description: Configuration for generating a Docker image


key: helm

description: Configuration for generating a Helm chart


key: archive

description: List of artifacts to archive (wildcards allowed). Check out https://www.jenkins.io/doc/pipeline/steps/core/#archiveartifacts-archive-the-artifacts

type: array


key: timeout

description: Build timeout in seconds


key: source

description: Path to the source directory, defaults to ./src

type: string

format: uri-reference


key: repositories

description: The default repositories to use if no repository is specified for a plugin

type: object

format: uri


key: maven

description: The url to the maven repository to use, defaults to https://repo.maven.apache.org/maven2


key: items

description: A local plugin, should most likely not be used in production

required: type path

const: local


description: A maven plugin in POM-like notation, will be downloaded from the provided repository

required: type groupId artifactId version

const: maven


description: A maven plugin in gradle-like notation, will be downloaded from the provided repository

required: type dependency

const: gradle


key: generators

description: Which SAMT generators to use


description: A collection of definitions that make up a schema or a data model.

required: source description

required: tag value

format: date-time

type: integer

enum: SUBJECT OBJECT PREDICATE NODE OTHER_ROLE


key: AliasPredicateEnum

description: permissible values for the relationship between an element and an alias


key: AltDescription

description: an attributed description


key: description

description: text of an attributed description


description: the source of an attributed description


description: an attributed description


key: Annotation

description: a tag/value pair with the semantics of OWL Annotation


key: annotations

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


key: extensions

description: a tag/text tuple attached to an arbitrary element


key: tag

description: a tag associated with an extension


key: value

description: the actual annotation


key: AnonymousClassExpression


key: aliases

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


description: holds if all of the expressions hold


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


description: holds if at least one of the expressions hold


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


description: a textual description of the element's purpose and use


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


description: holds if only one of the expressions hold


key: examples

description: example usages of an element


description: id of the schema that defined the element


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


description: the primary language used in the sources


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


description: A primary parent class or slot from which inheritable metaslots are propagated from. While multiple inheritance is not allowed, mixins can be provided effectively providing the same thing. The semantics are the same when translated to formalisms that allow MI (e.g. RDFS/OWL). When translating to a SI framework (e.g. java classes, python classes) then is a is used. When translating a framework without polymorphism (e.g. json-schema, solr document schema) then is a and mixins are recursively unfolded


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: agent that modified the element


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


description: holds if none of the expressions hold


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: rank

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


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


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


description: expresses constraints on a group of slots for a class expression


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: AnonymousEnumExpression

description: An enum_expression that is not named


description: the identifier of an enumeration code set.


description: the version tag of the enumeration code set


description: the version identifier of the enumeration code set


key: concepts

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


key: include

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


key: inherits

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


key: matches

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


key: minus

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


description: A list of possible values for a slot range


Defines the specific formula to be used to generate the permissible values.


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


key: AnonymousSlotExpression

type: boolean


key: aliases

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


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


description: holds if all of the expressions hold


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: holds if at least one of the expressions hold


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


An inlined enumeration


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


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


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


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


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


description: holds if only one of the expressions hold


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


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


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


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


description: the primary language used in the sources


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


key: inlined

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


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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: the maximum number of entries for a multivalued slot


description: for slots with ranges of type number, the value must be equal to or lowe than this


description: the minimum number of entries for a multivalued slot


description: for slots with ranges of type number, the value must be equal to or higher than this


description: agent that modified the element


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


description: holds if none of the expressions hold


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: pattern

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


key: range

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

implicitly asserts Y is an instance of C2


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


key: rank

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


key: recommended

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


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


key: required

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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


description: 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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: unit

description: an encoding of a unit


if true then a value must be present (for lists there must be at least one value). If false then a value must be absent (for lists, must be empty)


key: AnonymousTypeExpression

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


description: holds if all of the expressions hold


description: holds if at least one of the expressions hold


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


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


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


description: holds if only one of the expressions hold


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


description: for slots with ranges of type number, the value must be equal to or lowe than this


description: for slots with ranges of type number, the value must be equal to or higher than this


description: holds if none of the expressions hold


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


key: ClassDefinition

description: an element whose instances are complex objects that may have slot-value assignments


key: abstract

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


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.


key: attributes

description: Inline definition of slots


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


key: categories

description: Controlled terms used to categorize an element.


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


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


description: The collection of classification rules that apply to all members of this class. Classification rules allow for automatically assigning the instantiated type of an instance.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


description: The combination of is a plus defining slots form a genus-differentia definition, or the set of necessary and sufficient conditions that can be transformed into an OWL equivalence axiom


description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


description: Two classes are disjoint if they have no instances in common, two slots are disjoint if they can never hold between the same two instances


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


description: holds if only one of the expressions hold


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix


key: implements

description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element.


