{
  "schema_version": "2.1.0",
  "note": "Registry of susceptibility/conversion factors, mirroring the Measure registry. Namespaced ids by domain (host:/gene:/prior:/acute:/lab:/pathogen:/tx:/immune:/psych:/care:/env:). harmonised_construct is the cross-pathogen key (acute_severity | viral_burden | inflammatory_burden), null where no harmonisation is defined in v2.1. native_scales lists the concrete instruments this abstract factor stands in for. The native factor_verbatim on each Predictor is never overwritten; harmonisation is an additive, versioned opinion (see pais-severity-harmony-v1.md).",
  "factors": [
    { "id": "acute:illness-severity-composite", "domain": "acute_clinical", "label": "Acute illness severity (composite index)", "harmonised_construct": "acute_severity", "native_scales": ["Dubbo somatic symptom severity score", "WHO dengue severity grade", "WHO ordinal scale for COVID-19", "self-reported acute symptom burden"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "acute:hospitalisation", "domain": "acute_clinical", "label": "Hospitalisation for acute illness", "harmonised_construct": "acute_severity", "native_scales": ["hospital admission (binary)"], "ontology": { "snomed": "32485007", "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "acute:icu-admission", "domain": "acute_clinical", "label": "ICU admission", "harmonised_construct": "acute_severity", "native_scales": ["ICU admission (binary)"], "ontology": { "snomed": "305351004", "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "acute:fever-duration", "domain": "acute_clinical", "label": "Fever duration (days)", "harmonised_construct": null, "native_scales": ["days of fever"], "ontology": { "snomed": null, "loinc": null }, "unit": "days", "unit_ucum": "d" },
    { "id": "acute:peak-temperature", "domain": "acute_clinical", "label": "Peak temperature", "harmonised_construct": null, "native_scales": ["max recorded temperature"], "ontology": { "snomed": null, "loinc": "8310-5" }, "unit": "degC", "unit_ucum": "Cel" },
    { "id": "acute:symptom-count-presentation", "domain": "acute_clinical", "label": "Symptom count at presentation", "harmonised_construct": "acute_severity", "native_scales": ["number of acute symptoms in first week"], "ontology": { "snomed": null, "loinc": null }, "unit": "count", "unit_ucum": "1" },
    { "id": "acute:oxygen-requirement", "domain": "acute_clinical", "label": "Supplemental oxygen requirement", "harmonised_construct": "acute_severity", "native_scales": ["oxygen requirement (binary)"], "ontology": { "snomed": "371825009", "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "acute:neurological-involvement", "domain": "acute_clinical", "label": "Acute neurological involvement", "harmonised_construct": null, "native_scales": ["encephalitis/meningitis at presentation"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "acute:warning-signs", "domain": "acute_clinical", "label": "WHO warning signs (dengue)", "harmonised_construct": "acute_severity", "native_scales": ["WHO 2009 dengue warning signs"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "acute:time-onset-to-presentation", "domain": "acute_clinical", "label": "Time from onset to presentation", "harmonised_construct": null, "native_scales": ["days from symptom onset to care"], "ontology": { "snomed": null, "loinc": null }, "unit": "days", "unit_ucum": "d" },

