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Class: File

Abstract class for various kinds of files. Subclasses may be defined for specific file types.

URI: bdchm:File

classDiagram class File Entity <|-- File File : associated_participant File --> Participant : associated_participant File : data_category File : data_type File : derived_from File --> File : derived_from File : description File : file_location File : file_name File : file_size File : format File : id File : identity File : md5sum

Inheritance

Slots

Name Cardinality and Range Description Inheritance
identity 0..*
Uriorcurie		 A 'business' identifier or accession number for the entity, typically as prov... direct
file_name 0..1
String		 The name (or part of a name) of a file (of any type) direct
file_size 0..1
Integer		 The size of the data file (object) in bytes direct
file_location 0..*
Uriorcurie		 A unique identifier or url for identifying or locating the file direct
md5sum 0..1
String		 The 128-bit hash value expressed as a 32 digit hexadecimal number used as a f... direct
data_type 0..1
String		 The nature or genre of the resource direct
data_category 0..1
String		 A broad categorization of the contents of the data file direct
format 0..1
String		 The file format, physical medium, or dimensions of the resource direct
description 0..1
String		 An account of the resource direct
associated_participant 0..1
Participant		 A reference to the Participant to which this file relates direct
derived_from 0..1
File		 A File from which this File is derived direct
id 1..1
Uriorcurie		 The 'logical' identifier of the entity within the system of record Entity

Usages

used by used in type used
File derived_from range File

Comments

  • This is taken largely from the Gen3 Core Metadata Collection definition.
  • Gen3 apparently took most of the attributes listed here from the Dublin Core /elements/1.1/ namespace.
  • Attributes different from those in Dublin Core are noted as such in the comments.
  • The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this?
  • Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here?
  • Tentatively including three attribute for addressing this -- identifier, file_path, and uri.
  • There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files.

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/nhlbidatastage/bdchm

Mappings

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

LinkML Source

Direct

name: File
description: Abstract class for various kinds of files. Subclasses may be defined
  for specific file types.
comments:
- This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD)
  definition.
- Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/
  namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3).
- Attributes different from those in Dublin Core are noted as such in the comments.
- The Document entity was defined in this model prior to defining this File entity.
  Should it be modified to be a subclass of this?
- Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't
  have a file location or unique identifier. Should that be left to specific File
  subclasses or defined here?
- Tentatively including three attribute for addressing this -- identifier, file_path,
  and uri.
- There appear to be 11 specific file types defined in Gen3, 8 types classified as
  Data Files and 3 classified as Index Files.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
slots:
- identity
attributes:
  file_name:
    name: file_name
    description: The name (or part of a name) of a file (of any type).
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: string
  file_size:
    name: file_size
    description: The size of the data file (object) in bytes.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: integer
  file_location:
    name: file_location
    description: A unique identifier or url for identifying or locating the file.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: uriorcurie
  md5sum:
    name: md5sum
    description: The 128-bit hash value expressed as a 32 digit hexadecimal number
      used as a file's digital fingerprint.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: string
  data_type:
    name: data_type
    description: The nature or genre of the resource. Recommended best practice is
      to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7).
      To describe the file format, physical medium, or dimensions of the resource,
      use the Format element.
    comments:
    - Called 'type' in Dublin Core.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: string
  data_category:
    name: data_category
    description: A broad categorization of the contents of the data file.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: string
  format:
    name: format
    description: The file format, physical medium, or dimensions of the resource.
      Examples of dimensions include size and duration. Recommended best practice
      is to use a controlled vocabulary such as the list of Internet Media Types [MIME]
      (http://www.iana.org/assignments/media-types/).
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: string
  description:
    name: description
    description: 'An account of the resource. Description may include but is not limited
      to: an abstract, a table of contents, a graphical representation, or a free-text
      account of the resource.'
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    range: string
  associated_participant:
    name: associated_participant
    description: A reference to the Participant to which this file relates.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    range: Participant
  derived_from:
    name: derived_from
    description: A File from which this File is derived.  A derivation is a transformation
      of an entity into another, an update of an entity resulting in a new one, or
      the construction of a new entity based on a pre-existing entity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    range: File

