diff --git a/CodeSystem/CodeSystem-Genomics-mds-questiontag.json b/CodeSystem/CodeSystem-Genomics-mds-questiontag.json index 5cfb140..d1bf919 100644 --- a/CodeSystem/CodeSystem-Genomics-mds-questiontag.json +++ b/CodeSystem/CodeSystem-Genomics-mds-questiontag.json @@ -2,11 +2,11 @@ "resourceType": "CodeSystem", "id": "mds-questiontag-genomics", "url": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "version": "0.1.0", + "version": "0.1.1", "name": "MDSQuestionTagGenomics", "title": "MDS Question Tag Genomics", "status": "draft", - "date": "2025-07-29T00:00:00.000Z", + "date": "2025-12-15T00:00:00.000Z", "publisher": "NHS England", "contact": [ { @@ -28,7 +28,7 @@ { "code": "datagroup-healthcare-professional", "display": "Healthcare Professional", - "definition":"Data group - Healthcare professional", + "definition": "Data group - Healthcare professional", "concept": [ { "code": "HCP-1", @@ -37,8 +37,13 @@ }, { "code": "HCP-2", - "display": "HCP - Full name", - "definition": "HCP's full name." + "display": "HCP - First name", + "definition": "HCP's first name." + }, + { + "code": "HCP-13", + "display": "HCP - surname", + "definition": "HCP'surname " }, { "code": "HCP-3", @@ -52,8 +57,8 @@ }, { "code": "HCP-5", - "display": "HCP - Phone", - "definition": "HCP's phone number." + "display": "HCP - Telephone number", + "definition": "HCP's telephone number." }, { "code": "HCP-6", @@ -63,17 +68,12 @@ { "code": "HCP-7", "display": "HCP - Organisation name", - "definition": "HCP's organisation name." - }, - { - "code": "HCP-8", - "display": "HCP - Organisation address", - "definition": "HCP's organisation address." + "definition": "HCP's requesting organisation name." }, { "code": "HCP-9", "display": "HCP - Organisation ODS code", - "definition": "HCP's organisation ODS code (ORGANISATION IDENTIFIER (CODE OF ORDERING ENTITY))" + "definition": "HCP's organisation ODS code" }, { "code": "HCP-10", @@ -89,23 +89,13 @@ "code": "HCP-12", "display": "HCP - Professional registration number type", "definition": "HCP's professional registration number type such as 'GMC'." - }, - { - "code": "HCP-13", - "display": "HCP - Genomic report delivery method", - "definition": "HCP's report preferred delivery method." - }, - { - "code": "HCP-14", - "display": "HCP - Central email for address and reporting (many)", - "definition": "Central email address provided by a HCP." } ] }, { "code": "datagroup-patient", "display": "Patient", - "definition": "Data group - Patient", + "definition": "Data group - Patient", "concept": [ { "code": "P-1", @@ -117,21 +107,26 @@ "display": "Patient - First name", "definition": "Patient's first name." }, + { + "code": "P-40", + "display": "Patient - Middlename", + "definition": "Patient's middle name." + }, { "code": "P-3", "display": "Patient - Surname", "definition": "Patient's last name." }, + { + "code": "P-41", + "display": "Patient - Name use", + "definition": "Links each patient name entry to confirm if current, previous or what the patient is known as." + }, { "code": "P-4", "display": "Patient - Date of birth", "definition": "Patient's date of birth." }, - { - "code": "P-5", - "display": "Patient - Address", - "definition": "Patient's home address." - }, { "code": "P-6", "display": "Patient - Postcode", @@ -139,44 +134,29 @@ }, { "code": "P-7", - "display": "Patient - Country", + "display": "Patient - Country of residence", "definition": "Patient's home country." }, - { - "code": "P-8", - "display": "Patient - Life status at time of request", - "definition": "Patient's alive or deceased status when ordering the test." - }, { "code": "P-9", "display": "Patient - Ethnicity", - "definition": "Patient's ethnicity. Includes 'other' / 'not stated'." + "definition": "Patient's ethnicity." }, { "code": "P-10", - "display": "Patient - Sex registered at birth", - "definition": "Patient's phenotypic sex classification. Physical characteristic. Currently determined by the Dr at birth. Gender for PLCM." - }, - { - "code": "P-11", - "display": "Patient - Organisation responsible for GP practice ODS code", - "definition": "ODS code of organisation responsible for the GP Practice where the patient is registered." + "display": "Patient - Sex defined at birth", + "definition": "Patient's phenotypic sex classification as defined at birth based on physical characteristic." }, { "code": "P-12", "display": "Patient - GP practice's ODS Code", - "definition": "Patient's GP practice ODS code. Includes 'N/A' and 'Not Known'." + "definition": "Patient's GP practice ODS code." }, { "code": "P-13", "display": "Patient - Is from consanguineous union", "definition": "The fact of the patient's biological parents being descended from the same ancestor." }, - { - "code": "P-14", - "display": "Patient - GP's full name", - "definition": "Patient's GP's full name." - }, { "code": "P-15", "display": "Patient - NHS number", @@ -185,7 +165,12 @@ { "code": "P-16", "display": "Patient - Local identifier", - "definition": "Patient's identification code other than NHS number. (LOCAL PATIENT IDENTIFIER (EXTENDED))" + "definition": "Patient's identification code other than NHS number." + }, + { + "code": "P-42", + "display": "Patient - ODS code of organisation which assigned local identifier", + "definition": "ODS code of the organisation which assigned the local identifier P-16." }, { "code": "P-17", @@ -204,111 +189,46 @@ }, { "code": "P-20", - "display": "Patient - Date of death", - "definition": "Patient's date/time of death." + "display": "Patient - Deceased date", + "definition": "Patient's date of death." }, { "code": "P-21", "display": "Patient - Chromosomal sex", "definition": "Patient's genomic / karyotypic characteristic. Determined by genomic testing." }, - { - "code": "P-22", - "display": "Patient - Pregnancy gestation period", - "definition": "Patient's term of active pregnancy at point of test request." - }, - { - "code": "P-23", - "display": "Patient - Fetal gestation", - "definition": "Stage during patient pregnancy at which it terminated." - }, - { - "code": "P-24", - "display": "Patient - Estimated delivery date (EDD)", - "definition": "Patient's estimated delivery date." - }, - { - "code": "P-25", - "display": "Patient - Pregnancy type", - "definition": "Type of conception" - }, - { - "code": "P-26", - "display": "Patient - IVF age of egg donor", - "definition": "The age of the patient who donated the egg at the time of donation." - }, - { - "code": "P-27", - "display": "Patient - Diagnosed with or being treated for cancer", - "definition": "Has the patient been diagnosed with or are they being treated for cancer." - }, - { - "code": "P-28", - "display": "Patient - Had transplant", - "definition": "Has the patient ever had a transplant." - }, - { - "code": "P-29", - "display": "Patient - Type of transplant", - "definition": "What type of transplant the patient had." - }, - { - "code": "P-30", - "display": "Patient - Transplant date", - "definition": "When the patient had the transplant." - }, - { - "code": "P-31", - "display": "Patient - Had transfusion in the last 6 weeks", - "definition": "Has the patient had a transfusion in the last 6 weeks." - }, - { - "code": "P-32", - "display": "Patient - Type of transfusion", - "definition": "What type of transfusion the patient has had." - }, - { - "code": "P-33", - "display": "Patient - Transfusion date", - "definition": "When the patient had the transfusion." - }, - { - "code": "P-34", - "display": "Patient - Height (m)", - "definition": "Patient's height." - }, { "code": "P-35", "display": "Patient - Withheld identity reason", "definition": "Confirmation why the patient is withholding identity details." }, - { - "code": "P-36", - "display": "Patient - GP's professional registration number", - "definition": "Patient's GP's professional registration number." - }, { "code": "P-37", - "display": "Patient - Pedigree / Family identifier", + "display": "Patient - Locaal Pedigree / Family identifier", "definition": "Patient's pedigree or family identifying id." }, { - "code": "P-38", - "display": "Patient - Pregnancy status", - "definition": "Patient's pregnancy status." + "code": "P-39", + "display": "Patient - Reason for inclusion in genomic test request", + "definition": "Reason patient has been included in genomic test request, such as to support proband testing or providing own genomic reporting" } ] }, { "code": "datagroup-fetus", "display": "Fetus", - "definition": "Data group - Fetus", + "definition": "Data group - Fetus", "concept": [ { "code": "F-1", "display": "Fetus - Local identifier", "definition": "Fetus' identification code other than NHS number." }, + { + "code": "F-7", + "display": "Fetus - ODS code of organisation which assigned local identifier", + "definition": "ODS code of the organisation which assigned the local identifier F-1." + }, { "code": "F-2", "display": "Fetus - Observed sex", @@ -319,129 +239,47 @@ "display": "Fetus - Chromosomal sex", "definition": "Fetus' genomic / karyotypic characteristic. Determined by genomic testing." }, - { - "code": "F-4", - "display": "Fetus - Are multiple fetuses being tested", - "definition": "Confirmation that multiple fetuses are being tested." - }, - { - "code": "F-5", - "display": "Fetus - Is testing for fetal loss from 24 weeks of gestation", - "definition": "Confirmation that the test is for a loss of pregnancy after 24 weeks gestation." - }, { "code": "F-6", "display": "Fetus - Life status at time of request", "definition": "Fetus' alive or deceased status details at the point of test ordering." - } - ] - }, - { - "code": "datagroup-record-of-discussion", - "display": "Record of Discussion", - "definition": "Data group - Record of discussion", - "concept": [ - { - "code": "ROD-1", - "display": "RoD - Included", - "definition": "Has RoD been included with request." - }, - { - "code": "ROD-2", - "display": "RoD - Patient category", - "definition": "Confirmation of who made the RoD decisions." - }, - { - "code": "ROD-3", - "display": "RoD - Recording clinician name", - "definition": "Name of the clinician who recorded the RoD details." - }, - { - "code": "ROD-4", - "display": "RoD - Record of discussion form - copy attached", - "definition": "Marker to confirm on a test request form that an RoD has been included." - }, - { - "code": "ROD-5", - "display": "RoD - Patient choice status", - "definition": "Indication of the patient consenting to the genomic test request." - }, - { - "code": "ROD-6", - "display": "RoD - Has research participation been discussed", - "definition": "Marker to confirm RoD conversation has taken place." - }, - { - "code": "ROD-7", - "display": "RoD - Remote consent", - "definition": "Where consent has been recorded on behalf of the patient via remote confirmation." }, { - "code": "ROD-8", - "display": "RoD - Test type", - "definition": "If the test is WGS cancer or WGS rare disease." - }, - { - "code": "ROD-9", - "display": "RoD - Research opt out reason", - "definition": "Why patient has opted out of research." - }, - { - "code": "ROD-10", - "display": "RoD - Responsible clinician name", - "definition": "Name of the clinician who is responsible for the patient's genomic test request." - }, - { - "code": "ROD-11", - "display": "RoD - Patient conversation taken place, ROD form to follow", - "definition": "Marker to confirm RoD conversation has taken place but will be sent separately." - }, - { - "code": "ROD-12", - "display": "RoD - Signature", - "definition": "Copy of wet signature or valid e-signature." - }, - { - "code": "ROD-13", - "display": "RoD - Document/Link", - "definition": "A copy of/or link to the previous genomic or non-genomic report." + "code": "F-8", + "display": "Fetus - Pregnancy id", + "definition": "The id of a given pregnancy which this fetus belongs to." } ] }, { "code": "datagroup-test-request", "display": "Test Request", - "definition": "Data group - Test Request", + "definition": "Data group - Test Request", "concept": [ - { - "code": "TR-1", - "display": "Test Request - Test request id", - "definition": "Unique id to identify this test request." - }, { "code": "TR-2", "display": "Test Request - Payment status", "definition": "How the test request is funded" }, { - "code": "TR-3", - "display": "Test Request - Date and time request sent", - "definition": "Date and time the test request was sent from the requesting clinician (TEST REQUEST DATE)." + "code": "TR-4", + "display": "Test Request - Requesting reason rare disease", + "definition": "The reason for a rare disease genomic test." }, { - "code": "TR-4", - "display": "Test Request - Reason for testing", - "definition": "The reason for a genomic test." + "code": "TR-38", + "display": "Test Request - Requesting reason cancer", + "definition": "The reason for a cancer genomic test." }, { "code": "TR-5", "display": "Test Request - High level test identifier", - "definition": "The high level id which identifies the requested test. Options provided by Test Directory." + "definition": "Legacy high level ids which identify the requested test. Options provided by old Test Directory." }, { "code": "TR-6", "display": "Test Request - High level test identifier description", - "definition": "The high level name of the CI referred to." + "definition": "Legacy high level name of the id requested" }, { "code": "TR-7", @@ -464,685 +302,546 @@ "definition": "The low level name of the test to be actioned when the CITT code is multipurpose." }, { - "code": "TR-11", - "display": "Test Request - Count of patients to be tested", - "definition": "Count of patients to be tested including the proband/primary patient." - }, - { - "code": "TR-12", - "display": "Test Request - Urgency reason", - "definition": "The test request urgency reason." - }, - { - "code": "TR-13", - "display": "Test