diff --git a/.DS_Store b/.DS_Store index 17556db9..bdb9c9c3 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/.gitignore b/.gitignore index cba8be5f..3f503cd6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ /.vscode .DS_Store +.DS_Store diff --git a/parking_lot/CBC-Hold.txt b/parking_lot/CBC-Hold.txt index 73e8f595..ba0c6026 100644 --- a/parking_lot/CBC-Hold.txt +++ b/parking_lot/CBC-Hold.txt @@ -21,80 +21,80 @@ includes 0..1 PlateletMeanVolumeEntVolPtBldQnAutomatedCount EntryElement: LeukocytesNCncPtBldQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Leukocytes [#/​volume] in Blood by Automated count" Code is LNC#6690-2 "Leukocytes [#/​volume] in Blood by Automated count" DataValue.Quantity.Units is UCUM#10*3/uL EntryElement: ErythrocytesNCncPtBldQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Erythrocytes [#/​volume] in Blood by Automated count" Code is LNC#789-8 "Erythrocytes [#/​volume] in Blood by Automated count" DataValue.Quantity.Units is UCUM#10*6/uL EntryElement: HemoglobinMCncPtBldQn -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Hemoglobin [Mass/​volume] in Blood" Code is LNC#718-7 "Hemoglobin [Mass/​volume] in Blood" DataValue.Quantity.Units is UCUM#g/dL EntryElement: HematocritVFrPtBldQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Hematocrit [Volume Fraction] of Blood by Automated count" Code is LNC#4544-3 "Hematocrit [Volume Fraction] of Blood by Automated count" DataValue.Quantity.Units is UCUM#% EntryElement: ErythrocyteMeanCorpuscularVolumeEntVolPtRBCQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "MCV [Entitic volume] by Automated count" Code is LNC#787-2 "MCV [Entitic volume] by Automated count" DataValue.Quantity.Units is UCUM#fL EntryElement: ErythrocyteMeanCorpuscularHemoglobinEntMassPtRBCQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "MCH [Entitic mass] by Automated count" Code is LNC#785-6 "MCH [Entitic mass] by Automated count" DataValue.Quantity.Units is UCUM#pg EntryElement: ErythrocyteMeanCorpuscularHemoglobinConcentrationMCncPtRBCQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "MCHC [Mass/​volume] by Automated count" Code is LNC#786-4 "MCHC [Mass/​volume] by Automated count" DataValue.Quantity.Units is UCUM#g/dL EntryElement: ErythrocyteDistributionWidthEntVolPtRBCQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Erythrocyte distribution width [Entitic volume] by Automated count" Code is LNC#21000-5 "Erythrocyte distribution width [Entitic volume] by Automated count" DataValue.Quantity.Units is UCUM#fL EntryElement: ErythrocyteDistributionWidthRatioPtRBCQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Erythrocyte distribution width [Ratio] by Automated count" Code is LNC#788-0 "Erythrocyte distribution width [Ratio] by Automated count" DataValue.Quantity.Units is UCUM#% EntryElement: PlateletsNCncPtBldQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Platelets [#/​volume] in Blood by Automated count" Code is LNC#777-3 "Platelets [#/​volume] in Blood by Automated count" DataValue.Quantity.Units is UCUM#10*3/uL EntryElement: PlateletDistributionWidthEntVolPtBldQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Platelet distribution width [Entitic volume] in Blood by Automated count" Code is LNC#32207-3 "Platelet distribution width [Entitic volume] in Blood by Automated count" DataValue.Quantity.Units is UCUM#fL EntryElement: PlateletMeanVolumeEntVolPtBldQnAutomatedCount -SimpleQuantitativeLaboratoryObservation +Parent: SimpleQuantitativeLaboratoryObservation Description: "Platelet mean volume [Entitic volume] in Blood by Automated count" Code is LNC#32623-1 "Platelet mean volume [Entitic volume] in Blood by Automated count" DataValue.Quantity.Units is UCUM#fL EntryElement: UrinalysisDipstickPanelPtUrineTestStripAutomated -Based on: Panel +Parent: Panel Description: "Urinalysis dipstick panel - Urine by Automated test strip" 1..1 SubjectOfRecord value is type ref(Patient) Code is LNC#50556-0 "Urinalysis dipstick panel - Urine by Automated test strip" @@ -102,18 +102,18 @@ Description: "Urinalysis dipstick panel - Urine by Automated test strip" includes 0..* UrinalysisDipstickPanelMember EntryElement: UrinalysisDipstickPanelMember - Based on: LaboratoryObservation + Parent: LaboratoryObservation Description: "Members of Urinalysis dipstick panel LNC#50556-0" Code from UrinalysisDipstickPanelMembersVS EntryElement: HepaticFunction2000Panel-SerumOrPlasma -Based on: Panel +Parent: Panel Description: "24325-3 Hepatic function 2000 panel - Serum or Plasma" Code is LNC#24325-3 "Hepatic function 2000 panel - Serum or Plasma" PanelMembers.Observation includes 0..* HepaticFunction2000PanelMember EntryElement: HepaticFunction2000PanelMember - Based on: LaboratoryObservation + Parent: LaboratoryObservation Description: "Members of Hepatic Function 2000 panel LNC#24325-3" Code from HepaticFunctionPanelMembersVS \ No newline at end of file diff --git a/spec/.DS_Store b/spec/.DS_Store index 6b418ba4..06b4b281 100644 Binary files a/spec/.DS_Store and b/spec/.DS_Store differ diff --git a/spec/.vscode/settings.json b/spec/.vscode/settings.json new file mode 100644 index 00000000..7a73a41b --- /dev/null +++ b/spec/.vscode/settings.json @@ -0,0 +1,2 @@ +{ +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODECancerStageGroupExample01.json b/spec/Examples_mCODE_dstu2/mCODECancerStageGroupExample01.json similarity index 89% rename from spec/Examples_mCODE/mCODECancerStageGroupExample01.json rename to spec/Examples_mCODE_dstu2/mCODECancerStageGroupExample01.json index 43f2a848..adb50267 100644 --- a/spec/Examples_mCODE/mCODECancerStageGroupExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODECancerStageGroupExample01.json @@ -41,7 +41,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://cancerstaging.org", + "system": "http://cancerstaging.org", "code": "3C", "display": "IIIC" } @@ -50,7 +50,9 @@ "extension": [ { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", - "reference": "Condition/mCODEPrimaryCancerConditionExample01" + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } } ] } \ No newline at end of file diff --git a/spec/Examples_mCODE_dstu2/mCODECancerStageGroupExample02.json b/spec/Examples_mCODE_dstu2/mCODECancerStageGroupExample02.json new file mode 100644 index 00000000..d0598e36 --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODECancerStageGroupExample02.json @@ -0,0 +1,58 @@ +{ + "resourceType": "Observation", + "id": "mCODECancerStageGroupExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-CancerStageGroup" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Cancer Stage Group ***

