Module org.phenopackets.phenopackettools.validator.core

Package org.phenopackets.phenopackettools.validator.core.phenotype

Class HpoPhenotypeValidators.Ancestry

java.lang.Object

org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.Ancestry

Enclosing class:

HpoPhenotypeValidators

public static class HpoPhenotypeValidators.Ancestry
extends Object

A static factory class for providing validators for pointing out violations of the annotation propagation rule.

The validator checks observed and excluded phenotype terms. The observed terms are checked for a presence of an observed or an excluded ancestor, and a presence of such ancestor is pointed out as an error. For instance, Abnormality of finger or "NOT" Abnormality of finger must not be present in a patient annotated by Arachnodactyly. The most specific term (Arachnodactyly) must be used.

For the excluded terms, the validator checks for presence of an excluded children. Here, the least specific term must be used. For instance, "NOT" Arachnodactyly must not be present in a patient annotated with "NOT" Abnormality of finger. Only the "NOT" Abnormality of finger must be used.

Method Summary

Modifier and Type	Method	Description
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	cohortHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate ancestry Cohort using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	familyHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate ancestry Family using provided Ontology.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	phenopacketHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)	Get PhenopacketValidator to validate ancestry Phenopacket using provided Ontology.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

phenopacketHpoAncestryValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder> phenopacketHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)

Get PhenopacketValidator to validate ancestry Phenopacket using provided Ontology.

Parameters:

hpo - HPO ontology

familyHpoAncestryValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder> familyHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)

Get PhenopacketValidator to validate ancestry Family using provided Ontology.

Parameters:

hpo - HPO ontology

cohortHpoAncestryValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder> cohortHpoAncestryValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo)

Get PhenopacketValidator to validate ancestry Cohort using provided Ontology.

Parameters:

hpo - HPO ontology