Class: ClassDefinition
an element whose instances are complex objects that may have slot-value assignments
classDiagram
class ClassDefinition
ClassExpression <|-- ClassDefinition
Definition <|-- ClassDefinition
ClassDefinition : abstract
ClassDefinition : aliases
ClassDefinition : all_of
ClassDefinition --> anonymous_class_expression : all_of
ClassDefinition : alt_descriptions
ClassDefinition --> alt_description : alt_descriptions
ClassDefinition : annotations
ClassDefinition --> annotation : annotations
ClassDefinition : any_of
ClassDefinition --> anonymous_class_expression : any_of
ClassDefinition : apply_to
ClassDefinition --> class_definition : apply_to
ClassDefinition : attributes
ClassDefinition --> slot_definition : attributes
ClassDefinition : broad_mappings
ClassDefinition : categories
ClassDefinition : children_are_mutually_disjoint
ClassDefinition : class_uri
ClassDefinition : classification_rules
ClassDefinition --> anonymous_class_expression : classification_rules
ClassDefinition : close_mappings
ClassDefinition : comments
ClassDefinition : conforms_to
ClassDefinition : contributors
ClassDefinition : created_by
ClassDefinition : created_on
ClassDefinition : defining_slots
ClassDefinition --> slot_definition : defining_slots
ClassDefinition : definition_uri
ClassDefinition : deprecated
ClassDefinition : deprecated_element_has_exact_replacement
ClassDefinition : deprecated_element_has_possible_replacement
ClassDefinition : description
ClassDefinition : disjoint_with
ClassDefinition --> class_definition : disjoint_with
ClassDefinition : exact_mappings
ClassDefinition : exactly_one_of
ClassDefinition --> anonymous_class_expression : exactly_one_of
ClassDefinition : examples
ClassDefinition --> example : examples
ClassDefinition : extensions
ClassDefinition --> extension : extensions
ClassDefinition : from_schema
ClassDefinition : id_prefixes
ClassDefinition : id_prefixes_are_closed
ClassDefinition : implements
ClassDefinition : imported_from
ClassDefinition : in_language
ClassDefinition : in_subset
ClassDefinition --> subset_definition : in_subset
ClassDefinition : instantiates
ClassDefinition : is_a
ClassDefinition --> class_definition : is_a
ClassDefinition : keywords
ClassDefinition : last_updated_on
ClassDefinition : local_names
ClassDefinition --> local_name : local_names
ClassDefinition : mappings
ClassDefinition : mixin
ClassDefinition : mixins
ClassDefinition --> class_definition : mixins
ClassDefinition : modified_by
ClassDefinition : name
ClassDefinition : narrow_mappings
ClassDefinition : none_of
ClassDefinition --> anonymous_class_expression : none_of
ClassDefinition : notes
ClassDefinition : rank
ClassDefinition : related_mappings
ClassDefinition : represents_relationship
ClassDefinition : rules
ClassDefinition --> class_rule : rules
ClassDefinition : see_also
ClassDefinition : slot_conditions
ClassDefinition --> slot_definition : slot_conditions
ClassDefinition : slot_names_unique
ClassDefinition : slot_usage
ClassDefinition --> slot_definition : slot_usage
ClassDefinition : slots
ClassDefinition --> slot_definition : slots
ClassDefinition : source
ClassDefinition : status
ClassDefinition : string_serialization
ClassDefinition : structured_aliases
ClassDefinition --> structured_alias : structured_aliases
ClassDefinition : subclass_of
ClassDefinition : title
ClassDefinition : todos
ClassDefinition : tree_root
ClassDefinition : union_of
ClassDefinition --> class_definition : union_of
ClassDefinition : unique_keys
ClassDefinition --> unique_key : unique_keys
ClassDefinition : values_from
Inheritance
- Element [ Extensible Annotatable CommonMetadata]
- Definition
- ClassDefinition [ ClassExpression]
- Definition
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
slots | 0..* SlotDefinition |
collection of slot names that are applicable to a class | direct |
slot_usage | 0..* SlotDefinition |
the refinement of a slot in the context of the containing class definition | direct |
attributes | 0..* SlotDefinition |
Inline definition of slots | direct |
class_uri | 0..1 Uriorcurie |
URI of the class that provides a semantic interpretation of the element in a ... | direct |
subclass_of | 0..1 Uriorcurie |
DEPRECATED -- rdfs:subClassOf to be emitted in OWL generation | direct |
union_of | 0..* ClassDefinition |
indicates that the domain element consists exactly of the members of the elem... | direct |
defining_slots | 0..* SlotDefinition |
The combination of is a plus defining slots form a genus-differentia definiti... | direct |
