ARCHETYPE Reference sequence (openEHR-EHR-CLUSTER.reference_sequence.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.reference_sequence.v0
ConceptReference sequence
DescriptionA sequence file that is used as a reference to describe variants that are present in an analysed sequence.
PurposeTo record details about the reference sequence used to describe variants.
References"Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569".
Copyright© openEHR Foundation
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-08
Other Details LanguageAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-08
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, references="Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569"., original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=1C3D8C3C8BFD0511128AF4D967357745, build_uid=9198c3c9-c0b5-4389-81af-6d2759c54ec6, revision=0.0.1-alpha}
Keywordsgenetic findings, reference sequence, Genetic test, variant caling, genomic, variation
Lifecyclein_development
UID8df26362-590a-4a4e-901e-770a380652a5
Language useden
Citeable Identifier1246.145.400
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A sequence file that is used as a reference to describe variants that are present in an analysed sequence., archetypeConceptComment=null, otherContributors=Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Florian Kaercher, Charité Berlin, Germany
Francesca Frexia, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Gideon Giacomelli, Charité Berlin, Germany
Paolo Uva, CRS4, Italy
Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor)
Simon Schumacher, HiGHmed, Germany, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={relationships=[], provider=[], details=[], description=[], capabilities=[], activities=[], contacts=[], content=[], protocol=[], data=[], source=[], state=[], events=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0019], code=at0019, itemType=ELEMENT, level=1, text=Source name, description=The name of the data source containing the reference sequence., 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=/items[at0020], code=at0020, itemType=ELEMENT, level=1, text=Accession number, description=A unique identifier to refer to a sequence record in a sequence repository., 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=/items[at0021], code=at0021, itemType=ELEMENT, level=1, text=Version number, description=An attribute that provides a specific indication of the sequence used for annotation., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0022], code=at0022, itemType=ELEMENT, level=1, text=URL, description=Network address., comment=null, 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[at0023], code=at0023, itemType=ELEMENT, level=1, text=Chromosome label, description=Chromosome identifier., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Coded Text
    • Chromosome 1 [Chromosome 1.]
      [LOINC(2.65)::LA21254-0]
    • Chromosome 2 [Chromosome 2.]
      [LOINC(2.65)::LA21255-7]
    • Chromosome 3 [Chromosome 3.]
      [LOINC(2.65)::LA21256-5]
    • Chromosome 4 [Chromosome 4.]
      [LOINC(2.65)::LA21257-3]
    • Chromosome 5 [Chromosome 5.]
      [LOINC(2.65)::LA21258-1]
    • Chromosome 6 [Chromosome 6.]
      [LOINC(2.65)::LA21259-9]
    • Chromosome 7 [Chromosome 7.]
      [LOINC(2.65)::LA21260-7]
    • Chromosome 8 [Chromosome 8.]
      [LOINC(2.65)::LA21261-5]
    • Chromosome 9 [Chromosome 9.]
      [LOINC(2.65)::LA21262-3]
    • Chromosome 10 [Chromosome 10.]
      [LOINC(2.65)::LA21263-1]
    • Chromosome 11 [Chromosome 11.]
      [LOINC(2.65)::LA21264-9]
    • Chromosome 12 [Chromosome 12.]
      [LOINC(2.65)::LA21265-6]
    • Chromosome 13 [Chromosome 13.]
      [LOINC(2.65)::LA21266-4]
    • Chromosome 14 [Chromosome 14.]
      [LOINC(2.65)::LA21267-2]
    • Chromosome 15 [Chromosome 15.]
      [LOINC(2.65)::LA21268-0]
    • Chromosome 16 [Chromosome 16.]
      [LOINC(2.65)::LA21269-8]
    • Chromosome 17 [Chromosome 17.]
      [LOINC(2.65)::LA21270-6]
    • Chromosome 18 [Chromosome 18.]
      [LOINC(2.65)::LA21271-4]
    • Chromosome 19 [Chromosome 19.]
      [LOINC(2.65)::LA21272-2]
    • Chromosome 20 [Chromosome 20.]