Induced

name: File
description: Abstract class for various kinds of files. Subclasses may be defined
  for specific file types.
comments:
- This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD)
  definition.
- Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/
  namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3).
- Attributes different from those in Dublin Core are noted as such in the comments.
- The Document entity was defined in this model prior to defining this File entity.
  Should it be modified to be a subclass of this?
- Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't
  have a file location or unique identifier. Should that be left to specific File
  subclasses or defined here?
- Tentatively including three attribute for addressing this -- identifier, file_path,
  and uri.
- There appear to be 11 specific file types defined in Gen3, 8 types classified as
  Data Files and 3 classified as Index Files.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  file_name:
    name: file_name
    description: The name (or part of a name) of a file (of any type).
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: file_name
    owner: File
    domain_of:
    - File
    range: string
  file_size:
    name: file_size
    description: The size of the data file (object) in bytes.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: file_size
    owner: File
    domain_of:
    - File
    range: integer
  file_location:
    name: file_location
    description: A unique identifier or url for identifying or locating the file.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: file_location
    owner: File
    domain_of:
    - File
    range: uriorcurie
  md5sum:
    name: md5sum
    description: The 128-bit hash value expressed as a 32 digit hexadecimal number
      used as a file's digital fingerprint.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: md5sum
    owner: File
    domain_of:
    - File
    range: string
  data_type:
    name: data_type
    description: The nature or genre of the resource. Recommended best practice is
      to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7).
      To describe the file format, physical medium, or dimensions of the resource,
      use the Format element.
    comments:
    - Called 'type' in Dublin Core.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: data_type
    owner: File
    domain_of:
    - File
    range: string
  data_category:
    name: data_category
    description: A broad categorization of the contents of the data file.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: data_category
    owner: File
    domain_of:
    - File
    range: string
  format:
    name: format
    description: The file format, physical medium, or dimensions of the resource.
      Examples of dimensions include size and duration. Recommended best practice
      is to use a controlled vocabulary such as the list of Internet Media Types [MIME]
      (http://www.iana.org/assignments/media-types/).
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: format
    owner: File
    domain_of:
    - File
    range: string
  description:
    name: description
    description: 'An account of the resource. Description may include but is not limited
      to: an abstract, a table of contents, a graphical representation, or a free-text
      account of the resource.'
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    alias: description
    owner: File
    domain_of:
    - Participant
    - ResearchStudy
    - Questionnaire
    - File
    - Document
    - Specimen
    - BiologicProduct
    range: string
  associated_participant:
    name: associated_participant
    description: A reference to the Participant to which this file relates.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    alias: associated_participant
    owner: File
    domain_of:
    - Demography
    - Visit
    - Condition
    - Procedure
    - Exposure
    - File
    - ObservationSet
    - Observation
    range: Participant
  derived_from:
    name: derived_from
    description: A File from which this File is derived.  A derivation is a transformation
      of an entity into another, an update of an entity resulting in a new one, or
      the construction of a new entity based on a pre-existing entity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: derived_from
    owner: File
    domain_of:
    - File
    range: File
  identity:
    name: identity
    description: A 'business' identifier or accession number for the entity, typically
      as provided by an external system or authority, that are globally unique and
      persist across implementing systems. Also, since these identifiers are created
      outside the information system through a specific business process, the Identifier
      type has additional attributes to capture this additional metadata so the actual
      identifier values are qualified by the context that created those values. This
      additional context allows "identifier" instances to be transmitted as business
      data across systems while still being able to trace them back to the system
      of origin.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    slot_uri: schema:identifier
    multivalued: true
    alias: identity
    owner: File
    domain_of:
    - Person
    - Demography
    - Participant
    - ResearchStudy
    - Organization
    - Questionnaire
    - QuestionnaireItem
    - Condition
    - Procedure
    - Exposure
    - File
    - Document
    - Specimen
    - BiologicProduct
    range: uriorcurie
  id:
    name: id
    description: The 'logical' identifier of the entity within the system of record.  The
      simple value of this attribute stands for an identifier of this data object
      within the system, it can be used as a reference from other objects within the
      same system (i.e. primary and foreign keys), and it should be unique per type
      of object. The same data object copied to a different system will likely have
      a different "id" in the new system since "id" values are system specific and
      do not represent persistent business identifiers. Business identifiers are assigned
      outside the information system and are captured in the "identifier" field. The
      "id" field is more likely to be a serially or randomly generated value that
      is assigned to the data object as it is created in a system.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: File
    domain_of:
    - Entity
    range: uriorcurie
    required: true