PHA4GE: Improving the structure of pathogen genomics data for effective public health action
Creators: name: Griffiths, Emma
name: Timme, Ruth
name: Mendes, Catarina Inês
name: Aanensen, David
name: Alcock, Brian
name: Black, Allison
name: Campos, Josefina
name: Chindelevitch, Leonid
name: Christoffels, Alan
name: Coelho, Luis Pedro
name: Bede Constantinides
name: Cummins, Carla
name: Dallman, Timothy
name: Mugdha  Dave
name: Amadou  Diallo
name: Diaz, Paula
name: Feldgarden, Michael
name: Fornika, Dan
name: Hodcroft, Emma
name: Karsch-Mizrachi, Ilene
name: Lees, John
name: MacCannell, Duncan
name: Morey, Karim
name: Page, Andrew
name: Nasar, Muhammad I
name: Idowu  Olawoye
name: Oluniyi, Paul
name: Amogelang  Raphenya
name: Tausch, Simon
name: Vasconcelos, Ana Tereza
name: Thapa, Suchitra
name: Waheed, Zahra
name: Witney, Adam
name: Maguire, Finlay
Publisher: name: Gates Open Research
Year: 2022

description: Genomic sequencing and bioinformatic analysis are powerful tools for understanding the prevalence, diversity, and distribution of microbial pathogens (e.g. bacteria, viruses, parasites, fungi), as well as how they are transmitted to humans (from animals, environments or other humans), how they evolve, and how they cause outbreaks. An example of the utility of genomic sequencing for public health can be seen during the COVID-19 pandemic when genomic sequencing and surveillance were used to provide data for the development of diagnostics and vaccines, to track variants of concern, to identify and resolve outbreaks at local and global levels, and to understand the origins of the virus. Owing to its demonstrated utility for public health surveillance and decision-making, the WHO have recommended that pathogen genomic surveillance be a key part of their strategic pandemic preparedness plan.<br> <br> Pathogen genomic sequencing and bioinformatics analysis can be difficult for public health laboratories due to complex computing requirements, the range of tools and pipelines that each have their strengths and weaknesses, the lack of trained personnel and the difficulties of translating scientific findings into information which can be used by decision makers. The Public Health Alliance for Genomic Epidemiology (PHA4GE) is a BMGF-funded, international community of scientists and researchers from public health, industry and academia focused on addressing these challenges, as well as improving the reproducibility, interoperability, portability and openness of public health bioinformatics. <br> <br> Within PHA4GE, the Data Structures Working Group (DSWG) focuses on developing specifications, tools, and protocols to help public health labs standardize, harmonize, and organize genomics-based information so that datasets are more interoperable between labs, organizations, databases and platforms. <br> <br> A key question we ask ourselves in the DSWG is: How can we use data structures (i.e. data fields, terms and formats, and the way these are organized and linked to each other) to improve the way we transform pathogen genomics data into public health action? Where “data” includes the sequence data itself and also the accompanying epidemiological, clinical, laboratory and methods information, collectively known as contextual data. <br> In answering this question, the DSWG has identified challenges in three key areas for which we are now pursuing solutions. The projects include community consultation, technical development, implementation initiatives around the world, and information sharing/dissemination efforts, which will all be further described in the poster. These projects include:<br> <br> 1. The “hAMRonization” project: Aimed at streamlining antimicrobial resistance genomic surveillance data interoperability and reporting through the development of a specification and set of parsers for harmonizing gene/mutation outputs from widely used AMR detection tools. <br> <br> 2. The “SARS-CoV-2 contextual data specification package” project: Aimed at harmonizing genomic surveillance and outbreak data, and includes the development of a data specification that can map information between repositories, sequencing initiatives and organizations (e.g. WHO, INSDC, GISAID, AusTrakka, VirusSeq Data Portal, etc). Importantly, this framework for standardizing and harmonizing information about samples, hosts, exposures, outcomes, treatments/vaccination, sequencing methods, bioinformatics methods, lab testing etc can be reused for other pathogens and can be mapped to other organization-specific specifications. This standardization and mapping has led to the development of new data curation and transformation tools which help strengthen the data ecosystem. The package is part of the PHA4GE library of SARS-CoV-2 training and analysis resources to support turning data into public health decision-making.<br> <br> 3. The “INSDC Pathogen DOM” project: Aimed at providing guidance and recommendations for public health labs on how to organize and use data stored in INSDC repositories, as well as articulating the challenges and gaps faced by users in submitting and downloading data. The data model (known as the INSDC Pathogen DOM) works in parallel with other PHA4GE specifications under development for standardizing information about amplicon primer schemes important for viral pathogens like SARS-CoV-2 and Monkeypox, and standardized quality control tags for identifying quality issues in datasets. The package is also aimed at better supporting funders and organizations in setting priorities for data sharing.<br> <br> The PHA4GE DSWG is a group of scientists in the public health bioinformatics space, working to solve the challenges we face every day in using genomics data to reduce the burden of infectious disease. New members are always welcome. Participation can be in a consultation and/or technical capacity. For further information, please visit pha4ge.org.