A globally integrated structure of taxonomy supporting biodiversity science and conservation

OSF related project and underlying data https://osf.io/9rptq/

Repository content and contributions:

• Code to produce analysis of Box 1 and 2
• Contributors to analyses: A.A. Maureaud, M. Lucas, Y.V. Sica, E.L. Sandall
• Contributors to MOL taxonomies: Y.V. Sica, M.S Rogan, D.B. Booher, R. Edwards, M. Lucas, S. Pinkert, A. Ranipeta, A.A. Maureaud, E.L. Sandall

Data

All data files used for the analysis can be found on the OSF project linked at the top, except for butterfly synonym names that are not public (https://doi.org/10.1111/geb.13475).

Data and project should be cited as indicated on OSF as following: Sandall, E. L., Maureaud, A. A., Guralnick, R., McGeoch, M. A., Sica, Y. V., Rogan, M. S., … Jetz, W. (2023, July 27). Project data and code access underlying the globally integrated taxonomic structure. https://doi.org/10.17605/OSF.IO/9RPTQ

• MOL/: taxonomies from Map of Life (MOL) https://mol.org/
• COL/: downloaded data from Catalogue of Life (COL) for selected groups https://www.catalogueoflife.org/
• GBIF/: downloaded data from the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/
• GRIIS/: downloaded data from the Global Register of Introduced and Invasive Species (GRIIS) https://griis.org/
• IUCN/: downloaded data from the International Union for the Conservation of Nature (IUCN) https://www.iucnredlist.org/
• NCBI/: downloaded data from the National Center for Biotechnology Information https://www.ncbi.nlm.nih.gov/
• OpenTreePhylogeny: downloaded data from the Tree Of Life http://www.onezoom.org/
• taxonomies.csv: outputs file created when running count_names.R

Metadata

Description of the column names in the MOL taxonomy files:

• id unique name id per group
• accid value is 0 is name is considered accepted, id if synonym
• canonical combination of genus, species, and subspecies if relevant
• order follows DwC standard terms (https://dwc.tdwg.org/terms/)
• family follows DwC standard terms
• genus follows DwC standard terms
• species follows DwC standard terms
• subspecies correspond to infraspecificEpithet according to DwC standard terms
• group taxonomic group considered
• authorship correspond to scientificNameAuthorship according to DwC standard terms
• source data source used to access the names

Code

• count_names.R: create the taxonomy file for all MOL groups, including dragonflies, crabs, ants, daisies, mammals, reptiles, amphibians, birds, butterflies, and get simple summary of number of names per taxonomic group. Methods for compiling taxonomies are available in Text S1 and Table S3.
• get_silhouettes.R: for each taxonomic group, download and store a silhouette use for Box 1 and 2 from the rphylopic package http://phylopic.org/
• taxonomic_completeness.R: assess number of names added to master taxonomies on the last 2 decades
• col_coverage.R: assess taxonomic match with Catalogue of Life
• gbif_coverage.R: assess taxonomic match and data gaps with GBIF
• griis_coverage.R: assess taxonomic mismatch with GRIIS
• iucn_coverage.R: assess taxonomic match and data gaps with IUCN taxonomy and red list
• ncbi_coverage.R: assess taxonomic match and genetic data coverage with NCBI
• tree_coverage.R: assess taxonomic match and phylogenetic affiliation with TreeOfLife

Results

• match_XX_results.csv: tables with coverage and data gaps results per taxonomic group and database (either COL, GBIF, GRIIS, IUCN, NCBI, TreeOfLife)
• completeness.csv: table with completeness results
• numbers.csv: table with number of names
• matching_results.csv: table with matching results from all data sources, grading detailed in Table S5 and Text S2
• matching_results_scores.csv: table with matching results from all data sources and associated scores, grading detailed in Table S5

Figures

• All silhouettes downloaded from rphylopic