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
Field | Type | Multiplicity | Description |
---|---|---|---|
created | A Timestamp | 1..1 | Representation of the time when this object was created, e.g., 2019-04-01T15:10:17.808Z |
created_by | string | 1..1 | Name of person who created the phenopacket |
submitted_by | string | 0..1 | Name of person who submitted the phenopacket |
resources | list of :ref:rstresource |
1..* | Ontologies used to create the phenopacket |
updates | list of :ref:rstupdate |
0..* | List of updates to the phenopacket |
phenopacket_schema_version | string | 1..1 | schema version of the current phenopacket |
external_references | List of :ref:rstexternalreference |
0..* | (See text) |
The MetaData
element MUST have one :ref:rstresource
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
metadata:
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: "hp"
- id: "geno"
name: "Genotype Ontology"
url: "http://purl.obolibrary.org/obo/geno.owl"
version: "19-03-2018"
namespacePrefix: "GENO"
iriPrefix: "geno"
- id: "pubmed"
name: "PubMed"
url: "https://www.ncbi.nlm.nih.gov/pubmed/"
namespacePrefix: "PMID"
phenopacketSchemaVersion: "2.0"
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."
Explanations
- created
This element is a ISO8601 UTC timestamp <https://en.wikipedia.org/wiki/ISO_8601>
_ 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 :ref:rstupdate
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. Permitted values
MUST be one of 1.0.0
, 1.0
or 2.0
. Versions 1.0.0
and 1.0
are equivalent and the 1.0
string should be
preferred. This version of the schema is 2.0
.
- external_references
A list of :ref:rstexternalreference
(such as the PubMed id of a publication from which a
phenopacket was derived).