- Course overview
- Search within this course
- What is the Pathogens Portal?
- What can I do with the Pathogens Portal?
- Search data in 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.
Download data from the Pathogens Portal
The Pathogens Portal enables users to download data using two main methods.
Interactive
Individual data sections on the portal include a ‘Download’ button (Fig. 5). This enables users to:
- Either select a few accession IDs for data of interest, or all results in the data section.
- Choose a data format (often relevant to the type of data in the data section).
- Choose metadata, with the option between a list of accession IDs only, or a table of metadata.
Programmatic
The portal utilises the EBI Search API, and includes API Documentation to query data, and download datasets through links if available.
The Pathogens Portal also points users to underlying data resources that hold the datasets of interest, as these often provide different ways to download data, which may be more appropriate depending on the user’s needs.
Figure 5 Interactive downloads on the Pathogens Portal.
On the next page, we will see how to download data from the Cohort Browser instead.