ARCHETYPE Sequence variation (openEHR-EHR-CLUSTER.Sequence_variation_local.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.Sequence_variation_local.v0
ConceptSequence variation
DescriptionA difference between the reference sequence and the sample sequence
UseThis archetype is meant to be used in the SLOT 'Seq uence variation' within the 'CLUSTER.Genetic_findings' archetype. It should represent a single raw of a VCF file, corresponding to a single specific position in the genome.
PurposeTo record data about a single sequence variation derived from genetic tests
References"Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569 "
Copyright© HiGHmed
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-07
Other Details LanguageAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-07
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=HiGHmed, 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.highmed, original_publisher=HiGHmed, custodian_namespace=org.highmed, MD5-CAM-1.0.1=EAF2EFB26861C130421F5FC9C2D58F4C, build_uid=04dfcda4-d934-4147-a825-b198c8ecd0db, revision=0.0.1-alpha}
KeywordsVariation, Alternate, allele, VCF, Variant, genetic, genomic, variant calling, sequence
Lifecyclein_development
UID6985d31f-dbf2-4be0-b177-d39d3f233ed1
Language useden
Citeable Identifier867.109.29
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A difference between the reference sequence and the sample sequence, archetypeConceptComment=null, otherContributors=Paolo Uva, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Simone Leo, CRS4, Italy, originalLanguage=en, translators=, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={relationships=[], identities=[], provider=[], content=[], events=[], data=[], credentials=[], capabilities=[], target=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=CLUSTER, level=1, text=Genomic location, description=The position in respect to a genomic or coding sequence, following the HGVS nomenclature., comment=null, uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=4..*, cardinalityText=Minimum of 4 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0008], code=at0008, itemType=SLOT, level=2, text=Reference sequence, description=A sequence file that is used as a reference to describe variants that are present in a analysed sequence, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.Reference_sequence.v[0-9.]+ and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0096], code=at0096, itemType=ELEMENT, level=2, text=Genome assembly, description=The specific version of the human sequence assembly used for annotation (NCBI or UCSC), comment=null, uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0063], code=at0063, itemType=CLUSTER, level=2, text=Genomic region, description=Details about the specific position of the alteration, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=2..*, cardinalityText=Minimum of 2 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0063]/items[at0057], code=at0057, itemType=ELEMENT, level=3, text=Start position, description=Number(s) referring to the nucleotide(s) affected, according to the HGVS notation., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0063]/items[at0014], code=at0014, itemType=ELEMENT, level=3, text=Contig, description=, 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[at0002]/items[at0012], code=at0012, itemType=CLUSTER, level=2, text=Gene, description=A DNA region that contributes to phenotype/function specifying the amino acid sequence of a protein., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=1..*, cardinalityText=ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0012]/items[at0015], code=at0015, itemType=ELEMENT, level=3, text=Gene symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name, 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[at0002]/items[at0012]/items[at0024], code=at0024, itemType=ELEMENT, level=3, text=Full name, description=The full gene name approved by the HGNC that convey the character or function of the gene., 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[at0026], code=at0026, itemType=CLUSTER, level=1, text=Variation description, description=, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=5..*, cardinalityText=Minimum of 5 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0045], code=at0045, itemType=CLUSTER, level=2, text=Variation identifier, description=A reference to a specific variation recorded into a biological variation database, 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0045]/items[at0110], code=at0110, itemType=ELEMENT, level=3, text=Source name, description=The name of the public data source that gives the variant identification, 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[at0026]/items[at0045]/items[at0046], code=at0046, itemType=ELEMENT, level=3, text=Identification, description=The ID of a variation record, 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[at0026]/items[at0045]/items[at0048], code=at0048, itemType=ELEMENT, level=3, text=Version, description=, 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[at0026]/items[at0045]/items[at0050], code=at0050, itemType=ELEMENT, level=3, 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[at0026]/items[at0072], code=at0072, itemType=CLUSTER, level=2, text=Alternate, description=A variant form of the same gene, 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0072]/items[at0060], code=at0060, itemType=ELEMENT, level=3, text=Variant type, description=The type of the observed variant, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • del [deletion]
  • dup [duplication]
  • ins [insertion]
