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Merge pull request #153 from linkml/refining-array-model
refining array model
2 parents ba95ed4 + 6690c03 commit 356a065

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‎linkml_model/model/schema/array.yaml‎

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id: https://w3id.org/linkml/linkml-arrays
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name: linkml-arrays
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title: linkml-arrays
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id: https://w3id.org/linkml/lib/arrays
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name: arrays
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title: LinkML Arrays
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description: |-
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LinkML schema to store one-dimensional series and two-dimensional arrays.
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LinkML templates for storing one-dimensional series, two-dimensional arrays,
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and arrays of higher dimensionality.
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Status: Experimental
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Note that this model is not intended to be imported direcly. Instead,
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use `implements` to denote conformance.
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status: testing
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#contributors:
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# - github:rly
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# - github:oruebel
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# - github:jmchandonia
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# - github:realmarcin
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# - github:mavaylon1
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# - github:ialarmedalien
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# - github:cmungall
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prefixes:
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arrays: https://w3id.org/linkml/linkml-arrays
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linkml: https://w3id.org/linkml/
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github: https://github.com/
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gom: https://w3id.org/gom#
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default_prefix: arrays
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default_prefix: linkml
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default_range: string
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imports:
@@ -19,37 +36,245 @@ classes:
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Any:
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class_uri: linkml:Any
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DataStructure:
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abstract: true
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Array:
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description: >-
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a data structure consisting of a collection of *elements*, each identified by at least one array index tuple.
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abstract: true
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is_a: DataStructure
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slots:
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- dimensionality
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- elements
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- array_linearization_order
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slot_usage:
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elements:
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description: >-
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the collection of values that make up the array. The elements have a *direct* representation which is
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an ordered sequence of values. The elements also have an *array interpretation*, where each
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element has a unique index which is determined by array_linearization_order
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OneDimensionalSeries:
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attributes:
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name: # the row label
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key: true # unique when nested (unlike identifier, which is a global identifier)
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length:
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range: integer
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values:
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is_a: Array
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description: >-
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An array that has one dimension
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aliases:
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- axis
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- 1D array
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- vector
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- series
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- row
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slots:
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- series_label
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- length
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# TODO: consider offset and rate
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slot_usage:
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dimensionality:
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equals_expression: "1"
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TwoDimensionalArray:
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is_a: Array
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description: >-
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An array that has two dimensions
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aliases:
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- table
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- matrix
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- grid
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slots:
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- axis0
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- axis1
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slot_usage:
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dimensionality:
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equals_expression: "2"
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elements:
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description: >-
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this will be serialized as one big long list that should be interpreted as a 2D array
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ThreeDimensionalArray:
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is_a: Array
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description: >-
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An array that has two dimensions
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aliases:
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- 3D array
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slots:
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- axis0
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- axis1
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- axis2
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slot_usage:
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dimensionality:
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equals_expression: "3"
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OrderedArray:
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mixin: true
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description: >-
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A mixin that describes an array whose elements are mapped from a linear sequence to an array index
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via a specified mapping
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ColumnOrderedArray:
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mixin: true
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description: >-
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An array ordering that is column-order
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slots:
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- array_linearization_order
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slot_usage:
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array_linearization_order:
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equals_string: COLUMN_MAJOR_ARRAY_ORDER
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RowOrderedArray:
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mixin: true
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description: >-
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An array ordering that is row-order or generalizations thereof
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slots:
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- array_linearization_order
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slot_usage:
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array_linearization_order:
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equals_string: ROW_MAJOR_ARRAY_ORDER
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MultiDimensionalArray:
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is_a: Array
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abstract: true
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description: >-
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An array that has more than two dimensions
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ObjectAsTuple:
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comments:
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- not modeled as an array since this is used as a metaclass
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implements:
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- OneDimensionalSeries
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ArrayIndex:
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is_a: ObjectAsTuple
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Operation:
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abstract: true
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description: >-
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Represents the transformation of one or more inputs to one or more outputs determined by
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zero to many operation parameters
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slots:
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- specified_input
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- specified_output
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- operation_parameters
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ArrayIndexOperation:
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description: >-
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An operation that takes as input an Array and is parameterized by an array index tuple and
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yields an array element
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slot_usage:
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specified_input:
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range: Array
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maximum_cardinality: 1
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specified_output:
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range: Any
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multivalued: true
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required: true
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maximum_cardinality: 1
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operation_parameters:
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range: ArrayIndex
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maximum_cardinality: 1
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slots:
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dimensionality:
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description: >-
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The number of elements in the tuple used to access elements of an array
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aliases:
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- rank
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- dimension
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- number of axes
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- number of elements
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range: integer
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axis:
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abstract: true
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range: OneDimensionalSeries
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aliases:
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- dimension
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description: >-
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A one dimensional series that contains elements that form one part of a tuple used to access an array
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axis0:
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is_a: axis
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aliases:
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- x
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- dimension0
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description: >-
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An axis that is the zeroth index of the tuple used to access an array
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range: OneDimensionalSeries
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rank: 0
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required: true
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inlined: true
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inlined_as_list: true
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axis1:
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is_a: axis
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aliases:
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- y
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description: >-
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An axis that is the index after the zeroth of the tuple used to access an array
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range: OneDimensionalSeries
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rank: 1
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required: true
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inlined: true
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inlined_as_list: true
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axis2:
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is_a: axis
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aliases:
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- z
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range: OneDimensionalSeries
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rank: 2
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required: true
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inlined: true
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inlined_as_list: true
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elements:
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# this will be serialized as one big long list that should be interpreted as a 2D array
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range: Any
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aliases:
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- values
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required: true
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multivalued: true
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description: >-
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A collection of values that make up the contents of an array. These elements may be interpreted
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as a contiguous linear sequence (direct representation) or as elements to be accessed via an
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array index
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series_label: # the row label
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key: true
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description: >-
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A name that uniquely identifiers a series
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length:
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description: >-
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The number of elements in the array
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range: integer
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equals_expression: "length(elements)"
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array_linearization_order:
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range: ArrayLinearizationOrderOptions
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ifabsent: "string(ROW_MAJOR_ARRAY_ORDER)"
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TwoDimensionalArray:
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attributes:
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axis0:
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specified_input:
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range: DataStructure
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multivalued: true
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specified_output:
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range: DataStructure
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multivalued: true
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operation_parameters:
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range: Any
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multivalued: true
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enums:
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ArrayLinearizationOrderOptions:
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description: >-
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Determines how a linear contiguous representation of the elements of an array map
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to array indices
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permissible_values:
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COLUMN_MAJOR_ARRAY_ORDER:
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meaning: gom:columnMajorArray
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description: >-
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An array layout option in which the elements in each column is stored in consecutive positions,
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or any generalization thereof to dimensionality greater than 2
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aliases:
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- x
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range: OneDimensionalSeries
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rank: 0
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required: true
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inlined: true
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inlined_as_list: true
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axis1:
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- F order
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ROW_MAJOR_ARRAY_ORDER:
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meaning: gom:rowMajorArray
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description: >-
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An array layout option in which the elements in each row is stored in consecutive positions,
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or any generalization thereof to dimensionality greater than 2
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aliases:
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- y
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range: OneDimensionalSeries
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rank: 1
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required: true
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inlined: true
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inlined_as_list: true
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values:
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# this will be serialized as one big long list that should be interpreted as a 2D array
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range: Any
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required: true
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multivalued: true
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- C order
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aliases:
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- C order
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