TEMPLATE Genomics example template (71194c4f-28ad-44fd-834a-484a3eed2507)

TEMPLATE ID71194c4f-28ad-44fd-834a-484a3eed2507
ConceptGenomics example template
DescriptionExample of how the genomics archetypes are intended to be used together and within the OBSERVATION.laboratory_test_result archetype.
UseOnly for example use.
PurposeExample of how the genomics archetypes are intended to be used together and within the OBSERVATION.laboratory_test_result archetype.
References
Authorsdate: 2019-04-25; name: Silje Ljosland Bakke; organisation: Nasjonal IKT HF; email: silje.ljosland.bakke@nasjonalikt.no
Other Details Languagedate: 2019-04-25; name: Silje Ljosland Bakke; organisation: Nasjonal IKT HF; email: silje.ljosland.bakke@nasjonalikt.no
OtherDetails Language Independent{licence=licence, custodian_organisation=custodian_organisation, PARENT:MD5-CAM-1.0.1=PARENT:MD5-CAM-1.0.1, original_namespace=original_namespace, original_publisher=original_publisher, custodian_namespace=custodian_namespace, MD5-CAM-1.0.1=MD5-CAM-1.0.1}
Language useden
Citeable Identifier1013.26.223
AllOperationalTemplate [rootArchetypeId=openEHR-EHR-OBSERVATION.laboratory_test_result.v1, otherContributors=null, tshis=[ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1], code=at0000, itemType=OBSERVATION, level=0, text=Laboratory test result, description=The result, including findings and the laboratory's interpretation, of an investigation performed on specimens collected from an individual or related to that individual., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=OBSERVATION, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001], code=at0001, itemType=UNSUPPORTEDTOPLEVELATTRIBUTE, level=1, text=Data, description=, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=UNSUPPORTEDTOPLEVELATTRIBUTE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002], code=at0002, itemType=EVENT, level=2, text=Any event, description=Default, unspecified point in time or interval event which may be explicitly defined in a template or at run-time., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=EVENT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003], code=at0003, itemType=UNSUPPORTEDTOPLEVELATTRIBUTE, level=3, text=Data, description=, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=UNSUPPORTEDTOPLEVELATTRIBUTE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0005], code=at0005, itemType=ELEMENT, level=4, text=Test name, description=Name of the laboratory investigation performed on the specimen(s)., comment=A test result may be for a single analyte, or a group of items, including panel tests. It is strongly recommended that 'Test name' be coded with a terminology, for example LOINC or SNOMED CT. For example: 'Glucose', 'Urea and Electrolytes', 'Swab', 'Cortisol (am)', 'Potassium in perspiration' or 'Melanoma histopathology'. The name may sometimes include specimen type and patient state, for example 'Fasting blood glucose' or include other information, as 'Potassium (PNA blood gas)'., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0073], code=at0073, itemType=ELEMENT, level=4, text=Overall test status, description=The status of the laboratory test result as a whole., comment=The values have been specifically chosen to match those in the HL7 FHIR Diagnostic report, historically derived from HL7v2 practice. Other local codes/terms can be used via the Text 'choice'. This element is multiple occurrence to cater for the use cases where statuses for different aspects of the result have been split into several elements., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Coded Text
    • Registered  [The existence of the test is registered in the Laboratory Information System, but there is nothing yet available.]
    • Partial  [This is a partial (e.g. initial, interim or preliminary) Test Result: data in the Test Result may be incomplete or unverified.]
    • Preliminary  [Verified early results are available, but not all results are final. This is a sub-category of 'Partial'.]
    • Final  [The Test result is complete and verified by an authorised person.]
    • Amended  [The result has been modified subsequent to being Final, and is complete and verified by the responsible pathologist, and result data has been changed.]
    • Corrected  [The result has been modified subsequent to being Final, and is complete and verified by the responsible pathologist. This is a sub-category of 'Amended'.]
