meta.yaml

id: https://w3id.org/linkml/meta
title: LinkML Schema Metamodel
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)

license: https://creativecommons.org/publicdomain/zero/1.0/

prefixes:
  linkml: https://w3id.org/linkml/
  skos: http://www.w3.org/2004/02/skos/core#
  skosxl: http://www.w3.org/2008/05/skos-xl#
  OIO: http://www.geneontology.org/formats/oboInOwl#
  NCIT: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
  pav: http://purl.org/pav/
  oslc: http://open-services.net/ns/core#
  schema: http://schema.org/
  bibo: http://purl.org/ontology/bibo/
  swrl: http://www.w3.org/2003/11/swrl#
  sh: http://www.w3.org/ns/shacl#
  owl: http://www.w3.org/2002/07/owl#
  qb: http://purl.org/linked-data/cube#
  prov: http://www.w3.org/ns/prov#
  vann: https://vocab.org/vann/
  qudt: http://qudt.org/schema/qudt/
  cdisc: http://rdf.cdisc.org/mms#
  SIO: http://semanticscience.org/resource/SIO_

default_prefix: linkml
default_range: string

default_curi_maps:
  - semweb_context

emit_prefixes:
  - linkml
  - rdf
  - rdfs
  - xsd
  - skos
  - dcterms
  - OIO
  - owl
  - pav

imports:
  - linkml:types
  - linkml:mappings
  - linkml:extensions
  - linkml:annotations
#  - linkml:validation
  - linkml:units

subsets:
  MinimalSubset:
    rank: 0
    title: minimal subset
    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.
  BasicSubset:
    rank: 1
    title: basic subset
    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
  SpecificationSubset:
    rank: 2
    title: specification subset
    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)
  RelationalModelProfile:
    rank: 3
    title: relational model profile
    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.
  ObjectOrientedProfile:
    rank: 4
    title: object oriented profile
    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
  OwlProfile:
    title: owl profile
    description: |-
      A profile that includes all the metamodel elements whose semantics can be expressed in OWL

# ==================================
# Slots                            #
# ==================================
slots:

  # -----------------------------------
  # Common metadata shared by all elements
  # -----------------------------------
  name:
    rank: 1
    aliases:
      - short name
      - unique name
    domain: element
    identifier: true
    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.
    slot_uri: rdfs:label
    in_subset:
      - SpecificationSubset
      - OwlProfile
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile
    exact_mappings:
      - schema:name
    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

  title:
    rank: 3
    aliases:
      - long name
    domain: element
    description: >-
      A concise human-readable display label for the element. The title should mirror the name,
      and should use ordinary textual punctuation.
    slot_uri: dcterms:title
    in_subset:
      - BasicSubset

  conforms_to:
    domain: element
    description: An established standard to which the element conforms.
    slot_uri: dcterms:conformsTo
    in_subset:
      - BasicSubset
    see_also:
      - linkml:implements

  implements:
    domain: element
    range: uriorcurie
    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.
    multivalued: true

  instantiates:
    domain: element
    range: uriorcurie
    description: >-
      An element in another schema which this element instantiates.
    multivalued: true
      
  categories:
    range: uriorcurie
    singular_name: category
    slot_uri: dcterms:subject
    multivalued: true
    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

  keywords:
    domain: element
    singular_name: keyword
    description: >-
      Keywords or tags used to describe the element
    slot_uri: schema:keywords
    range: string
    multivalued: true
    in_subset:
      - BasicSubset

  definition_uri:
    domain: element
    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
    range: uriorcurie
    readonly: filled in by the schema loader or schema view
    see_also:
      - linkml:class_uri
      - linkml:slot_uri

  id_prefixes:
    domain: element
    multivalued: true
    range: ncname
    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)
    see_also:
      - https://github.com/linkml/linkml-model/issues/28
    in_subset:
      - SpecificationSubset
      - BasicSubset

  id_prefixes_are_closed:
    domain: element
    range: boolean
    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.
    see_also:
      - https://github.com/linkml/linkml/issues/194

  description:
    rank: 5
    aliases:
      - definition
    domain: element
    description: >-
      a textual description of the element's purpose and use
    slot_uri: skos:definition
    exact_mappings:
      - dcterms:description
      - schema:description
    recommended: true
    in_subset:
      - BasicSubset

  structured_aliases:
    slot_uri: skosxl:altLabel
    range: structured_alias
    multivalued: true
    inlined: true
    description: >-
      A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.
    see_also:
      - linkml:aliases
      
  aliases:
    aliases:
      - synonyms
      - alternate names
      - alternative labels
      - designations
    domain: element
    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.
    range: string
    multivalued: true
    slot_uri: skos:altLabel
    exact_mappings:
      - schema:alternateName
    in_subset:
      - BasicSubset

  deprecated:
    domain: element
    range: string
    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.
    close_mappings:
      - owl:deprecated
    in_subset:
      - BasicSubset

  todos:
    domain: element
    range: string
    description: Outstanding issues that needs resolution
    multivalued: true
    in_subset:
      - BasicSubset

  notes:
    domain: element
    multivalued: true
    description: editorial notes about an element intended primarily for internal consumption
    slot_uri: skos:editorialNote
    in_subset:
      - BasicSubset

  comments:
    domain: element
    multivalued: true
    description: notes and comments about an element intended primarily for external consumption
    slot_uri: skos:note
    exact_mappings:
      - rdfs:comment
    in_subset:
      - BasicSubset

  in_subset:
    domain: element
    multivalued: true
    range: subset_definition
    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
    slot_uri: OIO:inSubset
    in_subset:
      - BasicSubset

  from_schema:
    domain: element
    range: uri
    readonly: supplied by the schema loader or schema view
    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
    slot_uri: skos:inScheme
    in_subset:
      - SpecificationSubset

  imported_from:
    domain: element
    range: string
    readonly: supplied by the schema loader or schema view
    description: >-
      the imports entry that this element was derived from.  Empty means primary source

  see_also:
    domain: element
    multivalued: true
    range: uriorcurie
    description: A list of related entities or URLs that may be of relevance
    slot_uri: rdfs:seeAlso
    in_subset:
      - BasicSubset

  owned_by:
    aliases:
      - steward
      - owner
    domain: element
    range: uriorcurie
    description: agent that owns or is the steward of the element
    close_mappings:
      - rdfs:isDefinedBy
    in_subset:
      - BasicSubset

  created_by:
    domain: element
    range: uriorcurie
    description: agent that created the element
    slot_uri: pav:createdBy
    in_subset:
      - BasicSubset

  contributors:
    domain: element
    range: uriorcurie
    description: agent that contributed to the element
    slot_uri: dcterms:contributor
    multivalued: true
    in_subset:
      - BasicSubset

  created_on:
    domain: element
    range: datetime
    description: time at which the element was created
    slot_uri: pav:createdOn
    in_subset:
      - BasicSubset

  last_updated_on:
    domain: element
    range: datetime
    description: time at which the element was last updated
    slot_uri: pav:lastUpdatedOn
    in_subset:
      - BasicSubset

  modified_by:
    domain: element
    range: uriorcurie
    description: agent that modified the element
    slot_uri: oslc:modifiedBy
    in_subset:
      - BasicSubset

  status:
    aliases:
      - workflow status
    domain: element
    range: uriorcurie
    description: status of the element
    slot_uri: bibo:status
    examples:
      - value: "bibo:draft"
    see_also:
      - https://www.hl7.org/fhir/valueset-publication-status.html  ## Draft, Active, Retired, Unknown
      - https://www.hl7.org/fhir/versions.html#std-process  ## Draft, Trial Use, Normative, Informative, Deprecated
    in_subset:
      - BasicSubset

  literal_form:
    aliases:
      - alias_name
      - string_value
    domain: structured_alias
    range: string
    required: true
    slot_uri: skosxl:literalForm
    description: >-
      The literal lexical form of a structured alias; i.e the actual alias value.

  alias_predicate:
    alias: predicate
    recommended: true
    slot_uri: rdf:predicate
    domain: structured_alias
    range: alias_predicate_enum
    description: >-
      The relationship between an element and its alias.

  in_language:
    slot_uri: schema:inLanguage
    range: string
    description: >-
      the primary language used in the sources
    comments:
      - Recommended to use a string from IETF BCP 47
    conforms_to: https://www.rfc-editor.org/rfc/bcp/bcp47.txt

  source:
    aliases:
      - origin
      - derived from
    domain: element
    range: uriorcurie
    description: A related resource from which the element is derived.
    slot_uri: dcterms:source
    close_mappings:
      - prov:wasDerivedFrom
      - schema:isBasedOn
    comments:
      - The described resource may be derived from the related resource in whole or in part
    in_subset:
      - BasicSubset

  publisher:
    domain: element
    range: uriorcurie
    description: An entity responsible for making the resource available
    slot_uri: dcterms:publisher
    in_subset:
      - BasicSubset

  # --------------------------------------------------------------
  # Slots that are common to slot definition and class definition
  # --------------------------------------------------------------
  is_a:
    rank: 11
    domain: definition
    range: definition
    abstract: true
    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

  abstract:
    domain: definition
    range: boolean
    description: >-
      Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - ObjectOrientedProfile

  mixin:
    aliases:
      - trait
    domain: definition
    range: boolean
    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.
    see_also:
      - https://en.wikipedia.org/wiki/Mixin
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - ObjectOrientedProfile

  mixins:
    rank: 13
    aliases:
      - traits
    domain: definition
    multivalued: true
    range: definition
    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
    see_also:
      - https://en.wikipedia.org/wiki/Mixin
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - ObjectOrientedProfile
      - OwlProfile

  apply_to:
    domain: definition
    multivalued: true
    range: definition
    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.
    status: testing

  values_from:
    domain: definition
    multivalued: true
    range: uriorcurie
    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.
    status: testing

  # -----------------------------------
  # Enum definition slots
  # -----------------------------------
  code_set:
    domain: enum_expression
    range: uriorcurie
    description: >-
      the identifier of an enumeration code set.
    in_subset:
      - SpecificationSubset
      - BasicSubset

  code_set_version:
    domain: enum_expression
    range: string
    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

  code_set_tag:
    domain: enum_expression
    range: string
    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

  pv_formula:
    domain: enum_expression
    range: pv_formula_options
    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

  permissible_values:
    aliases:
      - coded values
    domain: enum_expression
    range: permissible_value
    multivalued: true
    inlined: true
    description: >-
      A list of possible values for a slot range
    in_subset:
      - SpecificationSubset
      - BasicSubset
    exact_mappings:
      - cdisc:PermissibleValue

  enum_uri:
    aliases:
      - public ID
    domain: enum_definition
    range: uriorcurie
    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
    ifabsent: class_curie
    in_subset:
      - SpecificationSubset
      - BasicSubset

  include:
    description: An enum expression that yields a list of permissible values that are to be included, after subtracting the minus set
    domain: enum_expression
    range: anonymous_enum_expression
    multivalued: true
    in_subset:
      - SpecificationSubset

  minus:
    description: An enum expression that yields a list of permissible values that are to be subtracted from the enum
    domain: enum_expression
    range: anonymous_enum_expression
    multivalued: true
    in_subset:
      - SpecificationSubset

  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
    domain: enum_expression
    range: enum_definition
    multivalued: true
    in_subset:
      - SpecificationSubset

  matches:
    description: Specifies a match query that is used to calculate the list of permissible values
    domain: enum_expression
    range: match_query
    in_subset:
      - SpecificationSubset

  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
    domain: match_query
    range: string
    in_subset:
      - SpecificationSubset

  concepts:
    description: A list of identifiers that are used to construct a set of permissible values
    domain: enum_expression
    range: uriorcurie
    multivalued: true
    in_subset:
      - SpecificationSubset

  reachable_from:
    description: Specifies a query for obtaining a list of permissible values based on graph reachability
    domain: enum_expression
    range: reachability_query
    in_subset:
      - SpecificationSubset

  source_ontology:
    aliases:
      - terminology
      - vocabulary
    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
    range: uriorcurie
    in_subset:
      - SpecificationSubset

  is_direct:
    aliases:
      - non-transitive
    description: True if the reachability query should only include directly related nodes, if False then include also transitively connected
    domain: reachability_query
    range: boolean
    in_subset:
      - SpecificationSubset

  traverse_up:
    aliases:
      - ancestors
    description: True if the direction of the reachability query is reversed and ancestors are retrieved
    domain: reachability_query
    range: boolean
    in_subset:
      - SpecificationSubset

  include_self:
    aliases:
      - reflexive
    description: True if the query is reflexive
    domain: reachability_query
    range: boolean
    in_subset:
      - SpecificationSubset

  relationship_types:
    description: A list of relationship types (properties) that are used in a reachability query
    aliases:
      - predicates
      - properties
    domain: reachability_query
    range: uriorcurie
    multivalued: true
    in_subset:
      - SpecificationSubset

  source_nodes:
    description: A list of nodes that are used in the reachability query
    domain: reachability_query
    range: uriorcurie
    multivalued: true
    in_subset:
      - SpecificationSubset

  # -----------------------------------
  # Slots for permissible_value
  # -----------------------------------
  text:
    rank: 21
    aliases:
      - value
    domain: permissible_value
    range: string
    description: >-
      The actual permissible value itself
    comments:
      - there are no constraints on the text of the permissible value, but for many applications you may want to consider following idiomatic forms and using computer-friendly forms
    identifier: true
    close_mappings:
      - skos:notation
    in_subset:
      - SpecificationSubset
      - BasicSubset

  meaning:
    rank: 23
    aliases:
      - PV meaning
    domain: permissible_value
    range: uriorcurie
    description: >-
      the value meaning of a permissible value
    notes:
      - we may want to change the range of this (and other) elements in the model to an entitydescription type construct
    in_subset:
      - SpecificationSubset
      - BasicSubset
    see_also:
      - https://en.wikipedia.org/wiki/ISO/IEC_11179

  # -----------------------------------
  # Schema definition slots
  # -----------------------------------
  id:
    rank: 0
    domain: schema_definition
    range: uri
    description: The official schema URI
    required: true
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - OwlProfile

  emit_prefixes:
    domain: schema_definition
    multivalued: true
    range: ncname
    description: >-
        a list of Curie prefixes that are used in the representation of instances of the model.  All prefixes in
        this list are added to the prefix sections of the target models.

  version:
    domain: schema_definition
    description: particular version of schema
    slot_uri: pav:version
    exact_mappings:
      - schema:schemaVersion
    in_subset:
      - BasicSubset

  imports:
    rank: 21
    domain: schema_definition
    range: uriorcurie
    multivalued: true
    description: A list of schemas that are to be included in this schema
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - OwlProfile

  structured_imports:
    domain: schema_definition
    range: import_expression
    multivalued: true
    description: >-
      A list of specifications for how to import elements from external schemas
    status: testing

  license:
    rank: 31
    domain: schema_definition
    description: license for the schema
    slot_uri: dcterms:license
    in_subset:
      - BasicSubset

  default_curi_maps:
    domain: schema_definition
    multivalued: true
    description: ordered list of prefixcommon biocontexts to be fetched to resolve id prefixes and inline prefix variables
    in_subset:
      - BasicSubset

  default_prefix:
    rank: 11
    domain: schema_definition
    range: string
    ifabsent: default_ns
    description: >-
      The prefix that is used for all elements within a schema
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset

  default_range:
    rank: 13
    domain: schema_definition
    range: type_definition
    description: default slot range to be used if range element is omitted from a slot definition
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset

  subsets:
    rank: 8
    domain: schema_definition
    multivalued: true
    range: subset_definition
    inlined: true
    description: An index to the collection of all subset definitions in the schema
    exact_mappings:
      - OIO:hasSubset
    in_subset:
      - SpecificationSubset
      - BasicSubset

  types:
    rank: 6
    domain: schema_definition
    range: type_definition
    multivalued: true
    inlined: true
    description: An index to the collection of all type definitions in the schema
    in_subset:
      - BasicSubset
      - ObjectOrientedProfile
      - OwlProfile

  enums:
    rank: 5
    domain: schema_definition
    range: enum_definition
    multivalued: true
    inlined: true
    description: An index to the collection of all enum definitions in the schema
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - ObjectOrientedProfile
      - OwlProfile

  slot_definitions:
    rank: 4
    domain: schema_definition
    multivalued: true
    range: slot_definition
    inlined: true
    alias: slots
    description: An index to the collection of all slot definitions in the schema
    comments:
      - note the formal name of this element is slot_definitions, but it has alias slots, which is the canonical form used in yaml/json serializes of schemas.
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - OwlProfile

  classes:
    rank: 3
    domain: schema_definition
    range: class_definition
    multivalued: true
    inlined: true
    description: An index to the collection of all class definitions in the schema
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile
      - OwlProfile

  metamodel_version:
    domain: schema_definition
    readonly: supplied by the schema loader or schema view
    description: Version of the metamodel used to load the schema
    in_subset:
      - BasicSubset

  source_file:
    domain: schema_definition
    readonly: supplied by the schema loader
    description: name, uri or description of the source of the schema
    in_subset:
      - BasicSubset

  source_file_date:
    domain: schema_definition
    range: datetime
    readonly: supplied by the loader
    description: modification date of the source of the schema
    in_subset:
      - BasicSubset

  source_file_size:
    domain: schema_definition
    range: integer
    readonly: supplied by the schema loader or schema view
    description: size in bytes of the source of the schema
    in_subset:
      - BasicSubset

  generation_date:
    domain: schema_definition
    range: datetime
    readonly: supplied by the schema loader or schema view
    description: date and time that the schema was loaded/generated
    in_subset:
      - BasicSubset


