- Course overview
- Search within this course
- What is the Pathogens Portal?
- What can I do with the Pathogens Portal?
- Download data from the Pathogens Portal
- Submit data to the Pathogens Portal
- Your feedback
- Get help and support on the Pathogens Portal
- Further material
- Funding and acknowledgements
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Search data in the Pathogens Portal
The Pathogens Portal can be accessed through a web browser to search a variety of pathogen-related data.
Searching for data in the Pathogens Portal is similar to the COVID-19 Data Portal, and includes the following key features:
- Main search bar: this allows for both free text search across fields (e.g. ‘Ebola virus’ or NCBI taxonomy ID searches – i.e ‘746128’ for Aspergillus fumigatus), and structured queries, where syntax can be generated using the ‘Advanced Search’ feature (see point 3).
- Facets on the left-hand side of each data type page: for example, on the Pathogen Sequences page, you can select from options such as classification, scientific name, and host name (name of the organism that is the host for the pathogen biological sample).
- ‘Advanced search’: here you can construct your query for your data type of interest and search, e.g. (country: “United Kingdom”) AND (collection_date:[“01/05/2022” TO “01/05/2025”]) for data from the United Kingdom, collected between 1st May 2022 and 1st May 2025.
Click on the ‘i’ symbols in Fig. 2 to further explore what data is accessible through the Pathogens Portal:
Figure 2 Navigating the Pathogens Portal.
The Pathogens Portal also presents infectious disease cohort studies that have been shared to data resources at EMBL-EBI, through the integrated Cohort Browser. This additionally presents cross-links to any data types generated from each cohort study.
Move on to the next page to find more information on the Cohort Browser.