  • inv [inversion]
  • sub [substitution]
  • indel [insertion/deletion]
  • rep [repeated sequence]
  • conv [conversion]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0072]/items[at0055], code=at0055, itemType=SLOT, level=3, text=Variant, description=The specific variation occurred, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.repeated_sequence_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.indel_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.duplication_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.insertion_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.deletion_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.conversion_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.substitution_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.inversion_variant.v[0-9.]+ and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0072]/items[at0086], code=at0086, itemType=ELEMENT, level=3, text=Allele depth, description=The number of reads that support the reported allele, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0071], code=at0071, itemType=ELEMENT, level=2, text=Quality, description=Phred-scaled quality score for the assertion made in the Observed nucleotide(s), comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0093], code=at0093, itemType=CLUSTER, level=2, text=Filtering, description=Section to describe the filters (if any) that has been applied to the data, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0093]/items[at0104], code=at0104, itemType=CLUSTER, level=3, text=Filter, description=Filter's details, 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0093]/items[at0104]/items[at0106], code=at0106, itemType=ELEMENT, level=4, text=ID, description=Identificative string, 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[at0026]/items[at0093]/items[at0104]/items[at0108], code=at0108, itemType=ELEMENT, level=4, text=Description, description=Description of how the filter works, 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[at0026]/items[at0093]/items[at0104]/items[at0097], code=at0097, itemType=ELEMENT, level=4, text=Filter passed, description=Wheter or not the position has passed the applied filter., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0087], code=at0087, itemType=ELEMENT, level=2, text=Total depth, description=Total number of reads, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0081], code=at0081, itemType=CLUSTER, level=2, text=Genotype characterization, description=Genotype information, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=3..*, cardinalityText=Minimum of 3 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0081]/items[at0082], code=at0082, itemType=ELEMENT, level=3, text=Genotype, description=Combination of the allele with regards to the specific gene of interests, encoded as allele separated values (0 for the reference allele, 1 for the first allternate, etc.), 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[at0026]/items[at0081]/items[at0084], code=at0084, itemType=ELEMENT, level=3, text=Genotype quality, description=Genotype quality, encoded as a phred quality, 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[at0026]/items[at0081]/items[at0085], code=at0085, itemType=ELEMENT, level=3, text=Genotype probability, description=, 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]], protocol=[], ism_transition=[], contacts=[], activities=[], context=[], other_participations=[], state=[], details=[], description=[], source=[]}, 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=2..*, cardinalityText=Minimum of 2 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0002], code=at0002, itemType=CLUSTER, level=1, text=Genomic location, description=The position in respect to a genomic or coding sequence, following the HGVS nomenclature., comment=null, uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=4..*, cardinalityText=Minimum of 4 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0008], code=at0008, itemType=SLOT, level=2, text=Reference sequence, description=A sequence file that is used as a reference to describe variants that are present in a analysed sequence, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.Reference_sequence.v[0-9.]+ and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0096], code=at0096, itemType=ELEMENT, level=2, text=Genome assembly, description=The specific version of the human sequence assembly used for annotation (NCBI or UCSC), comment=null, uncommonOntologyItems=null, occurencesFormal=1..*, occurencesText=Mandatory, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0063], code=at0063, itemType=CLUSTER, level=2, text=Genomic region, description=Details about the specific position of the alteration, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=2..*, cardinalityText=Minimum of 2 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0063]/items[at0057], code=at0057, itemType=ELEMENT, level=3, text=Start position, description=Number(s) referring to the nucleotide(s) affected, according to the HGVS notation., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0063]/items[at0014], code=at0014, itemType=ELEMENT, level=3, text=Contig, description=, 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[at0002]/items[at0012], code=at0012, itemType=CLUSTER, level=2, text=Gene, description=A DNA region that contributes to phenotype/function specifying the amino acid sequence of a protein., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=1..