    • Appended  [Subsequent to being final, the report has been modified by adding new content. The existing content is unchanged. This is a sub-category of 'Amended'.]
    • Cancelled  [The result is unavailable because the test was not started or not completed (also sometimes called 'aborted').]
    • Entered in error  [The Test Result has been withdrawn following previous Final release.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0075], code=at0075, itemType=ELEMENT, level=4, text=Overall test status timestamp, description=The date and/or time that ‘Overall test status’ was issued., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_DATE_TIME, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0077], code=at0077, itemType=ELEMENT, level=4, text=Diagnostic service category, description=The diagnostic service or discipline that is responsible for the laboratory test result., comment=This is intended to be a general categorisation and not to capture the organisational name of the laboratory. For example: anatomical pathology, immunology and transfusion medicine, medical microbiology, clinical pharmacology, medical genetics, medical biochemistry. Alternatively more granular sub categories or sub disciplines, such as endocrinology, haematology, and allergology services, may be used. This may assist clinicians in filtering between categories of results. Coding with a terminology is desirable, where possible., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0100], code=at0100, itemType=ELEMENT, level=4, text=Clinical information provided, description=Description of clinical information available at the time of interpretation of results., comment=This data element may include a link to the original clinical information provided in the test request., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0], code=at0000, itemType=CLUSTER, level=4, text=Genetic variant, description=Result of a genetic test for a single variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0070], code=at0070, itemType=ELEMENT, level=5, text=Tissue specimen identifier, description=Identifier for the specimen used for the genetic test., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_IDENTIFIER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.knowledge_base.v0], code=at0000, itemType=CLUSTER, level=5, text=Knowledge base, description=A reference to a software component or a knowledge base (e.g., a pipeline history, a database entry, an analysis tool, etc.)., comment=Software? Knowledge base (pipeline history, DB, analysis tool), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Namespace, description=The name of the software/DB/analysis tool., comment=Es. 1 Galaxy/Snakemake Es. 2 CADD Es. 3 dbSNP, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=6, text=Version, description=Resource version., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=URL, description=A unique link to the resource., comment=Es.1 Link to the History ID Es.2 -- Es.3 Link to the specific entry of the DB (e.g., rs139581412), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.reference_sequence.v0], code=at0018, itemType=CLUSTER, level=5, text=Reference sequence, description=A sequence file that is used as a reference to describe variants that are present in an analysed sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0019], code=at0019, itemType=ELEMENT, level=6, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0020], code=at0020, itemType=ELEMENT, level=6, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0021], code=at0021, itemType=ELEMENT, level=6, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0022], code=at0022, itemType=ELEMENT, level=6, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0023], code=at0023, itemType=ELEMENT, level=6, text=Chromosome label, description=Chromosome identifier., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Coded Text
    • Chromosome 1  [Chromosome 1.]
    • Chromosome 2  [Chromosome 2.]
    • Chromosome 3  [Chromosome 3.]
    • Chromosome 4  [Chromosome 4.]
    • Chromosome 5  [Chromosome 5.]
    • Chromosome 6  [Chromosome 6.]
    • Chromosome 7  [Chromosome 7.]
    • Chromosome 8  [Chromosome 8.]
    • Chromosome 9  [Chromosome 9.]
    • Chromosome 10  [Chromosome 10.]
    • Chromosome 11  [Chromosome 11.]
    • Chromosome 12  [Chromosome 12.]
    • Chromosome 13  [Chromosome 13.]
    • Chromosome 14  [Chromosome 14.]
    • Chromosome 15  [Chromosome 15.]
    • Chromosome 16  [Chromosome 16.]
    • Chromosome 17  [Chromosome 17.]
    • Chromosome 18  [Chromosome 18.]
    • Chromosome 19  [Chromosome 19.]
    • Chromosome 20  [Chromosome 20.]
    • Chromosome 21  [Chromosome 21.]
    • Chromosome 22  [Chromosome 22.]
    • Chromosome X  [Chromosome X.]
