Work Package 2
Harmonized Approaches to Data Collection and Analysis
Lead:
Dr. Lauren Maxwell- UKHD
Heidelberg Institute of Global Health (HIGH)
UNIVERSITÄTSKLINIKUM HEIDELBERG
Heidelberg, Germany
​​​
​
The overall aim of WP2 is to address challenges in the technical interoperability of the cohorts and to establish standards for future data sharing.
WP2 is designed to achieve the following 5 objectives:
Objective 1: Achieve consensus on modular content for syndromic approach to data dictionaries.
Researchers
Philippe Guerin
Kalynn Kennon
Caitlin Naylor
Lucie Kafkova
Jennie Lee
Affiliation
Infectious Diseases Data Observatory (IDDO)
University of Oxford (UOXF)
Task 2.1: Developing Syndromic Template CRFs for Arboviral and AFI Research brings together clinical and standardisation experts from around the world to develop syndromic, modular Case Report Forms (CRFs) tailored to acute febrile illness and major arboviral syndromes. These template CRFs will capture the key clinical features of diseases such as dengue, chikungunya, Zika, West Nile, yellow fever, and Oropouche. They can be rapidly adapted for future emerging infections.
Developed using the ISARIC WHO eCRF Community Development and Approval Process and built using CDISC standards and aligned with related ontologies, like SNOMED-CT, the CRFs are designed for interoperability and regulatory readiness. By creating a shared, modular library of community-derived variables, CONTAGIO will enable more comparable, reusable, and globally coordinated clinical data for epidemic-prone diseases.
Objective 2: Create a web-based tool for rapid generation of e-CRFs - ‘CRF Builder’.
Researchers
Gustavo Adolfo Gómez
Aidan Marler
Affiliations
Universidad Industrial de Santander (UIS)
University of Colorado, Anschutz Medical Campus (UCD)
Task 2.2 focuses on enhancing the existing ISARIC BRIDGE electronic Case Report Form (eCRF) tool by implementing two key software solutions: multi-language adaptability and a new variable manager. This involves developing automated translation workflows for Spanish, Portuguese, and French—including a validation system with native-language reviewers—and updating the BRIDGE interface to generate multilingual CRF exports with improved PDF layouts. In parallel, the task will deliver an administrative Variable Manager module, helping users adapt to specific studies and in the same time establish a clear path to integrate variables into the ARCH structure while preventing duplication and linking to standardized terminologies.
Objective 3: Generate machine-readable metadata.
Researchers
Lauren Maxwell
Ankur Krishnan
Affiliations
Heidelberg Institute of Global Health (HIGH) &
Tropical Medicine, Dept. of Infectious Diseases, Heidelberg University Hospital, Germany (UKHD)
Task 2.3 focuses on developing machine-readable, FAIR-aligned metadata that improve the discovery and reuse of data generated through arboviral diagnostic studies. Because metadata describe how clinical and laboratory data are produced, they are essential for comparing diagnostic performance, interpreting results across settings, and integrating findings into broader AFI research.
​
Working with clinical and laboratory experts, CONTAGIO is identifying the priority metadata elements needed to describe arboviral diagnostic workflows—spanning sample collection, assay characteristics, pathogen detection, and clinical context. To ensure interoperability, we are comparing metadata needs across major metadata catalogues (e.g., CoMeCT, GloPID-R, ECRIN, EMBL-EBI) and harmonising fields where possible.
We will adopt existing ontologies whenever available and develop new terms using robust ontology-engineering practices to ensure that all metadata are structured, standardised, and machine-readable. Draft metadata will be shared at external meetings for community review to ensure they meet the needs of the global arboviral research community. This work lays the groundwork for more consistent, comparable, and reusable arboviral diagnostic data worldwide.
Objective 4: Outline a standard data harmonization and sharing pipeline
Researchers
Gabriele Rinck
Nadim Rahman
Affiliations
EMBL European Bioinformatics Institute (EMBL-EBI)
Cambridge, UK
Task 2.4: Harmonisation with ReCoDID Cohort Data Flows focuses on making existing and planned data harmonisation and sharing workflows more visible and reusable, with a particular emphasis on the ReCoDID harmonisation pipeline, EMBL’s Cohort Browser, and key archives such as ENA and EGA. We will adapt these workflows as needed and identify legal or technical barriers that inform future work in WP3.
By coordinating with other major data infrastructure providers (e.g., IDDO), the task will map opportunities for cross-repository interoperability and explore long-term options for storing and disseminating project outputs. The outcome will be practical guidance to support interoperable data sharing across infectious disease research.
Objective 5: Design a novel Bayesian approach for addressing measurement error in arbovirus diagnostics.
Researchers
Neal Alexander
Affiliations
London School of Hygiene and Tropical Medicine, UK (LSHTM)
Task 2.5: Advancing Diagnostic Accuracy for Arboviruses Across Cohorts. To strengthen cross-cohort analyses of arboviral infections, CONTAGIO is developing a novel Bayesian framework that corrects for the measurement errors and cross-reactivity common in diagnostic tests. Instead of relying on study-specific classifications that cannot be compared across cohorts, this approach will generate a unified, probabilistic measure of infection—regardless of which tests were used or when they were introduced. By integrating test-performance estimates from the literature and expert elicitation, this method will deliver interoperable, transparent, and cohort-agnostic infection probabilities, enabling more reliable comparisons and insights during rapidly evolving outbreaks.