  # -----------------------------------
  # Class definition slots
  # -----------------------------------
  slots:
    rank: 19
    domain: class_definition
    multivalued: true
    range: slot_definition
    description: collection of slot names that are applicable to a class
    comments:
      - the list of applicable slots is inherited from parent classes
      - >-
        This defines the set of slots that are allowed to be used for a given class.
        The final list of slots for a class is the
        combination of the parent (is a) slots, mixins slots, apply to slots minus the slot usage entries.
    in_subset:
      - SpecificationSubset
      - BasicSubset

  slot_usage:
    rank: 23
    domain: class_definition
    multivalued: true
    range: slot_definition
    inlined: true
    description: the refinement of a slot in the context of the containing class definition.
    comments:
      - >-
        Many slots may be re-used across different classes, but the meaning of the slot may be refined by context.
        For example, a generic association model may use slots subject/predicate/object with generic semantics and
        minimal constraints. When this is subclasses, e.g. to disease-phenotype associations then slot usage may
        specify both local naming (e.g. subject=disease) and local constraints
    in_subset:
      - SpecificationSubset
      - BasicSubset

  enum_range:
    range: enum_expression
    description: An inlined enumeration
    in_subset:
      - SpecificationSubset
    status: testing

  range_expression:
    domain: slot_expression
    range: anonymous_class_expression
    description: A range that is described as a boolean expression combining existing ranges
    comments:
      - one use for this is being able to describe a range using any_of expressions, for example to combine two enums
    in_subset:
      - SpecificationSubset
    status: testing

  boolean_slot:
    abstract: true
    multivalued: true
    range: expression
    description: A grouping of slots that expression a boolean operator over a list of operands

  any_of:
    rank: 101
    description: holds if at least one of the expressions hold
    is_a: boolean_slot
    range: expression
    exact_mappings:
      - sh:or
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  exactly_one_of:
    rank: 103
    description: holds if only one of the expressions hold
    is_a: boolean_slot
    range: expression
    exact_mappings:
      - sh:xone
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  none_of:
    rank: 105
    description: holds if none of the expressions hold
    is_a: boolean_slot
    range: expression
    exact_mappings:
      - sh:not
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  all_of:
    rank: 107
    description: holds if all of the expressions hold
    is_a: boolean_slot
    range: expression
    exact_mappings:
      - sh:and
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  preconditions:
    rank: 111
    aliases:
      - if
      - body
      - antecedents
    slot_uri: sh:condition
    description: an expression that must hold in order for the rule to be applicable to an instance
    range: anonymous_class_expression
    inlined: true
    close_mappings:
      - swrl:body
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  postconditions:
    rank: 113
    aliases:
      - then
      - head
      - consequents
    description: an expression that must hold for an instance of the class, if the preconditions hold
    range: anonymous_class_expression
    inlined: true
    close_mappings:
      - swrl:body
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  elseconditions:
    rank: 115
    aliases:
      - else
    description: an expression that must hold for an instance of the class, if the preconditions no not hold
    range: anonymous_class_expression
    inlined: true
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/05validation/#rules"

  bidirectional:
    aliases:
      - iff
      - if and only if
    description: in addition to preconditions entailing postconditions, the postconditions entail the preconditions
    range: boolean
    in_subset:
      - SpecificationSubset

  open_world:
    description: if true, the the postconditions may be omitted in instance data, but it is valid for an inference engine to add these
    range: boolean
    in_subset:
      - SpecificationSubset

  rank:
    rank: 51
    aliases:
      - order
      - precedence
      - display order
    description: the relative order in which the element occurs, lower values are given precedence
    comments:
      - the rank of an element does not affect the semantics
    slot_uri: sh:order
    range: integer
    exact_mappings:
      - qudt:order
      - qb:order
    in_subset:
      - SpecificationSubset
      - BasicSubset

  deactivated:
    description: a deactivated rule is not executed by the rules engine
    slot_uri: sh:deactivated
    range: boolean

  rules:
    slot_uri: sh:rule
    domain: class_definition
    multivalued: true
    range: class_rule
    inlined: true
    description: the collection of rules that apply to all members of this class
    in_subset:
      - SpecificationSubset

  classification_rules:
    domain: class_definition
    multivalued: true
    range: anonymous_class_expression
    inlined: true
    description: >-
      The collection of classification rules that apply to all members of this class.
      Classification rules allow for automatically assigning the instantiated type of an instance.
    in_subset:
      - SpecificationSubset

  slot_conditions:
    domain: class_expression
    multivalued: true
    range: slot_definition
    inlined: true
    description: expresses constraints on a group of slots for a class expression
    in_subset:
      - SpecificationSubset

  attributes:
    rank: 29
    domain: class_definition
    multivalued: true
    range: slot_definition
    inlined: true
    description: Inline definition of slots
    comments:
      - >-
        attributes are an alternative way of defining new slots.  An attribute adds a slot to the global space in the
        form <class_name>__<slot_name> (lower case, double underscores).  Attributes can be specialized via slot_usage.
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile
      - OwlProfile

  class_uri:
    rank: 2
    aliases:
      - public ID
    domain: class_definition
    range: uriorcurie
    description: >-
      URI of the class 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
    comments:
      - Assigning class_uris can provide additional hooks for interoperation, indicating a common conceptual model
    ifabsent: class_curie
    in_subset:
      - SpecificationSubset
      - BasicSubset
    see_also:
      - linkml:definition_uri
      - https://linkml.io/linkml/schemas/uris-and-mappings.html

  subclass_of:
    domain: class_definition
    range: uriorcurie
    description: DEPRECATED -- rdfs:subClassOf to be emitted in OWL generation
    close_mappings:
      - rdfs:subClassOf
    deprecated: Use is_a instead

  defining_slots:
    domain: class_definition
    range: slot_definition
    multivalued: true
    inherited: true
    description: >-
      The combination of is a plus defining slots form a genus-differentia definition, or the set of
      necessary and sufficient conditions that can be transformed into an OWL equivalence axiom

  union_of:
    domain: element
    range: element
    multivalued: true
    description: indicates that the domain element consists exactly of the members of the element in the range.
    notes:
      - this only applies in the OWL generation
    in_subset:
      - SpecificationSubset
      - OwlProfile

  tree_root:
    rank: 31
    domain: class_definition
    range: boolean
    description: >-
      Indicates that this is the Container class which forms the root of the serialized document structure in tree serializations
    notes:
      - each schema should have at most one tree root
    in_subset:
      - SpecificationSubset
      - BasicSubset
    see_also:
      - https://linkml.io/linkml/intro/tutorial02.html

  unique_keys:
    domain: class_definition
    range: unique_key
    multivalued: true
    inlined: true
    description: A collection of named unique keys for this class. Unique keys may be singular or compound.
    exact_mappings:
      - owl:hasKey
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - RelationalModelProfile
    see_also:
      - https://linkml.io/linkml/schemas/constraints.html#unique-key

  unique_key_name:
    domain: unique_key
    key: true
    required: true
    description: name of the unique key
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - RelationalModelProfile

  consider_nulls_inequal:
    domain: unique_key
    range: boolean
    description: >-
      By default, None values are considered equal for the purposes of comparisons in determining uniqueness. Set this to true to treat
      missing values as per ANSI-SQL NULLs, i.e NULL=NULL is always False.