Name: Eve M. Anyperson

MRN: m456

Date: 05/01/19

Cancer staging system: AJCC Version 8

Stage group: IIIC

" + }, + "status": "final", + "category": + { + "coding": [ + { + "system": "http://hl7.org/fhir/observation-category", + "code": "laboratory" + } + ] + }, + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21908-9", + "display": "Stage group.clinical Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve M. Anyperson" + }, + "effectiveDateTime": "2019-05-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "3A", + "display": "IIIA" + } + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample02" + } + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODEGeneticVariantFoundExample01.json b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantFoundExample01.json similarity index 84% rename from spec/Examples_mCODE/mCODEGeneticVariantFoundExample01.json rename to spec/Examples_mCODE_dstu2/mCODEGeneticVariantFoundExample01.json index b2fefbf1..cd5bc9ac 100644 --- a/spec/Examples_mCODE/mCODEGeneticVariantFoundExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantFoundExample01.json @@ -11,20 +11,21 @@ "div": "
\n\t\t\t

\n\t\t\t\t*** mCODE Example: Genetic Variant Assessment ***\n\t\t\t

\n\t\t\t

\n\t\t\t\tPatient identifier: m123

\n\t\t\t

Name: John B. Anyperson

\n\t\t\t

\n\t\t\t\tTest date: April 1, 2019

\n\t\t\t

\n\t\t\t\tGenomic source class [Type]: Somatic

\n\t\t\t

\n\t\t\t\tVariant HGVS name: NM_000455.4:c.921-1G>C

\n\t\t\t

Variant common name: G242E

\n\t\t\t
" }, "status": "final", - "category": - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - }, + "category" : { + "coding" : [ + { + "system" : "http://hl7.org/fhir/observation-category", + "code" : "laboratory", + "userSelected": false + } + ], + "text" : "Laboratory" + }, "method": { "coding": [ { - "system": "https://ncit.nci.nih.gov", + "system": "http://ncit.nci.nih.gov", "code": "C101293", "display": "Next Generation Sequencing" } @@ -58,7 +59,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "http://hl7.org/fhir/us/mcode/onco-core/vs/GenomicSourceClassVS", + "system": "http://loinc.org", "code": "LA6684-0", "display": "Somatic" } @@ -72,14 +73,14 @@ { "system": "http://loinc.org", "code": "48003-8", - "display": "DNA sequence variation identifier" + "display": "DNA sequence variation identifier [Identifier]" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/clinvar", + "system": "http://www.ncbi.nlm.nih.gov/clinvar/", "code": "619728", "display": "NM_000455.4(STK11):c.725G>A (p.Gly242Glu)" } @@ -114,7 +115,7 @@ { "system": "http://loinc.org", "code": "47998-0", - "display": "DNA sequence variation display name" + "display": "DNA sequence variation display name [Text] Narrative" } ] }, diff --git a/spec/Examples_mCODE_dstu2/mCODEGeneticVariantFoundExample02.json b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantFoundExample02.json new file mode 100644 index 00000000..412c60be --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantFoundExample02.json @@ -0,0 +1,125 @@ +{ + "resourceType": "Observation", + "id": "mCODEGeneticVariantFoundExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantFound" + ] + }, + "text": { + "status": "generated", + "div": "
\n\t\t\t

\n\t\t\t\t*** mCODE Example: Genetic Variant Assessment ***\n\t\t\t

\n\t\t\t

\n\t\t\t\tPatient identifier: m456

\n\t\t\t

Name: Eve M. Anyperson

\n\t\t\t

\n\t\t\t\tTest date: June 5, 2019

\n\t\t\t

\n\t\t\t\tGenomic source class [Type]: Somatic

\n\t\t\t

\n\t\t\t\tVariant HGVS name: NM_001289938.1:c.836G>C

\n\t\t\t

Variant common name: G279A

\n\t\t\t
" + }, + "status": "final", + "category" : { + "coding" : [ + { + "system" : "http://hl7.org/fhir/observation-category", + "code" : "laboratory", + "userSelected": false + } + ], + "text" : "Laboratory" + }, + "method": + { + "coding": [ + { + "system": "http://ncit.nci.nih.gov", + "code": "C101293", + "display": "Next Generation Sequencing" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6", + "display": "Genetic variant assessment" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve M. Anyperson" + }, + "effectiveDateTime": "2019-06-05", + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48002-0", + "display": "Genomic source class [Type]" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6684-0", + "display": "Somatic" + } + ], + "text": "Somatic" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48003-8", + "display": "DNA sequence variation identifier [Identifier]" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/", + "code": "376205", + "display": "NM_001005862.2(ERBB2):c.836G>C (p.Gly279Ala)" + } + ], + "text": "NM_001005862.2(ERBB2):c.836G>C (p.Gly279Ala)" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "82154-6", + "display": "Genomic structural variant name" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://varnomen.hgvs.org", + "code": "NM_001289938.1:c.836G>C", + "display": "NM_001289938.1:c.836G>C" + } + ], + "text": "G279A" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "47998-0", + "display": "DNA sequence variation display name [Text] Narrative" + } + ] + }, + "valueString": "G279A" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODEGeneticVariantTestedExample01.json b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantTestedExample01.json similarity index 88% rename from spec/Examples_mCODE/mCODEGeneticVariantTestedExample01.json rename to spec/Examples_mCODE_dstu2/mCODEGeneticVariantTestedExample01.json index 75c57c17..286be6f2 100644 --- a/spec/Examples_mCODE/mCODEGeneticVariantTestedExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantTestedExample01.json @@ -11,20 +11,21 @@ "div": "

