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Class: Database

An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to collections.

URI: nmdc:Database

classDiagram class Database click Database href "../Database" Database : biosample_set Database --> "*" Biosample : biosample_set click Biosample href "../Biosample" Database : calibration_set Database --> "*" CalibrationInformation : calibration_set click CalibrationInformation href "../CalibrationInformation" Database : chemical_entity_set Database --> "*" ChemicalEntity : chemical_entity_set click ChemicalEntity href "../ChemicalEntity" Database : collecting_biosamples_from_site_set Database --> "*" CollectingBiosamplesFromSite : collecting_biosamples_from_site_set click CollectingBiosamplesFromSite href "../CollectingBiosamplesFromSite" Database : configuration_set Database --> "*" Configuration : configuration_set click Configuration href "../Configuration" Database : data_generation_set Database --> "*" DataGeneration : data_generation_set click DataGeneration href "../DataGeneration" Database : data_object_set Database --> "*" DataObject : data_object_set click DataObject href "../DataObject" Database : field_research_site_set Database --> "*" FieldResearchSite : field_research_site_set click FieldResearchSite href "../FieldResearchSite" Database : functional_annotation_agg Database --> "*" FunctionalAnnotationAggMember : functional_annotation_agg click FunctionalAnnotationAggMember href "../FunctionalAnnotationAggMember" Database : functional_annotation_set Database --> "*" FunctionalAnnotation : functional_annotation_set click FunctionalAnnotation href "../FunctionalAnnotation" Database : genome_feature_set Database --> "*" GenomeFeature : genome_feature_set click GenomeFeature href "../GenomeFeature" Database : instrument_set Database --> "*" Instrument : instrument_set click Instrument href "../Instrument" Database : manifest_set Database --> "*" Manifest : manifest_set click Manifest href "../Manifest" Database : material_processing_set Database --> "*" MaterialProcessing : material_processing_set click MaterialProcessing href "../MaterialProcessing" Database : processed_sample_set Database --> "*" ProcessedSample : processed_sample_set click ProcessedSample href "../ProcessedSample" Database : protocol_execution_set Database --> "*" ProtocolExecution : protocol_execution_set click ProtocolExecution href "../ProtocolExecution" Database : storage_process_set Database --> "*" StorageProcess : storage_process_set click StorageProcess href "../StorageProcess" Database : study_set Database --> "*" Study : study_set click Study href "../Study" Database : workflow_execution_set Database --> "*" WorkflowExecution : workflow_execution_set click WorkflowExecution href "../WorkflowExecution"

Slots

Name Cardinality and Range Description Inheritance
biosample_set *
Biosample		 This property links a database object to the set of samples within it direct
calibration_set *
CalibrationInformation		 This property links a database object to the set of calibrations within it direct
chemical_entity_set *
ChemicalEntity		 This property links a database object to the set of chemical entities within ... direct
collecting_biosamples_from_site_set *
CollectingBiosamplesFromSite		 direct
configuration_set *
Configuration		 This property links a database object to the set of configurations within it direct
data_generation_set *
DataGeneration		 This property links a database object to the set of data generations within i... direct
data_object_set *
DataObject		 This property links a database object to the set of data objects within it direct
field_research_site_set *
FieldResearchSite		 direct
functional_annotation_agg *
FunctionalAnnotationAggMember		 direct
functional_annotation_set *
FunctionalAnnotation		 This property links a database object to the set of all functional annotation... direct
genome_feature_set *
GenomeFeature		 This property links a database object to the set of all features direct
instrument_set *
Instrument		 This property links a database object to the set of instruments within it direct
manifest_set *
Manifest		 This property links a database object to the set of manifests within it direct
material_processing_set *
MaterialProcessing		 This property links a database object to the set of material processing withi... direct
processed_sample_set *
ProcessedSample		 This property links a database object to the set of processed samples within ... direct
protocol_execution_set *
ProtocolExecution		 This property links a database object to the set of protocol executions withi... direct
storage_process_set *
StorageProcess		 This property links a database object to the set of storage processes within ... direct
study_set *
Study		 This property links a database object to the set of studies within it direct
workflow_execution_set *
WorkflowExecution		 This property links a database object to the set of workflow executions direct

Aliases

  • NMDC metadata object

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: Database
description: An abstract holder for any set of metadata and data. It does not need
  to correspond to an actual managed database top level holder class. When translated
  to JSON-Schema this is the 'root' object. It should contain pointers to other objects
  of interest. For MongoDB, the lists of objects that Database slots point to correspond
  to **collections**.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- NMDC metadata object
slots:
- biosample_set
- calibration_set
- chemical_entity_set
- collecting_biosamples_from_site_set
- configuration_set
- data_generation_set
- data_object_set
- field_research_site_set
- functional_annotation_agg
- functional_annotation_set
- genome_feature_set
- instrument_set
- manifest_set
- material_processing_set
- processed_sample_set
- protocol_execution_set
- storage_process_set
- study_set
- workflow_execution_set
class_uri: nmdc:Database
tree_root: true

