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).