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


description: the primary language used in the sources


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


key: instantiates

description: An element in another schema which this element instantiates.


description: A primary parent class from which inheritable metaslots are propagated


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


description: a name assigned to an element in a given ontology


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


key: mixin

description: Indicates the class or slot is intended to be inherited from without being an is_a parent. mixins should not be inherited from using is_a, except by other mixins.


key: mixins

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


description: agent that modified the element


key: name

description: the unique name of the element within the context of the schema.  Name is combined with the default prefix to form the globally unique subject of the target class.


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


description: holds if none of the expressions hold


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: rank

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


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


description: true if this class represents a relationship rather than an entity


key: rules

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


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


description: expresses constraints on a group of slots for a class expression


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


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


key: slots

description: collection of slot names that are applicable to a class


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


description:
Used on a slot that stores the string serialization of the containing object. The syntax follows python formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.
We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the expansion.
Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of complex objects
For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of string_value shouldd be 2cm


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


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


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


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


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


description: The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot. Note: this is different than 'subproperty_of' in that 'subproperty_of' is intended to be a single ontology term while 'values_from' is the identifier of an entire value set.  Additionally, this is different than an enumeration in that in an enumeration, the values of the enumeration are listed directly in the model itself. Setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.


description: an element whose instances are complex objects that may have slot-value assignments


key: abstract

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


key: aliases

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


description: holds if all of the expressions hold


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: holds if at least one of the expressions hold


description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.


key: attributes

description: Inline definition of slots


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


key: categories

description: Controlled terms used to categorize an element.


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


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


description: The collection of classification rules that apply to all members of this class. Classification rules allow for automatically assigning the instantiated type of an instance.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


description: The combination of is a plus defining slots form a genus-differentia definition, or the set of necessary and sufficient conditions that can be transformed into an OWL equivalence axiom


description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


description: Two classes are disjoint if they have no instances in common, two slots are disjoint if they can never hold between the same two instances


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


description: holds if only one of the expressions hold


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix


key: implements

description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element.


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


description: the primary language used in the sources


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


key: instantiates

description: An element in another schema which this element instantiates.


description: A primary parent class from which inheritable metaslots are propagated


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


description: a name assigned to an element in a given ontology


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


key: mixin

description: Indicates the class or slot is intended to be inherited from without being an is_a parent. mixins should not be inherited from using is_a, except by other mixins.


key: mixins

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


description: agent that modified the element


key: name

description: the unique name of the element within the context of the schema.  Name is combined with the default prefix to form the globally unique subject of the target class.


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


description: holds if none of the expressions hold


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: rank

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


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


description: true if this class represents a relationship rather than an entity


key: rules

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


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


description: expresses constraints on a group of slots for a class expression


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


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


key: slots

description: collection of slot names that are applicable to a class


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


description:
Used on a slot that stores the string serialization of the containing object. The syntax follows python formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.
We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the expansion.
Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of complex objects
For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of string_value shouldd be 2cm


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


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


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


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


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


description: The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot. Note: this is different than 'subproperty_of' in that 'subproperty_of' is intended to be a single ontology term while 'values_from' is the identifier of an entire value set.  Additionally, this is different than an enumeration in that in an enumeration, the values of the enumeration are listed directly in the model itself. Setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.


key: ClassRule

description: A rule that applies to instances of a class


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


key: bidirectional

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


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deactivated

description: a deactivated rule is not executed by the rules engine


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


key: elseconditions

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


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


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


description: the primary language used in the sources


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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: agent that modified the element


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


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


key: postconditions

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


key: preconditions

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


key: rank

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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: EnumDefinition

description: an element whose instances must be drawn from a specified set of permissible values


key: abstract

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


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.


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


key: categories

description: Controlled terms used to categorize an element.


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


description: the identifier of an enumeration code set.


description: the version tag of the enumeration code set


description: the version identifier of the enumeration code set


key: comments

description: notes and comments about an element intended primarily for external consumption


key: concepts

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


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix


key: implements

description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element.


