Class: Definition

name: definition
description: abstract base class for core metaclasses
in_subset:
- BasicSubset
from_schema: https://w3id.org/linkml/meta
see_also:
- https://en.wikipedia.org/wiki/Data_element_definition
is_a: element
abstract: true
slots:
- is_a
- abstract
- mixin
- mixins
- apply_to
- values_from
- string_serialization

name: definition
description: abstract base class for core metaclasses
in_subset:
- BasicSubset
from_schema: https://w3id.org/linkml/meta
see_also:
- https://en.wikipedia.org/wiki/Data_element_definition
is_a: element
abstract: true
attributes:
  is_a:
    name: is_a
    description: A primary parent class or slot from which inheritable metaslots are
      propagated from. While multiple inheritance is not allowed, mixins can be provided
      effectively providing the same thing. The semantics are the same when translated
      to formalisms that allow MI (e.g. RDFS/OWL). When translating to a SI framework
      (e.g. java classes, python classes) then is a is used. When translating a framework
      without polymorphism (e.g. json-schema, solr document schema) then is a and
      mixins are recursively unfolded
    in_subset:
    - SpecificationSubset
    - BasicSubset
    - ObjectOrientedProfile
    - OwlProfile
    from_schema: https://w3id.org/linkml/meta
    rank: 11
    abstract: true
    domain: definition
    alias: is_a
    owner: definition
    domain_of:
    - definition
    - anonymous_class_expression
    range: definition
  abstract:
    name: abstract
    description: Indicates the class or slot cannot be directly instantiated and is
      intended for grouping purposes.
    in_subset:
    - SpecificationSubset
    - BasicSubset
    - ObjectOrientedProfile
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: definition
    alias: abstract
    owner: definition
    domain_of:
    - definition
    range: boolean
  mixin:
    name: mixin
    description: Indicates the class or slot is intended to be inherited from without
      being an is_a parent. mixins should not be inherited from using is_a, except
      by other mixins.
    in_subset:
    - SpecificationSubset
    - BasicSubset
    - ObjectOrientedProfile
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://en.wikipedia.org/wiki/Mixin
    aliases:
    - trait
    rank: 1000
    domain: definition
    alias: mixin
    owner: definition
    domain_of:
    - definition
    range: boolean
  mixins:
    name: mixins
    description: A collection of secondary parent classes or slots from which inheritable
      metaslots are propagated from.
    comments:
    - mixins act in the same way as parents (is_a). They allow a model to have a primary
      strict hierarchy, while keeping the benefits of multiple inheritance
    in_subset:
    - SpecificationSubset
    - BasicSubset
    - ObjectOrientedProfile
    - OwlProfile
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://en.wikipedia.org/wiki/Mixin
    aliases:
    - traits
    rank: 13
    domain: definition
    multivalued: true
    alias: mixins
    owner: definition
    domain_of:
    - definition
    range: definition
  apply_to:
    name: apply_to
    description: Used to extend class or slot definitions. For example, if we have
      a core schema where a gene has two slots for identifier and symbol, and we have
      a specialized schema for my_organism where we wish to add a slot systematic_name,
      we can avoid subclassing by defining a class gene_my_organism, adding the slot
      to this class, and then adding an apply_to pointing to the gene class. The new
      slot will be 'injected into' the gene class.
    from_schema: https://w3id.org/linkml/meta
    status: testing
    rank: 1000
    domain: definition
    multivalued: true
    alias: apply_to
    owner: definition
    domain_of:
    - definition
    range: definition
  values_from:
    name: values_from
    description: 'The identifier of a "value set" -- a set of identifiers that form
      the possible values for the range of a slot. Note: this is different than ''subproperty_of''
      in that ''subproperty_of'' is intended to be a single ontology term while ''values_from''
      is the identifier of an entire value set.  Additionally, this is different than
      an enumeration in that in an enumeration, the values of the enumeration are
      listed directly in the model itself. Setting this property on a slot does not
      guarantee an expansion of the ontological hierarchy into an enumerated list
      of possible values in every serialization of the model.'
    from_schema: https://w3id.org/linkml/meta
    status: testing
    rank: 1000
    domain: definition
    multivalued: true
    alias: values_from
    owner: definition
    domain_of:
    - definition
    range: uriorcurie
  string_serialization:
    name: string_serialization
    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'
    in_subset:
    - SpecificationSubset
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://github.com/linkml/issues/128
    rank: 1000
    domain: definition
    inherited: false
    alias: string_serialization
    owner: definition
    domain_of:
    - definition
    range: string
  name:
    name: name
    description: the unique name of the element within the context of the schema.  Name
      is combined with the default prefix to form the globally unique subject of the
      target class.