      [LOINC(2.65)::LA21273-0]
    • Chromosome 21 [Chromosome 21.]
      [LOINC(2.65)::LA21274-8]
    • Chromosome 22 [Chromosome 22.]
      [LOINC(2.65)::LA21275-5]
    • Chromosome X [Chromosome X.]
      [LOINC(2.65)::LA21276-3]
    • Chromosome Y [Chromosome Y.]
      [LOINC(2.65)::LA21277-1]
  •  Text
, extendedValues=null]], target=[], identities=[], credentials=[], other_participations=[], ism_transition=[], context=[]}, topLevelItems={items=ResourceSimplifiedHierarchyItem [path=ROOT_/, code=at0018, itemType=CLUSTER, level=0, text=null, description=null, comment=null, uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=3..*, cardinalityText=Minimum of 3 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0019], code=at0019, itemType=ELEMENT, level=1, text=Source name, description=The name of the data source containing the reference sequence., 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=/items[at0020], code=at0020, itemType=ELEMENT, level=1, text=Accession number, description=A unique identifier to refer to a sequence record in a sequence repository., 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=/items[at0021], code=at0021, itemType=ELEMENT, level=1, text=Version number, description=An attribute that provides a specific indication of the sequence used for annotation., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0022], code=at0022, itemType=ELEMENT, level=1, text=URL, description=Network address., comment=null, 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[at0023], code=at0023, itemType=ELEMENT, level=1, text=Chromosome label, description=Chromosome identifier., comment=null, uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=Choice of:
  •  Coded Text
    • Chromosome 1 [Chromosome 1.]
      [LOINC(2.65)::LA21254-0]
    • Chromosome 2 [Chromosome 2.]
      [LOINC(2.65)::LA21255-7]
    • Chromosome 3 [Chromosome 3.]
      [LOINC(2.65)::LA21256-5]
    • Chromosome 4 [Chromosome 4.]
      [LOINC(2.65)::LA21257-3]
    • Chromosome 5 [Chromosome 5.]
      [LOINC(2.65)::LA21258-1]
    • Chromosome 6 [Chromosome 6.]
      [LOINC(2.65)::LA21259-9]
    • Chromosome 7 [Chromosome 7.]
      [LOINC(2.65)::LA21260-7]
    • Chromosome 8 [Chromosome 8.]
      [LOINC(2.65)::LA21261-5]
    • Chromosome 9 [Chromosome 9.]
      [LOINC(2.65)::LA21262-3]
    • Chromosome 10 [Chromosome 10.]
      [LOINC(2.65)::LA21263-1]
    • Chromosome 11 [Chromosome 11.]
      [LOINC(2.65)::LA21264-9]
    • Chromosome 12 [Chromosome 12.]
      [LOINC(2.65)::LA21265-6]
    • Chromosome 13 [Chromosome 13.]
      [LOINC(2.65)::LA21266-4]
    • Chromosome 14 [Chromosome 14.]
      [LOINC(2.65)::LA21267-2]
    • Chromosome 15 [Chromosome 15.]
      [LOINC(2.65)::LA21268-0]
    • Chromosome 16 [Chromosome 16.]
      [LOINC(2.65)::LA21269-8]
    • Chromosome 17 [Chromosome 17.]
      [LOINC(2.65)::LA21270-6]
    • Chromosome 18 [Chromosome 18.]
      [LOINC(2.65)::LA21271-4]
    • Chromosome 19 [Chromosome 19.]
      [LOINC(2.65)::LA21272-2]
    • Chromosome 20 [Chromosome 20.]
      [LOINC(2.65)::LA21273-0]
    • Chromosome 21 [Chromosome 21.]
      [LOINC(2.65)::LA21274-8]
    • Chromosome 22 [Chromosome 22.]
      [LOINC(2.65)::LA21275-5]
    • Chromosome X [Chromosome X.]
      [LOINC(2.65)::LA21276-3]
    • Chromosome Y [Chromosome Y.]
      [LOINC(2.65)::LA21277-1]
  •  Text
, extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]