    • Chromosome Y  [Chromosome Y.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0003], code=at0003, itemType=CLUSTER, level=5, text=Variant identifier, description=A reference to a specific variation recorded into a biological variation database., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0003]/items[at0004], code=at0004, itemType=ELEMENT, level=6, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0003]/items[at0005], code=at0005, itemType=ELEMENT, level=6, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0003]/items[at0006], code=at0006, itemType=ELEMENT, level=6, text=Version, description=The version of the record., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0003]/items[at0007], code=at0007, itemType=ELEMENT, level=6, text=URL, description=A reference to a specific variation recorded into a biological variation database., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.conversion_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Conversion variant, description=A sequence change where, compared to a reference sequence, a range of nucleotides are replaced by a sequence from elsewhere in the genome., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.conversion_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=Start converted position, description=The position of the first nucleotide of the converted range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.conversion_variant.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=6, text=End converted position, description=The position of the last nucleotide of the converted range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.conversion_variant.v0]/items[at0009], code=at0009, itemType=ELEMENT, level=6, text=Replacing sequence start position, description=The position of the first nucleotide of the replacing sequence., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.conversion_variant.v0]/items[at0010], code=at0010, itemType=ELEMENT, level=6, text=Replacing sequence end position, description=The position of the last nucleotide of the replacing sequence., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.copy_number_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Copy number variant, description=Describes a Copy number variant, where any part of a genome was deleted or duplicated (gain or loss of an allele)., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.copy_number_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=Start position on the given reference sequence., comment=Number should not be treated as an absolute more as an estimation., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.copy_number_variant.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=6, text=End position, description=End position on the given reference sequence., comment=Number should not be treated as an absolute more as an estimation., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.copy_number_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=Total copy number, description=Number of appearance of the allele., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.copy_number_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=Copy number change type, description=Any copy number variant results in a gain or loss of the region e.g. a loss could result that a hetergozygous locus becomes homozygous since one gene was deleted., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • Gain  [Copy number gain.]
  • Loss  [Copy number loss.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.deletion_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Deletion variant, description=A sequence change where, compared to a reference sequence, one or more nucleotides are not present (deleted)., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.deletion_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=Position of the deleted nucleotide or the first nucleotide of the deleted range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.deletion_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=End position, description=Position of the last nucleotide of the deleted range., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.deletion_variant.v0]/items[at0008], code=at0008, itemType=ELEMENT, level=6, text=Deleted nucleotide(s), description=The deleted nucleotide or the sequence deleted., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.duplication_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Duplication variant, description=A sequence change where, compared to a reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.duplication_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=Position of the duplicated nucleotide or the first nucleotide of the duplicated range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.duplication_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=End position, description=Position of the last nucleotide of the duplicated range., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.duplication_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=Duplicated nucletide(s), description=The nucleotide or the sequence duplicated., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.indel_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Indel variant, description=A sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.indel_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=Position of the deleted nucleotide or the first nucleotide of the deleted range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.indel_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=End position, description=Position of the last nucleotide of the deleted range., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.indel_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=Deleted nucleotide(s), description=The deleted nucleotide or sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.indel_variant.v0]/items[at0007], code=at0007, itemType=ELEMENT, level=6, text=Inserted nucleotide(s), description=The sequence inserted., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.insertion_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Insertion variant, description=A sequence change where, compared to the reference sequence, one or more nucleotides are inserted and where the insertion is not a copy of a sequence immediately 5'., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.insertion_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=The position of the first of the two flanking nucleotides., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.insertion_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=End position, description=The position of the last of the two flanking nucleotides., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.insertion_variant.v0]/items[at0006], code=at0006, itemType=ELEMENT, level=6, text=Inserted nucleotide(s), description=The sequence inserted between the two flanking nucleotides., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.inversion_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Inversion variant, description=A sequence change where, compared to a reference sequence, more than one nucleotide replacing the original sequence are the reverse complement of the original sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.inversion_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=Position of the first nucleotide of the inverted range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.inversion_variant.