    in_subset:
    - SpecificationSubset
    - OwlProfile
    - MinimalSubset
    - BasicSubset
    - RelationalModelProfile
    - ObjectOrientedProfile
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://en.wikipedia.org/wiki/Data_element_name
    - https://linkml.io/linkml/faq/modeling.html#why-are-my-class-names-translated-to-camelcase
    aliases:
    - short name
    - unique name
    exact_mappings:
    - schema:name
    rank: 1
    domain: element
    slot_uri: rdfs:label
    identifier: true
    alias: name
    owner: definition
    domain_of:
    - element
    range: string
    required: true
  id_prefixes:
    name: id_prefixes
    description: An allowed list of prefixes for which identifiers must conform. The
      identifier of this class or slot must begin with the URIs referenced by this
      prefix
    comments:
    - Order of elements may be used to indicate priority order
    - If identifiers are treated as CURIEs, then the CURIE must start with one of
      the indicated prefixes followed by `:` (_should_ start if the list is open)
    - If identifiers are treated as URIs, then the URI string must start with the
      expanded for of the prefix (_should_ start if the list is open)
    in_subset:
    - SpecificationSubset
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://github.com/linkml/linkml-model/issues/28
    rank: 1000
    domain: element
    multivalued: true
    alias: id_prefixes
    owner: definition
    domain_of:
    - element
    range: ncname
  id_prefixes_are_closed:
    name: id_prefixes_are_closed
    description: If true, then the id_prefixes slot is treated as being closed, and
      any use of an id that does not have this prefix is considered a violation.
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://github.com/linkml/linkml/issues/194
    rank: 1000
    domain: element
    alias: id_prefixes_are_closed
    owner: definition
    domain_of:
    - element
    range: boolean
  definition_uri:
    name: definition_uri
    description: The native URI of the element. This is always within the namespace
      of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri
    comments:
    - Formed by combining the default_prefix with the normalized element name
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - linkml:class_uri
    - linkml:slot_uri
    rank: 1000
    domain: element
    readonly: filled in by the schema loader or schema view
    alias: definition_uri
    owner: definition
    domain_of:
    - element
    range: uriorcurie
  local_names:
    name: local_names
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    multivalued: true
    alias: local_names
    owner: definition
    domain_of:
    - element
    range: local_name
    inlined: true
  conforms_to:
    name: conforms_to
    description: An established standard to which the element conforms.
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - linkml:implements
    rank: 1000
    domain: element
    slot_uri: dcterms:conformsTo
    alias: conforms_to
    owner: definition
    domain_of:
    - element
    range: string
  implements:
    name: implements
    description: An element in another schema which this element conforms to. The
      referenced element is not imported into the schema for the implementing element.
      However, the referenced schema may be used to check conformance of the implementing
      element.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    multivalued: true
    alias: implements
    owner: definition
    domain_of:
    - element
    range: uriorcurie
  instantiates:
    name: instantiates
    description: An element in another schema which this element instantiates.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    multivalued: true
    alias: instantiates
    owner: definition
    domain_of:
    - element
    range: uriorcurie
  extensions:
    name: extensions
    description: a tag/text tuple attached to an arbitrary element
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: extensible
    multivalued: true
    alias: extensions
    owner: definition
    domain_of:
    - extension
    - extensible
    range: extension
    inlined: true
  annotations:
    name: annotations
    description: a collection of tag/text tuples with the semantics of OWL Annotation
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    is_a: extensions
    domain: annotatable
    multivalued: true
    alias: annotations
    owner: definition
    domain_of:
    - annotatable
    - annotation
    range: annotation
    inlined: true
  description:
    name: description
    description: a textual description of the element's purpose and use
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - definition
    exact_mappings:
    - dcterms:description
    - schema:description
    rank: 5
    domain: element
    slot_uri: skos:definition
    alias: description
    owner: definition
    domain_of:
    - common_metadata
    - permissible_value
    range: string
    recommended: true
  alt_descriptions:
    name: alt_descriptions
    description: A sourced alternative description for an element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - alternate definitions
    rank: 1000
    domain: element
    multivalued: true
    alias: alt_descriptions
    owner: definition
    domain_of:
    - common_metadata
    range: alt_description
    inlined: true
  title:
    name: title
    description: A concise human-readable display label for the element. The title
      should mirror the name, and should use ordinary textual punctuation.
