10.5281/zenodo.4416152
https://zenodo.org/records/4416152
oai:zenodo.org:4416152
Mast, Austin R.
Austin R.
Mast
0000-0002-4995-0467
Florida State University
Paul, Deborah L.
Deborah L.
Paul
0000-0003-2639-7520
Florida State University
Rios, Nelson
Nelson
Rios
0000-0003-4831-655X
Yale University Peabody Museum of Natural History
Bruhn, Robert
Robert
Bruhn
0000-0002-8081-5423
Florida State University
Dalton, Trevor
Trevor
Dalton
0000-0001-9210-1404
Florida State University
Krimmel, Erica R.
Erica R.
Krimmel
0000-0003-3192-0080
Florida State University
Pearson, Katelin D.
Katelin D.
Pearson
0000-0003-4947-7662
Florida State University
Sherman, Aja
Aja
Sherman
0000-0002-8295-9391
Florida State University
Shorthouse, David P.
David P.
Shorthouse
0000-0001-7618-5230
Agriculture and Agri-Food Canada
Simmons, Nancy B.
Nancy B.
Simmons
0000-0001-8807-7499
American Museum of Natural History
Soltis, Pam
Pam
Soltis
0000-0001-9310-8659
University of Florida
Upham, Nathan
Nathan
Upham
0000-0001-5412-9342
Arizona State University
Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses
Zenodo
2021
natural history collection
biodiversity collection
specimen
horseshoe bats
coronavirus
COVID-19
biodiversity informatics
2021-01-04
eng
10.5281/zenodo.3974999
https://zenodo.org/communities/covid-19
1.3
Creative Commons Public Domain Dedication and Certification
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
Funding by the U.S. National Science Foundation DBI 2033973.