Subset: SpecificationSubset
_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_
URI: SpecificationSubset
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/linkml/meta
Classes in subset
Class | Description |
---|---|
SchemaDefinition | a collection of subset, type, slot and class definitions |
ClassDefinition | an element whose instances are complex objects that may have slot-value assig... |
SlotDefinition | an element that describes how instances are related to other instances |
TypeDefinition | an element that whose instances are atomic scalar values that can be mapped t... |
EnumDefinition | an element whose instances must be drawn from a specified set of permissible ... |
SubsetDefinition | an element that can be used to group other metamodel elements |
Prefix | prefix URI tuple |
PermissibleValue | a permissible value, accompanied by intended text and an optional mapping to ... |
UniqueKey | a collection of slots whose values uniquely identify an instance of a class |
MatchQuery | A query that is used on an enum expression to dynamically obtain a set of per... |
ReachabilityQuery | A query that is used on an enum expression to dynamically obtain a set of per... |
ClassRule | A rule that applies to instances of a class |
Setting | assignment of a key to a value |
SchemaDefinition
a collection of subset, type, slot and class definitions
Name | Cardinality and Range | Description |
---|---|---|
id | 1..1 Uri |
The official schema URI |
name | 1..1 Ncname |
a unique name for the schema that is both human-readable and consists of only... identifier |
classes | 0..* ClassDefinition |
An index to the collection of all class definitions in the schema |
slot_definitions | 0..* SlotDefinition |
An index to the collection of all slot definitions in the schema |
enums | 0..* EnumDefinition |
An index to the collection of all enum definitions in the schema |
subsets | 0..* SubsetDefinition |
An index to the collection of all subset definitions in the schema |
prefixes | 0..* Prefix |
prefix / URI definitions to be added to the context beyond those fetched from... |
default_prefix | 0..1 String |
default and base prefix -- used for ':' identifiers, @base and @vocab |
default_range | 0..1 TypeDefinition |
default slot range to be used if range element is omitted from a slot definit... |
settings | 0..* Setting |
A collection of global variable settings |
imports | 0..* Uriorcurie |
other schemas that are included in this schema |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
id_prefixes | 0..* Ncname |
the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
ClassDefinition
an element whose instances are complex objects that may have slot-value assignments
Name | Cardinality and Range | Description |
---|---|---|
name | 1..1 String |
the unique name of the element within the context of the schema identifier |
class_uri | 0..1 Uriorcurie |
URI of the class that provides a semantic interpretation of the element in a ... |
is_a | 0..1 ClassDefinition |
A primary parent class from which inheritable metaslots are propagated |
mixins | 0..* ClassDefinition |
A collection of secondary parent mixin classes from which inheritable metaslo... |
slots | 0..* SlotDefinition |
collection of slot names that are applicable to a class |
slot_usage | 0..* SlotDefinition |
the refinement of a slot in the context of the containing class definition |
attributes | 0..* SlotDefinition |
Inline definition of slots |
tree_root | 0..1 Boolean |
indicator that this is the root class in tree structures |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
any_of | 0..* AnonymousClassExpression |
holds if at least one of the expressions hold |
exactly_one_of | 0..* AnonymousClassExpression |
holds if only one of the expressions hold |
none_of | 0..* AnonymousClassExpression |
holds if none of the expressions hold |
all_of | 0..* AnonymousClassExpression |
holds if all of the expressions hold |
union_of | 0..* ClassDefinition |
indicates that the domain element consists exactly of the members of the elem... |
unique_keys | 0..* UniqueKey |
A collection of unique keys for this class |
rules | 0..* ClassRule |
the collection of rules that apply to all members of this class |
classification_rules | 0..* AnonymousClassExpression |
the collection of classification rules that apply to all members of this clas... |
disjoint_with | 0..* ClassDefinition |
Two classes are disjoint if they have no instances in common, two slots are d... |
slot_conditions | 0..* SlotDefinition |
expresses constraints on a group of slots for a class expression |