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - long name
    rank: 3
    domain: element
    slot_uri: dcterms:title
    alias: title
    owner: definition
    domain_of:
    - common_metadata
    range: string
  deprecated:
    name: deprecated
    description: Description of why and when this element will no longer be used
    comments:
    - note that linkml does not use a boolean to indicate deprecation status - the
      presence of a string value in this field is sufficient to indicate deprecation.
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    close_mappings:
    - owl:deprecated
    rank: 1000
    domain: element
    alias: deprecated
    owner: definition
    domain_of:
    - common_metadata
    range: string
  todos:
    name: todos
    description: Outstanding issues that needs resolution
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    multivalued: true
    alias: todos
    owner: definition
    domain_of:
    - common_metadata
    range: string
  notes:
    name: notes
    description: editorial notes about an element intended primarily for internal
      consumption
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: skos:editorialNote
    multivalued: true
    alias: notes
    owner: definition
    domain_of:
    - common_metadata
    range: string
  comments:
    name: comments
    description: notes and comments about an element intended primarily for external
      consumption
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    exact_mappings:
    - rdfs:comment
    rank: 1000
    domain: element
    slot_uri: skos:note
    multivalued: true
    alias: comments
    owner: definition
    domain_of:
    - common_metadata
    range: string
  examples:
    name: examples
    description: example usages of an element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    close_mappings:
    - vann:example
    rank: 1000
    singular_name: example
    domain: element
    multivalued: true
    alias: examples
    owner: definition
    domain_of:
    - common_metadata
    range: example
    inlined: true
  in_subset:
    name: in_subset
    description: used to indicate membership of a term in a defined subset of terms
      used for a particular domain or application.
    comments:
    - an example of use in the translator_minimal subset in the biolink model, holding
      the minimal set of predicates used in a translator knowledge graph
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: OIO:inSubset
    multivalued: true
    alias: in_subset
    owner: definition
    domain_of:
    - common_metadata
    range: subset_definition
  from_schema:
    name: from_schema
    description: id of the schema that defined the element
    notes:
    - A stronger model would be range schema_definition, but this doesn't address
      the import model
    in_subset:
    - SpecificationSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: skos:inScheme
    readonly: supplied by the schema loader or schema view
    alias: from_schema
    owner: definition
    domain_of:
    - common_metadata
    range: uri
  imported_from:
    name: imported_from
    description: the imports entry that this element was derived from.  Empty means
      primary source
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    readonly: supplied by the schema loader or schema view
    alias: imported_from
    owner: definition
    domain_of:
    - common_metadata
    range: string
  source:
    name: source
    description: A related resource from which the element is derived.
    comments:
    - The described resource may be derived from the related resource in whole or
      in part
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - origin
    - derived from
    close_mappings:
    - prov:wasDerivedFrom
    - schema:isBasedOn
    rank: 1000
    domain: element
    slot_uri: dcterms:source
    alias: source
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  in_language:
    name: in_language
    conforms_to: https://www.rfc-editor.org/rfc/bcp/bcp47.txt
    description: the primary language used in the sources
    comments:
    - Recommended to use a string from IETF BCP 47
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    slot_uri: schema:inLanguage
    alias: in_language
    owner: definition
    domain_of:
    - common_metadata
    range: string
  see_also:
    name: see_also
    description: A list of related entities or URLs that may be of relevance
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: rdfs:seeAlso
    multivalued: true
    alias: see_also
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  deprecated element has exact replacement:
    name: deprecated element has exact replacement
    description: When an element is deprecated, it can be automatically replaced by
      this uri or curie
    from_schema: https://w3id.org/linkml/meta
    mappings:
    - IAO:0100001
    rank: 1000
    alias: deprecated_element_has_exact_replacement
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  deprecated element has possible replacement:
    name: deprecated element has possible replacement
    description: When an element is deprecated, it can be potentially replaced by
      this uri or curie
    from_schema: https://w3id.org/linkml/meta
    mappings:
    - OIO:consider
    rank: 1000
    alias: deprecated_element_has_possible_replacement
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  aliases:
    name: aliases
    description: Alternate names/labels for the element. These do not alter the semantics
      of the schema, but may be useful to support search and alignment.
    comments:
    - not be confused with the metaslot alias.
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - synonyms
    - alternate names
    - alternative labels
    - designations
    exact_mappings:
    - schema:alternateName
    rank: 1000
    domain: element
    slot_uri: skos:altLabel
    multivalued: true
    alias: aliases
    owner: definition
    domain_of:
    - common_metadata
    range: string
  structured_aliases:
    name: structured_aliases
    description: A list of structured_alias objects, used to provide aliases in conjunction
      with additional metadata.