Request - Reason for reanalysis", - "definition": "The reason reanalysis has been requested." - }, - { - "code": "TR-14", - "display": "Test Request - Detail of reason for reanalysis", - "definition": "Further detail associated to the reason reanalysis has been requested." - }, - { - "code": "TR-15", - "display": "Test Request - Type of reanalysis", - "definition": "The type of reanalysis which has been requested." - }, - { - "code": "TR-16", - "display": "Test Request - DNA storage information", - "definition": "If the reason for testing is DNA storage, this captures further detail." - }, - { - "code": "TR-17", - "display": "Test Request - Is urgent", - "definition": "Confirmation if the test request is urgent." - }, - { - "code": "TR-18", - "display": "Test Request - Date report required by", - "definition": "The date a completed genomic report is required by." + "code": "TR-21", + "display": "Test Request - Genomic package id", + "definition": "Id of the package requested." }, { - "code": "TR-19", - "display": "Test Request - Recipient ODS code", - "definition": "ODS code of the first organisation which receives the genomic test request." - } - ] - }, - { - "code": "datagroup-primary-sample", - "display": "Primary Sample", - "definition": "Data group - Primary Sample", - "concept": [ - { - "code": "PS-1", - "display": "Primary Sample - Destination organisation ODS code", - "definition": "Destination for primary sample." - }, - { - "code": "PS-2", - "display": "Primary Sample - Id (many)", - "definition": "Id of primary sample provided, linked to the stated assigning authority." - }, - { - "code": "PS-3", - "display": "Primary Sample - Id assigning authority ODS code (many)", - "definition": "Authority who assigned the primary sample id." - }, - { - "code": "PS-4", - "display": "Primary Sample - Received date", - "definition": "Date at which a primary sample was received at a laboratory (SAMPLE RECEIPT DATE)." - }, - { - "code": "PS-5", - "display": "Primary Sample - Sample storage details", - "definition": "Where a primary sample is in storage or where it needs to be stored." - }, - { - "code": "PS-6", - "display": "Primary Sample - Volume", - "definition": "Volume of provided primary sample." - }, - { - "code": "PS-7", - "display": "Primary Sample - Test request Id", - "definition": "The id of the associated genomic test being requested." + "code": "TR-22", + "display": "Test Request - Genomic package name", + "definition": "Name of the package requested." }, { - "code": "PS-8", - "display": "Primary Sample - Patient NHS number", - "definition": "Patient NHS number." + "code": "TR-23", + "display": "Test Request - Genomic package version", + "definition": "Version of the package requested." }, { - "code": "PS-9", - "display": "Primary Sample - Patient local identifier", - "definition": "Patient identification code other than NHS number." + "code": "TR-24", + "display": "Test Request - Genomic test id", + "definition": "Id of the test requested." }, { - "code": "PS-10", - "display": "Primary Sample - Obtained date", - "definition": "Date at which a specimen/biopsy was obtained from patient." - }, - { - "code": "PS-11", - "display": "Primary Sample - Primary sample", - "definition": "Initial sample from patient submitted into a laboratory." - }, - { - "code": "PS-12", - "display": "Primary Sample - Primary sample state", - "definition": "How the primary sample is preserved." + "code": "TR-25", + "display": "Test Request - Genomic test name", + "definition": "Name of the test requested." }, { - "code": "PS-13", - "display": "Primary Sample - Necrosis", - "definition": "% necrotic cells in primary sample." + "code": "TR-26", + "display": "Test Request - Genomic test version", + "definition": "Version of the test requested." }, { - "code": "PS-14", - "display": "Primary Sample - Nucleated cell count", - "definition": "Nucleated cell count in the primary sample (Solid Tumour and Haem-Onc)." + "code": "TR-27", + "display": "Test Request - Additional panels", + "definition": "Additional panels to test." }, { - "code": "PS-15", - "display": "Primary Sample - Tumour nuclear content", - "definition": "Neoplastic cell content in the primary sample(Solid Tumour) - sourced at local lab. (%)" + "code": "TR-28", + "display": "Test request - Target type", + "definition": "Type of target to test." }, { - "code": "PS-16", - "display": "Primary Sample - Tumour cellularity", - "definition": "The proportion of the primary sample which is tumour nuclei." + "code": "TR-29", + "display": "Test request - Target detail", + "definition": "Detail of target to test." }, { - "code": "PS-17", - "display": "Primary Sample - Solid tumour morphology", - "definition": "The histology and likely course of development of a tumour." + "code": "TR-11", + "display": "Test Request - Count of patients to be tested", + "definition": "Count of patients to be tested including the proband/primary patient." }, { - "code": "PS-18", - "display": "Primary Sample - Solid tumour topography", - "definition": "The tumour sample site. e.g. from colon, stomach etc." + "code": "TR-12", + "display": "Test Request - Urgency reason", + "definition": "The test request urgency reason." }, { - "code": "PS-19", - "display": "Primary Sample - Biopsy site", - "definition": "Site where the primary sample was taken from." + "code": "TR-13", + "display": "Test Request - Reanalysis reason", + "definition": "The reason reanalysis has been requested." }, { - "code": "PS-20", - "display": "Primary Sample - Skin/Bone sample affected", - "definition": "If the skin or bone provided is unaffected or affected." + "code": "TR-14", + "display": "Test Request - Detail of reason for request", + "definition": "Further detail associated to the reason reanalysis has been requested." }, { - "code": "PS-21", - "display": "Primary Sample - Maternal cell contamination (MCC)", - "definition": "Confirmation if MCC remains in the primary sample." + "code": "TR-15", + "display": "Test Request - Type of reanalysis", + "definition": "The type of reanalysis which has been requested." }, { - "code": "PS-22", - "display": "Primary Sample - Option for all products of conception", - "definition": "Future management for products of conception." + "code": "TR-17", + "display": "Test Request - Is urgent", + "definition": "Confirmation if the test request is urgent." }, { - "code": "PS-23", - "display": "Primary Sample - Blasts %", - "definition": "Blast count in the primary sample (Haemonc) - sourced at local SIHMDS." + "code": "TR-35", + "display": "Test Request - Purpose of linking", + "definition": "The reason a given test request has been linked to another test request." }, { - "code": "PS-24", - "display": "Primary Sample - High infection risk reason", - "definition": "The high contamination risk reason for a primary sample." - } - ] - }, - { - "code": "datagroup-sample-preparation", - "display": "Sample Preparation", - "definition": "Data group - Sample Preparation", - "concept": [ - { - "code": "SP-1", - "display": "Sample Preparation - Parent primary sample id", - "definition": "Id of primary sample this derived from" + "code": "TR-36", + "display": "Test Request - Central email address for reporting", + "definition": "Central email address for contingency in the event of not being able to obtain a report via the requester." }, { - "code": "SP-2", - "display": "Sample Preparation - Id (many)", - "definition": "Id of sample preparation provided, linked to the stated assigning authority. Occurs multiple times (SAMPLE IDENTIFIER)." + "code": "TR-20", + "display": "Test Request - Genomic report delivery method", + "definition": "Test Request - Genomic report delivery method" }, { - "code": "SP-3", - "display": "Sample Preparation - Id assigning authority ODS code (many)", - "definition": "Authority who assigned the sample preparation id(ORGANISATION IDENTIFIER (CODE OF HISTOPATHOLOGY LABORATORY ENTITY))" + "code": "TR-30", + "display": "Test Request - Add private genomic request and report to NHS record", + "definition": "Confirmation if the content of a private genomic test request should be added to an NHS record." }, { - "code": "SP-4", - "display": "Sample Preparation - Sample storage details", - "definition": "Where sample preparation is in storage or where it needs to be stored." + "code": "TR-31", + "display": "Test Request - Test request form version", + "definition": "Version of the test order form completed and submitted." }, { - "code": "SP-5", - "display": "Sample Preparation - Volume", - "definition": "Volume of provided sample preparation." + "code": "TR-32", + "display": "Test Request - File / Link to file", + "definition": "Upload of a file or a link to a file for adding documents such as previous genomic reports to a test order." }, { - "code": "SP-6", - "display": "Sample Preparation - Performed date", - "definition": "Date at which the sample preparation was completed." + "code": "TR-33", + "display": "Test Request - File detail", + "definition": "Detail to provide context to an uploaded file or document link." }, { - "code": "SP-7", - "display": "Sample Preparation - Received date", - "definition": "Date at which sample preparation was received at a laboratory (SAMPLE RECEIPT DATE)." + "code": "TR-34", + "display": "Test Request - Clinical utility", + "definition": "Clinical benefit to patient of obtaining a requested genomic report." }, { - "code": "SP-8", - "display": "Sample Preparation - Sample preparation", - "definition": "Cell separation applied to a primary sample." + "code": "TR-39", + "display": "Test Request - Linked test request reference", + "definition": "The reference to any associated test requests" } ] }, { - "code": "datagroup-final-sample", - "display": "Final Sample", - "definition": "Data group - Final Sample", + "code": "datagroup-ngrl-consent", + "display": "NGRL-consent", + "definition": "Data group - NGRL consent", "concept": [ { - "code": "FS-1", - "display": "Final Sample - Parent primary sample id", - "definition": "Id of primary this derived from." - }, - { - "code": "FS-2", - "display": "Final Sample - Parent sample preparation id", - "definition": "Id of sample preparation this derived from." + "code": "NGRL-1", + "display": "NGRL consent - Date of NGRL consent", + "definition": "The date NGRL consent was provided." }, { - "code": "FS-3", - "display": "Final Sample - Id (many)", - "definition": "Id of final sample provided, linked to the associated assigning authority. Occurs multiple times (SAMPLE IDENTIFIER)." + "code": "NGRL-2", + "display": "NGRL consent - Patient has made their own choice to consent to the NGRL", + "definition": "Confirmation if the patient to be tested has provided NGRL consent themselves." }, { - "code": "FS-4", - "display": "Final Sample - Id assigning authority ODS code (many)", - "definition": "Authority who assigned the final sample id ORGANISATION IDENTIFIER (CODE OF HISTOPATHOLOGY LABORATORY ENTITY)." + "code": "NGRL-3", + "display": "NGRL consent - Patient representative name (if patient cannot make their own choice)", + "definition": "The name of the patient representative." }, { - "code": "FS-5", - "display": "Final Sample - Sample storage details", - "definition": "Where a final sample is in storage or where it needs to be stored." + "code": "NGRL-4", + "display": "NGRL consent - I confirm that the patient (or their representative) agree to have their genomic and healthcare data used for research", + "definition": "The outcome of the patient or their representative’s choice in consenting to including their data used for research in the NGRL." }, { - "code": "FS-6", - "display": "Final Sample - Volume", - "definition": "Volume of provided final sample." - }, - { - "code": "FS-7", - "display": "Final Sample - Performed date", - "definition": "Date at which the final sample was extracted." - }, - { - "code": "FS-8", - "display": "Final Sample - Received date", - "definition": "Date at which a final sample was received at a laboratory (SAMPLE RECEIPT DATE)." - }, - { - "code": "FS-9", - "display": "Final Sample - Final sample", - "definition": "Material to be genomically tested." + "code": "NGRL-5", + "display": "NGRL consent - NGRL consent document link", + "definition":"A URL where a copy of a completed NGRL consent form may be found." } ] }, { - "code": "datagroup-previous-genomic-report", - "display": "Previous Genomic Report", - "definition": "Data group - Previous Genomic Report", + "code": "datagroup-primary-sample", + "display": "Primary Sample", + "definition": "Data group - Primary Sample", "concept": [ { - "code": "PGR-1", - "display": "Previous Genomic Report - Report referral summary", - "definition": "Referring clinician's summary of the previous genomic report to support test request." - }, - { - "code": "PGR-2", - "display": "Previous Genomic Report - Report file/link", - "definition": "A copy of/or link to the previous genomic report." - }, - { - "code": "PGR-3", - "display": "Previous Genomic Report - Test performed date", - "definition": "The date a previous genomic test was performed." - }, - { - "code": "PGR-4", - "display": "Previous Genomic Report - Report identifier", - "definition": "The identifier for the previous genomic report." - }, - { - "code": "PGR-5", - "display": "Previous Genomic Report - Patient's first name", - "definition": "The first name of the patient on the previous genomic report." - }, - { - "code": "PGR-6", - "display": "Previous Genomic Report - Patient's surname", - "definition": "The surname of the patient on the previous genomic report." - }, - { - "code": "PGR-7", - "display": "Previous Genomic Report - Patient's address", - "definition": "The address of the patient on the previous genomic