  unique_key_slots:
    domain: unique_key
    multivalued: true
    required: true
    range: slot_definition
    description: list of slot names that form a key. The tuple formed from the values of all these slots should be unique.
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - RelationalModelProfile

  slot_names_unique:
    domain: definition
    range: boolean
    description: if true then induced/mangled slot names are not created for class_usage and attributes
    status: testing
    

  # -----------------------------------
  # Slot definition slots
  # -----------------------------------
  domain:
    domain: slot_definition
    range: class_definition
    inherited: true
    description: |
      defines the type of the subject of the slot.  Given the following slot definition
        S1:
          domain: C1
          range:  C2
      the declaration
        X:
          S1: Y

      implicitly asserts that X is an instance of C1
    in_subset:
      - SpecificationSubset

  range:
    aliases:
      - value domain
    domain: slot_definition
    range: element
    ifabsent: default_range
    inherited: true
    comments:
      - range is underspecified, as not all elements can appear as the range of a slot.
    description: |
      defines the type of the object of the slot.  Given the following slot definition
        S1:
          domain: C1
          range:  C2
      the declaration
        X:
          S1: Y

      implicitly asserts Y is an instance of C2
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile

  slot_uri:
    rank: 2
    aliases:
      - public ID
    domain: slot_definition
    range: uriorcurie
    ifabsent: slot_curie
    description: >-
      URI of the class that provides a semantic interpretation of the slot in a linked data context. The URI may come from any namespace and may be shared between schemas.
    comments:
      - Assigning slot_uris can provide additional hooks for interoperation, indicating a common conceptual model
    in_subset:
      - SpecificationSubset
      - BasicSubset
    see_also:
      - linkml:definition_uri
      - https://linkml.io/linkml/schemas/uris-and-mappings.html

  multivalued:
    rank: 7
    domain: slot_definition
    range: boolean
    inherited: true
    description: true means that slot can have more than one value and should be represented using a list or collection structure.
    # ifabsent: False
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - ObjectOrientedProfile

  array:
    domain: slot_definition
    range: array_expression
    inherited: true
    description: coerces the value of the slot into an array and defines the dimensions of that array
    status: testing

  dimensions:
    aliases:
      - axes
    description: definitions of each axis in the array
    domain: array_expression
    range: dimension_expression
    multivalued: true
    list_elements_ordered: true
    status: testing

  minimum_number_dimensions:
    description: minimum number of dimensions in the array
    domain: array_expression
    range: integer
    status: testing
    # minimum_value: 1
    comments:
      - minimum_cardinality cannot be greater than maximum_cardinality

  maximum_number_dimensions:
    description: maximum number of dimensions in the array, or False if explicitly no maximum.
      If this is unset, and an explicit list of dimensions are passed using dimensions, then this is interpreted
      as a closed list and the maximum_number_dimensions is the length of the dimensions list, unless this
      value is set to False
    domain: array_expression
    range: Anything
    any_of:
      - range: integer
        # minimum_value: 1
      - range: boolean
    status: testing
    comments:
      - maximum_number_dimensions cannot be less than minimum_number_dimensions

  exact_number_dimensions:
    description: exact number of dimensions in the array
    domain: array_expression
    range: integer
    status: testing
    # minimum_value: 1
    comments:
      - if exact_number_dimensions is set, then minimum_number_dimensions and maximum_number_dimensions must be unset or have the same value

  inherited:
    domain: slot_definition
    range: boolean
    inherited: true
    description: true means that the *value* of a slot is inherited by subclasses
    comments:
      - the slot is to be used for defining *metamodels* only
      - Inherited applies to slot values.  Parent *slots* are always inherited by subclasses
    in_subset:
      - SpecificationSubset

  readonly:
    domain: slot_definition
    range: string
    inherited: true
    description: If present, slot is read only.  Text explains why
    comments:
      - the slot is to be used for defining *metamodels* only

  ifabsent:
    domain: slot_definition
    range: string
    inherited: true
    description: >-
      function that provides a default value for the slot.  Possible values for this slot are defined in
      linkml.utils.ifabsent_functions.default_library:
        * [Tt]rue -- boolean True
        * [Ff]alse -- boolean False
        * bnode -- blank node identifier
        * class_curie -- CURIE for the containing class
        * class_uri -- URI for the containing class
        * default_ns -- schema default namespace
        * default_range -- schema default range
        * int(value) -- integer value
        * slot_uri -- URI for the slot
        * slot_curie -- CURIE for the slot
        * string(value) -- string value
    close_mappings:
      - sh:defaultValue
    in_subset:
      - SpecificationSubset
    see_also:
      - linkml:equals_expression

  implicit_prefix:
    domain: slot_expression
    range: string
    description: >-
      Causes the slot value to be interpreted as a uriorcurie after prefixing with this string
    in_subset:
      - SpecificationSubset
    status: testing

  value_specification_constant:
    abstract: true
    description: Grouping for metamodel slots that constrain the a slot value to equal a specified constant
    status: testing

  list_value_specification_constant:
    abstract: true
    description: Grouping for metamodel slots that constrain members of a multivalued slot value to equal a specified constant
    status: testing

  value_presence:
    is_a: list_value_specification_constant
    domain: slot_definition
    range: presence_enum
    inherited: true
    description: if true then a value must be present (for lists there must be at least one value). If false then a value must be absent (for lists, must be empty)
    comments:
      - if set to true this has the same effect as required=true. In contrast, required=false allows a value to be present
    status: unstable

  equals_string:
    is_a: list_value_specification_constant
    range: string
    inherited: true
    description: the slot must have range string and the value of the slot must equal the specified value
    in_subset:
      - SpecificationSubset

  equals_number:
    is_a: list_value_specification_constant
    range: integer  ## todo, make the range a union
    inherited: true
    description: the slot must have range of a number and the value of the slot must equal the specified value
    status: unstable

  equals_expression:
    is_a: list_value_specification_constant
    range: string
    inherited: true
    description: the value of the slot must equal the value of the evaluated expression
    comments:
      - for example, a 'length' slot may have an equals_expression with value '(end-start)+1'
    see_also:
      - https://linkml.io/linkml/developers/inference.html
      - https://linkml.io/linkml/schemas/advanced.html#equals-expression
    in_subset:
      - SpecificationSubset

  exact_cardinality:
    is_a: list_value_specification_constant
    range: integer
    inherited: true
    description: the exact number of entries for a multivalued slot
    in_subset:
      - SpecificationSubset
    comments:
      - if exact_cardinality is set, then minimum_cardinalty and maximum_cardinality must be unset or have the same value

  minimum_cardinality:
    is_a: list_value_specification_constant
    range: integer
    inherited: true
    description: the minimum number of entries for a multivalued slot
    in_subset:
      - SpecificationSubset
    # minimum_value: 0
    comments:
      - minimum_cardinality cannot be greater than maximum_cardinality

  maximum_cardinality:
    is_a: list_value_specification_constant
    range: integer
    inherited: true
    description: the maximum number of entries for a multivalued slot
    in_subset:
      - SpecificationSubset
    comments:
      - maximum_cardinality cannot be less than minimum_cardinality
    # minimum_value: 0

  equals_string_in:
    is_a: list_value_specification_constant
    range: string
    multivalued: true
    inherited: true
    description: the slot must have range string and the value of the slot must equal one of the specified values
    status: testing
    in_subset:
      - SpecificationSubset

  equals_number_in:
    is_a: list_value_specification_constant
    range: integer
    multivalued: true
    inherited: true
    description: the slot must have range number and the value of the slot must equal one of the specified values
    status: testing
    in_subset:
      - SpecificationSubset

  has_member:
    is_a: list_value_specification_constant
    range: anonymous_slot_expression
    description: the value of the slot is multivalued with at least one member satisfying the condition
    status: testing
    in_subset:
      - SpecificationSubset

  all_members:
    is_a: list_value_specification_constant
    range: anonymous_slot_expression
    description: the value of the slot is multivalued with all members satisfying the condition
    status: testing
    in_subset:
      - SpecificationSubset

  singular_name:
    domain: slot_definition
    description: a name that is used in the singular form
    comments:
      - this may be used in some schema translations where use of a singular form is idiomatic, for example RDF
    close_mappings:
      - skos:altLabel
    in_subset:
      - BasicSubset

  required:
    rank: 8
    domain: slot_definition
    range: boolean
    inherited: true
    description: true means that the slot must be present in instances of the class definition
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile

  recommended:
    rank: 9
    domain: slot_definition
    range: boolean
    inherited: true
    description: true means that the slot should be present in instances of the class definition, but this is not required
    comments:
      - This is to be used where not all data is expected to conform to having a required field
      - If a slot is recommended, and it is not populated, applications must not treat this as an error. Applications may use this to inform the user of missing data
    see_also:
      - https://github.com/linkml/linkml/issues/177
    in_subset:
      - SpecificationSubset
      - BasicSubset

  inapplicable:
    domain: slot_definition
    range: boolean
    inherited: true
    description: true means that values for this slot must not be present
    comments:
      - By default all slots are applicable. The main use case for this slot is as an override in a subclass
    in_subset:
      - SpecificationSubset

  inlined:
    rank: 25
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      True means that keyed or identified slot appears in an outer structure by value.  False means that only the key
      or identifier for the slot appears within the domain, referencing a structure that appears elsewhere.
    comments:
      - classes without keys or identifiers are necessarily inlined as lists
      - only applicable in tree-like serializations, e.g json, yaml
    in_subset:
      - SpecificationSubset
      - BasicSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/06mapping/#collection-forms"
      - https://linkml.io/linkml/schemas/inlining.html

  inlined_as_list:
    rank: 27
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      True means that an inlined slot is represented as a list of range instances.  False means that an inlined slot
      is represented as a dictionary, whose key is the slot key or identifier and whose value is the range instance.
    comments:
      - |-
        The default loader will accept either list or dictionary form as input.  This parameter controls internal
        representation and output.
      - |-
        A keyed or identified class with one additional slot can be input in a third form, a dictionary whose key
        is the key or identifier and whose value is the one additional element.  This form is still stored according
        to the inlined_as_list setting.
    in_subset:
      - SpecificationSubset
      - BasicSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/06mapping/#collection-forms"
      - https://linkml.io/linkml/schemas/inlining.html

  inlined_as_simple_dict:
    rank: 28
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      True means that an inlined slot is represented as a simple dict whose values are all atoms
    in_subset:
      - SpecificationSubset
    see_also:
      - "https://w3id.org/linkml/docs/specification/06mapping/#collection-forms"
    status: testing

  list_elements_ordered:
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      If True, then the order of elements of a multivalued slot is guaranteed to be preserved. If False, the
      order may still be preserved but this is not guaranteed
    comments:
      - should only be used with multivalued slots
    in_subset:
      - SpecificationSubset
    status: testing

  list_elements_unique:
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      If True, then there must be no duplicates in the elements of a multivalued slot
    comments:
      - should only be used with multivalued slots
    in_subset:
      - SpecificationSubset

  shared:
    aliases:
      - inverse functional
      - many to one or many
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      If True, then the relationship between the slot domain and range is many to one or many to many
    in_subset:
      - SpecificationSubset

  key:
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      True means that the key slot(s) uniquely identify the elements within a single container
    comments:
      - key is inherited
      - a given domain can have at most one key slot (restriction to be removed in the future)
      - identifiers and keys are mutually exclusive.  A given domain cannot have both
      - a key slot is automatically required.  Keys cannot be optional
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - RelationalModelProfile
    see_also:
      - linkml:unique_keys

  identifier:
    rank: 5
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      True means that the key slot(s) uniquely identifies the elements. There can be at most one identifier or key per
      container
    aliases:
      - primary key
      - ID
      - UID
      - code
    see_also:
      - https://en.wikipedia.org/wiki/Identifier
      - linkml:unique_keys
    comments:
      - identifier is inherited
      - a key slot is automatically required.  Identifiers cannot be optional
      - a given domain can have at most one identifier
      - identifiers and keys are mutually exclusive.  A given domain cannot have both
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile

  designates_type:
    aliases:
      - type designator
    domain: slot_definition
    range: boolean
    inherited: true
    description: >-
      True means that the key slot(s) is used to determine the instantiation (types) relation between objects and a ClassDefinition
    in_subset:
      - SpecificationSubset
    see_also:
      - https://linkml.io/linkml/schemas/type-designators.html

  alias:
    rank: 6
    domain: slot_definition
    range: string
    slot_uri: skos:prefLabel
    description: >-
      the name used for a slot in the context of its owning class.  If present, this is used instead of the actual
      slot name.
    comments:
      - an example of alias is used within this metamodel, slot_definitions is aliases as slots
      - not to be confused with aliases, which indicates a set of terms to be used for search purposes.
    in_subset:
      - SpecificationSubset

  owner:
    domain: slot_definition
    range: definition
    description: >-
      the "owner" of the slot. It is the class if it appears in the slots list, otherwise the declaring slot
    readonly: filled in by loader -- either class domain or slot domain
    deprecated: Will be replaced by domain_of and eventually removed

  domain_of:
    domain: slot_definition
    range: class_definition
    description: the class(es) that reference the slot in a "slots" or "slot_usage" context
    readonly: filled in by the loader
    multivalued: true
    exact_mappings:
      - schema:domainIncludes
      - SIO:000011

  is_usage_slot:
    domain: slot_definition
    deprecated: Replaced by usage_slot_name
    range: boolean
    description: True means that this slot was defined in a slot_usage situation
    readonly: filled in by the loader

  usage_slot_name:
    domain: slot_definition
    range: string
    description: The name of the slot referenced in the slot_usage
    readonly: filled in by the loader

  subproperty_of:
    domain: slot_definition
    range: slot_definition
    description: >-
      Ontology property which this slot is a subproperty of.  Note: 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.
    examples:
      - value: RO:HOM0000001
        description: >-
          this is the RO term for "in homology relationship with", and used as a value of subproperty of this means
          that any ontological child (related to RO:HOM0000001 via an is_a relationship), is a valid value for the slot
          that declares this with the subproperty_of tag.  This differs from the 'values_from' meta model component
          in that 'values_from' requires the id of a value set (said another way, if an entire ontology had a curie/identifier
          that was the identifier for the entire ontology, then that identifier would be used in 'values_from.')
    slot_uri: rdfs:subPropertyOf

  disjoint_with:
    domain: definition
    range: definition
    multivalued: true
    description: Two classes are disjoint if they have no instances in common, two slots are disjoint if they can never hold between the same two instances
    in_subset:
      - SpecificationSubset

  children_are_mutually_disjoint:
    domain: definition
    range: boolean
    description: If true then all direct is_a children are mutually disjoint and share no instances in common

  relational_logical_characteristic:
    abstract: true
    domain: slot_definition
    range: boolean
    description: An abstract grouping for metaslots that describe logical properties of a slot

  symmetric:
    is_a: relational_logical_characteristic
    description: If s is symmetric, and i.s=v, then v.s=i
    close_mappings:
      - owl:SymmetricProperty
    in_subset:
      - SpecificationSubset

  asymmetric:
    is_a: relational_logical_characteristic
    description: If s is antisymmetric, and i.s=v where i is different from v, v.s cannot have value i
    comments:
      - asymmetry is the combination of antisymmetry and irreflexivity
    close_mappings:
      - owl:AsymmetricProperty
    in_subset:
      - SpecificationSubset

  reflexive:
    is_a: relational_logical_characteristic
    description: If s is reflexive, then i.s=i for all instances i
    comments:
      - it is rare for a property to be reflexive, this characteristic is added for completeness, consider instead locally_reflexive
    close_mappings:
      - owl:ReflexiveProperty
    in_subset:
      - SpecificationSubset

  irreflexive:
    is_a: relational_logical_characteristic
    description: If s is irreflexive, then there exists no i such i.s=i
    close_mappings:
      - owl:IrreflexiveProperty
    in_subset:
      - SpecificationSubset

  locally_reflexive:
    is_a: relational_logical_characteristic
    description: If s is locally_reflexive, then i.s=i for all instances i where s is a class slot for the type of i
    in_subset:
      - SpecificationSubset

  transitive:
    is_a: relational_logical_characteristic
    description: If s is transitive, and i.s=z, and s.s=j, then i.s=j
    close_mappings:
      - owl:TransitiveProperty
    in_subset:
      - SpecificationSubset

  transitive_form_of:
    range: slot_definition
    description: If s transitive_form_of d, then (1) s holds whenever d holds (2) s is transitive (3) d holds whenever s holds and there are no intermediates, and s is not reflexive
    comments:
      - "Example: ancestor_of is the transitive_form_of parent_of"
    in_subset:
      - SpecificationSubset

