Genomic Ranges


Genomic ranges, stored as a data frame inside a CSV file. Each row of the data frame corresponds to a genomic range. The data frame should contain at least the columns seqnames (character), start (integer), end (integer), and strand (character). If the genomic_ranges.names property is present, the first column of the CSV file contains the names of the ranges. The CSV file should comply with the comservatory specification.

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 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 genomic_ranges
Type: object
No Additional Properties

root allOf item 0 genomic_ranges compression
Type: enum (of string)

Type of compression applied to the file.

Must be one of:

  • "none"
  • "gzip"
  • "bzip2"

root allOf item 0 genomic_ranges length
Type: integer

Number of entries.

root allOf item 0 genomic_ranges names
Type: boolean Default: false

Whether the ranges are named. If true, the first column of CSV contains the names of the individual ranges.

root allOf item 0 genomic_ranges other_data
Type: object

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

root allOf item 0 genomic_ranges other_data resource
Type: object

root allOf item 0 genomic_ranges other_data resource path
Type: string

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

root allOf item 0 genomic_ranges 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 genomic_ranges range_data
Type: object

Location of additional annotations for each genomic range. If omitted, no additional annotations are present.

root allOf item 0 genomic_ranges range_data resource
Type: object

root allOf item 0 genomic_ranges range_data resource path
Type: string

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

root allOf item 0 genomic_ranges range_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 genomic_ranges sequence_information
Type: object

Location of the file containing the sequence information.

root allOf item 0 genomic_ranges sequence_information resource
Type: object

root allOf item 0 genomic_ranges sequence_information resource path
Type: string

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

root allOf item 0 genomic_ranges sequence_information 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 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 md5sum
Type: string

MD5 checksum for the file.

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