diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 00000000..49c69fdd --- /dev/null +++ b/docs/404.html @@ -0,0 +1,131 @@ + + + + + + + + + + + + LinkML Model + + + + + + + + + + + + + + +
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404

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Page not found

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+ + + + + + + + diff --git a/docs/AltDescription/index.html b/docs/AltDescription/index.html new file mode 100644 index 00000000..66a114e6 --- /dev/null +++ b/docs/AltDescription/index.html @@ -0,0 +1,157 @@ + + + + + + + + + + + + Class: alt_description - LinkML Model + + + + + + + + + + + + + + + + +
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  • Class: alt_description
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Class: alt_description

+

an attributed description

+

URI: linkml:AltDescription

+

img

+

Referenced by class

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Attributes

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Own

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+ + + + + + + + diff --git a/docs/Annotatable/index.html b/docs/Annotatable/index.html new file mode 100644 index 00000000..7bd80465 --- /dev/null +++ b/docs/Annotatable/index.html @@ -0,0 +1,156 @@ + + + + + + + + + + + + Class: annotatable - LinkML Model + + + + + + + + + + + + + + + + +
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  • Class: annotatable
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Class: annotatable

+

mixin for classes that support annotations

+

URI: linkml:Annotatable

+

img

+

Mixin for

+
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  • Annotation (mixin) - a tag/value pair with the semantics of OWL Annotation
    • +
  • Element (mixin) - a named element in the model
    • +
  • PermissibleValue (mixin) - a permissible value, accompanied by intended text and an optional mapping to a concept URI
    • +
  • UniqueKey (mixin) - a collection of slots whose values uniquely identify an instance of a class
    • +
+

Referenced by class

+

Attributes

+

Own

+
    +
  • annotations 0..*
      +
    • Description: a collection of tag/text tuples with the semantics of OWL Annotation
      • +
    • Range: Annotation
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+ + + + + + + + diff --git a/docs/Annotation/index.html b/docs/Annotation/index.html new file mode 100644 index 00000000..11c9c41d --- /dev/null +++ b/docs/Annotation/index.html @@ -0,0 +1,178 @@ + + + + + + + + + + + + Class: annotation - LinkML Model + + + + + + + + + + + + + + + + +
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  • Class: annotation
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Class: annotation

+

a tag/value pair with the semantics of OWL Annotation

+

URI: linkml:Annotation

+

img

+

Parents

+
    +
  • is_a: Extension - a tag/value pair used to add non-model information to an entry
    • +
+

Uses Mixins

+
    +
  • mixin: Annotatable - mixin for classes that support annotations
    • +
+

Referenced by class

+ +

Attributes

+

Own

+
    +
  • annotations 0..*
      +
    • Description: a collection of tag/text tuples with the semantics of OWL Annotation
      • +
    • Range: Annotation
      • +
    +
    • +
+

Inherited from extension:

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+ + + + + + + + diff --git a/docs/Boolean/index.html b/docs/Boolean/index.html new file mode 100644 index 00000000..71803528 --- /dev/null +++ b/docs/Boolean/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: boolean - LinkML Model + + + + + + + + + + + + + + + + +
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  • Type: boolean
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Type: boolean

+

A binary (true or false) value

+

URI: linkml:Boolean

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeBool
Representationbool
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+ + + + + + + + diff --git a/docs/ClassDefinition/index.html b/docs/ClassDefinition/index.html new file mode 100644 index 00000000..ed4169f3 --- /dev/null +++ b/docs/ClassDefinition/index.html @@ -0,0 +1,357 @@ + + + + + + + + + + + + Class: class_definition - LinkML Model + + + + + + + + + + + + + + + + +
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  • Class: class_definition
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Class: class_definition

+

the definition of a class or interface

+

URI: linkml:ClassDefinition

+

img

+

Parents

+ +

Referenced by class

+ +

Attributes

+

Own

+ +

Inherited from definition:

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
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    +
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  • id_prefixes 0..*
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    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
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  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
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    +
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  • aliases 0..* +
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  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
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    +
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  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
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  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
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    +
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  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
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  • abstract 0..1
      +
    • Description: an abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.
      • +
    • Range: Boolean
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  • mixin 0..1
      +
    • Description: this slot or class can only be used as a mixin.
      • +
    • Range: Boolean
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  • values_from 0..*
      +
    • Description: the identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
      • +
    • Range: Uriorcurie
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    +
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  • created_by 0..1
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    • Description: agent that created the element
      • +
    • Range: Uriorcurie
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    +
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  • created_on 0..1
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    • Description: time at which the element was created
      • +
    • Range: Datetime
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  • last_updated_on 0..1
      +
    • Description: time at which the element was last updated
      • +
    • Range: Datetime
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  • modified_by 0..1
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    • Description: agent that modified the element
      • +
    • Range: Uriorcurie
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  • status 0..1
      +
    • Description: status of the element
      • +
    • Range: Uriorcurie
      • +
    • Example: bibo:draft None
      • +
    +
    • +
  • string_serialization 0..1
      +
    • 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
      • +
    • Range: String
      • +
    +
    • +
+

Other properties

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Aliases:table
record
template
message
observation
Close Mappings:owl:Class
+ +
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+ + + + + + + + diff --git a/docs/CommonMetadata/index.html b/docs/CommonMetadata/index.html new file mode 100644 index 00000000..442b2847 --- /dev/null +++ b/docs/CommonMetadata/index.html @@ -0,0 +1,218 @@ + + + + + + + + + + + + Class: common_metadata - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Class: common_metadata
    • +
  • + +
    • +
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+
+ +

Class: common_metadata

+

Generic metadata shared across definitions

+

URI: linkml:CommonMetadata

+

img

+

Mixin for

+
    +
  • Element (mixin) - a named element in the model
    • +
  • PermissibleValue (mixin) - a permissible value, accompanied by intended text and an optional mapping to a concept URI
    • +
+

Referenced by class

+

Attributes

+

Own

+
    +
  • description 0..1
      +
    • Description: a description of the element's purpose and use
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • alt_descriptions 0..* +
    • +
  • deprecated 0..1
      +
    • Description: Description of why and when this element will no longer be used
      • +
    • Range: String
      • +
    +
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  • todos 0..*
      +
    • Description: Outstanding issue that needs resolution
      • +
    • Range: String
      • +
    +
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  • notes 0..*
      +
    • Description: editorial notes about an element intended for internal consumption
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • comments 0..*
      +
    • Description: notes and comments about an element intended for external consumption
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
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  • examples 0..*
      +
    • Description: example usages of an element
      • +
    • Range: Example
      • +
    • in subsets: (owl)
      • +
    +
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  • in_subset 0..*
      +
    • Description: used to indicate membership of a term in a defined subset of terms used for a particular domain or application (e.g. the translator_minimal subset holding the minimal set of predicates used in a translator knowledge graph)
      • +
    • Range: SubsetDefinition
      • +
    +
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  • from_schema 0..1
      +
    • Description: id of the schema that defined the element
      • +
    • Range: Uri
      • +
    +
    • +
  • imported_from 0..1
      +
    • Description: the imports entry that this element was derived from. Empty means primary source
      • +
    • Range: String
      • +
    +
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  • see_also 0..*
      +
    • Description: a reference
      • +
    • Range: Uriorcurie
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • deprecated element has exact replacement 0..1
      +
    • Description: When an element is deprecated, it can be automatically replaced by this uri or curie
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • deprecated element has possible replacement 0..1
      +
    • Description: When an element is deprecated, it can be potentially replaced by this uri or curie
      • +
    • Range: Uriorcurie
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+ + + + + + + + diff --git a/docs/Date/index.html b/docs/Date/index.html new file mode 100644 index 00000000..4900fa81 --- /dev/null +++ b/docs/Date/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: date - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Type: date
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: date

+

a date (year, month and day) in an idealized calendar

+

URI: linkml:Date

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeXSDDate
Representationstr
+ +
+
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+
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+ + + + + + + + diff --git a/docs/Datetime/index.html b/docs/Datetime/index.html new file mode 100644 index 00000000..f90d9da6 --- /dev/null +++ b/docs/Datetime/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: datetime - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Type: datetime
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: datetime

+

The combination of a date and time

+

URI: linkml:Datetime

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeXSDDateTime
Representationstr
+ +
+
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+
+ +
+ +
+ +
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+ + + + + + + + diff --git a/docs/Decimal/index.html b/docs/Decimal/index.html new file mode 100644 index 00000000..5b7d2e0e --- /dev/null +++ b/docs/Decimal/index.html @@ -0,0 +1,154 @@ + + + + + + + + + + + + Type: decimal - LinkML Model + + + + + + + + + + + + + + + + +
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    • + + + +
  • Type: decimal
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: decimal

+

A real number with arbitrary precision that conforms to the xsd:decimal specification

+

URI: linkml:Decimal

+ + + + + + + + + + + + + + + +
Root (builtin) typeDecimal
+ +
+
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+ + + + + + + + diff --git a/docs/Definition/index.html b/docs/Definition/index.html new file mode 100644 index 00000000..49d28629 --- /dev/null +++ b/docs/Definition/index.html @@ -0,0 +1,297 @@ + + + + + + + + + + + + Class: definition - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Docs »
    • + + + +
  • Class: definition
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: definition

+

base class for definitions

+

URI: linkml:Definition

+

img

+

Parents

+
    +
  • is_a: Element - a named element in the model
    • +
+

Children

+ +

Referenced by class

+ +

Attributes

+

Own

+
    +
  • is_a 0..1
      +
    • Description: specifies single-inheritance between classes or slots. 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
      • +
    • Range: Definition
      • +
    +
    • +
  • abstract 0..1
      +
    • Description: an abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.
      • +
    • Range: Boolean
      • +
    +
    • +
  • mixin 0..1
      +
    • Description: this slot or class can only be used as a mixin.
      • +
    • Range: Boolean
      • +
    +
    • +
  • mixins 0..*
      +
    • Description: List of definitions to be mixed in. Targets may be any definition of the same type
      • +
    • Range: Definition
      • +
    +
    • +
  • apply_to 0..*
      +
    • 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.
      • +
    • Range: Definition
      • +
    +
    • +
  • values_from 0..*
      +
    • Description: the identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • created_by 0..1
      +
    • Description: agent that created the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • created_on 0..1
      +
    • Description: time at which the element was created
      • +
    • Range: Datetime
      • +
    +
    • +
  • last_updated_on 0..1
      +
    • Description: time at which the element was last updated
      • +
    • Range: Datetime
      • +
    +
    • +
  • modified_by 0..1
      +
    • Description: agent that modified the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • status 0..1
      +
    • Description: status of the element
      • +
    • Range: Uriorcurie
      • +
    • Example: bibo:draft None
      • +
    +
    • +
  • string_serialization 0..1
      +
    • 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
      • +
    • Range: String
      • +
    +
    • +
+

