Subjects

This page details how subject (usually a patient) information is stored in the corresponding collection. This is the final form of the input data, and is structured to facilitate the queries used in Cafe Variome.

Subject Data Structure

Each subject is stored as an item within a specific collection belonging to a source. The subject is represented with a JSON object, with the following fields:

{
    "subjectID": "string",
    "HPO": [
        "0000002",
        "0000003",
        {
            "0000004": 25
        }
    ],
    "ORDO": ["1234"],
    "SNOMED": [
        "248153007",
        {
            "424144002": 25
        }
    ],
    "NCIT": ["C12345"],
    "ALLELES": [
        {
            "gene": "APOE",
            "alleles": ["e3", "e3"]
        }
    ],
    "VARIANT": [
        {
            "gene": "APOE",
            "mutation": "lossOfStart",
            "af": 0.01
        }
    ],
    "EAV": {
        "Attribute 1": "Value 1",
        "Attribute 2": 2,
        "Attribute 3": true,
        "Attribute 4": ["Value 4", "Value 5"]
    }
}

In the example:

subjectID is a unique identifier for the subject. If the original data source does not provide a unique identifier, Cafe Variome will generate one with UUID4 format. If the original data contains an ID and Cafe Variome is instructed to use it, it will not change anything. The ID should remain constant for the same subject within the same source, even across data updates, to allow correct association with other data.
HPO is an array of strings, containing the ID part (with no HPO: or similar prefixes) of Human Phenotype Ontology terms. It's kept as a string with front-padded zeros, as the HPO terms standard structure. It may also contain a dictionary, where the key is a descriptive term, and the value being the actual value of the attribute (could be a term, boolean, number, or anything).
ORDO is an array of strings, containing the ID part (with no ORDO: or similar prefixes) of Orphanet Rare Disease Ontology terms. Similar to HPO terms, it's the part taken from ORDO IDs directly, without the prefix.
SNOMED is an array of strings, containing the SNOMED CT term IDs. It may also contain a dictionary, where the key is a descriptive term, and the value being the actual value of the attribute (could be a term, boolean, number, or anything).
NCIT is an array of strings, containing the National Cancer Institute Thesaurus term IDs.
ALLELES is an array of objects designed to describ what type of alleles the subject has. Each object contains two fields: gene and allele. gene is the gene name (in HGNC format), and alleles are a pair of values representing the alleles of this gene that the subject has.
VARIANT is an array of objects designed to describe what type of genetic variants the subject has. Each object contains two fields: gene and mutation. The gene field is the gene name (in HGNC format), and the mutation field is the protein effect of the mutation. The af field is the allele frequency of the mutation. If the allele frequency is not provided, Cafe Variome will use the dataset itself to calculate it. This is to assume the dataset contains full information about each subject and their genetic variants.
EAV is a key-value pair object, where the key is the attribute name and the value is the attribute value. This is used to store any additional information that does not fit into the other fields. The values can be string, number, boolean, or an array of the above.

Last modified: 03 September 2024