@prefix amrf:    <https://w3id.org/amrf/> .
@prefix bibo:    <http://purl.org/ontology/bibo/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix edam:    <http://edamontology.org/> .
@prefix mod:     <https://w3id.org/mod#> .
@prefix obo:     <http://purl.obolibrary.org/obo/> .
@prefix owl:     <http://www.w3.org/2002/07/owl#> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema:  <https://schema.org/> .
@prefix skos:    <http://www.w3.org/2004/02/skos/core#> .
@prefix vann:    <http://purl.org/vocab/vann/> .
@prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .

# AMRF reuses EDAM, Bioschemas/schema.org, ARO, NCBITaxon, IAO and NCIT, and only defines a
# term when none of them fits. Each term explains in skos:editorialNote why it is needed.

<https://w3id.org/amrf/>
    a owl:Ontology ;
    dcterms:title "AMRF: AntiMicrobial Resistance Framework vocabulary"@en ;
    dcterms:description "Terms to describe antimicrobial resistance prediction models and the processing steps that prepare their inputs, so that a framework can discover which models can be applied to a sample. Complements EDAM, Bioschemas, ARO and NCBITaxon."@en ;
    dcterms:license <https://creativecommons.org/licenses/by/4.0/> ;
    dcterms:creator <https://orcid.org/0009-0005-7434-9883> ;
    dcterms:publisher <https://deal.us.es> ;
    dcterms:created "2026-10-15"^^xsd:date ;
    dcterms:issued "2026-10-20"^^xsd:date ;
    bibo:doi "10.5281/zenodo.24083396" ;
    dcterms:bibliographicCitation "Quirós Quiroga, M. (2026). AMRF: AntiMicrobial Resistance Framework vocabulary and SHACL shapes (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.24083396" ;
    dcterms:source <https://github.com/DEAL-US/Cocos> ;
    mod:status "Released"@en ;
    schema:logo <https://raw.githubusercontent.com/DEAL-US/Cocos/main/app/static/images/logo.svg> ;
    schema:includedInDataCatalog <https://bioportal.bioontology.org/ontologies/AMRF> ;
    owl:versionInfo "0.1.0" ;
    owl:versionIRI <https://w3id.org/amrf/0.1.0> ;
    vann:preferredNamespacePrefix "amrf" ;
    vann:preferredNamespaceUri "https://w3id.org/amrf/" .

amrf:predictsResistanceTo
    a owl:ObjectProperty ;
    rdfs:label "predicts resistance to"@en ;
    rdfs:comment "Relates a predictive model to an antibiotic for which it predicts whether a sample is resistant."@en ;
    rdfs:subPropertyOf obo:IAO_0000136 ;
    rdfs:range obo:ARO_1000003 ;
    rdfs:isDefinedBy <https://w3id.org/amrf/> ;
    skos:editorialNote "IAO 'is about' (obo:IAO_0000136) and schema:about only state that a model concerns an antibiotic, not that it predicts resistance to it rather than, for instance, susceptibility or minimum inhibitory concentration. ARO 'confers_resistance_to_antibiotic' (obo:ARO_2000000) relates genes and variants, not models. It is declared a subproperty of 'is about' so that consumers unaware of AMRF still read the model as being about the antibiotic. Proposed to ARO in https://github.com/arpcard/aro/issues/28; if accepted, this term will be deprecated in favour of the ARO one."@en .

amrf:BaktaJSON
    a owl:Class ;
    rdfs:label "Bakta JSON"@en ;
    rdfs:comment "JSON format of the genome annotations written by Bakta, with the annotated features of a genome and their database cross-references."@en ;
    rdfs:subClassOf edam:format_3464 ;
    rdfs:seeAlso <https://github.com/oschwengers/bakta> , <https://bio.tools/bakta> ;
    rdfs:isDefinedBy <https://w3id.org/amrf/> ;
    skos:editorialNote "EDAM has no format for Bakta's JSON output; bio.tools lists it only as generic JSON (edam:format_3464). A specific format is needed so that a parser of Bakta JSON is not offered any JSON feature table. It is a subclass of EDAM JSON so that consumers that accept any JSON accept it. Proposed to EDAM in https://github.com/edamontology/edamontology/issues/960; if accepted, this term will be deprecated in favour of the EDAM one."@en .