Inherited from element:

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
+

Other properties

+ + + + + + + + + + + + + + + +
See also:https://en.wikipedia.org/wiki/Data_element_definition
+ +
+
+ + +
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+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Double/index.html b/docs/Double/index.html new file mode 100644 index 00000000..3f1d9050 --- /dev/null +++ b/docs/Double/index.html @@ -0,0 +1,154 @@ + + + + + + + + + + + + Type: double - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Docs »
    • + + + +
  • Type: double
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: double

+

A real number that conforms to the xsd:double specification

+

URI: linkml:Double

+ + + + + + + + + + + + + + + +
Root (builtin) typefloat
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Element/index.html b/docs/Element/index.html new file mode 100644 index 00000000..e546abf2 --- /dev/null +++ b/docs/Element/index.html @@ -0,0 +1,356 @@ + + + + + + + + + + + + Class: element - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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+
+
    +
  • Docs »
    • + + + +
  • Class: element
    • +
  • + +
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+ +
+
+ +
+
+ +

Class: element

+

a named element in the model

+

URI: linkml:Element

+

img

+

Uses Mixins

+
    +
  • mixin: Extensible - mixin for classes that support extension
    • +
  • mixin: Annotatable - mixin for classes that support annotations
    • +
  • mixin: CommonMetadata - Generic metadata shared across definitions
    • +
+

Children

+ +

Referenced by class

+ +

Attributes

+

Own

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
+

Mixed in from extensible:

+
    +
  • extensions 0..*
      +
    • Description: a tag/text tuple attached to an arbitrary element
      • +
    • Range: Extension
      • +
    +
    • +
+

Mixed in from annotatable:

+
    +
  • annotations 0..*
      +
    • Description: a collection of tag/text tuples with the semantics of OWL Annotation
      • +
    • Range: Annotation
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • description 0..1
      +
    • Description: a description of the element's purpose and use
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+ +

Mixed in from common_metadata:

+
    +
  • deprecated 0..1
      +
    • Description: Description of why and when this element will no longer be used
      • +
    • Range: String
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • todos 0..*
      +
    • Description: Outstanding issue that needs resolution
      • +
    • Range: String
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • notes 0..*
      +
    • Description: editorial notes about an element intended for internal consumption
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • comments 0..*
      +
    • Description: notes and comments about an element intended for external consumption
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • examples 0..*
      +
    • Description: example usages of an element
      • +
    • Range: Example
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • in_subset 0..*
      +
    • Description: used to indicate membership of a term in a defined subset of terms used for a particular domain or application (e.g. the translator_minimal subset holding the minimal set of predicates used in a translator knowledge graph)
      • +
    • Range: SubsetDefinition
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • from_schema 0..1
      +
    • Description: id of the schema that defined the element
      • +
    • Range: Uri
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • imported_from 0..1
      +
    • Description: the imports entry that this element was derived from. Empty means primary source
      • +
    • Range: String
      • +
    +
    • +
+

Mixed in from common_metadata:

+ +

Mixed in from common_metadata:

+ +

Mixed in from common_metadata:

+ +

Other properties

+ + + + + + + + + + + + + + + +
See also:https://en.wikipedia.org/wiki/Data_element
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/EnumDefinition/index.html b/docs/EnumDefinition/index.html new file mode 100644 index 00000000..1da77ac9 --- /dev/null +++ b/docs/EnumDefinition/index.html @@ -0,0 +1,233 @@ + + + + + + + + + + + + Class: enum_definition - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: enum_definition
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: enum_definition

+

List of values that constrain the range of a slot

+

URI: linkml:EnumDefinition

+

img

+

Parents

+
    +
  • is_a: Element - a named element in the model
    • +
+

Referenced by class

+ +

Attributes

+

Own

+ +

Inherited from element:

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Example/index.html b/docs/Example/index.html new file mode 100644 index 00000000..fd7047ab --- /dev/null +++ b/docs/Example/index.html @@ -0,0 +1,157 @@ + + + + + + + + + + + + Class: example - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: example
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: example

+

usage example and description

+

URI: linkml:Example

+

img

+

Referenced by class

+ +

Attributes

+

Own

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Extensible/index.html b/docs/Extensible/index.html new file mode 100644 index 00000000..8b8655e3 --- /dev/null +++ b/docs/Extensible/index.html @@ -0,0 +1,155 @@ + + + + + + + + + + + + Class: extensible - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: extensible
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: extensible

+

mixin for classes that support extension

+

URI: linkml:Extensible

+

img

+

Mixin for

+
    +
  • Element (mixin) - a named element in the model
    • +
  • PermissibleValue (mixin) - a permissible value, accompanied by intended text and an optional mapping to a concept URI
    • +
  • UniqueKey (mixin) - a collection of slots whose values uniquely identify an instance of a class
    • +
+

Referenced by class

+

Attributes

+

Own

+
    +
  • extensions 0..*
      +
    • Description: a tag/text tuple attached to an arbitrary element
      • +
    • Range: Extension
      • +
    +
    • +
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Extension/index.html b/docs/Extension/index.html new file mode 100644 index 00000000..c64ab81a --- /dev/null +++ b/docs/Extension/index.html @@ -0,0 +1,166 @@ + + + + + + + + + + + + Class: extension - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: extension
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: extension

+

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

+

URI: linkml:Extension

+

img

+

Children

+
    +
  • Annotation - a tag/value pair with the semantics of OWL Annotation
    • +
+

Referenced by class

+ +

Attributes

+

Own

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Float/index.html b/docs/Float/index.html new file mode 100644 index 00000000..966d8f3e --- /dev/null +++ b/docs/Float/index.html @@ -0,0 +1,154 @@ + + + + + + + + + + + + Type: float - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: float
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: float

+

A real number that conforms to the xsd:float specification

+

URI: linkml:Float

+ + + + + + + + + + + + + + + +
Root (builtin) typefloat
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Integer/index.html b/docs/Integer/index.html new file mode 100644 index 00000000..780f8d1f --- /dev/null +++ b/docs/Integer/index.html @@ -0,0 +1,154 @@ + + + + + + + + + + + + Type: integer - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: integer
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: integer

+

An integer

+

URI: linkml:Integer

+ + + + + + + + + + + + + + + +
Root (builtin) typeint
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/LocalName/index.html b/docs/LocalName/index.html new file mode 100644 index 00000000..4b39e417 --- /dev/null +++ b/docs/LocalName/index.html @@ -0,0 +1,157 @@ + + + + + + + + + + + + Class: local_name - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: local_name
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: local_name

+

an attributed label

+

URI: linkml:LocalName

+

img

+

Referenced by class

+ +

Attributes

+

Own

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Ncname/index.html b/docs/Ncname/index.html new file mode 100644 index 00000000..8e9b9944 --- /dev/null +++ b/docs/Ncname/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: ncname - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: ncname
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: ncname

+

Prefix part of CURIE

+

URI: linkml:Ncname

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeNCName
Representationstr
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Nodeidentifier/index.html b/docs/Nodeidentifier/index.html new file mode 100644 index 00000000..7aeb6cfd --- /dev/null +++ b/docs/Nodeidentifier/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: nodeidentifier - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: nodeidentifier
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: nodeidentifier

+

A URI, CURIE or BNODE that represents a node in a model.

+

URI: linkml:Nodeidentifier

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeNodeIdentifier
Representationstr
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Objectidentifier/index.html b/docs/Objectidentifier/index.html new file mode 100644 index 00000000..76449301 --- /dev/null +++ b/docs/Objectidentifier/index.html @@ -0,0 +1,176 @@ + + + + + + + + + + + + Type: objectidentifier - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: objectidentifier
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: objectidentifier

+

A URI or CURIE that represents an object in the model.

+

URI: linkml:Objectidentifier

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeElementIdentifier
Representationstr
+

Other properties

+ + + + + + + + + + + + + + + +
Comments:Used for inheritence and type checking
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Owl/index.html b/docs/Owl/index.html new file mode 100644 index 00000000..d2916473 --- /dev/null +++ b/docs/Owl/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Subset: owl - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Subset: owl
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Subset: owl

+

Set of slots that appear in the OWL representation of a model

+

URI: linkml:owl

+

Classes

+

Mixins

+

Slots

+
    +
  • comments - notes and comments about an element intended for external consumption
    • +
  • description - a description of the element's purpose and use
    • +
  • examples - example usages of an element
    • +
  • generation_date - date and time that the schema was loaded/generated
    • +
  • license - license for the schema
    • +
  • metamodel_version - Version of the metamodel used to load the schema
    • +
  • name - 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.
    • +
  • notes - editorial notes about an element intended for internal consumption
    • +
  • see_also - a reference
    • +
  • source_file - name, uri or description of the source of the schema
    • +
  • source_file_date - modification date of the source of the schema
    • +
  • source_file_size - size in bytes of the source of the schema
    • +
  • title - the official title of the schema
    • +
  • version - particular version of schema
    • +
+

Types

+

Enums

+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/PermissibleValue/index.html b/docs/PermissibleValue/index.html new file mode 100644 index 00000000..cf967af5 --- /dev/null +++ b/docs/PermissibleValue/index.html @@ -0,0 +1,293 @@ + + + + + + + + + + + + Class: permissible_value - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: permissible_value
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: permissible_value

+

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

+

URI: linkml:PermissibleValue

+

img

+

Uses Mixins

+
    +
  • mixin: Extensible - mixin for classes that support extension
    • +
  • mixin: Annotatable - mixin for classes that support annotations
    • +
  • mixin: CommonMetadata - Generic metadata shared across definitions
    • +
+

Referenced by class

+ +

Attributes

+

Own

+ +

Mixed in from extensible:

+
    +
  • extensions 0..*
      +
    • Description: a tag/text tuple attached to an arbitrary element
      • +
    • Range: Extension
      • +
    +
    • +
+

Mixed in from annotatable:

+
    +
  • annotations 0..*
      +
    • Description: a collection of tag/text tuples with the semantics of OWL Annotation
      • +
    • Range: Annotation
      • +
    +
    • +
+

Mixed in from common_metadata:

+ +

Mixed in from common_metadata:

