Nmdc Metadata
nmdc_metadata
Tenant: NMDC · Snapshot 2026-04-29T21:35:53.838483+00:00
Schema status
discoveredCuration status
discoveredSource
berdl-spark-connect://metrics.berdl.kbase.us:443Citation & Attribution
Provider: NMDC
Schema Browser
Tables (47)
biosample_set biosample_set_agrochem_addition biosample_set_air_temp_regm biosample_set_associated_studies biosample_set_chem_administration biosample_set_fertilizer_regm biosample_set_gaseous_environment biosample_set_host_diet biosample_set_humidity_regm biosample_set_misc_param biosample_set_perturbation biosample_set_phaeopigments biosample_set_watering_regm calibration_set configuration_set configuration_set_ordered_mobile_phases data_generation_set data_generation_set_associated_studies data_generation_set_has_input data_generation_set_has_output data_generation_set_instrument_used data_object_set data_object_set_in_manifest field_research_site_set functional_annotation_agg instrument_set manifest_set material_processing_set material_processing_set_has_input material_processing_set_has_output material_processing_set_ordered_mobile_phases material_processing_set_substances_used processed_sample_set study_set study_set_associated_dois study_set_has_credit_associations study_set_part_of study_set_protocol_link study_set_study_image workflow_execution_set workflow_execution_set_has_failure_categorization workflow_execution_set_has_input workflow_execution_set_has_metabolite_identifications workflow_execution_set_has_output workflow_execution_set_mags_list workflow_execution_set_uses_calibration workflow_execution_set_was_informed_by
biosample_set_perturbation
| Column | Type | Description |
|---|
Atlas Pages
Lab fitness signals versus field ecology
Lab-derived fitness or tolerance scores can predict ecology in some settings, but metadata quality and field complexity limit broad generalization.
conflictMetal-AMR co-selection readiness
BERIL has the pieces to test metal-AMR co-selection, but the current evidence is a strong opportunity rather than a resolved result.
metaDerived Data Reuse Graph
Canonical Atlas page for project-to-project reuse, derived products, output artifacts, consumers, and review routes.
data typeEnvironment, Geochemistry, and Ecology
Environmental samples, coordinates, geochemistry, sample metadata, and ecology-facing observations used to validate laboratory predictions in the field.
data typeMulti-Omics, Embeddings, and Molecular Profiles
Metabolomics, proteomics, trait profiles, embeddings, and other matrix-style summaries that create reusable sample or organism representations.
derived productEnvironment Harmonization Labels
Reusable environment category and coordinate-quality labels that make cross-collection ecology joins safer.
derived productFunctional Innovation KO Atlas
Reusable clade-level functional innovation and acquisition-depth outputs from the ecological agora project.
derived productAMR Fitness Profiles
Reusable AMR mechanism, conservation, environment, and fitness-cost signals for resistance ecology questions.
data collectionNmdc Metadata
Live BERDL collection in the NMDC tenant with 47 discovered tables.
methodNew Project Integration Pattern
Procedure for integrating newly completed projects into the BERIL Atlas without turning topic pages into project-summary dumps.
opportunityMetal-AMR Site Co-Selection Analysis
Test whether metal contamination at BER-relevant sites co-selects antibiotic resistance mechanisms using metal fitness, AMR profiles, and environmental metadata.
opportunityEcotype Label Validation Benchmark
Build a benchmark that tests whether ecotype labels survive stricter metadata, batch, and holdout validation.
opportunityLab-to-Field Fitness Transfer Audit
Audit where laboratory fitness effects predict field ecology and where geochemistry, taxonomy, or metadata completeness blocks transfer.
topicMicrobial Ecotypes, Environment, and Field Validation
Synthesis of species-level ecotypes, environmental embeddings, lab-field validation, ENIGMA ecology, and metadata limitations.
topicMetabolic Capability, Dependency, and Community Design
Synthesis of GapMind capability, fitness dependency, metabolic models, community ecology, and design-ready derived data.
Atlas Reuse
Environment Harmonization Labels
promoted · 2 downstream projects
profile_tableAMR Fitness Profiles
promoted · 1 downstream projects
atlas_tableFunctional Innovation KO Atlas
candidate · 0 downstream projects
partially resolvedLab fitness signals versus field ecology
Lab-derived fitness or tolerance scores can predict ecology in some settings, but metadata quality and field complexity limit broad generalization.
unresolvedMetal-AMR co-selection readiness
BERIL has the pieces to test metal-AMR co-selection, but the current evidence is a strong opportunity rather than a resolved result.