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
Note
Mermaid class diagram too large to render.
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| planned_process_set | 0..* PlannedProcess |
This property links a database object to the set of planned processes within ... | direct |
| functional_annotation_agg | 0..* FunctionalAnnotationAggMember |
direct | |
| activity_set | 0..* WorkflowExecutionActivity |
This property links a database object to the set of workflow activities | direct |
| biosample_set | 0..* Biosample |
This property links a database object to the set of samples within it | direct |
| collecting_biosamples_from_site_set | 0..* CollectingBiosamplesFromSite |
direct | |
| data_object_set | 0..* DataObject |
This property links a database object to the set of data objects within it | direct |
| extraction_set | 0..* Extraction |
This property links a database object to the set of extractions within it | direct |
| field_research_site_set | 0..* FieldResearchSite |
direct | |
| functional_annotation_agg | 0..* FunctionalAnnotationAggMember |
direct | |
| functional_annotation_set | 0..* FunctionalAnnotation |
This property links a database object to the set of all functional annotation... | direct |
| genome_feature_set | 0..* GenomeFeature |
This property links a database object to the set of all features | direct |
| library_preparation_set | 0..* LibraryPreparation |
This property links a database object to the set of DNA extractions within it | direct |
| mags_activity_set | 0..* MagsAnalysisActivity |
This property links a database object to the set of MAGs analysis activities | direct |
| metabolomics_analysis_activity_set | 0..* MetabolomicsAnalysisActivity |
This property links a database object to the set of metabolomics analysis act... | direct |
| metagenome_annotation_activity_set | 0..* MetagenomeAnnotationActivity |
This property links a database object to the set of metagenome annotation act... | direct |
| metagenome_assembly_set | 0..* MetagenomeAssembly |
This property links a database object to the set of metagenome assembly activ... | direct |
| metagenome_sequencing_activity_set | 0..* MetagenomeSequencingActivity |
This property links a database object to the set of metagenome sequencing act... | direct |
| metaproteomics_analysis_activity_set | 0..* MetaproteomicsAnalysisActivity |
This property links a database object to the set of metaproteomics analysis a... | direct |
| metatranscriptome_activity_set | 0..* MetatranscriptomeActivity |
This property links a database object to the set of metatranscriptome analysi... | direct |
| nom_analysis_activity_set | 0..* NomAnalysisActivity |
This property links a database object to the set of natural organic matter (N... | direct |
| omics_processing_set | 0..* OmicsProcessing |
This property links a database object to the set of omics processings within ... | direct |
| planned_process_set | 0..* PlannedProcess |
This property links a database object to the set of planned processes within ... | direct |
| pooling_set | 0..* Pooling |
direct | |
| processed_sample_set | 0..* ProcessedSample |
This property links a database object to the set of processed samples within ... | direct |
| read_based_taxonomy_analysis_activity_set | 0..* ReadBasedTaxonomyAnalysisActivity |
This property links a database object to the set of read based analysis activ... | direct |
| read_qc_analysis_activity_set | 0..* ReadQcAnalysisActivity |
This property links a database object to the set of read QC analysis activiti... | direct |
| study_set | 0..* Study |
This property links a database object to the set of studies within it | direct |
Usages
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:
- planned_process_set
- functional_annotation_agg
- activity_set
- biosample_set
- collecting_biosamples_from_site_set
- data_object_set
- extraction_set
- field_research_site_set
- functional_annotation_agg
- functional_annotation_set
- genome_feature_set
- library_preparation_set
- mags_activity_set
- metabolomics_analysis_activity_set
- metagenome_annotation_activity_set
- metagenome_assembly_set
- metagenome_sequencing_activity_set
- metaproteomics_analysis_activity_set
- metatranscriptome_activity_set
- nom_analysis_activity_set
- omics_processing_set
- planned_process_set
- pooling_set
- processed_sample_set
- read_based_taxonomy_analysis_activity_set
- read_qc_analysis_activity_set
- study_set
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:
planned_process_set:
name: planned_process_set
description: This property links a database object to the set of planned processes
within it.
