Dataset


A dataset containing multiple summarized experiments, possibly with non-trivial relationships between the columns of different experiments. This is derived from Bioconductor's MultiAssayExperiment class. This document contains pointers to the various components including the sample data, sample mapping and experiments.

root allOf item 0
Type: object

root allOf item 0 $schema
Type: string

The schema to use.

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 dataset
Type: object
No Additional Properties

root allOf item 0 dataset experiments
Type: array of object

Array of pointers to the summarized experiments. Each experiment should contain column names that are unique within that experiment.

Must contain a minimum of 1 items

Each item of this array must be:

root allOf item 0 dataset experiments experiments items
Type: object

root allOf item 0 dataset experiments experiments items name
Type: string

Name of the experiment. This should be a non-empty string. Experiment names should also be unique within experiments.

Must be at least 1 characters long

root allOf item 0 dataset experiments experiments items resource
Type: object

root allOf item 0 dataset experiments experiments items resource path
Type: string

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

root allOf item 0 dataset experiments experiments 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 dataset other_data
Type: object

Pointer to additional metadata for this object, typically stored as a list (via the basic_list schema).

root allOf item 0 dataset other_data resource
Type: object

root allOf item 0 dataset other_data resource path
Type: string

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

root allOf item 0 dataset other_data 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 dataset sample_data
Type: object

Pointer to the sample data. This should be a data frame with one row per sample in the dataset, where each column contains sample annotations. Row names should be present and unique.

root allOf item 0 dataset sample_data resource
Type: object

root allOf item 0 dataset sample_data resource path
Type: string

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

root allOf item 0 dataset sample_data 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 dataset sample_mapping
Type: object

Pointer to the sample mappings. This defines the relationships between columns of the summarized experiments and the samples in the dataset. The data frame should always contain three string columns:

  • sample, the sample name.
  • 'experiment', the name of the experiment.
  • 'column', the name of the column in that experiment.

Each row defines a single relationship between a sample and an experiment's column.

root allOf item 0 dataset sample_mapping resource
Type: object

root allOf item 0 dataset sample_mapping resource path
Type: string

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

root allOf item 0 dataset sample_mapping 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 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