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ayates/amr_portal

AMR Portal — Multi-Dataset Release (Phenotype + Genotype) This repository contains multiple datasets from the EMBL-EBI AMR Portal, distributed in Apache Parquet format: phenotype.parquet – phenotypic antimicrobial susceptibility data genotype.parquet – AMR genes and mutations from in silico methods All datasets are released under CC-BY-4.0. Source documentation: https://www.ebi.ac.uk/amr/developers/ Dataset Summary This dataset contains phenotypic antimicrobial… See the full description on the dataset page: https://huggingface.co/datasets/ayates/amr_portal.

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AMR Portal — Multi-Dataset Release (Phenotype + Genotype)

This repository contains multiple datasets from the EMBL-EBI AMR Portal, distributed in Apache Parquet format:

  • —phenotype.parquet – phenotypic antimicrobial susceptibility data
  • —genotype.parquet – AMR genes and mutations from in silico methods

All datasets are released under CC-BY-4.0.

Source documentation: <https://www.ebi.ac.uk/amr/developers/>

Dataset Summary

This dataset contains phenotypic antimicrobial resistance (AMR) data derived from antibiograms submitted to BioSamples from the CABBAGE data set. It provides curated experimental measurements such as MIC values, AMR gene annotation, and metadata describing geography, organism taxonomy, and antibiotics. The dataset is stored in Apache Parquet. This release corresponds to:

FTP location: https://ftp.ebi.ac.uk/pub/databases/amr_portal/releases/2025-11/

Portal documentation: <https://www.ebi.ac.uk/amr/developers/>

Dataset Contents

This dataset represents AMR phenotypic experimental outcomes collected from antibiograms.

Each row corresponds to an individual antibiotic test performed on an isolate.

Typical use cases include:

  • —AMR prediction
  • —Taxonomic/epidemiological AMR analysis
  • —Linking phenotypes to genomic or genotypic data

Data Schema

phenotype.parquet: AMR phenotypes

FieldTypeNullableDescription
BioSample_IDstringNoThe unique identifier for the biological sample (e.g. SAMEA1028830)
SRA_accessionstringYesThe SRA accession number
assembly_IDstringYesThe unique accession number of the genome assembly (e.g. GCA_001096525.1)
collection_yearint32YesThe year the sample was collected
ISOcountrycodestringYesThe 3-letter ISO country code where the sample was collected (e.g. THA for Thailand)
hoststringYesThe organism the sample was isolated from (e.g. Homo sapiens)
host_agestringYesThe age of the host (empty/NULL in the sample data, but should be a string to allow for various formats or NULLs)
host_sexstringYesThe sex of the host (empty/NULL in the sample data)
isolatestringYesA unique identifier for the specific isolate (e.g. SMRU2695)
isolation_sourcestringYesThe specific anatomical source or environment the isolate came from (e.g. nasopharynx)
isolationsourcecategorystringYesThe general category of the isolation source (e.g. respiratory tract)
isolation_latitudestringYesGeographic latitude for the sample
isolation_longitudestringYesGeographic longitude for the sample
genusstringNoThe genus of the organism (e.g. Streptococcus)
organismstringNoThe full name of the organism (e.g. Streptococcus pneumoniae)
AMRassociatedpublicationsstringYesThe PubMed ID of the publication associated with the data. Can be a set of values joined with a ;
UpdatedphenotypeCLSIstringYesThe updated antimicrobial susceptibility testing (AST) phenotype based on CLSI standards (empty/NULL in the sample data)
UpdatedphenotypeEUCASTstringYesThe updated AST phenotype based on EUCAST standards (empty/NULL in the sample data)
used_ECOFFstringYesIndicates if the Epidemiological Cut-Off (ECOFF) was used (empty/NULL in the sample data)
databasestringYesDatabase of annotation
antibiotic_namestringYesThe name of the antibiotic tested (e.g. beta-lactams, trimethoprim-sulfamethoxazole)
ast_standardstringYesThe standard or guideline used for Antimicrobial Susceptibility Testing (e.g. CLSI, EUCAST)
laboratorytypingmethodstringYesThe method used to test the antibiotic sensitivity (e.g. disk diffusion, E-test)
measurementstringYesThe raw measurement value, typically MIC or zone size (e.g. 2, 1, 0.5, 12/0.125).
measurement_signstringYesThe sign indicating the nature of the measurement (e.g. '==' for exact value, or '>', '<')
measurement_unitsstringYesThe units for the measurement (e.g. mg/l)
platformstringYesThe platform used for analysis (empty/NULL in the sample data)
resistance_phenotypestringYesThe final result of the interpretation (e.g. susceptible, non-susceptible, resistant)
speciesstringNoThe species of the organism (e.g. Streptococcus pneumoniae)
antibiotic_ontologystringYesAn ontology ID for the antibiotic (e.g. ARO_3004024)
antibioticontologylinkstringYesLink to the ontology resource for the ID
countrystringYesFull country name where the sample was collected from. Converted from ISO_country_code.
geographical_regionstringYesGeographical region as defined by UN M49. e.g Asia, Europe, Oceania, Africa or Americas.
geographical_subregionstringYesGeographical subregion as defined by UN M49. e.g.Eastern Asia, Northern Europe.