*** mCODE Example: Genetic Mutation Test Result ***

Name: John B. Anyperson

MRN: m123

Observation date: 04/01/19

Gene studied [ID]: STK11

Gene variant Description: NM_000455.4(STK11):c.921-1G>C

Gene variant presence: DETECTED

" }, "status": "final", - "category": - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - }, + "category" : { + "coding" : [ + { + "system" : "http://hl7.org/fhir/observation-category", + "code" : "laboratory", + "userSelected": false + } + ], + "text" : "Laboratory" + }, "method": { "coding": [ { - "system": "https://ncit.nci.nih.gov", + "system": "http://ncit.nci.nih.gov", "code": "C101293", "display": "Next Generation Sequencing" } @@ -74,7 +75,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://www.genenames.org/", + "system": "http://www.genenames.org/", "code": "HGNC:11389", "display": "STK11" } diff --git a/spec/Examples_mCODE_dstu2/mCODEGeneticVariantTestedExample02.json b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantTestedExample02.json new file mode 100644 index 00000000..0020366a --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODEGeneticVariantTestedExample02.json @@ -0,0 +1,92 @@ +{ + "resourceType": "Observation", + "id": "mCODEGeneticVariantTestedExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantTested" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Genetic Variant Test Result ***

Name: Eve M. Anyperson

MRN: m456

Observation date: 06/05/19

Gene studied [ID]: ERBB2

Gene variant Description: NM_001289938.1:c.836G>C

Gene variant presence: DETECTED

" + }, + "status": "final", + "category" : { + "coding" : [ + { + "system" : "http://hl7.org/fhir/observation-category", + "code" : "laboratory", + "userSelected": false + } + ], + "text" : "Laboratory" + }, + "method": + { + "coding": [ + { + "system": "http://ncit.nci.nih.gov", + "code": "C101293", + "display": "Next Generation Sequencing" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "41103-3", + "display": "Gene XXX mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve M. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "10828004", + "display":"Positive (qualifier value)" + } + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantTested-extension", + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneStudied-extension", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48018-6", + "display": "Gene studied [ID]" + } + ] + } + }, + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantIdentifier-extension", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.genenames.org/", + "code": "HGNC:3430", + "display": "ERBB2" + } + ] + } + }, + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantDescription-extension", + "valueString": "NM_001289938.1:c.836G>C" + } + ] + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODEGenomicsReportExample01.json b/spec/Examples_mCODE_dstu2/mCODEGenomicsReportExample01.json similarity index 88% rename from spec/Examples_mCODE/mCODEGenomicsReportExample01.json rename to spec/Examples_mCODE_dstu2/mCODEGenomicsReportExample01.json index 54a4edf6..d177de79 100644 --- a/spec/Examples_mCODE/mCODEGenomicsReportExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODEGenomicsReportExample01.json @@ -13,14 +13,14 @@ "div": "

*** mCODE Example: Genomics Report ***

Test id: mCODEGenomicsReportExample01

Performer: Foundation Medicine

Test Name: FoundationOne

Status: final

Subject: John B. Anyperson

Generated Summary:

id: Medical Record Number = m123 (USUAL)

Effective: 04/01/2019

Genetic Mutation Tested: STK11

Gene variant presence: DETECTED

Genomic source class: Somatic

Variant HGVS name: NM_000455.4:c.921-1G>C

Variant common name: G242E

" }, "status": "final", - "category": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE", - "display": "Genetics" - } - ] + "category": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE", + "display": "Genetics" + } + ] }, "code": { "text": "FoundationOne" @@ -31,10 +31,9 @@ }, "effectiveDateTime": "2019-04-01", "issued": "2019-04-01T11:45:33+11:00", - "performer": - { + "performer": { "reference": "Organization/mCODEOrganizationExampleFM1" - }, + }, "result": [ { "reference": "Observation/mCODEGeneticVariantTestedExample01", diff --git a/spec/Examples_mCODE_dstu2/mCODEGenomicsReportExample02.json b/spec/Examples_mCODE_dstu2/mCODEGenomicsReportExample02.json new file mode 100644 index 00000000..a8f9fc84 --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODEGenomicsReportExample02.json @@ -0,0 +1,47 @@ +{ + "resourceType": "DiagnosticReport", + "id": "mCODEGenomicsReportExample02", + "meta": { + "versionId": "0.1", + "lastUpdated": "2019-06-05T14:00:00+11:00", + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GenomicsReport" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Genomics Report ***

Test id: mCODEGenomicsReportExample02

Performer: Foundation Medicine

Test Name: FoundationOne

Status: final

Subject: Eve M. Anyperson

Generated Summary:

id: Medical Record Number = m456 (USUAL)

