LinkML Metamodel

text of an attributed description

the source of an attributed description

text of an attributed description

the source of an attributed description

a tag associated with an extension

a collection of tag/text tuples with the semantics of OWL Annotation

a tag/text tuple attached to an arbitrary element

a collection of tag/text tuples with the semantics of OWL Annotation

a tag/text tuple attached to an arbitrary element

a tag associated with an extension

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

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

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

expresses constraints on a group of slots for a class expression

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

the identifier of an enumeration code set.

the version tag of the enumeration code set

the version identifier of the enumeration code set

A list of identifiers that are used to construct a set of permissible values

An enum expression that yields a list of permissible values that are to be included, after subtracting the minus set

An enum definition that is used as the basis to create a new enum

Specifies a match query that is used to calculate the list of permissible values

An enum expression that yields a list of permissible values that are to be subtracted from the enum

A list of possible values for a slot range

The formula used to generate the set of permissible values from the code_set values

Specifies a query for obtaining a list of permissible values based on graph reachability

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

the value of the slot is multivalued with all members satisfying the condition

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

coerces the value of the slot into an array and defines the dimensions of that array

A collection of enum bindings that specify how a slot can be bound to a permissible value from an enumeration. LinkML provides enums to allow string values to be restricted to one of a set of permissible values (specified statically or dynamically). Enum bindings allow enums to be bound to any object, including complex nested objects. For example, given a (generic) class Concept with slots id and label, it may be desirable to restrict the values the id takes on in a given context. For example, a HumanSample class may have a slot for representing sample site, with a range of concept, but the values of that slot may be restricted to concepts from a particular branch of an anatomy ontology.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

An inlined enumeration

the value of the slot must equal the value of the evaluated expression

the slot must have range of a number and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal one of the specified values

the exact number of entries for a multivalued slot

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the value of the slot is multivalued with at least one member satisfying the condition

Causes the slot value to be interpreted as a uriorcurie after prefixing with this string

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

True means that keyed or identified slot appears in an outer structure by value. False means that only the key or identifier for the slot appears within the domain, referencing a structure that appears elsewhere.

True means that an inlined slot is represented as a list of range instances. False means that an inlined slot is represented as a dictionary, whose key is the slot key or identifier and whose value is the range instance.

Keywords or tags used to describe the element

time at which the element was last updated

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.

the maximum number of entries for a multivalued slot

For ordinal ranges, the value must be equal to or lower than this

the minimum number of entries for a multivalued slot

For ordinal ranges, the value must be equal to or higher than this

agent that modified the element

true means that slot can have more than one value and should be represented using a list or collection structure.

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

the string value of the slot must conform to this regular expression expressed in the string

defines the type of the object of the slot. Given the following slot definition S1: domain: C1 range: C2 the declaration X: S1: Y

implicitly asserts Y is an instance of C2

A range that is described as a boolean expression combining existing ranges

the relative order in which the element occurs, lower values are given precedence

true means that the slot should be present in instances of the class definition, but this is not required

A list of terms from different schemas or terminology systems that have related meaning.

true means that the slot must be present in instances of the class definition

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

the string value of the slot must conform to the regular expression in the pattern expression

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

an encoding of a unit

enumeration of conditions by which a slot value should be set

holds if all of the expressions hold

holds if at least one of the expressions hold

the slot must have range of a number and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal one of the specified values

holds if only one of the expressions hold

Causes the slot value to be interpreted as a uriorcurie after prefixing with this string

For ordinal ranges, the value must be equal to or lower than this

For ordinal ranges, the value must be equal to or higher than this

holds if none of the expressions hold

the string value of the slot must conform to this regular expression expressed in the string

the string value of the slot must conform to the regular expression in the pattern expression

an encoding of a unit

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

definitions of each axis in the array

A list of terms from different schemas or terminology systems that have identical meaning.

exact number of dimensions in the array

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

maximum number of dimensions in the array, or False if explicitly no maximum. If this is unset, and an explicit list of dimensions are passed using dimensions, then this is interpreted as a closed list and the maximum_number_dimensions is the length of the dimensions list, unless this value is set to False

minimum number of dimensions in the array

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

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.

Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.

the name used for a slot in the context of its owning class. If present, this is used instead of the actual slot name.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

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.

Inline definition of slots

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

If true then all direct is_a children are mutually disjoint and share no instances in common

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

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.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

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

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

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

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

How a class instance handles extra data not specified in the class definition. Note that this does not define the constraints that are placed on additional slots defined by inheriting classes.

Possible values:

• allowed: true - allow all additional data
• allowed: false (or allowed: or allowed: null while range_expression is null) - forbid all additional data (default)
• range_expression: ... - allow additional data if it matches the slot expression (see examples)

id of the schema that defined the element

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

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.

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.

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An element in another schema which this element instantiates.

A primary parent class from which inheritable metaslots are propagated

Keywords or tags used to describe the element

time at which the element was last updated

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.

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.

A collection of secondary parent mixin classes from which inheritable metaslots are propagated

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

true if this class represents a relationship rather than an entity

the collection of rules that apply to all members of this class

A list of related entities or URLs that may be of relevance

expresses constraints on a group of slots for a class expression

if true then induced/mangled slot names are not created for class_usage and attributes

the refinement of a slot in the context of the containing class definition.

collection of slot names that are applicable to a class

A related resource from which the element is derived.

status of the element

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) GENERATE: 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

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

DEPRECATED -- rdfs:subClassOf to be emitted in OWL generation

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

Indicates that this is the Container class which forms the root of the serialized document structure in tree serializations

indicates that the domain element consists exactly of the members of the element in the range.

A collection of named unique keys for this class. Unique keys may be singular or compound.

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.

Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.

the name used for a slot in the context of its owning class. If present, this is used instead of the actual slot name.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

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.

Inline definition of slots

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

If true then all direct is_a children are mutually disjoint and share no instances in common

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

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.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

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

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

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

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

How a class instance handles extra data not specified in the class definition. Note that this does not define the constraints that are placed on additional slots defined by inheriting classes.

Possible values:

• allowed: true - allow all additional data
• allowed: false (or allowed: or allowed: null while range_expression is null) - forbid all additional data (default)
• range_expression: ... - allow additional data if it matches the slot expression (see examples)

id of the schema that defined the element

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

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.

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.

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An element in another schema which this element instantiates.

A primary parent class from which inheritable metaslots are propagated

Keywords or tags used to describe the element

time at which the element was last updated

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.

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.

A collection of secondary parent mixin classes from which inheritable metaslots are propagated

agent that modified the element

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.

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

true if this class represents a relationship rather than an entity

the collection of rules that apply to all members of this class

A list of related entities or URLs that may be of relevance

expresses constraints on a group of slots for a class expression

if true then induced/mangled slot names are not created for class_usage and attributes

the refinement of a slot in the context of the containing class definition.

collection of slot names that are applicable to a class

A related resource from which the element is derived.

status of the element

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) GENERATE: 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

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

DEPRECATED -- rdfs:subClassOf to be emitted in OWL generation

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

Indicates that this is the Container class which forms the root of the serialized document structure in tree serializations

indicates that the domain element consists exactly of the members of the element in the range.

A collection of named unique keys for this class. Unique keys may be singular or compound.

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.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

in addition to preconditions entailing postconditions, the postconditions entail the preconditions

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

a deactivated rule is not executed by the rules engine

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

an expression that must hold for an instance of the class, if the preconditions no not hold

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

if true, the the postconditions may be omitted in instance data, but it is valid for an inference engine to add these

an expression that must hold for an instance of the class, if the preconditions hold

an expression that must hold in order for the rule to be applicable to an instance

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

the name used for a slot in the context of its owning class. If present, this is used instead of the actual slot name.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

the exact number of entries for a multivalued slot

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

the maximum number of entries for a multivalued slot

the minimum number of entries for a multivalued slot

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A path to a slot that is being bound to a permissible value from an enumeration.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

The level of obligation or recommendation strength for a metadata element

The formula used to generate the set of permissible values from the code_set values

defines the type of the object of the slot. Given the following slot definition S1: domain: C1 range: C2 the declaration X: S1: Y

implicitly asserts Y is an instance of C2

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

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.

Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

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.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

the identifier of an enumeration code set.

the version tag of the enumeration code set

the version identifier of the enumeration code set

notes and comments about an element intended primarily for external consumption

A list of identifiers that are used to construct a set of permissible values

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

URI of the enum that provides a semantic interpretation of the element in a linked data context. The URI may come from any namespace and may be shared between schemas

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

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

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.

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.

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An enum expression that yields a list of permissible values that are to be included, after subtracting the minus set

An enum definition that is used as the basis to create a new enum

An element in another schema which this element instantiates.

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

Keywords or tags used to describe the element

time at which the element was last updated

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.

Specifies a match query that is used to calculate the list of permissible values

An enum expression that yields a list of permissible values that are to be subtracted from the enum

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.

A collection of secondary parent classes or slots from which inheritable metaslots are propagated from.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

A list of possible values for a slot range

The formula used to generate the set of permissible values from the code_set values

the relative order in which the element occurs, lower values are given precedence

Specifies a query for obtaining a list of permissible values based on graph reachability

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

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) GENERATE: 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

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

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.

Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

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.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

the identifier of an enumeration code set.

the version tag of the enumeration code set

the version identifier of the enumeration code set

notes and comments about an element intended primarily for external consumption

A list of identifiers that are used to construct a set of permissible values

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

URI of the enum that provides a semantic interpretation of the element in a linked data context. The URI may come from any namespace and may be shared between schemas

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

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

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.

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.

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An enum expression that yields a list of permissible values that are to be included, after subtracting the minus set

An enum definition that is used as the basis to create a new enum

An element in another schema which this element instantiates.

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

Keywords or tags used to describe the element

time at which the element was last updated

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.

Specifies a match query that is used to calculate the list of permissible values

An enum expression that yields a list of permissible values that are to be subtracted from the enum

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.

A collection of secondary parent classes or slots from which inheritable metaslots are propagated from.

agent that modified the element

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.

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

A list of possible values for a slot range

The formula used to generate the set of permissible values from the code_set values

the relative order in which the element occurs, lower values are given precedence

Specifies a query for obtaining a list of permissible values based on graph reachability

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

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) GENERATE: 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

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

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.

the identifier of an enumeration code set.

the version tag of the enumeration code set

the version identifier of the enumeration code set

A list of identifiers that are used to construct a set of permissible values

An enum expression that yields a list of permissible values that are to be included, after subtracting the minus set

An enum definition that is used as the basis to create a new enum

Specifies a match query that is used to calculate the list of permissible values

An enum expression that yields a list of permissible values that are to be subtracted from the enum

A list of possible values for a slot range

The formula used to generate the set of permissible values from the code_set values

Specifies a query for obtaining a list of permissible values based on graph reachability

description of what the value is doing

direct object representation of the example

example value

a tag associated with an extension

a tag/text tuple attached to an arbitrary element

a tag/text tuple attached to an arbitrary element

a tag associated with an extension

Whether or not something is allowed. Usage defined by context.

A range that is described as a boolean expression combining existing ranges

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

the ncname of the source of the name

a name assigned to an element in a given ontology

a name assigned to an element in a given ontology

the ncname of the source of the name

A regular expression that is used to obtain a set of identifiers from a source_ontology to construct a set of permissible values

An ontology or vocabulary or terminology that is used in a query to obtain a set of permissible values

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

in a sequential list, this indicates the next member

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

A range that is described as a boolean expression combining existing ranges

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

true if the slot is to be inversed

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

the slot to traverse

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

if true then the pattern is first string interpolated

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

if not true then the pattern must match the whole string, as if enclosed in ^...$

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

the string value of the slot must conform to this regular expression expressed in the string. May be interpolated.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

The actual permissible value itself

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

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.

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An element in another schema which this element instantiates.

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

Keywords or tags used to describe the element

time at which the element was last updated

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.

the value meaning of a permissible value

A collection of secondary parent classes or slots from which inheritable metaslots are propagated from.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

an encoding of a unit

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

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.