tree_root | 0..1 Boolean |
Indicates that this is the Container class which forms the root of the serial... | direct |
unique_keys | 0..* UniqueKey |
A collection of named unique keys for this class | direct |
rules | 0..* ClassRule |
the collection of rules that apply to all members of this class | direct |
classification_rules | 0..* AnonymousClassExpression |
The collection of classification rules that apply to all members of this clas... | direct |
slot_names_unique | 0..1 Boolean |
if true then induced/mangled slot names are not created for class_usage and a... | direct |
represents_relationship | 0..1 Boolean |
true if this class represents a relationship rather than an entity | direct |
disjoint_with | 0..* ClassDefinition |
Two classes are disjoint if they have no instances in common, two slots are d... | direct |
children_are_mutually_disjoint | 0..1 Boolean |
If true then all direct is_a children are mutually disjoint and share no inst... | direct |
any_of | 0..* AnonymousClassExpression |
holds if at least one of the expressions hold | ClassExpression |
exactly_one_of | 0..* AnonymousClassExpression |
holds if only one of the expressions hold | ClassExpression |
none_of | 0..* AnonymousClassExpression |
holds if none of the expressions hold | ClassExpression |
all_of | 0..* AnonymousClassExpression |
holds if all of the expressions hold | ClassExpression |
slot_conditions | 0..* SlotDefinition |
expresses constraints on a group of slots for a class expression | ClassExpression |
is_a | 0..1 ClassDefinition |
A primary parent class from which inheritable metaslots are propagated | Definition |
abstract | 0..1 Boolean |
Indicates the class or slot cannot be directly instantiated and is intended f... | Definition |
mixin | 0..1 Boolean |
Indicates the class or slot is intended to be inherited from without being an... | Definition |
mixins | 0..* ClassDefinition |
A collection of secondary parent mixin classes from which inheritable metaslo... | Definition |
apply_to | 0..* ClassDefinition |
Used to extend class or slot definitions | Definition |
values_from | 0..* Uriorcurie |
The identifier of a "value set" -- a set of identifiers that form the possibl... | Definition |
string_serialization | 0..1 String |
Used on a slot that stores the string serialization of the containing object | Definition |
name | 1..1 String |
the unique name of the element within the context of the schema | Element |
id_prefixes | 0..* Ncname |
An allowed list of prefixes for which identifiers must conform | Element |
id_prefixes_are_closed | 0..1 Boolean |
If true, then the id_prefixes slot is treated as being closed, and any use of... | Element |
definition_uri | 0..1 Uriorcurie |
The native URI of the element | Element |
local_names | 0..* LocalName |
Element | |
conforms_to | 0..1 String |
An established standard to which the element conforms | Element |
implements | 0..* Uriorcurie |
An element in another schema which this element conforms to | Element |
instantiates | 0..* Uriorcurie |
An element in another schema which this element instantiates | Element |
extensions | 0..* Extension |
a tag/text tuple attached to an arbitrary element | Extensible |
annotations | 0..* Annotation |
a collection of tag/text tuples with the semantics of OWL Annotation | Annotatable |
description | 0..1 recommended String |
a textual description of the element's purpose and use | CommonMetadata |
alt_descriptions | 0..* AltDescription |
A sourced alternative description for an element | CommonMetadata |
title | 0..1 String |
A concise human-readable display label for the element | CommonMetadata |
deprecated | 0..1 String |
Description of why and when this element will no longer be used | CommonMetadata |
todos | 0..* String |
Outstanding issues that needs resolution | CommonMetadata |
notes | 0..* String |
editorial notes about an element intended primarily for internal consumption | CommonMetadata |
comments | 0..* String |
notes and comments about an element intended primarily for external consumpti... | CommonMetadata |
examples | 0..* Example |
example usages of an element | CommonMetadata |
in_subset | 0..* SubsetDefinition |
used to indicate membership of a term in a defined subset of terms used for a... | CommonMetadata |
from_schema | 0..1 Uri |
id of the schema that defined the element | CommonMetadata |
imported_from | 0..1 String |
the imports entry that this element was derived from | CommonMetadata |
