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

Name: Reference sequence
License: http://creativecommons.org/licenses/by-sa/4.0/

ARCHETYPE ID	openEHR-EHR-CLUSTER.reference_sequence.v1
Concept	Reference sequence
Description	A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence.
Use	This archetype has been specifically designed to be used in the 'Reference Genome' and in the 'Transcript reference sequence' SLOTs within the CLUSTER.genomic_variant_result archetype and in the 'Reference sequence' SLOT within other specific genetic variant archetypes, such as the CLUSTER.genomic_insertion_variant and the CLUSTER.genomic_deletion_variant. Itt can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate.
Purpose	To record details about the reference sequence used to describe variants.
References	den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183.
Copyright	© openEHR Foundation
Authors	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-08
Other Details Language	Author 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 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/., custodian_organisation=openEHR Foundation, references=den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183., original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=96CF5AA5A83A89FF4CCD34E3278102D1, build_uid=d80acb5c-7ce4-4d47-991b-5e1eb8712f4d, revision=1.0.9}
Keywords	genetic findings, reference sequence, Genetic test, variant calling, genomic, variation
Lifecycle	published
UID	0d76b26d-8cbd-4e0d-a7ac-e83bf4dfcae9
Language used	en
Citeable Identifier	1013.1.3762
Revision Number	1.0.9
All	Archetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A sequence file that is used as a reference to describe genetic 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= German: Natalia Strauch, Medizinische Hochschule Hannover, Strauch.Natalia@mh-hannover.de Swedish: Therese Lindberg, Cambio CDS, therese.lindberg@cambio.se Norwegian Bokmål: Vebjørn Arntzen, Liv Laugen,, Oslo University Hospital, Norway, Oslo University Hospital, Norway, varntzen@ous-hf.no, liv.laugen@ous-hf.no , subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={state=[], contacts=[], details=[], description=[], content=[], provider=[], data=[], identities=[], other_participations=[], activities=[], protocol=[], credentials=[], events=[], context=[], relationships=[], target=[], capabilities=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0048], code=at0048, itemType=ELEMENT, level=1, text=Reference genome assembly, description=The reference genome assembled as a representative model of the human genome., 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[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=0..1, occurencesText=Optional, 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=0..1, occurencesText=Optional, 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=The version number of the data record of the reference sequence., comment=For example: 'hg38', 'hg19'., 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=0..1, occurencesText=Optional, 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=[LOINC(2.65)::48000-4 \| Chromosome [Identifier] in Blood or Tissue by Molecular genetics method], values=Choice of:* Coded Text at0024::Chromosome 1 [Chromosome 1.] [LOINC(2.65)::LA21254-0] at0025::Chromosome 2 [Chromosome 2.] [LOINC(2.65)::LA21255-7] at0026::Chromosome 3 [Chromosome 3.] [LOINC(2.65)::LA21256-5] at0027::Chromosome 4 [Chromosome 4.] [LOINC(2.65)::LA21257-3] at0028::Chromosome 5 [Chromosome 5.] [LOINC(2.65)::LA21258-1] at0029::Chromosome 6 [Chromosome 6.] [LOINC(2.65)::LA21259-9] at0030::Chromosome 7 [Chromosome 