README
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GNdb
GNdb provides tools to create and populate database for a local gnverifier app.
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
Architecture
See ARCHITECTURE.md for detailed information about the project's Clean Architecture design, package structure, and design patterns.
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
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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.
Source Files
Directories
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| Path | Synopsis |
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internal
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iodb
Package iodb implements database operations using pgxpool.
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Package iodb implements database operations using pgxpool. |
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iologger
Package iologger provides slog-based logging initialization and configuration.
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Package iologger provides slog-based logging initialization and configuration. |
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iooptimize
Package iooptimize implements Optimizer interface for database performance optimization.
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Package iooptimize implements Optimizer interface for database performance optimization. |
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iopopulate
Package populate implements cache management for SFGA file handling.
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Package populate implements cache management for SFGA file handling. |
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ioschema
Package ioschema implements SchemaManager interface for database schema management.
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Package ioschema implements SchemaManager interface for database schema management. |
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pkg
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config
Package config provides configuration management for GNdb.
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Package config provides configuration management for GNdb. |
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schema
Package schema provides database schema models for GNdb.
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Package schema provides database schema models for GNdb. |
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sources
Package sources provides configuration and validation for SFGA data sources.
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Package sources provides configuration and validation for SFGA data sources. |
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compare_sources compares a data source between gnames (to-gn) and gndb databases.
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compare_sources compares a data source between gnames (to-gn) and gndb databases. |