Class: DataObject

An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.

URI: nmdc:DataObject

classDiagram class DataObject click DataObject href "../DataObject" NamedThing <|-- DataObject click NamedThing href "../NamedThing" DataObject : alternative_identifiers DataObject : compression_type DataObject : data_object_type DataObject --> "1" FileTypeEnum : data_object_type click FileTypeEnum href "../FileTypeEnum" DataObject : description DataObject : file_size_bytes DataObject : id DataObject : md5_checksum DataObject : name DataObject : type DataObject : url DataObject : was_generated_by DataObject --> "1" Activity : was_generated_by click Activity href "../Activity"

Inheritance

NamedThing
- DataObject

Slots

Name	Cardinality and Range	Description	Inheritance
file_size_bytes	0..1 Bytes	Size of the file in bytes	direct
md5_checksum	0..1 String	MD5 checksum of file (pre-compressed)	direct
data_object_type	0..1 FileTypeEnum	The type of file represented by the data object	direct
compression_type	0..1 String	If provided, specifies the compression type	direct
was_generated_by	0..1 Activity		direct
url	0..1 String		direct
type	0..1 String	An optional string that specifies the type object	direct
id	1..1 Uriorcurie	A unique identifier for a thing	NamedThing
name	1..1 String	A human readable label for an entity	NamedThing
description	1..1 String	a human-readable description of a thing	NamedThing
alternative_identifiers	0..* Uriorcurie	A list of alternative identifiers for the entity	NamedThing

Usages

used by	used in	type	used
Database	data_object_set	range	DataObject
DataObject	file_size_bytes	domain	DataObject
OmicsProcessing	has_output	range	DataObject

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:DataObject
native	nmdc:DataObject

LinkML Source

Direct

name: DataObject
description: An object that primarily consists of symbols that represent information.   Files,
  records, and omics data are examples of data objects.
in_subset:
- data object subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: NamedThing
slots:
- file_size_bytes
- md5_checksum
- data_object_type
- compression_type
- was_generated_by
- url
- type
slot_usage:
  name:
    name: name
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    required: true
  description:
    name: description
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    required: true
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true

Induced

name: DataObject
description: An object that primarily consists of symbols that represent information.   Files,
  records, and omics data are examples of data objects.
in_subset:
- data object subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: NamedThing
slot_usage:
  name:
    name: name
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    required: true
  description:
    name: description
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    required: true
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
attributes:
  file_size_bytes:
    name: file_size_bytes
    description: Size of the file in bytes
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: DataObject
    alias: file_size_bytes
    owner: DataObject
    domain_of:
    - DataObject
    range: bytes
  md5_checksum:
    name: md5_checksum
    description: MD5 checksum of file (pre-compressed)
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: md5_checksum
    owner: DataObject
    domain_of:
    - DataObject
    range: string
  data_object_type:
    name: data_object_type
    description: The type of file represented by the data object.
    examples:
    - value: FT ICR-MS Analysis Results
    - value: GC-MS Metabolomics Results
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: data_object_type
    owner: DataObject
    domain_of:
    - DataObject
    range: FileTypeEnum
  compression_type:
    name: compression_type
    description: If provided, specifies the compression type
    todos:
    - consider setting the range to an enum
    examples:
    - value: gzip
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: compression_type
    owner: DataObject
    domain_of:
    - DataObject
    range: string
  was_generated_by:
    name: was_generated_by
    from_schema: https://w3id.org/nmdc/nmdc
    mappings:
    - prov:wasGeneratedBy
    rank: 1000
    alias: was_generated_by
    owner: DataObject
    domain_of:
    - DataObject
    - AttributeValue
    - FunctionalAnnotation
    range: Activity
  url:
    name: url
    notes:
    - See issue 207 - this clashes with the mixs field
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: url
    owner: DataObject
    domain_of:
    - Protocol
    - DataObject
    - ImageValue
    range: string
  type:
    name: type
    description: An optional string that specifies the type object.  This is used
      to allow for searches for different kinds of objects.
    deprecated: Due to confusion about what values are used for this slot, it is best
      not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.
      MAM removed designates_type and rdf:type slot uri 2022-11-30
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    rank: 1000
    alias: type
    owner: DataObject
    domain_of:
    - DataObject
    - Biosample
    - Study
    - OmicsProcessing
    - CreditAssociation
    - MagBin
    - GenomeFeature
    - WorkflowExecutionActivity
    - MetagenomeAssembly
    - MetagenomeAnnotationActivity
    - MetatranscriptomeAnnotationActivity
    - MetatranscriptomeActivity
    - MagsAnalysisActivity
    - ReadQcAnalysisActivity
    - ReadBasedTaxonomyAnalysisActivity
    range: string
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: DataObject
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: DataObject
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    range: string
    required: true
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: DataObject
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    range: string
    required: true
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: DataObject
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - MetaboliteQuantification
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$