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 (See text)

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 specificy the disease and HPO terms are used to specificy 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).