How to use the Antimicrobial resistance (AMR) portal

The antimicrobial resistance (AMR) portal contains three main data resources:

• AMR phenotypes - AMR was determined experimentally and taken from CABBAGE antibiograms catalogue.
• AMR genotypes - AMR was predicted computationally using Genotype data.
• Combined phenotypes and genotypes - AMR for which both phenotypic and genotypic data is available.

How to access portal data via FTP

Genome annotation (available in GFF format) and AMFinderPlus results are available from our genomes FTP site. Our denormalised AMR data representations are available in parquet, CSV and DuckDB formats all of which are available from our releases FTP site. Information on how to navigate and use these resources are available via our download and developer documentation pages.

How to explore the AMR data in the portal

You can start exploring from the portal home page. The home page provides:

• A global search box that searches across all sections of the website.
• Links to each of the three data resources: AMR phenotypes, AMR genotypes, and Combined phenotypes and genotypes.

Selecting a data-resource link opens the data explorer with a faceted search panel on the left and a results table on the right.

Choosing a data resource

Within the explorer, switch between data resources using the Result type cards at the top of the left panel:

• AMR phenotypes
• AMR genotypes
• Combined phenotypes and genotypes

Only one result type is active at a time. The available facet filters and table columns change when you switch type.

Global search

Global search lets you find records by sample accession, assembly accession, gene symbol, species name, antibiotic name, and other indexed text.

You can start a search from:

• The home page search box, which opens the combined data resource with your query applied.
• The Global search field at the top of the facet sidebar while browsing any data resource.

When active, your search query appears as a tag under Active filters, and result-type cards show match counts for your query.

Global search can be combined with facet filters. Both narrow the results table together.

Faceted search (filters)

Filters are organised as collapsible facets in the left panel under the Filters heading. Each facet corresponds to an attribute such as antibiotic, species, or collection year.

Each data resource has its own set of facets:

AMR phenotypes

• Antibiotic
• Species
• Genus
• Resistance phenotype
• Isolation source category
• Testing method
• Collection year
• Geographical subregion
• Country

AMR genotypes

• Antibiotic
• Species
• Genus
• Annotation tool mode

Combined phenotypes and genotypes

• Antibiotic
• Species
• Genus
• Resistance phenotype
• Isolation source category
• Testing method
• Collection year
• Geographical subregion
• Country
• Annotation tool mode

Using facets

To filter the data:

1. Expand a facet by clicking its heading (for example, Antibiotic or Species).
2. Optionally use the facet's own search box to find specific terms in long lists.
3. Tick one or more checkboxes. Selected items appear under Active filters at the top of the panel.
4. Add further facets to narrow results. Match counts update as filters are applied.
5. Click Load all at the bottom of a facet to display the complete list of options when only a subset is shown initially.

To remove a single filter, click the ✕ on its tag under Active filters. To remove all filters and the active global search at once, click Clear all.

When you switch result type, the facet list and table columns change to match the new resource. Your global search is kept; facet selections are reset.

The results table

The results table shows the records that match your current result type, global search, and facet selections.

The columns shown depend on the active data resource. For example, the AMR phenotypes table includes fields such as antibiotic name, resistance phenotype, BioSample ID, assembly ID, genus, species, and collection metadata. AMR genotypes and the combined resource include additional annotation fields (for example gene symbol, region coordinates, and AMR element details).

Pagination and sorting

Above the table you can:

• Change rows per page (100, 200, 500, or 1000).
• Move between pages with the previous/next controls, or type a page number directly.
• Sort by clicking a column heading where a sort arrow is shown.

Many columns contain links (for example to BioSample or assembly records) that open in a new browser tab.

Column selector

As of now, every column is shown by default. To choose which columns appear:

1. Click the column selector icon in the action rail on the right-hand side of the table.
2. Tick or untick columns in the Select columns to display panel.
3. Use Select all or Deselect all to show or hide every column at once.

Clearing and downloading results

The action rail on the right of the table provides three further actions:

• Clear filters — removes all facet selections, the global search, and column visibility choices (after confirmation).
• Download — downloads the current result set as a CSV file, or links to the FTP site for full data releases.

The number of rows in the results table depends on your global search, facet filters, and pagination settings. The CSV download includes all records matching the current filters, not only the current page.

Genome browser

The portal includes an integrated genome browser (based on JBrowse 2) for inspecting assembly annotation alongside your search results.

When the genome browser is enabled, a collapsible panel appears above the explorer. To use it:

1. Click the View in Browser button in the first column of a row (only available for rows that include an assembly ID).
2. The genome browser panel expands and loads the assembly, zooming to the relevant region.
3. Click a feature in the browser track to see annotation details in the panel beside the genome view.
4. Collapse the panel with the toggle control at the left edge when you want more space for the table.