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


description: the primary language used in the sources


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


key: include

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


key: inherits

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


key: instantiates

description: An element in another schema which this element instantiates.


description: A primary parent class or slot from which inheritable metaslots are propagated from. While multiple inheritance is not allowed, mixins can be provided effectively providing the same thing. The semantics are the same when translated to formalisms that allow MI (e.g. RDFS/OWL). When translating to a SI framework (e.g. java classes, python classes) then is a is used. When translating a framework without polymorphism (e.g. json-schema, solr document schema) then is a and mixins are recursively unfolded


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


description: a name assigned to an element in a given ontology


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


key: matches

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


key: minus

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


key: mixin

description: Indicates the class or slot is intended to be inherited from without being an is_a parent. mixins should not be inherited from using is_a, except by other mixins.


key: mixins

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


description: agent that modified the element


key: name

description: the unique name of the element within the context of the schema.  Name is combined with the default prefix to form the globally unique subject of the target class.


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


description: A list of possible values for a slot range


Defines the specific formula to be used to generate the permissible values.


key: rank

description: 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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


description:
Used on a slot that stores the string serialization of the containing object. The syntax follows python formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.
We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the expansion.
Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of complex objects
For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of string_value shouldd be 2cm


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


description: The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot. Note: this is different than 'subproperty_of' in that 'subproperty_of' is intended to be a single ontology term while 'values_from' is the identifier of an entire value set.  Additionally, this is different than an enumeration in that in an enumeration, the values of the enumeration are listed directly in the model itself. Setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.


description: an element whose instances must be drawn from a specified set of permissible values


key: abstract

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


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.


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


key: categories

description: Controlled terms used to categorize an element.


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


description: the identifier of an enumeration code set.


description: the version tag of the enumeration code set


description: the version identifier of the enumeration code set


key: comments

description: notes and comments about an element intended primarily for external consumption


key: concepts

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


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix


key: implements

description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element.


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


description: the primary language used in the sources


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


key: include

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


key: inherits

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


key: instantiates

description: An element in another schema which this element instantiates.


description: A primary parent class or slot from which inheritable metaslots are propagated from. While multiple inheritance is not allowed, mixins can be provided effectively providing the same thing. The semantics are the same when translated to formalisms that allow MI (e.g. RDFS/OWL). When translating to a SI framework (e.g. java classes, python classes) then is a is used. When translating a framework without polymorphism (e.g. json-schema, solr document schema) then is a and mixins are recursively unfolded


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


description: a name assigned to an element in a given ontology


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


key: matches

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


key: minus

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


key: mixin

description: Indicates the class or slot is intended to be inherited from without being an is_a parent. mixins should not be inherited from using is_a, except by other mixins.


key: mixins

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


description: agent that modified the element


key: name

description: the unique name of the element within the context of the schema.  Name is combined with the default prefix to form the globally unique subject of the target class.


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


description: A list of possible values for a slot range


Defines the specific formula to be used to generate the permissible values.


key: rank

description: 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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


description:
Used on a slot that stores the string serialization of the containing object. The syntax follows python formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.
We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the expansion.
Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of complex objects
For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of string_value shouldd be 2cm


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


description: The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot. Note: this is different than 'subproperty_of' in that 'subproperty_of' is intended to be a single ontology term while 'values_from' is the identifier of an entire value set.  Additionally, this is different than an enumeration in that in an enumeration, the values of the enumeration are listed directly in the model itself. Setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.


key: EnumExpression

description: An expression that constrains the range of a slot


description: the identifier of an enumeration code set.


description: the version tag of the enumeration code set


description: the version identifier of the enumeration code set


key: concepts

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


key: include

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


key: inherits

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


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


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


description: A list of possible values for a slot range


Defines the specific formula to be used to generate the permissible values.


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


key: Example

description: usage example and description


key: description

description: description of what the value is doing


key: object

description: direct object representation of the example


key: value

description: example value


key: Extension

description: a tag/value pair used to add non-model information to an entry


key: extensions

description: a tag/text tuple attached to an arbitrary element


key: tag

description: a tag associated with an extension


description: the actual annotation


key: ImportExpression

description: an expression describing an import


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


description: a textual description of the element's purpose and use


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


key: examples

description: example usages of an element


description: id of the schema that defined the element


description: The value assigned for a setting


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


description: the primary language used in the sources


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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: agent that modified the element


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: rank

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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: LocalName

description: an attributed label


description: the ncname of the source of the name


description: a name assigned to an element in a given ontology


description: an attributed label


key: MatchQuery

description: A query that is used on an enum expression to dynamically obtain a set of permissivle values via a query that matches on properties of the external concepts


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


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


key: PathExpression

description: An expression that describes an abstract path from an object to another through a sequence of slot lookups


key: aliases

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


description: holds if all of the expressions hold


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: holds if at least one of the expressions hold