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=6, text=End position, description=Position of the last nucleotide of the inverted range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.inversion_variant.v0]/items[at0006], code=at0006, itemType=ELEMENT, level=6, text=Inverted sequence, description=The nucleotide sequence of the reference sequence at th given positions., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.repeated_sequence_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Repeated sequence variant, description=A sequence where, compared to a reference sequence, a segment of one or more nucleotides (the repeat unit) is present several times, one after the other., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.repeated_sequence_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Start position, description=Position of the first nucleotide of the repeated range., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.repeated_sequence_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=End position, description=Position of the last nucleotide of the repeated range., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.repeated_sequence_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=Repeated sequence, description=The sequence of nucleotides that has been repeated., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.repeated_sequence_variant.v0]/items[at0007], code=at0007, itemType=ELEMENT, level=6, text=Copy number, description=Number of repeat units., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.substitution_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Substitution variant, description=A sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.substitution_variant.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=6, text=Position substituted, description=The position of the sustituted nucleotide., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.substitution_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=Reference nucleotide, description=The nucleotide at reference position., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.substitution_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=New nucleotide, description=Substituted nucleotide., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.translocation_variant.v0], code=at0000, itemType=CLUSTER, level=5, text=Translocation variant, description=Translocation variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.translocation_variant.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=Breakpoint position 1, description=Position of first breakpoint relative to start of "Chromosome 1"., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.translocation_variant.v0]/items[at0005], code=at0005, itemType=ELEMENT, level=6, text=Strand 1, description=A value of "+" indicates that the chromosomal segment at the second breakpoint is connected to the chromosomal segment at the first breakpoint right of "Breakpoint position 1". A value of "-" indicates that the chromosomal segment at the second breakpoint is connected to the chromosomal segment of the first breakpoint left of "Breakpoint position 1"., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.translocation_variant.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=6, text=Breakpoint position 2, description=Position of second breakpoint relative to start of "Chromosome 2"., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.translocation_variant.v0]/items[at0006], code=at0006, itemType=ELEMENT, level=6, text=Strand 2, description=A value of "+" indicates that the chromosomal segment at the first breakpoint is connected to the chromosomal segment at the second breakpoint right of "Breakpoint position 2". A value of "-" indicates that the chromosomal segment at the first breakpoint is connected to the chromosomal segment of the second breakpoint left of "Breakpoint position 2"., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[openEHR-EHR-CLUSTER.translocation_variant.v0]/items[at0009], code=at0009, itemType=ELEMENT, level=6, text=HGVS term, description=The description of the variant using the recommendations of the accepted HGVS nomeclature named extension ISCN., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008], code=at0008, itemType=CLUSTER, level=5, text=Transcript, description=Structured details about the transcript which is potentially affected by the variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[openEHR-EHR-CLUSTER.reference_sequence.v0], code=at0018, itemType=CLUSTER, level=6, text=Reference sequence, description=A sequence file that is used as a reference to describe variants that are present in an analysed sequence., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0019], code=at0019, itemType=ELEMENT, level=7, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0020], code=at0020, itemType=ELEMENT, level=7, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0021], code=at0021, itemType=ELEMENT, level=7, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0022], code=at0022, itemType=ELEMENT, level=7, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[openEHR-EHR-CLUSTER.reference_sequence.v0]/items[at0023], code=at0023, itemType=ELEMENT, level=7, text=Chromosome label, description=Chromosome identifier., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Coded Text
    • Chromosome 1  [Chromosome 1.]
    • Chromosome 2  [Chromosome 2.]
    • Chromosome 3  [Chromosome 3.]
    • Chromosome 4  [Chromosome 4.]
    • Chromosome 5  [Chromosome 5.]
    • Chromosome 6  [Chromosome 6.]
    • Chromosome 7  [Chromosome 7.]