+
    +
  • deprecated 0..1
      +
    • Description: Description of why and when this element will no longer be used
      • +
    • Range: String
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • todos 0..*
      +
    • Description: Outstanding issue that needs resolution
      • +
    • Range: String
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • notes 0..*
      +
    • Description: editorial notes about an element intended for internal consumption
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • comments 0..*
      +
    • Description: notes and comments about an element intended for external consumption
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • examples 0..*
      +
    • Description: example usages of an element
      • +
    • Range: Example
      • +
    • in subsets: (owl)
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • in_subset 0..*
      +
    • Description: used to indicate membership of a term in a defined subset of terms used for a particular domain or application (e.g. the translator_minimal subset holding the minimal set of predicates used in a translator knowledge graph)
      • +
    • Range: SubsetDefinition
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • from_schema 0..1
      +
    • Description: id of the schema that defined the element
      • +
    • Range: Uri
      • +
    +
    • +
+

Mixed in from common_metadata:

+
    +
  • imported_from 0..1
      +
    • Description: the imports entry that this element was derived from. Empty means primary source
      • +
    • Range: String
      • +
    +
    • +
+

Mixed in from common_metadata:

+ +

Mixed in from common_metadata:

+ +

Mixed in from common_metadata:

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Prefix/index.html b/docs/Prefix/index.html new file mode 100644 index 00000000..97442247 --- /dev/null +++ b/docs/Prefix/index.html @@ -0,0 +1,157 @@ + + + + + + + + + + + + Class: prefix - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: prefix
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: prefix

+

prefix URI tuple

+

URI: linkml:Prefix

+

img

+

Referenced by class

+ +

Attributes

+

Own

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/SchemaDefinition/index.html b/docs/SchemaDefinition/index.html new file mode 100644 index 00000000..1166edd6 --- /dev/null +++ b/docs/SchemaDefinition/index.html @@ -0,0 +1,333 @@ + + + + + + + + + + + + Class: schema_definition - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: schema_definition
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: schema_definition

+

a collection of subset, type, slot and class definitions

+

URI: linkml:SchemaDefinition

+

img

+

Parents

+
    +
  • is_a: Element - a named element in the model
    • +
+

Referenced by class

+

Attributes

+

Own

+
    +
  • id 1..1
      +
    • Description: The official schema URI
      • +
    • Range: Uri
      • +
    +
    • +
  • title 0..1
      +
    • Description: the official title of the schema
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • version 0..1
      +
    • Description: particular version of schema
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • imports 0..*
      +
    • Description: other schemas that are included in this schema
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • license 0..1
      +
    • Description: license for the schema
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • prefixes 0..*
      +
    • Description: prefix / URI definitions to be added to the context beyond those fetched from prefixcommons in id prefixes
      • +
    • Range: Prefix
      • +
    +
    • +
  • emit_prefixes 0..*
      +
    • 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.
      • +
    • Range: Ncname
      • +
    +
    • +
  • default_curi_maps 0..*
      +
    • Description: ordered list of prefixcommon biocontexts to be fetched to resolve id prefixes and inline prefix variables
      • +
    • Range: String
      • +
    +
    • +
  • default_prefix 0..1
      +
    • Description: default and base prefix -- used for ':' identifiers, @base and @vocab
      • +
    • Range: String
      • +
    +
    • +
  • default_range 0..1
      +
    • Description: default slot range to be used if range element is omitted from a slot definition
      • +
    • Range: TypeDefinition
      • +
    +
    • +
  • subsets 0..*
      +
    • Description: list of subsets referenced in this model
      • +
    • Range: SubsetDefinition
      • +
    +
    • +
  • types 0..* +
    • +
  • enums 0..* +
    • +
  • schema_definition➞slots 0..* +
    • +
  • classes 0..* +
    • +
  • metamodel_version 0..1
      +
    • Description: Version of the metamodel used to load the schema
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • source_file 0..1
      +
    • Description: name, uri or description of the source of the schema
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • source_file_date 0..1
      +
    • Description: modification date of the source of the schema
      • +
    • Range: Datetime
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • source_file_size 0..1
      +
    • Description: size in bytes of the source of the schema
      • +
    • Range: Integer
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • generation_date 0..1
      +
    • Description: date and time that the schema was loaded/generated
      • +
    • Range: Datetime
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • schema_definition➞name 1..1 +
    • +
+

Inherited from element:

+
    +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
+

Other properties

+ + + + + + + + + + + + + + + + + + + + +
Aliases:data dictionary
See also:https://en.wikipedia.org/wiki/Data_dictionary
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/SlotDefinition/index.html b/docs/SlotDefinition/index.html new file mode 100644 index 00000000..9ffd6093 --- /dev/null +++ b/docs/SlotDefinition/index.html @@ -0,0 +1,497 @@ + + + + + + + + + + + + Class: slot_definition - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: slot_definition
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: slot_definition

+

the definition of a property or a slot

+

URI: linkml:SlotDefinition

+

img

+

Parents

+ +

Referenced by class

+ +

Attributes

+

Own

+
    +
  • singular_name 0..1
      +
    • Description: a name that is used in the singular form
      • +
    • Range: String
      • +
    +
    • +
  • domain 0..1
      +
    • 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

+
 * Range: [ClassDefinition](ClassDefinition.md)
+
+
    +
  • range 0..1
      +
    • 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

+
 * Range: [Element](Element.md)
+
+
    +
  • slot_uri 0..1
      +
    • Description: predicate of this slot for semantic web application
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • multivalued 0..1
      +
    • Description: true means that slot can have more than one value
      • +
    • Range: Boolean
      • +
    +
    • +
  • inherited 0..1
      +
    • Description: true means that the value of a slot is inherited by subclasses
      • +
    • Range: Boolean
      • +
    +
    • +
  • readonly 0..1
      +
    • Description: If present, slot is read only. Text explains why
      • +
    • Range: String
      • +
    +
    • +
  • ifabsent 0..1
      +
    • Description: function that provides a default value for the slot. Possible values for this slot are defined in biolink.utils.ifabsent_functions.default_library:
      • +
    +
    • +
  • [Tt]rue -- boolean True
    • +
  • [Ff]alse -- boolean False
    • +
  • int(value) -- integer value
    • +
  • str(value) -- string value
    • +
  • default_range -- schema default range
    • +
  • bnode -- blank node identifier
    • +
  • slot_uri -- URI for the slot
    • +
  • class_curie -- CURIE for the containing class
    • +
  • class_uri -- URI for the containing class +
    • +
  • required 0..1
      +
    • Description: true means that the slot must be present in the loaded definition
      • +
    • Range: Boolean
      • +
    +
    • +
  • recommended 0..1
      +
    • Description: true means that the slot should be present in the loaded definition, but this is not required
      • +
    • Range: Boolean
      • +
    +
    • +
  • inlined 0..1
      +
    • 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.
      • +
    • Range: Boolean
      • +
    +
    • +
  • inlined_as_list 0..1
      +
    • 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.
      • +
    • Range: Boolean
      • +
    +
    • +
  • key 0..1
      +
    • Description: True means that the key slot(s) uniquely identify the container.
      • +
    • Range: Boolean
      • +
    +
    • +
  • identifier 0..1
      +
    • Description: True means that the key slot(s) uniquely identify the container. There can be at most one identifier or key per container
      • +
    • Range: Boolean
      • +
    +
    • +
  • designates_type 0..1
      +
    • Description: True means that the key slot(s) is used to determine the instantiation (types) relation between objects and a ClassDefinition
      • +
    • Range: Boolean
      • +
    +
    • +
  • alias 0..1
      +
    • 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.
      • +
    • Range: String
      • +
    +
    • +
  • owner 0..1
      +
    • Description: the "owner" of the slot. It is the class if it appears in the slots list, otherwise the declaring slot
      • +
    • Range: Definition
      • +
    +
    • +
  • domain_of 0..*
      +
    • Description: the class(es) that reference the slot in a "slots" or "slot_usage" context
      • +
    • Range: ClassDefinition
      • +
    +
    • +
  • subproperty_of 0..1
      +
    • Description: Ontology property which this slot is a subproperty of
      • +
    • Range: SlotDefinition
      • +
    +
    • +
  • symmetric 0..1
      +
    • Description: True means that any instance of d s r implies that there is also an instance of r s d
      • +
    • Range: Boolean
      • +
    +
    • +
  • inverse 0..1
      +
    • Description: indicates that any instance of d s r implies that there is also an instance of r s' d
      • +
    • Range: SlotDefinition
      • +
    +
    • +
  • is_class_field 0..1
      +
    • Description: indicates that any instance, i, the domain of this slot will include an assert of i s range
      • +
    • Range: Boolean
      • +
    +
    • +
  • role 0..1
      +
    • Description: the role played by the slot range
      • +
    • Range: String
      • +
    +
    • +
  • is_usage_slot 0..1
      +
    • Description: True means that this slot was defined in a slot_usage situation
      • +
    • Range: Boolean
      • +
    +
    • +
  • usage_slot_name 0..1
      +
    • Description: The name of the slot referenced in the slot_usage
      • +
    • Range: String
      • +
    +
    • +
  • minimum_value 0..1
      +
    • Description: for slots with ranges of type number, the value must be equal to or higher than this
      • +
    • Range: Integer
      • +
    +
    • +
  • maximum_value 0..1
      +
    • Description: for slots with ranges of type number, the value must be equal to or lowe than this
      • +
    • Range: Integer
      • +
    +
    • +
  • pattern 0..1
      +
    • Description: the string value of the slot must conform to this regular expression
      • +
    • Range: String
      • +
    +
    • +
  • slot_definition➞is_a 0..1 +
    • +
  • slot_definition➞mixins 0..* +
    • +
  • slot_definition➞apply_to 0..* +
    • +
+

Inherited from definition:

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • abstract 0..1
      +
    • Description: an abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.
      • +
    • Range: Boolean
      • +
    +
    • +
  • mixin 0..1
      +
    • Description: this slot or class can only be used as a mixin.
      • +
    • Range: Boolean
      • +
    +
    • +
  • values_from 0..*
      +
    • Description: the identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • created_by 0..1
      +
    • Description: agent that created the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • created_on 0..1
      +
    • Description: time at which the element was created
      • +
    • Range: Datetime
      • +
    +
    • +
  • last_updated_on 0..1
      +
    • Description: time at which the element was last updated
      • +
    • Range: Datetime
      • +
    +
    • +
  • modified_by 0..1
      +
    • Description: agent that modified the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • status 0..1
      +
    • Description: status of the element
      • +
    • Range: Uriorcurie
      • +
    • Example: bibo:draft None
      • +
    +
    • +
  • string_serialization 0..1
      +
    • 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
      • +
    • Range: String
      • +
    +
    • +
+