    { "id": "lab:platelet-nadir", "domain": "acute_laboratory", "label": "Platelet nadir", "harmonised_construct": "acute_severity", "native_scales": ["lowest platelet count"], "ontology": { "snomed": null, "loinc": "777-3" }, "unit": "10^9/L", "unit_ucum": "10*9/L" },
    { "id": "lab:haematocrit-peak", "domain": "acute_laboratory", "label": "Haematocrit peak / haemoconcentration", "harmonised_construct": "acute_severity", "native_scales": ["peak haematocrit"], "ontology": { "snomed": null, "loinc": "4544-3" }, "unit": "%", "unit_ucum": "%" },
    { "id": "lab:lymphocyte-count", "domain": "acute_laboratory", "label": "Lymphocyte count", "harmonised_construct": null, "native_scales": ["absolute lymphocyte count"], "ontology": { "snomed": null, "loinc": "731-0" }, "unit": "10^9/L", "unit_ucum": "10*9/L" },
    { "id": "lab:nlr", "domain": "acute_laboratory", "label": "Neutrophil-lymphocyte ratio", "harmonised_construct": "inflammatory_burden", "native_scales": ["NLR"], "ontology": { "snomed": null, "loinc": null }, "unit": "ratio", "unit_ucum": "1" },
    { "id": "lab:crp", "domain": "acute_laboratory", "label": "C-reactive protein", "harmonised_construct": "inflammatory_burden", "native_scales": ["CRP"], "ontology": { "snomed": null, "loinc": "1988-5" }, "unit": "mg/L", "unit_ucum": "mg/L" },
    { "id": "lab:ferritin", "domain": "acute_laboratory", "label": "Ferritin", "harmonised_construct": "inflammatory_burden", "native_scales": ["serum ferritin"], "ontology": { "snomed": null, "loinc": "2276-4" }, "unit": "ng/mL", "unit_ucum": "ng/mL" },
    { "id": "lab:ldh", "domain": "acute_laboratory", "label": "Lactate dehydrogenase", "harmonised_construct": null, "native_scales": ["LDH"], "ontology": { "snomed": null, "loinc": "2532-0" }, "unit": "U/L", "unit_ucum": "U/L" },
    { "id": "lab:alt-ast", "domain": "acute_laboratory", "label": "Transaminases (ALT/AST)", "harmonised_construct": null, "native_scales": ["ALT", "AST"], "ontology": { "snomed": null, "loinc": "1742-6" }, "unit": "U/L", "unit_ucum": "U/L" },
    { "id": "lab:d-dimer", "domain": "acute_laboratory", "label": "D-dimer", "harmonised_construct": null, "native_scales": ["D-dimer"], "ontology": { "snomed": null, "loinc": "48065-7" }, "unit": "mg/L FEU", "unit_ucum": "mg/L" },
    { "id": "lab:albumin", "domain": "acute_laboratory", "label": "Serum albumin", "harmonised_construct": null, "native_scales": ["albumin"], "ontology": { "snomed": null, "loinc": "1751-7" }, "unit": "g/L", "unit_ucum": "g/L" },

    { "id": "pathogen:viral-load", "domain": "acute_pathogen", "label": "Viral load / Ct value", "harmonised_construct": "viral_burden", "native_scales": ["RT-PCR Ct value", "copies/mL"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "pathogen:ns1-antigenaemia", "domain": "acute_pathogen", "label": "NS1 antigenaemia (dengue)", "harmonised_construct": "viral_burden", "native_scales": ["NS1 antigen level"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "pathogen:serotype-dengue", "domain": "acute_pathogen", "label": "Dengue serotype", "harmonised_construct": null, "native_scales": ["DENV-1..4"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "pathogen:primary-vs-secondary", "domain": "acute_pathogen", "label": "Primary vs secondary infection (serostatus)", "harmonised_construct": null, "native_scales": ["IgG serostatus at acute phase"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "pathogen:variant-strain", "domain": "acute_pathogen", "label": "Variant / strain", "harmonised_construct": null, "native_scales": ["viral variant"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "pathogen:viraemia-duration", "domain": "acute_pathogen", "label": "Duration of viraemia / shedding", "harmonised_construct": "viral_burden", "native_scales": ["days of detectable virus"], "ontology": { "snomed": null, "loinc": null }, "unit": "days", "unit_ucum": "d" },
    { "id": "pathogen:antigen-persistence", "domain": "acute_pathogen", "label": "Antigen persistence at convalescence", "harmonised_construct": null, "native_scales": ["circulating antigen at follow-up"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "pathogen:infecting-agent", "domain": "acute_pathogen", "label": "Infecting pathogen (which agent)", "harmonised_construct": null, "native_scales": ["EBV vs RRV vs Coxiella"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },

    { "id": "tx:corticosteroids", "domain": "acute_treatment", "label": "Corticosteroids in acute phase", "harmonised_construct": null, "native_scales": ["corticosteroid use (binary)"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "tx:antivirals", "domain": "acute_treatment", "label": "Antiviral therapy", "harmonised_construct": null, "native_scales": ["antiviral use (binary)"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "tx:antibiotics", "domain": "acute_treatment", "label": "Antibiotic therapy", "harmonised_construct": null, "native_scales": ["antibiotic use (binary)"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },

