New portal a key tool for better global pathogen surveillance
An online platform has been launched that gives researchers, clinicians and policymakers access to an extensive collection of biomolecular data about pathogens. Called Pathogens Portal, it can serve as an important aid in infection biology and pathogen surveillance. The portal is supported by the EU-funded RECODID, VEO and BY-COVID projects, and it builds on infrastructure developed and funded by EU projects ELIXIR-CONVERGE, EOSC-Life, COMPARE and CORBEL. It is also supported with core funding from BY-COVID project coordinator and RECORDID and VEO project partner European Molecular Biology Laboratory (EMBL), Germany. The Pathogens Portal contains data on more than 200 000 pathogen species and strains. Its list of pathogens ranges from those we all know, such as HIV, influenza, Hepatitis B and the malaria parasite Plasmodium falciparum, to lesser-known pathogens that affect humans, such as Lassa mammarenavirus that causes Lassa haemorrhagic fever. However, as reported in a news item posted on the portal, it does not only include pathogens affecting humans but also hundreds that affect other animals, making it a useful tool for food security and biodiversity. Included in the portal are nucleotide sequences, raw genomic data, sample metadata and relevant scientific literature. The aim is to also add data types such as protein sequence and structure and chemistry data from other public data resources. “The unique feature of the Pathogens Portal is that it brings together different data types, which are currently scattered in lots of different places,” observes Dr Guy Cochrane, who is Team Leader at EMBL’s European Bioinformatics Institute (EBI). “This new approach enables researchers, clinical scientists, and public health agencies to access all publicly-available data about their pathogen of interest with just one quick search. The portal also contains intuitive tools for discovery, which make it easy for users to refine their searches.”
Preparing for the next pandemic
The data is available to anyone with an internet connection, which can be of great value during a public health emergency when speed is vital in the sharing of information. “The COVID-19 pandemic demonstrated that having robust and easy-to-use data sharing structures in place can save lives because these enable a quick and informed public health response,” explains Marianna Ventouratou, who is Data Platform Manager at EMBL-EBI. “Building on the lessons learned from [the] COVID-19 pandemic, EMBL-EBI and partners have now developed the Pathogens Portal, which researchers and public health authorities around the world can use to enhance global pathogen surveillance efforts.” Data Hubs, a key component of the portal, enables researchers and health agencies to keep their data private at first. This is important for researchers who have not yet published their work but still need to analyse it together with other data accessible through the portal. The portal also includes a cohort browser containing highly sought-after clinical-epidemiological data from patient cohorts. “The Cohort Browser interoperates genomic data with clinical epidemiological data, which enables deep interrogation of disease data by linking infomation [sic] on the pathogen and the host it directly infected,” states Lauren Maxwell of RECODID project coordinator Universitätsklinikum Heidelberg, Germany. RECODID (Integrated human data repositories for infectious disease-related international cohorts to foster personalized medicine approaches to infectious disease research) ends in December 2023. VEO (Versatile Emerging infectious disease Observatory) and BY-COVID (Beyond COVID) end the following year. For more information, please see: RECODID project website VEO project website BY-COVID project website Pathogens Portal
Keywords
RECODID, VEO, BY-COVID, portal, data, Pathogens Portal, pathogen, COVID-19
