Harmonization of sediment diatoms from hundreds of lakes in the northeastern United States
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 R.zip” 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).
Resources
4 resources available
-
DiatomHarmonization_032222_files for R.zip
APPLICATION/X-ZIP-COMPRESSED -
NE_Lakes_Voucher_Flora_102421.pdf
APPLICATION/PDF -
Slide_accession_numbers_102421.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
VoucherFloraTranslation_102421.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET
Complete Metadata
| accessLevel | public |
|---|---|
| bureauCode |
[
"020:00"
]
|
| contactPoint |
{
"fn": "Sylvia Lee",
"hasEmail": "mailto:lee.sylvia@epa.gov"
}
|
| description | 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 R.zip” 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). |
| distribution |
[
{
"title": "DiatomHarmonization_032222_files for R.zip",
"mediaType": "application/x-zip-compressed",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524246/DiatomHarmonization_032222_files%20for%20R.zip"
},
{
"title": "NE_Lakes_Voucher_Flora_102421.pdf",
"mediaType": "application/pdf",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524246/NE_Lakes_Voucher_Flora_102421.pdf"
},
{
"title": "Slide_accession_numbers_102421.xlsx",
"mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524246/Slide_accession_numbers_102421.xlsx"
},
{
"title": "VoucherFloraTranslation_102421.xlsx",
"mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524246/VoucherFloraTranslation_102421.xlsx"
}
]
|
| identifier | https://doi.org/10.23719/1524246 |
| keyword |
[
"data quality",
"diatoms",
"lakes",
"paleolimnology",
"taxonomic harmonization",
"water quality"
]
|
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2022-03-22 |
| programCode |
[
"020:000"
]
|
| publisher |
{
"name": "U.S. EPA Office of Research and Development (ORD)",
"subOrganizationOf": {
"name": "U.S. Environmental Protection Agency",
"subOrganizationOf": {
"name": "U.S. Government"
}
}
}
|
| references |
[
"https://doi.org/10.1038/s41597-022-01661-3"
]
|
| rights |
null
|
| title | Harmonization of sediment diatoms from hundreds of lakes in the northeastern United States |