Effective: 06/05/2019

Genetic Mutation Tested: ERBB2

Gene variant presence: DETECTED

Genomic source class: Somatic

Variant HGVS name: NM_001289938.1:c.836G>C

Variant common name: G279A

" + }, + "status": "final", + "category": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE", + "display": "Genetics" + } + ] + }, + "code": { + "text": "FoundationOne" + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "Eve M. Anyperson" + }, + "effectiveDateTime": "2019-06-05", + "issued": "2019-06-05T14:00:00+11:00", + "performer": { + "reference": "Organization/mCODEOrganizationExampleFM1" + }, + "result": [ + { + "reference": "Observation/mCODEGeneticVariantTestedExample02", + "display": "GeneticVariantTested" + }, + { + "reference": "Observation/mCODEGeneticVariantFoundExample02", + "display": "GeneticVariantFound" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODEOrganizationExampleFM1.json b/spec/Examples_mCODE_dstu2/mCODEOrganizationExampleFM1.json similarity index 98% rename from spec/Examples_mCODE/mCODEOrganizationExampleFM1.json rename to spec/Examples_mCODE_dstu2/mCODEOrganizationExampleFM1.json index de56e73b..4a7e6e34 100644 --- a/spec/Examples_mCODE/mCODEOrganizationExampleFM1.json +++ b/spec/Examples_mCODE_dstu2/mCODEOrganizationExampleFM1.json @@ -16,6 +16,7 @@ "value": "1265714091" } ], + "active": true, "extension": [ { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Status-extension", diff --git a/spec/Examples_mCODE/mCODEPatientExample01.json b/spec/Examples_mCODE_dstu2/mCODEPatientExample01.json similarity index 90% rename from spec/Examples_mCODE/mCODEPatientExample01.json rename to spec/Examples_mCODE_dstu2/mCODEPatientExample01.json index ea2368c8..4a724a59 100644 --- a/spec/Examples_mCODE/mCODEPatientExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODEPatientExample01.json @@ -91,19 +91,5 @@ "postalCode": "12345", "country": "US" } - ], - "communication": [ - { - "language": { - "coding": [ - { - "system": "urn:ietf:bcp:47", - "code": "en-US", - "display": "English (Region=United States)" - } - ], - "text": "English" - } - } ] } \ No newline at end of file diff --git a/spec/Examples_mCODE_dstu2/mCODEPatientExample02.json b/spec/Examples_mCODE_dstu2/mCODEPatientExample02.json new file mode 100644 index 00000000..4a38f714 --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODEPatientExample02.json @@ -0,0 +1,95 @@ +{ + "resourceType": "Patient", + "id": "mCODEPatientExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Patient" + ] + }, + "text": { + "status": "generated", + "div": "
\n\t\t\t

\n\t\t\t\t*** mCODE Example: Patient ***\n\t\t\t

\n\t\t\t

\n\t\t\t\tid: example

\n\t\t\t

\n\t\t\t\tidentifier: Medical Record Number = m456 (USUAL)

\n\t\t\t

\n\t\t\t\tname: Eve M. Anyperson

\n\t\t\t

\n\t\t\t\ttelecom: ph: 555-555-5555(HOME), eve.anyperson@example.com

\n\t\t\t

\n\t\t\t\tgender: female

\n\t\t\t

\n\t\t\t\tbirthsex: F

\n\t\t\t

\n\t\t\t\tbirthDate: Mar 25, 1952

\n\t\t\t

\n\t\t\t\taddress: 123 Main St Anytown MA 12345 US

\n\t\t\t

\n\t\t\t\trace: Black

\n\t\t\t

\n\t\t\t\tethnicity: Not Hispanic or Latino

\n\t\t
" + }, + "extension": [ + { + "url": "http://fhir.org/guides/argonaut/StructureDefinition/argo-race", + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2054-5", + "display": "Black or African American" + } + } + ] + }, + { + "url": "http://fhir.org/guides/argonaut/StructureDefinition/argo-ethnicity", + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2186-5", + "display": "Not Hispanic or Latino" + } + } + ] + }, + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/argo-birthsex", + "valueCode": "F" + } + ], + "identifier": [ + { + "use": "usual", + "type": { + "coding": [ + { + "system": "http://hl7.org/fhir/v2/0203", + "code": "MR", + "display": "Medical Record Number" + } + ], + "text": "Medical Record Number" + }, + "system": "http://hospital.example.org", + "value": "m456" + } + ], + "name": [ + { + "family": "Anyperson", + "given": [ + "Eve", + "M." + ] + } + ], + "telecom": [ + { + "system": "phone", + "value": "555-555-5555", + "use": "home" + }, + { + "system": "email", + "value": "eve.anyperson@example.com" + } + ], + "gender": "female", + "birthDate": "1952-03-25", + "address": [ + { + "line": [ + "123 Main St" + ], + "city": "Anytown", + "state": "MA", + "postalCode": "12345", + "country": "US" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODEPractitionerExample01.json b/spec/Examples_mCODE_dstu2/mCODEPractitionerExample01.json similarity index 97% rename from spec/Examples_mCODE/mCODEPractitionerExample01.json rename to spec/Examples_mCODE_dstu2/mCODEPractitionerExample01.json index 48e21ff9..11d57000 100644 --- a/spec/Examples_mCODE/mCODEPractitionerExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODEPractitionerExample01.json @@ -30,9 +30,7 @@ "Dr." ] }, - "gender": { - "code": "male" - }, + "gender": "male", "address": [ { "use": "home", diff --git a/spec/Examples_mCODE/mCODEPrimaryCancerConditionExample01.json b/spec/Examples_mCODE_dstu2/mCODEPrimaryCancerConditionExample01.json similarity index 93% rename from spec/Examples_mCODE/mCODEPrimaryCancerConditionExample01.json rename to spec/Examples_mCODE_dstu2/mCODEPrimaryCancerConditionExample01.json index 3ad88a68..a75aa99b 100644 --- a/spec/Examples_mCODE/mCODEPrimaryCancerConditionExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODEPrimaryCancerConditionExample01.json @@ -41,10 +41,6 @@ }, "onsetDateTime": "2019-04-01", "extension": [ - { - "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-DateOfDiagnosis-extension", - "valueDate": "2019-04-01" - }, { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-HistologyMorphologyBehavior-extension", "valueCodeableConcept": { @@ -66,11 +62,13 @@ "code": "48105005", "display": "Clinical stage III C (finding)" } - ], - "assessment": { + ] + }, + "assessment": [ + { "reference": "Observation/mCODECancerStageGroupExample01" } - } + ] }, "bodySite": [ { @@ -84,7 +82,7 @@ ], "extension": [ { - "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Laterality-extension", + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-datatype-Laterality-extension", "valueCodeableConcept": { "coding": [ { diff --git a/spec/Examples_mCODE_dstu2/mCODEPrimaryCancerConditionExample02.json b/spec/Examples_mCODE_dstu2/mCODEPrimaryCancerConditionExample02.json new file mode 100644 index 00000000..707f6caf --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODEPrimaryCancerConditionExample02.json @@ -0,0 +1,99 @@ +{ + "resourceType": "Condition", + "id": "mCODEPrimaryCancerConditionExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Primary Cancer Condition Generated Narrative ***

id: mCODE_CancerCondition_m456_01

Patient: Eve M. Anyperson

Medical Record Number: m1456 (USUAL)

