Class: Disease

Message to indicate a disease (diagnosis) and its recorded onset.

erDiagram Disease { boolean excluded } OntologyClass { string id string label } TimeElement { string timestamp } TimeInterval { string end string start } GestationalAge { integer days integer weeks } AgeRange { } Age { string iso8601duration } Disease ||--}o OntologyClass : "clinicalTnmFinding" Disease ||--}o OntologyClass : "diseaseStage" Disease ||--|o OntologyClass : "laterality" Disease ||--|o TimeElement : "onset" Disease ||--|o OntologyClass : "primarySite" Disease ||--|o TimeElement : "resolution" Disease ||--|o OntologyClass : "term" TimeElement ||--|o Age : "age" TimeElement ||--|o AgeRange : "ageRange" TimeElement ||--|o GestationalAge : "gestationalAge" TimeElement ||--|o TimeInterval : "interval" TimeElement ||--|o OntologyClass : "ontologyClass" AgeRange ||--|o Age : "end" AgeRange ||--|o Age : "start"

Slots

Name	Cardinality and Range	Description	Inheritance
clinicalTnmFinding	0..* OntologyClass	Cancer findings in the TNM system that is relevant to the diagnosis of cancer	direct
diseaseStage	0..* OntologyClass	Disease staging, the extent to which a disease has developed	direct
excluded	0..1 Boolean	Flag to indicate whether the disease was observed or not	direct
laterality	0..1 OntologyClass	The term used to indicate laterality of diagnosis, if applicable	direct
onset	0..1 TimeElement	The onset of the disease	direct
primarySite	0..1 OntologyClass	The text term used to describe the primary site of disease, as categorized by...	direct
resolution	0..1 TimeElement		direct
term	0..1 OntologyClass	The identifier of this disease e	direct

Usages

used by	used in	type	used
Phenopacket	diseases	range	Disease

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type	Mapped Value
self	phenopackets:Disease
native	phenopackets:Disease

LinkML Source

Direct

name: Disease
description: Message to indicate a disease (diagnosis) and its recorded onset.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  clinicalTnmFinding:
    name: clinicalTnmFinding
    annotations:
      rank:
        tag: rank
        value: 6
    description: Cancer findings in the TNM system that is relevant to the diagnosis
      of cancer. See https://www.cancer.gov/about-cancer/diagnosis-staging/staging
      Valid values include child terms of NCIT:C48232 (Cancer TNM Finding) ARGO mapping
      primary_diagnosis::clinical_t_category ARGO mapping primary_diagnosis::clinical_n_category
      ARGO mapping primary_diagnosis::clinical_m_category
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.clinical_t_category
    rank: 1000
    multivalued: true
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  diseaseStage:
    name: diseaseStage
    annotations:
      rank:
        tag: rank
        value: 5
    description: Disease staging, the extent to which a disease has developed. For
      cancers, see https://www.cancer.gov/about-cancer/diagnosis-staging/staging Valid
      values include child terms of NCIT:C28108 (Disease Stage Qualifier) ARGO mapping
      primary_diagnosis::clinical_tumour_staging_system ARGO mapping primary_diagnosis::clinical_stage_group
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.clinical_tumour_staging_system
    rank: 1000
    multivalued: true
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  excluded:
    name: excluded
    annotations:
      rank:
        tag: rank
        value: 2
    description: Flag to indicate whether the disease was observed or not. Default
      is 'false', in other words the disease was observed. Therefore it is only required
      in cases to indicate that the disease was looked for, but found to be absent.
      More formally, this modifier indicates the logical negation of the OntologyClass
      used in the 'term' field. *CAUTION* It is imperative to check this field for
      correct interpretation of the disease!
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - PhenotypicFeature
    - Disease
    range: boolean
  laterality:
    name: laterality
    annotations:
      rank:
        tag: rank
        value: 8
    description: 'The term used to indicate laterality of diagnosis, if applicable.
      (Codelist reference: NCI CDE: 4122391)'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  onset:
    name: onset
    annotations:
      rank:
        tag: rank
        value: 3
    description: 'The onset of the disease. The values of this will come from the
      HPO onset hierarchy i.e. subclasses of HP:0003674 FHIR mapping: Condition.onset
      ARGO mapping primary_diagnosis::age_at_diagnosis'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.age_at_diagnosis
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  primarySite:
    name: primarySite
    annotations:
      rank:
        tag: rank
        value: 7
    description: The text term used to describe the primary site of disease, as categorized
      by the World Health Organization's (WHO) International Classification of Diseases
      for Oncology (ICD-O). This categorization groups cases into general
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  resolution:
    name: resolution
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  term:
    name: term
    annotations:
      rank:
        tag: rank
        value: 1
    description: The identifier of this disease e.g. MONDO:0007043, OMIM:101600, Orphanet:710,
      DOID:14705 (note these are all equivalent) ARGO mapping primary_diagnosis::submitter_primary_diagnosis_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.submitter_primary_diagnosis_id
    rank: 1000
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true