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An element in another schema which this element instantiates.

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

Keywords or tags used to describe the element

time at which the element was last updated

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.

the value meaning of a permissible value

A collection of secondary parent classes or slots from which inheritable metaslots are propagated from.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

The actual permissible value itself

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

an encoding of a unit

The prefix components of a prefix expansions. This is the part that appears before the colon in a CURIE.

The namespace to which a prefix expands to.

The namespace to which a prefix expands to.

The prefix components of a prefix expansions. This is the part that appears before the colon in a CURIE.

True if the query is reflexive

True if the reachability query should only include directly related nodes, if False then include also transitively connected

A list of relationship types (properties) that are used in a reachability query

A list of nodes that are used in the reachability query

An ontology or vocabulary or terminology that is used in a query to obtain a set of permissible values

True if the direction of the reachability query is reversed and ancestors are retrieved

The official schema URI

a unique name for the schema that is both human-readable and consists of only characters from the NCName set

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A collection of enum bindings that specify how a slot can be bound to a permissible value from an enumeration. LinkML provides enums to allow string values to be restricted to one of a set of permissible values (specified statically or dynamically). Enum bindings allow enums to be bound to any object, including complex nested objects. For example, given a (generic) class Concept with slots id and label, it may be desirable to restrict the values the id takes on in a given context. For example, a HumanSample class may have a slot for representing sample site, with a range of concept, but the values of that slot may be restricted to concepts from a particular branch of an anatomy ontology.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

An index to the collection of all class definitions in the schema

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

ordered list of prefixcommon biocontexts to be fetched to resolve id prefixes and inline prefix variables

The prefix that is used for all elements within a schema

default slot range to be used if range element is omitted from a slot definition

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

a list of Curie prefixes that are used in the representation of instances of the model. All prefixes in this list are added to the prefix sections of the target models.

An index to the collection of all enum definitions in the schema

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

date and time that the schema was loaded/generated

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

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.

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.

the imports entry that this element was derived from. Empty means primary source

A list of schemas that are to be included in this schema

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

An element in another schema which this element instantiates.

Keywords or tags used to describe the element

time at which the element was last updated

license for the schema

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.

Version of the metamodel used to load the schema

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

A collection of prefix expansions that specify how CURIEs can be expanded to URIs

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A collection of global variable settings

if true then induced/mangled slot names are not created for class_usage and attributes

An index to the collection of all slot definitions in the schema

A related resource from which the element is derived.

name, uri or description of the source of the schema

modification date of the source of the schema

size in bytes of the source of the schema

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

An index to the collection of all subset definitions in the schema

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

An index to the collection of all type definitions in the schema

particular version of schema

the variable name for a setting

The value assigned for a setting

The value assigned for a setting

the variable name for a setting

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.

Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.

the name used for a slot in the context of its owning class. If present, this is used instead of the actual slot name.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

the value of the slot is multivalued with all members satisfying the condition

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

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.

coerces the value of the slot into an array and defines the dimensions of that array

If s is antisymmetric, and i.s=v where i is different from v, v.s cannot have value i

A collection of enum bindings that specify how a slot can be bound to a permissible value from an enumeration. LinkML provides enums to allow string values to be restricted to one of a set of permissible values (specified statically or dynamically). Enum bindings allow enums to be bound to any object, including complex nested objects. For example, given a (generic) class Concept with slots id and label, it may be desirable to restrict the values the id takes on in a given context. For example, a HumanSample class may have a slot for representing sample site, with a range of concept, but the values of that slot may be restricted to concepts from a particular branch of an anatomy ontology.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

If true then all direct is_a children are mutually disjoint and share no instances in common

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

True means that the key slot(s) is used to determine the instantiation (types) relation between objects and a ClassDefinition

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

defines the type of the subject of the slot. Given the following slot definition S1: domain: C1 range: C2 the declaration X: S1: Y

implicitly asserts that X is an instance of C1

the class(es) that reference the slot in a "slots" or "slot_usage" context

An inlined enumeration

the value of the slot must equal the value of the evaluated expression

the slot must have range of a number and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal one of the specified values

the exact number of entries for a multivalued slot

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the value of the slot is multivalued with at least one member satisfying the condition

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

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.