Phone: 555-555-5555 (HOME)

Gender: female

Birth Date: 03/25/1952

Diagnosed by: Kyle Anydoc, MD

Disease: Malignant neoplasm of breast, unspecified

Morphology: Carcinoma, no subtype

Body site: Breast structure; laterality: Unilateral right

Clinical status: active

Verification status: confirmed

Onset date: 05/01/2019

" + }, + "clinicalStatus": "active", + "verificationStatus": "confirmed", + "category": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "64572001", + "display": "Disease" + } + ], + "text": "Disease" + }, + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "254837009", + "display": "Malignant neoplasm of breast (disorder)" + } + ] + }, + "patient": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve M. Anyperson" + }, + "asserter": { + "reference": "Practitioner/mCODEPractitionerExample01", + "display": "Kyle Anydoc, MD" + }, + "onsetDateTime": "2019-05-01", + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-HistologyMorphologyBehavior-extension", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "68453008", + "display": "Carcinoma, no subtype (morphologic abnormality)" + } + ] + } + } + ], + "stage": { + "summary": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "48105005", + "display": "Clinical stage III C (finding)" + } + ] + }, + "assessment": [ + { + "reference": "Observation/mCODECancerStageGroupExample02" + } + ] + }, + "bodySite": [ + { + "coding": + [ + { + "system": "http://snomed.info/sct", + "code": "76752008", + "display": "Breast structure (body structure)" + } + ], + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-datatype-Laterality-extension", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "419465000", + "display": "Unilateral right" + } + ] + } + } + ] + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODETNMClinicalDistantMetastasesCategoryExample01.json b/spec/Examples_mCODE_dstu2/mCODETNMClinicalDistantMetastasesCategoryExample01.json similarity index 90% rename from spec/Examples_mCODE/mCODETNMClinicalDistantMetastasesCategoryExample01.json rename to spec/Examples_mCODE_dstu2/mCODETNMClinicalDistantMetastasesCategoryExample01.json index 18301eee..a5f6c31d 100644 --- a/spec/Examples_mCODE/mCODETNMClinicalDistantMetastasesCategoryExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODETNMClinicalDistantMetastasesCategoryExample01.json @@ -41,7 +41,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://cancerstaging.org", + "system": "http://cancerstaging.org", "code": "M0", "display": "M0" } @@ -50,7 +50,9 @@ "extension": [ { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", - "valueReference": "Condition/mCODEPrimaryCancerConditionExample01" + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } } ] } \ No newline at end of file diff --git a/spec/Examples_mCODE_dstu2/mCODETNMClinicalDistantMetastasesCategoryExample02.json b/spec/Examples_mCODE_dstu2/mCODETNMClinicalDistantMetastasesCategoryExample02.json new file mode 100644 index 00000000..b0943985 --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODETNMClinicalDistantMetastasesCategoryExample02.json @@ -0,0 +1,58 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalDistantMetastasesCategoryExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalDistantMetastasesCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Distant Metastases Category ***

Name: Eve M. Anyperson

MRN: m456

Date: 05/01/19

Cancer staging system: AJCC Version 8

M Category: cM0

" + }, + "status": "final", + "category": + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + }, + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21907-1", + "display": "Distant metastases.clinical [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve m. Anyperson" + }, + "effectiveDateTime": "2019-05-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "cM0", + "display": "cM0" + } + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample02" + } + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODETNMClinicalPrimaryTumorCategoryExample01.json b/spec/Examples_mCODE_dstu2/mCODETNMClinicalPrimaryTumorCategoryExample01.json similarity index 90% rename from spec/Examples_mCODE/mCODETNMClinicalPrimaryTumorCategoryExample01.json rename to spec/Examples_mCODE_dstu2/mCODETNMClinicalPrimaryTumorCategoryExample01.json index bbba5130..69a77a01 100644 --- a/spec/Examples_mCODE/mCODETNMClinicalPrimaryTumorCategoryExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODETNMClinicalPrimaryTumorCategoryExample01.json @@ -41,7 +41,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://cancerstaging.org", + "system": "http://cancerstaging.org", "code": "T3", "display": "T3" } @@ -50,7 +50,9 @@ "extension": [ { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", - "valueReference": "Condition/mCODEPrimaryCancerConditionExample01" + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } } ] } \ No newline at end of file diff --git a/spec/Examples_mCODE_dstu2/mCODETNMClinicalPrimaryTumorCategoryExample02.json b/spec/Examples_mCODE_dstu2/mCODETNMClinicalPrimaryTumorCategoryExample02.json new file mode 100644 index 00000000..ac093473 --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODETNMClinicalPrimaryTumorCategoryExample02.json @@ -0,0 +1,58 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalPrimaryTumorCategoryExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalPrimaryTumorCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Primary Tumor Category ***

