2019 novel coronavirus repository

MIDAS 2019 Novel Coronavirus Repository

Disclaimer
Most sections in this repository are under active development and may be incomplete. Information posted in this repository was created by those listed as creators in the metadata and not by the MIDAS Coordination Center. Creators should be acknowledged when using the information for scientific or other work (see Information for Users).

Introduction

This repository serves as a central platform to share resources relevant for modeling of the COVID-19 outbreak. The MIDAS Coordination Center (MCC) has created and will maintain it in collaboration with the broader modeling community. Community members are encouraged to contribute resources to the repository and thus support the overall COVID-19 research effort. See Information for Contributors for guidance on how to contribute material. Contact questions@midasnetwork.us for any questions or ideas for improvements, or to send/request any material to be included.

MIDAS 2019 Novel Coronavirus Mailing List

The MIDAS Coordination Center maintains a dedicated mailing list for updates and news about COVID-19 modeling research. To join the mailing list, please email questions@midasnetwork.us.

Community contributions

We highly encourage community member to contribute to COVID-19 repository and we would like to acknowledged those that send us data, papers, links or pointed us to resources. Please find below a short presentation of each of them and a summary of their contributions to the repository:

Data

Data Curation Tracker

All data sources relevant for COVID-19 modeling can be uploaded/found here, including case count data and line listings. Data can be in many different formats and levels of curation. The sources by country are listed in a curation tracking table indicating the data available or in the process of being published in the repository. We encourage everybody who wants to contribute to the repository to send resources not yet listed in this table or not yet extracted so we can add it to our workflow to avoid duplication. See Information for Contributors for more information.

Data Catalog

All data published in the repository are uploaded/found here. Data are uploaded by the MCC and by community members. Sets of related data files are presented as “collections”. For example, a collection can be a set of related outbreak situation updates from a country, a set of time-stamped backup files, or another set of related files. Each collection has its own metadata, data guide, and location dictionary that maps geographic locations listed in the collection to international standards.

Parameter Estimates

Parameter estimates are stored in one CSV file with estimates for epidemiological parameters relevant for nCoV modeling. Estimates are extracted from a variety of sources including preliminary model reports, pre-prints, and peer-reviewed publications. For each parameter, metadata are also extracted. Parameter estimates are extracted by a team of curators from the MIDAS Coordination Center and community members. A subset of the CSV file is displayed in a README file. New parameter estimates can be added by appending to the CSV file (see Information for Contributors).

Parameter Estimates for 2019 Novel Coronavirus

Parameter Estimates for SARS

Forthcoming

Parameter Estimates for MERS

Forthcoming

Parameter Estimates for Seasonal influenza

Forthcoming

Software Tools

Software tools for data-processing, modeling, and visualizations will be included in this section together with relevant metadata. One CSV catalog file includes all tools, each on a separate row, and all tools are listed here. New tools can be added by appending to the CSV file or by submitting an issue.

Documents

All documents relevant to COVID-19 are posted in this section. Documents are mostly organized by country or by topic. Pre-prints and peer-reviewd manuscripts are posted with links to external webpages only while all other documents are also stored in this repository as collections in the documents folder. Add new documents by submitting an issue with the document information.

Documents include:

• Reports, inlcuding outbreak situation reports/updates, modeling reports and other “gray literature”
• Pre-prints and peer-reviewed publications, organized by topic
• Guidelines by WHO, China, and US CDC related to COVID-19

Information for Contributors

Anybody can contribute to this repository through pull requests. Community members are encouraged to contribute new data and findings, and help make this repository increasingly complete and useful. This section includes detailed instructions for pull requests and templates for metadata, data guides, and other files formats and content standards. Email questions@midasnetwork.us in case of questions or ideas.

Information for Users

Many people have contributed to the creation of this repository and of its content. Please cite the creators of data or other content listed in the respective metadata if you use any of their contributions. Also cite this repository as the source for those contributions as per the following suggested citation: “Creators of object, name of object, Retrieved from: MIDAS 2019 Novel Coronavirus GitHub Repository, URL. Accessed date”

Contact Information

For any questions or comments related to this repository, submit an issue or contact the MIDAS Coordination Center.

MIDAS Coordination Center
University of Pittsburgh
A737 Public Health
130 DeSoto Street
Pittsburgh PA 15261
United States
Tel: +1 412-624-7693
Email: questions@midasnetwork.us