True means that the key slot(s) uniquely identifies the elements. There can be at most one identifier or key per container

function that provides a default value for the slot.

• [Tt]rue -- boolean True
• [Ff]alse -- boolean False
• bnode -- blank node identifier
• class_curie -- CURIE for the containing class
• class_uri -- URI for the containing class
• default_ns -- schema default namespace
• default_range -- schema default range
• int(value) -- integer value
• slot_uri -- URI for the slot
• slot_curie -- CURIE for the slot
• string(value) -- string value
• EnumName(PermissibleValue) -- enum value

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.

Causes the slot value to be interpreted as a uriorcurie after prefixing with this string

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

true means that the value of a slot is inherited by subclasses

True means that keyed or identified slot appears in an outer structure by value. False means that only the key or identifier for the slot appears within the domain, referencing a structure that appears elsewhere.

True means that an inlined slot is represented as a list of range instances. False means that an inlined slot is represented as a dictionary, whose key is the slot key or identifier and whose value is the range instance.

An element in another schema which this element instantiates.

indicates that any instance of d s r implies that there is also an instance of r s' d

If s is irreflexive, then there exists no i such i.s=i

A primary parent slot from which inheritable metaslots are propagated

indicates that for any instance, i, the domain of this slot will include an assertion of i s range

true if this slot is a grouping slot

True means that this slot was defined in a slot_usage situation

True means that the key slot(s) uniquely identify the elements within a single container

Keywords or tags used to describe the element

time at which the element was last updated

If True, then the order of elements of a multivalued slot is guaranteed to be preserved. If False, the order may still be preserved but this is not guaranteed

If True, then there must be no duplicates in the elements of a multivalued slot

If s is locally_reflexive, then i.s=i for all instances i where s is a class slot for the type of i

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.

the maximum number of entries for a multivalued slot

For ordinal ranges, the value must be equal to or lower than this

the minimum number of entries for a multivalued slot

For ordinal ranges, the value must be equal to or higher than this

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.

A collection of secondary parent mixin slots from which inheritable metaslots are propagated

agent that modified the element

true means that slot can have more than one value and should be represented using a list or collection structure.

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

the "owner" of the slot. It is the class if it appears in the slots list, otherwise the declaring slot

a rule for inferring a slot assignment based on evaluating a path through a sequence of slot assignments

the string value of the slot must conform to this regular expression expressed in the string

defines the type of the object of the slot. Given the following slot definition S1: domain: C1 range: C2 the declaration X: S1: Y

implicitly asserts Y is an instance of C2

A range that is described as a boolean expression combining existing ranges

the relative order in which the element occurs, lower values are given precedence

If present, slot is read only. Text explains why

true means that the slot should be present in instances of the class definition, but this is not required

If s is reflexive, then i.s=i for all instances i

transitive_form_of including the reflexive case

A list of terms from different schemas or terminology systems that have related meaning.

enumeration of roles a slot on a relationship class can play

true means that the slot must be present in instances of the class definition

a textual descriptor that indicates the role played by the slot range

A list of related entities or URLs that may be of relevance

If True, then the relationship between the slot domain and range is many to one or many to many

a name that is used in the singular form

allows for grouping of related slots into a grouping slot that serves the role of a group

URI of the class that provides a semantic interpretation of the slot in a linked data context. The URI may come from any namespace and may be shared between schemas.

A related resource from which the element is derived.

status of the element

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) GENERATE: 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

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

the string value of the slot must conform to the regular expression in the pattern expression

Ontology property which this slot is a subproperty of. Note: setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.

If s is symmetric, and i.s=v, then v.s=i

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

If s is transitive, and i.s=z, and s.s=j, then i.s=j

If s transitive_form_of d, then (1) s holds whenever d holds (2) s is transitive (3) d holds whenever s holds and there are no intermediates, and s is not reflexive

A collection of type mappings that specify how a slot's range should be mapped or serialized in different frameworks

indicates that the domain element consists exactly of the members of the element in the range.

an encoding of a unit

The name of the slot referenced in the slot_usage

enumeration of conditions by which a slot value should be set

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.

