Class: File

A stable digital asset

classDiagram class File File : analysis_type File : assay_type File : bundle_collection_id_namespace File : bundle_collection_local_id File : compression_format File : creation_time File : data_type File : dbgap_study_id File : file_format File : filename File : id_namespace File : local_id File : md5 File : mime_type File : persistent_id File : project_id_namespace File : project_local_id File : sha256 File : size_in_bytes File : uncompressed_size_in_bytes

Slots

Name	Range	Cardinality	Description	Info
id_namespace	IdNamespace	1..1	A CFDE-cleared identifier representing the top-level data space containing this file [part 1 of 2-component composite primary key]	.
local_id	xsd:string	1..1	An identifier representing this file, unique within this id_namespace [part 2 of 2-component composite primary key]	.
project_id_namespace	xsd:string	1..1	The id_namespace of the primary project within which this file was created [part 1 of 2-component composite foreign key]	.
project_local_id	xsd:string	1..1	The local_id of the primary project within which this file was created [part 2 of 2-component composite foreign key]	.
persistent_id	xsd:string	0..1	A persistent, resolvable (not necessarily retrievable) URI or compact ID permanently attached to this file	.
creation_time	xsd:dateTime	0..1	An ISO 8601 -- RFC 3339 (subset)-compliant timestamp documenting this file's creation time: YYYY-MM-DDTHH:MM:SS±NN:NN	.
size_in_bytes	xsd:integer	0..1	The size of this file in bytes	.
uncompressed_size_in_bytes	xsd:integer	0..1	The total decompressed size in bytes of the contents of this file: null if this file is not compressed	.
sha256	xsd:string	0..1	(preferred) SHA-256 checksum for this file [sha256, md5 cannot both be null]	.
md5	xsd:string	0..1	(allowed) MD5 checksum for this file [sha256, md5 cannot both be null]	.
filename	xsd:string	0..1	A filename with no prepended PATH information	.
file_format	FileFormat	0..1	An EDAM CV term ID identifying the digital format of this file (e.g. TSV or FASTQ): if this file is compressed, this should be its uncompressed format	.
compression_format	FileFormat	0..1	An EDAM CV term ID identifying the compression format of this file (e.g. gzip or bzip2): null if this file is not compressed	.
data_type	DataType	0..1	An EDAM CV term ID identifying the type of information stored in this file (e.g. RNA sequence reads): null if is_bundle is set to true	.
assay_type	AssayType	0..1	An OBI CV term ID describing the type of experiment that generated the results summarized by this file	.
analysis_type	AnalysisType	0..1	An OBI CV term ID describing the type of analytic operation that generated this file	.
mime_type	xsd:string	0..1	A MIME type describing this file	.
bundle_collection_id_namespace	xsd:string	0..1	If this file is a bundle encoding more than one sub-file, this field gives the id_namespace of a collection listing the bundle's sub-file contents; null otherwise	.
bundle_collection_local_id	xsd:string	0..1	If this file is a bundle encoding more than one sub-file, this field gives the local_id of a collection listing the bundle's sub-file contents; null otherwise	.
dbgap_study_id	xsd:string	0..1	The name of a dbGaP study ID governing access control for this file, compatible for comparison to RAS user-level access control metadata	.

Usages

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/linkml/cfde

Mappings

Mapping Type	Mapped Value
self	['cfde_schema:File']
native	['cfde_schema:File']

