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Harmonization of sediment diatoms from hundreds of lakes in the northeastern United States

Metadata Updated: September 13, 2022

Sediment diatoms are widely used to track environmental histories of lakes and their watersheds, but merging datasets generated by different researchers for further large-scale studies is challenging because of the taxonomic discrepancies caused by rapidly evolving diatom nomenclature and taxonomic concepts. Here we collated five datasets of lake sediment diatoms from the northeastern USA using a harmonization process which included updating synonyms, tracking the identity of inconsistently identified taxa and grouping those that could not be resolved taxonomically. The Dataset consists of a Portable Document Format (.pdf) file of the Voucher Flora, six Microsoft Excel (.xlsx) data files, an R script, and five output Comma Separated Values (.csv) files.

The Voucher Flora documents the morphological species concepts in the dataset using diatom images compiled into plates (NE_Lakes_Voucher_Flora_102421.pdf) and the translation scheme of the OTU codes to diatom scientific or provisional names with identification sources, references, and notes (VoucherFloraTranslation_102421.xlsx).

The file Slide_accession_numbers_102421.xlsx has slide accession numbers in the ANS Diatom Herbarium.

The “DiatomHarmonization_032222_files for” archive contains four Excel input data files, the R code, and a subfolder “OUTPUT” with five .csv files. The file Counts_original_long_102421.xlsx contains original diatom count data in long format. The file Harmonization_102421.xlsx is the taxonomic harmonization scheme with notes and references. The file SiteInfo_031922.xlsx contains sampling site- and sample-level information. WaterQualityData_021822.xlsx is a supplementary file with water quality data. R code (DiatomHarmonization_032222.R) was used to apply the harmonization scheme to the original diatom counts to produce the output files. The resulting output files are five wide format files containing diatom count data at different harmonization steps (Counts_1327_wide.csv, Step1_1327_wide.csv, Step2_1327_wide.csv, Step3_1327_wide.csv) and the summary of the Indicator Species Analysis (INDVAL_RESULT.csv). The harmonization scheme (Harmonization_102421.xlsx) can be further modified based on additional taxonomic investigations, while the associated R code (DiatomHarmonization_032222.R) provides a straightforward mechanism to diatom data versioning.

This dataset is associated with the following publication: Potapova, M., S. Lee, S. Spaulding, and N. Schulte. A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States. Scientific Data. Springer Nature, New York, NY, 9(540): 1-8, (2022).

Access & Use Information

Public: This dataset is intended for public access and use. License: See this page for license information.

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Metadata Created Date February 21, 2022
Metadata Updated Date September 13, 2022

Metadata Source

Harvested from EPA ScienceHub

Additional Metadata

Resource Type Dataset
Metadata Created Date February 21, 2022
Metadata Updated Date September 13, 2022
Publisher U.S. EPA Office of Research and Development (ORD)
Data Last Modified 2022-03-22
Public Access Level public
Bureau Code 020:00
Schema Version
Harvest Object Id 293334e7-7a55-4a5d-92c0-1d5afe144892
Harvest Source Id 04b59eaf-ae53-4066-93db-80f2ed0df446
Harvest Source Title EPA ScienceHub
Program Code 020:000
Publisher Hierarchy U.S. Government > U.S. Environmental Protection Agency > U.S. EPA Office of Research and Development (ORD)
Related Documents
Source Datajson Identifier True
Source Hash f4b7b12545314db22ab4dfd28227078a101dd460
Source Schema Version 1.1

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