    • Chromosome 8  [Chromosome 8.]
    • Chromosome 9  [Chromosome 9.]
    • Chromosome 10  [Chromosome 10.]
    • Chromosome 11  [Chromosome 11.]
    • Chromosome 12  [Chromosome 12.]
    • Chromosome 13  [Chromosome 13.]
    • Chromosome 14  [Chromosome 14.]
    • Chromosome 15  [Chromosome 15.]
    • Chromosome 16  [Chromosome 16.]
    • Chromosome 17  [Chromosome 17.]
    • Chromosome 18  [Chromosome 18.]
    • Chromosome 19  [Chromosome 19.]
    • Chromosome 20  [Chromosome 20.]
    • Chromosome 21  [Chromosome 21.]
    • Chromosome 22  [Chromosome 22.]
    • Chromosome X  [Chromosome X.]
    • Chromosome Y  [Chromosome Y.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0010], code=at0010, itemType=ELEMENT, level=6, text=DNARegionName, description=A human readable name for the region of interest. Typically Exon #, Intron # or other., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0011], code=at0011, itemType=ELEMENT, level=6, text=DNA change, description=Description of the variation at the DNA-level following the HGVS nomenclature., comment=For example: "c.5249C>T" NC_000023.10:g.33038255C>A, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0012], code=at0012, itemType=ELEMENT, level=6, text=Amino Acid Change, description=Description of the variation at the protein-level following the HGVS nomenclature., comment=For example "p.T1750M", uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0013], code=at0013, itemType=ELEMENT, level=6, text=Amino Acid Change Type, description=Codified type for associated Amino Acid Marker., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Coded Text
    • Wild Type  [Wild Type.]
    • Deletion  [A deletion in the amino acid sequence.]
    • Duplication  [A duplication in the amino acid sequence.]
    • Frameshift  [A frameshift in the amino acid sequence.]
    • Initiating Methionine  [Initiating Methionine.]
    • Insertion  [A insertion in the amino acid sequence.]
    • Insertion and Deletion  [An insertion/deletion in the amino acid sequence.]
    • Missense  [Missense.]
    • Nonsense  [Nonsense.]
    • Silent  [Silent.]
    • Stop Codon Mutation  [Stop Codon Mutation.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015], code=at0015, itemType=CLUSTER, level=6, text=Predicted impact, description=Estimate of the effects that each variant may have on the transcript., comment=Calculation is based on a precise data source and only done by software., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015]/items[openEHR-EHR-CLUSTER.knowledge_base.v0], code=at0000, itemType=CLUSTER, level=7, text=Knowledge base, description=A reference to a software component or a knowledge base (e.g., a pipeline history, a database entry, an analysis tool, etc.)., comment=Software? Knowledge base (pipeline history, DB, analysis tool), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=8, text=Namespace, description=The name of the software/DB/analysis tool., comment=Es. 1 Galaxy/Snakemake Es. 2 CADD Es. 3 dbSNP, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=8, text=Version, description=Resource version., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=8, text=URL, description=A unique link to the resource., comment=Es.1 Link to the History ID Es.2 -- Es.3 Link to the specific entry of the DB (e.g., rs139581412), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015]/items[at0017], code=at0017, itemType=ELEMENT, level=7, text=Score, description=The calculated value., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=Units: 1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0015]/items[at0018], code=at0018, itemType=ELEMENT, level=7, text=Qualitative prediction, description=Human readable version of the predicted impact., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052], code=at0052, itemType=CLUSTER, level=6, text=Reported impact, description=Intepretation of the Mutation linked to a specific paper (e.g. activation, deactivating, dysfunction…)., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052]/items[openEHR-EHR-CLUSTER.citation.v0], code=at0000, itemType=CLUSTER, level=7, text=Citation, description=Reference to information held elsewhere, in the same EHR or external to the EHR., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052]/items[openEHR-EHR-CLUSTER.citation.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=8, text=Description, description=Description about the citation., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052]/items[openEHR-EHR-CLUSTER.citation.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=8, text=Citation, description=Representation of the citation., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Parsable
  •  Multimedia
