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

ARCHETYPE IDopenEHR-EHR-CLUSTER.pp_htsfile.v0
ConceptPhenopacket HtsFile
DescriptionPhenopacket HtsFile
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=BBA0FCB5CC8A2003B542B2399D7539AE, build_uid=c66eebab-f654-4fc4-acc0-e84f57b3f226, revision=0.0.1-alpha}
Keywords
Lifecyclein_development
UID13286611-babd-4403-b5a9-c608b8220dd6
Language useden
Citeable Identifier1013.1.4147
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=Phenopacket HtsFile, archetypeConceptComment=null, otherContributors=, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={identities=[], other_participations=[], credentials=[], description=[], relationships=[], ism_transition=[], activities=[], 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=
  • UNKNOWN [An HTS file of unknown type.]
  • SAM [A SAM format file.]
  • BAM [A BAM format file.]
  • CRAM [A CRAM format file.]
  • VCF [A VCF format file.]
  • BCF [A BCF format file.]
  • 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]], data=[], capabilities=[], state=[], context=[], events=[], source=[], content=[], target=[], details=[], provider=[], protocol=[], contacts=[]}, 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=, 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=
  • UNKNOWN [An HTS file of unknown type.]
  • SAM [A SAM format file.]
  • BAM [A BAM format file.]
  • CRAM [A CRAM format file.]
  • VCF [A VCF format file.]
  • BCF [A BCF format file.]
  • 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]