comments:
- PlannedProcess instances aggregated by this slot will require the designated_class
slot
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: planned_process_set
owner: Database
domain_of:
- Database
range: PlannedProcess
inlined_as_list: true
functional_annotation_agg:
name: functional_annotation_agg
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Database
multivalued: true
alias: functional_annotation_agg
owner: Database
domain_of:
- Database
range: FunctionalAnnotationAggMember
inlined: true
inlined_as_list: true
activity_set:
name: activity_set
description: This property links a database object to the set of workflow activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: activity_set
owner: Database
domain_of:
- Database
range: WorkflowExecutionActivity
inlined_as_list: true
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
domain: Database
multivalued: true
alias: biosample_set
owner: Database
domain_of:
- Database
range: Biosample
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
domain: Database
multivalued: true
alias: collecting_biosamples_from_site_set
owner: Database
domain_of:
- Database
range: CollectingBiosamplesFromSite
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
domain: Database
multivalued: true
alias: data_object_set
owner: Database
domain_of:
- Database
range: DataObject
inlined_as_list: true
extraction_set:
name: extraction_set
description: This property links a database object to the set of extractions within
it.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: extraction_set
owner: Database
domain_of:
- Database
range: Extraction
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
domain: Database
multivalued: true
alias: field_research_site_set
owner: Database
domain_of:
- Database
range: FieldResearchSite
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
domain: Database
multivalued: true
alias: functional_annotation_set
owner: Database
domain_of:
- Database
range: FunctionalAnnotation
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
domain: Database
multivalued: true
alias: genome_feature_set
owner: Database
domain_of:
- Database
range: GenomeFeature
inlined_as_list: true
library_preparation_set:
name: library_preparation_set
description: This property links a database object to the set of DNA extractions
within it.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- library_construction_set
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: library_preparation_set
owner: Database
domain_of:
- Database
range: LibraryPreparation
inlined_as_list: true
mags_activity_set:
name: mags_activity_set
description: This property links a database object to the set of MAGs analysis
activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: mags_activity_set
owner: Database
domain_of:
- Database
range: MagsAnalysisActivity
inlined_as_list: true
metabolomics_analysis_activity_set:
name: metabolomics_analysis_activity_set
description: This property links a database object to the set of metabolomics
analysis activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: metabolomics_analysis_activity_set
owner: Database
domain_of:
- Database
range: MetabolomicsAnalysisActivity
inlined_as_list: true
metagenome_annotation_activity_set:
name: metagenome_annotation_activity_set
description: This property links a database object to the set of metagenome annotation
activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: metagenome_annotation_activity_set
owner: Database
domain_of:
- Database
range: MetagenomeAnnotationActivity
inlined_as_list: true
metagenome_assembly_set:
name: metagenome_assembly_set
description: This property links a database object to the set of metagenome assembly
activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: metagenome_assembly_set
owner: Database
domain_of:
- Database
range: MetagenomeAssembly
inlined_as_list: true
metagenome_sequencing_activity_set:
name: metagenome_sequencing_activity_set
description: This property links a database object to the set of metagenome sequencing
activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: metagenome_sequencing_activity_set
owner: Database
domain_of:
- Database
range: MetagenomeSequencingActivity
inlined_as_list: true
metaproteomics_analysis_activity_set:
name: metaproteomics_analysis_activity_set
description: This property links a database object to the set of metaproteomics
analysis activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: metaproteomics_analysis_activity_set
owner: Database
domain_of:
- Database
range: MetaproteomicsAnalysisActivity
inlined_as_list: true
metatranscriptome_activity_set:
name: metatranscriptome_activity_set
description: This property links a database object to the set of metatranscriptome
analysis activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: metatranscriptome_activity_set
owner: Database
domain_of:
- Database
range: MetatranscriptomeActivity
inlined_as_list: true
nom_analysis_activity_set:
name: nom_analysis_activity_set
description: This property links a database object to the set of natural organic
matter (NOM) analysis activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: nom_analysis_activity_set
owner: Database
domain_of:
- Database
range: NomAnalysisActivity
inlined_as_list: true
omics_processing_set:
name: omics_processing_set
description: This property links a database object to the set of omics processings
within it.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: omics_processing_set
owner: Database
domain_of:
- Database
range: OmicsProcessing
inlined_as_list: true
pooling_set:
name: pooling_set
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: pooling_set
owner: Database
domain_of:
- Database
range: Pooling
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
domain: Database
multivalued: true
alias: processed_sample_set
owner: Database
domain_of:
- Database
range: ProcessedSample
inlined_as_list: true
read_based_taxonomy_analysis_activity_set:
name: read_based_taxonomy_analysis_activity_set
description: This property links a database object to the set of read based analysis
activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: read_based_taxonomy_analysis_activity_set
owner: Database
domain_of:
- Database
range: ReadBasedTaxonomyAnalysisActivity
inlined_as_list: true
read_qc_analysis_activity_set:
name: read_qc_analysis_activity_set
description: This property links a database object to the set of read QC analysis
activities.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
mixins:
- object_set
domain: Database
multivalued: true
alias: read_qc_analysis_activity_set
owner: Database
domain_of:
- Database
range: ReadQcAnalysisActivity
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
domain: Database
multivalued: true
alias: study_set
owner: Database
domain_of:
- Database
range: Study
inlined_as_list: true
tree_root: true