cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nfyxhh
title: Occurrence Download

description: A dataset containing 3899 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phyllastrephus strepitans)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 3899 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020537-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xj8j65
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Rhyticeros undulatus)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020540-250802193616735/datasets/export for details.
DOI: 10.15468/dl.p9dejj
title: Occurrence Download

description: A dataset containing 15145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Rhyticeros undulatus)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 15145 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020538-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10888508
title: 1000 Soils Pilot Dataset, version 6, March 2024

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data.

A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback.

Data completed include:



Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry

Microbial biomass C and N; TOC/TDN of water-extractable OM; X-ray computed tomography

Metagenomes; raw data available upon request


Data in progress:



Soil hydraulic properties, in development, timeline TBD (specific samples may be available upon request)

LC-MS/MS in development, timeline TBD, inquire for status


1000S_Dataset_Biogeochem_Biomass_Tomography_WEOM_2023_06_12.csv contains all available biogeochemical data; microbial biomass C and N; TOC/TDN of water-extractable OM; and X-ray computed tomography.

icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates.

1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information.

Readme File_v2.xlsx is the readme file.

Please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions.

The following file and all raw data are available upon request:

icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.13210467
title: 1000 Soils Pilot Dataset, version 7, August 2024

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data.

A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback.

Data completed include:



Geochemistry, texture, respiration, and enzyme activities

FTICR-MS organic matter chemistry

Microbial biomass C and N

TOC/TDN of water-extractable OM

X-ray computed tomography (derived metrics available here, raw data available upon request)

Metagenomes; a variety of data formats are available upon request

Soil hydraulic properties


Data in progress:



LC-MS/MS in development, timeline TBD, inquire for status


1000S_Dataset_Biogeochem_Biomass_Tomography_WEOM_2023_06_12.csv contains all available biogeochemical data; microbial biomass C and N; TOC/TDN of water-extractable OM; and X-ray computed tomography.

icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates.

1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information.

Soil Hydraulics.xlsx contains soil hydraulics information.

Readme File_v3.xlsx is the readme file.

Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions.

The following file and all raw data are available upon request:

icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.7406533
title: 1000 Soils Pilot Dataset, version 1, December 2022

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. Our estimated timeline is as follows: Early-to-mid December: Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry Mid-to-late January: Microbial biomass C and N; TOC/TDN of water-extractable OM Mid-February: Metagenomes and LC-MS organic matter chemistry Mid-March: X-ray computed tomography Mid-April: Soil hydraulic properties 1000S_Dataset_Biogeochemistry_2022-12-01.csv contains all available biogeochemical data and will be updated as more data become available. icr_by_formula.csv contains FTICR-MS data processed by CoreMS. These data are merged by formula across instrument runs to enable cross-sample comparisons. Readme files will be available shortly. In the interim, please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file is available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.7606753
title: 1000 Soils Pilot Dataset, version 2, February 2023

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. Our estimated timeline is as follows: Early-to-mid December: Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry Late February: Microbial biomass C and N; TOC/TDN of water-extractable OM; X-ray computed tomography Mid-April: Metagenomes July: LC-MS organic matter chemistry September: Soil hydraulic properties (specific samples may be available upon request) 1000S_Dataset_Biogeochemistry_2022-12-01.csv contains all available biogeochemical data and will be updated as more data become available. icr.reps.combined_v1.csv contains FTICR-MS data processed by CoreMS. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file is available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.15328215
title: 1000 Soils Pilot Dataset, version 8, May 2025

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data.

A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback.

Data completed include:



Geochemistry, texture, respiration, and enzyme activities

FTICR-MS organic matter chemistry

Microbial biomass C and N

TOC/TDN of water-extractable OM

X-ray computed tomography (derived metrics available here, raw data available upon request)

Metagenomes; a variety of data formats are available upon request

Soil hydraulic properties


Data in progress:



LC-MS/MS in development, timeline TBD, inquire for status


1000S_processed_BGC_summary.csv contains all available biogeochemical data; microbial biomass C and N; and TOC/TDN of water-extractable OM; and 

1000S_Tomography.xslx contains a summary of data generated via X-ray computed tomography.

icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates.

1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information.

Soil Hydraulics_corrected_02042025.xlsx contains soil hydraulics information.

Readme File_v4.xlsx is the readme file.

Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions.

The following file and all raw data are available upon request:

icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.

For more information, please see: https://www.emsl.pnnl.gov/monet and https://sc-data.emsl.pnnl.gov/monet

Acknowledgment: 

Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. 

The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.
DOI: 10.5281/zenodo.7406532
title: 1000 Soils Pilot Dataset, version 8, May 2025

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data.

