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Mammal Diversity Database (MDD) — Web Map & API

MDD web map — type localities coloured by IUCN status

Overview

An interactive web map and REST API built on the Mammal Diversity Database v2.4 — 6,871 mammal species with nomenclatural synonyms, type localities, and optional GBIF occurrence overlays. DuckDB is the analysis backbone; a React + MapLibre frontend and FastAPI backend are packaged in a single Docker image for deployment.

Data: MDD v2.4 (Zenodo) + GBIF Occurrence API
Role: Solo project
Status: Active — live on Render
Live demo: mdd-map.onrender.com Repository: github.com/ulfboge/MDD

What it does

Component Description
Taxonomy DB DuckDB built from five MDD CSV files — species, ~100k synonyms, type specimen metadata, version diff
Harmonization Resolve any reported name (GBIF, field CSV, literature) to the current MDD accepted name via the synonyms table
Type localities ~1,941 geocoded holotype collection sites, coloured by IUCN status on the map
GBIF pipeline gbif_import.py fetches occurrences, harmonizes names, and stores them in DuckDB + GeoParquet
Web map Species / genus / family search, museum & country coverage filters, CSV export for missing coordinates, IUCN popups
API FastAPI — species lookup, type-localities GeoJSON, occurrences per species, health check
Deploy Single-container Docker (nginx + uvicorn + baked DuckDB); render.yaml for Render

Methods & Tools

Layer Technology
Database DuckDB (spatial extension, GeoParquet export)
Backend Python 3.11, FastAPI, uvicorn
Frontend React, TypeScript, Vite, MapLibre GL JS
Data ingest SQL scripts + setup_database.py, gbif_import.py, harmonize_names.py
GIS export GeoParquet for QGIS; PostgreSQL/PostGIS migration scripts
Container Docker, nginx reverse proxy
Hosting Render Blueprint (render.yaml)

Design principle: MDD is the taxonomy backbone — external datasets (GBIF, IUCN, field CSVs) are harmonized to MDD via species_id and the synonyms table, not the other way around. Coordinates in MDD are type specimen localities (where the holotype was collected), not species range centroids.

Key features

  • Global map of ~1,941 geocoded type localities with IUCN colour symbology
  • Species autocomplete across 6,871 accepted names
  • Per-species type locality highlight and optional “show all” layer
  • GBIF occurrence layer (populated locally via import pipeline; not at container startup on free tier)
  • Reproducible build: setup_database.py regenerates the full DuckDB from raw CSVs
  • QGIS-ready GeoParquet exports and documented PostGIS migration path

Live Demo View Code on GitHub MDD data source

Citation

Mammal Diversity Database. (2026). Mammal Diversity Database (Version 2.4) [Data set].
Zenodo. https://doi.org/10.5281/zenodo.18135819