Evidence (Java)

The evidence code is used to document the support for an assertion. Here, we will show an example for the assertion that flexion contractures are found in stiff skin syndrome.

import org.phenopackets.schema.v1.core.Evidence;
import org.phenopackets.schema.v1.core.ExternalReference;
import org.phenopackets.schema.v1.core.OntologyClass;

OntologyClass publishedClinicalStudy = OntologyClass.
            newBuilder().
            setId("ECO:0006017").
            setLabel("author statement from published clinical study used in manual assertion").
            build();
    ExternalReference reference = ExternalReference.newBuilder().
            setId("PMID:20375004").
            setDescription("Mutations in fibrillin-1 cause congenital scleroderma: stiff skin syndrome").
            build();
    Evidence evidence = Evidence.newBuilder().
            setEvidenceCode(publishedClinicalStudy).
            setReference(reference).
            build();

This code produces the following Evidence element.

{
    evidence_code {
        id: "ECO:0006017"
        label: "author statement from published clinical study used in manual assertion"
    }
    reference {
        id: "PMID:20375004"
        description: "Mutations in fibrillin-1 cause congenital scleroderma: stiff skin syndrome"
    }
}