report." - }, - { - "code": "PGR-8", - "display": "Previous Genomic Report - Patient's post code", - "definition": "The postcode of the patient on the previous genomic report." - }, - { - "code": "PGR-9", - "display": "Previous Genomic Report - Patient's country", - "definition": "The country of the patient on the previous genomic report." - }, - { - "code": "PGR-10", - "display": "Previous Genomic Report - Patient's date of birth", - "definition": "The date of birth of the patient on the previous genomic report." - }, - { - "code": "PGR-11", - "display": "Previous Genomic Report - Patient's NHS number", - "definition": "The NHS number of the patient on the previous genomic report." - }, - { - "code": "PGR-12", - "display": "Previous Genomic Report - Patient's alternative identifier", - "definition": "The alternative identifier of the patient on the previous genomic report." - }, - { - "code": "PGR-13", - "display": "Previous Genomic Report - Patient's relationship to requesting patient", - "definition": "The relationship of the patient on the previous genomic report to the requesting patient." - }, - { - "code": "PGR-14", - "display": "Previous Genomic Report - Patient's clinical genetic number", - "definition": "The individual clinical genetic number of the patient on the previous genomic report." - }, - { - "code": "PGR-15", - "display": "Previous Genomic Report - Patient's pedigree number", - "definition": "The pedigree number of the patient on the previous genomic report which links their family." + "code": "PS-2", + "display": "Primary Sample - Local identifier", + "definition": "Local ids applied to a sample" }, { - "code": "PGR-16", - "display": "Previous Genomic Report - Report lab test number", - "definition": "The lab test number from the previous genomic report." + "code": "PS-3", + "display": "Primary Sample - ODS code of organisation which assigned local id", + "definition": "ODS code of the organisation which assigned the local sample id." }, { - "code": "PGR-17", - "display": "Previous Genomic Report - Report of genetic analysis", - "definition": "The clinical outcomes from the previous genomic report." + "code": "PS-10", + "display": "Primary Sample - Obtained date", + "definition": "Date at which a specimen/biopsy was obtained from patient." }, { - "code": "PGR-18", - "display": "Previous Genomic Report - Report performer full name", - "definition": "The full name of the individual that authored the previous genomic test report." + "code": "PS-11", + "display": "Primary Sample - Primary sample", + "definition": "The primary sample material." }, { - "code": "PGR-19", - "display": "Previous Genomic Report - Report performer organisation ODS code", - "definition": "The organisation ODS code of the individual that authored the previous genomic test report." + "code": "PS-12", + "display": "Primary Sample - Primary sample state", + "definition": "The state of the primary sample." }, { - "code": "PGR-20", - "display": "Previous Genomic Report - Original requester full name", - "definition": "The full name of the individual that requested the previous genomic test report." + "code": "PS-25", + "display": "Primary Sample - Preservative/Container", + "definition": "How the primary sample is preserved." }, { - "code": "PGR-21", - "display": "Previous Genomic Report - Original requester organisation ODS code", - "definition": "The organisation ODS code of the individual that requested the previous genomic test report." + "code": "PS-30", + "display": "Primary Sample - Block identifier", + "definition": "Sample block identifier" }, { - "code": "PGR-22", - "display": "Previous Genomic Report - Original requester reason for request", - "definition": "The reason for requesting the previous genomic test report." - } - ] - }, - { - "code": "datagroup-relevant-clinical-report", - "display": "Relevant Clinical Report", - "definition": "Data group - Relevant Clinical Report ", - "concept": [ - { - "code": "RCP-1", - "display": "Relevant Clinical Report - Report title", - "definition": "Title of relevant clinical report." + "code": "PS-31", + "display": "Primary Sample - Fixative type", + "definition": "Sample fixative type" }, { - "code": "RCP-2", - "display": "Relevant Clinical Report - Report referral summary", - "definition": "Referring clinician's summary of the previous relevant clinical report to support test request." + "code": "PS-32", + "display": "Primary Sample - Hours to fixation", + "definition": "Sample hours to fixation" }, { - "code": "RCP-3", - "display": "Relevant Clinical Report - Report file/link", - "definition": "A copy of/or link to the relevant clinical report." + "code": "PS-33", + "display": "Primary Sample - Hours in fixative", + "definition": "Sample hours in fixative" }, { - "code": "RCP-4", - "display": "Relevant Clinical Report - Test performed date", - "definition": "The date a relevant clinical report was performed." + "code": "PS-34", + "display": "Primary Sample - Tumour enrichment method", + "definition": "Method used for tumour enrichment." }, { - "code": "RCP-5", - "display": "Relevant Clinical Report - Report identifier", - "definition": "The identifier for the relevant clinical report." + "code": "PS-13", + "display": "Primary Sample - Necrosis", + "definition": "% necrotic (dead) cells in primary sample." }, { - "code": "RCP-6", - "display": "Relevant Clinical Report - Test type", - "definition": "A name that describes the relevant clinical report." + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count", + "definition": "Nucleated (with nucleous) cell (non tumour and tumour) count in the primary sample (Solid Tumour and Haem-Onc)." }, { - "code": "RCP-7", - "display": "Relevant Clinical Report - Test result value comparator", - "definition": "A comparator that may be used to indicate whether the actual value is greater or less than the stated value. Applies to numeric values only." + "code": "PS-15", + "display": "Primary Sample - Tumour nuclear content in whole section", + "definition": "Neoplastic (tumour) cell content in the primary sample whole section(Solid Tumour) - sourced at local lab. (%)" }, { - "code": "RCP-8", - "display": "Relevant Clinical Report - Test result value unit of measure", - "definition": "The name and code of the unit of measure associated with the test result value. Applies to numeric values only." + "code": "PS-26", + "display": "Primary Sample - Tumour nuclear content in marked area", + "definition": "Neoplastic (tumour) cell content in the primary sample marked area(Solid Tumour) - sourced at local lab. (%)" }, { - "code": "RCP-9", - "display": "Relevant Clinical Report - Test result reference range low", - "definition": "The reference range low value." + "code": "PS-17", + "display": "Primary Sample - Solid tumour morphology", + "definition": "The histology and likely course of development of a tumour." }, { - "code": "RCP-10", - "display": "Relevant Clinical Report - Test result reference range high", - "definition": "The reference range high value." + "code": "PS-18", + "display": "Primary Sample - Solid tumour topography", + "definition": "The tumour sample site. e.g. from colon, stomach etc." }, { - "code": "RCP-11", - "display": "Relevant Clinical Report - Test result test method", - "definition": "The method of testing/observation that was used." + "code": "PS-29", + "display": "Primary Sample - Is biopsy", + "definition": "Primary Sample - Is biopsy" }, { - "code": "RCP-12", - "display": "Relevant Clinical Report - Test result reference range text", - "definition": "A human readable text-based description to provide additional information about the reference range. For example, the target population that the reference range applies to and/or differences based on factors such as age or sex." + "code": "PS-19", + "display": "Primary Sample - Biopsy site", + "definition": "Digital confirmation that the sample is a biopsy." }, { - "code": "RCP-13", - "display": "Relevant Clinical Report - Test result clinical summary", - "definition": "A human readable text-based clinical interpretation of the test result and any additional notes provided by the performing organisation." + "code": "PS-21", + "display": "Primary Sample - Observed maternal cell contamination (MCC)", + "definition": "An observed outcome which may indicate MCC" }, { - "code": "RCP-14", - "display": "Relevant Clinical Report - Report result", - "definition": "Reference to the result(s)/result groups contained in the relevant clinical report" + "code": "PS-27", + "display": "Primary Sample - Test confirmed maternal cell contamination (MCC)", + "definition": "Analytically confirmed MCC levels" }, { - "code": "RCP-15", - "display": "Relevant Clinical Report - Report performer full name", - "definition": "The full name of the individual that authored the relevant clinical report." + "code": "PS-22", + "display": "Primary Sample - Option for all products of conception", + "definition": "Primary Sample - Option for all products of conception" }, { - "code": "RCP-16", - "display": "Relevant Clinical Report - Report performer organisation ODS code", - "definition": "The identifier of the org which authored the patient's relevant clinical report." + "code": "PS-23", + "display": "Primary Sample - Blasts %", + "definition": "Future management for products of conception." }, { - "code": "RCP-17", - "display": "Relevant Clinical Report - Original requester full name", - "definition": "The full name of the individual that requested the relevant clinical report." + "code": "PS-24", + "display": "Primary Sample - High infection risk reason", + "definition": "The high contamination risk reason for a primary sample." }, { - "code": "RCP-18", - "display": "Relevant Clinical Report - Original requester organisation ODS code", - "definition": "The organisation ODS code of the individual that requested the relevant clinical report." + "code": "PS-28", + "display": "Primary Sample - Patient life status at the time of collection", + "definition": "If the patient was alive or deceased at the point of collecting a sample." }, { - "code": "RCP-19", - "display": "Relevant Clinical Report - Original requester reason for request", - "definition": "The reason for requesting the relevant clinical report." + "code": "PS-35", + "display": "Primary Sample - Solid tumour type", + "definition": "The origin or context of a tumour sample." } ] }, { "code": "datagroup-patient-clinical-information", "display": "Patient Clinical Information", - "definition": "Data group - Patient Clinical Information", + "definition": "Data group - Patient Clinical Information", "concept": [ { "code": "PCI-1", - "display": "Genomic Ethnicity", + "display": "Patient clinical information - Genomic Ethnicity", "definition": "Patient's ethnicity where 'Patient - Ethnicity field' doesn't provide an adequate description. E.g Ashkenazi Jewish" }, { "code": "PCI-2", - "display": "Disease Status", + "display": "Patient clinical information - Disease Status", "definition": "If the patient is affected, unaffected, or it is unknown." }, - { - "code": "PCI-3", - "display": "Date of Diagnosis", - "definition": "The patient's date of diagnosis." - }, { "code": "PCI-4", - "display": "Age at disease onset", + "display": "Patient clinical information - Age at disease onset", "definition": "The age when a change in patients' health was first noted in line with suspected diagnosis." }, { "code": "PCI-5", - "display": "Known/Suspected Disease", + "display": "Patient clinical information - Known/Suspected Disease", "definition": "Disease a patient is believed, known to have, or be at risk of developing." }, { "code": "PCI-6", - "display": "Phenotypic details (many)", + "display": "Patient clinical information - Phenotypic details", "definition": "The HPO (or alternative ontology as appropriate) term names for the observable disease traits." }, { "code": "PCI-7", - "display": "Symptoms at onset", - "definition": "The patient's symptoms at onset." - }, - { - "code": "PCI-8", - "display": "Disease penetrance", - "definition": "Confirms if all individuals with a disease show clinical symptoms or if there are carriers who do not." - }, - { - "code": "PCI-9", - "display": "Has multiple tumours", - "definition": "Does the patient have multiple tumours." + "display": "Patient clinical information - Symptoms", + "definition": "The patient's symptoms" }, { "code": "PCI-10", - "display": "Count of tumours", + "display": "Patient clinical information - Count of tumours", "definition": "How many tumours the patient has." }, { "code": "PCI-11", - "display": "Site of tumour (many)", + "display": "Patient clinical information - Site of tumour", "definition": "Location of the tumours on the body." }, - { - "code": "PCI-12", - "display": "Solid Tumour Type", - "definition": "The patient's solid tumour type." - }, - { - "code": "PCI-13", - "display": "Liquid Tumour Type", - "definition": "The patient's liquid tumour type." - }, { "code": "PCI-14", - "display": "Tumour sites - Body image diagram", + "display": "Patient clinical information - Tumour sites - Body image diagram", "definition": "Image attachment of body with tumour sites highlighted." }, { "code": "PCI-15", - "display": "Pedigree details / Relevant family history", + "display": "Patient clinical information - Pedigree details / Relevant family history", "definition": "The patient's pedigree/family history details (inc family history of cancer)." }, { "code": "PCI-16", - "display": "Pedigree diagram", + "display": "Patient clinical information - Pedigree diagram", "definition": "Image attachment of pedigree details" }, { "code": "PCI-17", - "display": "Laterality of hearing loss", + "display": "Patient clinical information - Laterality of