Induced

name: Database
description: An abstract holder for any set of metadata and data. It does not need
  to correspond to an actual managed database top level holder class. When translated
  to JSON-Schema this is the 'root' object. It should contain pointers to other objects
  of interest. For MongoDB, the lists of objects that Database slots point to correspond
  to **collections**.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- NMDC metadata object
attributes:
  biosample_set:
    name: biosample_set
    description: This property links a database object to the set of samples within
      it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: biosample_set
    owner: Database
    domain_of:
    - Database
    range: Biosample
    multivalued: true
    inlined_as_list: true
  calibration_set:
    name: calibration_set
    description: This property links a database object to the set of calibrations
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: calibration_set
    owner: Database
    domain_of:
    - Database
    range: CalibrationInformation
    multivalued: true
    inlined_as_list: true
  chemical_entity_set:
    name: chemical_entity_set
    description: This property links a database object to the set of chemical entities
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: chemical_entity_set
    owner: Database
    domain_of:
    - Database
    range: ChemicalEntity
    multivalued: true
    inlined_as_list: true
  collecting_biosamples_from_site_set:
    name: collecting_biosamples_from_site_set
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: collecting_biosamples_from_site_set
    owner: Database
    domain_of:
    - Database
    range: CollectingBiosamplesFromSite
    multivalued: true
    inlined_as_list: true
  configuration_set:
    name: configuration_set
    description: This property links a database object to the set of configurations
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: configuration_set
    owner: Database
    domain_of:
    - Database
    range: Configuration
    multivalued: true
    inlined_as_list: true
  data_generation_set:
    name: data_generation_set
    description: This property links a database object to the set of data generations
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: data_generation_set
    owner: Database
    domain_of:
    - Database
    range: DataGeneration
    multivalued: true
    inlined_as_list: true
  data_object_set:
    name: data_object_set
    description: This property links a database object to the set of data objects
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: data_object_set
    owner: Database
    domain_of:
    - Database
    range: DataObject
    multivalued: true
    inlined_as_list: true
  field_research_site_set:
    name: field_research_site_set
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: field_research_site_set
    owner: Database
    domain_of:
    - Database
    range: FieldResearchSite
    multivalued: true
    inlined_as_list: true
  functional_annotation_agg:
    name: functional_annotation_agg
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: functional_annotation_agg
    owner: Database
    domain_of:
    - Database
    range: FunctionalAnnotationAggMember
    multivalued: true
    inlined: true
    inlined_as_list: true
  functional_annotation_set:
    name: functional_annotation_set
    description: This property links a database object to the set of all functional
      annotations
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: functional_annotation_set
    owner: Database
    domain_of:
    - Database
    range: FunctionalAnnotation
    multivalued: true
    inlined_as_list: true
  genome_feature_set:
    name: genome_feature_set
    description: This property links a database object to the set of all features
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: genome_feature_set
    owner: Database
    domain_of:
    - Database
    range: GenomeFeature
    multivalued: true
    inlined_as_list: true
  instrument_set:
    name: instrument_set
    description: This property links a database object to the set of instruments within
      it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: instrument_set
    owner: Database
    domain_of:
    - Database
    range: Instrument
    multivalued: true
    inlined_as_list: true
  manifest_set:
    name: manifest_set
    description: This property links a database object to the set of manifests within
      it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: manifest_set
    owner: Database
    domain_of:
    - Database
    range: Manifest
    multivalued: true
    inlined_as_list: true
  material_processing_set:
    name: material_processing_set
    description: This property links a database object to the set of material processing
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: material_processing_set
    owner: Database
    domain_of:
    - Database
    range: MaterialProcessing
    multivalued: true
    inlined_as_list: true
  processed_sample_set:
    name: processed_sample_set
    description: This property links a database object to the set of processed samples
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: processed_sample_set
    owner: Database
    domain_of:
    - Database
    range: ProcessedSample
    multivalued: true
    inlined_as_list: true
  protocol_execution_set:
    name: protocol_execution_set
    description: This property links a database object to the set of protocol executions
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: protocol_execution_set
    owner: Database
    domain_of:
    - Database
    range: ProtocolExecution
    multivalued: true
    inlined_as_list: true
  storage_process_set:
    name: storage_process_set
    description: This property links a database object to the set of storage processes
      within it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: storage_process_set
    owner: Database
    domain_of:
    - Database
    range: StorageProcess
    multivalued: true
    inlined_as_list: true
  study_set:
    name: study_set
    description: This property links a database object to the set of studies within
      it.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: study_set
    owner: Database
    domain_of:
    - Database
    range: Study
    multivalued: true
    inlined_as_list: true
  workflow_execution_set:
    name: workflow_execution_set
    description: This property links a database object to the set of workflow executions.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    mixins:
    - object_set
    alias: workflow_execution_set
    owner: Database
    domain_of:
    - Database
    range: WorkflowExecution
    multivalued: true
    inlined_as_list: true
class_uri: nmdc:Database
tree_root: true