TEMPLATE Cohort (Cohort)

TEMPLATE IDCohort
ConceptCohort
DescriptionThis dataset describes a group of individuals related in some phenotypic or genotypic aspect. For instance, a cohort can consist of individuals all of whom have been diagnosed with a certain disease or have been found to have a certain phenotypic feature.
PurposeThis dataset describes a group of individuals related in some phenotypic or genotypic aspect. For instance, a cohort can consist of individuals all of whom have been diagnosed with a certain disease or have been found to have a certain phenotypic feature.
References
Authorsdate: 2019-09-26; name: Heather Leslie; organisation: Atomica Informatics; email: heather.leslie@atomicainformatics.com
Other Details Languagedate: 2019-09-26; name: Heather Leslie; organisation: Atomica Informatics; email: heather.leslie@atomicainformatics.com
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/., custodian_organisation=openEHR Foundation, PARENT:MD5-CAM-1.0.1=F1AE88E842C8441C1505E7DEBF69C395, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=93b4ff978ac05ffae32a89139be30b3c}
Language useden
Citeable Identifier1013.26.236
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For example: "UBERON::0001256 | wall of urinary bladder |"., uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_biosample.v0]/items[at0008], code=at0008, itemType=ELEMENT, level=4, text=taxonomy, description=Species of the sampled individual., comment=To be represented as a code and a text label pair., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_biosample.v0]/items[at0010], code=at0010, itemType=ELEMENT, level=4, text=individual_age_at_collection, description=Age, or age range, of the proband at the time the sample was taken, comment=For example: "P52Y2M"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Duration
  •  Interval of Duration
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_biosample.v0]/items[at0011], code=at0011, itemType=ELEMENT, level=4, text=histological diagnosis, description=Disease diagnosis that was inferred from the histological examination., comment=To be represented as a code and a text label pair. 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For example: "NCIT::C28743|Punch Biopsy"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_biosample.v0]/items[openEHR-EHR-CLUSTER.pp_procedure.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=5, text=body_site, description=Specific body site if unable to represent this as the code., comment=To be represented as a code and a text label pair. For example: "UBERON::0003403|skin of forearm"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_biosample.v0]/items[at0018], code=at0018, itemType=ELEMENT, level=4, text=is_control_sample, description=Whether the sample is being used as a normal control., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=Assumed value: false, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_gene.v0], code=at0000, itemType=CLUSTER, level=3, text=Gene, description=Phenopacket gene, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_gene.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=4, text=gene symbol, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0], code=at0000, itemType=CLUSTER, level=3, text=Variant, description=This archetype should be used to describe candidate variants or diagnosed causative variants. There is currently no standard variant nomenclature that can represent all kinds of genetic variation that is relevant to human medicine, science, and model organisms. Therefore, we represent variants using the keyword oneof, which is used in protobuf for an item with many optional fields where at most one field will be set at the same time. Variant messages contain an allele and the zygosity of the allele. Alleles can be listed using HGVS, VCF, SPDI or ISCN notation. The phenopacket schema will implement the GA4GH Variation Representation Specification once that is mature. The VR-Spec will be the recommended option in some settings. See: https://vr-spec.readthedocs.io/en/1.0rc/ See: https://github.com/ga4gh-beacon/specification/blob/master/beacon.yaml The Variant element itself is an optional element of a Phenopacket or Biosample. If it is present, the Phenopacket standard has the following requirements. Alleles can refer to external sources, for example the ClinGen allele registry, ClinVar, dbSNP, dbVAR etc. using the id field. It is RECOMMENDED to use a CURIE identifier and corresponding Resource. N.B. phase information for alleles are not represented in this model., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_hgvsallele.v0], code=at0000, itemType=CLUSTER, level=4, text=HgvsAllele, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=1..4, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_hgvsallele.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=5, text=id, description=An arbitrary identifier., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_hgvsallele.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=5, text=hgvs, description=*, comment=For example: NM_000226.3:c.470T>G., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_iscnallele.v0], code=at0000, itemType=CLUSTER, level=4, text=IscnAllele, description=IscnAllele, comment=null, uncommonOntologyItems=null, occurencesFormal=1..4, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_iscnallele.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=5, text=id, description=An arbitrary identifier., comment=For example: ""ISCN:12345"", uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_iscnallele.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=5, text=iscn, description=*, comment=For example: "t(8;9;11)(q12;p24;p12)"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_spdiallele.v0], code=at0000, itemType=CLUSTER, level=4, text=SpdiAllele, description=SpdiAllele, comment=null, uncommonOntologyItems=null, occurencesFormal=1..4, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_spdiallele.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=5, text=id, description=An arbitrary identifier., comment=For example: "clinvar:13294"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_spdiallele.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=5, text=seq_id, description=*, comment=For example: "NC_000001.10"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_spdiallele.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=5, text=position, description=*, comment=For example: "12346"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_spdiallele.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=5, text=deleted_sequence, description=*, comment=For example: "A"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_spdiallele.