Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses

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 <strong>(1) </strong>raw data from iDigBio (http://portal.idigbio.org) and GBIF (https://www.gbif.org), <strong>(2) </strong>R code for reproducible data wrangling and improvement, <strong>(3)</strong> protocols associated with data enhancements, and <strong>(4)</strong> 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. <strong>Grant abstract:</strong> "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." <strong>Files included in this resource</strong> <em>9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip</em>: Raw data from iDigBio, DwC-A format <em>0067804-200613084148143.zip</em>: Raw data from GBIF, DwC-A format <em>0067806-200613084148143.zip</em>: Raw data from GBIF, DwC-A format <em>1620226888.zip</em>: Full export of this project's data (enhanced and raw) from BIOSPEX, CSV format <em>bionomia-datasets-attributions.zip</em>: 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. <em>bionomia-problem-dates-all-datasets_2021-02-25.csv</em>: List of 21 Hipposiderid or Rhinolophid records whose eventDate or dateIdentified mismatches a wikidata recipient’s date of birth or death across all datasets. <em>flagEventDate.txt</em>: file containing term definition to reference in DwC-A <em>flagExclude.txt</em>: file containing term definition to reference in DwC-A <em>flagGeoreference.txt</em>: file containing term definition to reference in DwC-A <em>flagTaxonomy.txt</em>: file containing term definition to reference in DwC-A <em>georeferencedByID.txt</em>: file containing term definition to reference in DwC-A <em>identifiedByNames.txt</em>: file containing term definition to reference in DwC-A <em>RAPID-code_collection-date.R</em>: code associated with enhancing collection dates <em>RAPID-code_compile-deduplicate.R</em>: code associated with compiling and deduplicating raw data <em>RAPID-code_standardize-country.R</em>: code associated with standardizing country data <em>RAPID-code_external-linkages-bold.R</em>: code associated with enhancing external linkages <em>RAPID-code_external-linkages-genbank.R</em>: code associated with enhancing external linkages <em>RAPID-code_external-linkages-standardize.R</em>: code associated with enhancing external linkages <em>RAPID-code_people.R</em>: code associated with enhancing data about people <em>RAPID-code_standardize-country.R</em>: code associated with standardizing country data <em>rapid-data-providers_2021-05-03.csv</em>: list of data providers and number of records provided to rapid-joined-records_country-cleanup_2020-09-23.csv <em>rapid-final-data-product_2021-05-07.csv</em>: Enhanced dataset, final version from BIOSPEX <em>rapid-joined-records_country-cleanup_2020-09-23.csv</em>: data product initial version where raw data