Other properties

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Aliases:slot
field
property
attribute
column
variable
Close Mappings:rdf:Property
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/String/index.html b/docs/String/index.html new file mode 100644 index 00000000..80608e61 --- /dev/null +++ b/docs/String/index.html @@ -0,0 +1,154 @@ + + + + + + + + + + + + Type: string - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: string
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: string

+

A character string

+

URI: linkml:String

+ + + + + + + + + + + + + + + +
Root (builtin) typestr
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/SubsetDefinition/index.html b/docs/SubsetDefinition/index.html new file mode 100644 index 00000000..6bcbf657 --- /dev/null +++ b/docs/SubsetDefinition/index.html @@ -0,0 +1,206 @@ + + + + + + + + + + + + Class: subset_definition - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: subset_definition
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: subset_definition

+

the name and description of a subset

+

URI: linkml:SubsetDefinition

+

img

+

Parents

+
    +
  • is_a: Element - a named element in the model
    • +
+

Referenced by class

+ +

Attributes

+

Inherited from element:

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Time/index.html b/docs/Time/index.html new file mode 100644 index 00000000..9dfbd865 --- /dev/null +++ b/docs/Time/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: time - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: time
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: time

+

A time object represents a (local) time of day, independent of any particular day

+

URI: linkml:Time

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeXSDTime
Representationstr
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/TypeDefinition/index.html b/docs/TypeDefinition/index.html new file mode 100644 index 00000000..0e12af6f --- /dev/null +++ b/docs/TypeDefinition/index.html @@ -0,0 +1,230 @@ + + + + + + + + + + + + Class: type_definition - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: type_definition
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: type_definition

+

A data type definition.

+

URI: linkml:TypeDefinition

+

img

+

Parents

+
    +
  • is_a: Element - a named element in the model
    • +
+

Referenced by class

+ +

Attributes

+

Own

+
    +
  • typeof 0..1 +
    • +
  • base 0..1
      +
    • Description: python base type that implements this type definition
      • +
    • Range: String
      • +
    +
    • +
  • type_definition➞uri 0..1
      +
    • Description: The uri that defines the possible values for the type definition
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • repr 0..1
      +
    • Description: the name of the python object that implements this type definition
      • +
    • Range: String
      • +
    +
    • +
+

Inherited from element:

+
    +
  • name 1..1
      +
    • 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.
      • +
    • Range: String
      • +
    • in subsets: (owl)
      • +
    +
    • +
  • id_prefixes 0..*
      +
    • Description: the identifier of this class or slot must begin with the URIs referenced by this prefix
      • +
    • Range: Ncname
      • +
    +
    • +
  • definition_uri 0..1
      +
    • Description: the "native" URI of the element
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • aliases 0..* +
    • +
  • local_names 0..* +
    • +
  • mappings 0..*
      +
    • 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.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • exact mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • close mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • related mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have related meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • narrow mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
  • broad mappings 0..*
      +
    • Description: A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • Range: Uriorcurie
      • +
    +
    • +
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/UniqueKey/index.html b/docs/UniqueKey/index.html new file mode 100644 index 00000000..a4111565 --- /dev/null +++ b/docs/UniqueKey/index.html @@ -0,0 +1,173 @@ + + + + + + + + + + + + Class: unique_key - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Class: unique_key
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Class: unique_key

+

a collection of slots whose values uniquely identify an instance of a class

+

URI: linkml:UniqueKey

+

img

+

Uses Mixins

+
    +
  • mixin: Extensible - mixin for classes that support extension
    • +
  • mixin: Annotatable - mixin for classes that support annotations
    • +
+

Referenced by class

+ +

Attributes

+

Own

+ +

Mixed in from extensible:

+
    +
  • extensions 0..*
      +
    • Description: a tag/text tuple attached to an arbitrary element
      • +
    • Range: Extension
      • +
    +
    • +
+

Mixed in from annotatable:

+
    +
  • annotations 0..*
      +
    • Description: a collection of tag/text tuples with the semantics of OWL Annotation
      • +
    • Range: Annotation
      • +
    +
    • +
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Uri/index.html b/docs/Uri/index.html new file mode 100644 index 00000000..b7c575ba --- /dev/null +++ b/docs/Uri/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: uri - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: uri
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: uri

+

a complete URI

+

URI: linkml:Uri

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeURI
Representationstr
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/Uriorcurie/index.html b/docs/Uriorcurie/index.html new file mode 100644 index 00000000..462172e9 --- /dev/null +++ b/docs/Uriorcurie/index.html @@ -0,0 +1,159 @@ + + + + + + + + + + + + Type: uriorcurie - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Type: uriorcurie
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Type: uriorcurie

+

a URI or a CURIE

+

URI: linkml:Uriorcurie

+ + + + + + + + + + + + + + + + + + + + +
Root (builtin) typeURIorCURIE
Representationstr
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/abstract/index.html b/docs/abstract/index.html new file mode 100644 index 00000000..232e50e9 --- /dev/null +++ b/docs/abstract/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + Slot: abstract - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: abstract
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: abstract

+

an abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.

+

URI: linkml:abstract

+

Domain and Range

+

Definition → 0..1 Boolean

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/alias/index.html b/docs/alias/index.html new file mode 100644 index 00000000..a2da95ab --- /dev/null +++ b/docs/alias/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: alias - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: alias
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: alias

+

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

+

URI: linkml:alias

+

Domain and Range

+

SlotDefinition → 0..1 String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/aliases/index.html b/docs/aliases/index.html new file mode 100644 index 00000000..ed4a7840 --- /dev/null +++ b/docs/aliases/index.html @@ -0,0 +1,169 @@ + + + + + + + + + + + + Slot: aliases - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: aliases
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: aliases

+

URI: linkml:aliases

+

Domain and Range

+

Element → 0..* String

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:skos:altLabel
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/alt_description_source/index.html b/docs/alt_description_source/index.html new file mode 100644 index 00000000..f9d9d8ec --- /dev/null +++ b/docs/alt_description_source/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: source - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: source
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: source

+

the source of an attributed description

+

URI: linkml:alt_description_source

+

Domain and Range

+

AltDescription → 1..1 String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/alt_description_text/index.html b/docs/alt_description_text/index.html new file mode 100644 index 00000000..c3492382 --- /dev/null +++ b/docs/alt_description_text/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: description - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: description
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: description

+

text of an attributed description

+

URI: linkml:alt_description_text

+

Domain and Range

+

AltDescription → 1..1 String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/alt_descriptions/index.html b/docs/alt_descriptions/index.html new file mode 100644 index 00000000..eb9d2f2c --- /dev/null +++ b/docs/alt_descriptions/index.html @@ -0,0 +1,154 @@ + + + + + + + + + + + + Slot: alt_descriptions - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: alt_descriptions
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: alt_descriptions

+

URI: linkml:alt_descriptions

+

Domain and Range

+

Element → 0..* AltDescription

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/annotations/index.html b/docs/annotations/index.html new file mode 100644 index 00000000..276b2541 --- /dev/null +++ b/docs/annotations/index.html @@ -0,0 +1,160 @@ + + + + + + + + + + + + Slot: annotations - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: annotations
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: annotations

+

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

+

URI: linkml:annotations

+

Domain and Range

+

Annotatable → 0..* Annotation

+

Parents

+ +

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/apply_to/index.html b/docs/apply_to/index.html new file mode 100644 index 00000000..bf328689 --- /dev/null +++ b/docs/apply_to/index.html @@ -0,0 +1,150 @@ + + + + + + + + + + + + Slot: apply_to - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: apply_to
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: apply_to

+

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.

+

URI: linkml:apply_to

+

Domain and Range

+

Definition → 0..* Definition

+

Parents

+

Children

+ +

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/attributes/index.html b/docs/attributes/index.html new file mode 100644 index 00000000..c2b32663 --- /dev/null +++ b/docs/attributes/index.html @@ -0,0 +1,163 @@ + + + + + + + + + + + + Slot: attributes - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: attributes
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: attributes

+

Inline definition of slots

+

URI: linkml:attributes

+

Domain and Range

+

ClassDefinition → 0..* SlotDefinition

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Comments:attributes are an alternative way of defining new slots. An attribute adds a slot to the global space in the form __ (lower case, double underscores). Attributes can be specialized via slot_usage.
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/base/index.html b/docs/base/index.html new file mode 100644 index 00000000..15ad6ef4 --- /dev/null +++ b/docs/base/index.html @@ -0,0 +1,168 @@ + + + + + + + + + + + + Slot: base - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: base
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: base

+

python base type that implements this type definition

+

URI: linkml:base

+

Domain and Range

+

TypeDefinition → 0..1 String

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + + + + + + +
Comments:every root type must have a base
the base is inherited by child types but may be overriden. Base compatibility is not checked.
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/broad_mappings/index.html b/docs/broad_mappings/index.html new file mode 100644 index 00000000..b1f500a2 --- /dev/null +++ b/docs/broad_mappings/index.html @@ -0,0 +1,173 @@ + + + + + + + + + + + + Slot: broad mappings - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: broad mappings
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: broad mappings

+

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

+

URI: linkml:broad_mappings

+

Domain and Range

+

None → 0..* Uriorcurie

+

Parents

+ +

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:skos:broadMatch
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/class_definition_apply_to/index.html b/docs/class_definition_apply_to/index.html new file mode 100644 index 00000000..3aa9a485 --- /dev/null +++ b/docs/class_definition_apply_to/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + Slot: apply_to - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: apply_to
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: apply_to

+

URI: linkml:class_definition_apply_to

+

Domain and Range

+

ClassDefinition → 0..* ClassDefinition

+

Parents

+ +

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/class_definition_is_a/index.html b/docs/class_definition_is_a/index.html new file mode 100644 index 00000000..0c6568c7 --- /dev/null +++ b/docs/class_definition_is_a/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + Slot: is_a - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: is_a
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: is_a

+

URI: linkml:class_definition_is_a

+

Domain and Range

+

ClassDefinition → 0..1 ClassDefinition

+

Parents

+ +

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/class_definition_mixins/index.html b/docs/class_definition_mixins/index.html new file mode 100644 index 00000000..70b6db15 --- /dev/null +++ b/docs/class_definition_mixins/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + Slot: mixins - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: mixins
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: mixins

+

URI: linkml:class_definition_mixins

+

Domain and Range

+

ClassDefinition → 0..* ClassDefinition

+

Parents

+ +

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/class_uri/index.html b/docs/class_uri/index.html new file mode 100644 index 00000000..cd293646 --- /dev/null +++ b/docs/class_uri/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: class_uri - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: class_uri
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: class_uri

+

URI of the class in an RDF environment

+

URI: linkml:class_uri

+

Domain and Range

+

ClassDefinition → 0..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/classes/index.html b/docs/classes/index.html new file mode 100644 index 00000000..ba4add8e --- /dev/null +++ b/docs/classes/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: classes - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: classes
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: classes

+

class definitions

+

URI: linkml:classes

+

Domain and Range

+

SchemaDefinition → 0..* ClassDefinition

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/close_mappings/index.html b/docs/close_mappings/index.html new file mode 100644 index 00000000..9a86bff6 --- /dev/null +++ b/docs/close_mappings/index.html @@ -0,0 +1,173 @@ + + + + + + + + + + + + Slot: close mappings - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: close mappings
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: close mappings

+

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

+

URI: linkml:close_mappings

+

Domain and Range

+

None → 0..* Uriorcurie

+

Parents

+ +

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:skos:closeMatch
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/code_set/index.html b/docs/code_set/index.html new file mode 100644 index 00000000..50e5c048 --- /dev/null +++ b/docs/code_set/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: code_set - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: code_set
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: code_set

+

the identifier of an enumeration code set.

