Outcomes
Progress
BY-COVID runs from October 2021 to October 2024. The ultimate outcome of the project is that SARS-CoV-2 and other infectious disease data will be easier to access, share and analyse. This will enable the world to respond more quickly to infectious disease outbreaks. During the project there will also be specific outputs such as publications and deliverables. Deliverables will include reports and best practice guidelines. These outputs will appear here as the project progresses.
Publications
Host genomes for the unique SARS-CoV-2 variant leaked into Antarctic soil metagenomic sequencing data
Recently Csabai et al.1 have found a most likely contaminated metagenomic sample set from Antarctica that contained traces of unique SARS-CoV-2 variants. This is a short followup of that report where we attempt to find genetic footprint of the hosts.
Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development
Using a fragment-based screening strategy by NMR, we identified 311 small molecule binders of 25 SARS-CoV-2 proteins, thus expanding the previously unexplored chemical and target space. Further, using experimental and bioinformatic analysis we identify potential binding sites. This comprehensive data would greatly assist medicinal chemistry efforts even beyond COVID-19.
Identification of mutations in SARS-CoV-2 PCR primer regions
The aim of this paper is to propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets and provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples.
Lightweight Distributed Provenance Model for Complex Real–world Environments
Provenance is information describing the lineage of an object, such as a dataset or biological material. In this paper, we define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments.
BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment - Common Data Model Specification
This publication corresponds to the Common Data Model (CDM) specification of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “COVID-19 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection.”
COVID-19: An exploration of consecutive systemic barriers to pathogen-related data sharing during a pandemic
In this paper we report results of a study, where we interviewed data professionals working with COVID-19-relevant data types including social media, mobility, viral genome, testing, infection, hospital admission, and deaths.
Selection analysis identifies clusters of unusual mutational changes in Omicron lineage [BA].1 that likely impact Spike function
This paper shows that, based on both the rarity of the 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred.
10 Simple Rules for making a software tool workflow-ready
Workflows have become a core part of computational scientific analysis in recent years. This paper presents 10 simple rules for how a software tool can be prepared for workflow use.
Packaging research artefacts with RO-Crate
The aim of this paper is to introduce RO-Crate (an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner) and assess it as a strategy for making multiple types of research artefacts FAIR.
Unique SARS-CoV-2 variant found in public sequence data of Antarctic soil samples collected in 2018-2019
This paper is about an investigation to know whether the huge public sequencing data archives’ samples collected earlier than the earliest known cases of the pandemic might contain traces of SARS-CoV-2.
The response of the scholarly communication system to the COVID-19 pandemic
This paper analyses how the scholarly communication system – involving the production, evaluation, and dissemination of research outputs – has responded to this crisis, focusing on the period until mid-2021.
FAIR, ethical, and coordinated data sharing for COVID-19 response
Data sharing is central to the rapid translation of research into advances in clinical medicine and public health practice. This paper is a review of COVID-19 data sharing platforms and registries.
Ready-to-use public infrastructure for global [SARS]-[CoV]-2 monitoring
This paper presents the COVID-19 effort by the Galaxy Project, which pools free worldwide public computational infrastructure, making the analysis of deep sequencing data accessible to anyone while also providing an analytical framework for global pathogen genomic surveillance based on raw sequencing-read data.
Deliverables and Milestones
| Code | Due | Description | Responsibility |
|---|---|---|---|
| D8.1 | 11/21 | Project Handbook initial release and periodic updates | WP8 |
| D3.1 | 03/22 | Metadata standards | WP3 |
| D7.1 | 03/22 | Dissemination, exploitation and communication Plan | WP7 |
| D8.2.1 | 02/22 | Project Data Management Plan initial release and periodic updates | WP8 |
| D2.1 | 06/22 | Initial data and metadata harmonisation at domain level to enable fast responses to COVID-19 | WP2 |
| D1.1 | 09/22 | Extended workflows | WP1 |
| D3.2 | 09/22 | Implementation of cloud-based, high performance, scalable indexing system | WP3 |
| D8.2.2 | 12/22 | Project Data Management Plan initial release and periodic updates | WP8 |
| D8.1.2 | 03/23 | Project Handbook initial release and periodic updates | WP8 |
| D2.2 | 06/23 | Data Access and Transfer across research domains and jurisdictions | WP2 |
| D1.2 | 09/23 | Preparedness Data Hub | WP1 |
| D3.3.1 | 09/23 | COVID-19 Data Portal | WP3 |
| D7.3 | 09/23 | Report on public engagement activities | WP7 |
| D5.3 | 11/23 | Hot Spot detection, samples data collection and mechanistic analyses | WP5 |
| D1.3 | 03/24 | Tracking and open analytics tools | WP1 |
| D2.3 | 03/24 | Enabling data discovery at source using beacon-like mechanisms | WP2 |
| D4.3 | 03/24 | Provenance model | WP4 |
| D7.2 | 03/24 | Public report showcasing industry value from infectious disease data | WP7 |
| D4.2 | 04/24 | Common analysis environment | WP4 |
| D5.1 | 05/24 | Enriched report viral variants and health outcomes | WP5 |
| D4.1 | 06/24 | Infectious diseases toolkit | WP4 |
| D3.3.2 | 07/24 | COVID-19 Data Portal | WP3 |
| D6.1 | 07/24 | Stakeholder engagement report | WP6 |
| D6.2 | 07/24 | The training efforts report | WP6 |
| D8.2.3 | 07/24 | Project Data Management Plan initial release and periodic updates | WP8 |
| D8.3 | 07/24 | Report on sustainability plans | WP8 |
| D2.4 | 09/24 | Report on data sources discovery and integration for enabling data use and re-use in response to future outbreaks | WP2 |
| D5.2 | 09/24 | Secondary use of vaccine trial data and biosamples | WP5 |
| D8.1.3 | 09/24 | Project Handbook initial release and periodic updates | WP8 |
| Code | Due | Description | Responsibility |
|---|---|---|---|
| M7.1 | 10/21 | Branding and communications guidelines | WP7 |
| M7.2 | 11/21 | Launch of project website | WP7 |
| M8.1 | 11/21 | Project mobilised. All governing boards and WPs established | WP8 |
| M8.2 | 02/22 | DMP approved by the relevant project boards before submission | WP8 |
| M1.1 | 03/22 | First support services in operation | WP1 |
| M2.1 | 03/22 | Identified data sources have been registered in the BY-COVID reference catalogue | WP2 |
| M5.1 | 02/22 | Compiled research questions and requirements Workshop 1 | WP5 |
| M6.1 | 03/22 | Stakeholder engagement (initial scoping and draft monitoring approach) | WP6 |
| M5.4 | 09/22 | FAIR open-source pipeline | WP5 |
| M6.2 | 09/22 | Identified training needs and roadmap | WP6 |
| M7.3 | 09/22 | Industry sector mapping report | WP7 |
| M4.1 | 09/22 | Common analysis environment | WP4 |
| M4.2 | 09/22 | Prototype Infectious diseases toolkit | WP4 |
| M2.2 | 01/23 | Identified the preferred mechanisms for data access and use of Real-world data | WP2 |
| M1.2 | 03/23 | First globally comprehensive data set | WP1 |
| M3.1 | 03/23 | Initial set of resources metadata mapped, indexed, and discoverable in COVID-19 Data Portal | WP3 |
| M5.2 | 03/23 | Compiled research questions and requirements Workshop 2 | WP5 |
| M5.5 | 03/23 | Viral variant and health outcomes | WP5 |
| M5.3 | 03/24 | Compiled research questions and requirements Workshop 3 | WP5 |
| M2.3 | 07/24 | Report on upgrade of clinical trial data and metadata | WP2 |