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - linkml:aliases
    rank: 1000
    slot_uri: skosxl:altLabel
    multivalued: true
    alias: structured_aliases
    owner: definition
    domain_of:
    - common_metadata
    range: structured_alias
    inlined: true
  mappings:
    name: mappings
    description: A list of terms from different schemas or terminology systems that
      have comparable meaning. These may include terms that are precisely equivalent,
      broader or narrower in meaning, or otherwise semantically related but not equivalent
      from a strict ontological perspective.
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - xrefs
    - identifiers
    - alternate identifiers
    - alternate ids
    rank: 1000
    slot_uri: skos:mappingRelation
    multivalued: true
    alias: mappings
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  exact mappings:
    name: exact mappings
    description: A list of terms from different schemas or terminology systems that
      have identical meaning.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    is_a: mappings
    slot_uri: skos:exactMatch
    multivalued: true
    inherited: false
    alias: exact_mappings
    owner: definition
    domain_of:
    - common_metadata
    - UnitOfMeasure
    range: uriorcurie
  close mappings:
    name: close mappings
    description: A list of terms from different schemas or terminology systems that
      have close meaning.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    is_a: mappings
    slot_uri: skos:closeMatch
    multivalued: true
    inherited: false
    alias: close_mappings
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  related mappings:
    name: related mappings
    description: A list of terms from different schemas or terminology systems that
      have related meaning.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    is_a: mappings
    slot_uri: skos:relatedMatch
    multivalued: true
    inherited: false
    alias: related_mappings
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  narrow mappings:
    name: narrow mappings
    description: A list of terms from different schemas or terminology systems that
      have narrower meaning.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    is_a: mappings
    slot_uri: skos:narrowMatch
    multivalued: true
    inherited: false
    alias: narrow_mappings
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  broad mappings:
    name: broad mappings
    description: A list of terms from different schemas or terminology systems that
      have broader meaning.
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    is_a: mappings
    slot_uri: skos:broadMatch
    multivalued: true
    inherited: false
    alias: broad_mappings
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  created_by:
    name: created_by
    description: agent that created the element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: pav:createdBy
    alias: created_by
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  contributors:
    name: contributors
    description: agent that contributed to the element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: dcterms:contributor
    multivalued: true
    alias: contributors
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  created_on:
    name: created_on
    description: time at which the element was created
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: pav:createdOn
    alias: created_on
    owner: definition
    domain_of:
    - common_metadata
    range: datetime
  last_updated_on:
    name: last_updated_on
    description: time at which the element was last updated
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: pav:lastUpdatedOn
    alias: last_updated_on
    owner: definition
    domain_of:
    - common_metadata
    range: datetime
  modified_by:
    name: modified_by
    description: agent that modified the element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    domain: element
    slot_uri: oslc:modifiedBy
    alias: modified_by
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  status:
    name: status
    description: status of the element
    examples:
    - value: bibo:draft
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    see_also:
    - https://www.hl7.org/fhir/valueset-publication-status.html
    - https://www.hl7.org/fhir/versions.html#std-process
    aliases:
    - workflow status
    rank: 1000
    domain: element
    slot_uri: bibo:status
    alias: status
    owner: definition
    domain_of:
    - common_metadata
    range: uriorcurie
  rank:
    name: rank
    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
    in_subset:
    - SpecificationSubset
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    aliases:
    - order
    - precedence
    - display order
    exact_mappings:
    - qudt:order
    - qb:order
    rank: 51
    slot_uri: sh:order
    alias: rank
    owner: definition
    domain_of:
    - common_metadata
    - class_rule
    range: integer
  categories:
    name: categories
    description: Controlled terms used to categorize an element.
    comments:
    - if you wish to use uncontrolled terms or terms that lack identifiers then use
      the keywords element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    singular_name: category
    slot_uri: dcterms:subject
    multivalued: true
    alias: categories
    owner: definition
    domain_of:
    - common_metadata
    - structured_alias
    range: uriorcurie
  keywords:
    name: keywords
    description: Keywords or tags used to describe the element
    in_subset:
    - BasicSubset
    from_schema: https://w3id.org/linkml/meta
    rank: 1000
    singular_name: keyword
    domain: element
    slot_uri: schema:keywords
    multivalued: true
    alias: keywords
    owner: definition
    domain_of:
    - common_metadata
    range: string