hearing loss", "definition": "Laterality of the hearing loss i.e. bilateral or unilateral." }, { "code": "PCI-18", - "display": "Fetal maternal screening genotype", + "display": "Patient clinical information - Fetal haemoglobinopathy maternal screening genotype", "definition": "Maternal screening genotype for haemoglobinopathy testing." }, - { - "code": "PCI-19", - "display": "Is patient on TKI therapy", - "definition": "If the patient is on tyrosine kinase inhibitor therapy." - }, - { - "code": "PCI-20", - "display": "Is patient in treatment free remission", - "definition": "If the patient is in treatment free remission." - }, { "code": "PCI-21", - "display": "Legal considerations", + "display": "Patient clinical information - Legal considerations", "definition": "Legal considerations for a given request." }, { "code": "PCI-22", - "display": "Fetal paternal screening genotype", - "definition": "Paternal screening genotype for haemoglobinopathy testing." + "display": "Patient clinical information - Fetal haemoglobinopathy paternal screening genotype", + "definition": "Paternal screening genotype for haemoglobinopathy testing" }, { "code": "PCI-23", - "display": "Expected Maternity Unit - Organisation name", + "display": "Patient clinical information - Expected Maternity Unit - Organisation name", "definition": "Requesting clinician's organisation name." }, { "code": "PCI-24", - "display": "Expected Maternity Unit - Organisation address", + "display": "Patient clinical information - Expected Maternity Unit - Organisation address", "definition": "Requesting clinician's organisation address." }, { "code": "PCI-25", - "display": "Expected Maternity Unit - Organisation ODS code", + "display": "Patient clinical information - Expected Maternity Unit - Organisation ODS code", "definition": "Requesting clinician's organisation ODS code." }, { "code": "PCI-26", - "display": "Expected Maternity Unit - Department name", + "display": "Patient clinical information - Expected Maternity Unit - Department name", "definition": "Requesting clinician's department name." }, { "code": "PCI-27", - "display": "Growth history", + "display": "Patient clinical information - Growth history", "definition": "Summary passage of text to highlight patient centile history e.g. head circumference, weight, etc." }, { "code": "PCI-28", - "display": "Severity of hearing loss", + "display": "Patient clinical information - Severity of hearing loss", "definition": "Free text regarding hearing loss" }, { "code": "PCI-29", - "display": "Retinal degeneration", + "display": "Patient clinical information - Retinal degeneration", "definition": "Free text regarding retinal degeneration" }, { "code": "PCI-30", - "display": "Risk factors", + "display": "Patient clinical information - Risk factors", "definition": "Toxic medication - Prematurity (risk factor for hearing loss) e.g. Baby early birth - Ototoxic medication." }, { "code": "PCI-31", - "display": "Suspected inborn error type(s)", + "display": "Patient clinical information - Suspected inborn error type(s)", "definition": "Suspected inborn error type(s)" }, { "code": "PCI-32", - "display": "Abnormal infection history site", + "display": "Patient clinical information - Abnormal infection history site", "definition": "Abnormal infection history site organism" }, { "code": "PCI-33", - "display": "Abnormal infection history site organism", + "display": "Patient clinical information - Abnormal infection history site organism", "definition": "Abnormal infection history site organism" }, { "code": "PCI-34", "display": "Is on ig replacement", "definition": "If the patient is on immunoglobin replacement treatment." + }, + { + "code": "PCI-35", + "display": "Patient clinical information - Current and previous treatment detail", + "definition": "Detail regarding relevant current and previous medical treatments." + }, + { + "code": "PCI-36", + "display": "Patient clinical information - Pregnancy status", + "definition": "Patient`s pregnancy status" + }, + { + "code": "PCI-37", + "display": "Patient clinical information - Pregnancy type", + "definition": "Type of conception" + }, + { + "code": "PCI-38", + "display": "Patient clinical information - Pregnancy gestation period", + "definition": "Patient's term of active pregnancy at point of test request." + }, + { + "code": "PCI-39", + "display": "Patient clinical information - Fetal gestation", + "definition": "Stage during patient pregnancy at which it terminated." + }, + { + "code": "PCI-40", + "display": "Patient clinical information - Estimated delivery date (EDD)", + "definition": "Patient's estimated delivery date." + }, + { + "code": "PCI-41", + "display": "Patient clinical information - IVF age of egg donor", + "definition": "The age of the patient who donated the egg at the time of donation." + }, + { + "code": "PCI-42", + "display": "Patient clinical information - Had transplant", + "definition": "Has the patient ever had a transplant." + }, + { + "code": "PCI-43", + "display": "Patient clinical information - Type of transplant", + "definition": "What type of transplant the patient had." + }, + { + "code": "PCI-44", + "display": "Patient clinical information - Transplant date", + "definition": "When the patient had the transplant." + }, + { + "code": "PCI-45", + "display": "Patient clinical information - Had transfusion in the last 6 weeks", + "definition": "Has the patient had a transfusion in the last 6 weeks." + }, + { + "code": "PCI-46", + "display": "Patient clinical information - Type of transfusion", + "definition": "What type of transfusion the patient has had." + }, + { + "code": "PCI-47", + "display": "Patient clinical information - Transfusion date", + "definition": "When the patient had the transfusion." + }, + { + "code": "PCI-48", + "display": "Patient clinical information - Height (m)", + "definition": "Patient's height." } ] }, { - "code": "further-supporting-information", - "display": "Further Supporting Information", - "definition": "Data group - Further Supporting Information", + "code": "datagroup-miscellaneous", + "display": "Miscellaneous", + "definition": "Data group - Miscellaneous", "concept": [ { - "code": "FSI-1", - "display": "Further Supporting Information", + "code": "MIS-1", + "display": "Further supporting information", "definition": "Supporting information which has not been captured elsewhere." } ] + }, + { + "code": "datagroup-hospital-encounter", + "display": "Hospital encounter", + "definition": "Data group - Hospital encounter", + "concept": [ + { + "code": "HE-1", + "display": "Treatment function code (TFC)", + "definition": "The identifier for the clinical specialty or service under which the patient is being treated." + }, + { + "code": "HE-2", + "display": "Hospital provider spell identifier", + "definition": "The identifier for the patient's continuous period of care in a hospital provider setting, from admission to discharge." + }, + { + "code": "HE-3", + "display": "Outpatient attendance identifier", + "definition": "The identifier for the patient's specific outpatient appointment at which the genomic test may have been ordered." + }, + { + "code": "HE-4", + "display": "Hospital point of delivery code", + "definition": "The identifier that defines the type of care setting in which the genomic test was requested." + } + ] } ] } \ No newline at end of file diff --git a/Observation/Observation-AutisticBehaviour-Example.json b/Observation/Observation-AutisticBehaviour-Example.json index 20cddb8..87bd0e5 100644 --- a/Observation/Observation-AutisticBehaviour-Example.json +++ b/Observation/Observation-AutisticBehaviour-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-AutisticBehaviour-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-BlastPercentage-Example.json b/Observation/Observation-BlastPercentage-Example.json index 11e7610..700c699 100644 --- a/Observation/Observation-BlastPercentage-Example.json +++ b/Observation/Observation-BlastPercentage-Example.json @@ -1,40 +1,49 @@ { - "resourceType": "Observation", - "id": "Observation-BlastPercentage-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1015521000000107", - "display": "Percentage blast cells" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", + "resourceType": "Observation", + "id": "Observation-BlastPercentage-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-23", + "display": "Primary Sample - Blasts %" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1015521000000107", + "display": "Percentage blast cells" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", + "value": "RR81234", + "assigner": { "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" } - }, - "specimen": { - "identifier": { - "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", - "value": "RR81234", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "696B0" - } - } - } - }, - "valueQuantity": { - "value": 25, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-08-29" + } + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-08-29" } \ No newline at end of file diff --git a/Observation/Observation-BlastPercentageWGSSample-Example.json b/Observation/Observation-BlastPercentageWGSSample-Example.json index 0d07da8..ea25686 100644 --- a/Observation/Observation-BlastPercentageWGSSample-Example.json +++ b/Observation/Observation-BlastPercentageWGSSample-Example.json @@ -1,40 +1,49 @@ { - "resourceType": "Observation", - "id": "Observation-BlastPercentageWGSSample-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1015521000000107", - "display": "Percentage blast cells" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", + "resourceType": "Observation", + "id": "Observation-BlastPercentageWGSSample-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-23", + "display": "Primary Sample - Blasts %" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1015521000000107", + "display": "Percentage blast cells" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", + "value": "RR81235", + "assigner": { "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" } - }, - "specimen": { - "identifier": { - "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", - "value": "RR81235", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "696B0" - } - } - } - }, - "valueQuantity": { - "value": 25, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-08-05" + } + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-08-05" } \ No newline at end of file diff --git a/Observation/Observation-Bruising-Example.json b/Observation/Observation-Bruising-Example.json index c7449f8..6238592 100644 --- a/Observation/Observation-Bruising-Example.json +++ b/Observation/Observation-Bruising-Example.json @@ -1,22 +1,31 @@ { - "resourceType": "Observation", - "id": "Observation-Bruising-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "308492005", - "display": "Bruising" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "effectiveDateTime": "2023-09-03" + "resourceType": "Observation", + "id": "Observation-Bruising-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-7", + "display": "Patient clinical information - Symptoms" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "308492005", + "display": "Bruising" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-09-03" } \ No newline at end of file diff --git a/Observation/Observation-Cellularity-Example.json b/Observation/Observation-Cellularity-Example.json index 5d6da60..f3ac678 100644 --- a/Observation/Observation-Cellularity-Example.json +++ b/Observation/Observation-Cellularity-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-Cellularity-Example", - "status": "final", - "code": { - "text": "Cellularity" - }, - "subject": { - "reference": "Patient/Patient-ZelmaHadjkiss-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307555" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "RA257630" - } - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "75540009", - "display": "High" - } - ] - }, - "effectiveDateTime": "2023-09-08T10:00:00Z" + "resourceType": "Observation", + "id": "Observation-Cellularity-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "text": "Cellularity" + }, + "subject": { + "reference": "Patient/Patient-ZelmaHadjkiss-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307555" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257630" + } + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "75540009", + "display": "High" + } + ] + }, + "effectiveDateTime": "2023-09-08T10:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-CellularityKayBurbridge-Example.json b/Observation/Observation-CellularityKayBurbridge-Example.json index 04dea41..671d2e5 100644 --- a/Observation/Observation-CellularityKayBurbridge-Example.json +++ b/Observation/Observation-CellularityKayBurbridge-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-CellularityKayBurbridge-Example", - "status": "final", - "code": { - "text": "Cellularity" - }, - "subject": { - "reference": "Patient/Patient-KayBurbridge-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "8449303541" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "699F01231423" - } - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "75540009", - "display": "High" - } - ] - }, - "effectiveDateTime": "2023-11-01T11:00:00Z" + "resourceType": "Observation", + "id": "Observation-CellularityKayBurbridge-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "text": "Cellularity" + }, + "subject": { + "reference": "Patient/Patient-KayBurbridge-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "8449303541" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "699F01231423" + } + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "75540009", + "display": "High" + } + ] + }, + "effectiveDateTime": "2023-11-01T11:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-CellularityPatrickSammy-Example.json