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052]/items[openEHR-EHR-CLUSTER.citation.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=8, text=URI to original data, description=Link to the original data., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052]/items[openEHR-EHR-CLUSTER.citation.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=8, text=Comment, description=Comment about the citation., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0052]/items[at0054], code=at0054, itemType=ELEMENT, level=7, text=Impact, description=Interpretative data about the specific variant., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0019], code=at0019, itemType=CLUSTER, level=6, text=Gene, description=Structured details about the gene harboring the variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0019]/items[at0020], code=at0020, itemType=ELEMENT, level=7, text=Gene symbol, description=The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name., comment=For example "CHD5"., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0019]/items[at0021], code=at0021, itemType=ELEMENT, level=7, text=Full name, description=The full gene name approved by the HGNC that convey the character or function of the gene., comment=For example "Chromodomain helicase DNA binding protein 5"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0019]/items[at0056], code=at0056, itemType=ELEMENT, level=7, text=Copy number overlap, description=The fraction of gene region covered by copy number., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_PROPORTION, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0019]/items[at0057], code=at0057, itemType=ELEMENT, level=7, text=Part of fusion, description=States if the Gene is part of a Fusion Gene and if it is the first or second part of the Fusion Gene., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • First  [First part of a Fusion Gene.]
  • Second  [Second part of a Fusion Gene.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0058], code=at0058, itemType=ELEMENT, level=6, text=ACMG classification, description=Single DNA marker or individual allele interpretation in the context of the assessed genetic disease according to the ACMG recommendations., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • Pathogenic  [Pathogenic variant.]
  • Likely pathogenic  [Likely pathogenic variant.]
  • Uncertain significance  [Variant of uncertain significance.]
  • Likely benign  [Likely benign variant.]
  • Benign  [Benign variant.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0008]/items[at0059], code=at0059, itemType=ELEMENT, level=6, text=Fusion exon, description=The number of the exon which is either the end or the beginning of the fusion., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0023], code=at0023, itemType=ELEMENT, level=5, text=Best transcript candidate, description=The ID of the transcript with the highest predicted impact., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0024], code=at0024, itemType=CLUSTER, level=5, text=Conservation, description=Structured details about the evolutionary conservation., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0024]/items[openEHR-EHR-CLUSTER.knowledge_base.v0], code=at0000, itemType=CLUSTER, level=6, text=Knowledge base, description=A reference to a software component or a knowledge base (e.g., a pipeline history, a database entry, an analysis tool, etc.)., comment=Software? Knowledge base (pipeline history, DB, analysis tool), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0024]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=7, text=Namespace, description=The name of the software/DB/analysis tool., comment=Es. 1 Galaxy/Snakemake Es. 2 CADD Es. 3 dbSNP, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0024]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=7, text=Version, description=Resource version., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0024]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=7, text=URL, description=A unique link to the resource., comment=Es.1 Link to the History ID Es.2 -- Es.3 Link to the specific entry of the DB (e.g., rs139581412), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0024]/items[at0026], code=at0026, itemType=ELEMENT, level=6, text=Score, description=The conservation score., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=Units: 1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0060], code=at0060, itemType=ELEMENT, level=5, text=Read depth, description=Total number of reads mapped at this specific location., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0028], code=at0028, itemType=ELEMENT, level=5, text=Allele depth, description=The number of reads that support the reported variant., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0047], code=at0047, itemType=ELEMENT, level=5, text=Allele frequency, description=The relative frequency of an allele at a particular locus, expressed as a number from 0 to 1., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=0..1 1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0029], code=at0029, itemType=CLUSTER, level=5, text=Population allele frequency details, description=The relative frequency of a particular allele in the population, expressed as a number from 0 to 1., comment=null, uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0029]/items[openEHR-EHR-CLUSTER.knowledge_base.v0], code=at0000, itemType=CLUSTER, level=6, text=Knowledge base, description=A reference to a software component or a knowledge base (e.g., a pipeline history, a database entry, an analysis tool, etc.)