Reconciliation of Avian NCBI Taxonomy
This repository includes programs used to reconcile the avian taxonomy used by NCBI with the eBird taxonomy. It is intended to serve the avian biodiversity research community, providing a means to link genetic sequence data available from NCBI with a standardized taxonomy. A complete description of the reconciliation and analysis of the taxonomic distribution of sequence data is available in Hosner et al. (2022).
Citation: Hosner, P. A., Zhao, M., Kimball, R. T., Braun, E. L., & Burleigh, J. G. (2022). Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies. Ornithology, 139(4), ukac045. https://doi.org/10.1093/ornithology/ukac045 (please cite this publication if you use these resources)
Primary data file:
The primary data file likely to be of interest to end user are the csv files with information on csv file with the GenBank taxon IDs, Genbank and eBird names, number of nucletide sequences (as of the version date), and the flag indicating whether name reconcilation was necessary.
eBird/Clements 2019 (NCBI data downloaded May 3, 2020):
File = GenBank_eBird_Clements_2019_taxonomic_reconciliation_20210120.csv
eBird/Clements 2022 (NCBI data downloaded Nov 4, 2022):
File = GenBank_eBird_Clements_2022_taxonomic_reconciliation.csv
eBird/Clements 2023 (NCBI data downloaded Feb 26, 2024):
File = GenBank_eBird_Clements_2023_taxonomic_reconciliation.csv