eDNA Schema

Environmental DNA (eDNA) analysis is a key method in the AI4SH project for characterising soil biodiversity. Two schemas handle this data: edna_utility holds the method and workflow reference catalogues, and edna holds the observations.

Process files

File	Schema	Purpose
edna/edna_utility_v10_sql.json	edna_utility	Creates eDNA method and workflow reference tables
edna/edna_observation_v10_sql.json	edna	Creates eDNA observation tables

Schema: edna_utility

The edna_utility schema holds reference tables for the specific methods and reagents used in eDNA workflows. eDNA processing involves several distinct steps, each with its own catalogue:

Reference table	Description
Extraction method	Method for extracting DNA from a soil sample
Amplification (PCR)	PCR amplification protocol
Purification method	Clean-up of extracted or amplified DNA
Sequencing platform	Sequencing technology used (e.g. Illumina, Nanopore)
Metabarcoding protocol	Protocol for amplicon-based community profiling

Each reference table must be populated before eDNA observations can be entered.

Schema: edna

The edna schema stores actual eDNA observations. An eDNA observation in the AI4SH context typically represents a metabarcoding result: the detected presence, abundance, or diversity of taxa in a soil sample identified via DNA sequencing.

eDNA observations link back to:

• The soil sample from which DNA was extracted (via observation schema infrastructure)
• edna_utility reference records describing the extraction, amplification, and sequencing workflow
• observation_utility.taxa for the detected organisms (using the Linnean classification hierarchy)

Relationship to other schemas

eDNA observations use the same sample infrastructure as physicochemical soil observations — the same sampling_log, sample, and campaign hierarchy applies. What differs is the analytical pipeline: instead of a chemical or spectral measurement, the result is a sequence-based taxon detection. The edna_utility schema captures the specific reagents and protocols of that pipeline in a structured, queryable form.

This design allows combining eDNA biodiversity results with physicochemical soil properties from the same sample, which is a core analytical goal of the AI4SH project.