+

URI: linkml:code_set

+

Domain and Range

+

EnumDefinition → 0..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/code_set_tag/index.html b/docs/code_set_tag/index.html new file mode 100644 index 00000000..8c8d1a47 --- /dev/null +++ b/docs/code_set_tag/index.html @@ -0,0 +1,163 @@ + + + + + + + + + + + + Slot: code_set_tag - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: code_set_tag
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: code_set_tag

+

the version tag of the enumeration code set

+

URI: linkml:code_set_tag

+

Domain and Range

+

EnumDefinition → 0..1 String

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Comments:enum_definition cannot have both a code_set_tag and a code_set_version
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/code_set_version/index.html b/docs/code_set_version/index.html new file mode 100644 index 00000000..7d1daa20 --- /dev/null +++ b/docs/code_set_version/index.html @@ -0,0 +1,163 @@ + + + + + + + + + + + + Slot: code_set_version - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: code_set_version
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: code_set_version

+

the version identifier of the enumeration code set

+

URI: linkml:code_set_version

+

Domain and Range

+

EnumDefinition → 0..1 String

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Comments:we assume that version identifiers lexically sort in temporal order. Recommend semver when possible
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/comments/index.html b/docs/comments/index.html new file mode 100644 index 00000000..50aea773 --- /dev/null +++ b/docs/comments/index.html @@ -0,0 +1,177 @@ + + + + + + + + + + + + Slot: comments - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Slot: comments
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Slot: comments

+

notes and comments about an element intended for external consumption

+

URI: linkml:comments

+

Domain and Range

+

Element → 0..* String

+

Parents

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Children

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Used by

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Other properties

+ + + + + + + + + + + + + + + + + + + + +
Mappings:skos:note
In Subsets:owl
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+ + + + + + + + diff --git a/docs/created_by/index.html b/docs/created_by/index.html new file mode 100644 index 00000000..cd4f28c0 --- /dev/null +++ b/docs/created_by/index.html @@ -0,0 +1,165 @@ + + + + + + + + + + + + Slot: created_by - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Slot: created_by
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Slot: created_by

+

agent that created the element

+

URI: linkml:created_by

+

Domain and Range

+

Element → 0..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:pav:createdBy
+ +
+
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+
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+ + + + + + + + diff --git a/docs/created_on/index.html b/docs/created_on/index.html new file mode 100644 index 00000000..73ebbd00 --- /dev/null +++ b/docs/created_on/index.html @@ -0,0 +1,165 @@ + + + + + + + + + + + + Slot: created_on - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
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  • Docs »
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  • Slot: created_on
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+ +
+
+ +
+
+ +

Slot: created_on

+

time at which the element was created

+

URI: linkml:created_on

+

Domain and Range

+

Element → 0..1 Datetime

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:pav:createdOn
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+ + + + + + + + diff --git a/docs/credits/index.html b/docs/credits/index.html new file mode 100644 index 00000000..99f9dd81 --- /dev/null +++ b/docs/credits/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + Credits - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
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  • Docs »
    • + + + +
  • Credits
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Credits

+

this project was made using the Link Model Language (LinkML) framework

+ +
+
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+ +
+ + + + « Previous + + + +
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Mono","Courier New",Courier,monospace;padding:2px 5px}.rst-content tt big,.rst-content tt em,.rst-content tt big,.rst-content code big,.rst-content tt em,.rst-content code em{font-size:100% !important;line-height:normal}.rst-content tt.literal,.rst-content tt.literal,.rst-content code.literal{color:#E74C3C}.rst-content tt.xref,a .rst-content tt,.rst-content tt.xref,.rst-content code.xref,a .rst-content tt,a .rst-content code{font-weight:bold;color:#404040}.rst-content pre,.rst-content kbd,.rst-content samp{font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",Courier,monospace}.rst-content a tt,.rst-content a tt,.rst-content a code{color:#2980B9}.rst-content dl{margin-bottom:24px}.rst-content dl dt{font-weight:bold;margin-bottom:12px}.rst-content dl p,.rst-content dl table,.rst-content dl ul,.rst-content dl ol{margin-bottom:12px !important}.rst-content dl dd{margin:0 0 12px 24px;line-height:24px}.rst-content dl:not(.docutils){margin-bottom:24px}.rst-content dl:not(.docutils) dt{display:table;margin:6px 0;font-size:90%;line-height:normal;background:#e7f2fa;color:#2980B9;border-top:solid 3px #6ab0de;padding:6px;position:relative}.rst-content dl:not(.docutils) dt:before{color:#6ab0de}.rst-content dl:not(.docutils) dt .headerlink{color:#404040;font-size:100% !important}.rst-content dl:not(.docutils) dl dt{margin-bottom:6px;border:none;border-left:solid 3px #ccc;background:#f0f0f0;color:#555}.rst-content dl:not(.docutils) dl dt .headerlink{color:#404040;font-size:100% !important}.rst-content dl:not(.docutils) dt:first-child{margin-top:0}.rst-content dl:not(.docutils) tt,.rst-content dl:not(.docutils) tt,.rst-content dl:not(.docutils) code{font-weight:bold}.rst-content dl:not(.docutils) tt.descname,.rst-content dl:not(.docutils) tt.descclassname,.rst-content dl:not(.docutils) tt.descname,.rst-content dl:not(.docutils) code.descname,.rst-content dl:not(.docutils) tt.descclassname,.rst-content dl:not(.docutils) code.descclassname{background-color:transparent;border:none;padding:0;font-size:100% !important}.rst-content dl:not(.docutils) tt.descname,.rst-content dl:not(.docutils) tt.descname,.rst-content dl:not(.docutils) code.descname{font-weight:bold}.rst-content dl:not(.docutils) .optional{display:inline-block;padding:0 4px;color:#000;font-weight:bold}.rst-content dl:not(.docutils) .property{display:inline-block;padding-right:8px}.rst-content .viewcode-link,.rst-content .viewcode-back{display:inline-block;color:#27AE60;font-size:80%;padding-left:24px}.rst-content .viewcode-back{display:block;float:right}.rst-content p.rubric{margin-bottom:12px;font-weight:bold}.rst-content tt.download,.rst-content code.download{background:inherit;padding:inherit;font-weight:normal;font-family:inherit;font-size:inherit;color:inherit;border:inherit;white-space:inherit}.rst-content tt.download span:first-child,.rst-content code.download span:first-child{-webkit-font-smoothing:subpixel-antialiased}.rst-content tt.download span:first-child:before,.rst-content code.download span:first-child:before{margin-right:4px}.rst-content .guilabel{border:1px solid #7fbbe3;background:#e7f2fa;font-size:80%;font-weight:700;border-radius:4px;padding:2.4px 6px;margin:auto 2px}.rst-content .versionmodified{font-style:italic}@media screen and (max-width: 480px){.rst-content .sidebar{width:100%}}span[id*='MathJax-Span']{color:#404040}.math{text-align:center}@font-face{font-family:"Lato";src:url("../fonts/Lato/lato-regular.eot");src:url("../fonts/Lato/lato-regular.eot?#iefix") format("embedded-opentype"),url("../fonts/Lato/lato-regular.woff2") format("woff2"),url("../fonts/Lato/lato-regular.woff") format("woff"),url("../fonts/Lato/lato-regular.ttf") format("truetype");font-weight:400;font-style:normal}@font-face{font-family:"Lato";src:url("../fonts/Lato/lato-bold.eot");src:url("../fonts/Lato/lato-bold.eot?#iefix") format("embedded-opentype"),url("../fonts/Lato/lato-bold.woff2") format("woff2"),url("../fonts/Lato/lato-bold.woff") format("woff"),url("../fonts/Lato/lato-bold.ttf") format("truetype");font-weight:700;font-style:normal}@font-face{font-family:"Lato";src:url("../fonts/Lato/lato-bolditalic.eot");src:url("../fonts/Lato/lato-bolditalic.eot?#iefix") format("embedded-opentype"),url("../fonts/Lato/lato-bolditalic.woff2") format("woff2"),url("../fonts/Lato/lato-bolditalic.woff") format("woff"),url("../fonts/Lato/lato-bolditalic.ttf") format("truetype");font-weight:700;font-style:italic}@font-face{font-family:"Lato";src:url("../fonts/Lato/lato-italic.eot");src:url("../fonts/Lato/lato-italic.eot?#iefix") format("embedded-opentype"),url("../fonts/Lato/lato-italic.woff2") format("woff2"),url("../fonts/Lato/lato-italic.woff") format("woff"),url("../fonts/Lato/lato-italic.ttf") format("truetype");font-weight:400;font-style:italic}@font-face{font-family:"Roboto Slab";font-style:normal;font-weight:400;src:url("../fonts/RobotoSlab/roboto-slab.eot");src:url("../fonts/RobotoSlab/roboto-slab-v7-regular.eot?#iefix") format("embedded-opentype"),url("../fonts/RobotoSlab/roboto-slab-v7-regular.woff2") format("woff2"),url("../fonts/RobotoSlab/roboto-slab-v7-regular.woff") format("woff"),url("../fonts/RobotoSlab/roboto-slab-v7-regular.ttf") format("truetype")}@font-face{font-family:"Roboto Slab";font-style:normal;font-weight:700;src:url("../fonts/RobotoSlab/roboto-slab-v7-bold.eot");src:url("../fonts/RobotoSlab/roboto-slab-v7-bold.eot?#iefix") format("embedded-opentype"),url("../fonts/RobotoSlab/roboto-slab-v7-bold.woff2") format("woff2"),url("../fonts/RobotoSlab/roboto-slab-v7-bold.woff") format("woff"),url("../fonts/RobotoSlab/roboto-slab-v7-bold.ttf") format("truetype")} diff --git a/docs/css/theme_extra.css b/docs/css/theme_extra.css new file mode 100644 index 00000000..ec7002a6 --- /dev/null +++ b/docs/css/theme_extra.css @@ -0,0 +1,191 @@ +/* + * Wrap inline code samples otherwise they shoot of the side and + * can't be read at all. + * + * https://github.com/mkdocs/mkdocs/issues/313 + * https://github.com/mkdocs/mkdocs/issues/233 + * https://github.com/mkdocs/mkdocs/issues/834 + */ +.rst-content code { + white-space: pre-wrap; + word-wrap: break-word; + padding: 2px 5px; +} + +/** + * Make code blocks display as blocks and give them the appropriate + * font size and padding. + * + * https://github.com/mkdocs/mkdocs/issues/855 + * https://github.com/mkdocs/mkdocs/issues/834 + * https://github.com/mkdocs/mkdocs/issues/233 + */ +.rst-content pre code { + white-space: pre; + word-wrap: normal; + display: block; + padding: 12px; + font-size: 12px; +} + +/** + * Fix code colors + * + * https://github.com/mkdocs/mkdocs/issues/2027 + */ +.rst-content code { + color: #E74C3C; +} + +.rst-content pre code { + color: #000; + background: #f8f8f8; +} + +/* + * Fix link colors when the link text is inline code. + * + * https://github.com/mkdocs/mkdocs/issues/718 + */ +a code { + color: #2980B9; +} +a:hover code { + color: #3091d1; +} +a:visited code { + color: #9B59B6; +} + +/* + * The CSS classes from highlight.js seem to clash with the + * ReadTheDocs theme causing some code to be incorrectly made + * bold and italic. + * + * https://github.com/mkdocs/mkdocs/issues/411 + */ +pre .cs, pre .c { + font-weight: inherit; + font-style: inherit; +} + +/* + * Fix some issues with the theme and non-highlighted code + * samples. Without and highlighting styles attached the + * formatting is broken. + * + * https://github.com/mkdocs/mkdocs/issues/319 + */ +.rst-content .no-highlight { + display: block; + padding: 0.5em; + color: #333; +} + + +/* + * Additions specific to the search functionality provided by MkDocs + */ + +.search-results { + margin-top: 23px; +} + +.search-results article { + border-top: 1px solid #E1E4E5; + padding-top: 24px; +} + +.search-results article:first-child { + border-top: none; +} + +form .search-query { + width: 100%; + border-radius: 50px; + padding: 6px 12px; /* csslint allow: box-model */ + border-color: #D1D4D5; +} + +/* + * Improve inline code blocks within admonitions. + * + * https://github.com/mkdocs/mkdocs/issues/656 + */ + .rst-content .admonition code { + color: #404040; + border: 1px solid #c7c9cb; + border: 1px solid rgba(0, 0, 0, 0.2); + background: #f8fbfd; + background: rgba(255, 255, 255, 0.7); +} + +/* + * Account for wide tables which go off the side. + * Override borders to avoid wierdness on narrow tables. + * + * https://github.com/mkdocs/mkdocs/issues/834 + * https://github.com/mkdocs/mkdocs/pull/1034 + */ +.rst-content .section .docutils { + width: 100%; + overflow: auto; + display: block; + border: none; +} + +td, th { + border: 1px solid #e1e4e5 !important; /* csslint allow: important */ + border-collapse: collapse; +} + +/* + * Without the following amendments, the navigation in the theme will be + * slightly cut off. This is due to the fact that the .wy-nav-side has a + * padding-bottom of 2em, which must not necessarily align with the font-size of + * 90 % on the .rst-current-version container, combined with the padding of 12px + * above and below. These amendments fix this in two steps: First, make sure the + * .rst-current-version container has a fixed height of 40px, achieved using + * line-height, and then applying a padding-bottom of 40px to this container. In + * a second step, the items within that container are re-aligned using flexbox. + * + * https://github.com/mkdocs/mkdocs/issues/2012 + */ + .wy-nav-side { + padding-bottom: 40px; +} + +/* + * The second step of above amendment: Here we make sure the items are aligned + * correctly within the .rst-current-version container. Using flexbox, we + * achieve it in such a way that it will look like the following: + * + * [No repo_name] + * Next >> // On the first page + * << Previous Next >> // On all subsequent pages + * + * [With repo_name] + * Next >> // On the first page + * << Previous Next >> // On all subsequent pages + * + * https://github.com/mkdocs/mkdocs/issues/2012 + */ +.rst-versions .rst-current-version { + padding: 0 12px; + display: flex; + font-size: initial; + justify-content: space-between; + align-items: center; + line-height: 40px; +} + +/* + * Please note that this amendment also involves removing certain inline-styles + * from the file ./mkdocs/themes/readthedocs/versions.html. + * + * https://github.com/mkdocs/mkdocs/issues/2012 + */ +.rst-current-version span { + flex: 1; + text-align: center; +} diff --git a/docs/default_curi_maps/index.html b/docs/default_curi_maps/index.html new file mode 100644 index 00000000..012e5466 --- /dev/null +++ b/docs/default_curi_maps/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: default_curi_maps - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: default_curi_maps
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: default_curi_maps