LinkML Specification

Direct

name: file
description: A stable digital asset
title: file
from_schema: https://w3id.org/linkml/cfde
attributes:
  id_namespace:
    name: id_namespace
    description: A CFDE-cleared identifier representing the top-level data space containing
      this file [part 1 of 2-component composite primary key]
    from_schema: https://w3id.org/linkml/cfde
    range: id_namespace
    required: true
  local_id:
    name: local_id
    description: An identifier representing this file, unique within this id_namespace
      [part 2 of 2-component composite primary key]
    from_schema: https://w3id.org/linkml/cfde
    range: string
    required: true
  project_id_namespace:
    name: project_id_namespace
    description: The id_namespace of the primary project within which this file was
      created [part 1 of 2-component composite foreign key]
    from_schema: https://w3id.org/linkml/cfde
    range: string
    required: true
  project_local_id:
    name: project_local_id
    description: The local_id of the primary project within which this file was created
      [part 2 of 2-component composite foreign key]
    from_schema: https://w3id.org/linkml/cfde
    range: string
    required: true
  persistent_id:
    name: persistent_id
    description: A persistent, resolvable (not necessarily retrievable) URI or compact
      ID permanently attached to this file
    from_schema: https://w3id.org/linkml/cfde
    range: string
  creation_time:
    name: creation_time
    description: 'An ISO 8601 -- RFC 3339 (subset)-compliant timestamp documenting
      this file''s creation time: YYYY-MM-DDTHH:MM:SS±NN:NN'
    from_schema: https://w3id.org/linkml/cfde
    range: datetime
  size_in_bytes:
    name: size_in_bytes
    description: The size of this file in bytes
    from_schema: https://w3id.org/linkml/cfde
    range: integer
  uncompressed_size_in_bytes:
    name: uncompressed_size_in_bytes
    description: 'The total decompressed size in bytes of the contents of this file:
      null if this file is not compressed'
    from_schema: https://w3id.org/linkml/cfde
    range: integer
  sha256:
    name: sha256
    description: (preferred) SHA-256 checksum for this file [sha256, md5 cannot both
      be null]
    from_schema: https://w3id.org/linkml/cfde
    range: string
  md5:
    name: md5
    description: (allowed) MD5 checksum for this file [sha256, md5 cannot both be
      null]
    from_schema: https://w3id.org/linkml/cfde
    range: string
  filename:
    name: filename
    description: A filename with no prepended PATH information
    from_schema: https://w3id.org/linkml/cfde
    range: string
    pattern: ^[^/\:]+$
  file_format:
    name: file_format
    description: 'An EDAM CV term ID identifying the digital format of this file (e.g.
      TSV or FASTQ): if this file is compressed, this should be its _uncompressed_
      format'
    from_schema: https://w3id.org/linkml/cfde
    range: file_format
  compression_format:
    name: compression_format
    description: 'An EDAM CV term ID identifying the compression format of this file
      (e.g. gzip or bzip2): null if this file is not compressed'
    from_schema: https://w3id.org/linkml/cfde
    range: file_format
  data_type:
    name: data_type
    description: 'An EDAM CV term ID identifying the type of information stored in
      this file (e.g. RNA sequence reads): null if is_bundle is set to true'
    from_schema: https://w3id.org/linkml/cfde
    range: data_type
  assay_type:
    name: assay_type
    description: An OBI CV term ID describing the type of experiment that generated
      the results summarized by this file
    from_schema: https://w3id.org/linkml/cfde
    range: assay_type
  analysis_type:
    name: analysis_type
    description: An OBI CV term ID describing the type of analytic operation that
      generated this file
    from_schema: https://w3id.org/linkml/cfde
    range: analysis_type
  mime_type:
    name: mime_type
    description: A MIME type describing this file
    from_schema: https://w3id.org/linkml/cfde
    range: string
  bundle_collection_id_namespace:
    name: bundle_collection_id_namespace
    description: If this file is a bundle encoding more than one sub-file, this field
      gives the id_namespace of a collection listing the bundle's sub-file contents;
      null otherwise
    from_schema: https://w3id.org/linkml/cfde
    range: string
  bundle_collection_local_id:
    name: bundle_collection_local_id
    description: If this file is a bundle encoding more than one sub-file, this field
      gives the local_id of a collection listing the bundle's sub-file contents; null
      otherwise
    from_schema: https://w3id.org/linkml/cfde
    range: string
  dbgap_study_id:
    name: dbgap_study_id
    description: The name of a dbGaP study ID governing access control for this file,
      compatible for comparison to RAS user-level access control metadata
    from_schema: https://w3id.org/linkml/cfde
    range: string
unique_keys:
  file_primary_key:
    unique_key_name: file_primary_key
    unique_key_slots:
    - '[''id_namespace'', ''local_id'']'