*, cardinalityText=ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0002]/items[at0012]/items[at0015], code=at0015, itemType=ELEMENT, level=3, text=Gene symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name, 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[at0002]/items[at0012]/items[at0024], code=at0024, itemType=ELEMENT, level=3, text=Full name, description=The full gene name approved by the HGNC that convey the character or function of the gene., 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[at0026], code=at0026, itemType=CLUSTER, level=1, text=Variation description, description=, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=5..*, cardinalityText=Minimum of 5 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0045], code=at0045, itemType=CLUSTER, level=2, text=Variation identifier, description=A reference to a specific variation recorded into a biological variation database, 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0045]/items[at0110], code=at0110, itemType=ELEMENT, level=3, text=Source name, description=The name of the public data source that gives the variant identification, 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[at0026]/items[at0045]/items[at0046], code=at0046, itemType=ELEMENT, level=3, text=Identification, description=The ID of a variation record, 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[at0026]/items[at0045]/items[at0048], code=at0048, itemType=ELEMENT, level=3, text=Version, description=, 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[at0026]/items[at0045]/items[at0050], code=at0050, itemType=ELEMENT, level=3, 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[at0026]/items[at0072], code=at0072, itemType=CLUSTER, level=2, text=Alternate, description=A variant form of the same gene, 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0072]/items[at0060], code=at0060, itemType=ELEMENT, level=3, text=Variant type, description=The type of the observed variant, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • del [deletion]
  • dup [duplication]
  • ins [insertion]
  • inv [inversion]
  • sub [substitution]
  • indel [insertion/deletion]
  • rep [repeated sequence]
  • conv [conversion]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0072]/items[at0055], code=at0055, itemType=SLOT, level=3, text=Variant, description=The specific variation occurred, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:
openEHR-EHR-CLUSTER.repeated_sequence_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.indel_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.duplication_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.insertion_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.deletion_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.conversion_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.substitution_variant.v[0-9.]+ and specialisations Or
openEHR-EHR-CLUSTER.inversion_variant.v[0-9.]+ and specialisations, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0072]/items[at0086], code=at0086, itemType=ELEMENT, level=3, text=Allele depth, description=The number of reads that support the reported allele, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0071], code=at0071, itemType=ELEMENT, level=2, text=Quality, description=Phred-scaled quality score for the assertion made in the Observed nucleotide(s), comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0093], code=at0093, itemType=CLUSTER, level=2, text=Filtering, description=Section to describe the filters (if any) that has been applied to the data, comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=1..*, cardinalityText=ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0093]/items[at0104], code=at0104, itemType=CLUSTER, level=3, text=Filter, description=Filter's details, 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=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0093]/items[at0104]/items[at0106], code=at0106, itemType=ELEMENT, level=4, text=ID, description=Identificative string, 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[at0026]/items[at0093]/items[at0104]/items[at0108], code=at0108, itemType=ELEMENT, level=4, text=Description, description=Description of how the filter works, 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[at0026]/items[at0093]/items[at0104]/items[at0097], code=at0097, itemType=ELEMENT, level=4, text=Filter passed, description=Wheter or not the position has passed the applied filter., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0087], code=at0087, itemType=ELEMENT, level=2, text=Total depth, description=Total number of reads, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=C_DV_QUANTITY, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0081], code=at0081, itemType=CLUSTER, level=2, text=Genotype characterization, description=Genotype information, comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=3..*, cardinalityText=Minimum of 3 items, ordered, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0026]/items[at0081]/items[at0082], code=at0082, itemType=ELEMENT, level=3, text=Genotype, description=Combination of the allele with regards to the specific gene of interests, encoded as allele separated values (0 for the reference allele, 1 for the first allternate, etc.), 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[at0026]/items[at0081]/items[at0084], code=at0084, itemType=ELEMENT, level=3, text=Genotype quality, description=Genotype quality, encoded as a phred quality, 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[at0026]/items[at0081]/items[at0085], code=at0085, itemType=ELEMENT, level=3, text=Genotype probability, description=, 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]], minIndents={}, termBindingRetrievalErrorMessage=null]