prefixes owner: element domain_of: - element range: ncname multivalued: true id_prefixes_are_closed: name: id_prefixes_are_closed definition_uri: https://w3id.org/linkml/id_prefixes_are_closed description: If true, then the id_prefixes slot is treated as being closed, and any use of an id that does not have this prefix is considered a violation. from_schema: https://w3id.org/linkml/meta see_also: - https://github.com/linkml/linkml/issues/194 domain: element slot_uri: linkml:id_prefixes_are_closed owner: element domain_of: - element range: boolean description: name: description definition_uri: https://w3id.org/linkml/description description: a textual description of the element's purpose and use in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - definition mappings: - skos:definition exact_mappings: - dcterms:description - schema:description rank: 5 domain: element slot_uri: skos:definition owner: description domain_of: - common_metadata - permissible_value range: string recommended: true structured_aliases: name: structured_aliases definition_uri: https://w3id.org/linkml/structured_aliases description: A list of structured_alias objects, used to provide aliases in conjunction with additional metadata. from_schema: https://w3id.org/linkml/meta see_also: - linkml:aliases mappings: - skosxl:altLabel slot_uri: skosxl:altLabel owner: common_metadata domain_of: - common_metadata range: structured_alias multivalued: true inlined: true aliases: name: aliases definition_uri: https://w3id.org/linkml/aliases description: Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment. comments: - not be confused with the metaslot alias. in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - synonyms - alternate names - alternative labels - designations mappings: - skos:altLabel exact_mappings: - schema:alternateName domain: element slot_uri: skos:altLabel owner: aliases domain_of: - common_metadata range: string multivalued: true deprecated: name: deprecated definition_uri: https://w3id.org/linkml/deprecated description: Description of why and when this element will no longer be used comments: - note that linkml does not use a boolean to indicate deprecation status - the presence of a string value in this field is sufficient to indicate deprecation. in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta close_mappings: - owl:deprecated domain: element slot_uri: linkml:deprecated owner: deprecated domain_of: - common_metadata range: string todos: name: todos definition_uri: https://w3id.org/linkml/todos description: Outstanding issues that needs resolution in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta domain: element slot_uri: linkml:todos owner: todos domain_of: - common_metadata range: string multivalued: true notes: name: notes definition_uri: https://w3id.org/linkml/notes description: editorial notes about an element intended primarily for internal consumption in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - skos:editorialNote domain: element slot_uri: skos:editorialNote owner: notes domain_of: - common_metadata range: string multivalued: true comments: name: comments definition_uri: https://w3id.org/linkml/comments description: notes and comments about an element intended primarily for external consumption in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - skos:note exact_mappings: - rdfs:comment domain: element slot_uri: skos:note owner: comments domain_of: - common_metadata range: string multivalued: true in_subset: name: in_subset definition_uri: https://w3id.org/linkml/in_subset description: used to indicate membership of a term in a defined subset of terms used for a particular domain or application. comments: - an example of use in the translator_minimal subset in the biolink model, holding the minimal set of predicates used in a translator knowledge graph in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - OIO:inSubset domain: element slot_uri: OIO:inSubset owner: in_subset domain_of: - common_metadata range: subset_definition multivalued: true from_schema: name: from_schema definition_uri: https://w3id.org/linkml/from_schema description: id of the schema that defined the element notes: - A stronger model would be range schema_definition, but this doesn't address the import model in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta mappings: - skos:inScheme domain: element slot_uri: skos:inScheme readonly: supplied by the schema loader or schema view owner: from_schema domain_of: - common_metadata range: uri imported_from: name: imported_from definition_uri: https://w3id.org/linkml/imported_from description: the imports entry that this element was derived from. Empty means primary source from_schema: https://w3id.org/linkml/meta domain: element slot_uri: linkml:imported_from readonly: supplied by the schema loader or schema view owner: imported_from domain_of: - common_metadata range: string see_also: name: see_also definition_uri: https://w3id.org/linkml/see_also description: A list of related entities or URLs that may be