What is the Pathogens Portal?

The Pathogens Portal is part of the broader Pathogens Platform, which also includes the Pathogen Data Hubs. The Platform facilitates data sharing and supports research and discovery in response to infectious diseases.

The Pathogens Portal was developed to support access and retrieval of biological data related to microorganisms that can cause infections in humans, animals and/or plants. Data in the Pathogens Portal can therefore be used in the context of research, outbreaks, surveillance, or other public health purposes (Fig. 1). 

Building on the success of the COVID-19 Data Portal, it aims to expand and utilise the same infrastructure, tools, and knowledge, bringing together and continuously updating relevant pathogen-related datasets and tools to accelerate infectious disease research. The Pathogens Portal integrates access to different data types (including nucleotide sequences, cohort data, etc.), thus facilitating their retrieval and use. Note that currently the Pathogens Portal excludes SARS-CoV-2 data, which can be found in the COVID-19 Data Portal instead.

The Pathogens Portal currently acts as an interface to infectious disease biological data held in ELIXIR core data resources at EMBL-EBI, such as the European Nucleotide Archive (ENA) and Europe PMC. You can visit the “Database resources” page for the full list of resources feeding into the Pathogens Portal. The Portal also includes a network of Pathogens Portal Nodes that provides information, guidelines, tools, and services to highlight pathogen research data from participating countries or regions.

Figure 1 The Pathogens Portal fetches human, animals and/or plants pathogens data from a variety of online databases and resources. Through the integration of different data types, the Pathogens Portal facilitates data access and retrieval, and acts as a support for research, public health purposes (including policymaking), surveillance, and outbreak response.

What is a pathogen?

Defining what is or is not a “pathogen” is challenging. Therefore, the Portal relies on external sources to classify organisms as pathogens. These sources include pathogen lists produced by the World Health Organisation (WHO), Health and Safety Executive (HSE) in the UK, the National Institute of Allergy and Infectious Diseases (NIAID), and others. For more information, you can visit the “Pathogens classifications” page. The Pathogens Portal will continue to include a variety of well-established sources in its definition of a pathogen, ensuring the portal is kept up-to-date. In addition, it is open to feedback and inclusion of further sources to help the definition evolve as new relevant information arises.

In the next section, we will explore what you can do on the Pathogens Portal website.