Name: Eve M. Anyperson

MRN: m456

Date: 05/01/19

Cancer staging system: AJCC Version 8

T category: cT3

" + }, + "status": "final", + "category": + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + }, + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21905-5", + "display": "Primary tumor.clinical [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve M. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "T3", + "display": "T3" + } + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample02" + } + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODETNMClinicalRegionalNodesCategoryExample01.json b/spec/Examples_mCODE_dstu2/mCODETNMClinicalRegionalNodesCategoryExample01.json similarity index 86% rename from spec/Examples_mCODE/mCODETNMClinicalRegionalNodesCategoryExample01.json rename to spec/Examples_mCODE_dstu2/mCODETNMClinicalRegionalNodesCategoryExample01.json index 9cceb19e..14d5af57 100644 --- a/spec/Examples_mCODE/mCODETNMClinicalRegionalNodesCategoryExample01.json +++ b/spec/Examples_mCODE_dstu2/mCODETNMClinicalRegionalNodesCategoryExample01.json @@ -41,17 +41,19 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://cancerstaging.org", - "code": "N3", - "display": "N3" + "system": "http://cancerstaging.org", + "code": "cN3", + "display": "cN3" } ], - "text": "N3" + "text": "cN3" }, "extension": [ { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", - "valueReference": "Condition/mCODEPrimaryCancerConditionExample01" + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } } ] } \ No newline at end of file diff --git a/spec/Examples_mCODE_dstu2/mCODETNMClinicalRegionalNodesCategoryExample02.json b/spec/Examples_mCODE_dstu2/mCODETNMClinicalRegionalNodesCategoryExample02.json new file mode 100644 index 00000000..b7c3ca1d --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODETNMClinicalRegionalNodesCategoryExample02.json @@ -0,0 +1,59 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalRegionalNodesCategoryExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalRegionalNodesCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Regional Nodes Category ***

Name: Eve M. Anyperson

MRN: m456

Date: 05/01/19

Cancer staging system: AJCC Version 8

N Category: cN2

" + }, + "status": "final", + "category": + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + }, + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21906-3", + "display": "Regional lymph nodes.clinical [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample02", + "display": "Eve M. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "cN2", + "display": "cN2" + } + ], + "text": "cN2" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension", + "valueReference": { + "reference": "Condition/mCODEPrimaryCancerConditionExample02" + } + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_dstu2/mCODETumorMarkerTestExample02.json b/spec/Examples_mCODE_dstu2/mCODETumorMarkerTestExample02.json new file mode 100644 index 00000000..7daaeb1d --- /dev/null +++ b/spec/Examples_mCODE_dstu2/mCODETumorMarkerTestExample02.json @@ -0,0 +1,48 @@ +{ + "resourceType" : "Observation", + "id": "mCODETumorMarkerTestExample02", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TumorMarkerTest" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Tumor Marker Test Example: ER Status ***

Patient Name: Eve M. Anyperson

MRN: m456

Test Date: 05/01/19

ER Status: Positive

" + }, + "status": "final", + "category" : { + "coding" : [ + { + "system" : "http://hl7.org/fhir/observation-category", + "code" : "laboratory", + "userSelected": false + } + ], + "text" : "Laboratory" + }, + "code" : { + "coding" : [ + { + "system" : "http://loinc.org", + "code" : "16112-5", + "display" : "Estrogen receptor [Interpretation] in Tissue" + } + ], + "text" : "Estrogen receptor [Interpretation] in Tissue" + }, + "subject" : { + "reference" : "Patient/mCODEPatientExample02dstu2", + "display" : "Eve M. Anyperson" + }, + "effectiveDateTime" : "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "10828004", + "display": "Positive (qualifier value)" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODEGeneticVariantFoundExample01.json b/spec/Examples_mCODE_r4/mCODEGeneticVariantFoundExample01.json new file mode 100644 index 00000000..c9194a78 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODEGeneticVariantFoundExample01.json @@ -0,0 +1,116 @@ +{ + "resourceType": "Observation", + "id": "mCODEGeneticVariantFoundExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantFound" + ] + }, + "text": { + "status": "generated", + "div": "
\n\t\t\t

\n\t\t\t\t*** mCODE Example: Genetic Variant Assessment ***\n\t\t\t

\n\t\t\t

\n\t\t\t\tPatient identifier: m123

\n\t\t\t

Name: John B. Anyperson

\n\t\t\t

\n\t\t\t\tTest date: April 1, 2019

\n\t\t\t

\n\t\t\t\tGenomic source class [Type]: Somatic

\n\t\t\t

\n\t\t\t\tVariant HGVS name: NM_000455.4:c.921-1G>C

\n\t\t\t

Variant common name: G242E

\n\t\t\t
" + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "coding": [ + { + "system": "http://ncit.nci.nih.gov", + "code": "C101293", + "display": "Next Generation Sequencing" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6", + "display": "Genetic variant assessment" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48002-0", + "display": "Genomic source class [Type]" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6684-0", + "display": "Somatic" + } + ], + "text": "Somatic" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48003-8", + "display": "DNA sequence variation identifier [Identifier]" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/", + "code": "619728", + "display": "NM_000455.4(STK11):c.725G>A (p.Gly242Glu)" + } + ], + "text": "NM_000455.4(STK11):c.725G>A (p.Gly242Glu)" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "82154-6", + "display": "Genomic structural variant name" + } + ] + }, + "valueString": "NM_000455.4:c.725G>A" + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "47998-0", + "display": "DNA sequence variation display name [Text] Narrative" + } + ] + }, + "valueString": "G242E" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE/mCODEGeneticMutationTestResultExample01.json b/spec/Examples_mCODE_r4/mCODEGeneticVariantTestedExample01.json similarity index 78% rename from spec/Examples_mCODE/mCODEGeneticMutationTestResultExample01.json rename to spec/Examples_mCODE_r4/mCODEGeneticVariantTestedExample01.json index 4d413b10..c0f8e662 100644 --- a/spec/Examples_mCODE/mCODEGeneticMutationTestResultExample01.json +++ b/spec/Examples_mCODE_r4/mCODEGeneticVariantTestedExample01.json @@ -1,9 +1,9 @@ { "resourceType": "Observation", - "id": "mCODEGeneticMutationTestResultExample01", + "id": "mCODEGeneticVariantTestedExample01", "meta": { "profile": [ - "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticMutationTestResult" + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantTested" ] }, "text": { @@ -11,20 +11,22 @@ "div": "