+

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

+

URI: linkml:default_curi_maps

+

Domain and Range

+

SchemaDefinition → 0..* String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/default_prefix/index.html b/docs/default_prefix/index.html new file mode 100644 index 00000000..2f65d3ee --- /dev/null +++ b/docs/default_prefix/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: default_prefix - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: default_prefix
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: default_prefix

+

default and base prefix -- used for ':' identifiers, @base and @vocab

+

URI: linkml:default_prefix

+

Domain and Range

+

SchemaDefinition → 0..1 String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/default_range/index.html b/docs/default_range/index.html new file mode 100644 index 00000000..cf7e22cd --- /dev/null +++ b/docs/default_range/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: default_range - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: default_range
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: default_range

+

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

+

URI: linkml:default_range

+

Domain and Range

+

SchemaDefinition → 0..1 TypeDefinition

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/defining_slots/index.html b/docs/defining_slots/index.html new file mode 100644 index 00000000..9d7ecac5 --- /dev/null +++ b/docs/defining_slots/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: defining_slots - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: defining_slots
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: defining_slots

+

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

+

URI: linkml:defining_slots

+

Domain and Range

+

ClassDefinition → 0..* SlotDefinition

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/definition_uri/index.html b/docs/definition_uri/index.html new file mode 100644 index 00000000..5296924b --- /dev/null +++ b/docs/definition_uri/index.html @@ -0,0 +1,170 @@ + + + + + + + + + + + + Slot: definition_uri - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: definition_uri
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: definition_uri

+

the "native" URI of the element

+

URI: linkml:definition_uri

+

Domain and Range

+

Element → 0..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Comments:Formed by combining the default_prefix with the mangled element
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/deprecated/index.html b/docs/deprecated/index.html new file mode 100644 index 00000000..fa57d79c --- /dev/null +++ b/docs/deprecated/index.html @@ -0,0 +1,155 @@ + + + + + + + + + + + + Slot: deprecated - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: deprecated
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: deprecated

+

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

+

URI: linkml:deprecated

+

Domain and Range

+

Element → 0..1 String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/deprecated_element_has_exact_replacement/index.html b/docs/deprecated_element_has_exact_replacement/index.html new file mode 100644 index 00000000..f09582a1 --- /dev/null +++ b/docs/deprecated_element_has_exact_replacement/index.html @@ -0,0 +1,172 @@ + + + + + + + + + + + + Slot: deprecated element has exact replacement - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: deprecated element has exact replacement
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: deprecated element has exact replacement

+

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

+

URI: linkml:deprecated_element_has_exact_replacement

+

Domain and Range

+

None → 0..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:IAO:0100001
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/deprecated_element_has_possible_replacement/index.html b/docs/deprecated_element_has_possible_replacement/index.html new file mode 100644 index 00000000..90d4bccd --- /dev/null +++ b/docs/deprecated_element_has_possible_replacement/index.html @@ -0,0 +1,172 @@ + + + + + + + + + + + + Slot: deprecated element has possible replacement - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: deprecated element has possible replacement
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: deprecated element has possible replacement

+

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

+

URI: linkml:deprecated_element_has_possible_replacement

+

Domain and Range

+

None → 0..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:OIO:consider
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/description/index.html b/docs/description/index.html new file mode 100644 index 00000000..60f65179 --- /dev/null +++ b/docs/description/index.html @@ -0,0 +1,177 @@ + + + + + + + + + + + + Slot: description - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: description
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: description

+

a description of the element's purpose and use

+

URI: linkml:description

+

Domain and Range

+

Element → 0..1 String

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + + + + + + +
Mappings:skos:definition
In Subsets:owl
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/designates_type/index.html b/docs/designates_type/index.html new file mode 100644 index 00000000..b14ecf1c --- /dev/null +++ b/docs/designates_type/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: designates_type - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: designates_type
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: designates_type

+

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

+

URI: linkml:designates_type

+

Domain and Range

+

SlotDefinition → 0..1 Boolean

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/domain/index.html b/docs/domain/index.html new file mode 100644 index 00000000..1748f089 --- /dev/null +++ b/docs/domain/index.html @@ -0,0 +1,153 @@ + + + + + + + + + + + + Slot: domain - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: domain
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: domain

+

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

+

URI: linkml:domain

+

Domain and Range

+

SlotDefinition → 0..1 ClassDefinition

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/domain_of/index.html b/docs/domain_of/index.html new file mode 100644 index 00000000..5f0928bc --- /dev/null +++ b/docs/domain_of/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: domain_of - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: domain_of
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: domain_of

+

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

+

URI: linkml:domain_of

+

Domain and Range

+

SlotDefinition → 0..* ClassDefinition

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/emit_prefixes/index.html b/docs/emit_prefixes/index.html new file mode 100644 index 00000000..96ccae13 --- /dev/null +++ b/docs/emit_prefixes/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: emit_prefixes - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: emit_prefixes
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: emit_prefixes

+

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.

