This repo contains material for an hour and a half lecture on taxonomic harmonization, which is the process to 'align' differents datasets on a similar taxonomy prior to merging them.
The lecture was developed and given in the context of the NFDI4Biodiversity and GfÖ joint Winter School 2022.
This course aims to give first clues about taxonomic harmonization and how to deal with it. Giving the following points:
- What is taxonomy and how does it work?
- What are taxonomic reference databases and their different types?
- What is taxonomic harmonization and why is it needed?
- Where to start when trying to harmonize the taxonomy of datasets?
- Some practical considerations when performing taxonomic harmonization: considering author names, fuzzy matching, and larger databases.
The first important resource is the main work on which is this lecture is based:
Grenié, M., Berti, E., Carvajal-Quintero, J., Dädlow, G. M., Sagouis, A. & Winter, M. (2022). Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices. Methods in Ecology and Evolution, 00, 1– 14. https://doi.org/10.1111/2041-210X.13802
Then there are several other interesting resources:
taxharmonizexplorerthe companion shiny app that displays a network of searchable taxonomic resourcesgnparserone of the parser suggested to parse taxonomic names- the GBIF name parser another name parsing tool useful to preprocess taxonomic names
- Global Names Verifier one of these "mega-aggregator" database that contains many other databases to search for unmatched names
These materials are made available following the CC-BY 4.0 License.