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

Class HpoOrganSystems

java.lang.Object
org.phenopackets.phenopackettools.validator.core.phenotype.HpoOrganSystems
public class HpoOrganSystems extends Object
A class with constants that correspond to the upper-level HPO organ-system phenotypic abnormalities.

The constants can be used together with the HpoPhenotypeValidators.OrganSystem validators, which enforce that a phenopacket contains at least one term from a set of organ systems (observed or excluded).

Note that users can also use any HPO term in this way -- the validator will enforce that the phenopacket has an HPO term that descends from it, but the most common use cases are these organ-level terms. 

 Ontology hpo = ...; // get the ontology
 var requiredOrganSystems = Set.of(BLOOD, CARDIOVASCULAR, SKELETAL);
 var validator = HpoPhenotypeValidators.OrganSystem.phenopacketHpoOrganSystemValidator(hpo, requiredOrganSystems);

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final org.monarchinitiative.phenol.ontology.data.TermId
    ABNORMAL_CELLULAR
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    BLOOD
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    BREAST
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    CARDIOVASCULAR
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    CONNECTIVE_TISSUE
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    CONSTITUTIONAL
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    DIGESTIVE
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    EAR
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    ENDOCRINE
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    EYE
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    GENITOURINARY
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    GROWTH
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    HEAD_AND_NECK
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    IMMUNOLOGY
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    INTEGUMENT
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    LIMBS
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    METABOLISM
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    MUSCLE
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    NEOPLASM
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    NERVOUS_SYSTEM
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    PRENATAL
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    RESPIRATORY
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    SKELETAL
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    THORACIC_CAVITY
     
    static final org.monarchinitiative.phenol.ontology.data.TermId
    VOICE
     

  • Method Summary

    Methods inherited from class java.lang.Object

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

  • Field Details

    • ABNORMAL_CELLULAR

      public static final org.monarchinitiative.phenol.ontology.data.TermId ABNORMAL_CELLULAR

    • BLOOD

      public static final org.monarchinitiative.phenol.ontology.data.TermId BLOOD

    • CONNECTIVE_TISSUE

      public static final org.monarchinitiative.phenol.ontology.data.TermId CONNECTIVE_TISSUE

    • HEAD_AND_NECK

      public static final org.monarchinitiative.phenol.ontology.data.TermId HEAD_AND_NECK

    • LIMBS

      public static final org.monarchinitiative.phenol.ontology.data.TermId LIMBS

    • METABOLISM

      public static final org.monarchinitiative.phenol.ontology.data.TermId METABOLISM

    • PRENATAL

      public static final org.monarchinitiative.phenol.ontology.data.TermId PRENATAL

    • BREAST

      public static final org.monarchinitiative.phenol.ontology.data.TermId BREAST

    • CARDIOVASCULAR

      public static final org.monarchinitiative.phenol.ontology.data.TermId CARDIOVASCULAR

    • DIGESTIVE

      public static final org.monarchinitiative.phenol.ontology.data.TermId DIGESTIVE

    • EAR

      public static final org.monarchinitiative.phenol.ontology.data.TermId EAR

    • ENDOCRINE

      public static final org.monarchinitiative.phenol.ontology.data.TermId ENDOCRINE

    • EYE

      public static final org.monarchinitiative.phenol.ontology.data.TermId EYE

    • GENITOURINARY

      public static final org.monarchinitiative.phenol.ontology.data.TermId GENITOURINARY

    • IMMUNOLOGY

      public static final org.monarchinitiative.phenol.ontology.data.TermId IMMUNOLOGY

    • INTEGUMENT

      public static final org.monarchinitiative.phenol.ontology.data.TermId INTEGUMENT

    • MUSCLE

      public static final org.monarchinitiative.phenol.ontology.data.TermId MUSCLE

    • NERVOUS_SYSTEM

      public static final org.monarchinitiative.phenol.ontology.data.TermId NERVOUS_SYSTEM

    • RESPIRATORY

      public static final org.monarchinitiative.phenol.ontology.data.TermId RESPIRATORY

    • SKELETAL

      public static final org.monarchinitiative.phenol.ontology.data.TermId SKELETAL

    • THORACIC_CAVITY

      public static final org.monarchinitiative.phenol.ontology.data.TermId THORACIC_CAVITY

    • VOICE

      public static final org.monarchinitiative.phenol.ontology.data.TermId VOICE

    • CONSTITUTIONAL

      public static final org.monarchinitiative.phenol.ontology.data.TermId CONSTITUTIONAL

    • GROWTH

      public static final org.monarchinitiative.phenol.ontology.data.TermId GROWTH

    • NEOPLASM

      public static final org.monarchinitiative.phenol.ontology.data.TermId NEOPLASM