Accessing, handling, and referencing open biodiversity data using the Global Biodiversity Information Facility (GBIF)
In the age of changes and threat to the Ecosphere at macroecological scales, big data has crystallized as a go-to tool for ecological research. To facilitate the creation of, access to, and referencing of contributors to such big data repositories, the Global Biodiversity Information Facility (GBIF) has established data streams that make readily available a wealth of biodiversity data. Navigating and accessing such large data sets and ensuring fair use and accreditation of observations can seem daunting. In this workshop, we will introduce GBIF, show how to navigate its data portal, demonstrate data streams to obtain and handle data programmatically, and communicate accreditation procedures.
Throughout this workshop material, I present practical examples for obtaining GBIF data using rgbif. Much of this work has been directly inspired or adapted from the official
rgbif website and a
previous GBIF workshop.
Learning Goals
Throughout this workshop, you will be introduced to:
- The Global Biodiversity Information Facility (GBIF)
- What it is
- What data it makes available
- How to navigate the data
- How to query and obtain specific records
- What to consider with regards to data content, richness and quality
- How to reference and accredit GBIF-mediated data
- The
rgbifpackage
- Functionality for querying, accessing, and handling GBIF data programmatically
- Data handling practices in
R
Study Organism
Most of the time, GBIF users query data for individual species so we will establish a comparable use-case here. For most of this material, I will be focussing on Lagopus muta - the rock ptarmigan (see below). I have particularly fond memories of these birds flying alongside an uncle of mine and I on a topptur-ski trip in Lofoten earlier this year. It also lends itself well to a demonstration of rgbif functionality.
Disclaimer
If you find any typos in my material, are unhappy with some of what or how I am presenting or simply unclear about thing, do not hesitate to contact me.
All the best, Erik