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 🔴

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

Before installing, ensure your system meets the following requirements:

• Docker (optional): For containerized deployment

Installation Steps

1. Clone the repository:

   git clone https://github.com/TaiBIF/naturedb.git
   cd naturedb

2. Create .env: copy dotenv.sample & edit

   cp dotenv.sample .env

3. Build docker image:

   docker compose -f compose.yml -f compose.override.yml -f compose.upgrade.yml build

4. Initialize database

   postgres: create database naturedb;
   flask migrate
   insert init-db.sql
   

5. Start the application:

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

6. Set local DNS:

edit /etc/hosts

127.0.0.1 foo.bar.com

database table: site add domain field

insert site admin account

7. Visit http://foo.bar.com:5000 in your browser to access the platform.

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: [email protected]
• Issue Tracker: GitHub Issues