*** mCODE Example: Genetic Mutation Test Result ***

Name: John B. Anyperson

MRN: m123

Observation date: 04/01/19

Gene studied [ID]: STK11

Gene variant Description: NM_000455.4(STK11):c.921-1G>C

Gene variant presence: DETECTED

" }, "status": "final", - "category": + "category": [ { "coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "display": "Laboratory" } ] - }, + } + ], "method": { "coding": [ { - "system": "https://ncit.nci.nih.gov", + "system": "http://ncit.nci.nih.gov", "code": "C101293", "display": "Next Generation Sequencing" } @@ -55,26 +57,18 @@ }, "extension": [ { - "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-MutationTested-extension", + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantTested-extension", "extension": [ { - "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneStudied-extension", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied [ID]" - } - ] - } + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantHGVSName-extension", + "valueString": "NM_000455.4:c.921-1G>C" }, { "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantIdentifier-extension", "valueCodeableConcept": { "coding": [ { - "system": "https://www.genenames.org/", + "system": "http://www.genenames.org/", "code": "HGNC:11389", "display": "STK11" } diff --git a/spec/Examples_mCODE_r4/mCODEGenomicsReportExample01.json b/spec/Examples_mCODE_r4/mCODEGenomicsReportExample01.json new file mode 100644 index 00000000..49be6180 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODEGenomicsReportExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "DiagnosticReport", + "id": "mCODEGenomicsReportExample01", + "meta": { + "versionId": "0.1", + "lastUpdated": "2019-04-01T15:35:58.045+00:00", + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GenomicsReport" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Genomics Report ***

Test id: mCODEGenomicsReportExample01

Performer: Foundation Medicine

Test Name: FoundationOne

Status: final

Subject: John B. Anyperson

Generated Summary:

id: Medical Record Number = m123 (USUAL)

Effective: 04/01/2019

Genetic Mutation Tested: STK11

Gene variant presence: DETECTED

Genomic source class: Somatic

Variant HGVS name: NM_000455.4:c.921-1G>C

Variant common name: G242E

" + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE", + "display": "Genetics" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://www.ncbi.nlm.nih.gov/gtr", + "code": "GTR000527976.2", + "display": "FoundationOne" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "issued": "2019-04-01T11:45:33+11:00", + "performer": [ + { + "reference": "Organization/mCODEOrganizationExampleFM1" + } + ], + "result": [ + + { + "reference": "Observation/mCODEGeneticVariantTestedExample01" + }, + { + "reference": "Observation/mCODEGeneticVariantFoundExample01" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODEOrganizationExampleFM1.json b/spec/Examples_mCODE_r4/mCODEOrganizationExampleFM1.json new file mode 100644 index 00000000..38ee4d66 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODEOrganizationExampleFM1.json @@ -0,0 +1,48 @@ +{ + "resourceType": "Organization", + "id": "mCODEOrganizationExampleFM1", + "text": { + "status": "generated", + "div": "
\n Foundation Medicine\n
\n\t\t\t\t150 Second Street\n
\n\t\t\t\tCambridge, MA 02141\n
\n\t\t\t\tUSA\n
\n\t\t\t\t(+1) 617-418-2200 (phone)\n
" + }, + "identifier": [ + { + "system": "http://hl7.org.fhir/sid/us-npi", + "value": "1265714091" + } + ], + "active": true, + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Status-extension", + "valueCodeableConcept": + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "55561003", + "display": "Active" + } + ] + } + } + ], + "name": "Foundation Medicine", + "telecom": [ + { + "system": "phone", + "value": "(+1) 617-418-2200" + } + ], + "address": [ + { + "line": [ + "150 Second Street" + ], + "city": "Cambridge", + "state": "MA", + "postalCode": "02141", + "country": "USA" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODEPatientExample01.json b/spec/Examples_mCODE_r4/mCODEPatientExample01.json new file mode 100644 index 00000000..6105bf5f --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODEPatientExample01.json @@ -0,0 +1,117 @@ +{ + "resourceType": "Patient", + "id": "mCODEPatientExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Patient" + ] + }, + "text": { + "status": "generated", + "div": "
\n\t\t\t

\n\t\t\t\t*** mCODE Example: Patient ***\n\t\t\t

\n\t\t\t

\n\t\t\t\tid: example

\n\t\t\t

\n\t\t\t\tidentifier: Medical Record Number = m123 (USUAL)

\n\t\t\t

\n\t\t\t\tname: John B. Anyperson

\n\t\t\t

\n\t\t\t\ttelecom: ph: 555-555-5555(HOME), john.anyperson@example.com

\n\t\t\t

\n\t\t\t\tgender: male

\n\t\t\t

\n\t\t\t\tbirthsex: M

\n\t\t\t

\n\t\t\t\tbirthDate: Jan 20, 1951

\n\t\t\t

\n\t\t\t\taddress: 123 Main St Anytown MA 12345 US

\n\t\t\t

\n\t\t\t\trace: Black

\n\t\t\t

\n\t\t\t\tethnicity: Not Hispanic or Latino

\n\t\t
" + }, + "extension": [ + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2054-5", + "display": "Black or African American" + } + }, + { + "url": "text", + "valueString": "Black" + } + ] + }, + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", + "extension": [ + { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2186-5", + "display": "Not Hispanic or Latino" + } + }, + { + "url": "text", + "valueString": "Not Latino" + } + ] + }, + { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", + "valueCode": "M" + } + ], + "identifier": [ + { + "use": "usual", + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "MR", + "display": "Medical Record Number" + } + ], + "text": "Medical Record Number" + }, + "system": "http://hospital.example.org", + "value": "m123" + } + ], + "name": [ + { + "family": "Anyperson", + "given": [ + "John", + "B." + ] + } + ], + "telecom": [ + { + "system": "phone", + "value": "555-555-5555", + "use": "home" + }, + { + "system": "email", + "value": "john.anyperson@example.com" + } + ], + "gender": "male", + "birthDate": "1951-01-20", + "address": [ + { + "line": [ + "123 Main St" + ], + "city": "Anytown", + "state": "MA", + "postalCode": "12345", + "country": "US" + } + ], + "communication": [ + { + "language": { + "coding": [ + { + "system": "urn:ietf:bcp:47", + "code": "en-US", + "display": "English (Region=United States)" + } + ], + "text": "English" + } + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODEPractitionerExample01.json b/spec/Examples_mCODE_r4/mCODEPractitionerExample01.json new file mode 100644 index 00000000..ad69e4a8 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODEPractitionerExample01.json @@ -0,0 +1,55 @@ +{ + "resourceType": "Practitioner", + "id": "mCODEPractitionerExample01", + "text": { + "status": "generated", + "div": "

