Amalgamated array


An amalgalm of multiple arrays, combined into a single object for downstream use. This is typically used to combine data from different samples or conditions into a single array, e.g., to store in a consolidated SummarizedExperiment object. The key feature of this schema is that the individual component matrices are still represented by separate files; this means that it can be very cheap to add or remove components by just modifying the metadata rather than making a new copy of the entire combined array.

Derived from array/v1.json: some kind of multi-dimensional array, where we store metadata about the dimensions and type of data. The exact implementation of the array is left to concrete subclasses.

root allOf item 0
Type: object

root allOf item 0 $schema
Type: string

The schema to use.

root allOf item 0 amalgamated_array
Type: object
No Additional Properties

root allOf item 0 amalgamated_array along
Type: integer

Index of the dimension on which the various component arrays are combined. This should be a non-negative value that is less than the length of array.dimensions. For matrices, a value of 0 indicates that the arrays are combined by row, while a value of 1 indicates a combination by column.

Value must be greater or equal to 0

root allOf item 0 amalgamated_array components
Type: array of object

Components of the amalgamated array. Each component should be an array of the same dimensionality, with the same extents for all dimensions other than extent. The amalgamated array is formed by combining the component arrays in the order listed here; the sum of extents of dimension along across components should be equal to the corresponding entry of array.dimensions.

Each item of this array must be:

root allOf item 0 amalgamated_array components components items
Type: object
No Additional Properties

root allOf item 0 amalgamated_array components components items name
Type: string

Name of the component. Typically used to specify the sample or condition of origin.

root allOf item 0 amalgamated_array components components items resource
Type: object

root allOf item 0 amalgamated_array components components items resource path
Type: string

Relative path of the resource from the root of the project directory.

root allOf item 0 amalgamated_array components components items resource type
Type: enum (of string)

Type of file. Local files should be present in the same project directory.

Must be one of:

  • "local"

root allOf item 0 array
Type: object
No Additional Properties

root allOf item 0 array dimensions
Type: array of integer

Dimensions of an n-dimensional array.

Must contain a minimum of 1 items

Each item of this array must be:

root allOf item 0 array dimensions dimensions items
Type: integer

root allOf item 0 array type
Type: enum (of string)

Type of data stored in this array.

Must be one of:

  • "boolean"
  • "number"
  • "integer"
  • "string"
  • "other"

root allOf item 0 authors
Type: array of object

Authors of this resource.

Each item of this array must be:

root allOf item 0 authors authors items
Type: object

root allOf item 0 authors authors items email
Type: string

Email of the author.

Must match regular expression: ^[^@]+@[^@]+$

root allOf item 0 authors authors items name
Type: string

Name of the author.

root allOf item 0 authors authors items orcid
Type: string

ORCID of the author.

Must match regular expression: ^[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}$

root allOf item 0 description
Type: string

Description of the resource.

root allOf item 0 genome
Type: array of object

UCSC, Ensembl or other genome builds involved in generating this resource.

Each item of this array must be:

root allOf item 0 genome genome items
Type: object

root allOf item 0 genome genome items id
Type: string

Identifier for this genome build.
Examples:

"mm10"

"NCBIm37"

root allOf item 0 genome genome items source
Type: enum (of string)

Source of the genome build identifier.

Must be one of:

  • "Ensembl"
  • "UCSC"
  • "Wormbase"
  • "Flybase"

root allOf item 0 is_child
Type: boolean Default: false

Is this a child document, only to be interpreted in the context of the parent document from which it is linked? This may have implications for search and metadata requirements.

root allOf item 0 origin
Type: array of object

Origins of this resource.

Each item of this array must be:

root allOf item 0 origin origin items

root allOf item 0 origin origin items allOf item 0
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 origin origin items allOf item 0 if
Type: object

root allOf item 0 origin origin items allOf item 0 if source
Type: const
Specific value: "PubMed"
root allOf item 0 origin origin items allOf item 0 then
Type: object

root allOf item 0 origin origin items allOf item 0 then id
Type: string
Must match regular expression: ^[0-9]+$
root allOf item 0 origin origin items allOf item 1
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 origin origin items allOf item 1 if
Type: object

root allOf item 0 origin origin items allOf item 1 if source
Type: const
Specific value: "GEO"
root allOf item 0 origin origin items allOf item 1 then
Type: object

root allOf item 0 origin origin items allOf item 1 then id
Type: string
Must match regular expression: ^GSE[0-9]+$
root allOf item 0 origin origin items allOf item 2
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 origin origin items allOf item 2 if
Type: object

