Microbial Discovery Forge

Schema status

discovered

Curation status

curated

Source

berdl-spark-connect://metrics.berdl.kbase.us:443

Philosophy

Standardize biosample metadata for cross-study comparisons. Enable sample discovery and integration across microbiome studies.

Data sources: NCBI BioSample NMDC

Citation & Attribution

Provider: NMDC / NCBI

Website: https://microbiomedata.org/

Scale

17

tables

Schema Browser

Tables (17)

attribute_harmonized_pairings bioprojects_flattened biosamples_attributes biosamples_flattened biosamples_ids biosamples_links content_pairs_aggregated env_triads_flattened harmonized_name_dimensional_stats harmonized_name_usage_stats measurement_evidence_percentages measurement_results_skip_filtered mixed_content_counts ncbi_attributes_flattened ncbi_packages_flattened sra_biosamples_bioprojects unit_assertion_counts

Key Tables

Table	Description	Rows
`biosamples_flattened`	Flattened biosample records	—
`env_triads_flattened`	Environmental triads (broad/local/medium)	—
`biosamples_attributes`	Biosample attributes	—

Sample Queries

Get biosamples

SELECT *
FROM nmdc_ncbi_biosamples.biosamples_flattened
LIMIT 20

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Atlas Pages

data type

Environment, Geochemistry, and Ecology

Environmental samples, coordinates, geochemistry, sample metadata, and ecology-facing observations used to validate laboratory predictions in the field.

data type

Host, Clinical, Pathogen, and Isolate Data

Collections organized around host-associated samples, pathogen isolates, clinical context, or strain-level interpretation.

data collection

NMDC BioSamples

Harmonized NCBI BioSample metadata

Start Exploring

Access the full NMDC BioSamples data through BERDL JupyterHub.

Open JupyterHub