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BASALT Schema

BASALT (Broad Analytical Schema for Samples and Laboratory Techniques) is a comprehensive schema for representing multimodal environmental and microbiological analysis data, including soil characterization and high-throughput microbial culture workflows. It supports diverse experimental techniques including mass spectrometry, metagenomics sequencing, X-ray fluorescence/diffraction, and 96-well plate-based growth assays. It is a production model in ongoing development to support the open, user-driven science the Environmental Molecular Sciences Laboratory (EMSL).

NOTE: This schema is under active development and integrates metadata standards from multiple collaborating institutions (EMSL, GLBRC, NMDC, and more). Some areas are marked with TODOs for future refinement.

Schema Organization

The schema follows a relational design with flat entity collections, explicit association tables for many-to-many relationships, and a pre-computed linkage cache for efficient provenance traversal. This supports flexible data reuse across studies and proposals.

The top-level entity is a Study (or Proposal), which serves as a container for related research. A study might represent all data from a specific EMSL proposal, user project, or collaborative investigation.

Entity Tables

All entities are stored in flat collections linked to studies:

Biological Materials

  • Samples: Physical specimens submitted for analysis (soil, aerosol, user-submitted microbial cultures). Each sample includes collection metadata, storage conditions, and analysis type specifications.

  • Organisms: Reference data representing biological identities (strains, isolates, engineered constructs) that can be instantiated by multiple physical samples. This separates the "what" (strain identity) from the "this tube" (physical sample).

  • Processed Samples: Samples that have undergone laboratory processing—subsampling, extraction, digestion, or culture growth. These form chains linking back to original samples.

Laboratory Resources

  • Media: Growth media preparations with detailed recipes, pH adjustments, sterilization methods, and storage conditions. Supports strain purity, stock culture, pre-culture, and experimental culture media types.

  • Instruments: Physical instrument metadata including manufacturer, model, and serial number. Activities reference instruments via association tables.

  • Purchased Materials: Commercial reagents, standards, and supplies with catalog information and lot tracking.

AMP2-Specific Culture-to-Phenotyping Workflows

Culture Growth Activities: Laboratory activities for microbial culture workflows on the Anaerobic Microbial Phenotyping Platform (AMP2) including:

  • Strain Purity: Initial purity verification of user samples

  • Stock Culture Preparation: Creating glycerol stocks for long-term storage

  • Pre-Culture Growth: Starter cultures before experimental conditions

  • Experimental Culture: Growth under defined treatment conditions

Plate Setup Activities: Configuration of 96-well plates for optical density measurements or Ecoplate metabolic profiling, with well-level sample/media assignments. Coming Soon: HPLC and Flow Cytometry

Data Generation

Data Generation Activities: Instrument runs that produce raw data, specialized by technique:

  • Mass Spectrometry: LC-MS, GC-MS, direct infusion FT-ICR with ionization and chromatography configurations

  • Nucleotide Sequencing: Metagenomics and metatranscriptomics sequencing runs

  • X-ray Analysis: XRF elemental analysis and XRD mineralogical diffraction

  • Plate Reading: Optical density and fluorescence measurements from plate readers

Data Processing

Data Processing Activities: Computational workflows applied to raw data, including: - Mass spectrometry molecular identification (CoreMS) - Metagenomics assembly, annotation, and binning - XRD Rietveld refinement [10]

Workflow Chaining: Parent-child relationships between processing activities enable multi-step pipeline tracking via parent_workflow_id.

Data Products

Processed Data: Abstract base for all analytical results, with concrete subclasses by technique:

  • Mass Spectrometry Products: Molecular identification tables, MS images, metaproteomics results

  • Metagenomics Products: Annotation, binning, and gene phylogeny outputs

  • Soil Characterization Products: pH, texture, bulk density, hydraulic properties, elemental analysis, microbial biomass

  • Plate Products: Well-level readings with timepoints, blanks, and quality metrics

  • X-ray Products: XRF elemental concentrations and XRD mineral phase percentages

Supporting Classes

  • Sites: Location metadata for field sampling including coordinates, land use, vegetation, and climate information.

  • Methods: Analytical method specifications with instrument parameters, calibration details, and detection limits.

  • Value Tables: Structured representations for quantities (with units), controlled terms, timestamps, and person records.

Association Tables

Many-to-many relationships are represented via explicit association tables:

  • ProcessingSampleLink: Links samples to processing activities with step number and role (input/output)

  • Instrument Associations: Links instruments to activities with custodian tracking

  • Workflow Associations: Links functional annotations and other outputs to workflow executions

LAMBDA-BER Schema

This is an externally-developed schema, linked via the sidebar and with separate versioning, used for multimodal structural biology imaging data. The bridging concept between that schema and BASALT is the study class (link to LAMBDA-BER.study, link to BASALT.study).

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