Geospatial Integration of Population Genomics and Metagenomic Metadata

Technical Specifications for the YEA "Genetic Address" Module

Document ID: CNL-TN-2026-026
Version: 1.4
Date: March 7, 2026
Author: Gemini (AI Assistance)

AI Assistance Disclosure: This technical note was developed with assistance from Gemini (Google). The AI contributed to the synthesis of biodiversity genomics databases, API endpoint mapping, and the architectural design for radial genomic searching based on the GenDivRange dataset and the YEA system specification.

1. Abstract

This technical note details the integration of three high-resolution genomic data streams into the Your Ecological Address (YEA) profiling engine. While traditional biodiversity inventories rely on species-level presence/absence data (e.g., GBIF, iNaturalist), the "Genetic Address" protocol described herein enables the characterization of intra-specific genetic health and environmental DNA (eDNA) signatures. We evaluate the technical practicality of querying the GenDivRange dataset, GEOME (Genomic Observatories Metadatabase), and MGnify (metagenomics) within a 1–5 km radial buffer. The proposed architecture utilizes a parallel-fetch PHP sub-parser to append molecular biodiversity metrics to the existing YEA Ecological Identity panel.

2. Background and Scientific Rationale

The "Ecological Address" concept seeks to provide a comprehensive digital twin of a geographic coordinate. However, species lists alone mask critical evolutionary data, such as genetic bottlenecks or local adaptations. By integrating population-level metrics like Expected Heterozygosity ($H_e$) and Allelic Richness ($A_r$), YEA can inform users of the "genomic vitality" of their location. Furthermore, the inclusion of eDNA metadata via MGnify captures microbial and cryptic diversity typically absent from macroscopic field observations.

3. Data Source Evaluation and API Registry

3.1 GenDivRange (Population-Level Diversity)

The GenDivRange dataset serves as the foundational layer for intra-specific variation. It aggregates 19,173 populations across 1,109 species, geo-referenced and placed on range maps.

• Technical Parameters: $H_e$ (Expected Heterozygosity), $A_r$ (Allelic Richness), and Nei’s gene diversity.
• Practicality: High, but requires local indexing. Since GenDivRange is a static dataset (Parquet/CSV), it must be ingested into the YEA Data Tier (PostgreSQL/PostGIS) to facilitate $O(1)$ spatial lookups.
• Access: https://doi.org/10.5281/zenodo.11183350

3.2 GEOME (Sample Metadata)

GEOME is the authoritative registry for biological samples linked to the NCBI Sequence Read Archive (SRA).

• Technical Parameters: Metadata includes collection depth, microhabitat, preservation method, and links to raw FASTQ files.
• Practicality: Essential for "Scientific History." It allows YEA to show users exactly which physical specimens were collected at their "Ecological Address."
• API Endpoint: https://api.geome-db.org/apidocs/

3.3 MGnify (Metagenomics & eDNA)

MGnify provides taxonomic assignments from environmental sequencing (soil, water, air).

• Technical Parameters: OTU/ASV counts, biome classification, and sequence assembly metadata.
• Practicality: High for "Hidden Diversity." It captures the microbiome of the specific ecoregion or soil type identified by the YEA "Physical Place" panel.
• API Endpoint: https://www.ebi.ac.uk/metagenomics/api/v1/

4. Proposed Methodology for Integration

4.1 Radial Buffer Normalization (The "Search Silo")

Following the "Silo Independence" principle, each genomic source is treated as an independent fetcher.

1. Polygon Generation: For APIs requiring WKT (Well-Known Text) geometries (GBIF, GEOME), the PHP sub-parser will calculate a 16-point circular approximation of the 1–5 km user-selected radius.
2. Point Search: MGnify queries will utilize the native latitude, longitude, and accuracy (radius) parameters.
3. Local Spatial Join: The system will execute a ST_DWithin query against the local GenDivRange index to retrieve species-specific diversity scores for any taxon identified in the broader biodiversity inventory.

4.2 Data Hierarchy and The "Genetic Address" Card

The results will be synthesized into a new Genetic Address card within the YEA interface, organized into three technical sections:

• Section I: Genomic Health: Aggregated $H_e$ and $A_r$ scores for local populations, providing a relative "Vitality Percentile" compared to global averages for that taxon.
• Section II: Molecular Inventory: A list of unique taxonomic IDs (TaxonKeys) identified via eDNA (MGnify), highlighting life forms not detected in iNaturalist/eBird.
• Section III: Research Legacy: A list of physical biosamples (GEOME) collected within the radius, linking users to the researchers and institutions involved.

5. Architectural Implementation

Integration into the four-layer platform:

1. Data Tier: Integration of GenDivRange Parquet files into the PostGIS genetics_cache.
2. Logic Tier: A new genetics.php sub-parser to handle parallel REST requests to GEOME and MGnify.
3. Presentation Tier: Development of fg-genetics.js (Module 14) to render the "Genetic Address" card with interactive SVG charts for $H_e$ distribution.

6. References

• CNL-SG-2025-002: CNL Technical Note Style Guide.
• CNL-TN-2026-025: Your Ecological Address (YEA) — System Specification.
• CNL-TN-2026-033: Structural State Vector Extraction from ecoSPLAT.
• Csilléry et al. (2025): GenDivRange: A global dataset of geo-referenced population genetic diversity.