    { "id": "immune:acute-cytokines", "domain": "acute_immune", "label": "Acute cytokine levels (IL-6/IL-1β/IFN-γ/TNF-α/IL-10)", "harmonised_construct": "inflammatory_burden", "native_scales": ["serum cytokine panel"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "immune:convalescent-antibody-titre", "domain": "acute_immune", "label": "Convalescent antibody titre", "harmonised_construct": null, "native_scales": ["convalescent anti-pathogen antibody titre"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "immune:autoantibody-presence", "domain": "acute_immune", "label": "Autoantibody presence", "harmonised_construct": null, "native_scales": ["autoantibody panel"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },

    { "id": "host:age", "domain": "host_demographic", "label": "Age", "harmonised_construct": null, "native_scales": ["age in years", "age band"], "ontology": { "snomed": null, "loinc": "30525-0" }, "unit": "years", "unit_ucum": "a" },
    { "id": "host:sex-female", "domain": "host_demographic", "label": "Female sex", "harmonised_construct": null, "native_scales": ["female vs male"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "host:bmi", "domain": "host_demographic", "label": "Body mass index / obesity", "harmonised_construct": null, "native_scales": ["BMI", "obesity (binary)"], "ontology": { "snomed": null, "loinc": "39156-5" }, "unit": "kg/m2", "unit_ucum": "kg/m2" },

    { "id": "prior:comorbidity-count", "domain": "host_prior_health", "label": "Pre-existing comorbidity count", "harmonised_construct": null, "native_scales": ["number of comorbidities"], "ontology": { "snomed": null, "loinc": null }, "unit": "count", "unit_ucum": "1" },
    { "id": "prior:chronic-lung-disease", "domain": "host_prior_health", "label": "Pre-existing chronic lung disease", "harmonised_construct": null, "native_scales": ["asthma/COPD (binary)"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "prior:mecfs-fibromyalgia", "domain": "host_prior_health", "label": "Prior ME/CFS or fibromyalgia", "harmonised_construct": null, "native_scales": ["prior ME/CFS or FM diagnosis"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "prior:atopy-allergy", "domain": "host_prior_health", "label": "Atopy / allergy", "harmonised_construct": null, "native_scales": ["atopy (binary)"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "prior:premorbid-psychiatric", "domain": "host_prior_health", "label": "Premorbid psychiatric history", "harmonised_construct": null, "native_scales": ["prior depression/anxiety diagnosis", "neuroticism score"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },

    { "id": "gene:hla-type", "domain": "host_genetic", "label": "HLA type", "harmonised_construct": null, "native_scales": ["HLA alleles"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:cytokine-polymorphism", "domain": "host_genetic", "label": "Cytokine gene polymorphism", "harmonised_construct": null, "native_scales": ["IFNG, IL10, TNF SNPs"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:gwas-locus", "domain": "host_genetic", "label": "GWAS susceptibility locus (generic)", "harmonised_construct": null, "native_scales": ["any genome-wide significant locus"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:hla-dqb1-0602", "domain": "host_genetic", "label": "HLA-DQB1*06:02 carriage", "harmonised_construct": null, "native_scales": ["HLA-DQB1*06:02 positive vs negative"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:foxp4-locus", "domain": "host_genetic", "label": "FOXP4 locus (rs9367106)", "harmonised_construct": null, "native_scales": ["FOXP4 rs9367106 risk allele"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:rabgap1l", "domain": "host_genetic", "label": "RABGAP1L locus", "harmonised_construct": null, "native_scales": ["RABGAP1L GWAS signal"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:olfm4", "domain": "host_genetic", "label": "OLFM4 locus", "harmonised_construct": null, "native_scales": ["OLFM4 GWAS signal"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:fbxl4", "domain": "host_genetic", "label": "FBXL4 locus", "harmonised_construct": null, "native_scales": ["FBXL4 GWAS signal"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },
    { "id": "gene:ca10", "domain": "host_genetic", "label": "CA10 locus", "harmonised_construct": null, "native_scales": ["CA10 GWAS signal (colocalises with chronic pain)"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null },

    { "id": "psych:acute-distress", "domain": "psychosocial", "label": "Acute psychological distress", "harmonised_construct": null, "native_scales": ["acute anxiety/depression score"], "ontology": { "snomed": null, "loinc": null }, "unit": null, "unit_ucum": null }
  ]
}