A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback.

Data completed include:



Geochemistry, texture, respiration, and enzyme activities

FTICR-MS organic matter chemistry

Microbial biomass C and N

TOC/TDN of water-extractable OM

X-ray computed tomography (derived metrics available here, raw data available upon request)

Metagenomes; a variety of data formats are available upon request

Soil hydraulic properties


Data in progress:



LC-MS/MS in development, timeline TBD, inquire for status


1000S_processed_BGC_summary.csv contains all available biogeochemical data; microbial biomass C and N; and TOC/TDN of water-extractable OM; and 

1000S_Tomography.xslx contains a summary of data generated via X-ray computed tomography.

icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates.

1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information.

Soil Hydraulics_corrected_02042025.xlsx contains soil hydraulics information.

Readme File_v4.xlsx is the readme file.

Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions.

The following file and all raw data are available upon request:

icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.

For more information, please see: https://www.emsl.pnnl.gov/monet and https://sc-data.emsl.pnnl.gov/monet

Acknowledgment: 

Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. 

The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.
DOI: 10.5281/zenodo.7706774
title: 1000 Soils Pilot Dataset, version 3, March 2023

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. Our estimated timeline is as follows: Early-to-mid December: Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry Late February: Microbial biomass C and N; TOC/TDN of water-extractable OM; X-ray computed tomography Mid-April: Metagenomes July: LC-MS organic matter chemistry September: Soil hydraulic properties (specific samples may be available upon request) 1000S_Dataset_Biogeochemistry_2022-12-01.csv contains all available biogeochemical data and will be updated as more data become available. 1000S_Dataset_Biomass_Tomography_WEOM_2023_03_01.xlsx contains microbial biomass C and N; TOC/TDN of water-extractable OM; and X-ray computed tomography. icr.reps.combined_v1.csv contains FTICR-MS data processed by CoreMS. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file is available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.7765003
title: 1000 Soils Pilot Dataset, version 4, March 2023

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. Our estimated timeline is as follows: Early-to-mid December: Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry Late February: Microbial biomass C and N; TOC/TDN of water-extractable OM; X-ray computed tomography June: Metagenomes; raw data available September: Soil hydraulic properties (specific samples may be available upon request) LC-MS/MS in development, timeline TBD, estimated late summer/early fall, inquire for status 1000S_Dataset_Biogeochemistry_2022-12-01.csv contains all available biogeochemical data and will be updated as more data become available. 1000S_Dataset_Biomass_Tomography_WEOM_2023_03_01.xlsx contains microbial biomass C and N; TOC/TDN of water-extractable OM; and X-ray computed tomography. icr.reps.combined_v1.csv contains FTICR-MS data processed by CoreMS. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file is available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.8118357
title: 1000 Soils Pilot Dataset, version 5, July 2023

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. Data completed include: Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry Microbial biomass C and N; TOC/TDN of water-extractable OM; X-ray computed tomography Metagenomes; raw data available upon request Data in progress: Soil hydraulic properties, in development, timeline TBD (specific samples may be available upon request) LC-MS/MS in development, timeline TBD, estimated late summer/early fall, inquire for status 1000S_Dataset_Biogeochem_Biomass_Tomography_WEOM_2023_06_12.csv contains all available biogeochemical data; microbial biomass C and N; TOC/TDN of water-extractable OM; and X-ray computed tomography. icr.reps.combined_v1.csv contains FTICR-MS data processed by CoreMS. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Readme File_v2.xlsx is the readme file. Please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file and all raw data are available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.5281/zenodo.8122488
title: 1000 Soils Pilot Dataset, version 5, July 2023

description: This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback. Data completed include: Geochemistry, texture, respiration, enzyme activities, and FTICR-MS organic matter chemistry Microbial biomass C and N; TOC/TDN of water-extractable OM; X-ray computed tomography Metagenomes; raw data available upon request Data in progress: Soil hydraulic properties, in development, timeline TBD (specific samples may be available upon request) LC-MS/MS in development, timeline TBD, estimated late summer/early fall, inquire for status 1000S_Dataset_Biogeochem_Biomass_Tomography_WEOM_2023_06_12.csv contains all available biogeochemical data; microbial biomass C and N; TOC/TDN of water-extractable OM; and X-ray computed tomography. icr.reps.combined_v1.csv contains FTICR-MS data processed by CoreMS. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Readme File_v2.xlsx is the readme file. Please contact Qian Zhao (qian.zhao@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file and all raw data are available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs.
DOI: 10.15468/dl.9bdhfj
title: Occurrence Download

description: A dataset containing 4459 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myrica gale L.",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4459 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012473-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.