., comment=Software? Knowledge base (pipeline history, DB, analysis tool), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0029]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0001], code=at0001, itemType=ELEMENT, level=7, text=Namespace, description=The name of the software/DB/analysis tool., comment=Es. 1 Galaxy/Snakemake Es. 2 CADD Es. 3 dbSNP, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0029]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0002], code=at0002, itemType=ELEMENT, level=7, text=Version, description=Resource version., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0029]/items[openEHR-EHR-CLUSTER.knowledge_base.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=7, text=URL, description=A unique link to the resource., comment=Es.1 Link to the History ID Es.2 -- Es.3 Link to the specific entry of the DB (e.g., rs139581412), uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_URI, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0029]/items[at0031], code=at0031, itemType=ELEMENT, level=6, text=Population allele frequency, description=The population allele frequency., comment=null, uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=0..1 1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0061], code=at0061, itemType=CLUSTER, level=5, text=VCF Quality Filter, description=Structured details about the quality filters that have been applied to the data., comment=This field is derived from the FILTER column of VCF., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0061]/items[at0062], code=at0062, itemType=ELEMENT, level=6, text=Filter name, description=Name of the quality filter., comment=For example "q10"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0061]/items[at0063], code=at0063, itemType=ELEMENT, level=6, text=Description, description=Quality filter extended description., comment=For example "at this site the quality is below 10"., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0061]/items[at0064], code=at0064, itemType=ELEMENT, level=6, text=Filter passed, description=Whether the variant passed the quality 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0067], code=at0067, itemType=ELEMENT, level=5, text=Strand bias ratio, description=The ratio of the strand bias., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=Units: 1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0068], code=at0068, itemType=ELEMENT, level=5, text=Strand bias p-value, description=The Phred-scaled p-value of the strand bias., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=Units: 1, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0039], code=at0039, itemType=ELEMENT, level=5, text=Genotype, description=Genotype encoded as allele values separated by either of / or | (0 for the reference allele, 1 for the first alternate, 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0040], code=at0040, itemType=ELEMENT, level=5, text=Allelic State, description=The level of occurrence of a single DNA Marker within a set of chromosomes., comment=This is the human readable version of genotype, e.g.: Heterozygous, Homozygous., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Coded Text
    • Heteroplasmic  [Heteroplasmic.]
    • Homoplasmic  [Homoplasmic.]
    • Homozygous  [Homozygous.]
    • Heterozygous  [Heterozygous.]
    • Hemizygous  [Hemizygous.]
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0041], code=at0041, itemType=ELEMENT, level=5, text=Genotype quality, description=Conditional genotype quality, encoded as a phred quality., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0069], code=at0069, itemType=ELEMENT, level=5, text=Genotype probability, description=A comma separated list of the log10-scaled genotype likelihoods for all possible genotypes, given the reference and the alternate alleles., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.genetic_variant.v0]/items[at0050], code=at0050, itemType=ELEMENT, level=5, text=Genetic Variant Assessment, description=Assessment of the presence or absence of a specific DNA variants., comment='No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presence or absence. This may be due to test failure or specimen specific context which renders the test ineffective., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=
  • Present  [The target variant is present.]
  • Absent  [The target variant is absent.]
  • No call  [No data are available to confirm the presence/absence of the variant.]
  • Indeterminate  [The result is indeterminate.]
