MetaData

This element contains structured definitions of the resources and ontologies used within the phenopacket. It is considered to be a required element of a valid Phenopacket and application Q/C software should check this.

Data model

Definition of the MetaData element
Field Type Status Description
created A Timestamp required Representation of the time when this object was created, e.g., 2019-04-01T15:10:17.808Z
created_by string required Name of person who created the phenopacket
submitted_by string optional Name of person who submitted the phenopacket
resources list of Resource required Ontologies used to create the phenopacket
updates list of Update optional List of updates to the phenopacket
phenopacket_schema_version string optional schema version of the current phenopacket
external_references List of ExternalReference optional (See text)

The MetaData element MUST have one Resource element for each ontology or terminology whose terms are used in the Phenopacket. For instance, if a MONDO term is used to specify the disease and HPO terms are used to specify the phenotypes of a patient, then the MetaData element MUST have one Resource element each for MONDO and HPO.

Example

{
  "created": "2019-07-21T00:25:54.662Z",
  "createdBy": "Peter R.",
  "resources": [{
    "id": "hp",
    "name": "human phenotype ontology",
    "url": "http://purl.obolibrary.org/obo/hp.owl",
    "version": "2018-03-08",
    "namespacePrefix": "HP",
    "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
  }, {
    "id": "geno",
    "name": "Genotype Ontology",
    "url": "http://purl.obolibrary.org/obo/geno.owl",
    "version": "19-03-2018",
    "namespacePrefix": "GENO",
    "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
  }, {
    "id": "pubmed",
    "name": "PubMed",
    "namespacePrefix": "PMID",
    "iriPrefix": "https://www.ncbi.nlm.nih.gov/pubmed/"
  }],
  "externalReferences": [{
    "id": "PMID:30808312",
    "description": "Bao M, et al. COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report. BMC Neurol. 2019;19(1):32."
  }]
}

created

This element is a ISO8601 UTC timestamp for when this phenopacket was created in ISO, e.g., “2018-03-01T00:00:00Z”.

created_by

This is a string that represents an identifier for the contributor/ program. The expected syntax and semantics are application-dependent.

submitted_by

This is a string that represents an identifier for the person who submitted the phenopacket (who may not be the person who created the phenopacket).

resources

This element contains a listing of the ontologies/resources referenced in the phenopacket.

updates

This element contains a list of Update objects which contain information about when, what and who updated a phenopacket. This is only necessary when a phenopacket is being used as a persistent record and is being continuously updated. Resources should provide information about how this is being used.

phenopacket_schema_version

A string representing the version of the phenopacket-schema according to which a phenopacket was made.

external_references

A list of ExternalReference (such as the PubMed id of a publication from which a phenopacket was derived).