b/Observation/Observation-CellularityPatrickSammy-Example.json index 625354a..f52c1a6 100644 --- a/Observation/Observation-CellularityPatrickSammy-Example.json +++ b/Observation/Observation-CellularityPatrickSammy-Example.json @@ -1,37 +1,46 @@ { - "resourceType": "Observation", - "id": "Observation-CellularityPatrickSammy-Example", - "status": "final", - "code": { - "text": "Cellularity" - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", + "resourceType": "Observation", + "id": "Observation-CellularityPatrickSammy-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "text": "Cellularity" + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", + "value": "RR81234", + "assigner": { "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" } - }, - "specimen": { - "identifier": { - "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", - "value": "RR81234", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "696B0" - } - } - } - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "75540009", - "display": "High" - } - ] - }, - "effectiveDateTime": "2023-08-29" + } + } + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "75540009", + "display": "High" + } + ] + }, + "effectiveDateTime": "2023-08-29" } \ No newline at end of file diff --git a/Observation/Observation-DelayedSpeechLanguageDevt-Example.json b/Observation/Observation-DelayedSpeechLanguageDevt-Example.json index 60b8b5d..4749a0c 100644 --- a/Observation/Observation-DelayedSpeechLanguageDevt-Example.json +++ b/Observation/Observation-DelayedSpeechLanguageDevt-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-DelayedSpeechLanguageDevt-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-31", + "display": "Patient clinical information - Suspected inborn error type(s)" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-DiseasePenetrance-Example.json b/Observation/Observation-DiseasePenetrance-Example.json index 0bdf7ab..4fec8b9 100644 --- a/Observation/Observation-DiseasePenetrance-Example.json +++ b/Observation/Observation-DiseasePenetrance-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-DiseasePenetrance-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-2", + "display": "Patient clinical information - Disease status" + } + ] + }, "status": "final", "code": { "coding": [ @@ -8,7 +17,7 @@ "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", "code": "R14", "display": "Acutely unwell children with a likely monogenic disorder", - "version": "7" + "version": "7" } ] }, diff --git a/Observation/Observation-DiseasePenetrancePheobeSmitham-Example.json b/Observation/Observation-DiseasePenetrancePheobeSmitham-Example.json index 8104c77..0a0d5ec 100644 --- a/Observation/Observation-DiseasePenetrancePheobeSmitham-Example.json +++ b/Observation/Observation-DiseasePenetrancePheobeSmitham-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-DiseasePenetrancePheobeSmitham-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-2", + "display": "Patient clinical information - Disease status" + } + ] + }, "status": "final", "code": { "coding": [ @@ -8,7 +17,7 @@ "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", "code": "R14", "display": "Acutely unwell children with a likely monogenic disorder", - "version": "7" + "version": "7" } ] }, diff --git a/Observation/Observation-DutchLipidScore-Example.json b/Observation/Observation-DutchLipidScore-Example.json index 685728b..f67053f 100644 --- a/Observation/Observation-DutchLipidScore-Example.json +++ b/Observation/Observation-DutchLipidScore-Example.json @@ -1,24 +1,33 @@ { - "resourceType": "Observation", - "id": "Observation-DutchLipidScore-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "872541000000104", - "display": "Dutch Lipid Clinic Network diagnostic criteria for familial hypercholesterolaemia score" - } - ], - "text": "Dutch or (Welsh) Lipid score" - }, - "subject": { - "reference": "Patient/Patient-FayMutlow-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307806" - } - }, - "effectiveDateTime": "2023-08-05", - "valueInteger": 7 + "resourceType": "Observation", + "id": "Observation-DutchLipidScore-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-2", + "display": "Patient clinical information - Disease status" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "872541000000104", + "display": "Dutch Lipid Clinic Network diagnostic criteria for familial hypercholesterolaemia score" + } + ], + "text": "Dutch or (Welsh) Lipid score" + }, + "subject": { + "reference": "Patient/Patient-FayMutlow-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307806" + } + }, + "effectiveDateTime": "2023-08-05", + "valueInteger": 7 } \ No newline at end of file diff --git a/Observation/Observation-EnlargedKidney-Example.json b/Observation/Observation-EnlargedKidney-Example.json index c20fe89..72674ab 100644 --- a/Observation/Observation-EnlargedKidney-Example.json +++ b/Observation/Observation-EnlargedKidney-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-EnlargedKidney-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-GenomicEthnicity-Example.json b/Observation/Observation-GenomicEthnicity-Example.json index d1cc744..e63ff54 100644 --- a/Observation/Observation-GenomicEthnicity-Example.json +++ b/Observation/Observation-GenomicEthnicity-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-GenomicEthnicity-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-1", + "display": "Patient clinical information - Genomic ethnicity" + } + ] + }, "status": "preliminary", "code": { "coding": [ diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index cf03581..28fe500 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -1,99 +1,108 @@ { - "resourceType": "Observation", - "id": "Observation-GenomicTherapeuticImplication-Example", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" - ] - }, - "status": "final", - "category": [ + "resourceType": "Observation", + "id": "Observation-GenomicTherapeuticImplication-Example", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" + ], + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "TR-39", + "display": "Test request - Linked test request reference" + } + ] + }, + "status": "final", + "category": [ + { + "coding": [ { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - }, + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + }, + { + "coding": [ { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" - } - ] + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE" } - ], - "code": { + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "2023-09-16", + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" + } + ], + "component": [ + { + "code": { "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication", + "display": "Therapeutic Implication" + } ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9661-5", + "display": "Presumed responsive" + } + ] + } }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" - }, - "effectiveDateTime": "2023-09-16", - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "derivedFrom": [ - { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication", - "display": "Therapeutic Implication" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9661-5", - "display": "Presumed responsive" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "Medication assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "438481000124108", - "display": "Riboflavin supplement" - } - ] - } - } - ], - "note" : [{ - "text" : "High dose riboflavin supplementation has been reported to ameliorate the progression of this disorder (Foley et al 2014 PMID22740598)" - }] + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "Medication assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "438481000124108", + "display": "Riboflavin supplement" + } + ] + } + } + ], + "note": [ + { + "text": "High dose riboflavin supplementation has been reported to ameliorate the progression of this disorder (Foley et al 2014 PMID22740598)" + } + ] } \ No newline at end of file diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 7a43773..817890c 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -5,6 +5,13 @@ "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" + ], + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "TR-28", + "display": "Test Request - Target type" + } ] }, "status": "final", @@ -220,9 +227,9 @@ } } ], - "partOf": [ - { - "reference": "Procedure/Procedure-GenomicStudy-Example" - } - ] + "partOf": [ + { + "reference": "Procedure/Procedure-GenomicStudy-Example" + } + ] } \ No newline at end of file diff --git a/Observation/Observation-Haemoglobin-Example.json b/Observation/Observation-Haemoglobin-Example.json index d47bc7e..30f6206 100644 --- a/Observation/Observation-Haemoglobin-Example.json +++ b/Observation/Observation-Haemoglobin-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-Haemoglobin-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "38082009", - "display": "Haemoglobin" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "valueQuantity": { - "value": 83, - "unit": "g/dl", - "system": "http://unitsofmeasure.org", - "code": "g/dL" - }, - "effectiveDateTime": "2023-09-03" + "resourceType": "Observation", + "id": "Observation-Haemoglobin-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-22", + "display": "Patient clinical information - Fetal haemoglobinopathy paternal screening genotype" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "38082009", + "display": "Haemoglobin" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "valueQuantity": { + "value": 83, + "unit": "g/dl", + "system": "http://unitsofmeasure.org", + "code": "g/dL" + }, + "effectiveDateTime": "2023-09-03" } \ No newline at end of file diff --git a/Observation/Observation-HepaticCysts-Example.json b/Observation/Observation-HepaticCysts-Example.json index 082d158..215bc14 100644 --- a/Observation/Observation-HepaticCysts-Example.json +++ b/Observation/Observation-HepaticCysts-Example.json @@ -1,24 +1,33 @@ { - "resourceType": "Observation", - "id": "Observation-HepaticCysts-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://human-phenotype-ontology.org", - "version": "20221005", - "code": "HP:0001407", - "display": "Hepatic cysts" - } - ] - }, - "subject": { - "reference": "Patient/Patient-LindsaySorrell-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307946" - } - }, - "effectiveDateTime": "2023-08-05", - "valueBoolean": false + "resourceType": "Observation", + "id": "Observation-HepaticCysts-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://human-phenotype-ontology.org", + "version": "20221005", + "code": "HP:0001407", + "display": "Hepatic cysts" + } + ] + }, + "subject": { + "reference": "Patient/Patient-LindsaySorrell-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307946" + } + }, + "effectiveDateTime": "2023-08-05", + "valueBoolean": false } \ No newline at end of file diff --git a/Observation/Observation-HistoryOfFetalLoss-Example.json b/Observation/Observation-HistoryOfFetalLoss-Example.json index 5ad7625..fdf3bf2 100644 --- a/Observation/Observation-HistoryOfFetalLoss-Example.json +++ b/Observation/Observation-HistoryOfFetalLoss-Example.json @@ -1,24 +1,33 @@ { - "resourceType": "Observation", - "id": "Observation-HistoryOfFetalLoss-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "161743003", - "display": "Past pregnancy history of stillbirth" - } - ], - "text": "Is the testing for a fetal loss from 24+0 or more weeks of gestation?" - }, - "subject": { - "reference": "Patient/Patient-RyanneBoulder-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307687" - } - }, - "effectiveDateTime": "2023-09-25", - "valueBoolean": false + "resourceType": "Observation", + "id": "Observation-HistoryOfFetalLoss-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-39", + "display": "Patient clinical information - Fetal gestation" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "161743003", + "display": "Past pregnancy history of stillbirth" + } + ], + "text": "Is the testing for a fetal loss from 24+0 or more weeks of gestation?" + }, + "subject": { + "reference": "Patient/Patient-RyanneBoulder-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307687" + } + }, + "effectiveDateTime": "2023-09-25", + "valueBoolean": false } \ No newline at end of file diff --git a/Observation/Observation-Immunodeficiency-Example.json b/Observation/Observation-Immunodeficiency-Example.json index 7341f38..34daa20 100644 --- a/Observation/Observation-Immunodeficiency-Example.json +++ b/Observation/Observation-Immunodeficiency-Example.json @@ -1,24 +1,33 @@ { - "resourceType": "Observation", - "id": "Observation-Immunodefficiency-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://human-phenotype-ontology.org", - "version": "20221005", - "code": "HP:0002721", - "display": "Immunodefficiency" - } - ] - }, - "subject": { - "reference": "Patient/Patient-JamesMetcalfe-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "7449306524" - } - }, - "effectiveDateTime": "2023-10-01", - "valueBoolean": true + "resourceType": "Observation", + "id": "Observation-Immunodefficiency-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://human-phenotype-ontology.org", + "version": "20221005", + "code": "HP:0002721", + "display": "Immunodefficiency" + } + ] + }, + "subject": { + "reference": "Patient/Patient-JamesMetcalfe-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "7449306524" + } + }, + "effectiveDateTime": "2023-10-01", + "valueBoolean": true } \ No newline at end of file diff --git a/Observation/Observation-IntellectualDisabilityMild-Example.json b/Observation/Observation-IntellectualDisabilityMild-Example.json index 7887c3c..4182ca1 100644 --- a/Observation/Observation-IntellectualDisabilityMild-Example.json +++ b/Observation/Observation-IntellectualDisabilityMild-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-IntellectualDisabilityMild-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-IntellectualDisabilityProfound-Example.json b/Observation/Observation-IntellectualDisabilityProfound-Example.json index 3469bf1..a1e0eef 100644 --- a/Observation/Observation-IntellectualDisabilityProfound-Example.json +++ b/Observation/Observation-IntellectualDisabilityProfound-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-IntellectualDisabilityProfound-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-MultipleRenalCysts-Example.json b/Observation/Observation-MultipleRenalCysts-Example.json index 8d6d3b5..f335edf 100644 --- a/Observation/Observation-MultipleRenalCysts-Example.json +++ b/Observation/Observation-MultipleRenalCysts-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-MultipleRenalCysts-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-NatureAndAgeOfHearingLoss-Example.json b/Observation/Observation-NatureAndAgeOfHearingLoss-Example.json index d6cb512..72def82 100644 --- a/Observation/Observation-NatureAndAgeOfHearingLoss-Example.json +++ b/Observation/Observation-NatureAndAgeOfHearingLoss-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-NatureAndAgeOfHearingLoss-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-17", + "display": "Patient clinical information - Laterality of hearing loss" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-Necrosis-Example.json b/Observation/Observation-Necrosis-Example.json index 11c671a..9b1cfb9 100644 --- a/Observation/Observation-Necrosis-Example.json +++ b/Observation/Observation-Necrosis-Example.json @@ -1,34 +1,43 @@ { - "resourceType": "Observation", - "id": "Observation-Necrosis-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "405921002", - "display": "Percentage of neoplasm involved by necrosis" - } - ] - }, - "subject": { - "reference": "Patient/Patient-ZelmaHadjkiss-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307555" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "RA257630" - } - }, - "valueQuantity": { - "value": 5, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-09-08" + "resourceType": "Observation", + "id": "Observation-Necrosis-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-13", + "display": "Primary Sample - Necrosis" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "405921002", + "display": "Percentage of neoplasm involved by necrosis" + } + ] + }, + "subject": { + "reference": "Patient/Patient-ZelmaHadjkiss-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307555" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257630" + } + }, + "valueQuantity": { + "value": 5, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-09-08" } \ No newline at end of file diff --git a/Observation/Observation-NecrosisKayBurbridge-Example.json b/Observation/Observation-NecrosisKayBurbridge-Example.json index eecc095..e8f72e5 100644 --- a/Observation/Observation-NecrosisKayBurbridge-Example.json +++ b/Observation/Observation-NecrosisKayBurbridge-Example.json @@ -1,34 +1,43 @@ { - "resourceType": "Observation", - "id": "Observation-NecrosisKayBurbridge-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "405921002", - "display": "Percentage of neoplasm involved by necrosis" - } - ] - }, - "subject": { - "reference": "Patient/Patient-KayBurbridge-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "8449303541" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "699F01231423" - } - }, - "valueQuantity": { - "value": 5, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-11-01T11:00:00Z" + "resourceType": "Observation", + "id": "Observation-NecrosisKayBurbridge-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-13", + "display": "Primary Sample - Necrosis" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "405921002", + "display": "Percentage of neoplasm involved by necrosis" + } + ] + }, + "subject": { + "reference": "Patient/Patient-KayBurbridge-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "8449303541" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "699F01231423" + } + }, + "valueQuantity": { + "value": 5, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-11-01T11:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-NeoplasticCell-Example.json b/Observation/Observation-NeoplasticCell-Example.json index 926cdf8..be0e9a0 100644 --- a/Observation/Observation-NeoplasticCell-Example.json +++ b/Observation/Observation-NeoplasticCell-Example.json @@ -1,34 +1,43 @@ { - "resourceType": "Observation", - "id": "Observation-NeoplasticCell-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "371510003", - "display": "Proportion of specimen involved by tumour" - } - ] - }, - "subject": { - "reference": "Patient/Patient-ZelmaHadjkiss-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307555" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "RA257630" - } - }, - "valueQuantity": { - "value": 25, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-09-08T10:00:00Z" + "resourceType": "Observation", + "id": "Observation-NeoplasticCell-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-26", + "display": "Primary Sample - Tumour nuclear content in marked area" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "371510003", + "display": "Proportion of specimen involved by tumour" + } + ] + }, + "subject": { + "reference": "Patient/Patient-ZelmaHadjkiss-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307555" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257630" + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-09-08T10:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-NeoplasticCellKayBurbridge-Example.json b/Observation/Observation-NeoplasticCellKayBurbridge-Example.json index b74356f..8754f63 100644 --- a/Observation/Observation-NeoplasticCellKayBurbridge-Example.json +++ b/Observation/Observation-NeoplasticCellKayBurbridge-Example.json @@ -1,34 +1,43 @@ { - "resourceType": "Observation", - "id": "Observation-NeoplasticCellKayBurbridge-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "371510003", - "display": "Proportion of specimen involved by tumour" - } - ] - }, - "subject": { - "reference": "Patient/Patient-KayBurbridge-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "8449303541" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "699F01231423" - } - }, - "valueQuantity": { - "value": 25, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-11-01T11:00:00Z" + "resourceType": "Observation", + "id": "Observation-NeoplasticCellKayBurbridge-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-26", + "display": "Primary Sample - Tumour nuclear content in marked area" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "371510003", + "display": "Proportion of specimen involved by tumour" + } + ] + }, + "subject": { + "reference": "Patient/Patient-KayBurbridge-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "8449303541" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "699F01231423" + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-11-01T11:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-Nephronophthisis-Example.json b/Observation/Observation-Nephronophthisis-Example.json index 9f56f03..f6f21f2 100644 --- a/Observation/Observation-Nephronophthisis-Example.json +++ b/Observation/Observation-Nephronophthisis-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-Nephronophthisis-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-Neutrophils-Example.json b/Observation/Observation-Neutrophils-Example.json index d2eebb8..365e065 100644 --- a/Observation/Observation-Neutrophils-Example.json +++ b/Observation/Observation-Neutrophils-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-Neutrophils-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1022551000000104", - "display": "Neutrophil count" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "valueQuantity": { - "value": 0.51, - "unit": "10^9/l", - "system": "http://unitsofmeasure.org", - "code": "10^9/L" - }, - "effectiveDateTime": "2023-09-03" + "resourceType": "Observation", + "id": "Observation-Neutrophils-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1022551000000104", + "display": "Neutrophil count" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "valueQuantity": { + "value": 0.51, + "unit": "10^9/l", + "system": "http://unitsofmeasure.org", + "code": "10^9/L" + }, + "effectiveDateTime": "2023-09-03" } \ No newline at end of file diff --git a/Observation/Observation-NoBoneMarrowTransplant-Example.json b/Observation/Observation-NoBoneMarrowTransplant-Example.json index 7c4e464..bf69c79 100644 --- a/Observation/Observation-NoBoneMarrowTransplant-Example.json +++ b/Observation/Observation-NoBoneMarrowTransplant-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoBoneMarrowTransplant-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "445715009", - "display": "Blood and marrow transplantation" - } - ] - }, - "subject": { - "reference": "Patient/Patient-LindsaySorrell-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307946" - } - }, - "effectiveDateTime": "2023-08-05" + "resourceType": "Observation", + "id": "Observation-NoBoneMarrowTransplant-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-42", + "display": "Patient clinical information - Had transplant" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445715009", + "display": "Blood and marrow transplantation" + } + ] + }, + "subject": { + "reference": "Patient/Patient-LindsaySorrell-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307946" + } + }, + "effectiveDateTime": "2023-08-05" } \ No newline at end of file diff --git a/Observation/Observation-NoBoneMarrowTransplantProbandFather-Example.json b/Observation/Observation-NoBoneMarrowTransplantProbandFather-Example.json index 916ce56..803359b 100644 --- a/Observation/Observation-NoBoneMarrowTransplantProbandFather-Example.json +++ b/Observation/Observation-NoBoneMarrowTransplantProbandFather-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoBoneMarrowTransplantProbandFather-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "445715009", - "display": "Blood and marrow transplantation" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmithamFather-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307636" - } - }, - "effectiveDateTime": "2023-09-15T15:00:00Z" + "resourceType": "Observation", + "id": "Observation-NoBoneMarrowTransplantProbandFather-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-42", + "display": "Patient clinical information - Had transplant" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445715009", + "display": "Blood and marrow transplantation" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmithamFather-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307636" + } + }, + "effectiveDateTime": "2023-09-15T15:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-NoBoneMarrowTransplantProbandMother-Example.json b/Observation/Observation-NoBoneMarrowTransplantProbandMother-Example.json index f495146..be6b371 100644 --- a/Observation/Observation-NoBoneMarrowTransplantProbandMother-Example.json +++ b/Observation/Observation-NoBoneMarrowTransplantProbandMother-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoBoneMarrowTransplantProbandMother-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "445715009", - "display": "Blood and marrow transplantation" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmithamMother-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307246" - } - }, - "effectiveDateTime": "2023-09-15T15:00:00Z" + "resourceType": "Observation", + "id": "Observation-NoBoneMarrowTransplantProbandMother-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-42", + "display": "Patient clinical information - Had transplant" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445715009", + "display": "Blood and marrow transplantation" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmithamMother-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307246" + } + }, + "effectiveDateTime": "2023-09-15T15:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-NoFirstTrimesterFetalAnomalies-Example.json b/Observation/Observation-NoFirstTrimesterFetalAnomalies-Example.json index ee2c0c9..7fd7246 100644 --- a/Observation/Observation-NoFirstTrimesterFetalAnomalies-Example.json +++ b/Observation/Observation-NoFirstTrimesterFetalAnomalies-Example.json @@ -1,37 +1,46 @@ { - "resourceType": "Observation", - "id": "Observation-NoFirstTrimesterFetalAnomalies-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "609520005", - "display": "Disorder of fetal structure" - } - ], - "text": "First Trimester Anomalies?" - }, - "subject": { - "reference": "Patient/Patient-RyanneBoulder-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307687" - } - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "255246003", - "display": "First trimester" - } - ] - } - } + "resourceType": "Observation", + "id": "Observation-NoFirstTrimesterFetalAnomalies-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-39", + "display": "Patient clinical information - Fetal gestation" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "609520005", + "display": "Disorder of fetal structure" + } ], - "effectiveDateTime": "2023-09-25", - "valueBoolean": false + "text": "First Trimester Anomalies?" + }, + "subject": { + "reference": "Patient/Patient-RyanneBoulder-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307687" + } + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "255246003", + "display": "First trimester" + } + ] + } + } + ], + "effectiveDateTime": "2023-09-25", + "valueBoolean": false } \ No newline at end of file diff --git a/Observation/Observation-NoPregnancy-Example.json b/Observation/Observation-NoPregnancy-Example.json index 1d19221..1a6648d 100644 --- a/Observation/Observation-NoPregnancy-Example.json +++ b/Observation/Observation-NoPregnancy-Example.json @@ -1,22 +1,31 @@ { - "resourceType": "Observation", - "id": "Observation-NoPregnancy-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "60001007", - "display": "Not pregnant" - } - ] - }, - "subject": { - "reference": "Patient/Patient-MeirLieberman-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "effectiveDateTime": "2023-08-05" + "resourceType": "Observation", + "id": "Observation-NoPregnancy-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-36", + "display": "Patient clinical information - Pregnancy status" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "60001007", + "display": "Not pregnant" + } + ] + }, + "subject": { + "reference": "Patient/Patient-MeirLieberman-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-08-05" } \ No newline at end of file diff --git a/Observation/Observation-NoSecondTrimesterFetalAnomalies-Example.json b/Observation/Observation-NoSecondTrimesterFetalAnomalies-Example.json index 76efa8f..80c1474 100644 --- a/Observation/Observation-NoSecondTrimesterFetalAnomalies-Example.json +++ b/Observation/Observation-NoSecondTrimesterFetalAnomalies-Example.json @@ -1,38 +1,46 @@ { - "resourceType": "Observation", - "id": "Observation-NoSecondTrimesterFetalAnomalies-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "609520005", - "display": "Disorder of fetal structure" - } - ], - "text": "Second Trimester Anomalies?" - - }, - "subject": { - "reference": "Patient/Patient-RyanneBoulder-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307687" - } - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "255247007", - "display": "Second trimester" - } - ] - } - } + "resourceType": "Observation", + "id": "Observation-NoSecondTrimesterFetalAnomalies-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-39", + "display": "Patient clinical information - Fetal gestation" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "609520005", + "display": "Disorder of fetal structure" + } ], - "effectiveDateTime": "2023-09-25", - "valueBoolean": false + "text": "Second Trimester Anomalies?" + }, + "subject": { + "reference": "Patient/Patient-RyanneBoulder-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307687" + } + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "255247007", + "display": "Second trimester" + } + ] + } + } + ], + "effectiveDateTime": "2023-09-25", + "valueBoolean": false } \ No newline at end of file diff --git a/Observation/Observation-NoTransfusion-Example.json b/Observation/Observation-NoTransfusion-Example.json index 8f3b496..66eea21 100644 --- a/Observation/Observation-NoTransfusion-Example.json +++ b/Observation/Observation-NoTransfusion-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoTransfusion-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "303955003", - "display": "Transfusion - action" - } - ] - }, - "subject": { - "reference": "Patient/Patient-MeirLieberman-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "effectiveDateTime": "2023-08-05" + "resourceType": "Observation", + "id": "Observation-NoTransfusion-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-45", + "display": "Patient clinical information - Had transfusion in the last 6 weeks" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "303955003", + "display": "Transfusion - action" + } + ] + }, + "subject": { + "reference": "Patient/Patient-MeirLieberman-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-08-05" } \ No newline at end of file diff --git a/Observation/Observation-NoTransfusionProbandFather-Example.json b/Observation/Observation-NoTransfusionProbandFather-Example.json index 6e085cc..150c630 100644 --- a/Observation/Observation-NoTransfusionProbandFather-Example.json +++ b/Observation/Observation-NoTransfusionProbandFather-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoTransfusionProbandFather-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "303955003", - "display": "Transfusion - action" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmithamFather-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307636" - } - }, - "effectiveDateTime": "2023-09-15T15:00:00Z" + "resourceType": "Observation", + "id": "Observation-NoTransfusionProbandFather-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-45", + "display": "Patient clinical information - Had transfusion in the last 6 weeks" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "303955003", + "display": "Transfusion - action" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmithamFather-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307636" + } + }, + "effectiveDateTime": "2023-09-15T15:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-NoTransfusionProbandMother-Example.json b/Observation/Observation-NoTransfusionProbandMother-Example.json index 1789b7e..988958f 100644 --- a/Observation/Observation-NoTransfusionProbandMother-Example.json +++ b/Observation/Observation-NoTransfusionProbandMother-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoTransfusionProbandMother-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "303955003", - "display": "Transfusion - action" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmithamMother-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307246" - } - }, - "effectiveDateTime": "2023-09-15T15:00:00Z" + "resourceType": "Observation", + "id": "Observation-NoTransfusionProbandMother-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-45", + "display": "Patient clinical information - Had transfusion in the last 6 weeks" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "303955003", + "display": "Transfusion - action" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmithamMother-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307246" + } + }, + "effectiveDateTime": "2023-09-15T15:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-NoTransplant-Example.json b/Observation/Observation-NoTransplant-Example.json index f1954ca..7d93006 100644 --- a/Observation/Observation-NoTransplant-Example.json +++ b/Observation/Observation-NoTransplant-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-NoTransplant-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "263903005", - "display": "Transplant" - } - ] - }, - "subject": { - "reference": "Patient/Patient-MeirLieberman-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "effectiveDateTime": "2023-08-05" + "resourceType": "Observation", + "id": "Observation-NoTransplant-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-42", + "display": "Patient clinical information - Had transplant" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "263903005", + "display": "Transplant" + } + ] + }, + "subject": { + "reference": "Patient/Patient-MeirLieberman-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-08-05" } \ No newline at end of file diff --git a/Observation/Observation-NonConsanguinousUnion-Example.json b/Observation/Observation-NonConsanguinousUnion-Example.json index 85e5831..50bf3c8 100644 --- a/Observation/Observation-NonConsanguinousUnion-Example.json +++ b/Observation/Observation-NonConsanguinousUnion-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-NonConsanguinousUnion-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "P-13", + "display": "Patient - Is from consanguineous union" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-NonConsanguinousUnionProband-Example.json b/Observation/Observation-NonConsanguinousUnionProband-Example.json index 82e265a..d4815b6 100644 --- a/Observation/Observation-NonConsanguinousUnionProband-Example.json +++ b/Observation/Observation-NonConsanguinousUnionProband-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-NonConsanguinousUnionProband-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "P-13", + "display": "Patient - Is from consanguineous union" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-NonConsanguinousUnionProbandFather-Example.json b/Observation/Observation-NonConsanguinousUnionProbandFather-Example.json index 1d09119..2d9873a 100644 --- a/Observation/Observation-NonConsanguinousUnionProbandFather-Example.json +++ b/Observation/Observation-NonConsanguinousUnionProbandFather-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-NonConsanguinousUnionProbandFather-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "P-13", + "display": "Patient - Is from consanguineous union" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-NonConsanguinousUnionProbandMother-Example.json b/Observation/Observation-NonConsanguinousUnionProbandMother-Example.json index 8afe035..11543d2 100644 --- a/Observation/Observation-NonConsanguinousUnionProbandMother-Example.json +++ b/Observation/Observation-NonConsanguinousUnionProbandMother-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-NonConsanguinousUnionProbandMother-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "P-13", + "display": "Patient - Is from consanguineous union" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-NucleatedCellCount-Example.json b/Observation/Observation-NucleatedCellCount-Example.json index 42e4f1d..66ad2b5 100644 --- a/Observation/Observation-NucleatedCellCount-Example.json +++ b/Observation/Observation-NucleatedCellCount-Example.json @@ -1,40 +1,49 @@ { - "resourceType": "Observation", - "id": "Observation-NucleatedCellCount-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1022461000000100", - "display": "Nucleated red blood cell count" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", + "resourceType": "Observation", + "id": "Observation-NucleatedCellCount-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1022461000000100", + "display": "Nucleated red blood cell count" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", + "value": "RR81234", + "assigner": { "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" } - }, - "specimen": { - "identifier": { - "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", - "value": "RR81234", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "696B0" - } - } - } - }, - "valueQuantity": { - "value": 10, - "unit": "10^12/l", - "system": "http://unitsofmeasure.org", - "code": "10^12/L" - }, - "effectiveDateTime": "2023-08-29" + } + } + }, + "valueQuantity": { + "value": 10, + "unit": "10^12/l", + "system": "http://unitsofmeasure.org", + "code": "10^12/L" + }, + "effectiveDateTime": "2023-08-29" } \ No newline at end of file diff --git a/Observation/Observation-NucleatedCellCountWGSSample-Example.json b/Observation/Observation-NucleatedCellCountWGSSample-Example.json index 87509f3..e5343ea 100644 --- a/Observation/Observation-NucleatedCellCountWGSSample-Example.json +++ b/Observation/Observation-NucleatedCellCountWGSSample-Example.json @@ -1,40 +1,49 @@ { - "resourceType": "Observation", - "id": "Observation-NucleatedCellCountWGSSample-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1022461000000100", - "display": "Nucleated red blood cell count" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", + "resourceType": "Observation", + "id": "Observation-NucleatedCellCountWGSSample-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1022461000000100", + "display": "Nucleated red blood cell count" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", + "value": "RR81235", + "assigner": { "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" } - }, - "specimen": { - "identifier": { - "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19", - "value": "RR81235", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "696B0" - } - } - } - }, - "valueQuantity": { - "value": 10, - "unit": "10^12/l", - "system": "http://unitsofmeasure.org", - "code": "10^12/L" - }, - "effectiveDateTime": "2023-09-05" + } + } + }, + "valueQuantity": { + "value": 10, + "unit": "10^12/l", + "system": "http://unitsofmeasure.org", + "code": "10^12/L" + }, + "effectiveDateTime": "2023-09-05" } \ No newline at end of file diff --git a/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json b/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json index 3fcbe71..f0b6d38 100644 --- a/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json +++ b/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json @@ -1,31 +1,40 @@ { - "resourceType": "Observation", - "id": "Observation-PatrickSammyNoBoneMarrowTransplant-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "416128008", - "display": "No history of procedure" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "445715009", - "display": "Blood and marrow transplantation" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "effectiveDateTime": "2023-09-05" + "resourceType": "Observation", + "id": "Observation-PatrickSammyNoBoneMarrowTransplant-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-42", + "display": "Patient clinical information - Had transplant" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445715009", + "display": "Blood and marrow transplantation" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-09-05" } \ No newline at end of file diff --git a/Observation/Observation-PercentageMalignantNuclei-Example.json b/Observation/Observation-PercentageMalignantNuclei-Example.json index cf0f4c5..3a7700b 100644 --- a/Observation/Observation-PercentageMalignantNuclei-Example.json +++ b/Observation/Observation-PercentageMalignantNuclei-Example.json @@ -1,41 +1,50 @@ { - "resourceType": "Observation", - "id": "Observation-PercentageMalignantNuclei-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1015521000000107", - "display": "Percentage blast