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=5, text=inserted_sequence, description=*, comment=For example: "G"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0], code=at0000, itemType=CLUSTER, level=4, text=VcfAllele, description=null, comment=null, uncommonOntologyItems=null, occurencesFormal=1..4, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=5, text=genome_assembly, description=*, comment=For example: "GRCh38"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=5, text=id, description=An arbitrary identifier., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=5, text=chr, description=*, comment=For example: "2"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=5, text=pos, description=*, comment=For example: "134327882"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=5, text=re, description=*, comment=For example: "A"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0006], code=at0006, itemType=ELEMENT, level=5, text=alt, description=*, comment=For example: "C" or "<DUP>"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[openEHR-EHR-CLUSTER.pp_vcfallele.v0]/items[at0007], code=at0007, itemType=ELEMENT, level=5, text=info, description=*, comment=For example: "END=43500;SVTYPE=DUP;CHR2=1;SVLEN=29000;"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_variant.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=4, text=zygosity, description=*, comment=The zygosity of the variant as determined in all of the samples represented in this Phenopacket is represented using a list of terms taken from the Genotype Ontology (GENO). For instance, if a variant affects one of two alleles at a certain locus, we could record the zygosity using the term heterozygous (GENO:0000135)., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_disease.v0], code=at0000, itemType=CLUSTER, level=3, text=Disease, description=Phenopacket disease, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_disease.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=4, text=term, description=An coded term that represents the disease., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_disease.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=4, text=onset, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Duration>=P0D
    Units:
    • Year
    • Month
    • Day
  •  Coded TextValue set: external
  •  Interval of DurationLower constraint: >=P0D
    Units:
    • Year
    • Month
    • Day

    Upper constraint: >=P0D
    Units:
    • Year
    • Month
    • Day
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0]/items[openEHR-EHR-CLUSTER.pp_disease.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=4, text=tumor_stage, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0], code=at0000, itemType=CLUSTER, level=2, text=HtsFile, description=Phenopacket HtsFile, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=3, text=uri, description=A valid URI., comment=For example: "file://data/genomes/germline_wgs.vcf.gz"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=3, text=description, description=Arbitrary description of the file, comment=For example; "Matched normal germline sample"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=3, text=hts_format, description=*, comment=For example: "VCF"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • UNKNOWN 
  • SAM 
  • BAM 
  • CRAM 
  • VCF 
  • BCF 
  • GVCF 
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0]/items[at0011], code=at0011, itemType=ELEMENT, level=3, text=genome_assembly, description=*, comment=For example: "GRCh38"., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0]/items[at0012], code=at0012, itemType=ELEMENT, level=3, text=individual_identifier, description=The Individual.id component required for mapping between the Individual.id or Biosample.id to the sample identifier in the HTS file., comment=For example: "patient23456"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_htsfile.v0]/items[at0013], code=at0013, itemType=ELEMENT, level=3, text=sample_identifier, description=The Biosample.id component required for mapping between the Individual.id or Biosample.id to the sample identifier in the HTS file., comment=For example: "NA12345"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0], code=at0000, itemType=CLUSTER, level=2, text=MetaData, description=Phenopacket MetaData, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=3, text=created, description=Representation of the time when this object was created., comment=For example: "2019-04-01T15:10:17.808Z"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_DATE_TIME, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=3, text=created by, description=Name of person who created the phenopacket., comment=This is a string that represents an identifier for the contributor/ program. The expected syntax and semantics are application-dependent., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=3, text=submitted by, description=Name of person who submitted the phenopacket., comment=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)., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0], code=at0000, itemType=CLUSTER, level=3, text=Resource, description=Phenopacket resource, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=4, text=id, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=4, text=name, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=4, text=namespace_prefix, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=4, text=url, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=4, text=version, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_resource.v0]/items[at0006], code=at0006, itemType=ELEMENT, level=4, text=iri-prefix, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_update.v0], code=at0000, itemType=CLUSTER, level=3, text=Update, description=Phenopacket update, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_update.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=4, text=timestamp, description=ISO8601 UTC timestamp at which this record was updated, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_DATE_TIME, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_update.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=4, text=updated_by, description=Information about the person/organisation/network that has updated the phenopacket., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_update.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=4, text=comment, description=Textual comment about the changes made to the content and/or reason for the update., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[at0006], code=at0006, itemType=ELEMENT, level=3, text=phenopacket_schema_version, description=Schema version of the current phenopacket., comment=A string representing the version of the phenopacket-schema according to which a phenopacket was made., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_external_reference.v0], code=at0000, itemType=CLUSTER, level=3, text=External reference, description=Phenopacket external reference, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_external_reference.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=4, text=id, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-EVALUATION.pp_cohort.v0]/data[at0001]/items[openEHR-EHR-CLUSTER.pp_metadata.v0]/items[openEHR-EHR-CLUSTER.pp_external_reference.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=4, text=description, description=*, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null]], templateType=normal]