has been compiled and deduplicated, and country data has been standardized <em>RAPID-protocol_collection-date.pdf</em>: protocol associated with enhancing collection dates <em>RAPID-protocol_compile-deduplicate.pdf</em>: protocol associated with compiling and deduplicating raw data <em>RAPID-protocol_external-linkages.pdf</em>: protocol associated with enhancing external linkages <em>RAPID-protocol_georeference.pdf</em>: protocol associated with georeferencing <em>RAPID-protocol_people.pdf</em>: protocol associated with enhancing data about people <em>RAPID-protocol_standardize-country.pdf</em>: protocol associated with standardizing country data <em>RAPID-protocol_taxonomic-names.pdf</em>: protocol associated with enhancing taxonomic name data <em>RAPIDAgentStrings1_archivedCopy_30March2021.ods</em>: resource used in conjunction with RAPID people protocol <em>Rhinolophid-HipposideridAgentStrings_and_People2_archivedCopy_30March2021.ods</em>: resource used in conjunction with RAPID people protocol <em>recordedByNames.txt</em>: file containing term definition to reference in DwC-A <em>wikidata-notes-for-bat-collectors_leachman_2020.docx</em>: resource used in conjunction with RAPID people protocol <em>wikidata-notes-for-bat-collectors_leachman_2020.pdf</em>: resource used in conjunction with RAPID people protocol本仓库关联美国国家科学基金会（National Science Foundation, NSF）DBI 2033973号快速资助项目：快速构建针对全球菊头蝠及其近缘类群标本的数据产品——该类群是已知的冠状病毒自然宿主（项目链接：https://www.nsf.gov/awardsearch/showAward?AWD_ID=2033973）。具体而言，本仓库包含以下内容：<strong>(1)</strong> 来自集成生物多样性数据库（iDigBio, Integrated Digitized Biocollections）和全球生物多样性信息设施（GBIF, Global Biodiversity Information Facility）的原始数据；<strong>(2)</strong> 用于可复现的数据整理与优化的R语言代码；<strong>(3)</strong> 与数据增强相关的操作规程；<strong>(4)</strong> 项目各里程碑阶段发布的增强版数据集。本项目资助下的额外代码可在BIOSPEX仓库（https://github.com/iDigBio/Biospex）中获取。本项目生成的增强型标本数据的长期管理工作，将由收藏实体标本的自然历史馆藏机构完成，相关馆藏列表可在该Zenodo资源中查阅。 <strong>项目摘要：</strong>“本项目资助佛罗里达州立大学开展研究，旨在开发全球菊头蝠及其近缘类群标本的地理参考、经过审核且带版本号的数据产品，供研究类SARS冠状病毒（包括COVID-19病原体）起源与传播的科研人员使用。菊头蝠及其他近缘物种被证实为多种类SARS冠状病毒的自然宿主。此类蝙蝠主要分布于这些病毒已传入人类群体的区域。目前，此类蝙蝠标本的数据分散存储于全球各地的自然历史馆藏中，且标本对应的地点信息大多模糊不清，甚至多数情况下完全缺失。这降低了这些标本在解析SARS-CoV-2及同类病毒的源头、出现与传播规律时的应用价值。本项目将通过扩展标本模型，整合每件蝙蝠标本的附属信息，提供高质量的地理参考数据产品。最终成果将作为生物多样性馆藏数据如何用于解决人畜共患新兴疾病问题的示范案例。本项目成果将通过开源期刊、学术会议以及参与机构的官方网站广泛传播。本项目的支持将提供一个经过优化的高质量资源，助力提升我们对SARS-CoV-2的生物学特性与传播规律的认知。本项目的总体目标包括：通过开源仓库交付面向广大科研与生物多样性馆藏社区的版本化数据产品；通过GitHub平台发布项目操作规程与代码，并在同行评议期刊中予以说明；在项目全程与生物多样性馆藏机构保持持续互动，将优化后的数据重新整合至其本地标本数据管理系统，以改进长期馆藏管理工作。本快速资助项目将生成并交付菊头蝠及其近缘物种的地理参考、经过审核且整合完善的数据产品，以助力解析SARS-CoV-2及同类病毒的源头、分布与传播规律，这既是对当前SARS-CoV-2引发的全球大流行病的及时响应，也是对全球整合并提供与理解本次大流行及其他新发传染病相关的高质量数据工作的重要贡献。本快速资助项目由美国国家科学基金会生物基础设施分部（Division of Biological Infrastructure, DBI）通过《冠状病毒援助、救济与经济安全法案》（Coronavirus Aid, Relief, and Economic Security Act, CARES Act）的资金拨付设立。本资助符合美国国家科学基金会的法定使命，并通过基金会的知识价值（intellectual merit）与 broader 影响力（broader impacts）评审标准的评估，被认定为具备资助价值。” <strong>本资源包含的文件：</strong> <em>9d4b9069-48c4-4212-90d8-4dd6f4b7f2a5.zip</em>：来自iDigBio的原始数据，格式为达尔文核心归档（DwC-A, Darwin Core Archive） <em>0067804-200613084148143.zip</em>：来自GBIF的原始数据，格式为达尔文核心归档 <em>0067806-200613084148143.zip</em>：来自GBIF的原始数据，格式为达尔文核心归档 <em>1620226888.zip</em>：本项目数据（含原始与增强版）的完整导出文件，格式为CSV <em>bionomia-datasets-attributions.zip</em>：包含103个无摩擦数据（Frictionless Data）包的目录，对应所有涉及菊头蝠科（Rhinolophidae）或蹄蝠科（Hipposideridae）标本且已完成归属标注的数据集；每个数据包同时包含一份CSV文件，用于比对人员出生日期/逝世日期与标本事件日期（eventDate）的不匹配情况。本目录下的<b>bionomia-datasets-attributions-key_2021-02-25.csv</b>提供了数据集标识符（即无摩擦数据包文件的命名方式）与数据集名称之间的映射关系。 <em>bionomia-problem-dates-all-datasets_2021-02-25.csv</em>：涵盖所有数据集的21条蹄蝠科或菊头蝠科标本记录，其事件日期（eventDate）或鉴定日期（dateIdentified）与对应维基数据条目中记录的采集人员出生日期/逝世日期存在不匹配。 <em>flagEventDate.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>flagExclude.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>flagGeoreference.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>flagTaxonomy.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>georeferencedByID.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>identifiedByNames.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>RAPID-code_collection-date.R</em>：用于优化标本采集日期的代码 <em>RAPID-code_compile-deduplicate.R</em>：用于合并与去重原始数据的代码 <em>RAPID-code_standardize-country.R</em>：用于标准化国家/地区数据的代码 <em>RAPID-code_external-linkages-bold.R</em>：用于增强外部关联信息的代码（针对BOLD数据库） <em>RAPID-code_external-linkages-genbank.R</em>：用于增强外部关联信息的代码（针对GenBank数据库） <em>RAPID-code_external-linkages-standardize.R</em>：用于增强外部关联信息的标准化代码 <em>RAPID-code_people.R</em>：用于优化人员相关数据的代码 <em>RAPID-code_standardize-country.R</em>：用于标准化国家/地区数据的代码（注：原文存在重复） <em>rapid-data-providers_2021-05-03.csv</em>：数据提供方列表及各提供方提交至<b>rapid-joined-records_country-cleanup_2020-09-23.csv</b>的记录数量 <em>rapid-final-data-product_2021-05-07.csv</em>：增强版数据集，为来自BIOSPEX的最终版本 <em>rapid-joined-records_country-cleanup_2020-09-23.csv</em>：初始版数据产品，其中原始数据已完成合并与去重，且国家/地区数据已完成标准化 <em>RAPID-protocol_collection-date.pdf</em>：与优化标本采集日期相关的操作规程 <em>RAPID-protocol_compile-deduplicate.pdf</em>：与合并及去重原始数据相关的操作规程 <em>RAPID-protocol_external-linkages.pdf</em>：与增强外部关联信息相关的操作规程 <em>RAPID-protocol_georeference.pdf</em>：与地理配准相关的操作规程 <em>RAPID-protocol_people.pdf</em>：与优化人员相关数据相关的操作规程 <em>RAPID-protocol_standardize-country.pdf</em>：与标准化国家/地区数据相关的操作规程 <em>RAPID-protocol_taxonomic-names.pdf</em>：与优化分类学名称数据相关的操作规程 <em>RAPIDAgentStrings1_archivedCopy_30March2021.ods</em>：配合RAPID人员数据操作规程使用的资源文件 <em>Rhinolophid-HipposideridAgentStrings_and_People2_archivedCopy_30March2021.ods</em>：配合RAPID人员数据操作规程使用的资源文件 <em>recordedByNames.txt</em>：包含需在达尔文核心归档（DwC-A）中引用的术语定义文件 <em>wikidata-notes-for-bat-collectors_leachman_2020.docx</em>：配合RAPID人员数据操作规程使用的资源文件 <em>wikidata-notes-for-bat-collectors_leachman_2020.pdf</em>：配合RAPID人员数据操作规程使用的资源文件