Module org.phenopackets.phenopackettools.validator.core

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

Class HpoPhenotypeValidators.OrganSystem

java.lang.Object

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

Enclosing class:

HpoPhenotypeValidators

public static class HpoPhenotypeValidators.OrganSystem
extends Object

A static factory class for providing validators for checking annotation of organ systems.

The validators check if each phenopacket or family/cohort member have annotation for an organ system represented by a top-level HPO term (e.g. Abnormality of limbs). The annotation comprises either one or more observed descendants (e.g. Arachnodactyly), or excluded top-level HPO term (NOT Abnormality of limbs).

Method Summary

Modifier and Type	Method	Description
static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder>	cohortHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo, Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)	Get PhenopacketValidator to validate annotation of organ systems in a Cohort using provided Ontology and a collection of organ system TermIds.
static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder>	familyHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo, Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)	Get PhenopacketValidator to validate annotation of organ systems in a Family using provided Ontology and a collection of organ system TermIds.
static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder>	phenopacketHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo, Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)	Get PhenopacketValidator to validate annotation of organ systems in a Phenopacket using provided Ontology and a collection of organ system TermIds.

Methods inherited from class java.lang.Object

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

Method Details

phenopacketHpoOrganSystemValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.PhenopacketOrBuilder> phenopacketHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo,
 Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)

Get PhenopacketValidator to validate annotation of organ systems in a Phenopacket using provided Ontology and a collection of organ system TermIds.

NOTE: the organ system TermId that is absent from the Ontology is disregarded and not used for validation.

Parameters:

hpo - HPO ontology

organSystemTermIds - a collection of HPO TermIds corresponding to organ systems.

familyHpoOrganSystemValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.FamilyOrBuilder> familyHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo,
 Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)

Get PhenopacketValidator to validate annotation of organ systems in a Family using provided Ontology and a collection of organ system TermIds.

NOTE: the organ system TermId that is absent from the Ontology is disregarded and not used for validation.

Parameters:

hpo - HPO ontology

organSystemTermIds - a collection of HPO TermIds corresponding to organ systems.

cohortHpoOrganSystemValidator

public static PhenopacketValidator<org.phenopackets.schema.v2.CohortOrBuilder> cohortHpoOrganSystemValidator(org.monarchinitiative.phenol.ontology.data.Ontology hpo,
 Collection<org.monarchinitiative.phenol.ontology.data.TermId> organSystemTermIds)

Get PhenopacketValidator to validate annotation of organ systems in a Cohort using provided Ontology and a collection of organ system TermIds.

NOTE: the organ system TermId that is absent from the Ontology is disregarded and not used for validation.

Parameters:

hpo - HPO ontology

organSystemTermIds - a collection of HPO TermIds corresponding to organ systems.