Summary: Proximate biochemistry of sponge species collected in 2017 and 2018 across the Caribbean Basin in Curacao, Belize, Grand Cayman, St. Croix. These data were published in Clayshulte Abraham et al. (2021). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/868047

Summary: Sponge volume at Virgin Islands Territorial Coral Reef Monitoring Program’s (TCRMP) permanent monitoring sites, 2015-2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/814490

Summary: Sponge density and morphology and percent cover of sponges and associated benthic community determined from videos of three transects at Virgin Islands Territorial Coral Reef Monitoring Program site, pre- and post-hurricane, 2015-2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/814267

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip: Raw data from iDigBio, DwC-A format
• 0067804-200613084148143.zip: Raw data from GBIF, DwC-A format
• 0067806-200613084148143.zip: Raw data from GBIF, DwC-A format
• 1623690110.zip: Full export of this project's data (enhanced and raw) from BIOSPEX, CSV format
• bionomia-datasets-attributions.zip: Directory containing 103 Frictionless Data packages for datasets that have attributions made containing Rhinolophids or Hipposiderids, each package also containing a CSV file for mismatches in person date of birth/death and specimen eventDate. File bionomia-datasets-attributions-key_2021-02-25.csv included in this directory provides a key between dataset identifier (how the Frictionless Data package files are named) and dataset name.
• bionomia-problem-dates-all-datasets_2021-02-25.csv: List of 21 Hipposiderid or Rhinolophid records whose eventDate or dateIdentified mismatches a wikidata recipient’s date of birth or death across all datasets.
• flagEventDate.txt: file containing term definition to reference in DwC-A
• flagExclude.txt: file containing term definition to reference in DwC-A
• flagGeoreference.txt: file containing term definition to reference in DwC-A
• flagTaxonomy.txt: file containing term definition to reference in DwC-A
• georeferencedByID.txt: file containing term definition to reference in DwC-A
• identifiedByNames.txt: file containing term definition to reference in DwC-A
• instructions-to-get-people-data-from-bionomia-via-datasetKey: instructions given to data providers
• RAPID-code_collection-date.R: code associated with enhancing collection dates
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_external-linkages-bold.R: code associated with enhancing external linkages
• RAPID-code_external-linkages-genbank.R: code associated with enhancing external linkages
• RAPID-code_external-linkages-standardize.R: code associated with enhancing external linkages
• RAPID-code_people.R: code associated with enhancing data about people
• RAPID-code_standardize-country.R: code associated with standardizing country data
• RAPID-data-dictionary.pdf: metadata about terms included in this project’s data, in PDF format
• RAPID-data-dictionary.xlsx: metadata about terms included in this project’s data, in spreadsheet format
• rapid-data-providers_2021-05-03.csv: list of data providers and number of records provided to rapid-joined-records_country-cleanup_2020-09-23.csv
• rapid-final-data-product_2021-06-29.zip: Enhanced data from BIOSPEX, DwC-A format
• rapid-final-gazetteer.zip: Gazetteer providing georeference data and metadata for 10,341 localities assessed as part of this project
• rapid-joined-records_country-cleanup_2020-09-23.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_collection-date.pdf: protocol associated with enhancing collection dates
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_external-linkages.pdf: protocol associated with enhancing external linkages
• RAPID-protocol_georeference.pdf: protocol associated with georeferencing
• RAPID-protocol_people.pdf: protocol associated with enhancing data about people
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data
• RAPID-protocol_taxonomic-names.pdf: protocol associated with enhancing taxonomic name data
• RAPIDAgentStrings1_archivedCopy_30March2021.ods: resource used in conjunction with RAPID people protocol
• recordedByNames.txt: file containing term definition to reference in DwC-A
• Rhinolophid-HipposideridAgentStrings_and_People2_archivedCopy_30March2021.ods: resource used in conjunction with RAPID people protocol
• wikidata-notes-for-bat-collectors_leachman_2020: please see https://zenodo.org/record/4724139 for this resource

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip: Raw data from iDigBio
• 0067804-200613084148143.zip: Raw data from GBIF
• 0067806-200613084148143.zip: Raw data from GBIF
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_standardize-country.R: code associated with standardizing country data
• rapid-data-providers_2020-09-23.csv: list of data providers and number of records provided to rapid-joined-records_country-cleanup_2020-09-23.csv
• rapid-joined-records_country-cleanup_2020-09-23.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 77dfb340-4ab1-4c06-9f0c-eecc0558a9c8.zip: Raw data from iDigBio
• 0019125-200613084148143.zip: Raw data from GBIF
• 0019126-200613084148143.zip: Raw data from GBIF
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_standardize-country.R: code associated with standardizing country data
• rapid-joined-records_country-cleanup_2020-07-31.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data