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


description: holds if only one of the expressions hold


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


in a sequential list, this indicates the next member


description: id of the schema that defined the element


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


description: the primary language used in the sources


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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: agent that modified the element


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


description: holds if none of the expressions hold


key: notes

description: editorial notes about an element intended primarily for internal consumption


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


key: rank

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


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


key: reversed

description: true if the slot is to be inversed


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: traverse

description: the slot to traverse


key: PatternExpression

description: a regular expression pattern used to evaluate conformance of a string


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


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


description: the primary language used in the sources


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


key: interpolated

description: if true then the pattern is first string interpolated


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: agent that modified the element


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


description: if true then the pattern must match the whole string, as if enclosed in ^...$


key: rank

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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: syntax

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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: PermissibleValue

description: a permissible value, accompanied by intended text and an optional mapping to a concept URI


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


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


description: the primary language used in the sources


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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


key: meaning

description: the value meaning of a permissible value


description: agent that modified the element


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: rank

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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: text

description: The actual permissible value itself


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: unit

description: an encoding of a unit


description: a permissible value, accompanied by intended text and an optional mapping to a concept URI


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


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


key: categories

description: Controlled terms used to categorize an element.


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


key: comments

description: notes and comments about an element intended primarily for external consumption


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


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


description: the primary language used in the sources


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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


key: meaning

description: the value meaning of a permissible value


description: agent that modified the element


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: rank

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


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


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


key: text

description: The actual permissible value itself


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: unit

description: an encoding of a unit


key: Prefix

description: prefix URI tuple


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


description: The namespace to which a prefix expands to.


description: prefix URI tuple


key: PresenceEnum

description: enumeration of conditions by which a slot value should be set

enum: UNCOMMITTED PRESENT ABSENT


key: PvFormulaOptions

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

enum: CODE CURIE URI FHIR_CODING


key: ReachabilityQuery

description: A query that is used on an enum expression to dynamically obtain a set of permissible values via walking from a set of source nodes to a set of descendants or ancestors over a set of relationship types


description: True if the query is reflexive


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


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


description: A list of nodes that are used in the reachability query


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


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


key: RelationalRoleEnum

description: enumeration of roles a slot on a relationship class can play


key: SchemaDefinition

description: A collection of definitions that make up a schema or a data model.

required: id name


key: aliases

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


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


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


key: categories

description: Controlled terms used to categorize an element.


key: classes

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


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


key: comments

description: notes and comments about an element intended primarily for external consumption


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


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


description: The prefix that is used for all elements within a schema


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


description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


key: enums

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


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


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


description: date and time that the schema was loaded/generated


key: id

description: The official schema URI


description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix


key: implements

description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element.


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


key: imports

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


description: the primary language used in the sources


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


key: instantiates

description: An element in another schema which this element instantiates.


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


key: license

description: license for the schema


key: additionalProperties

description: a name assigned to an element in a given ontology


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: Version of the metamodel used to load the schema


description: agent that modified the element


key: name

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


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


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: prefixes

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


description: The namespace to which a prefix expands to.


key: rank

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


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


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


key: settings

description: A collection of global variable settings


description: The value assigned for a setting


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


key: slots

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


key: source

description: A related resource from which the element is derived.


description: name, uri or description of the source of the schema


description: modification date of the source of the schema


description: size in bytes of the source of the schema


key: status

description: status of the element


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


key: subsets

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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: types

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


key: version

description: particular version of schema


key: Setting

description: assignment of a key to a value


description: the variable name for a setting


description: The value assigned for a setting


description: assignment of a key to a value


key: SlotDefinition

description: an element that describes how instances are related to other instances


key: abstract

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


key: alias

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


key: aliases

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


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


description: holds if all of the expressions hold


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: holds if at least one of the expressions hold


description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.


key: asymmetric

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


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


key: categories

description: Controlled terms used to categorize an element.


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


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


key: comments

description: notes and comments about an element intended primarily for external consumption


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created


description: The native URI of the element. This is always within the namespace of the containing schema. Contrast with the assigned URI, via class_uri or slot_uri


key: deprecated

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


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


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


key: description

description: a textual description of the element's purpose and use


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


description: Two classes are disjoint if they have no instances in common, two slots are disjoint if they can never hold between the same two instances


key: domain

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

implicitly asserts that X is an instance of C1


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


An inlined enumeration


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


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


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


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


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


description: holds if only one of the expressions hold


key: examples

description: example usages of an element


key: extensions

description: a tag/text tuple attached to an arbitrary element


description: id of the schema that defined the element


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


description: An allowed list of prefixes for which identifiers must conform. The identifier of this class or slot must begin with the URIs referenced by this prefix


key: identifier

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


key: ifabsent

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


key: implements

description: An element in another schema which this element conforms to. The referenced element is not imported into the schema for the implementing element. However, the referenced schema may be used to check conformance of the implementing element.