7.] [LOINC(2.65)::LA21260-7] at0031::Chromosome 8 [Chromosome 8.] [LOINC(2.65)::LA21261-5] at0032::Chromosome 9 [Chromosome 9.] [LOINC(2.65)::LA21262-3] at0033::Chromosome 10 [Chromosome 10.] [LOINC(2.65)::LA21263-1] at0034::Chromosome 11 [Chromosome 11.] [LOINC(2.65)::LA21264-9] at0035::Chromosome 12 [Chromosome 12.] [LOINC(2.65)::LA21265-6] at0036::Chromosome 13 [Chromosome 13.] [LOINC(2.65)::LA21266-4] at0037::Chromosome 14 [Chromosome 14.] [LOINC(2.65)::LA21267-2] at0038::Chromosome 15 [Chromosome 15.] [LOINC(2.65)::LA21268-0] at0039::Chromosome 16 [Chromosome 16.] [LOINC(2.65)::LA21269-8] at0040::Chromosome 17 [Chromosome 17.] [LOINC(2.65)::LA21270-6] at0041::Chromosome 18 [Chromosome 18.] [LOINC(2.65)::LA21271-4] at0042::Chromosome 19 [Chromosome 19.] [LOINC(2.65)::LA21272-2] at0043::Chromosome 20 [Chromosome 20.] [LOINC(2.65)::LA21273-0] at0044::Chromosome 21 [Chromosome 21.] [LOINC(2.65)::LA21274-8] at0045::Chromosome 22 [Chromosome 22.] [LOINC(2.65)::LA21275-5] at0046::Chromosome X [Chromosome X.] [LOINC(2.65)::LA21276-3] at0047::Chromosome Y [Chromosome Y.] [LOINC(2.65)::LA21277-1] Text , extendedValues=null]], source=[], ism_transition=[]}, 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 (Cardinality: 3.., ordered), subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0048], code=at0048, itemType=ELEMENT, level=1, text=Reference genome assembly, description=The reference genome assembled as a representative model of the human genome., 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[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=0..1, occurencesText=Optional, 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=0..1, occurencesText=Optional, 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=The version number of the data record of the reference sequence., comment=For example: 'hg38', 'hg19'., 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=0..1, occurencesText=Optional, 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=[LOINC(2.65)::48000-4 \| Chromosome [Identifier] in Blood or Tissue by Molecular genetics method], values=Choice of: Coded Text at0024::Chromosome 1 [Chromosome 1.] [LOINC(2.65)::LA21254-0] at0025::Chromosome 2 [Chromosome 2.] [LOINC(2.65)::LA21255-7] at0026::Chromosome 3 [Chromosome 3.] [LOINC(2.65)::LA21256-5] at0027::Chromosome 4 [Chromosome 4.] [LOINC(2.65)::LA21257-3] at0028::Chromosome 5 [Chromosome 5.] [LOINC(2.65)::LA21258-1] at0029::Chromosome 6 [Chromosome 6.] [LOINC(2.65)::LA21259-9] at0030::Chromosome 7 [Chromosome 7.] [LOINC(2.65)::LA21260-7] at0031::Chromosome 8 [Chromosome 8.] [LOINC(2.65)::LA21261-5] at0032::Chromosome 9 [Chromosome 9.] [LOINC(2.65)::LA21262-3] at0033::Chromosome 10 [Chromosome 10.] [LOINC(2.65)::LA21263-1] at0034::Chromosome 11 [Chromosome 11.] [LOINC(2.65)::LA21264-9] at0035::Chromosome 12 [Chromosome 12.] [LOINC(2.65)::LA21265-6] at0036::Chromosome 13 [Chromosome 13.] [LOINC(2.65)::LA21266-4] at0037::Chromosome 14 [Chromosome 14.] [LOINC(2.65)::LA21267-2] at0038::Chromosome 15 [Chromosome 15.] [LOINC(2.65)::LA21268-0] at0039::Chromosome 16 [Chromosome 16.] [LOINC(2.65)::LA21269-8] at0040::Chromosome 17 [Chromosome 17.] [LOINC(2.65)::LA21270-6] at0041::Chromosome 18 [Chromosome 18.] [LOINC(2.65)::LA21271-4] at0042::Chromosome 19 [Chromosome 19.] [LOINC(2.65)::LA21272-2] at0043::Chromosome 20 [Chromosome 20.] [LOINC(2.65)::LA21273-0] at0044::Chromosome 21 [Chromosome 21.] [LOINC(2.65)::LA21274-8] at0045::Chromosome 22 [Chromosome 22.] [LOINC(2.65)::LA21275-5] at0046::Chromosome X [Chromosome X.] [LOINC(2.65)::LA21276-3] at0047::Chromosome Y [Chromosome Y.] [LOINC(2.65)::LA21277-1] Text , extendedValues=null]], minIndents={}, termBindingRetrievalErrorMessage=null]