of relevance in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - rdfs:seeAlso domain: element slot_uri: rdfs:seeAlso owner: see_also domain_of: - common_metadata range: uriorcurie multivalued: true owned_by: name: owned_by definition_uri: https://w3id.org/linkml/owned_by description: agent that owns or is the steward of the element in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - steward - owner close_mappings: - rdfs:isDefinedBy domain: element slot_uri: linkml:owned_by owner: owned_by range: uriorcurie created_by: name: created_by definition_uri: https://w3id.org/linkml/created_by description: agent that created the element in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - pav:createdBy domain: element slot_uri: pav:createdBy owner: created_by domain_of: - common_metadata range: uriorcurie contributors: name: contributors definition_uri: https://w3id.org/linkml/contributors description: agent that contributed to the element in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - dcterms:contributor domain: element slot_uri: dcterms:contributor owner: contributors domain_of: - common_metadata range: uriorcurie multivalued: true created_on: name: created_on definition_uri: https://w3id.org/linkml/created_on description: time at which the element was created in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - pav:createdOn domain: element slot_uri: pav:createdOn owner: created_on domain_of: - common_metadata range: datetime last_updated_on: name: last_updated_on definition_uri: https://w3id.org/linkml/last_updated_on description: time at which the element was last updated in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - pav:lastUpdatedOn domain: element slot_uri: pav:lastUpdatedOn owner: last_updated_on domain_of: - common_metadata range: datetime modified_by: name: modified_by definition_uri: https://w3id.org/linkml/modified_by description: agent that modified the element in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - oslc:modifiedBy domain: element slot_uri: oslc:modifiedBy owner: modified_by domain_of: - common_metadata range: uriorcurie status: name: status definition_uri: https://w3id.org/linkml/status description: status of the element examples: - value: bibo:draft in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta see_also: - https://www.hl7.org/fhir/valueset-publication-status.html - https://www.hl7.org/fhir/versions.html#std-process aliases: - workflow status mappings: - bibo:status domain: element slot_uri: bibo:status owner: status domain_of: - common_metadata range: uriorcurie literal_form: name: literal_form definition_uri: https://w3id.org/linkml/literal_form description: The literal lexical form of a structured alias; i.e the actual alias value. from_schema: https://w3id.org/linkml/meta aliases: - alias_name - string_value mappings: - skosxl:literalForm domain: structured_alias slot_uri: skosxl:literalForm owner: structured_alias domain_of: - structured_alias range: string required: true alias_predicate: name: alias_predicate definition_uri: https://w3id.org/linkml/alias_predicate description: The relationship between an element and its alias. from_schema: https://w3id.org/linkml/meta mappings: - rdf:predicate domain: structured_alias slot_uri: rdf:predicate alias: predicate owner: structured_alias domain_of: - structured_alias range: alias_predicate_enum recommended: true alias_contexts: name: alias_contexts definition_uri: https://w3id.org/linkml/alias_contexts description: The context in which an alias should be applied from_schema: https://w3id.org/linkml/meta domain: structured_alias slot_uri: linkml:contexts alias: contexts owner: structured_alias domain_of: - structured_alias range: uri multivalued: true in_language: name: in_language definition_uri: https://w3id.org/linkml/in_language conforms_to: https://www.rfc-editor.org/rfc/bcp/bcp47.txt description: the primary language used in the sources comments: - Recommended to use a string from IETF BCP 47 from_schema: https://w3id.org/linkml/meta mappings: - schema:inLanguage slot_uri: schema:inLanguage owner: common_metadata domain_of: - common_metadata range: string source: name: source definition_uri: https://w3id.org/linkml/source description: A related resource from which the element is derived. comments: - The described resource may be derived from the related resource in whole or in part in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - origin - derived from mappings: - dcterms:source close_mappings: - prov:wasDerivedFrom - schema:isBasedOn domain: element slot_uri: dcterms:source owner: source domain_of: - common_metadata range: uriorcurie publisher: name: publisher definition_uri: https://w3id.org/linkml/publisher description: An entity responsible for making the resource available in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta mappings: - dcterms:publisher domain: element slot_uri: dcterms:publisher owner: publisher range: uriorcurie is_a: name: is_a definition_uri: https://w3id.org/linkml/is_a description: A primary