Summary: This dataset provides rates of nitrogen fixation for the coastal Chukchi Sea near Barrow, Alaska. Nitrogen fixation supplies ‘new’ nitrogen to the global ocean and supports primary production and impacts global biogeochemical cycles. Historically, nitrogen fixation in marine waters was considered a predominantly warm water process but this and other recent studies have shown that nitrogen fixation is occurring at low rates in polar waters. This dataset reports rates of 3.5 – 17.2 nmol N L-1 d-1 in the ice-free coastal Alaskan Arctic. Additional investigations of high-latitude marine diazotrophic physiology are required to refine these N2 fixation estimates. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/701789

Summary: Cruise event log from the R/V Atlantic Explorer AE0922 cruise in the North Atlantic, Bermuda BATS region during 2009 (TZEX project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3454

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip: Raw data from iDigBio, DwC-A format
• 0067804-200613084148143.zip: Raw data from GBIF, DwC-A format
• 0067806-200613084148143.zip: Raw data from GBIF, DwC-A format
• 1620226888.zip: Full export of this project's data (enhanced and raw) from BIOSPEX, CSV format
• bionomia-datasets-attributions.zip: Directory containing 103 Frictionless Data packages for datasets that have attributions made containing Rhinolophids or Hipposiderids, each package also containing a CSV file for mismatches in person date of birth/death and specimen eventDate. File bionomia-datasets-attributions-key_2021-02-25.csv included in this directory provides a key between dataset identifier (how the Frictionless Data package files are named) and dataset name.
• bionomia-problem-dates-all-datasets_2021-02-25.csv: List of 21 Hipposiderid or Rhinolophid records whose eventDate or dateIdentified mismatches a wikidata recipient’s date of birth or death across all datasets.
• RAPID-code_collection-date.R: code associated with enhancing collection dates
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_standardize-country.R: code associated with standardizing country data
• RAPID-code_external-linkages-bold.R: code associated with enhancing external linkages
• RAPID-code_external-linkages-genbank.R: code associated with enhancing external linkages
• RAPID-code_external-linkages-standardize.R: code associated with enhancing external linkages
• RAPID-code_people.R: code associated with enhancing data about people
• RAPID-code_standardize-country.R: code associated with standardizing country data
• rapid-data-providers_2021-05-03.csv: list of data providers and number of records provided to rapid-joined-records_country-cleanup_2020-09-23.csv
• rapid-final-data-product_2021-05-07.csv: Enhanced dataset, final version from BIOSPEX
• rapid-joined-records_country-cleanup_2020-09-23.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_collection-date.pdf: protocol associated with enhancing collection dates
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_external-linkages.pdf: protocol associated with enhancing external linkages
• RAPID-protocol_georeference.pdf: protocol associated with georeferencing
• RAPID-protocol_people.pdf: protocol associated with enhancing data about people
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data
• RAPID-protocol_taxonomic-names.pdf: protocol associated with enhancing taxonomic name data
• RAPIDAgentStrings1_archivedCopy_30March2021.ods: resource used in conjunction with RAPID people protocol
• Rhinolophid-HipposideridAgentStrings_and_People2_archivedCopy_30March2021.ods: resource used in conjunction with RAPID people protocol
• wikidata-notes-for-bat-collectors_leachman_2020.docx: resource used in conjunction with RAPID people protocol
• wikidata-notes-for-bat-collectors_leachman_2020.pdf: resource used in conjunction with RAPID people protocol