abstract | 0..1 Boolean |
Indicates the class or slot cannot be directly instantiated and is intended f... |
mixin | 0..1 Boolean |
Indicates the class or slot is intended to be inherited from without being an... |
string_serialization | 0..1 String |
Used on a slot that stores the string serialization of the containing object |
id_prefixes | 0..* Ncname |
the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
SlotDefinition
an element that describes how instances are related to other instances
Name | Cardinality and Range | Description |
---|---|---|
name | 1..1 String |
the unique name of the element within the context of the schema identifier |
slot_uri | 0..1 Uriorcurie |
predicate of this slot for semantic web application |
identifier | 0..1 Boolean |
True means that the key slot(s) uniquely identify the container |
alias | 0..1 String |
the name used for a slot in the context of its owning class |
multivalued | 0..1 Boolean |
true means that slot can have more than one value |
required | 0..1 Boolean |
true means that the slot must be present in the loaded definition |
recommended | 0..1 Boolean |
true means that the slot should be present in the loaded definition, but this... |
is_a | 0..1 SlotDefinition |
A primary parent slot from which inheritable metaslots are propagated |
mixins | 0..* SlotDefinition |
A collection of secondary parent mixin slots from which inheritable metaslots... |
inlined | 0..1 Boolean |
True means that keyed or identified slot appears in an outer structure by val... |
inlined_as_list | 0..1 Boolean |
True means that an inlined slot is represented as a list of range instances |
pattern | 0..1 String |
the string value of the slot must conform to this regular expression expresse... |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
any_of | 0..* AnonymousSlotExpression |
holds if at least one of the expressions hold |
exactly_one_of | 0..* AnonymousSlotExpression |
holds if only one of the expressions hold |
none_of | 0..* AnonymousSlotExpression |
holds if none of the expressions hold |
all_of | 0..* AnonymousSlotExpression |
holds if all of the expressions hold |
domain | 0..1 ClassDefinition |
defines the type of the subject of the slot |
inherited | 0..1 Boolean |
true means that the value of a slot is inherited by subclasses |
ifabsent | 0..1 String |
function that provides a default value for the slot |
list_elements_unique | 0..1 Boolean |
If True, then there must be no duplicates in the elements of a multivalued sl... |
list_elements_ordered | 0..1 Boolean |
If True, then the order of elements of a multivalued slot is guaranteed to be... |
shared | 0..1 Boolean |
If True, then the relationship between the slot domain and range is many to o... |
key | 0..1 Boolean |
True means that the key slot(s) uniquely identify the container |
designates_type | 0..1 Boolean |
True means that the key slot(s) is used to determine the instantiation (types... |
symmetric | 0..1 Boolean |
If s is symmetric, and i |
reflexive | 0..1 Boolean |
If s is reflexive, then i |
locally_reflexive | 0..1 Boolean |
If s is locally_reflexive, then i |
irreflexive | 0..1 Boolean |
If s is irreflexive, then there exists no i such i |
asymmetric | 0..1 Boolean |
If s is antisymmetric, and i |
transitive | 0..1 Boolean |
If s is transitive, and i |
inverse | 0..1 SlotDefinition |
indicates that any instance of d s r implies that there is also an instance o... |
transitive_form_of | 0..1 SlotDefinition |
If s transitive_form_of d, then (1) s holds whenever d holds (2) s is transit... |
reflexive_transitive_form_of | 0..1 SlotDefinition |
transitive_form_of including the reflexive case |
slot_group | 0..1 SlotDefinition |
allows for grouping of related slots into a grouping slot that serves the rol... |
is_grouping_slot | 0..1 Boolean |
true if this slot is a grouping slot |
disjoint_with | 0..* SlotDefinition |
Two classes are disjoint if they have no instances in common, two slots are d... |
union_of | 0..* SlotDefinition |
indicates that the domain element consists exactly of the members of the elem... |
range | 0..1 Element |
defines the type of the object of the slot |
range_expression | 0..1 AnonymousClassExpression |
A range that is described as a boolean expression combining existing ranges |
enum_range | 0..1 EnumExpression |
An inlined enumeration |
minimum_value | 0..1 Integer |
for slots with ranges of type number, the value must be equal to or higher th... |
maximum_value | 0..1 Integer |
