Nathanael Sheehan, Sabina Leonelli and Federico Botta
Two distinct modes of data governance have emerged in accessing and reusing viral data pertaining to COVID-19: an unrestricted model, espoused by data repositories part of the International Nucleotide Sequence Database Collaboration and a regulated model promoted by the Global Initiative on Sharing All Influenza data. In this paper, we focus on publications mentioning either infrastructure in the period between January 2020 and January 2023, thus capturing a period of acute response to the COVID-19 pandemic. Through a variety of bibliometric and network science methods, we compare the extent to which either data infrastructure facilitated collaboration from different countries around the globe to understand how data reuse can enhance forms of diversity between institutions, countries, and funding groups. Our findings reveal disparities in representation and usage between the two data infrastructures. We conclude that both approaches offer useful lessons, with the unrestricted model providing insights into complex data linkage and the regulated model demonstrating the importance of global representation.
This repository contains the code and data used to produce the results presented in the paper "Title of Paper" by [Author 1](link to author 1's website) and [Author 2](link to author 2's website), published in [Journal/Conference/Workshop](link to publication) in [Year of Publication].
To run the code in this repository, you will need:
A computer:
R: R is a free software environment for statistical computing and graphics. You can download the latest version of R from the R Project website.
RStudio: RStudio is an integrated development environment (IDE) for R that provides a user-friendly interface for coding and running R scripts. You can download the latest version of RStudio from the RStudio website. All additional packages are installed in the packages.r file.
git clone https://github.com/natesheehan/C2A.git
cd C2a
| Data | URL | Description |
|---|---|---|
| GISAID | https://www.gisaid.org/ | A global science initiative providing open access to genomic data of influenza viruses and SARS-CoV-2 |
| COVID-19 Data Portal | https://covid19dataportal.org/ | A global database of COVID-19 cases, deaths, hospitalizations, and other related genomic data |
| Dimensions API | https://docs.dimensions.ai/dsl/api.html | A database with various datasets, including COVID-19 research publications, patents, and grants |
| Our World in Data COVID-19 Cases | https://ourworldindata.org/covid-cases | A dataset with daily COVID-19 cases for countries and regions |
| Our World in Data Income Groups | https://ourworldindata.org/global-economic-inequality | A dataset with income group classifications for various countries and regions based on World Bank classifications |
All code can be found in the code/ folder.
The analysis of this work is full reproducible. However, before reproducing the results the reviewer must do two things after installing the repository:
(1) first you must unzip the /data-raw/submissions folder
(2) change reproducible = FALSE to TRUE in build.r
(3) sign up to GISAID and download the Clade/Lineage Variants (tsv) file from EPICov.
(4) sit and watch, a full run should take around 10 minutes
If you use the code or data from this repository in your research, please cite our paper:
@article{sheehan2023,
title={From collection to analysis: A comparison of GISAID and the Covid-19 Data Portal},
author={[Nathanael Sheehan,Sabina Leonelli,Federico Botta},
journal={Journal},
year={2023}
}
MIT License
Copyright (c) 2023 Nathanael Sheehan
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
This project has received funding from the European Research Council (ERC) under the European Union’s Horison 2020 research and innovation programme (grant agreement No. 101001145). This paper reflects only the author's view and that the Commission / Agency is not responsible for any use that may be made of the information it contains.