NatureDB, Yet Another Natural History Collection Management System

The "NaturalDB" is an open-source platform designed to manage, collect, and showcase natural history specimens and biodiversity data. This platform supports institutions in cataloging, curating, and publish the collections to other biodiversity information standards, like Darwin core.

The following are some online examples:

Cdoe	Title	Chinese Title	URL	status
HAST	Biodiversity Research Museum, Herbarium, Academia Sinica	中央研究院植物標本館	https://hast.biodiv.tw	release 🟢
TaiBOL	Taiwan Barcode of Life	台灣野生生物遺傳物質冷凍典藏計畫	https://taibol.biodiv.tw	beta🟡
PPI	National Pingtung University of Science and Technology	國立屏東科技大學森林系植物標本館	https://ppi.naturedb.org/data	alpha 🔴
ASIZ	Biodiversity Research Museum, Academia Sinica	中央研究院動物標本館	https://asiz.naturedb.org	alpha 🔴

Table of Contents

• Features
• Installation
• Usage
• Data Management
• Contributing
• License
• Contact

Features

• Specimen Data Integration: Collect, manage, and display natural history specimen data from museums and research institutions worldwide.
• Diversity Data Visualization: Offers rich data visualization tools to explore biodiversity patterns.
• API Support: Provides an open API for third-party application integration.
• Collection Management: Tools for cataloging and curating specimens, including metadata management, tagging, and categorization.
• Multilingual Support: The platform supports traditional Chinese and English.
• Dashboard: can edit specimen collection data, and generate reports on collection statistics, specimen inventory, and data usage.

Installation

Prerequisites

• Docker with the Compose plugin. Nothing else is needed on the host — Python, PostgreSQL/PostGIS, Redis and Node all run inside the containers.

Quick start (example site)

This gets you a running site with example data — one organization, one collection, a small taxon backbone, a gazetteer, 8 specimen records and an admin account — so you can click through the whole system before importing anything of your own.

git clone https://github.com/TaiBIF/naturedb.git
cd naturedb
cp dotenv.sample .env

docker compose up -d --build        # builds, starts, and runs the migrations
docker compose exec flask flask initdata

Then open:

What	URL	Notes
Frontend	http://localhost:5000/	browse, search, specimen detail
Admin	http://localhost:5000/admin/login	log in as admin / admin
Adminer	http://localhost:8080/	server postgres, credentials from .env

flask initdata is idempotent, so re-running it only fills in rows that are missing. It refuses to run if site id 1 already belongs to a site other than demo, so it will not touch a database restored from a production dump.

Non-default credentials:

docker compose exec flask flask initdata --admin-username curator --admin-password 's3cret'

(If your checkout has the optional Makefile, make init runs the same two steps and prints the URLs.)

What the example data contains

Defined in app/initdata.py — edit that file to reshape the example, or use it as a template for seeding a real institution.

• Site demo bound to host localhost:5000 (in dev, Site.find_by_host() also matches the first label of the Host header, so demo.localhost:5000 works too), with its per-site settings in app/settings/demo.json.
• Organization / collection: DEMO — "Demo Herbarium".
• Gazetteer: COUNTRY / ADM1 / ADM2 classes plus the custom national_park and locality classes. These carry fixed ids (5–10) that the record form, the exporters and the quick-edit country dropdown depend on — keep them if you replace the data.
• Taxa: a three-family backbone (Fagaceae, Lauraceae, Asteraceae) with the taxon_relation closure rows filled in.
• Specimens: 8 records / 9 units with collectors, identifications, coordinates, altitudes, named areas and assertions (植群型, 生長型, …).
• News: two article categories and three articles.
• User: a ROLE_ROOT site administrator.

There are no specimen images: media lives in object storage (see admin.uploads in the site settings), so a self-contained example ships without it.

Setting up your own site

1. Copy app/settings/demo.json to app/settings/<your-site-name>.json and edit it. Site.get_settings() reads that file by Site.name, so the filename must match.
2. Either edit app/initdata.py and re-run flask initdata, or create the site/organization/collection rows through Adminer and flask createuser <username> <password> <site_id> <role>.
3. Point a real hostname at the site by setting site.host in the database (dev also matches on Site.name, so /etc/hosts entries are optional locally).
4. Import your own specimens with flask importdata <csv_file> <collection_id> <record_group>.

Production / staging

docker compose -f compose.yml -f compose.prod.yml up -d --build

compose.prod.yml adds Traefik with Let's Encrypt (set ACME_EMAIL and CF_DNS_API_TOKEN in .env), gunicorn instead of the dev server, and the PostgreSQL tuning knobs. Per-host router labels go in compose.prod-vhosts.yml — see compose.prod-vhosts-sample.yml.

To start from a database dump instead of the example data, drop the gzipped dump into initdb/ before the first up; the postgres entrypoint loads everything in that directory in filename order, after initdb/00-extensions.sql has created PostGIS.

Usage

1. Browse Specimens: Visit the homepage of the platform to search and browse natural history specimens.
2. Pages: Visit static pages like: about us, contact and dynamic pages: news, related links...
3. API Usage: not ready.

Data Management (admin)

1. Cataloging Specimens: Use the collection management interface to catalog new specimens, including the input of metadata such as species name, collection date, location, and more.
2. Curating Collections: Organize specimens into collections, adding tags and categories to facilitate easy retrieval and browsing.
3. User Roles and Permissions: Assign roles such as administrator, curator, or researcher to manage who can add, edit, or view specific parts of the collection.
4. Reporting: Generate reports on the number of specimens, their condition, and other collection-related metrics to help manage the inventory and share insights with stakeholders.

Contributing

We welcome contributions from developers, curators, and researchers! Here’s how you can get involved:

1. Fork the repository and clone it locally.
2. Create a new branch for your changes:

   git checkout -b my-feature-branch

3. Commit your changes and push them to your remote repository:

   git push origin my-feature-branch

4. Create a Pull Request, describing your changes.

License

This project is licensed under the MIT License. You are free to use, modify, and distribute this project, but please retain the original author's credit.

Contact

If you have any questions or suggestions, feel free to reach out to us:

• Email: moogoo78@gmail.com
• Issue Tracker: GitHub Issues