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Access to biodiversity data through web services

This online course will focus on automated ways of retrieving and processing biodiversity data from public databases. You will mostly work in the R programming environment and be introduced to common R-packages and functions to retrieve publication-quality (DOI-assigned) species occurrence data from the Global Biodiversity Information Facility (GBIF). Further you will exercise the most important steps of data cleaning and filtering, including taxonomic filtering to account for the variation of species name synonyms and misspellings using the package taxise. The tutorial will also include common approaches to download occurrences of a larger taxonomic group, such as a family or order. Finally you will try some fancy plotting options to best display the retrieved biodiversity data, including plotting on interactive maps. We encourage you to bring your own scientific questions, and if possible run this course together in a small group – this will make the exercises more interesting and comprehensible.

Contact: Matthias Obst (

Creator: Gothenburg Global Biodiversity Center (GGBC)

Time effort: 4-6 hours

Course level: PhD level (motivated Master’s students welcome)

Recommended background: Basic R knowledge required

Link to module: