gndb

README

GNdb

GNdb provides tools to create and populate database for a local gnverifier app.

• Introduction
• Prerequisites
  • PostgreSQL
  • SQLite
• Installation
• Authors
• License

Introduction

GNverifier makes it possible to reconcile/resolve scientific names against multiple biodiversity data sources with high speed, accuracy. It makes it possible to find misspellings (via fuzzy matching), filter out 'bad' names, find out currently acceptable names for taxons, get vernacular/common names.

However GNverifier is a centralized service and might be lacking a particular data source, or do not have the most recent version of its data. GNdb app provides means to setup a local GNverifier service and populate it with data sources that a user needs for research.

However the data sources can be available in many different formats -- Darwin Core Archives (DwCA), Catalogue of Life Data Package (CoLDP), Excel spread sheets, simple list of names etc. We developed an intermediate normalization format Species File Group Archive (SFGA) which is simply a SQLite database, and as such is significantly easier for data handling than text-based alternatives.

SFGA is an fantastic format that gives you ability to easily query your biodiversity data. You can use SF tool for conversion of popular biodiversity formats into SFGA and then use the resulting files to populate GNdb.

Prerequisites

PostgreSQL

For GNverifier data that usually is kept in gnames database. Find installationg instructions for your operating system.

SQLite

Not a requirement, but it is very handy for examining SFGA archives. We recommend to setup SQLite DB viewer and SQLite tools to make most of produced SFGA files.

Installation

Authors

Dima Mozzherin with much assistance from Claude Code

All code generated by Claude Code was reviewed and reworked.

License

The project is released uner [MIT License]

Documentation

Overview

Copyright © 2025 Dmitry Mozzherin <dmozzherin@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.