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


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


description: the primary language used in the sources


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


key: inherited

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


key: inlined

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


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


key: instantiates

description: An element in another schema which this element instantiates.


key: inverse

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


key: irreflexive

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


description: A primary parent slot from which inheritable metaslots are propagated


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


description: true if this slot is a grouping slot


description: True means that this slot was defined in a slot_usage situation


key: key

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


key: keywords

description: Keywords or tags used to describe the element


description: time at which the element was last updated


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


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


key: additionalProperties

description: a name assigned to an element in a given ontology


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


key: mappings

description: A list of terms from different schemas or terminology systems that have comparable meaning. These may include terms that are precisely equivalent, broader or narrower in meaning, or otherwise semantically related but not equivalent from a strict ontological perspective.


description: the maximum number of entries for a multivalued slot


description: for slots with ranges of type number, the value must be equal to or lowe than this


description: the minimum number of entries for a multivalued slot


description: for slots with ranges of type number, the value must be equal to or higher than this


key: mixin

description: Indicates the class or slot is intended to be inherited from without being an is_a parent. mixins should not be inherited from using is_a, except by other mixins.


key: mixins

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


description: agent that modified the element


key: multivalued

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


key: name

description: the unique name of the element within the context of the schema.  Name is combined with the default prefix to form the globally unique subject of the target class.


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


description: holds if none of the expressions hold


key: notes

description: editorial notes about an element intended primarily for internal consumption


key: owner

description: 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


key: pattern

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


key: range

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

implicitly asserts Y is an instance of C2


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


key: rank

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


key: readonly

description: If present, slot is read only.  Text explains why


key: recommended

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


key: reflexive

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


description: transitive_form_of including the reflexive case


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


the role a slot on a relationship class plays, for example, the subject, object or predicate roles


key: required

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


key: role

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


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


key: shared

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


description: a name that is used in the singular form


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


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


key: source

description: A related resource from which the element is derived.


key: status

description: status of the element


description:
Used on a slot that stores the string serialization of the containing object. The syntax follows python formatted strings, with slot names enclosed in {}s. These are expanded using the values of those slots.
We call the slot with the serialization the s-slot, the slots used in the {}s are v-slots. If both s-slots and v-slots are populated on an object then the value of the s-slot should correspond to the expansion.
Implementations of frameworks may choose to use this property to either (a) PARSE: implement automated normalizations by parsing denormalized strings into complex objects (b) GENERARE: implement automated to_string labeling of complex objects
For example, a Measurement class may have 3 fields: unit, value, and string_value. The string_value slot may have a string_serialization of {value}{unit} such that if unit=cm and value=2, the value of string_value shouldd be 2cm


description: 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


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


key: symmetric

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


key: title

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


key: todos

description: Outstanding issues that needs resolution


key: transitive

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


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


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


key: unit

description: an encoding of a unit


description: The name of the slot referenced in the slot_usage


if true then a value must be present (for lists there must be at least one value). If false then a value must be absent (for lists, must be empty)


description: The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot. Note: this is different than 'subproperty_of' in that 'subproperty_of' is intended to be a single ontology term while 'values_from' is the identifier of an entire value set.  Additionally, this is different than an enumeration in that in an enumeration, the values of the enumeration are listed directly in the model itself. Setting this property on a slot does not guarantee an expansion of the ontological hierarchy into an enumerated list of possible values in every serialization of the model.


description: an element that describes how instances are related to other instances


key: abstract

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


key: alias

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


key: aliases

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


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


description: holds if all of the expressions hold


description: A sourced alternative description for an element


key: additionalProperties

description: text of an attributed description


key: annotations

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


description: holds if at least one of the expressions hold


description: Used to extend class or slot definitions. For example, if we have a core schema where a gene has two slots for identifier and symbol, and we have a specialized schema for my_organism where we wish to add a slot systematic_name, we can avoid subclassing by defining a class gene_my_organism, adding the slot to this class, and then adding an apply_to pointing to the gene class. The new slot will be 'injected into' the gene class.


key: asymmetric

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


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


key: categories

description: Controlled terms used to categorize an element.


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


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


key: comments

description: notes and comments about an element intended primarily for external consumption


description: An established standard to which the element conforms.


key: contributors

description: agent that contributed to the element


description: agent that created the element


description: time at which the element was created