Induced

name: Disease
description: Message to indicate a disease (diagnosis) and its recorded onset.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  clinicalTnmFinding:
    name: clinicalTnmFinding
    annotations:
      rank:
        tag: rank
        value: 6
    description: Cancer findings in the TNM system that is relevant to the diagnosis
      of cancer. See https://www.cancer.gov/about-cancer/diagnosis-staging/staging
      Valid values include child terms of NCIT:C48232 (Cancer TNM Finding) ARGO mapping
      primary_diagnosis::clinical_t_category ARGO mapping primary_diagnosis::clinical_n_category
      ARGO mapping primary_diagnosis::clinical_m_category
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.clinical_t_category
    rank: 1000
    multivalued: true
    alias: clinicalTnmFinding
    owner: Disease
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  diseaseStage:
    name: diseaseStage
    annotations:
      rank:
        tag: rank
        value: 5
    description: Disease staging, the extent to which a disease has developed. For
      cancers, see https://www.cancer.gov/about-cancer/diagnosis-staging/staging Valid
      values include child terms of NCIT:C28108 (Disease Stage Qualifier) ARGO mapping
      primary_diagnosis::clinical_tumour_staging_system ARGO mapping primary_diagnosis::clinical_stage_group
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.clinical_tumour_staging_system
    rank: 1000
    multivalued: true
    alias: diseaseStage
    owner: Disease
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  excluded:
    name: excluded
    annotations:
      rank:
        tag: rank
        value: 2
    description: Flag to indicate whether the disease was observed or not. Default
      is 'false', in other words the disease was observed. Therefore it is only required
      in cases to indicate that the disease was looked for, but found to be absent.
      More formally, this modifier indicates the logical negation of the OntologyClass
      used in the 'term' field. *CAUTION* It is imperative to check this field for
      correct interpretation of the disease!
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: excluded
    owner: Disease
    domain_of:
    - PhenotypicFeature
    - Disease
    range: boolean
  laterality:
    name: laterality
    annotations:
      rank:
        tag: rank
        value: 8
    description: 'The term used to indicate laterality of diagnosis, if applicable.
      (Codelist reference: NCI CDE: 4122391)'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: laterality
    owner: Disease
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  onset:
    name: onset
    annotations:
      rank:
        tag: rank
        value: 3
    description: 'The onset of the disease. The values of this will come from the
      HPO onset hierarchy i.e. subclasses of HP:0003674 FHIR mapping: Condition.onset
      ARGO mapping primary_diagnosis::age_at_diagnosis'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.age_at_diagnosis
    alias: onset
    owner: Disease
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  primarySite:
    name: primarySite
    annotations:
      rank:
        tag: rank
        value: 7
    description: The text term used to describe the primary site of disease, as categorized
      by the World Health Organization's (WHO) International Classification of Diseases
      for Oncology (ICD-O). This categorization groups cases into general
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: primarySite
    owner: Disease
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  resolution:
    name: resolution
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: resolution
    owner: Disease
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  term:
    name: term
    annotations:
      rank:
        tag: rank
        value: 1
    description: The identifier of this disease e.g. MONDO:0007043, OMIM:101600, Orphanet:710,
      DOID:14705 (note these are all equivalent) ARGO mapping primary_diagnosis::submitter_primary_diagnosis_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:primary_diagnosis.submitter_primary_diagnosis_id
    rank: 1000
    alias: term
    owner: Disease
    domain_of:
    - Disease
    range: OntologyClass
    inlined: true
    inlined_as_list: true