Class: File (File)

File

 classDiagram
    class File
    click File href "../File/"
      Record <|-- File
        click Record href "../Record/"

      File : access_policy_id





        File --> "0..1" AccessPolicy : access_policy_id
        click AccessPolicy href "../AccessPolicy/"



      File : availability





        File --> "0..1" EnumAvailabilityStatus : availability
        click EnumAvailabilityStatus href "../EnumAvailabilityStatus/"



      File : data_category





        File --> "0..1" Concept : data_category
        click Concept href "../Concept/"



      File : data_type





        File --> "0..1" EnumEDAMDataTypes : data_type
        click EnumEDAMDataTypes href "../EnumEDAMDataTypes/"



      File : drs_uri

      File : external_id

      File : file_extension

      File : file_id

      File : filename

      File : format





        File --> "0..1" EnumEDAMFormats : format
        click EnumEDAMFormats href "../EnumEDAMFormats/"



      File : hash





        File --> "*" FileHash : hash
        click FileHash href "../FileHash/"



      File : internal_uri

      File : release_uri

      File : sample_id





        File --> "*" Sample : sample_id
        click Sample href "../Sample/"



      File : size

      File : storage_class

      File : study_id





        File --> "0..1" Study : study_id
        click Study href "../Study/"



      File : subject_id





        File --> "*" Subject : subject_id
        click Subject href "../Subject/"

Inheritance

File [ Record]

Slots

Name	Cardinality and Range	Description	Inheritance
file_id	1 DrGlobalID	Unique identifier for this File	direct
subject_id	* Subject	INCLUDE Global ID for the Subject	direct
sample_id	* Sample	The unique identifier for this Sample	direct
filename	0..1 String	The name of the file	direct
format	0..1 EnumEDAMFormats	The format of the file	direct
file_extension	1 String	Typically a 3-4 letter code at the end of a filename that identifies the file...	direct
data_category	0..1 Concept or EnumDataCategory	General category of data in this Record (e	direct
data_type	0..1 EnumEDAMDataTypes	The type of data within this file	direct
format	0..1 EnumEDAMFormats	The format of the file	direct
size	0..1 Integer	Size of the file, in Bytes	direct
internal_uri	0..1 Uriorcurie	URI/URL for internal access to the data	direct
release_uri	0..1 Uriorcurie	URI/URL for controlled or open access to the data	direct
drs_uri	0..1 Uriorcurie	DRS location to access the data	direct
storage_class	0..1 String	Storage class of the object, reflecting cost and access characteristics	direct
hash	* FileHash	File hash information	direct
availability	0..1 EnumAvailabilityStatus	Is or was this file available to users?	direct
external_id	* Uriorcurie	Other identifiers for this entity, eg, from the submitting study or in system...	Record
access_policy_id	0..1 AccessPolicy	Global identifier for the access policy that applies to this row of data	Record
study_id	0..1 Study	INCLUDE Global ID for the study	Record

Usages

used by	used in	type	used
Assay	file_id	range	File
Dataset	file_id	range	File

Identifier and Mapping Information

Schema Source

from schema: https://includedcc.org/include-access-model

Mappings

Mapping Type	Mapped Value
self	includedcc:File
native	includedcc:File

LinkML Source

Direct

name: File
description: File
title: File
from_schema: https://includedcc.org/include-access-model
mixins:
- Record
slots:
- file_id
- subject_id
- sample_id
- filename
- format
- file_extension
- data_category
- data_type
- format
- size
- internal_uri
- release_uri
- drs_uri
- storage_class
- hash
- availability
slot_usage:
  file_id:
    name: file_id
    identifier: true
    range: drGlobalID
    required: true
  subject_id:
    name: subject_id
    multivalued: true
  sample_id:
    name: sample_id
    multivalued: true

Induced

name: File
description: File
title: File
from_schema: https://includedcc.org/include-access-model
mixins:
- Record
slot_usage:
  file_id:
    name: file_id
    identifier: true
    range: drGlobalID
    required: true
  subject_id:
    name: subject_id
    multivalued: true
  sample_id:
    name: sample_id
    multivalued: true
attributes:
  file_id:
    name: file_id
    description: Unique identifier for this File.
    title: File ID
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    identifier: true
    owner: File
    domain_of:
    - File
    - Assay
    - Dataset
    range: drGlobalID
    required: true
  subject_id:
    name: subject_id
    description: INCLUDE Global ID for the Subject
    title: Study ID
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - Subject
    - Demographics
    - FamilyRelationship
    - FamilyMembership
    - SubjectAssertion
    - Encounter
    - File
    - Assay
    range: Subject
    multivalued: true
  sample_id:
    name: sample_id
    description: The unique identifier for this Sample.
    title: Sample ID
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - Sample
    - Aliquot
    - File
    - Assay
    range: Sample
    multivalued: true
  filename:
    name: filename
    description: The name of the file.
    title: Filename
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: string
  format:
    name: format
    description: The format of the file.
    title: File Format
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: EnumEDAMFormats
  file_extension:
    name: file_extension
    description: Typically a 3-4 letter code at the end of a filename that identifies
      the file format. Empty string for no extension.
    title: File Extension
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: string
    required: true
  data_category:
    name: data_category
    description: General category of data in this Record (e.g. Clinical, Genomics,
      etc)
    title: Data Category
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - StudyMetadata
    - File
    range: Concept
    any_of:
    - range: Concept
    - range: EnumDataCategory
  data_type:
    name: data_type
    description: The type of data within this file.
    title: Data Type
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: EnumEDAMDataTypes
  size:
    name: size
    description: Size of the file, in Bytes. May require BigInt or similar.
    title: File Size
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: integer
    unit:
      ucum_code: By
  internal_uri:
    name: internal_uri
    description: URI/URL for internal access to the data. May be temporary.
    title: Internal Staging Location
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: uriorcurie
  release_uri:
    name: release_uri
    description: URI/URL for controlled or open access to the data.
    title: Release Location
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: uriorcurie
  drs_uri:
    name: drs_uri
    description: DRS location to access the data.
    title: DRS URI
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: uriorcurie
  storage_class:
    name: storage_class
    description: Storage class of the object, reflecting cost and access characteristics.
    title: Storage Class
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: string
  hash:
    name: hash
    description: File hash information
    title: File Hash
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: FileHash
    multivalued: true
  availability:
    name: availability
    description: Is or was this file available to users?
    title: File Availability
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - File
    range: EnumAvailabilityStatus
  external_id:
    name: external_id
    description: Other identifiers for this entity, eg, from the submitting study
      or in systems like dbGaP
    title: External Identifiers
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - Record
    range: uriorcurie
    required: false
    multivalued: true
  access_policy_id:
    name: access_policy_id
    description: Global identifier for the access policy that applies to this row
      of data.
    title: Access Policy ID
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - Record
    - AccessPolicy
    range: AccessPolicy
  study_id:
    name: study_id
    description: INCLUDE Global ID for the study
    title: Study ID
    from_schema: https://includedcc.org/include-access-model
    rank: 1000
    owner: File
    domain_of:
    - Record
    - StudyMetadata
    range: Study
    multivalued: false