TEMPLATE Pharmacogenetic test result (Pharmacogenetic test result)

TEMPLATE IDPharmacogenetic test result
ConceptPharmacogenetic test result
DescriptionNot Specified
PurposeNot Specified
References
Authorsdate: 2023-04-21
Other Details Languagedate: 2023-04-21
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/., custodian_organisation=openEHR Foundation, PARENT:MD5-CAM-1.0.1=D02DE57ACD4A04C1ADAE1F8B28197890, original_language=ISO_639-1::en, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=ada44e6c5502ab3530af7a7d7cc1b205, sem_ver=4.0.0}
Language useden
Citeable Identifier1013.26.891
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=Pharmacogenetic 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=Point in time, 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=null, occurencesText=null, 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=Default value: Pharmacogenetics screening panel, 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.laboratory_test_analyte.v1], code=at0000, itemType=CLUSTER, level=4, text=Laboratory analyte result, description=The result of a laboratory test for a single analyte value., 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.laboratory_test_analyte.v1]/items[at0024], code=at0024, itemType=ELEMENT, level=5, text=Analyte name, description=The name of the analyte result., comment=The value for this element is normally supplied in a specialisation, in a template or at run-time to reflect the actual analyte. For example: 'Serum sodium', 'Haemoglobin'. Coding with an external terminology is strongly recommended, such as LOINC, NPU, SNOMED CT, or local lab terminologies., uncommonOntologyItems={fhir_mapping=Observation.code, hl7v2_mapping=OBX.3}, 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0], code=at0000, itemType=CLUSTER, level=5, text=Pharmacogenetic analyte result, description=Details of the result of pharmacogenetic testing against a single gene, including the detected genotype, pharmacognetic phenotype, activity score to support prescribing decision support., 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0003], code=at0003, itemType=ELEMENT, level=6, text=Gene name, description=A term which identifies the gene concerned., comment=Preferably this should be coded with terms from the HGNC nomenclature (HUGO Gene Nomenclature Committee). For example: 'http://www.genenames.org::CYP2C9 | CYP2C9 |' See https://terminology.hl7.org/CodeSystem-v3-hgnc.json.html Note that CPIC currently recommends the use of LOINC-based "Phenotypic interpretation" terms and not the Gene names, e.g. "TPMT Gene Product Metabolic Activity Interpretation"., 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0004], code=at0004, itemType=ELEMENT, level=6, text=Diplotype, description=A textual representation of the diplotype, normally as string of characters, either as as gene change descriptors or star allele diplotypes., comment=For example: 'g.94938683A>G' (Gene changes) '*1/*36' (Star allele diplotype)., 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0052], code=at0052, itemType=ELEMENT, level=6, text=Phenotype, description=The estimated pharmacological impact of the identified genotype., comment=The internal terms are based on CPIC phenotype recommendations - see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/ . For example: 'local::at0057 | Poor metaboliser |' These terms are bound to SNOMED CT and LOINC equivalents. The list is left open as other terms may be required., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CHOICE, bindings=null, values=
  •  Coded Text
    • Normal metaboliser 
    • Rapid metaboliser 
    • Ultrarapid metaboliser 
    • Intermediate metaboliser 
    • Poor metaboliser 
    • Increased function 
    • Decreased function 
    • Normal function 
    • Poor function 
    • Negative 
    • Positive 
    • Normal risk of aminoglycoside-induced hearing loss 
    • Increased risk of aminoglycoside-induced hearing loss 
    • Uncertain risk of aminoglycoside-induced hearing loss 
  •  Text
, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0080], code=at0080, itemType=ELEMENT, level=6, text=Overall activity score, description=An associated derived activity score, based on known association with specific genotypes and individual allele activity values, which is required to assess metaboliser status for some phenotypes., comment=null, uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=>=0 , extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0084], code=at0084, itemType=CLUSTER, level=6, text=Individual activity value, description=A list of enzyme activity values each associated with a specific allele, which are used to derive the Overall activity score., 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0084]/items[at0086], code=at0086, itemType=ELEMENT, level=7, text=Allele, description=The allele descriptor associated with the activity value., comment=For example: '*36'., 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0084]/items[at0085], code=at0085, itemType=ELEMENT, level=7, text=Activity value, description=An associated derived activity score, based on known association with specific genotypes, which is required to assess metaboliser status for some phenotypes., comment=For example: '0.5'., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_QUANTITY, bindings=null, values=>=0 , extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0075], code=at0075, itemType=CLUSTER, level=6, text=Per-allele tested, description=A list of the specific alleles tested by this pharmacogenetic test, as the specific alleles may vary between tests., 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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0075]/items[at0078], code=at0078, itemType=ELEMENT, level=7, text=SNP rsNumber, description=The rsNumber (rs ID) of the allele tested, based on the the dbSNP identifier using terminology ID 'http://terminology.hl7.org/NamingSystem/v3-dbSNP'., comment=For example: 'http://terminology.hl7.org/NamingSystem/v3-dbSNP::rs3918290 | rs3918290 |'., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_CODED_TEXT, bindings=null, values=Value set: external, extendedValues=null], ResourceSimplifiedHierarchyItem [path=[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]/data[at0001]/events[at0002]/data[at0003]/items[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0075]/items[at0083], code=at0083, itemType=ELEMENT, level=7, text=Reference allele, description=A text descriptor of the expected reference content of the tested allele., comment=For example: 'A/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.laboratory_test_analyte.v1]/items[openEHR-EHR-CLUSTER.pharmacogenetic_analyte_result.v0]/items[at0075]/items[at0082], code=at0082, itemType=ELEMENT, level=7, text=Detected allele, description=A text descriptor of the detected content of the tested allele., comment=For example: 'A/G'., 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[at0057], code=at0057, itemType=ELEMENT, level=4, text=Overall recommendation, 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]/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[openEHR-EHR-CLUSTER.device.v1], code=at0000, itemType=CLUSTER, level=2, text=Medical device, description=An instrument, apparatus, implant, material or similar, used in the provision of healthcare. In this context, a medical device includes a broad range of devices which act through a variety of physical, mechanical, thermal or similar means but specifically excludes devices which act through medicinal means such as pharmacological, metabolic or immunological methods. The scope is inclusive of disposable devices as well as durable or persisting devices that require tracking, maintenance activities or regular calibration, recognising that each type of device has specific data recording requirements., 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]/protocol[at0004]/items[openEHR-EHR-CLUSTER.device.v1]/items[at0001], code=at0001, itemType=ELEMENT, level=3, text=Device name, description=Identification of the medical device, preferably by a common name, a formal fully descriptive name or, if required, by class or category of device., comment=This data element will capture the term, phrase or category used in clinical practice. For example: <brand name><machine> (XYZ Audiometer); <size> <brand name> <intravenous catheter> (14G Jelco IV catheter); or <brand name/type> <implant>. Coding with a terminology is desirable, where possible, although this may be local and depending on local supplies available., 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]/protocol[at0004]/items[openEHR-EHR-CLUSTER.device.v1]/items[at0003], code=at0003, itemType=ELEMENT, level=3, text=Type, description=The category or kind of device., comment=Not applicable if a category is already recorded in 'Device name'. Example: if the 'Device' is named as a 'urinary catheter'; the 'Type' may be recorded as 'indwelling' or 'condom'.Coding with a terminology is desirable, where possible. This may include use of GTIN or EAN numbers., uncommonOntologyItems=null, occurencesFormal=null, occurencesText=null, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null]], templateType=normal]