root allOf item 0 origin origin items allOf item 2 if source
Type: const
Specific value: "ArrayExpress"
root allOf item 0 origin origin items allOf item 2 then
Type: object

root allOf item 0 origin origin items allOf item 2 then id
Type: string
Must match regular expression: ^E-MTAB-[0-9]+$
root allOf item 0 origin origin items allOf item 3
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 origin origin items allOf item 3 if
Type: object

root allOf item 0 origin origin items allOf item 3 if source
Type: const
Specific value: "DOI"
root allOf item 0 origin origin items allOf item 3 then
Type: object

root allOf item 0 origin origin items allOf item 3 then id
Type: string
Must match regular expression: ^[0-9a-zA-Z\._-]+/[0-9a-zA-Z\._-]+$
root allOf item 0 origin origin items allOf item 4
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 origin origin items allOf item 4 if
Type: object

root allOf item 0 origin origin items allOf item 4 if source
Type: const
Specific value: "URI"
root allOf item 0 origin origin items allOf item 4 then
Type: object

root allOf item 0 origin origin items allOf item 4 then id
Type: string
Must match regular expression: ^(http|ftp|https|s3|sftp)://

root allOf item 0 origin origin items id
Type: string

Identifier for the resource in the specified type.

root allOf item 0 origin origin items source
Type: enum (of string)

Source database or repository.

Must be one of:

  • "PubMed"
  • "GEO"
  • "ArrayExpress"
  • "DOI"
  • "URI"

root allOf item 0 path
Type: string

Path to the file in the project directory.

root allOf item 0 species
Type: array of integer

Each item of this array must be:

root allOf item 0 species species items
Type: integer

NCBI taxonomy IDs of the species involved in this resource.

root allOf item 0 terms
Type: array of object

Terms from a controlled vocabulary, used to annotate this resource in a machine-readable manner.

Each item of this array must be:

root allOf item 0 terms terms items

No Additional Properties

root allOf item 0 terms terms items allOf item 0
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 terms terms items allOf item 0 if
Type: object

root allOf item 0 terms terms items allOf item 0 if source
Type: const
Specific value: "Experimental Factor Ontology"
root allOf item 0 terms terms items allOf item 0 then
Type: object

root allOf item 0 terms terms items allOf item 0 then id
Type: object
Must match regular expression: ^EFO:[0-9]{7}$
root allOf item 0 terms terms items allOf item 1
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 terms terms items allOf item 1 if
Type: object

root allOf item 0 terms terms items allOf item 1 if source
Type: const
Specific value: "Human Disease Ontology"
root allOf item 0 terms terms items allOf item 1 then
Type: object

root allOf item 0 terms terms items allOf item 1 then id
Type: object
Must match regular expression: ^DOID:[0-9]+$
root allOf item 0 terms terms items allOf item 2
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 terms terms items allOf item 2 if
Type: object

root allOf item 0 terms terms items allOf item 2 if source
Type: const
Specific value: "Cell Ontology"
root allOf item 0 terms terms items allOf item 2 then
Type: object

root allOf item 0 terms terms items allOf item 2 then id
Type: object
Must match regular expression: ^CL:[0-9]{7}$
root allOf item 0 terms terms items allOf item 3
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 0 terms terms items allOf item 3 if
Type: object

root allOf item 0 terms terms items allOf item 3 if source
Type: const
Specific value: "UBERON"
root allOf item 0 terms terms items allOf item 3 then
Type: object

root allOf item 0 terms terms items allOf item 3 then source
Type: const
Specific value: "^UBERON:[0-9]{7}$"

root allOf item 0 terms terms items id
Type: string

Identifier for the term.
Examples:

"EFO:0008913"

"DOID:13250"

"CL:0000097"

"UBERON:0005870"

root allOf item 0 terms terms items source
Type: enum (of string)

Name of the vocabulary or ontology that is the source for this term.

Must be one of:

  • "Experimental Factor Ontology"
  • "Human Disease Ontology"
  • "Cell Ontology"
  • "UBERON"

root allOf item 0 terms terms items version
Type: string

Version of the vocabulary.

root allOf item 0 title
Type: string

Title of the resource.
root allOf item 1
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

root allOf item 1 if

Must not be:

root allOf item 1 if not
Type: object

root allOf item 1 if not is_child
Type: const
Specific value: true
root allOf item 1 then
Type: object

The following properties are required:

  • title
  • description
  • authors
  • species
  • genome
  • origin
  • terms