The PHA4GE Data Repositories Working Group works with the global community and major sequence repositories to improve community-driven standards for sequence submission, query, retrieval, and metadata management. Our aim is to make public health sequence data easier to share, discover, and use while supporting equitable data sharing and FAIR (Findable, Accessible, Interoperable, Reusable) principles.
A current focus of the Working Group is Pathoplexus, a community-driven platform designed to support rapid and equitable sequence data sharing for public health.
This Working Group brings together public health users, repository developers, and data stewards to improve repository workflows and tools.
Key focus areas include:
Sequence submission, query, and retrieval workflows
Repository-based tools, databases, and APIs (Application Programming Interfaces)
Management and standards for sequence-associated metadata
Community-driven repository development, including Pathoplexus
SRA management for community projects (e.g. umbrella BioProjects, organizational standards)
Link-outs to sensitive epidemiologic, clinical, and commercial data resources
Data sharing and governance, including equitable use and reuse
Engagement with major public repositories (NCBI, ENA, DDBJ / INSDC)
Cloud-based repository interfaces and integrations
Key deliverables include:
Consensus recommendations for public health–relevant submission and metadata practices
Community feedback on repository features, APIs, and user interfaces
Guidance to improve documentation, usability, and discoverability of repository tools
Support for training, workshops, and hackathons focused on repository use
Recommendations that help repositories better support pathogens of public health interest
If you submit data to public repositories, build tools that depend on them, or rely on repository data for surveillance and research, your experience can help shape systems used worldwide.
By joining, you can:
Influence how repositories support public health needs
Help improve usability and accessibility of sequence data
Contribute to more equitable and FAIR data sharing practices
Collaborate directly with repository developers and global stakeholders
Inception: August 2024
# of Members: 20+
Swiss TPH
Independent Consultant
Contact: [email protected]
Pathoplexus is an open-source viral genomics database designed to support transparent data sharing, flexible attribution, and advanced analysis of pathogens of public health importance. Built as a community-driven platform with open governance and interoperable data access, Pathoplexus aims to strengthen global research and public health responses to infectious diseases.
Remigio Arteaga | Laboratorio Para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador | Ecuador
Sunday Ayuba Buru | Genomic Research Lab, College of Health Sciences, Kaduna State University Kaduna | Nigeria
Swapan Bhuiyan | NYC Public Health Laboratory | United States
Anderson Brito | Instituto Todos pela Saúde (ITpS) | Brazil
Chaoran Chen | ETH Zurich | Switzerland
Nyasha Chin’Ombe | University of Zimbabwe | Zimbabwe
Alan Christoffels | SANBI-UWC | South Africa
Matheus de Andrade Silva | Instituto Todos pela Saúde | Brazil
Karthikeyan Govindan | Wellcome Trust Research Laboratory, Christian Medical College and Hospital | India
Eneida Hatcher | NIH/NLM/NCBI | United States
Emma Hodcroft | Institute for Social and Preventive Medicine at the University of Bern | Switzerland
Kathryn Holt | LSHTM | United Kingdom
Arthur Shem Kasambula | Makerere University | Uganda
No’emie Lefrancq | ETH Zürich | Switzerland
Duncan MacCannell | CDC | United States
Francis Mubigalo | National Institute of Biomedical Research | Congo, The Democratic Republic of the
Kingsley Achilike Njoku | Georgetown Global Health Nigeria | Nigeria
Purity Oreng’ | Kenya Institute Of Primate Research | Kenya
Theo Sanderson | Francis Crick Institute | United Kingdom
Kin-Ming (Clement) Tsui | University of British Columbia | Canada
Tesfahun Wubetu | Addis Ababa university | Ethiopia
Tesfahun Wubetu | Addis Ababa university | Ethiopia
This piece highlights Pathoplexus, a community-driven viral genomics database developed with input from PHA4GE to advance open data sharing, ethical use, and transparent governance in public health genomics.