cells" - } - ] - }, - "subject": { - "reference": "Patient/Patient-DemeizaSeo-Example", + "resourceType": "Observation", + "id": "Observation-PercentageMalignantNuclei-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-23", + "display": "Primary Sample - Blasts %" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1015521000000107", + "display": "Percentage blast cells" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "specimen": { + "reference": "Specimen/Specimen-SolidTumorDemeizaSeo-Example", + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257631", + "assigner": { "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449306559" + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" } - }, - "specimen": { - "reference":"Specimen/Specimen-SolidTumorDemeizaSeo-Example", - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "RA257631", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "696B0" - } - } - } - }, - "valueQuantity": { - "value": 25, - "unit": "%", - "system": "http://unitsofmeasure.org", - "code": "%" - }, - "effectiveDateTime": "2023-08-09" + } + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-08-09" } \ No newline at end of file diff --git a/Observation/Observation-Platelets-Example.json b/Observation/Observation-Platelets-Example.json index 2daeb55..c7018dc 100644 --- a/Observation/Observation-Platelets-Example.json +++ b/Observation/Observation-Platelets-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-Platelets-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1022651000000100", - "display": "Platelet count" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "valueQuantity": { - "value": 100, - "unit": "10^9/l", - "system": "http://unitsofmeasure.org", - "code": "10^9/L" - }, - "effectiveDateTime": "2023-09-03" + "resourceType": "Observation", + "id": "Observation-Platelets-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1022651000000100", + "display": "Platelet count" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "valueQuantity": { + "value": 100, + "unit": "10^9/l", + "system": "http://unitsofmeasure.org", + "code": "10^9/L" + }, + "effectiveDateTime": "2023-09-03" } \ No newline at end of file diff --git a/Observation/Observation-PregnancyConfirmation-Example.json b/Observation/Observation-PregnancyConfirmation-Example.json index 284586b..ba41025 100644 --- a/Observation/Observation-PregnancyConfirmation-Example.json +++ b/Observation/Observation-PregnancyConfirmation-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-PregnancyConfirmation-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-36", + "display": "Patient clinical information - Pregnancy status" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-QueryXanthoma-Example.json b/Observation/Observation-QueryXanthoma-Example.json index fa390b5..a45618f 100644 --- a/Observation/Observation-QueryXanthoma-Example.json +++ b/Observation/Observation-QueryXanthoma-Example.json @@ -1,23 +1,32 @@ { - "resourceType": "Observation", - "id": "Observation-QueryXanthoma-Example", - "status": "final", -"code": { + "resourceType": "Observation", + "id": "Observation-QueryXanthoma-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-2", + "display": "Patient clinical information - Disease status" + } + ] + }, + "status": "final", + "code": { "coding": [ - { - "system": "http://snomed.info/sct", - "code": "75594004", - "display": "Xanthomatous deposition" - } + { + "system": "http://snomed.info/sct", + "code": "75594004", + "display": "Xanthomatous deposition" + } ], "text": "Physical Characteristics = query xanthoma" - }, - "subject": { - "reference": "Patient/Patient-FayMutlow-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307806" - } - }, - "effectiveDateTime": "2023-08-05" + }, + "subject": { + "reference": "Patient/Patient-FayMutlow-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307806" + } + }, + "effectiveDateTime": "2023-08-05" } \ No newline at end of file diff --git a/Observation/Observation-RenalInsufficiency-Example.json b/Observation/Observation-RenalInsufficiency-Example.json index 20d17e8..58f98fc 100644 --- a/Observation/Observation-RenalInsufficiency-Example.json +++ b/Observation/Observation-RenalInsufficiency-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-RenalInsufficiency-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-6", + "display": "Patient clinical information - Phenotypic details" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-SimonBroomeCriteria-Example.json b/Observation/Observation-SimonBroomeCriteria-Example.json index 2347ef5..ceda546 100644 --- a/Observation/Observation-SimonBroomeCriteria-Example.json +++ b/Observation/Observation-SimonBroomeCriteria-Example.json @@ -1,24 +1,33 @@ { - "resourceType": "Observation", - "id": "Observation-SimonBroomeCriteria-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "149611000000100", - "display": "Simon Broome diagnostic criteria for familial hypercholesterolaemia result" - } - ], - "text": "Simon Broome Criteria" - }, - "subject": { - "reference": "Patient/Patient-FayMutlow-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307806" - } - }, - "effectiveDateTime": "2023-08-05", + "resourceType": "Observation", + "id": "Observation-SimonBroomeCriteria-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PCI-2", + "display": "Patient clinical information - Disease status" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "149611000000100", + "display": "Simon Broome diagnostic criteria for familial hypercholesterolaemia result" + } + ], + "text": "Simon Broome Criteria" + }, + "subject": { + "reference": "Patient/Patient-FayMutlow-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307806" + } + }, + "effectiveDateTime": "2023-08-05", "valueString": "Suspected FH" } \ No newline at end of file diff --git a/Observation/Observation-TumourType-Example.json b/Observation/Observation-TumourType-Example.json index a88599e..c96371d 100644 --- a/Observation/Observation-TumourType-Example.json +++ b/Observation/Observation-TumourType-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-TumourType-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "14799000", - "display": "Neoplasm, metastatic" - } - ] - }, - "subject": { - "reference": "Patient/Patient-KayBurbridge-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307555" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "RA257630" - } - }, - "effectiveDateTime": "2023-09-08T10:00:00Z" + "resourceType": "Observation", + "id": "Observation-TumourType-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-35", + "display": "Primary Sample - Solid tumour type" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "14799000", + "display": "Neoplasm, metastatic" + } + ] + }, + "subject": { + "reference": "Patient/Patient-KayBurbridge-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307555" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257630" + } + }, + "effectiveDateTime": "2023-09-08T10:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-TumourTypeDemeizaSeo-Example.json b/Observation/Observation-TumourTypeDemeizaSeo-Example.json index 861df03..e68f9b0 100644 --- a/Observation/Observation-TumourTypeDemeizaSeo-Example.json +++ b/Observation/Observation-TumourTypeDemeizaSeo-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-TumourTypeDemeizaSeo-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "369757002", - "display": "Solid tumor configuration" - } - ] - }, - "subject": { - "reference": "Patient/Patient-DemeizaSeo-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449306559" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "RA257631" - } - }, - "effectiveDateTime": "2023-09-08T11:00:00Z" + "resourceType": "Observation", + "id": "Observation-TumourTypeDemeizaSeo-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-26", + "display": "Primary Sample - Tumour nuclear content in marked area" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "369757002", + "display": "Solid tumor configuration" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257631" + } + }, + "effectiveDateTime": "2023-09-08T11:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-TumourTypeKayBurbridge-Example.json b/Observation/Observation-TumourTypeKayBurbridge-Example.json index 58c4cac..3e1efa2 100644 --- a/Observation/Observation-TumourTypeKayBurbridge-Example.json +++ b/Observation/Observation-TumourTypeKayBurbridge-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-TumourTypeKayBurbridge-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "14799000", - "display": "Neoplasm, metastatic" - } - ] - }, - "subject": { - "reference": "Patient/Patient-KayBurbridge-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "8449303541" - } - }, - "specimen": { - "identifier": { - "system": "https://fhir.add.nhs.uk/Id/specimenId", - "value": "699F01231423" - } - }, - "effectiveDateTime": "2023-11-01T11:00:00Z" + "resourceType": "Observation", + "id": "Observation-TumourTypeKayBurbridge-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-35", + "display": "Primary Sample - Solid tumour type" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "14799000", + "display": "Neoplasm, metastatic" + } + ] + }, + "subject": { + "reference": "Patient/Patient-KayBurbridge-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "8449303541" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "699F01231423" + } + }, + "effectiveDateTime": "2023-11-01T11:00:00Z" } \ No newline at end of file diff --git a/Observation/Observation-UnknownConsanguinousUnionStatus-Example.json b/Observation/Observation-UnknownConsanguinousUnionStatus-Example.json index 43baefc..4deaad2 100644 --- a/Observation/Observation-UnknownConsanguinousUnionStatus-Example.json +++ b/Observation/Observation-UnknownConsanguinousUnionStatus-Example.json @@ -1,6 +1,15 @@ { "resourceType": "Observation", "id": "Observation-UnknownConsanguinousUnionStatus-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "P-13", + "display": "Patient - Is from consanguineous union" + } + ] + }, "status": "final", "code": { "coding": [ diff --git a/Observation/Observation-WhiteBloodCell-Example.json b/Observation/Observation-WhiteBloodCell-Example.json index a899d3c..c292f6d 100644 --- a/Observation/Observation-WhiteBloodCell-Example.json +++ b/Observation/Observation-WhiteBloodCell-Example.json @@ -1,28 +1,37 @@ { - "resourceType": "Observation", - "id": "Observation-WhiteBloodCell-Example", - "status": "final", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "767002", - "display": "White blood cell count - observation" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PatrickSammy-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307873" - } - }, - "valueQuantity": { - "value": 11.9, - "unit": "10^9/L", - "system": "http://unitsofmeasure.org", - "code": "10^9/L" - }, - "effectiveDateTime": "2023-09-03" + "resourceType": "Observation", + "id": "Observation-WhiteBloodCell-Example", + "meta": { + "tag": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", + "code": "PS-14", + "display": "Primary Sample - Nucleated cell count" + } + ] + }, + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "767002", + "display": "White blood cell count - observation" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "valueQuantity": { + "value": 11.9, + "unit": "10^9/L", + "system": "http://unitsofmeasure.org", + "code": "10^9/L" + }, + "effectiveDateTime": "2023-09-03" } \ No newline at end of file diff --git a/ValueSet/ValueSet-Genomics-mds-questiontag.json b/ValueSet/ValueSet-Genomics-mds-questiontag.json deleted file mode 100644 index b52c712..0000000 --- a/ValueSet/ValueSet-Genomics-mds-questiontag.json +++ /dev/null @@ -1,1158 +0,0 @@ -{ - "resourceType": "ValueSet", - "id": "genomics-mdsquestiontag", - "url": "https://fhir.nhs.uk/ValueSet/genomics-mdsquestiontag", - "version": "0.1.0", - "name": "GenomicsmdsQuestionTag", - "title": "Genomics MDS Question Tag", - "status": "draft", - "date": "2025-07-29T00:00:00.000Z", - "publisher": "NHS England", - "contact": [ - { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net" - } - ] - } - ], - "description": "A ValueSet used to map MDS Dataset to FHIR Resources.This is intended to be used on Resource.meta.tag.", - "copyright": "Copyright © 2025+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "compose": { - "include": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "version": "0.1.0" - } - ] - }, - "expansion": { - "timestamp": "2025-07-29T00:00:00Z", - "total": 219, - "offset": 0, - "contains": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "datagroup-healthcare-professional", - "display": "Healthcare Professional", - "contains": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-1", - "display": "HCP - Genomic test order role" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-2", - "display": "HCP - Full name" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-3", - "display": "HCP - Job title" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-4", - "display": "HCP - Current specialty" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-5", - "display": "HCP - Phone" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-6", - "display": "HCP - Email address" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-7", - "display": "HCP - Organisation name" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-8", - "display": "HCP - Organisation address" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-9", - "display": "HCP - Organisation ODS code" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-10", - "display": "HCP - Department name" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/mds-questiontag-genomics", - "code": "HCP-11", - "display": "HCP - Professional registration number" - 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