for slots with ranges of type number, the value must be equal to or lowe than... |
structured_pattern | 0..1 PatternExpression |
the string value of the slot must conform to the regular expression in the pa... |
implicit_prefix | 0..1 String |
Causes the slot value to be interpreted as a uriorcurie after prefixing with ... |
equals_string | 0..1 String |
the slot must have range string and the value of the slot must equal the spec... |
equals_string_in | 0..* String |
the slot must have range string and the value of the slot must equal one of t... |
equals_expression | 0..1 String |
the value of the slot must equal the value of the evaluated expression |
minimum_cardinality | 0..1 Integer |
the minimum number of entries for a multivalued slot |
maximum_cardinality | 0..1 Integer |
the maximum number of entries for a multivalued slot |
has_member | 0..1 AnonymousSlotExpression |
the value of the slot is multivalued with at least one member satisfying the ... |
all_members | 0..1 AnonymousSlotExpression |
the value of the slot is multivalued with all members satisfying the conditio... |
abstract | 0..1 Boolean |
Indicates the class or slot cannot be directly instantiated and is intended f... |
mixin | 0..1 Boolean |
Indicates the class or slot is intended to be inherited from without being an... |
string_serialization | 0..1 String |
Used on a slot that stores the string serialization of the containing object |
id_prefixes | 0..* Ncname |
the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
TypeDefinition
an element that whose instances are atomic scalar values that can be mapped to primitive types
Name | Cardinality and Range | Description |
---|---|---|
name | 1..1 String |
the unique name of the element within the context of the schema identifier |
type_uri | 0..1 Uriorcurie |
The uri that defines the possible values for the type definition |
typeof | 0..1 TypeDefinition |
Names a parent type |
base | 0..1 String |
python base type that implements this type definition |
repr | 0..1 String |
the name of the python object that implements this type definition |
pattern | 0..1 String |
the string value of the slot must conform to this regular expression expresse... |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
any_of | 0..* AnonymousTypeExpression |
holds if at least one of the expressions hold |
exactly_one_of | 0..* AnonymousTypeExpression |
holds if only one of the expressions hold |
none_of | 0..* AnonymousTypeExpression |
holds if none of the expressions hold |
all_of | 0..* AnonymousTypeExpression |
holds if all of the expressions hold |
union_of | 0..* TypeDefinition |
indicates that the domain element consists exactly of the members of the elem... |
structured_pattern | 0..1 PatternExpression |
the string value of the slot must conform to the regular expression in the pa... |
implicit_prefix | 0..1 String |
Causes the slot value to be interpreted as a uriorcurie after prefixing with ... |
equals_string | 0..1 String |
the slot must have range string and the value of the slot must equal the spec... |
equals_string_in | 0..* String |
the slot must have range string and the value of the slot must equal one of t... |
minimum_value | 0..1 Integer |
for slots with ranges of type number, the value must be equal to or higher th... |
maximum_value | 0..1 Integer |
for slots with ranges of type number, the value must be equal to or lowe than... |
id_prefixes | 0..* Ncname |
the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
EnumDefinition
an element whose instances must be drawn from a specified set of permissible values
Name | Cardinality and Range | Description |
---|---|---|
name | 1..1 String |
the unique name of the element within the context of the schema identifier |
is_a | 0..1 Definition |
A primary parent class or slot from which inheritable metaslots are propagate... |
mixins | 0..* Definition |
A collection of secondary parent classes or slots from which inheritable meta... |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
enum_uri | 0..1 Uriorcurie |
URI of the enum that provides a semantic interpretation of the element in a l... |
code_set | 0..1 Uriorcurie |
the identifier of an enumeration code set |
pv_formula | 0..1 PvFormulaOptions |
Defines the specific formula to be used to generate the permissible values |
permissible_values | 0..* PermissibleValue |
A list of possible values for a slot range |
include | 0..* AnonymousEnumExpression |
An enum expression that yields a list of permissible values that are to be in... |
minus | 0..* AnonymousEnumExpression |