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0057], code=at0057, itemType=ELEMENT, level=4, text=Conclusion, description=Narrative description of the key findings., comment=For example: 'Pattern suggests significant renal impairment'. The content of the conclusion will vary, depending on the investigation performed. This conclusion should be aligned with the coded 'Test diagnosis'., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0098], code=at0098, itemType=ELEMENT, level=4, text=Test diagnosis, description=Single word, phrase or brief description that represents the clinical meaning and significance of the laboratory test result., comment=For example: 'Severe hepatic impairment', 'Salmonella contamination'. Coding of the diagnosis with a terminology is strongly recommended, where possible. This diagnosis should be aligned with the narrative in the 'Conclusion'., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[at0101], code=at0101, itemType=ELEMENT, level=4, text=Comment, description=Additional narrative about the test result not captured in other fields., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/state[at0112], code=at0112, itemType=UNSUPPORTEDTOPLEVELATTRIBUTE, level=3, text=State, description=, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=UNSUPPORTEDTOPLEVELATTRIBUTE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/state[at0112]/items[at0113], code=at0113, itemType=ELEMENT, level=4, text=Confounding factors, description=Issues or circumstances that impact on the accurate interpretation of the measurement or test result., comment='Confounding factors' should be reserved for uncontrolled/unplanned issues of patient state/physiology that might affect interpretation, for example 'recent exercise' or 'recent tobacco smoking'. Known or required preconditions, such as 'fasting' should be carried in the 'Sampling conditions' element within the CLUSTER.specimen archetype . In some cases preconditions are captured as part of the test name, for example 'Fasting blood glucose'. Known issues with specimen collection or handling, such as 'prolonged use of tourniquet' or 'sample haemolysed', should be carried in the 'Specimen quality' elements within CLUSTER.specimen archetype. Coding with a terminology is desirable, where possible., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004], code=at0004, itemType=UNSUPPORTEDTOPLEVELATTRIBUTE, level=1, text=Protocol, description=, comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=UNSUPPORTEDTOPLEVELATTRIBUTE, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0068], code=at0068, itemType=ELEMENT, level=2, text=Laboratory internal identifier, description=A local identifier assigned by the receiving Laboratory Information System (LIS) to track the test process., comment=This identifier is an internal tracking number assigned by the LIS, and it not intended to be the name of the test., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Identifier
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0094], code=at0094, itemType=CLUSTER, level=2, text=Test request details, description=Details about the test request., comment=In most situations there is one test request and a single corresponding test result, however this repeating cluster allows for the situation where there may be multiple test requests reported using a single test result. As an example: 'a clinician asks for blood glucose in one request and Urea/electrolytes in a second request, but the lab analyser does both and the lab wishes to report these together'., uncommonOntologyItems=null, occurencesFormal=0..*, occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0094]/items[at0106], code=at0106, itemType=ELEMENT, level=3, text=Original test requested name, description=Name of the original laboratory test requested., comment=This data element is to be used when the test requested differs from the test actually performed by the laboratory., 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=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0094]/items[at0062], code=at0062, itemType=ELEMENT, level=3, text=Requester order identifier, description=The local identifier assigned by the requesting clinical system., comment=Equivalent to the HL7 Placer Order Identifier., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Identifier
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0094]/items[at0063], code=at0063, itemType=ELEMENT, level=3, text=Receiver order identifier, description=The local identifier assigned to the test order by the order filler, usually by the Laboratory Information System (LIS)., comment=Assigning an identifier to a request by the Laboratory lnformation System (LIS) enables tracking progress of the request and enables linking results to requests. It also provides a reference to assist with enquiries and it is usually equivalent to the HL7 Filler Order Identifier., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Identifier
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0111], code=at0111, itemType=ELEMENT, level=2, text=Point-of-care test, description=This indicates whether the test was performed directly at Point-of-Care (POCT) as opposed to a formal result from a laboratory or other service delivery organisation., comment=True if the test was performed directly at Point-of-Care (POCT)., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_BOOLEAN, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/protocol[at0004]/items[at0121], code=at0121, itemType=ELEMENT, level=2, text=Test method, description=Description about the method used to perform the test., comment=Coding with a terminology is desirable, where possible., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=ANY, bindings=null, values=, extendedValues=null]], templateType=normal]