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