An enum expression that yields a list of permissible values that are to be su... |
inherits | 0..* EnumDefinition |
An enum definition that is used as the basis to create a new enum |
reachable_from | 0..1 ReachabilityQuery |
Specifies a query for obtaining a list of permissible values based on graph r... |
matches | 0..1 MatchQuery |
Specifies a match query that is used to calculate the list of permissible val... |
concepts | 0..* Uriorcurie |
A list of identifiers that are used to construct a set of permissible values |
abstract | 0..1 Boolean |
Indicates the class or slot cannot be directly instantiated and is intended f... |
mixin | 0..1 Boolean |
Indicates the class or slot is intended to be inherited from without being an... |
string_serialization | 0..1 String |
Used on a slot that stores the string serialization of the containing object |
id_prefixes | 0..* Ncname |
the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
SubsetDefinition
an element that can be used to group other metamodel elements
Name | Cardinality and Range | Description |
---|---|---|
name | 1..1 String |
the unique name of the element within the context of the schema identifier |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
id_prefixes | 0..* Ncname |
the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
Prefix
prefix URI tuple
Name | Cardinality and Range | Description |
---|---|---|
prefix_prefix | 0..1 Ncname |
the nsname (sans ':' for a given prefix) |
prefix_reference | 1..1 Uri |
A URI associated with a given prefix |
PermissibleValue
a permissible value, accompanied by intended text and an optional mapping to a concept URI
Name | Cardinality and Range | Description |
---|---|---|
text | 1..1 String |
identifier |
meaning | 0..1 Uriorcurie |
the value meaning of a permissible value |
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
UniqueKey
a collection of slots whose values uniquely identify an instance of a class
Name | Cardinality and Range | Description |
---|---|---|
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
unique_key_name | 1..1 String |
name of the unique key |
unique_key_slots | 1..* SlotDefinition |
list of slot names that form a key |
from_schema | 0..1 Uri |
id of the schema that defined the element |
MatchQuery
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
Name | Cardinality and Range | Description |
---|---|---|
identifier_pattern | 0..1 String |
A regular expression that is used to obtain a set of identifiers from a sourc... |
source_ontology | 0..1 Uriorcurie |
An ontology or vocabulary or terminology that is used in a query to obtain a ... |
ReachabilityQuery
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
Name | Cardinality and Range | Description |
---|---|---|
source_ontology | 0..1 Uriorcurie |
An ontology or vocabulary or terminology that is used in a query to obtain a ... |
source_nodes | 0..* Uriorcurie |
A list of nodes that are used in the reachability query |
relationship_types | 0..* Uriorcurie |
A list of relationship types (properties) that are used in a reachability que... |
is_direct | 0..1 Boolean |
True if the reachability query should only include directly related nodes, if... |
include_self | 0..1 Boolean |
True if the query is reflexive |
traverse_up | 0..1 Boolean |
True if the direction of the reachability query is reversed and ancestors are... |
ClassRule
A rule that applies to instances of a class
Name | Cardinality and Range | Description |
---|---|---|
rank | 0..1 Integer |
the relative order in which the element occurs, lower values are given preced... |
preconditions | 0..1 AnonymousClassExpression |
an expression that must hold in order for the rule to be applicable to an ins... |
postconditions | 0..1 AnonymousClassExpression |
an expression that must hold for an instance of the class, if the preconditio... |
elseconditions | 0..1 AnonymousClassExpression |
an expression that must hold for an instance of the class, if the preconditio... |
bidirectional | 0..1 Boolean |
in addition to preconditions entailing postconditions, the postconditions ent... |
open_world | 0..1 Boolean |
if true, the the postconditions may be omitted in instance data, but it is va... |
from_schema | 0..1 Uri |
id of the schema that defined the element |
Setting
assignment of a key to a value
Name | Cardinality and Range | Description |
---|---|---|
setting_key | 0..1 Ncname |
the variable name for a setting |
setting_value | 1..1 String |
The value assigned for a setting |
Slots in subset
Slot | Description |
---|---|
id | The official schema URI |
