RT Journal Article
SR Electronic
T1 APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.02.02.578715
DO 10.1101/2024.02.02.578715
A1 Wenk, Elizabeth
A1 Cornwell, William
A1 Fuchs, Anne
A1 Kar, Fonti
A1 Monro, Anna
A1 Sauquet, Hervé
A1 Stephens, Ruby
A1 Falster, Daniel S
YR 2024
UL http://biorxiv.org/content/early/2024/02/05/2024.02.02.578715.abstract
AB Here we present “APCalign”, an R package and accompanying browser-sourced application to align and update scientific names for Australian vascular plants to the most likely currently accepted name using the Australian Plant Census (APC) or a name in the Australian Plant Names Index (APNI). Scientific names are the label assigned to unique taxon concepts by the scientific community, but this common terminology is most useful if a taxon concept is consistently referred to by the same name. These links can be broken due to either spelling mistakes or taxonomic changes. Automated tools are required to resolve taxon lists, aligning and updating long lists of possibly erroneous scientific names to the most likely currently accepted names. It is essential that tools specific to the APC/APNI be developed, as these lists specify an endorsed national-level nomenclature used in government legislation and include the uniquely Australian concept of phrase names, absent in global taxonomic datasets. To align input names to names within the APC or APNI, “APCalign” works progressively through a sequence of checks that combine different permutations of the input name, exact versus fuzzy matches, matches that consider the entire name input versus a subset of words, and character strings that indicate a name can only be resolved to a genus or family. The aligned names are then, when possible, updated to a currently accepted taxon concept within the APC. This package should facilitate all research outputs that require diverse scientific name lists to be merged or outdated lists to be updated.Competing Interest StatementThe authors have declared no competing interest.