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 77dfb340-4ab1-4c06-9f0c-eecc0558a9c8.zip: Raw data from iDigBio
• 0019125-200613084148143.zip: Raw data from GBIF
• 0019126-200613084148143.zip: Raw data from GBIF
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_standardize-country.R: code associated with standardizing country data
• rapid-joined-records_country-cleanup_2020-07-31.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip: Raw data from iDigBio, DwC-A format
• 0067804-200613084148143.zip: Raw data from GBIF, DwC-A format
• 0067806-200613084148143.zip: Raw data from GBIF, DwC-A format
• 1620226888.zip: Full export of this project's data (enhanced and raw) from BIOSPEX, CSV format
• bionomia-datasets-attributions.zip: Directory containing 103 Frictionless Data packages for datasets that have attributions made containing Rhinolophids or Hipposiderids, each package also containing a CSV file for mismatches in person date of birth/death and specimen eventDate. File bionomia-datasets-attributions-key_2021-02-25.csv included in this directory provides a key between dataset identifier (how the Frictionless Data package files are named) and dataset name.
• bionomia-problem-dates-all-datasets_2021-02-25.csv: List of 21 Hipposiderid or Rhinolophid records whose eventDate or dateIdentified mismatches a wikidata recipient’s date of birth or death across all datasets.
• flagEventDate.txt: file containing term definition to reference in DwC-A
• flagExclude.txt: file containing term definition to reference in DwC-A
• flagGeoreference.txt: file containing term definition to reference in DwC-A
• flagTaxonomy.txt: file containing term definition to reference in DwC-A
• georeferencedByID.txt: file containing term definition to reference in DwC-A
• identifiedByNames.txt: file containing term definition to reference in DwC-A
• RAPID-code_collection-date.R: code associated with enhancing collection dates
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_standardize-country.R: code associated with standardizing country data
• RAPID-code_external-linkages-bold.R: code associated with enhancing external linkages
• RAPID-code_external-linkages-genbank.R: code associated with enhancing external linkages
• RAPID-code_external-linkages-standardize.R: code associated with enhancing external linkages
• RAPID-code_people.R: code associated with enhancing data about people
• RAPID-code_standardize-country.R: code associated with standardizing country data
• rapid-data-providers_2021-05-03.csv: list of data providers and number of records provided to rapid-joined-records_country-cleanup_2020-09-23.csv
• rapid-final-data-product_2021-05-07.csv: Enhanced dataset, final version from BIOSPEX
• rapid-joined-records_country-cleanup_2020-09-23.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_collection-date.pdf: protocol associated with enhancing collection dates
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_external-linkages.pdf: protocol associated with enhancing external linkages
• RAPID-protocol_georeference.pdf: protocol associated with georeferencing
• RAPID-protocol_people.pdf: protocol associated with enhancing data about people
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data
• RAPID-protocol_taxonomic-names.pdf: protocol associated with enhancing taxonomic name data
• RAPIDAgentStrings1_archivedCopy_30March2021.ods: resource used in conjunction with RAPID people protocol
• Rhinolophid-HipposideridAgentStrings_and_People2_archivedCopy_30March2021.ods: resource used in conjunction with RAPID people protocol
• recordedByNames.txt: file containing term definition to reference in DwC-A
• wikidata-notes-for-bat-collectors_leachman_2020.docx: resource used in conjunction with RAPID people protocol
• wikidata-notes-for-bat-collectors_leachman_2020.pdf: resource used in conjunction with RAPID people protocol

Summary:

This repository is associated with NSF DBI 2033973, RAPID Grant: Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses (https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973). Specifically, this repository contains (1) raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), (2) R code for reproducible data wrangling and improvement, (3) protocols associated with data enhancements, and (4) enhanced versions of the dataset published at various project milestones. Additional code associated with this grant can be found in the BIOSPEX repository (https://github.com/iDigBio/Biospex). Long-term data management of the enhanced specimen data created by this project is expected to be accomplished by the natural history collections curating the physical specimens, a list of which can be found in this Zenodo resource.

Grant abstract: "The award to Florida State University will support research contributing to the development of georeferenced, vetted, and versioned data products of the world's specimens of horseshoe bats and their relatives for use by researchers studying the origins and spread of SARS-like coronaviruses, including the causative agent of COVID-19. Horseshoe bats and other closely related species are reported to be reservoirs of several SARS-like coronaviruses. Species of these bats are primarily distributed in regions where these viruses have been introduced to populations of humans. Currently, data associated with specimens of these bats are housed in natural history collections that are widely distributed both nationally and globally. Additionally, information tying these specimens to localities are mostly vague, or in many instances missing. This decreases the utility of the specimens for understanding the source, emergence, and distribution of SARS-COV-2 and similar viruses. This project will provide quality georeferenced data products through the consolidation of ancillary information linked to each bat specimen, using the extended specimen model. The resulting product will serve as a model of how data in biodiversity collections might be used to address emerging diseases of zoonotic origin. Results from the project will be disseminated widely in opensource journals, at scientific meetings, and via websites associated with the participating organizations and institutions. Support of this project provides a quality resource optimized to inform research relevant to improving our understanding of the biology and spread of SARS-CoV-2. The overall objectives are to deliver versioned data products, in formats used by the wider research and biodiversity collections communities, through an open-access repository; project protocols and code via GitHub and described in a peer-reviewed paper, and; sustained engagement with biodiversity collections throughout the project for reintegration of improved data into their local specimen data management systems improving long-term curation.