name | the unique name of the element within the context of the schema |
prefix_prefix | the nsname (sans ':' for a given prefix) |
class_uri | URI of the class that provides a semantic interpretation of the element in a ... |
slot_uri | predicate of this slot for semantic web application |
type_uri | The uri that defines the possible values for the type definition |
prefix_reference | A URI associated with a given prefix |
classes | An index to the collection of all class definitions in the schema |
slot_definitions | An index to the collection of all slot definitions in the schema |
enums | An index to the collection of all enum definitions in the schema |
identifier | True means that the key slot(s) uniquely identify the container |
alias | the name used for a slot in the context of its owning class |
multivalued | true means that slot can have more than one value |
typeof | Names a parent type |
subsets | An index to the collection of all subset definitions in the schema |
required | true means that the slot must be present in the loaded definition |
base | python base type that implements this type definition |
recommended | true means that the slot should be present in the loaded definition, but this... |
repr | the name of the python object that implements this type definition |
prefixes | prefix / URI definitions to be added to the context beyond those fetched from... |
is_a | A primary parent class or slot from which inheritable metaslots are propagate... |
default_prefix | default and base prefix -- used for ':' identifiers, @base and @vocab |
mixins | A collection of secondary parent classes or slots from which inheritable meta... |
default_range | default slot range to be used if range element is omitted from a slot definit... |
slots | collection of slot names that are applicable to a class |
settings | A collection of global variable settings |
text | |
imports | other schemas that are included in this schema |
meaning | the value meaning of a permissible value |
slot_usage | the refinement of a slot in the context of the containing class definition |
inlined | True means that keyed or identified slot appears in an outer structure by val... |
inlined_as_list | True means that an inlined slot is represented as a list of range instances |
attributes | Inline definition of slots |
tree_root | indicator that this is the root class in tree structures |
pattern | the string value of the slot must conform to this regular expression expresse... |
rank | the relative order in which the element occurs, lower values are given preced... |
any_of | holds if at least one of the expressions hold |
exactly_one_of | holds if only one of the expressions hold |
none_of | holds if none of the expressions hold |
all_of | holds if all of the expressions hold |
preconditions | an expression that must hold in order for the rule to be applicable to an ins... |
postconditions | an expression that must hold for an instance of the class, if the preconditio... |
elseconditions | an expression that must hold for an instance of the class, if the preconditio... |
id_prefixes | the identifier of this class or slot must begin with the URIs referenced by t... |
from_schema | id of the schema that defined the element |
abstract | Indicates the class or slot cannot be directly instantiated and is intended f... |
mixin | Indicates the class or slot is intended to be inherited from without being an... |
code_set | the identifier of an enumeration code set |
pv_formula | Defines the specific formula to be used to generate the permissible values |
permissible_values | A list of possible values for a slot range |
enum_uri | URI of the enum that provides a semantic interpretation of the element in a l... |
include | An enum expression that yields a list of permissible values that are to be in... |
minus | An enum expression that yields a list of permissible values that are to be su... |
inherits | An enum definition that is used as the basis to create a new enum |
matches | Specifies a match query that is used to calculate the list of permissible val... |
identifier_pattern | A regular expression that is used to obtain a set of identifiers from a sourc... |
concepts | A list of identifiers that are used to construct a set of permissible values |
reachable_from | Specifies a query for obtaining a list of permissible values based on graph r... |
source_ontology | An ontology or vocabulary or terminology that is used in a query to obtain a ... |
is_direct | True if the reachability query should only include directly related nodes, if... |