  reflexive_transitive_form_of:
    is_a: transitive_form_of
    description: transitive_form_of including the reflexive case
    in_subset:
      - SpecificationSubset

  inverse:
    domain: slot_definition
    range: slot_definition
    description: indicates that any instance of d s r implies that there is also an instance of r s' d
    slot_uri: owl:inverseOf
    in_subset:
      - SpecificationSubset

  is_class_field:
    domain: slot_definition
    range: boolean
    description: indicates that for any instance, i, the domain of this slot will include an assertion of i s range

  role:
    domain: slot_definition
    range: string
    description: a textual descriptor that indicates the role played by the slot range
    comments:
      - the primary use case for this slot is to provide a textual descriptor of a generic slot name when used in the context of a more specific class
    inherited: true

  minimum_value:
    aliases:
      - low value
    domain: slot_definition
    range: Anything
    description: For ordinal ranges, the value must be equal to or higher than this
    notes:
      - Range to be refined to an "Ordinal" metaclass - see https://github.com/linkml/linkml/issues/1384#issuecomment-1892721142
    inherited: true
    in_subset:
      - SpecificationSubset
      - BasicSubset

  maximum_value:
    aliases:
      - high value
    domain: slot_definition
    range: Anything
    description: For ordinal ranges, the value must be equal to or lower than this
    notes:
      - Range to be refined to an "Ordinal" metaclass - see https://github.com/linkml/linkml/issues/1384#issuecomment-1892721142
    inherited: true
    in_subset:
      - SpecificationSubset
      - BasicSubset

  interpolated:
    domain: pattern_expression
    range: boolean
    description: if true then the pattern is first string interpolated
    in_subset:
      - SpecificationSubset

  partial_match:
    domain: pattern_expression
    range: boolean
    description: if not true then the pattern must match the whole string, as if enclosed in ^...$
    in_subset:
      - SpecificationSubset

  pattern:
    rank: 35
    domain: definition
    range: string
    description: the string value of the slot must conform to this regular expression expressed in the string
    inherited: true
    in_subset:
      - SpecificationSubset
      - BasicSubset

  syntax:
    domain: pattern_expression
    range: string
    description: the string value of the slot must conform to this regular expression expressed in the string. May be interpolated.
    inherited: true
    in_subset:
      - SpecificationSubset

  structured_pattern:
    domain: definition
    range: pattern_expression
    description: the string value of the slot must conform to the regular expression in the pattern expression
    inherited: true
    in_subset:
      - SpecificationSubset
    see_also:
      - https://linkml.io/linkml/schemas/constraints.html#structured-patterns

  string_serialization:
    domain: definition
    range: string
    description: >-
      Used on a slot that stores the string serialization of the containing object. The syntax follows python
      formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.

      We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both
      s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the
      expansion.

      Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations
      by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of
      complex objects

      For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot
      may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of
      string_value shouldd be 2cm
    inherited: false
    see_also:
      - https://github.com/linkml/issues/128
    in_subset:
      - SpecificationSubset


  # -----------------------------------
  # Slots for type definition
  # -----------------------------------
  typeof:
    rank: 7
    domain: type_definition
    range: type_definition
    description: >-
      A parent type from which type properties are inherited
    comments:
      - the target type definition of the typeof slot is referred to as the "parent type"
      - the type definition containing the typeof slot is referred to as the "child type"
      - type definitions without a typeof slot are referred to as a "root type"
    in_subset:
      - SpecificationSubset
      - BasicSubset

  base:
    rank: 8
    domain: type_definition
    description: python base type in the LinkML runtime that implements this type definition
    inherited: true
    comments:
      - every root type must have a base
      - the base is inherited by child types but may be overridden.  Base compatibility is not checked.
    in_subset:
      - SpecificationSubset
      - BasicSubset

  type_uri:
    rank: 2
    domain: type_definition
    range: uriorcurie
    alias: uri
    inherited: true
    description: The uri that defines the possible values for the type definition
    comments:
      - uri is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)
      - every root type must have a type uri
    in_subset:
      - SpecificationSubset
      - BasicSubset

  repr:
    rank: 10
    domain: type_definition
    range: string
    description: the name of the python object that implements this type definition
    inherited: true
    in_subset:
      - SpecificationSubset
      - BasicSubset

  # -----------------------------------
  # Slots for alt description
  # -----------------------------------
  alt_description_text:
    domain: alt_description
    range: string
    required: true
    description: text of an attributed description
    alias: description
    in_subset:
      - BasicSubset

  alt_description_source:
    domain: alt_description
    range: string
    key: true
    alias: source
    description: the source of an attributed description
    in_subset:
      - BasicSubset

  alt_descriptions:
    aliases:
      - alternate definitions
    domain: element
    description: A sourced alternative description for an element
    range: alt_description
    multivalued: true
    inlined: true
    in_subset:
      - BasicSubset

  # -----------------------------------
  # Slots for example
  # -----------------------------------
  value:
    domain: example
    description: example value
    slot_uri: skos:example
    in_subset:
      - BasicSubset

  value_description:
    domain: example
    alias: description
    description: description of what the value is doing
    in_subset:
      - BasicSubset

  value_object:
    domain: example
    alias: object
    description: direct object representation of the example
    range: Anything
    in_subset:
      - BasicSubset

  examples:
    singular_name: example
    domain: element
    multivalued: true
    range: example
    inlined: true
    description: example usages of an element
    close_mappings:
      - vann:example
    in_subset:
      - BasicSubset

  # -----------------------------------
  # Slots for prefix
  # -----------------------------------
  prefix_prefix:
    slot_uri: sh:prefix
    rank: 1
    domain: prefix
    range: ncname
    key: true
    description: >-
      The prefix components of a prefix expansions. This is the part that appears before the colon in a CURIE.
    in_subset:
      - SpecificationSubset
      - BasicSubset

  prefix_reference:
    slot_uri: sh:namespace
    rank: 2
    domain: prefix
    range: uri
    required: true
    description: >-
      The namespace to which a prefix expands to.
    in_subset:
      - SpecificationSubset
      - BasicSubset

  prefixes:
    slot_uri: sh:declare
    rank: 10
    domain: schema_definition
    range: prefix
    multivalued: true
    inlined: true
    description: >-
      A collection of prefix expansions that specify how CURIEs can be expanded to URIs
    in_subset:
      - SpecificationSubset
      - BasicSubset

  # -----------------------------------
  # Slots for settings
  # -----------------------------------
  setting_key:
    domain: setting
    range: ncname
    key: true
    description: the variable name for a setting
    in_subset:
      - SpecificationSubset

  setting_value:
    domain: setting
    range: string
    required: true
    description: The value assigned for a setting
    in_subset:
      - SpecificationSubset

  settings:
    aliases:
      - constants
    rank: 20
    domain: schema_definition
    range: setting
    multivalued: true
    inlined: true
    description: A collection of global variable settings
    comments:
      - global variables are used in string interpolation in structured patterns
    in_subset:
      - SpecificationSubset

  # -----------------------------------
  # Slots for import expressions
  # -----------------------------------

  import_from:
    domain: import_expression
    required: true
    range: uriorcurie
    status: testing

  import_as:
    domain: import_expression
    range: ncname
    status: testing

  import_map:
    domain: import_expression
    multivalued: true
    inlined: true
    range: setting
    status: testing

  # -----------------------------------
  # Slots for local_name
  # -----------------------------------
  local_name_source:
    domain: local_name
    range: ncname
    key: true
    description: the ncname of the source of the name

  local_name_value:
    domain: local_name
    range: string
    required: true
    description: a name assigned to an element in a given ontology
    slot_uri: skos:altLabel

  local_names:
    domain: element
    range: local_name
    multivalued: true
    inlined: true

  slot_group:
    domain: slot_definition
    range: slot_definition
    description: allows for grouping of related slots into a grouping slot that serves the role of a group
    comments:
      - slot groups do not change the semantics of a model but are a useful way of visually grouping related slots
    slot_uri: sh:group
    range_expression:
      slot_conditions:
        is_grouping_slot:
          equals_expression: "True"
    in_subset:
      - SpecificationSubset
      - BasicSubset

  is_grouping_slot:
    domain: slot_definition
    range: boolean
    description: true if this slot is a grouping slot
    close_mappings:
      - sh:PropertyGroup
    in_subset:
      - SpecificationSubset
      - BasicSubset