source | 0..1 Uriorcurie |
A related resource from which the element is derived | CommonMetadata |
in_language | 0..1 String |
the primary language used in the sources | CommonMetadata |
see_also | 0..* Uriorcurie |
A list of related entities or URLs that may be of relevance | CommonMetadata |
deprecated_element_has_exact_replacement | 0..1 Uriorcurie |
When an element is deprecated, it can be automatically replaced by this uri o... | CommonMetadata |
deprecated_element_has_possible_replacement | 0..1 Uriorcurie |
When an element is deprecated, it can be potentially replaced by this uri or ... | CommonMetadata |
aliases | 0..* String |
Alternate names/labels for the element | CommonMetadata |
structured_aliases | 0..* StructuredAlias |
A list of structured_alias objects, used to provide aliases in conjunction wi... | CommonMetadata |
mappings | 0..* Uriorcurie |
A list of terms from different schemas or terminology systems that have compa... | CommonMetadata |
exact_mappings | 0..* Uriorcurie |
A list of terms from different schemas or terminology systems that have ident... | CommonMetadata |
close_mappings | 0..* Uriorcurie |
A list of terms from different schemas or terminology systems that have close... | CommonMetadata |
related_mappings | 0..* Uriorcurie |
A list of terms from different schemas or terminology systems that have relat... | CommonMetadata |
narrow_mappings | 0..* Uriorcurie |
A list of terms from different schemas or terminology systems that have narro... | CommonMetadata |
broad_mappings | 0..* Uriorcurie |
A list of terms from different schemas or terminology systems that have broad... | CommonMetadata |
created_by | 0..1 Uriorcurie |
agent that created the element | CommonMetadata |
contributors | 0..* Uriorcurie |
agent that contributed to the element | CommonMetadata |
created_on | 0..1 Datetime |
time at which the element was created | CommonMetadata |
last_updated_on | 0..1 Datetime |
time at which the element was last updated | CommonMetadata |
modified_by | 0..1 Uriorcurie |
agent that modified the element | CommonMetadata |
status | 0..1 Uriorcurie |
status of the element | CommonMetadata |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... | CommonMetadata |
categories | 0..* Uriorcurie |
Controlled terms used to categorize an element | CommonMetadata |
keywords | 0..* String |
Keywords or tags used to describe the element | CommonMetadata |
Usages
used by | used in | type | used |
---|---|---|---|
SchemaDefinition | classes | range | ClassDefinition |
SlotDefinition | domain | range | ClassDefinition |
SlotDefinition | domain_of | range | ClassDefinition |
ClassDefinition | slots | domain | ClassDefinition |
ClassDefinition | slot_usage | domain | ClassDefinition |
ClassDefinition | attributes | domain | ClassDefinition |
ClassDefinition | class_uri | domain | ClassDefinition |
ClassDefinition | subclass_of | domain | ClassDefinition |
ClassDefinition | union_of | range | ClassDefinition |
ClassDefinition | defining_slots | domain | ClassDefinition |
ClassDefinition | tree_root | domain | ClassDefinition |
ClassDefinition | unique_keys | domain | ClassDefinition |
ClassDefinition | rules | domain | ClassDefinition |
ClassDefinition | classification_rules | domain | ClassDefinition |
ClassDefinition | represents_relationship | domain | ClassDefinition |
ClassDefinition | disjoint_with | range | ClassDefinition |
ClassDefinition | is_a | range | ClassDefinition |
ClassDefinition | mixins | range | ClassDefinition |
ClassDefinition | apply_to | range | ClassDefinition |
Aliases
- table
- record
- template
- message
- observation
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/linkml/meta
Mappings
Mapping Type | Mapped Value |
---|---|
self | linkml:ClassDefinition |
native | linkml:ClassDefinition |
close | owl:Class |
LinkML Source
Direct
name: class_definition
description: an element whose instances are complex objects that may have slot-value
assignments
in_subset:
- SpecificationSubset
- MinimalSubset
- BasicSubset
- RelationalModelProfile
- ObjectOrientedProfile
- OwlProfile
from_schema: https://w3id.org/linkml/meta
aliases:
- table
- record
- template
- message
- observation
close_mappings:
- owl:Class
rank: 2
is_a: definition
mixins:
- class_expression
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:
name: is_a
description: A primary parent class from which inheritable metaslots are propagated
domain_of:
- definition
- anonymous_class_expression