This RAPID award will produce and deliver a georeferenced, vetted and consolidated data product for horseshoe bats and related species to facilitate understanding of the sources, distribution, and spread of SARS-CoV-2 and related viruses, a timely response to the ongoing global pandemic caused by SARS-CoV-2 and an important contribution to the global effort to consolidate and provide quality data that are relevant to understanding emergent and other properties the current pandemic. This RAPID award is made by the Division of Biological Infrastructure (DBI) using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria."

Files included in this resource

• 9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip: Raw data from iDigBio
• 0067804-200613084148143.zip: Raw data from GBIF
• 0067806-200613084148143.zip: Raw data from GBIF
• RAPID-code_compile-deduplicate.R: code associated with compiling and deduplicating raw data
• RAPID-code_standardize-country.R: code associated with standardizing country data
• rapid-data-providers_2020-09-23.csv: list of data providers and number of records provided to rapid-joined-records_country-cleanup_2020-09-23.csv
• rapid-joined-records_country-cleanup_2020-09-23.csv: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized
• RAPID-protocol_compile-deduplicate.pdf: protocol associated with compiling and deduplicating raw data
• RAPID-protocol_standardize-country.pdf: protocol associated with standardizing country data
• wikidata-notes-for-bat-collectors_leachman_2020.docx: resource used in conjunction with RAPID people protocol
• wikidata-notes-for-bat-collectors_leachman_2020.pdf: resource used in conjunction with RAPID people protocol

Summary:

This is the source code required to reproduce data analysis figures from the manuscript, "System-wide automatic extraction of functional signatures in Pseudomonas aeruginosa with eADAGE." This includes the eADAGE method as well as code for the comparison methods.

Summary: The Eddies Dynamics, Mixing, Export, and Species composition (EDDIES) mesozooplankton biomass data set includes estimates of mesozooplankton biomass determined from MOCNESS plankton net tows. Zooplankton biomass estimates were determined from 1 m^2, 150 micron mesh MOCNESS (Multiple Opening/Closing Net and Environmental Sensing System) tows. The following discrete depth intervals were sampled on the upcast: 0-50, 50-100, 100-150, 150-200, 200-300, 300-400, 400-500, 500-600, and 600-700 m. Generally paired tows during the day (9:30-15:00 local time) and night (21:30-03:00) were performed at each station. A single tow generally covered 5-15 km. The nominal position (lat_n and lon_n) for each tow is the position at the mid depth 200-300m sampling interval. Table 1 (pg 1362) of Goldthwait and Steinberg (2008) is a sequential list of all MOCNESS mesozooplankton tows and includes eddy identification number and location. Each sample was size-fractionated using nested sieves of 0.15 mm, 0.5 mm, 1 mm, 2mm, and 5 mm mesh. Zooplankton in each size class were transferred onto pre-weighed 0.15 mm nitex mesh filters and rinsed with deionized water. Samples were then dried for 24 hours at 60 degrees C and weighed.

Summary: Summary of samples collected by the Hydrothermal Organic Geochemistry (HOG) sampler on AT-4201 with ROV Jason, on dives J2_1107 through J2_1111, during R/V Atlantic cruise AT42-01, September 9 - October 1, 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/782197

Summary: Cruise event log from the R/V Atlantic Explorer AE0922 cruise in the North Atlantic, Bermuda BATS region during 2009 (TZEX project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3454

Summary: CTD stations from the R/V Atlantic Explorer AE0922 in the North Atlantic, Bermuda BATS region during 2009 (TZEX project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3457

Summary: Zooplankton taxonomic data from MOCNESS and IONESS tows from VERTIGO cruises KM0414, ZHNG09RR from the Hawaiian Islands HOT Site, NW SubArctic Pacific Ocean K2 Site, 2004-2005 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3014

Summary: Using data from a randomized experiment, we find that poor rural Mexican households invested part of their cash transfers from the Oportunidades program in productive assets, increasing agricultural income by almost 10 percent after 18 months of benefits. We estimate that for each peso transferred, households consume 74 cents and invest the rest, permanently increasing long-term consumption by about 1.6 cents. Results suggest that cash transfers can achieve long-term increases in consumption through investment in productive activities, thereby permitting beneficiary households to attain higher living standards that are sustained even after transitioning off the program.