+

URI: linkml:emit_prefixes

+

Domain and Range

+

SchemaDefinition → 0..* Ncname

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/enums/index.html b/docs/enums/index.html new file mode 100644 index 00000000..282c54b1 --- /dev/null +++ b/docs/enums/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: enums - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: enums
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: enums

+

enumerated ranges

+

URI: linkml:enums

+

Domain and Range

+

SchemaDefinition → 0..* EnumDefinition

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/exact_mappings/index.html b/docs/exact_mappings/index.html new file mode 100644 index 00000000..7b6893a8 --- /dev/null +++ b/docs/exact_mappings/index.html @@ -0,0 +1,173 @@ + + + + + + + + + + + + Slot: exact mappings - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
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    +
  • Docs »
    • + + + +
  • Slot: exact mappings
    • +
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    • +
+ +
+
+ +
+
+ +

Slot: exact mappings

+

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

+

URI: linkml:exact_mappings

+

Domain and Range

+

None → 0..* Uriorcurie

+

Parents

+ +

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:skos:exactMatch
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/examples/index.html b/docs/examples/index.html new file mode 100644 index 00000000..8fc4246e --- /dev/null +++ b/docs/examples/index.html @@ -0,0 +1,172 @@ + + + + + + + + + + + + Slot: examples - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
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    +
  • Docs »
    • + + + +
  • Slot: examples
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: examples

+

example usages of an element

+

URI: linkml:examples

+

Domain and Range

+

Element → 0..* Example

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
In Subsets:owl
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/extension_tag/index.html b/docs/extension_tag/index.html new file mode 100644 index 00000000..6f98fcbf --- /dev/null +++ b/docs/extension_tag/index.html @@ -0,0 +1,147 @@ + + + + + + + + + + + + Slot: tag - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: tag
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: tag

+

a tag associated with an extension

+

URI: linkml:extension_tag

+

Domain and Range

+

Extension → 1..1 Uriorcurie

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/extension_value/index.html b/docs/extension_value/index.html new file mode 100644 index 00000000..729b2542 --- /dev/null +++ b/docs/extension_value/index.html @@ -0,0 +1,147 @@ + + + + + + + + + + + + Slot: value - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: value
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: value

+

the actual annotation

+

URI: linkml:extension_value

+

Domain and Range

+

Extension → 1..1 String

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/extensions/index.html b/docs/extensions/index.html new file mode 100644 index 00000000..828b3e06 --- /dev/null +++ b/docs/extensions/index.html @@ -0,0 +1,161 @@ + + + + + + + + + + + + Slot: extensions - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: extensions
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: extensions

+

a tag/text tuple attached to an arbitrary element

+

URI: linkml:extensions

+

Domain and Range

+

Extensible → 0..* Extension

+

Parents

+

Children

+ +

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/fonts/Lato/lato-bold.eot b/docs/fonts/Lato/lato-bold.eot new file mode 100644 index 00000000..3361183a Binary files /dev/null and b/docs/fonts/Lato/lato-bold.eot differ diff --git a/docs/fonts/Lato/lato-bold.ttf b/docs/fonts/Lato/lato-bold.ttf new file mode 100644 index 00000000..29f691d5 Binary files /dev/null and b/docs/fonts/Lato/lato-bold.ttf differ diff --git a/docs/fonts/Lato/lato-bold.woff b/docs/fonts/Lato/lato-bold.woff new file mode 100644 index 00000000..c6dff51f Binary files /dev/null and b/docs/fonts/Lato/lato-bold.woff differ diff --git a/docs/fonts/Lato/lato-bold.woff2 b/docs/fonts/Lato/lato-bold.woff2 new file mode 100644 index 00000000..bb195043 Binary files /dev/null and b/docs/fonts/Lato/lato-bold.woff2 differ diff --git a/docs/fonts/Lato/lato-bolditalic.eot b/docs/fonts/Lato/lato-bolditalic.eot new file mode 100644 index 00000000..3d415493 Binary files /dev/null and b/docs/fonts/Lato/lato-bolditalic.eot differ diff --git 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All rights reserved. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/fonts/fontawesome-webfont.ttf b/docs/fonts/fontawesome-webfont.ttf new file mode 100644 index 00000000..35acda2f Binary files /dev/null and b/docs/fonts/fontawesome-webfont.ttf differ diff --git a/docs/fonts/fontawesome-webfont.woff b/docs/fonts/fontawesome-webfont.woff new file mode 100644 index 00000000..400014a4 Binary files /dev/null and b/docs/fonts/fontawesome-webfont.woff differ diff --git a/docs/fonts/fontawesome-webfont.woff2 b/docs/fonts/fontawesome-webfont.woff2 new file mode 100644 index 00000000..4d13fc60 Binary files /dev/null and b/docs/fonts/fontawesome-webfont.woff2 differ diff --git a/docs/from_schema/index.html b/docs/from_schema/index.html new file mode 100644 index 00000000..70909cdf --- /dev/null +++ b/docs/from_schema/index.html @@ -0,0 +1,172 @@ + + + + + + + + + + + + Slot: from_schema - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: from_schema
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: from_schema

+

id of the schema that defined the element

+

URI: linkml:from_schema

+

Domain and Range

+

Element → 0..1 Uri

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
Mappings:skos:inScheme
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/generation_date/index.html b/docs/generation_date/index.html new file mode 100644 index 00000000..7e25770a --- /dev/null +++ b/docs/generation_date/index.html @@ -0,0 +1,163 @@ + + + + + + + + + + + + Slot: generation_date - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: generation_date
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: generation_date

+

date and time that the schema was loaded/generated

+

URI: linkml:generation_date

+

Domain and Range

+

SchemaDefinition → 0..1 Datetime

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + +
In Subsets:owl
+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/home/index.html b/docs/home/index.html new file mode 100644 index 00000000..3da9b75c --- /dev/null +++ b/docs/home/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + Home - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Home
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Introduction

+

about my_schema

+ +
+
+ + +
+
+ +
+ +
+ +
+ + + + + Next » + + +
+ + + + + + + + diff --git a/docs/id/index.html b/docs/id/index.html new file mode 100644 index 00000000..263273b1 --- /dev/null +++ b/docs/id/index.html @@ -0,0 +1,146 @@ + + + + + + + + + + + + Slot: id - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: id
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: id

+

The official schema URI

+

URI: linkml:id

+

Domain and Range

+

SchemaDefinition → 1..1 Uri

+

Parents

+

Children

+

Used by

+ + +
+
+ + +
+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/id_prefixes/index.html b/docs/id_prefixes/index.html new file mode 100644 index 00000000..63480877 --- /dev/null +++ b/docs/id_prefixes/index.html @@ -0,0 +1,190 @@ + + + + + + + + + + + + Slot: id_prefixes - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: id_prefixes
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: id_prefixes

+

the identifier of this class or slot must begin with the URIs referenced by this prefix

+

URI: linkml:id_prefixes

+

Domain and Range

+

Element → 0..* Ncname

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Comments:Order of elements may be used to indicate priority order
If identifiers are treated as CURIEs, then the CURIE must start with one of the indicated prefixes followed by : (should start if the list is open)
If identifiers are treated as URIs, then the URI string must start with the expanded for of the prefix (should start if the list is open)
See also:https://github.com/linkml/linkml/issues/194
https://github.com/linkml/linkml-model/issues/28
+ +
+
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+
+ +
+ +
+ +
+ + + + + +
+ + + + + + + + diff --git a/docs/identifier/index.html b/docs/identifier/index.html new file mode 100644 index 00000000..b6b3473d --- /dev/null +++ b/docs/identifier/index.html @@ -0,0 +1,203 @@ + + + + + + + + + + + + Slot: identifier - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: identifier
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: identifier

+

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

+

URI: linkml:identifier

+

Domain and Range

+

SlotDefinition → 0..1 Boolean

+

Parents

+

Children

+

Used by

+ +

Other properties

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Aliases:primary key
ID
UID
code
Comments:identifier is inherited
a key slot is automatically required. Identifiers cannot be optional
a given domain can have at most one identifier
identifiers and keys are mutually exclusive. A given domain cannot have both
See also:https://en.wikipedia.org/wiki/Identifier
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+ + + + + + + + diff --git a/docs/ifabsent/index.html b/docs/ifabsent/index.html new file mode 100644 index 00000000..b180492f --- /dev/null +++ b/docs/ifabsent/index.html @@ -0,0 +1,155 @@ + + + + + + + + + + + + Slot: ifabsent - LinkML Model + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + +
+
+
+
    +
  • Docs »
    • + + + +
  • Slot: ifabsent
    • +
  • + +
    • +
+ +
+
+ +
+
+ +

Slot: ifabsent

+

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

+

URI: linkml:ifabsent

+

Domain and Range

+

SlotDefinition → 0..1 String

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Parents

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Used by

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  • Slot: imported_from
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Slot: imported_from

+

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

+

URI: linkml:imported_from

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Domain and Range

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Element → 0..1 String

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Parents

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Children

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Used by

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  • Slot: imports
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Slot: imports

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other schemas that are included in this schema

+

URI: linkml:imports

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Domain and Range

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SchemaDefinition → 0..* Uriorcurie

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Parents

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Children

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Used by

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+ + + + + + + + diff --git a/docs/in_subset/index.html b/docs/in_subset/index.html new file mode 100644 index 00000000..bd7a049e --- /dev/null +++ b/docs/in_subset/index.html @@ -0,0 +1,172 @@ + + + + + + + + + + + + Slot: in_subset - LinkML Model + + + + + + + + + + + + + + + + +
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  • Slot: in_subset
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Slot: in_subset

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used to indicate membership of a term in a defined subset of terms used for a particular domain or application (e.g. the translator_minimal subset holding the minimal set of predicates used in a translator knowledge graph)

+

URI: linkml:in_subset

+

Domain and Range

+

Element → 0..* SubsetDefinition

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Parents

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Children

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Used by

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Other properties

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Mappings:OIO:inSubset
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  • Index
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meta schema

+

A metamodel for defining linked open data schemas

+

Classes

+
    +
  • AltDescription - an attributed description
    • +
  • Element - a named element in the model +
    • +
  • Example - usage example and description
    • +
  • Extension - a tag/value pair used to add non-model information to an entry
      +
    • Annotation - a tag/value pair with the semantics of OWL Annotation
      • +
    +
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  • LocalName - an attributed label
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  • PermissibleValue - a permissible value, accompanied by intended text and an optional mapping to a concept URI
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  • Prefix - prefix URI tuple
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  • UniqueKey - a collection of slots whose values uniquely identify an instance of a class
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Mixins

