Factor


Virtual factor-like object where the unique levels are some vector-like object, corresponding to the Factor class in the S4Vectors Bioconductor package. Each element of the factor is a 1-based integer index that refers to a specific level. The path property points to a comservatory-formatted CSV file containing a data frame with one index integer column with the indices for all factor elements. If the factor.names property is present, the first column of the data frame contains the names of the factor elements.

Concrete subclasses are expected to define a levels property that points to a vector-like object containing the levels.

Type: object

Type: string

The schema to use.

Type: array of object

Authors of this resource.

Each item of this array must be:

Type: object

Type: string

Email of the author.

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

Type: string

Name of the author.

Type: string

ORCID of the author.

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

Type: string

Description of the resource.

Type: object
No Additional Properties

Type: enum (of string)

Type of compression applied to the file.

Must be one of:

  • "none"
  • "gzip"
  • "bzip2"

Type: object

Pointer to a data frame additional annotations for each element in the factor. If omitted, no additional annotations are present.

Type: object

Type: string

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

Type: enum (of string)

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

Must be one of:

  • "local"

Type: integer

Length of the factor.

Type: boolean Default: false

Whether the factor is named. If true, the first column of CSV contains the names of the factor elements.

Type: object

Pointer to a list of additional metadata for this object.

Type: object

Type: string

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

Type: enum (of string)

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

Must be one of:

  • "local"

Type: array of object

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

Each item of this array must be:

Type: object

Type: string

Identifier for this genome build.


Examples:

"mm10"
"NCBIm37"

Type: enum (of string)

Source of the genome build identifier.

Must be one of:

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

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.

Type: string

MD5 checksum for the file.

Type: array of object

Origins of this resource.

Each item of this array must be:


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.

Type: object

Type: const
Specific value: "PubMed"
Type: object

Type: string
Must match regular expression: ^[0-9]+$
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.

Type: object

Type: const
Specific value: "GEO"
Type: object

Type: string
Must match regular expression: ^GSE[0-9]+$
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.

Type: object

Type: const
Specific value: "ArrayExpress"
Type: object

Type: string
Must match regular expression: ^E-MTAB-[0-9]+$
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.

Type: object

Type: const
Specific value: "DOI"
Type: object

Type: string
Must match regular expression: ^[0-9a-zA-Z\._-]+/[0-9a-zA-Z\._-]+$
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.

Type: object

Type: const
Specific value: "URI"
Type: object

Type: string
Must match regular expression: ^(http|ftp|https|s3|sftp)://

Type: string

Identifier for the resource in the specified type.

Type: enum (of string)

Source database or repository.

Must be one of:

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

Type: string

Path to the file in the project directory.

Type: array of integer

Each item of this array must be:

Type: integer

NCBI taxonomy IDs of the species involved in this resource.

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:


No Additional Properties

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.

Type: object

Type: const
Specific value: "Experimental Factor Ontology"
Type: object

Type: object
Must match regular expression: ^EFO:[0-9]{7}$
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.

Type: object

Type: const
Specific value: "Human Disease Ontology"
Type: object

Type: object
Must match regular expression: ^DOID:[0-9]+$
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.

Type: object

Type: const
Specific value: "Cell Ontology"
Type: object

Type: object
Must match regular expression: ^CL:[0-9]{7}$
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.

Type: object

Type: const
Specific value: "UBERON"
Type: object

Type: const
Specific value: "^UBERON:[0-9]{7}$"

Type: string

Identifier for the term.


Examples:

"EFO:0008913"
"DOID:13250"
"CL:0000097"
"UBERON:0005870"

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"

Type: string

Version of the vocabulary.

Type: string

Title of the resource.

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.


Must not be:

Type: object

Type: const
Specific value: true
Type: object

The following properties are required:

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