Disease

The word phenotype is used with many different meanings, including “the observable traits of an organism”. In medicine, the word can be used with at least two different meanings. It is used to refer to some observed deviation from normal morphology, physiology, or behavior. In contrast, the disease is a diagnosis, i.e., and inference or hypothesis about the cause underlying the observed phenotypic abnormalities. Occasionally, physicians use the word phenotype to refer to a disease, but we do not use this meaning here.

Data model

Field Type Status Description
term OntologyClass required An ontology class that represents the disease
onset Age or AgeRange or OntologyClass optional an element representing the age of onset of the disease
tumor_stage OntologyClass optional List of terms representing the tumor stage (TNM findings)

Example

{
"term": {
  "id": "OMIM:164400",
  "label": "Spinocerebellar ataxia 1 "
  },
"ageOfOnset": {
  "age": "P38Y7M"
  }
}

See A complete example: Oncology for a usage of the Disease element that includes information about tumor staging.

term

In the phenopacket schema, the disease element denotes the diagnosis by means of an ontology class. For rare diseases, we recommend using a term from Online Mendelian Inheritance in Man (OMIM) (e.g., OMIM:101600), Orphanet (e.g., Orphanet:710), or MONDO (e.g., MONDO:0007043). There are many other ontologies and terminologies that can be used including Disease Ontology, SNOMED, and ICD.

tumor_stage

This element can be used if the phenopacket is described cancer. Tumor staging describes the extent of growth of cancer. including the tumor and if applicable affected lymph nodes, and distant metastases. See staging. This element should be derived from child terms of NCIT:C48232 (Cancer TNM Finding) or equivalent.

age_of_onset

The onset element provides three possibilities of describing the onset of the disease. It is also possible to denote the onset of individual phenotypic features of disease in the Phenopacket element. If an ontology class is used to refer to the age of onset of the disease, we recommend using a term from the HPO onset hierarchy.