  # paths

  followed_by:
    description: in a sequential list, this indicates the next member
    range: expression
  reversed:
    description: true if the slot is to be inversed
    range: boolean
  traverse:
    description: the slot to traverse
    range: slot_definition
  path_rule:
    description: a rule for inferring a slot assignment based on evaluating a path through a sequence of slot assignments
    domain: slot_definition
    range: path_expression

  # -----------------------------------
  # Relational Roles
  # -----------------------------------
  represents_relationship:
    aliases:
      - is_reified
    description: true if this class represents a relationship rather than an entity
    domain: class_definition
    range: boolean
    inherited: true
    status: testing
    see_also:
      - rdf:Statement
      - https://patterns.dataincubator.org/book/qualified-relation.html
    comments:
      - in the context of Entity-Relationship (ER) modeling, this is used to state that a class models a relationship between entities, and should be drawn with a diamond
      - in the context of RDF, this should be used when instances of the class are `rdf:Statement`s
      - in the context of property graphs, this should be used when a class is used to represent an edge that connects nodes

  relational_role:
    aliases:
      - reification_role
    description: the role a slot on a relationship class plays, for example, the subject, object or predicate roles
    domain: slot_definition
    range: relational_role_enum
    inherited: true
    status: testing
    comments:
      - this should only be used on slots that are applicable to class that represent relationships
      - in the context of RDF, this should be used for slots that can be modeled using the RDF reification vocabulary
      - in the context of property graphs, this should be used on edge classes to indicate which slots represent the input and output nodes


# ==================================
# Classes                          #
# ==================================
classes:

  Anything:
    class_uri: linkml:Any
  
  common_metadata:
    description: Generic metadata shared across definitions
    mixin: true
    slots:
      - description
      - alt_descriptions
      - title
      - deprecated
      - todos
      - notes
      - comments
      - examples
      - in_subset
      - from_schema
      - imported_from
      - source
      - in_language
      - see_also
      - deprecated element has exact replacement
      - deprecated element has possible replacement
      - aliases
      - structured_aliases
      - mappings
      - exact mappings
      - close mappings
      - related mappings
      - narrow mappings
      - broad mappings
      - created_by
      - contributors
      - created_on
      - last_updated_on
      - modified_by
      - status
      - rank
      - categories
      - keywords
    in_subset:
      - BasicSubset

  element:
    aliases:
      - data element
      - object
    description: >-
      A named element in the model
    abstract: true
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - name
      - id_prefixes
      - id_prefixes_are_closed
      - definition_uri
      - local_names
      - conforms_to
      - implements
      - instantiates
    see_also:
      - https://en.wikipedia.org/wiki/Data_element
    in_subset:
      - BasicSubset

  schema_definition:
    rank: 1
    description: >-
      A collection of definitions that make up a schema or a data model.
    tree_root: true
    aliases:
      - data dictionary
      - data model
      - information model
      - logical model
      - schema
      - model
    is_a: element
    slots:
      - id
      - version
      - imports
      - license
      - prefixes
      - emit_prefixes
      - default_curi_maps
      - default_prefix
      - default_range
      - subsets
      - types
      - enums
      - slot_definitions
      - classes
      - metamodel_version
      - source_file
      - source_file_date
      - source_file_size
      - generation_date
      - slot_names_unique
      - settings
    see_also:
      - https://en.wikipedia.org/wiki/Data_dictionary
    close_mappings:
      - qb:ComponentSet
      - owl:Ontology
    slot_usage:
      name:
        range: ncname
        description: a unique name for the schema that is both human-readable and consists of only characters from the NCName set
#    slot_usage:
#      description:
#        slot_uri: dcterms:description
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile
      - OwlProfile

  type_expression:
    description: >-
      An abstract class grouping named types and anonymous type expressions
    is_a: expression
    mixin: true
    slots:
      - pattern
      - structured_pattern
      - unit
      - implicit_prefix
      - equals_string
      - equals_string_in
      - equals_number
      - minimum_value
      - maximum_value
      - none_of
      - exactly_one_of
      - any_of
      - all_of
    slot_usage:
      any_of:
        range: anonymous_type_expression
      all_of:
        range: anonymous_type_expression
      exactly_one_of:
        range: anonymous_type_expression
      none_of:
        range: anonymous_type_expression

  anonymous_type_expression:
    mixins:
      - type_expression
    description: >-
      A type expression that is not a top-level named type definition. Used for nesting.

  type_definition:
    rank: 4
    mixins:
      - type_expression
    description: an element that whose instances are atomic scalar values that can be mapped to primitive types
    is_a: element
    slots:
      - typeof
      - base
      - type_uri
      - repr
      - union_of
    slot_usage:
      union_of:
        range: type_definition
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - OwlProfile

  subset_definition:
    rank: 6
    description: an element that can be used to group other metamodel elements
    is_a: element
    in_subset:
      - SpecificationSubset
      - BasicSubset

  definition:
    description: abstract base class for core metaclasses
    abstract: true
    is_a: element
    slots:
      - is_a
      - abstract
      - mixin
      - mixins
      - apply_to
      - values_from
      - string_serialization
    see_also:
      - https://en.wikipedia.org/wiki/Data_element_definition
    in_subset:
      - BasicSubset

  enum_expression:
    description: An expression that constrains the range of a slot
    is_a: expression
    slots:
      - code_set
      - code_set_tag
      - code_set_version
      - pv_formula
      - permissible_values
      - include
      - minus
      - inherits
      - reachable_from
      - matches
      - concepts

  anonymous_enum_expression:
    description: An enum_expression that is not named
    mixins:
      - enum_expression

  enum_definition:
    rank: 5
    aliases:
      - enum
      - enumeration
      - semantic enumeration
      - value set
      - term set
      - concept set
      - code set
      - Terminology Value Set
      - answer list
      - value domain
    description: an element whose instances must be drawn from a specified set of permissible values
    is_a: definition
    mixins:
      - enum_expression
    exact_mappings:
      - qb:HierarchicalCodeList
      - NCIT:C113497
      - cdisc:ValueDomain
    close_mappings:
      - skos:ConceptScheme
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile
      - OwlProfile
    slots:
      - enum_uri

  match_query:
    description: >-
      A query that is used on an enum expression to dynamically obtain a set of permissivle values via a query that 
      matches on properties of the external concepts.
    slots:
      - identifier_pattern
      - source_ontology
    in_subset:
      - SpecificationSubset

  reachability_query:
    description: >-
      A query that is used on an enum expression to dynamically obtain a set of permissible values via walking from a 
      set of source nodes to a set of descendants or ancestors over a set of relationship types.
    slots:
      - source_ontology
      - source_nodes
      - relationship_types
      - is_direct
      - include_self
      - traverse_up
    in_subset:
      - SpecificationSubset

  structured_alias:
    description: >-
      object that contains meta data about a synonym or alias including where it came from (source)
      and its scope (narrow, broad, etc.)
    class_uri: skosxl:Label
    mixins:
      - expression
      - extensible
      - annotatable
      - common_metadata
    slots:
      - literal_form
      - alias_predicate
      - categories
    slot_usage:
      categories:
        description: >-
          The category or categories of an alias. This can be drawn from any relevant vocabulary
        examples:
          - value: "https://w3id.org/mod#acronym"
            description: An acronym

  expression:
    mixin: true
    abstract: true
    description: general mixin for any class that can represent some form of expression

  anonymous_expression:
    abstract: true
    mixins:
      - expression
      - extensible
      - annotatable
      - common_metadata
    description: >-
      An abstract parent class for any nested expression
    comments:
      - anonymous expressions are useful for when it is necessary to build a complex expression without introducing a named element for each sub-expression

  path_expression:
    description: An expression that describes an abstract path from an object to another through a sequence of slot lookups
    mixins:
      - expression
      - extensible
      - annotatable
      - common_metadata
    slots:
      - followed_by
      - none_of
      - any_of
      - all_of
      - exactly_one_of
      - reversed
      - traverse
      - range_expression
    slot_usage:
      followed_by:
        range: path_expression
      any_of:
        range: path_expression
      exactly_one_of:
        range: path_expression
      none_of:
        range: path_expression
      all_of:
        range: path_expression

