ARCHETYPE Phenopacket biosample (openEHR-EHR-CLUSTER.pp_biosample.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.pp_biosample.v0
ConceptPhenopacket biosample
Descriptionbiosample
Purpose
References
Copyright© openEHR Foundation
AuthorsAuthor name: Heather Leslie
Organisation: Atomica Informatics
Email: heather.leslie@atomicainformatics.com
Date originally authored: 2019-09-25
Other Details LanguageAuthor name: Heather Leslie
Organisation: Atomica Informatics
Email: heather.leslie@atomicainformatics.com
Date originally authored: 2019-09-25
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, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=DAF8772578930B5C7EF35C9382FCACDC, build_uid=1fab9318-a552-48f2-a219-b4a00ff3c251, revision=0.0.1-alpha}
Keywords
Lifecyclein_development
UID208c36cf-16ec-4981-b4e2-4e79743ac345
Language useden
Citeable Identifier1013.1.4150
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=biosample, archetypeConceptComment=null, otherContributors=, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={identities=[], other_participations=[], events=[], details=[], provider=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=id, description=Arbitrary identifier., comment=For example: "sample1"., 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=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=individual id, description=Arbitrary identifier., comment=For example: "patient1"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=description, description=Arbitrary text, comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=ELEMENT, level=1, text=sampled_tissue, description=Tissue from which the sample was taken., comment=To be represented as a code and a text label pair. 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0007], code=at0007, itemType=SLOT, level=1, text=phenotypic_features, description=List of phenotypic abnormalities of the sample., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_phenotypic_feature.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, itemType=ELEMENT, level=1, text=taxonomy, description=Species of the sampled individual., comment=To be represented as a code and a text label pair., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0010], code=at0010, itemType=ELEMENT, level=1, 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=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Duration
  •  Interval of Duration

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0011], code=at0011, itemType=ELEMENT, level=1, 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. For example: NCIT::C39853|Infiltrating Urothelial Carcinoma|"., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0012], code=at0012, itemType=ELEMENT, level=1, text=tumor_progression, description=Indicates primary, metastatic, recurrent., comment=To be represented as a code and a text label pair. For example: "NCIT::C84509|Primary Malignant Neoplasm|"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0013], code=at0013, itemType=ELEMENT, level=1, text=tumor_grade, description=List of terms representing the tumor grade or stage., comment=To be represented as a code and a text label pair. For example: "NCIT::C48766|pT2b Stage Finding|" or "NCIT::C48750|pN2 Stage Finding|"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0014], code=at0014, itemType=ELEMENT, level=1, text=diagnostic_markers, description=Clinically relevant biomarkers., comment=To be represented as a code and a text label pair., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0015], code=at0015, itemType=SLOT, level=1, text=procedure, description=The procedure used to extract the biosample., comment=For example: "NCIT:C5189|Radical Cystoprostatectomy|"., uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_procedure.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0016], code=at0016, itemType=SLOT, level=1, text=hts_files, description=list of high-throughput sequencing files derived from the biosample, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_htsfile.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0017], code=at0017, itemType=SLOT, level=1, text=variants, description=List of variants determined to be present in the biosample., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_variant.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0018], code=at0018, itemType=ELEMENT, level=1, text=is_control_sample, description=Whether the sample is being used as a normal control., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=Assumed value: false, extendedValues=null]], description=[], protocol=[], ism_transition=[], context=[], data=[], activities=[], relationships=[], credentials=[], target=[], source=[], state=[], content=[], contacts=[], capabilities=[]}, topLevelItems={items=ResourceSimplifiedHierarchyItem [path=ROOT_/, code=at0000, itemType=CLUSTER, level=0, text=null, description=null, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=0..*, cardinalityText=Minimum of 0 items, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=id, description=Arbitrary identifier., comment=For example: "sample1"., 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=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=individual id, description=Arbitrary identifier., comment=For example: "patient1"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0004], code=at0004, itemType=ELEMENT, level=1, text=description, description=Arbitrary text, comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0006], code=at0006, itemType=ELEMENT, level=1, text=sampled_tissue, description=Tissue from which the sample was taken., comment=To be represented as a code and a text label pair. 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0007], code=at0007, itemType=SLOT, level=1, text=phenotypic_features, description=List of phenotypic abnormalities of the sample., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_phenotypic_feature.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, itemType=ELEMENT, level=1, text=taxonomy, description=Species of the sampled individual., comment=To be represented as a code and a text label pair., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0010], code=at0010, itemType=ELEMENT, level=1, 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=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Duration
  •  Interval of Duration

, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0011], code=at0011, itemType=ELEMENT, level=1, 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. For example: NCIT::C39853|Infiltrating Urothelial Carcinoma|"., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0012], code=at0012, itemType=ELEMENT, level=1, text=tumor_progression, description=Indicates primary, metastatic, recurrent., comment=To be represented as a code and a text label pair. For example: "NCIT::C84509|Primary Malignant Neoplasm|"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0013], code=at0013, itemType=ELEMENT, level=1, text=tumor_grade, description=List of terms representing the tumor grade or stage., comment=To be represented as a code and a text label pair. For example: "NCIT::C48766|pT2b Stage Finding|" or "NCIT::C48750|pN2 Stage Finding|"., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0014], code=at0014, itemType=ELEMENT, level=1, text=diagnostic_markers, description=Clinically relevant biomarkers., comment=To be represented as a code and a text label pair., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0015], code=at0015, itemType=SLOT, level=1, text=procedure, description=The procedure used to extract the biosample., comment=For example: "NCIT:C5189|Radical Cystoprostatectomy|"., uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_procedure.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0016], code=at0016, itemType=SLOT, level=1, text=hts_files, description=list of high-throughput sequencing files derived from the biosample, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_htsfile.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0017], code=at0017, itemType=SLOT, level=1, text=variants, description=List of variants determined to be present in the biosample., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.pp_variant.v0, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0018], code=at0018, itemType=ELEMENT, level=1, text=is_control_sample, description=Whether the sample is being used as a normal control., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=Assumed value: false, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]