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  • Annotatable - mixin for classes that support annotations
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  • CommonMetadata - Generic metadata shared across definitions
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  • Extensible - mixin for classes that support extension
    • +
+

Slots

+
    +
  • abstract - an abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.
    • +
  • alias - the name used for a slot in the context of its owning class. If present, this is used instead of the actual slot name.
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  • aliases
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  • alt_description➞source - the source of an attributed description
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  • alt_description➞description - text of an attributed description
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  • alt_descriptions
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  • apply_to - 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. +
    • +
  • attributes - Inline definition of slots
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  • base - python base type that implements this type definition
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  • class_uri - URI of the class in an RDF environment
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  • classes - class definitions
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  • code_set - the identifier of an enumeration code set.
    • +
  • code_set_tag - the version tag of the enumeration code set
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  • code_set_version - the version identifier of the enumeration code set
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  • comments - notes and comments about an element intended for external consumption
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  • created_by - agent that created the element
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  • created_on - time at which the element was created
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  • default_curi_maps - ordered list of prefixcommon biocontexts to be fetched to resolve id prefixes and inline prefix variables
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  • default_prefix - default and base prefix -- used for ':' identifiers, @base and @vocab
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  • default_range - default slot range to be used if range element is omitted from a slot definition
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  • defining_slots - 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
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  • definition_uri - the "native" URI of the element
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  • deprecated - Description of why and when this element will no longer be used
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  • deprecated element has exact replacement - When an element is deprecated, it can be automatically replaced by this uri or curie
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  • deprecated element has possible replacement - When an element is deprecated, it can be potentially replaced by this uri or curie
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  • description - a description of the element's purpose and use
    • +
  • designates_type - True means that the key slot(s) is used to determine the instantiation (types) relation between objects and a ClassDefinition
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  • domain - defines the type of the subject of the slot. Given the following slot definition
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  • domain_of - the class(es) that reference the slot in a "slots" or "slot_usage" context
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  • emit_prefixes - 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.
    • +
  • enums - enumerated ranges
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  • examples - example usages of an element
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  • extension➞tag - a tag associated with an extension
    • +
  • extension➞value - the actual annotation
    • +
  • extensions - a tag/text tuple attached to an arbitrary element
      +
    • annotations - a collection of tag/text tuples with the semantics of OWL Annotation
      • +
    +
    • +
  • from_schema - id of the schema that defined the element
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  • generation_date - date and time that the schema was loaded/generated
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  • id - The official schema URI
    • +
  • id_prefixes - the identifier of this class or slot must begin with the URIs referenced by this prefix
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  • identifier - True means that the key slot(s) uniquely identify the container. There can be at most one identifier or key per container
    • +
  • ifabsent - function that provides a default value for the slot. Possible values for this slot are defined in biolink.utils.ifabsent_functions.default_library:
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  • imported_from - the imports entry that this element was derived from. Empty means primary source
    • +
  • imports - other schemas that are included in this schema
    • +
  • in_subset - used to indicate membership of a term in a defined subset of terms used for a particular domain or application (e.g. the translator_minimal subset holding the minimal set of predicates used in a translator knowledge graph)
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  • inherited - true means that the value of a slot is inherited by subclasses
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  • inlined - 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.
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  • inlined_as_list - 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.
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  • inverse - indicates that any instance of d s r implies that there is also an instance of r s' d
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  • is_a - specifies single-inheritance between classes or slots. 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 +
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  • is_class_field - indicates that any instance, i, the domain of this slot will include an assert of i s range
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  • is_usage_slot - True means that this slot was defined in a slot_usage situation
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  • key - True means that the key slot(s) uniquely identify the container.
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  • last_updated_on - time at which the element was last updated
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  • license - license for the schema
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  • local_name_source - the ncname of the source of the name
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  • local_name_value - a name assigned to an element in a given ontology
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  • local_names
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  • mappings - 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.
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    • broad mappings - A list of terms from different schemas or terminology systems that have broader meaning.
      • +
    • close mappings - A list of terms from different schemas or terminology systems that have close meaning.
      • +
    • exact mappings - A list of terms from different schemas or terminology systems that have identical meaning.
      • +
    • narrow mappings - A list of terms from different schemas or terminology systems that have narrower meaning.
      • +
    • related mappings - A list of terms from different schemas or terminology systems that have related meaning.
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  • maximum_value - for slots with ranges of type number, the value must be equal to or lowe than this
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  • meaning - the value meaning (in the 11179 sense) of a permissible value
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  • metamodel_version - Version of the metamodel used to load the schema
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  • minimum_value - for slots with ranges of type number, the value must be equal to or higher than this
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  • mixin - this slot or class can only be used as a mixin.
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  • mixins - List of definitions to be mixed in. Targets may be any definition of the same type +
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  • modified_by - agent that modified the element
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  • multivalued - true means that slot can have more than one value
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  • name - 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. +
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  • notes - editorial notes about an element intended for internal consumption
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  • owner - the "owner" of the slot. It is the class if it appears in the slots list, otherwise the declaring slot
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  • pattern - the string value of the slot must conform to this regular expression
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  • permissible_values - A list of possible values for a slot range
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  • prefix_prefix - the nsname (sans ':' for a given prefix)
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  • prefix_reference - A URI associated with a given prefix
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  • prefixes - prefix / URI definitions to be added to the context beyond those fetched from prefixcommons in id prefixes
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  • pv_formula - Defines the specific formula to be used to generate the permissible values.
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  • range - defines the type of the object of the slot. Given the following slot definition
    • +
  • readonly - If present, slot is read only. Text explains why
    • +
  • recommended - true means that the slot should be present in the loaded definition, but this is not required
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  • repr - the name of the python object that implements this type definition
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  • required - true means that the slot must be present in the loaded definition
    • +
  • role - the role played by the slot range
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  • see_also - a reference
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  • singular_name - a name that is used in the singular form
    • +
  • schema_definition➞slots - slot definitions
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  • slot_uri - predicate of this slot for semantic web application
    • +
  • slot_usage - the redefinition of a slot in the context of the containing class definition.
    • +
  • slots - list of slot names that are applicable to a class
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  • source_file - name, uri or description of the source of the schema
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  • source_file_date - modification date of the source of the schema
    • +
  • source_file_size - size in bytes of the source of the schema
    • +
  • status - status of the element
    • +
  • string_serialization - 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.
    • +
  • subclass_of - rdfs:subClassOf to be emitted in OWL generation
    • +
  • subproperty_of - Ontology property which this slot is a subproperty of
    • +
  • subsets - list of subsets referenced in this model
    • +
  • symmetric - True means that any instance of d s r implies that there is also an instance of r s d
    • +
  • text
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  • title - the official title of the schema
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  • todos - Outstanding issue that needs resolution
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  • tree_root - indicator that this is the root class in tree structures
    • +
  • type_definition➞uri - The uri that defines the possible values for the type definition
    • +
  • typeof - Names a parent type
    • +
  • types - data types used in the model
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  • union_of - indicates that the domain class consists exactly of the members of the classes in the range
    • +
  • unique_key_slots - list of slot names that form a key
    • +
  • unique_keys - Set of unique keys for this slot
    • +
  • usage_slot_name - The name of the slot referenced in the slot_usage
    • +
  • value - example value
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  • example➞description - description of what the value is doing
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  • values_from - the identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot
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  • version - particular version of schema
    • +
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Enums

+
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  • pv_formula_options - The formula used to generate the set of permissible values from the code_set values
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Subsets

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  • Owl - Set of slots that appear in the OWL representation of a model
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Types

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Built in

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  • Bool
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  • Decimal
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  • ElementIdentifier
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  • NCName
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  • NodeIdentifier
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  • URI
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  • URIorCURIE
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  • XSDDate
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  • XSDDateTime
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  • XSDTime
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  • float
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  • int
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  • str
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Defined

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  • Boolean (Bool) - A binary (true or false) value
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  • Date (XSDDate) - a date (year, month and day) in an idealized calendar
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  • Datetime (XSDDateTime) - The combination of a date and time
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  • Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
    • +
  • Double (float) - A real number that conforms to the xsd:double specification
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  • Float (float) - A real number that conforms to the xsd:float specification
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  • Integer (int) - An integer
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  • Ncname (NCName) - Prefix part of CURIE
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  • Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
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  • Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
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  • String (str) - A character string
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  • Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
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  • Uri (URI) - a complete URI
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  • Uriorcurie (URIorCURIE) - a URI or a CURIE
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  • Slot: inherited
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Slot: inherited

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

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URI: linkml:inherited

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Domain and Range

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SlotDefinition → 0..1 Boolean

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Parents

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Children

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Used by

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Other properties

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Comments:Inherited applies to slot values. Parent slots are always inherited by subclasses
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  • Slot: inlined
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Slot: inlined

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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.

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URI: linkml:inlined

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Domain and Range

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SlotDefinition → 0..1 Boolean

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Parents

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Children

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Used by

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Other properties

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Comments:classes without keys or identifiers are necessarily inlined as lists
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  • Slot: inlined_as_list
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Slot: inlined_as_list

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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.

+

URI: linkml:inlined_as_list

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Domain and Range

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SlotDefinition → 0..1 Boolean

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Parents

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Children

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Used by

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Other properties

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Comments:The default loader will accept either list or dictionary form as input. This parameter controls internal
representation and output.
A keyed or identified class with one additional slot can be input in a third form, a dictionary whose key
is the key or identifier and whose value is the one additional element. This form is still stored according
to the inlined_as_list setting.
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  • Slot: inverse
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Slot: inverse

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

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URI: linkml:inverse

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Domain and Range

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SlotDefinition → 0..1 SlotDefinition

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Parents

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Children

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Used by

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Other properties

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Mappings:owl:inverseOf
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  • Slot: is_a
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Slot: is_a

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specifies single-inheritance between classes or slots. 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

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URI: linkml:is_a

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Domain and Range

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Definition → 0..1 Definition

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Parents

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Children

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Used by

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  • Slot: is_class_field
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Slot: is_class_field

+

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

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URI: linkml:is_class_field

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Domain and Range

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SlotDefinition → 0..1 Boolean

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Parents

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Children

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Used by

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  • Slot: is_usage_slot _(deprecated)_
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Slot: is_usage_slot (deprecated)

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True means that this slot was defined in a slot_usage situation

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URI: linkml:is_usage_slot

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Domain and Range

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SlotDefinition → 0..1 Boolean

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Parents

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Children

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Used by

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