parent class or slot from which inheritable metaslots are propagated from. While multiple inheritance is not allowed, mixins can be provided effectively providing the same thing. The semantics are the same when translated to formalisms that allow MI (e.g. RDFS/OWL). When translating to a SI framework (e.g. java classes, python classes) then is a is used. When translating a framework without polymorphism (e.g. json-schema, solr document schema) then is a and mixins are recursively unfolded in_subset: - SpecificationSubset - BasicSubset - ObjectOrientedProfile - OwlProfile from_schema: https://w3id.org/linkml/meta rank: 11 abstract: true slot_uri: linkml:is_a owner: permissible_value domain_of: - definition - anonymous_class_expression - permissible_value range: definition abstract: name: abstract definition_uri: https://w3id.org/linkml/abstract description: Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes. in_subset: - SpecificationSubset - BasicSubset - ObjectOrientedProfile from_schema: https://w3id.org/linkml/meta domain: definition slot_uri: linkml:abstract owner: definition domain_of: - definition range: boolean mixin: name: mixin definition_uri: https://w3id.org/linkml/mixin description: Indicates the class or slot is intended to be inherited from without being an is_a parent. mixins should not be inherited from using is_a, except by other mixins. in_subset: - SpecificationSubset - BasicSubset - ObjectOrientedProfile from_schema: https://w3id.org/linkml/meta see_also: - https://en.wikipedia.org/wiki/Mixin aliases: - trait domain: definition slot_uri: linkml:mixin owner: definition domain_of: - definition range: boolean mixins: name: mixins definition_uri: https://w3id.org/linkml/mixins description: A collection of secondary parent classes or slots from which inheritable metaslots are propagated from. comments: - mixins act in the same way as parents (is_a). They allow a model to have a primary strict hierarchy, while keeping the benefits of multiple inheritance in_subset: - SpecificationSubset - BasicSubset - ObjectOrientedProfile - OwlProfile from_schema: https://w3id.org/linkml/meta see_also: - https://en.wikipedia.org/wiki/Mixin aliases: - traits rank: 13 slot_uri: linkml:mixins owner: permissible_value domain_of: - definition - permissible_value range: definition multivalued: true apply_to: name: apply_to definition_uri: https://w3id.org/linkml/apply_to description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class. from_schema: https://w3id.org/linkml/meta status: testing domain: definition slot_uri: linkml:apply_to owner: definition domain_of: - definition range: definition multivalued: true values_from: name: values_from definition_uri: https://w3id.org/linkml/values_from description: 'The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot. Note: this is different than ''subproperty_of'' in that ''subproperty_of'' is intended to be a single ontology term while ''values_from'' is the identifier of an entire value set. Additionally, this is different than an enumeration in that in an enumeration, the values of the enumeration are listed directly in the model itself. Setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.' from_schema: https://w3id.org/linkml/meta status: testing domain: definition slot_uri: linkml:values_from owner: definition domain_of: - definition range: uriorcurie multivalued: true code_set: name: code_set definition_uri: https://w3id.org/linkml/code_set description: the identifier of an enumeration code set. in_subset: - SpecificationSubset - BasicSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:code_set owner: enum_expression domain_of: - enum_expression range: uriorcurie code_set_version: name: code_set_version definition_uri: https://w3id.org/linkml/code_set_version description: the version identifier of the enumeration code set comments: - we assume that version identifiers lexically sort in temporal order. Recommend semver when possible in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:code_set_version owner: enum_expression domain_of: - enum_expression range: string code_set_tag: name: code_set_tag definition_uri: https://w3id.org/linkml/code_set_tag description: the version tag of the enumeration code set comments: - enum_expression cannot have both a code_set_tag and a code_set_version in_subset: - BasicSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:code_set_tag owner: enum_expression domain_of: - enum_expression range: string pv_formula: name: pv_formula definition_uri: https://w3id.org/linkml/pv_formula description: Defines the specific formula to be used to generate the permissible values. comments: - you cannot have BOTH the permissible_values and permissible_value_formula tag - code_set must be supplied for this to be valid in_subset: - SpecificationSubset - BasicSubset from_schema: https://w3id.org/linkml/meta slot_uri: linkml:pv_formula owner: enum_binding domain_of: - enum_expression - enum_binding range: pv_formula_options permissible_values: name: permissible_values definition_uri: https://w3id.org/linkml/permissible_values description: A list of possible values for a slot range in_subset: - SpecificationSubset - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - coded values exact_mappings: - cdisc:PermissibleValue domain: enum_expression slot_uri: linkml:permissible_values owner: enum_expression domain_of: - enum_expression range: permissible_value multivalued: true inlined: true enum_uri: name: enum_uri definition_uri: https://w3id.org/linkml/enum_uri description: URI of the enum that provides a semantic interpretation of the element in a linked data context. The URI may come from any namespace and may be shared between schemas in_subset: - SpecificationSubset - BasicSubset from_schema: https://w3id.org/linkml/meta aliases: - public ID domain: enum_definition slot_uri: linkml:enum_uri ifabsent: class_curie owner: enum_definition domain_of: - enum_definition range: uriorcurie include: name: include definition_uri: https://w3id.org/linkml/include description: An enum expression that yields a list of permissible values that are to be included, after subtracting the minus set in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:include owner: enum_expression domain_of: - enum_expression range: anonymous_enum_expression multivalued: true inlined: true minus: name: minus definition_uri: https://w3id.org/linkml/minus description: An enum expression that yields a list of permissible values that are to be subtracted from the enum in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:minus owner: enum_expression domain_of: - enum_expression range: anonymous_enum_expression multivalued: true inlined: true inherits: name: inherits definition_uri: https://w3id.org/linkml/inherits description: An enum definition that is used as the basis to create a new enum comments: - All permissible values for all inherited enums are copied to form the initial seed set in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:inherits owner: enum_expression domain_of: - enum_expression range: enum_definition multivalued: true matches: name: matches definition_uri: https://w3id.org/linkml/matches description: Specifies a match query that is used to calculate the list of permissible values in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:matches owner: enum_expression domain_of: - enum_expression range: match_query inlined: true identifier_pattern: name: identifier_pattern definition_uri: https://w3id.org/linkml/identifier_pattern description: A regular expression that is used to obtain a set of identifiers from a source_ontology to construct a set of permissible values in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: match_query slot_uri: linkml:identifier_pattern owner: match_query domain_of: - match_query range: string concepts: name: concepts definition_uri: https://w3id.org/linkml/concepts description: A list of identifiers that are used to construct a set of permissible values in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:concepts owner: enum_expression domain_of: - enum_expression range: uriorcurie multivalued: true reachable_from: name: reachable_from definition_uri: https://w3id.org/linkml/reachable_from description: Specifies a query for obtaining a list of permissible values based on graph reachability in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta domain: enum_expression slot_uri: linkml:reachable_from owner: enum_expression domain_of: - enum_expression range: reachability_query inlined: true source_ontology: name: source_ontology definition_uri: https://w3id.org/linkml/source_ontology description: An ontology or vocabulary or terminology that is used in a query to obtain a set of permissible values comments: - examples include schema.org, wikidata, or an OBO ontology - for obo ontologies we recommend CURIEs of the form obo:cl, obo:envo, etc in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta aliases: - terminology - vocabulary slot_uri: linkml:source_ontology owner: reachability_query domain_of: - match_query - reachability_query range: uriorcurie is_direct: name: is_direct definition_uri: https://w3id.org/linkml/is_direct description: True if the reachability query should only include directly related nodes, if False then include also transitively connected in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta aliases: - non-transitive domain: reachability_query slot_uri: linkml:is_direct owner: reachability_query domain_of: - reachability_query range: boolean traverse_up: name: traverse_up definition_uri: https://w3id.org/linkml/traverse_up description: True if the direction of the reachability query is reversed and ancestors are retrieved in_subset: - SpecificationSubset from_schema: https://w3id.org/linkml/meta aliases: - ancestors domain: reachability_query slot_uri: linkml:traverse_up owner: reachability_query domain_of: - reachability_query range: boolean include_self: name: include_self definition_uri: https://w3id.org/linkml/include_self description: True if the query is reflexive in_subset: