CO-CONNECT: COVID - Curated and Open aNalysis aNd rEsearCh plaTform

Lead Research Organisation: University of Nottingham
Department Name: School of Computer Science

Abstract

CO-CONNECT is a collaborative project and it has four CO-PIs: Jefferson (Dundee), Sheikh (Edinburgh), Hopkins (PHE) and Quinlan (Nottingham).

The current COVID-19 pandemic has caused hundreds of thousands of deaths, severely strained health systems and damaged economies across the world. At this time there is limited evidence that people who have recovered from COVID-19 and have antibodies are protected from a second infection and if so, how long that lasts. Understanding who is immune is vital to protect vulnerable individuals, to safely scale back population-based interventions and for managing disease transmission.
The data which can help us to answer these key questions have been collected across the UK by a range of research groups and within clinical primary and secondary care settings. As this is a new disease, the standards for antibody data capture are in their infancy so some of the details need to answer the key questions are not being captured systematically. The fragmented landscape of data means that it can be challenging for public health groups and researchers to find and access the high-quality data they need at pace.
We will:
- Standardise antibody data collection across the UK
- Configure an infrastructure which enables trustworthy, fast, de-identified, secure analysis of data sets from across multiple sources
- Answer key questions about immunity to COVID-19 and the implications for patient outcomes.

Technical Summary

CO-CONNECT is a collaborative project and it has four CO-PIs: Jefferson (Dundee), Sheikh (Edinburgh), Hopkins (PHE) and Quinlan (Nottingham).

The UK has rich, globally important COVID-19 datasets, including large serology cohort studies funded by UKRI, Wellcome, DHSC/NHS, NIHR and the devolved administrations. However, this breadth of data creates a risk of fragmentation, inconsistent structure and access processes, severely limiting utility, timeliness and impact.

Our vision is to transform UK COVID-19 diagnostic datasets to be Findable, Accessible, Interoperable and Reusable (FAIR) and couple this with expert data engineering, enabled by Health Data Research (HDR) UK, to catalyse responsible and trustworthy use of the data for research and innovation.

We propose to support PIs and data custodians to link COVID-19 cohort, serology and other health and non-health datasets. This longitudinal linkage is vital to derive new scientific insights and deliver informed decisions about how best to control the spread of SARS-CoV-2. At present there are >30 independent studies with no streamlined approach to linkage to other health and non-health related datasets, lack of data standardisation, and no strategic approach to synthesise analyses across studies.

SAGE (9th June) requested HDR to work with partners to develop the UK-wide serology and testing data research asset that is linkable to other data sources.

This proposal has been prepared in response to this request. We have bought together 41 leaders from 29 different organisations and 44 data sources to address a major data engineering challenge by building upon existing UKRI investments, including the HDR BREATHE Hub, to create a 'one-stop' service for trustworthy, multi-stakeholder utilisation of curated COVID-19 data for public, private and third sector benefit.

People

ORCID iD

Philip Quinlan (Principal Investigator)
Susan Hopkins (Co-Investigator) orcid http://orcid.org/0000-0001-5179-5702
Ian Hall (Co-Investigator)
Ana Valdes (Co-Investigator) orcid http://orcid.org/0000-0003-1141-4471
Amir Gander (Co-Investigator)
David Vincent Ford (Co-Investigator)
Gerry Reilly (Co-Investigator) orcid http://orcid.org/0000-0003-1427-3598
Tim Gentry (Co-Investigator) orcid http://orcid.org/0000-0001-8486-5797
Charlotte Manisty (Co-Investigator) orcid http://orcid.org/0000-0003-0245-7090
Malcolm Gracie Semple (Co-Investigator) orcid http://orcid.org/0000-0001-9700-0418
Shamez Ladhani (Co-Investigator)
Emma Lawrence (Co-Investigator) orcid http://orcid.org/0000-0001-9018-6010
Susheel Varma (Co-Investigator)
Emily Jefferson (Co-Investigator) orcid http://orcid.org/0000-0003-2992-7582
John Danesh (Co-Investigator)
Laura Shallcross (Co-Investigator) orcid http://orcid.org/0000-0003-1713-2555
Aziz Sheikh (Co-Investigator)
Declan Terence Bradley (Co-Investigator) orcid http://orcid.org/0000-0003-1468-1823
Andrew David Morris (Co-Investigator)
Jessica Mai Sims (Co-Investigator)
Katie Jeffery (Co-Investigator) orcid http://orcid.org/0000-0002-6506-2689
Paul Moss (Co-Investigator)
Victoria Chico (Co-Investigator)
Louis Grandjean (Co-Investigator)
Emanuele Di Angelantonio (Co-Investigator)
Simon Thompson (Co-Investigator)
Nicholas John Timpson (Co-Investigator) orcid http://orcid.org/0000-0002-7141-9189
James D Chalmers (Co-Investigator)
Joanne Martin (Co-Investigator)
Neil Sebire (Co-Investigator)
Jim McMenamin (Co-Investigator)
David Robert Seymour (Co-Investigator) orcid http://orcid.org/0000-0003-4194-2056
David Wells (Co-Investigator)
John Kenneth Baillie (Co-Investigator) orcid http://orcid.org/0000-0001-5258-793X
Ming Tang (Co-Investigator)
Benjamin Ollivere (Co-Investigator) orcid http://orcid.org/0000-0002-1410-1756
Paul Elliott (Co-Investigator) orcid http://orcid.org/0000-0002-7511-5684
Daniel Morales (Co-Investigator)
Tom Charles Giles (Researcher)
Roberto Santos (Researcher) orcid http://orcid.org/0000-0003-1333-2605

Publications

10 25 50
 
Description New Information Governance Framework for Federated Aggregate Level Queries on Unconsented Data
Geographic Reach National 
Policy Influence Type Contribution to new or Improved professional practice
Impact A new framework for researchers to discovery data relevant to their research across the UK.
 
Description Alleviate: Hub for Pain
Amount £2,032,575 (GBP)
Funding ID MR/W014335/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 06/2021 
End 06/2024
 
Description Guidelines and Resources for AI Model Access from TrusTEd Researchenvironments (GRAIMatter)
Amount £315,488 (GBP)
Funding ID MC_PC_21033 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 08/2022
 
Description MICA - DEfining MechanIsms Shared across mulTI-organ FIbrosis to prevent the development of long-term multi-morbidity DEMISTIFI-Multi Morbidity
Amount £2,856,188 (GBP)
Funding ID MR/W014491/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 11/2021 
End 10/2025
 
Description Trusted Research Environment and Enclave for Hosting Open Original Science Exploration (TREEHOOSE)
Amount £202,664 (GBP)
Funding ID MC_PC_21032 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 08/2022
 
Description Federated search across TREs 
Organisation Health Data Research UK
Country United Kingdom 
Sector Private 
PI Contribution We are supporting the roll out of the federated tool across the National Core Studies Data and Connectivity piece
Collaborator Contribution Project management and technical insight.
Impact None to date. Impact expected in 2021.
Start Year 2020
 
Description Health Data Research UK, National Core Studies Programme 
Organisation Health Data Research UK
Country United Kingdom 
Sector Private 
PI Contribution We are supporting the NCS programme with the roll out of the cohort discovery tooling that has been generated in CO-CONNECT.
Collaborator Contribution Supporting the work with the NCS partners.
Impact The development of the HDR UK Cohort Discovery tool: https://www.healthdatagateway.org/about/cohort-discovery
Start Year 2021
 
Description Royal Surrey NHS Foundation Trust 
Organisation Royal Surrey County Hospital NHS Foundation Trust
Country United Kingdom 
Sector Public 
PI Contribution Collaborated on building the National COVID-19 Chest Imaging Database (NCCID). This collaboration was highly successful and we then went on to collaborate on the National COVID-19 Chest Imaging Database (NCCID) Validation project
Collaborator Contribution Expertise in image data handling and infrastructures
Impact New funding for NCCID Validation project. A UK wide COVID imaging dataset for research and innovation. Talked about to the G7.
Start Year 2020
 
Title CO-CONNECT/co-connect-tools: 0.3.1 
Description No description provided. 
Type Of Technology Software 
Year Produced 2021 
Impact The primary functionality is used for performing ETL on health datasets, converting them to the OHDSI Common Data Model (CDM), via a command line interface. 
URL https://zenodo.org/record/5529834
 
Title HDR UK Cohort Discovery 
Description The system allows researchers to find cohorts of patients via an online platform. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Impact It is now embedded within the HDR Innovation Gateway. 
URL https://www.healthdatagateway.org/about/cohort-discovery
 
Title Link lite 
Description An open source version of the BC Platforms link software 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact A POC for the HDR Innovation Gateway 
 
Title OMOP Mapping tool 
Description The platform allows rules to be generated to convert data from source to OMOP. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Open Source License? Yes  
Impact It has helped mapped several datasets in the UK and is now being utilised across EU projects in BBMRI-ERIC 
URL https://github.com/CO-CONNECT/mapping-pipeline
 
Description CO-CONNECT: Linking COVID-19 immunity data 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact .
Year(s) Of Engagement Activity 2021
URL https://www.hdruk.ac.uk/news/co-connect-linking-covid-19-immunity-data/
 
Description CO-CONNECT Explainer Video 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This video aims to support the Data Governance Teams, to describe the intentions of CO-CONNECT and to support the approvals process.
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=68E3-GEwl-U
 
Description CO-CONNECT Website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our CO-CONNECT Website is a central communication tool to let our audiences aware of our project and activities. It has sparked interested from organisations not on the original grant to come forward and enquiry about onboarding their data into CO-CONNECT to make it discoverable to other groups of public health officials and the research community.
Year(s) Of Engagement Activity 2020
URL https://co-connect.ac.uk/
 
Description Data Partner Tracker Dashboard 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tracking the onboarding process of our Data Partners onto CO-CONNECT in this clear and transparent manor has increased engagement and communication across our partners, public engagement group, advisory steering group and funders.
Year(s) Of Engagement Activity 2021
URL https://ccdashboard-drs.azurewebsites.net/
 
Description Data Standardisation (OMOP) 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact CO-CONNECT Data Pipeline Part 2 Data Standardisation OMOP
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=zP1UF_3U5Ic
 
Description Discovery Day Lecture: Data saves lives: the fight against COVID-19 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A lecture for the general public about our research.
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=CKuuY1LNv-0
 
Description Input into HDR UK Data Standards Paper 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Input into HDR UK Data Standards Paper
Year(s) Of Engagement Activity 2020
 
Description Input into HDR UK Trusted Research Environments Green Paper 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Input into HDR UK Trusted Research Environments Green Paper.
Year(s) Of Engagement Activity 2020
URL https://ukhealthdata.org/wp-content/uploads/2020/07/200723-Alliance-Board_Paper-E_TRE-Green-Paper.pd...
 
Description Introduction to CO-CONNECT & HDR Innovation Gateway 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The video describes the Data Pipeline. This video is Part One and gives an introduction to CO-CONNECT and the HDR Innovation Gateway.
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=3pCAfO3Sy-o&t=23s
 
Description Invited Member of MRC Population Health Sciences Group (PHSG) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Oversee population health sciences investment across MRC Boards and panels. Advise MRC Strategy Board, boards and panels on development and implementation of strategies and policies. Advise on strategic funding initiatives and partnership activities. Carry out gap analyses and horizon scanning.
Year(s) Of Engagement Activity 2020
 
Description Invited Speaker HDR UK Data Federation Initiatives, 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact UK Health Data Research Alliance Symposium
Year(s) Of Engagement Activity 2020
 
Description Invited Speaker: EAVE II Steering Group 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited Speaker: CO-CONNECT - COVID-Curated and Open aNalysis aNd rEsearCh platform
Year(s) Of Engagement Activity 2021
 
Description Invited Speaker: Exciting developments of HIC's Next Generation Safe Haven and new COVID research initiatives 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Public Health Scotland Research Talks
Year(s) Of Engagement Activity 2020
 
Description Invited speaker: Data and Intelligence Network 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited Speaker - CO-CONNECT - COVID-Curated and Open aNalysis aNd rEsearCh platform
Year(s) Of Engagement Activity 2021
 
Description Mapping Rules 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact CO-CONNECT Data Pipeline Part 4 - Mapping Rules Generation using CO-CONNECT Mapping Tool
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=rSkVqll_ah4
 
Description Pre-Processing and Metadata 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact CO-CONNECT Data Pipeline Part 3 Meta data and Pre Processing
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=9kVrP_jhC_o&t=393s