Indicates the class or slot cannot be directly instantiated and is intended for grouping purposes.

the name used for a slot in the context of its owning class. If present, this is used instead of the actual slot name.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

the value of the slot is multivalued with all members satisfying the condition

holds if all of the expressions hold

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

holds if at least one of the expressions hold

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.

coerces the value of the slot into an array and defines the dimensions of that array

If s is antisymmetric, and i.s=v where i is different from v, v.s cannot have value i

A collection of enum bindings that specify how a slot can be bound to a permissible value from an enumeration. LinkML provides enums to allow string values to be restricted to one of a set of permissible values (specified statically or dynamically). Enum bindings allow enums to be bound to any object, including complex nested objects. For example, given a (generic) class Concept with slots id and label, it may be desirable to restrict the values the id takes on in a given context. For example, a HumanSample class may have a slot for representing sample site, with a range of concept, but the values of that slot may be restricted to concepts from a particular branch of an anatomy ontology.

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

If true then all direct is_a children are mutually disjoint and share no instances in common

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

An established standard to which the element conforms.

agent that contributed to the element

agent that created the element

time at which the element was created

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

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

True means that the key slot(s) is used to determine the instantiation (types) relation between objects and a ClassDefinition

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

defines the type of the subject of the slot. Given the following slot definition S1: domain: C1 range: C2 the declaration X: S1: Y

implicitly asserts that X is an instance of C1

the class(es) that reference the slot in a "slots" or "slot_usage" context

An inlined enumeration

the value of the slot must equal the value of the evaluated expression

the slot must have range of a number and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal the specified value

the slot must have range string and the value of the slot must equal one of the specified values

the exact number of entries for a multivalued slot

A list of terms from different schemas or terminology systems that have identical meaning.

holds if only one of the expressions hold

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the value of the slot is multivalued with at least one member satisfying the condition

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

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.

True means that the key slot(s) uniquely identifies the elements. There can be at most one identifier or key per container

function that provides a default value for the slot.

• [Tt]rue -- boolean True
• [Ff]alse -- boolean False
• bnode -- blank node identifier
• class_curie -- CURIE for the containing class
• class_uri -- URI for the containing class
• default_ns -- schema default namespace
• default_range -- schema default range
• int(value) -- integer value
• slot_uri -- URI for the slot
• slot_curie -- CURIE for the slot
• string(value) -- string value
• EnumName(PermissibleValue) -- enum value

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.

Causes the slot value to be interpreted as a uriorcurie after prefixing with this string

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

true means that the value of a slot is inherited by subclasses

True means that keyed or identified slot appears in an outer structure by value. False means that only the key or identifier for the slot appears within the domain, referencing a structure that appears elsewhere.

True means that an inlined slot is represented as a list of range instances. False means that an inlined slot is represented as a dictionary, whose key is the slot key or identifier and whose value is the range instance.

An element in another schema which this element instantiates.

indicates that any instance of d s r implies that there is also an instance of r s' d

If s is irreflexive, then there exists no i such i.s=i

A primary parent slot from which inheritable metaslots are propagated

indicates that for any instance, i, the domain of this slot will include an assertion of i s range

true if this slot is a grouping slot

True means that this slot was defined in a slot_usage situation

True means that the key slot(s) uniquely identify the elements within a single container

Keywords or tags used to describe the element

time at which the element was last updated

If True, then the order of elements of a multivalued slot is guaranteed to be preserved. If False, the order may still be preserved but this is not guaranteed

If True, then there must be no duplicates in the elements of a multivalued slot

If s is locally_reflexive, then i.s=i for all instances i where s is a class slot for the type of i

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.

the maximum number of entries for a multivalued slot

For ordinal ranges, the value must be equal to or lower than this

the minimum number of entries for a multivalued slot

For ordinal ranges, the value must be equal to or higher than this

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.