genotype.parquet: AMR genotypes

FieldTypeNullableDescription
BioSample_IDstringNoThe unique identifier for the biological sample (e.g., SAMEA1028830)
assembly_IDstringNoThe unique accession number of genome assembly (e.g., GCA_001096525.1)
genusstringNoThe genus of the organism (e.g., Streptococcus)
speciesstringNoThe species name of the organism
organismstringNoThe full name of the organism (e.g., Streptococcus pneumoniae)
isolatestringYesIsolate information
taxon_idint64NoNCBI Taxonomy identifier of the organism
regionstringNoName of a genomic region
region_startint64NoStart of the annotated gene
region_endint64NoEnd of the annotated gene
strandstringNoStrand of the annotated gene. '+' indicates the forward strand, '-' indicates the reverse strand
_binint64NoUCSC bin number for the genomic region. See UCSC's wiki for further details. Internal field
idstringNoIdentifier of the gene
gene_symbolstringNoSymbol of the gene
amrelementsymbolstringNoAMRFinderPlus assigned symbol for the AMR element
element_typestringNoBroad type of AMR element. Normally set to AMR
element_subtypestringNoSubtype of AMR element. Normally set to AMR
classstringNoOverall class of AMR compound as given by AMRFinderPlus. Normally a broad representation of antibiotics
subclassstringNoSubclass of AMR compound as given by AMRFinderPlus. Can also be set to the same as class
split_subclassstringNoSubclass can represent multiple individual compounds separated by a '/'. This field contains the individual element of subclass.
antibiotic_namestringYesNormalised name of the antibiotic tested (e.g., beta-lactams, trimethoprim-sulfamethoxazole)
antibiotic_ontologystringYesOntology ID for the antibiotic (e.g., ARO_3004024)
antibioticontologylinkstringYesLink to ontology entry for the antibiotic
evidence_accessionstringYesAccession number for evidence supporting the predicted AMR resistance
evidence_typestringYesType of evidence supporting the predicted AMR resistance
evidence_linkstringYesLink to the evidence supporting the predicted AMR resistance
evidence_descriptionstringYesEvidence description supporting the predicted AMR resistance

How to Load the Dataset

Load phenotype data

python
from datasets import load_dataset

phenotype = load_dataset(
    "ayates/amr_portal",
    data_files="phenotype.parquet",
    split="train"
)

Load genotype data

python
genotype = load_dataset(
    "ayates/amr_portal",
    data_files="genotype.parquet",
    split="train"
)

Load everything at once

python
ds = load_dataset(
    "ayates/amr_portal",
    data_files={
        "phenotype": "phenotype.parquet",
        "genotype": "genotype.parquet"
    }
)

You can then access:

python
ds["phenotype"]
ds["genotype"]

License

Creative Commons Attribution 4.0 (CC-BY-4.0) <https://creativecommons.org/licenses/by/4.0/>

Citation

Please cite Dickens E et al. 2025 10.1101/2025.11.12.688105.

txt
@article {Dickens2025.11.12.688105,
  author = {Dickens, Emily and Derelle, Romain and Beardmore, Robert and Suresh, Anita and Uplekar, Swapna and Yates, Andrew D and Keatley, Jon and Winterbottom, Andrea and Azov, Andrey G and El Houdaigui, Bilal and Ochkalova, Sofiia and Gurbich, Tatiana A and Shivalikanjli, Anu and Yordanova, Galabina and Lees, John A and Chindelevitch, Leonid},
  title = {A comprehensive AMR genotype-phenotype database (CABBAGE)},
  elocation-id = {2025.11.12.688105},
  year = {2025},
  doi = {10.1101/2025.11.12.688105},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2025/11/13/2025.11.12.688105},
  eprint = {https://www.biorxiv.org/content/early/2025/11/13/2025.11.12.688105.full.pdf},
  journal = {bioRxiv}
}