GBIF - Extinct

DOI

A Tool for Exploring Global Biodiversity Information Facility (GBIF) Data with Enhanced Filtering Capabilities and Potential Applications in Uncovering “Forgotten Taxa”

GBIF-Extinct introduces a tool that facilitates the exploration of the Global Biodiversity Information Facility (GBIF) data with unique filtering functionalities not readily available on the official GBIF website. The homepage enables users to search for the latest observation of specific taxa across different countries. Users can refine their search by applying filters based on taxon name, taxonomic rank, and country.

This user-friendly interface provides several advantages:

Overall, it offers a valuable contribution to the field of biodiversity research by providing a user-friendly and versatile platform for exploring GBIF data, potentially leading to the identification of “forgotten taxa” and promoting a deeper understanding of global biodiversity patterns.

Caveats

Data Quality

The GBIF data is not perfect and contains errors and biases. The data is only as good as the data providers and the data cleaning process.

Completeness

Usage

Above the table you find a filter form. You can filter by taxon name, taxonomic rank, and country. The taxon name search will return all taxa which contain the search string, eg. “apis” will also return “Caledanapis peckorum”. The taxonomic rank is a dropdown and will return all taxa which are of the selected rank or higher, the search term itself will match with the start of the string, eg. Family “Ap”, will return Apidae, Apiaceae etc. The country code is two letter ISO standard, eg. “AT” for Austria. The synonym checkbox will hide all synonyms from the result.

Table Columns

Reference and Citation

You can download our white paper please see gbif-extinct-white-paper. If you use GBIF-Extinct in your research, please cite the following:

Oberreiter, H. und Duenser, A. (2024) „HannesOberreiter/gbif-extinct: v1.3.1“. Zenodo. doi: 10.5281/zenodo.12599948.

@software{oberreiter_2024_12599948,
  author       = {Oberreiter, Hannes and Duenser, Anna},
  title        = {HannesOberreiter/gbif-extinct: v1.3.1},
  month        = jun,
  year         = 2024,
  publisher    = {Zenodo},
  version      = {v1.3.1},
  doi          = {10.5281/zenodo.12599948},
  url          = {https://doi.org/10.5281/zenodo.12599948}
}

Development

The project is open-source and contributions are welcome github.com/HannesOberreiter/gbif-extinct. The project is written in Go and uses Echo as a web framework. HTMX, Tailwind CSS and templ are used to build the frontend. As database we use DuckDB as it can be deployed as binary inside the go application and offers fast self-joining queries.

Pre-requisites

To get development running you will need Go the standalone version of Tailwind CSS Standalone CLI and templ.

Localhost

For ease of development we use cosmtrek/air to automatically reload the server when changes are made. See the config file for the configuration.

air

Taxa Data

To migrate taxa into our database, we use the backbone taxonomy from GBIF, see hosted-datasets.gbif.org/datasets/backbone/README.html for details. To fill the database the Taxon.tsv and the simple.txt (github.com/gbif/…/backbone-ddl.sql).

Running the mutate script will fill the database with the latest backbone taxonomy from GBIF, set synonyms and delete possible taxa which are synonyms for non species rank taxa.

go run ./scripts/mutate/mutate.go

Other scripts

The cron script does run manually a cron job on a defined TaxonID as a parameter or if no parameter is given it will run a few at random.

go run ./scripts/cron/cron.go <TaxonID>

The import script will import occurrence zip files from GBIF into the database. The format must be “simple”, when exporting from GBIF. The script will take the path to the zip file as a parameter.

go run ./scripts/import/import.go <path-to-zip-file>

Testing

To run the tests you will need to set the SQL_PATH and ROOT environment variables. The SQL_PATH is the path to the database file (from the root) and ROOT is the path to the root of the project.

SQL_PATH="memory" ROOT=/gbif-extinct go test -v ./...

Docker

GitHub action is used to generate the web-sever as a docker container hub.docker.com/r/hannesoberreiter/gbif-extinct. See the Dockerfile for details of the build and the docker-compose.yml for the deployment.

Current Server Setup