ARCHETYPE Reference sequence (openEHR-EHR-CLUSTER.reference_sequence.v1)

ARCHETYPE IDopenEHR-EHR-CLUSTER.reference_sequence.v1
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=E3475CF4AF445B569257A3B61ED1B539, build_uid=e11d3b58-4bcb-4fa5-9e1d-e1330e385b44, revision=1.0.1}
Keywordsgenetic findings, reference sequence, Genetic test, variant calling, genomic, variation
Lifecyclepublished
UID0d76b26d-8cbd-4e0d-a7ac-e83bf4dfcae9
Language useden
Citeable Identifier1013.1.3762
Revision Number1.0.1
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=Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor)
SB Bhattacharyya, Sudisa Consultancy Services, India
Francesca Frexia, CRS4 - Center for advanced studies, research and development in Sardinia, Italy
Gideon Giacomelli, Charité Berlin, Germany
Evelyn Hovenga, EJSH Consulting, Australia
Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Florian Kaercher, Charité Berlin, Germany
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Cecilia Mascia, CRS4, Italy (openEHR Editor)
Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (openEHR Editor)
Andrej Orel, Marand d.o.o., Slovenia
Simon Schumacher, HiGHmed, Germany
Aurelie Tomczak, Uniklinikum Heidelberg, Germany
Paolo Uva, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy, originalLanguage=en, translators=Norwegian Bokmål: Liv Laugen, Oslo University Hospital, Norway, liv.laugen@ous-hf.no
, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={identities=[], other_participations=[], credentials=[], description=[], relationships=[], ism_transition=[], activities=[], 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]], data=[], capabilities=[], state=[], context=[], events=[], source=[], content=[], target=[], details=[], provider=[], protocol=[], contacts=[]}, 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]