Main Content

Collectomics & Ecoinformatics

How can we reliably use 300 year old herbarium specimen for modern biodiversity research?


The public availability of biodiversity data is drastically increasing. For instance information of species geographic occurrence from digitized herbarium collections, molecular data on species relationships from high throughput sequencing, and information on species traits, from mobilized data in floras. Currently methods to process “big data” are a bottleneck for harnessing the full potential of large datasets and transitioning biodiversity research into a data driven discipline. We develop software methods for standardized and reproducible analysis of large-scale biodiversity data with a focus on georeferenced species occurrence records mobilized from collection records. Among other we develop CoordinateCleaner, an R-package to quality control large scale species occurrences from collections (Zizka et al., 2019), SampBias, an R-package to quantify geographic sampling bias in occurrence records (Zizka et al. 2021) and Bio-Dem, a graphical user interface tool to visually link scientific collection activity to socio-political conditions in countries worldwide, including colonial history (Zizka et al. 2021, 1st prize at the 2021 GBIF Ebbe Nielsen Challenge)