- permissible_value
range: class_definition
mixins:
name: mixins
description: A collection of secondary parent mixin classes from which inheritable
metaslots are propagated
domain_of:
- definition
- permissible_value
range: class_definition
apply_to:
name: apply_to
domain_of:
- definition
range: class_definition
rules:
name: rules
domain_of:
- class_definition
range: class_rule
disjoint_with:
name: disjoint_with
domain_of:
- slot_definition
- class_definition
range: class_definition
union_of:
name: union_of
domain_of:
- type_definition
- slot_definition
- class_definition
range: class_definition
Induced
name: class_definition
description: an element whose instances are complex objects that may have slot-value
assignments
in_subset:
- SpecificationSubset
- MinimalSubset
- BasicSubset
- RelationalModelProfile
- ObjectOrientedProfile
- OwlProfile
from_schema: https://w3id.org/linkml/meta
aliases:
- table
- record
- template
- message
- observation
close_mappings:
- owl:Class
rank: 2
is_a: definition
mixins:
- class_expression
slot_usage:
is_a:
name: is_a
description: A primary parent class from which inheritable metaslots are propagated
domain_of:
- definition
- anonymous_class_expression
- permissible_value
range: class_definition
mixins:
name: mixins
description: A collection of secondary parent mixin classes from which inheritable
metaslots are propagated
domain_of:
- definition
- permissible_value
range: class_definition
apply_to:
name: apply_to
domain_of:
- definition
range: class_definition
rules:
name: rules
domain_of:
- class_definition
range: class_rule
disjoint_with:
name: disjoint_with
domain_of:
- slot_definition
- class_definition
range: class_definition
union_of:
name: union_of
domain_of:
- type_definition
- slot_definition
- class_definition
range: class_definition
attributes:
slots:
name: slots
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
from_schema: https://w3id.org/linkml/meta
rank: 19
domain: class_definition
multivalued: true
alias: slots
owner: class_definition
domain_of:
- class_definition
range: slot_definition
slot_usage:
name: slot_usage
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
from_schema: https://w3id.org/linkml/meta
rank: 23
domain: class_definition
multivalued: true
alias: slot_usage
owner: class_definition
domain_of:
- class_definition
range: slot_definition
inlined: true
attributes:
name: attributes
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
from_schema: https://w3id.org/linkml/meta
rank: 29
domain: class_definition
multivalued: true
alias: attributes
owner: class_definition
domain_of:
- class_definition
range: slot_definition
inlined: true
class_uri:
name: class_uri
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
in_subset:
- SpecificationSubset
- BasicSubset
from_schema: https://w3id.org/linkml/meta
see_also:
- linkml:definition_uri
- https://linkml.io/linkml/schemas/uris-and-mappings.html
aliases:
- public ID
rank: 2
domain: class_definition
ifabsent: class_curie
alias: class_uri
owner: class_definition
domain_of:
- class_definition
range: uriorcurie
subclass_of:
name: subclass_of
description: DEPRECATED -- rdfs:subClassOf to be emitted in OWL generation
deprecated: Use is_a instead
from_schema: https://w3id.org/linkml/meta
close_mappings:
- rdfs:subClassOf
rank: 1000
domain: class_definition
alias: subclass_of
owner: class_definition
domain_of:
- class_definition
range: uriorcurie
union_of:
name: union_of
description: indicates that the domain element consists exactly of the members
of the element in the range.
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: element
multivalued: true
alias: union_of
owner: class_definition
domain_of:
- type_definition
- slot_definition
- class_definition
range: class_definition
defining_slots:
name: defining_slots
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
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: class_definition
multivalued: true
inherited: true
alias: defining_slots
owner: class_definition
domain_of:
- class_definition
range: slot_definition
tree_root:
name: tree_root
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
from_schema: https://w3id.org/linkml/meta
see_also:
- https://linkml.io/linkml/intro/tutorial02.html
rank: 31
domain: class_definition
alias: tree_root
owner: class_definition
domain_of:
- class_definition
range: boolean
unique_keys:
name: unique_keys
description: A collection of named unique keys for this class. Unique keys may
be singular or compound.
in_subset:
- SpecificationSubset
- BasicSubset
- RelationalModelProfile
from_schema: https://w3id.org/linkml/meta
see_also:
- https://linkml.io/linkml/schemas/constraints.html#unique-key
exact_mappings:
- owl:hasKey
rank: 1000
domain: class_definition
multivalued: true
alias: unique_keys
owner: class_definition
domain_of:
- class_definition
range: unique_key
inlined: true
rules:
name: rules
description: the collection of rules that apply to all members of this class
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: class_definition
slot_uri: sh:rule
multivalued: true
alias: rules
owner: class_definition
domain_of:
- class_definition
range: class_rule
inlined: true
classification_rules:
name: classification_rules
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
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: class_definition
multivalued: true
alias: classification_rules
owner: class_definition
domain_of:
- class_definition
range: anonymous_class_expression
inlined: true
slot_names_unique:
name: slot_names_unique
description: if true then induced/mangled slot names are not created for class_usage
and attributes
from_schema: https://w3id.org/linkml/meta
status: testing
rank: 1000
domain: definition
alias: slot_names_unique
owner: class_definition
domain_of:
- schema_definition
- class_definition
range: boolean
represents_relationship:
name: represents_relationship
description: true if this class represents a relationship rather than an entity
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
from_schema: https://w3id.org/linkml/meta
see_also:
- rdf:Statement
- https://patterns.dataincubator.org/book/qualified-relation.html
aliases:
- is_reified
status: testing
rank: 1000
domain: class_definition
inherited: true
alias: represents_relationship
owner: class_definition
domain_of:
- class_definition
range: boolean
disjoint_with:
name: disjoint_with
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
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: definition
multivalued: true
alias: disjoint_with
owner: class_definition
domain_of:
- slot_definition
- class_definition
range: class_definition
children_are_mutually_disjoint:
name: children_are_mutually_disjoint
description: If true then all direct is_a children are mutually disjoint and share
no instances in common
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: definition
alias: children_are_mutually_disjoint
owner: class_definition
domain_of:
- slot_definition
- class_definition
range: boolean
any_of:
name: any_of
description: holds if at least one of the expressions hold
from_schema: https://w3id.org/linkml/meta
rank: 101
is_a: boolean_slot
multivalued: true
alias: any_of
owner: class_definition
domain_of:
- type_expression
- path_expression
- slot_expression
- class_expression
range: anonymous_class_expression
exactly_one_of:
name: exactly_one_of
description: holds if only one of the expressions hold
from_schema: https://w3id.org/linkml/meta
rank: 103
is_a: boolean_slot
multivalued: true
alias: exactly_one_of
owner: class_definition
domain_of:
- type_expression
- path_expression
- slot_expression
- class_expression
range: anonymous_class_expression
none_of:
name: none_of
description: holds if none of the expressions hold
from_schema: https://w3id.org/linkml/meta
rank: 105
is_a: boolean_slot
multivalued: true
alias: none_of
owner: class_definition
domain_of:
- type_expression
- path_expression
- slot_expression
- class_expression
range: anonymous_class_expression
all_of:
name: all_of
description: holds if all of the expressions hold
from_schema: https://w3id.org/linkml/meta
rank: 107
is_a: boolean_slot
multivalued: true
alias: all_of
owner: class_definition
domain_of:
- type_expression
- path_expression
- slot_expression
- class_expression
range: anonymous_class_expression
slot_conditions:
name: slot_conditions
description: expresses constraints on a group of slots for a class expression
in_subset:
- SpecificationSubset
from_schema: https://w3id.org/linkml/meta
rank: 1000
domain: class_expression
multivalued: true
alias: slot_conditions
owner: class_definition
domain_of:
- class_expression
range: slot_definition
inlined: true
is_a:
name: is_a
description: A primary parent class from which inheritable metaslots are propagated
from_schema: https://w3id.org/linkml/meta
rank: 11
abstract: true
alias: is_a
owner: class_definition
domain_of:
- definition
- anonymous_class_expression
- permissible_value
range: class_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: class_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: class_definition
domain_of:
- definition
range: boolean
mixins:
name: mixins
description: A collection of secondary parent mixin classes from which inheritable
metaslots are propagated
from_schema: https://w3id.org/linkml/meta
rank: 13
multivalued: true
alias: mixins
owner: class_definition
domain_of:
- definition
- permissible_value
range: class_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: class_definition
domain_of:
- definition
range: class_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: class_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: class_definition
domain_of:
- definition
- type_mapping
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: class_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: class_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: class_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: class_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: class_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: class_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: class_definition
domain_of:
- element
- permissible_value
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: class_definition
domain_of:
- element
- permissible_value
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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_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: class_definition
domain_of:
- common_metadata
range: string