traverse_up | True if the direction of the reachability query is reversed and ancestors are... |
include_self | True if the query is reflexive |
relationship_types | A list of relationship types (properties) that are used in a reachability que... |
source_nodes | A list of nodes that are used in the reachability query |
enum_range | An inlined enumeration |
range_expression | A range that is described as a boolean expression combining existing ranges |
bidirectional | in addition to preconditions entailing postconditions, the postconditions ent... |
open_world | if true, the the postconditions may be omitted in instance data, but it is va... |
rules | the collection of rules that apply to all members of this class |
classification_rules | the collection of classification rules that apply to all members of this clas... |
slot_conditions | expresses constraints on a group of slots for a class expression |
union_of | indicates that the domain element consists exactly of the members of the elem... |
unique_keys | A collection of unique keys for this class |
unique_key_name | name of the unique key |
unique_key_slots | list of slot names that form a key |
domain | defines the type of the subject of the slot |
range | defines the type of the object of the slot |
inherited | true means that the value of a slot is inherited by subclasses |
ifabsent | function that provides a default value for the slot |
implicit_prefix | Causes the slot value to be interpreted as a uriorcurie after prefixing with ... |
equals_string | the slot must have range string and the value of the slot must equal the spec... |
equals_expression | the value of the slot must equal the value of the evaluated expression |
minimum_cardinality | the minimum number of entries for a multivalued slot |
maximum_cardinality | the maximum number of entries for a multivalued slot |
equals_string_in | the slot must have range string and the value of the slot must equal one of t... |
equals_number_in | the slot must have range number and the value of the slot must equal one of t... |
has_member | the value of the slot is multivalued with at least one member satisfying the ... |
all_members | the value of the slot is multivalued with all members satisfying the conditio... |
inapplicable | true means that the slot must not be present |
list_elements_ordered | If True, then the order of elements of a multivalued slot is guaranteed to be... |
list_elements_unique | If True, then there must be no duplicates in the elements of a multivalued sl... |
shared | If True, then the relationship between the slot domain and range is many to o... |
key | True means that the key slot(s) uniquely identify the container |
designates_type | True means that the key slot(s) is used to determine the instantiation (types... |
disjoint_with | Two classes are disjoint if they have no instances in common, two slots are d... |
symmetric | If s is symmetric, and i |
asymmetric | If s is antisymmetric, and i |
reflexive | If s is reflexive, then i |
irreflexive | If s is irreflexive, then there exists no i such i |
locally_reflexive | If s is locally_reflexive, then i |
transitive | If s is transitive, and i |
transitive_form_of | If s transitive_form_of d, then (1) s holds whenever d holds (2) s is transit... |
reflexive_transitive_form_of | transitive_form_of including the reflexive case |
inverse | indicates that any instance of d s r implies that there is also an instance o... |
minimum_value | for slots with ranges of type number, the value must be equal to or higher th... |
maximum_value | for slots with ranges of type number, the value must be equal to or lowe than... |
interpolated | if true then the pattern is first string interpolated |
partial_match | if true then the pattern must match the whole string, as if enclosed in ^ |
syntax | the string value of the slot must conform to this regular expression expresse... |
structured_pattern | the string value of the slot must conform to the regular expression in the pa... |
string_serialization | Used on a slot that stores the string serialization of the containing object |
setting_key | the variable name for a setting |
setting_value | The value assigned for a setting |
slot_group | allows for grouping of related slots into a grouping slot that serves the rol... |
is_grouping_slot | true if this slot is a grouping slot |
Enumerations in subset
Enumeration | Description |
---|---|
PvFormulaOptions | The formula used to generate the set of permissible values from the code_set ... |