  slot_expression:
    description: an expression that constrains the range of values a slot can take
    mixin: true
    is_a: expression
    slots:
      - range
      - range_expression
      - enum_range
      - required
      - recommended
      - inlined
      - inlined_as_list
      - minimum_value
      - maximum_value
      - pattern
      - structured_pattern
      - unit
      - implicit_prefix
      - value_presence
      - equals_string
      - equals_string_in
      - equals_number
      - equals_expression
      - exact_cardinality
      - minimum_cardinality
      - maximum_cardinality
      - has_member
      - all_members
      - none_of
      - exactly_one_of
      - any_of
      - all_of
    slot_usage:
      any_of:
        range: anonymous_slot_expression
      all_of:
        range: anonymous_slot_expression
      exactly_one_of:
        range: anonymous_slot_expression
      none_of:
        range: anonymous_slot_expression

  anonymous_slot_expression:
    is_a: anonymous_expression
    mixins:
      - slot_expression

  slot_definition:
    rank: 3
    description: an element that describes how instances are related to other instances
    aliases:
      - slot
      - field
      - property
      - attribute
      - column
      - variable
    is_a: definition
    close_mappings:
      - rdf:Property
      - qb:ComponentProperty
    mixins:
      - slot_expression
    slots:
      - singular_name
      - domain
      - slot_uri
      - multivalued
      - array
      - inherited
      - readonly
      - ifabsent
      - list_elements_unique
      - list_elements_ordered
      - shared
      - key
      - identifier
      - designates_type
      - alias
      - owner
      - domain_of
      - subproperty_of
      - symmetric
      - reflexive
      - locally_reflexive
      - irreflexive
      - asymmetric
      - transitive
      - inverse
      - is_class_field
      - transitive_form_of
      - reflexive_transitive_form_of
      - role
      - is_usage_slot
      - usage_slot_name
      - relational_role
      - slot_group
      - is_grouping_slot
      - path_rule
      - disjoint_with
      - children_are_mutually_disjoint
      - union_of
    slot_usage:
      is_a:
        range: slot_definition
        description: A primary parent slot from which inheritable metaslots are propagated
      mixins:
        range: slot_definition
        description: A collection of secondary parent mixin slots from which inheritable metaslots are propagated
      apply_to:
        range: slot_definition
      disjoint_with:
        range: slot_definition
      union_of:
        range: slot_definition
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - OwlProfile

  class_expression:
    mixin: true
    description: A boolean expression that can be used to dynamically determine membership of a class
    slots:
      - any_of
      - exactly_one_of
      - none_of
      - all_of
      - slot_conditions
    slot_usage:
      any_of:
        range: anonymous_class_expression
      all_of:
        range: anonymous_class_expression
      exactly_one_of:
        range: anonymous_class_expression
      none_of:
        range: anonymous_class_expression

  anonymous_class_expression:
    is_a: anonymous_expression
    mixins:
      - class_expression
    slots:
      - is_a

  class_definition:
    rank: 2
    mixins:
      - class_expression
    description: an element whose instances are complex objects that may have slot-value assignments
    aliases:
      - table
      - record
      - template
      - message
      - observation
    is_a: definition
    slots:
      - slots
      - slot_usage
      - attributes
      - class_uri
      - subclass_of
      - union_of
      - defining_slots
      - tree_root
      - unique_keys
      - rules
      - classification_rules
      - slot_names_unique
      - represents_relationship
      - disjoint_with
      - children_are_mutually_disjoint
    slot_usage:
      is_a:
        range: class_definition
        description: A primary parent class from which inheritable metaslots are propagated
      mixins:
        range: class_definition
        description: A collection of secondary parent mixin classes from which inheritable metaslots are propagated
      apply_to:
        range: class_definition
      rules:
        range: class_rule
      disjoint_with:
        range: class_definition
      union_of:
        range: class_definition
    close_mappings:
      - owl:Class
    in_subset:
      - SpecificationSubset
      - MinimalSubset
      - BasicSubset
      - RelationalModelProfile
      - ObjectOrientedProfile
      - OwlProfile

  class_level_rule:
    abstract: true
    description: A rule that is applied to classes

  class_rule:
    is_a: class_level_rule
    aliases:
      - if rule
    description: A rule that applies to instances of a class
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - preconditions
      - postconditions
      - elseconditions
      - bidirectional
      - open_world
      - rank
      - deactivated
    close_mappings:
      - sh:TripleRule
      - swrl:Imp
    in_subset:
      - SpecificationSubset

  array_expression:
    description: defines the dimensions of an array
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - exact_number_dimensions
      - minimum_number_dimensions
      - maximum_number_dimensions
      - dimensions
    status: testing

  dimension_expression:
    description: defines one of the dimensions of an array
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - alias
      - maximum_cardinality
      - minimum_cardinality
      - exact_cardinality
    status: testing

  pattern_expression:
    description: a regular expression pattern used to evaluate conformance of a string
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - syntax
      - interpolated
      - partial_match

  import_expression:
    description: an expression describing an import
    status: testing
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - import_from
      - import_as
      - import_map

  setting:
    description: assignment of a key to a value
    slots:
      - setting_key
      - setting_value
    in_subset:
      - SpecificationSubset

  prefix:
    rank: 12
    description: prefix URI tuple
    slots:
      - prefix_prefix
      - prefix_reference
    in_subset:
      - SpecificationSubset
      - BasicSubset

  local_name:
    description: an attributed label
    slots:
      - local_name_source
      - local_name_value

  example:
    description: usage example and description
    slots:
      - value
      - value_description
      - value_object
    in_subset:
      - BasicSubset

  alt_description:
    aliases:
      - structured description
    description: an attributed description
    slots:
      - alt_description_source
      - alt_description_text
    in_subset:
      - BasicSubset

  permissible_value:
    rank: 16
    aliases:
      - PV
    description: a permissible value, accompanied by intended text and an optional mapping to a concept URI
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slot_usage:
      is_a:
        range: permissible_value
      mixins:
        range: permissible_value
    close_mappings:
      - skos:Concept
    slots:
      - text
      - description
      - meaning
      - unit
    in_subset:
      - SpecificationSubset
      - BasicSubset

  unique_key:
    rank: 20
    description: a collection of slots whose values uniquely identify an instance of a class
    mixins:
      - extensible
      - annotatable
      - common_metadata
    slots:
      - unique_key_name
      - unique_key_slots
      - consider_nulls_inequal
    in_subset:
      - SpecificationSubset
      - BasicSubset
      - RelationalModelProfile

# ==================================
# Enumerations                     #
# ==================================
enums:
  pv_formula_options:
    rank: 1
    description: >-
      The formula used to generate the set of permissible values from the code_set values
    permissible_values:
      CODE:
        description: The permissible values are the set of possible codes in the code set
      CURIE:
        description: The permissible values are the set of CURIES in the code set
      URI:
        description: The permissible values are the set of code URIs in the code set
      FHIR_CODING:
        description: The permissible values are the set of FHIR coding elements derived from the code set
      LABEL:
        description: The permissible values are the set of human readable labels in the code set
    in_subset:
      - SpecificationSubset
      - BasicSubset

  presence_enum:
    rank: 11
    description: enumeration of conditions by which a slot value should be set
    permissible_values:
      UNCOMMITTED:
      PRESENT:
      ABSENT:
    status: testing

  relational_role_enum:
    rank: 3
    description: enumeration of roles a slot on a relationship class can play
    permissible_values:
      SUBJECT:
        meaning: rdf:subject
        description: a slot with this role connects a relationship to its subject/source node
        exact_mappings:
          - owl:annotatedSource
      OBJECT:
        meaning: rdf:object
        description: a slot with this role connects a relationship to its object/target node
        exact_mappings:
          - owl:annotatedTarget
      PREDICATE:
        meaning: rdf:predicate
        description: a slot with this role connects a relationship to its predicate/property
        exact_mappings:
          - owl:annotatedProperty
      NODE:
        description: a slot with this role connects a symmetric relationship to a node that represents either subject or object node
      OTHER_ROLE:
        description: a slot with this role connects a relationship to a node that is not subject/object/predicate

  alias_predicate_enum:
    rank: 5
    description: permissible values for the relationship between an element and an alias
    permissible_values:
      EXACT_SYNONYM:
        meaning: skos:exactMatch
      RELATED_SYNONYM:
        meaning: skos:relatedMatch
      BROAD_SYNONYM:
        meaning: skos:broaderMatch
      NARROW_SYNONYM:
        meaning: skos:narrowerMatch