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
disease_stage	OntologyClass	optional	List of terms representing the disease stage e.g. AJCC stage group.
tnm_finding	OntologyClass	optional	List of terms representing the tumor TNM score

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. For cancers, we recommend using terms from domain-specific ontologies, such as NCIthesaurus (e.g., NCIT:C9049).

disease_stage

This attribute is used to describe the stage of disease. If the disease is a cancer, this attribute describes the extent of cancer development, typically including an AJCC stage group (i.e., Stage 0, I-IV), though other staging systems are used for some cancers. See staging. The list of elements constituting this attribute should be derived from child terms of NCIT:C28108 (Disease Stage Qualifier) or equivalent hierarchy from another ontology.

tnm_finding

This attribute can be used if the phenopacket is describing cancer. TNM findings score the progression of cancer with respect to the originating tumor (T), spread to lymph nodes (N), and presence of metastases (M). These findings are commonly reported for tumors, and support the stage classifications stored in the disease_stage attribute. See staging. The list of elements constituting this attribute should be derived from child terms of NCIT:C48232 (Cancer TNM Finding) or equivalent hierarchy from another ontology.

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.