ARCHETYPE Phenopacket HtsFile (openEHR-EHR-CLUSTER.pp_htsfile.v0)

Name: Phenopacket HtsFile
License: http://creativecommons.org/licenses/by-sa/3.0/

ARCHETYPE ID	openEHR-EHR-CLUSTER.pp_htsfile.v0
Concept	Phenopacket HtsFile
Description	Phenopacket HtsFile
Purpose
References
Copyright	© openEHR Foundation
Authors	Author name: Heather Leslie Organisation: Atomica Informatics Email: heather.leslie@atomicainformatics.com Date originally authored: 2019-09-25
Other Details Language	Author 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=BBA0FCB5CC8A2003B542B2399D7539AE, build_uid=c66eebab-f654-4fc4-acc0-e84f57b3f226, revision=0.0.1-alpha}
Keywords
Lifecycle	in_development
UID	13286611-babd-4403-b5a9-c608b8220dd6
Language used	en
Citeable Identifier	1013.1.4147
Revision Number	0.0.1-alpha
All	Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Phenopacket HtsFile, archetypeConceptComment=null, otherContributors=, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={source=[], identities=[], contacts=[], ism_transition=[], provider=[], protocol=[], description=[], events=[], details=[], context=[], target=[], capabilities=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, 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=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=description, description=Arbitrary description of the file, comment=For example; "Matched normal germline sample"., 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[at0003], code=at0003, itemType=ELEMENT, level=1, 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= at0004::UNKNOWN [An HTS file of unknown type.] at0005::SAM [A SAM format file.] at0006::BAM [A BAM format file.] at0007::CRAM [A CRAM format file.] at0008::VCF [A VCF format file.] at0009::BCF [A BCF format file.] at0010::GVCF [A GVCF format file.] , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0011], code=at0011, itemType=ELEMENT, level=1, 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=/items[at0012], code=at0012, itemType=ELEMENT, level=1, 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=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0013], code=at0013, itemType=ELEMENT, level=1, 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=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null]], other_participations=[], content=[], state=[], activities=[], data=[], relationships=[], credentials=[]}, 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=1.., cardinalityText= (Cardinality: 1.., unordered), subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, 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=/items[at0002], code=at0002, itemType=ELEMENT, level=1, text=description, description=Arbitrary description of the file, comment=For example; "Matched normal germline sample"., 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[at0003], code=at0003, itemType=ELEMENT, level=1, 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= at0004::UNKNOWN [An HTS file of unknown type.] at0005::SAM [A SAM format file.] at0006::BAM [A BAM format file.] at0007::CRAM [A CRAM format file.] at0008::VCF [A VCF format file.] at0009::BCF [A BCF format file.] at0010::GVCF [A GVCF format file.] , extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0011], code=at0011, itemType=ELEMENT, level=1, 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=/items[at0012], code=at0012, itemType=ELEMENT, level=1, 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=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0013], code=at0013, itemType=ELEMENT, level=1, 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=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]