A collection of secondary parent mixin slots from which inheritable metaslots are propagated

agent that modified the element

true means that slot can have more than one value and should be represented using a list or collection structure.

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.

A list of terms from different schemas or terminology systems that have narrower meaning.

holds if none of the expressions hold

editorial notes about an element intended primarily for internal consumption

the "owner" of the slot. It is the class if it appears in the slots list, otherwise the declaring slot

a rule for inferring a slot assignment based on evaluating a path through a sequence of slot assignments

the string value of the slot must conform to this regular expression expressed in the string

defines the type of the object of the slot. Given the following slot definition S1: domain: C1 range: C2 the declaration X: S1: Y

implicitly asserts Y is an instance of C2

A range that is described as a boolean expression combining existing ranges

the relative order in which the element occurs, lower values are given precedence

If present, slot is read only. Text explains why

true means that the slot should be present in instances of the class definition, but this is not required

If s is reflexive, then i.s=i for all instances i

transitive_form_of including the reflexive case

A list of terms from different schemas or terminology systems that have related meaning.

enumeration of roles a slot on a relationship class can play

true means that the slot must be present in instances of the class definition

a textual descriptor that indicates the role played by the slot range

A list of related entities or URLs that may be of relevance

If True, then the relationship between the slot domain and range is many to one or many to many

a name that is used in the singular form

allows for grouping of related slots into a grouping slot that serves the role of a group

URI of the class that provides a semantic interpretation of the slot in a linked data context. The URI may come from any namespace and may be shared between schemas.

A related resource from which the element is derived.

status of the element

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) GENERATE: 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

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

the string value of the slot must conform to the regular expression in the pattern expression

Ontology property which this slot is a subproperty of. Note: setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.

If s is symmetric, and i.s=v, then v.s=i

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

If s is transitive, and i.s=z, and s.s=j, then i.s=j

If s transitive_form_of d, then (1) s holds whenever d holds (2) s is transitive (3) d holds whenever s holds and there are no intermediates, and s is not reflexive

A collection of type mappings that specify how a slot's range should be mapped or serialized in different frameworks

indicates that the domain element consists exactly of the members of the element in the range.

an encoding of a unit

The name of the slot referenced in the slot_usage

enumeration of conditions by which a slot value should be set

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.

The literal lexical form of a structured alias; i.e the actual alias value.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

The category or categories of an alias. This can be drawn from any relevant vocabulary

A list of terms from different schemas or terminology systems that have close meaning.

notes and comments about an element intended primarily for external consumption

The context in which an alias should be applied

agent that contributed to the element

agent that created the element

time at which the element was created

Description of why and when this element will no longer be used

When an element is deprecated, it can be automatically replaced by this uri or curie

When an element is deprecated, it can be potentially replaced by this uri or curie

a textual description of the element's purpose and use

A list of terms from different schemas or terminology systems that have identical meaning.

example usages of an element

a tag/text tuple attached to an arbitrary element

id of the schema that defined the element

the imports entry that this element was derived from. Empty means primary source

the primary language used in the sources

used to indicate membership of a term in a defined subset of terms used for a particular domain or application.

Keywords or tags used to describe the element

time at which the element was last updated

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.

agent that modified the element

A list of terms from different schemas or terminology systems that have narrower meaning.

editorial notes about an element intended primarily for internal consumption

permissible values for the relationship between an element and an alias

the relative order in which the element occurs, lower values are given precedence

A list of terms from different schemas or terminology systems that have related meaning.

A list of related entities or URLs that may be of relevance

A related resource from which the element is derived.

status of the element

A list of structured_alias objects, used to provide aliases in conjunction with additional metadata.

A concise human-readable display label for the element. The title should mirror the name, and should use ordinary textual punctuation.

Outstanding issues that needs resolution

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.

Alternate names/labels for the element. These do not alter the semantics of the schema, but may be useful to support search and alignment.

A sourced alternative description for an element

a collection of tag/text tuples with the semantics of OWL Annotation

A list of terms from different schemas or terminology systems that have broader meaning.

Controlled terms used to categorize an element.

A list of terms from different schemas or terminology systems that have close meaning.