Induced

name: file
description: A stable digital asset
title: file
from_schema: https://w3id.org/linkml/cfde
attributes:
  id_namespace:
    name: id_namespace
    description: A CFDE-cleared identifier representing the top-level data space containing
      this file [part 1 of 2-component composite primary key]
    from_schema: https://w3id.org/linkml/cfde
    alias: id_namespace
    owner: file
    range: id_namespace
    required: true
  local_id:
    name: local_id
    description: An identifier representing this file, unique within this id_namespace
      [part 2 of 2-component composite primary key]
    from_schema: https://w3id.org/linkml/cfde
    alias: local_id
    owner: file
    range: string
    required: true
  project_id_namespace:
    name: project_id_namespace
    description: The id_namespace of the primary project within which this file was
      created [part 1 of 2-component composite foreign key]
    from_schema: https://w3id.org/linkml/cfde
    alias: project_id_namespace
    owner: file
    range: string
    required: true
  project_local_id:
    name: project_local_id
    description: The local_id of the primary project within which this file was created
      [part 2 of 2-component composite foreign key]
    from_schema: https://w3id.org/linkml/cfde
    alias: project_local_id
    owner: file
    range: string
    required: true
  persistent_id:
    name: persistent_id
    description: A persistent, resolvable (not necessarily retrievable) URI or compact
      ID permanently attached to this file
    from_schema: https://w3id.org/linkml/cfde
    alias: persistent_id
    owner: file
    range: string
  creation_time:
    name: creation_time
    description: 'An ISO 8601 -- RFC 3339 (subset)-compliant timestamp documenting
      this file''s creation time: YYYY-MM-DDTHH:MM:SS±NN:NN'
    from_schema: https://w3id.org/linkml/cfde
    alias: creation_time
    owner: file
    range: datetime
  size_in_bytes:
    name: size_in_bytes
    description: The size of this file in bytes
    from_schema: https://w3id.org/linkml/cfde
    alias: size_in_bytes
    owner: file
    range: integer
  uncompressed_size_in_bytes:
    name: uncompressed_size_in_bytes
    description: 'The total decompressed size in bytes of the contents of this file:
      null if this file is not compressed'
    from_schema: https://w3id.org/linkml/cfde
    alias: uncompressed_size_in_bytes
    owner: file
    range: integer
  sha256:
    name: sha256
    description: (preferred) SHA-256 checksum for this file [sha256, md5 cannot both
      be null]
    from_schema: https://w3id.org/linkml/cfde
    alias: sha256
    owner: file
    range: string
  md5:
    name: md5
    description: (allowed) MD5 checksum for this file [sha256, md5 cannot both be
      null]
    from_schema: https://w3id.org/linkml/cfde
    alias: md5
    owner: file
    range: string
  filename:
    name: filename
    description: A filename with no prepended PATH information
    from_schema: https://w3id.org/linkml/cfde
    alias: filename
    owner: file
    range: string
    pattern: ^[^/\:]+$
  file_format:
    name: file_format
    description: 'An EDAM CV term ID identifying the digital format of this file (e.g.
      TSV or FASTQ): if this file is compressed, this should be its _uncompressed_
      format'
    from_schema: https://w3id.org/linkml/cfde
    alias: file_format
    owner: file
    range: file_format
  compression_format:
    name: compression_format
    description: 'An EDAM CV term ID identifying the compression format of this file
      (e.g. gzip or bzip2): null if this file is not compressed'
    from_schema: https://w3id.org/linkml/cfde
    alias: compression_format
    owner: file
    range: file_format
  data_type:
    name: data_type
    description: 'An EDAM CV term ID identifying the type of information stored in
      this file (e.g. RNA sequence reads): null if is_bundle is set to true'
    from_schema: https://w3id.org/linkml/cfde
    alias: data_type
    owner: file
    range: data_type
  assay_type:
    name: assay_type
    description: An OBI CV term ID describing the type of experiment that generated
      the results summarized by this file
    from_schema: https://w3id.org/linkml/cfde
    alias: assay_type
    owner: file
    range: assay_type
  analysis_type:
    name: analysis_type
    description: An OBI CV term ID describing the type of analytic operation that
      generated this file
    from_schema: https://w3id.org/linkml/cfde
    alias: analysis_type
    owner: file
    range: analysis_type
  mime_type:
    name: mime_type
    description: A MIME type describing this file
    from_schema: https://w3id.org/linkml/cfde
    alias: mime_type
    owner: file
    range: string
  bundle_collection_id_namespace:
    name: bundle_collection_id_namespace
    description: If this file is a bundle encoding more than one sub-file, this field
      gives the id_namespace of a collection listing the bundle's sub-file contents;
      null otherwise
    from_schema: https://w3id.org/linkml/cfde
    alias: bundle_collection_id_namespace
    owner: file
    range: string
  bundle_collection_local_id:
    name: bundle_collection_local_id
    description: If this file is a bundle encoding more than one sub-file, this field
      gives the local_id of a collection listing the bundle's sub-file contents; null
      otherwise
    from_schema: https://w3id.org/linkml/cfde
    alias: bundle_collection_local_id
    owner: file
    range: string
  dbgap_study_id:
    name: dbgap_study_id
    description: The name of a dbGaP study ID governing access control for this file,
      compatible for comparison to RAS user-level access control metadata
    from_schema: https://w3id.org/linkml/cfde
    alias: dbgap_study_id
    owner: file
    range: string
unique_keys:
  file_primary_key:
    unique_key_name: file_primary_key
    unique_key_slots:
    - '[''id_namespace'', ''local_id'']'