- Course overview
- Search within this course
- What is antimicrobial resistance?
- How do we study pathogens?
- A guide to the Pathogens Portal
- Analysing genomic data from pathogens
- Identification and investigation of antimicrobial resistance genes
- Looking for antimicrobial resistance genes in different environments
- Data sharing
- The future of AMR
- Crossword: Test your knowledge
- Your feedback
- Further resources
- Help and support
- Glossary
- References
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.
Public pathogen data
The scientific community has generated enormous amounts of pathogen data, much of which is freely available through public online databases and data resources. These open access resources are important as they facilitate data sharing, allowing researchers to explore, analyse, and test hypotheses on diverse data from across the world.
What EMBL-EBI resources and databases are available for sharing and investigating pathogen data?
- Pathogens portal – A centralised platform for sharing and accessing data on key pathogens, vectors, and hosts.
- Ensembl – A genome browser that provides a single point of access to annotated genomes. It has separate sites for different organisms, including microorganisms such as bacteria, fungi, protists, and COVID-19.
- Uniprot – A comprehensive resource for protein sequence and annotation data.
- MGnify – An automated pipeline for the analysis and archiving of microbiome data.
These resources are all available online through their web platforms however many can also be accessed programmatically using an API (application programming interface). To learn more about accessing these resources programmatically check out our online tutorial ‘EMBL-EBI, programmatically‘.
We will discover more about these resources and data types throughout the tutorial.