*** mCODE Example: Practitioner ***

id: mCODEPractitionerExample01

meta:

identifier: 9941339108, 25456

name: Kyle Anydoc, MD

address: 567 Healthcare Drive Anytown MA 12345 (HOME)

" + }, + "identifier": [ + { + "system": "http://hl7.org.fhir/sid/us-npi", + "value": "9988776655" + }, + { + "system": "http://www.acme.org/practitioners", + "value": "25456" + } + ], + "name": [ + { + "family": "Anydoc", + "given": [ + "Kyle" + ], + "prefix": [ + "Dr." + ] + } + ], + "gender": "male", + "address": [ + { + "use": "home", + "line": [ + "567 Healthcare Drive" + ], + "city": "Anytown", + "state": "MA", + "postalCode": "12345", + "country": "US" + } + ], + "qualification": [ + { + "code": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0360|2.7", + "code": "MD", + "display": "Doctor of Medicine" + } + ] + } + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODEPrimaryCancerConditionExample01.json b/spec/Examples_mCODE_r4/mCODEPrimaryCancerConditionExample01.json new file mode 100644 index 00000000..af10ea11 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODEPrimaryCancerConditionExample01.json @@ -0,0 +1,122 @@ +{ + "resourceType": "Condition", + "id": "mCODEPrimaryCancerConditionExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Primary Cancer Condition Generated Narrative ***

id: mCODE_CancerCondition_m123_01

Patient: John B. Anyperson

Medical Record Number: m123 (USUAL)

Phone: 555-555-5555 (HOME)

Gender: male

Birth Date: 01/20/1951

Diagnosed by: Kyle Anydoc, MD

Disease: Non-small cell lung cancer

TNM Stage Group: clinical stage IIIC

Morphology: Adenocarcinoma, no subtype

Body site: Lung structure; laterality: Unilateral right

Clinical status: active

Verification status: confirmed

Onset date: 04/01/2019

" + }, + "clinicalStatus": + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", + "code": "active", + "display": "Active" + } + ] + }, + "verificationStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "confirmed", + "display": "Confirmed" + } + ] +}, + "category": + [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "64572001", + "display": "Disease" + } + ], + "text": "Disease" + } + ], + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "254637007", + "display": "Non-small cell lung cancer (disorder)" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "asserter": { + "reference": "Practitioner/mCODEPractitionerExample01", + "display": "Kyle Anydoc, MD" + }, + "onsetDateTime": "2019-04-01", + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-HistologyMorphologyBehavior-extension", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "35917007", + "display": "Adenocarcinoma, no subtype (morphologic abnormality)" + } + ] + } + } + ], + "stage": [ + { + "summary": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "3C", + "display": "IIIC" + } + ], + "text": "clinical stage IIIC" + }, + "assessment": [ + { + "reference": "Observation/mCODETNMClinicalStageGroupExample01" + } + ] + } +], + "bodySite": [ + { + "coding": + [ + { + "system": "http://snomed.info/sct", + "code": "39607008", + "display": "Lung structure (body structure)" + } + ], + "extension": [ + { + "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-datatype-Laterality-extension", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "419465000", + "display": "Unilateral right" + } + ] + } + } + ] + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMClinicalDistantMetastasesCategoryExample01.json b/spec/Examples_mCODE_r4/mCODETNMClinicalDistantMetastasesCategoryExample01.json new file mode 100644 index 00000000..bba49228 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMClinicalDistantMetastasesCategoryExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalDistantMetastasesCategoryExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalDistantMetastasesCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Distant Metastases Category ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

M Category: cM0

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21907-1", + "display": "Distant metastases.clinical [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "cM0", + "display": "M0" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMClinicalPrimaryTumorCategoryExample01.json b/spec/Examples_mCODE_r4/mCODETNMClinicalPrimaryTumorCategoryExample01.json new file mode 100644 index 00000000..42877842 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMClinicalPrimaryTumorCategoryExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalPrimaryTumorCategoryExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalPrimaryTumorCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Primary Tumor Category ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

T category: cT3

" + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21905-5", + "display": "Primary tumor.clinical [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "cT3", + "display": "T3" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMClinicalRegionalNodesCategoryExample01.json b/spec/Examples_mCODE_r4/mCODETNMClinicalRegionalNodesCategoryExample01.json new file mode 100644 index 00000000..697a591d --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMClinicalRegionalNodesCategoryExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalRegionalNodesCategoryExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalRegionalNodesCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Regional Nodes Category ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

N Category: cN3

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21906-3", + "display": "Regional lymph nodes.clinical [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "cN3", + "display": "N3" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMClinicalStageGroupExample01.json b/spec/Examples_mCODE_r4/mCODETNMClinicalStageGroupExample01.json new file mode 100644 index 00000000..2adf41db --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMClinicalStageGroupExample01.json @@ -0,0 +1,67 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMClinicalStageGroupExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalStageGroup" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Clinical Stage Group ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

Stage group: IIIC

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21908-9", + "display": "Stage group.clinical Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "3C", + "display": "IIIC" + } + ] + }, + "hasMember": [ + { + "reference": "Observation/mCODETNMClinicalPrimaryTumorCategoryExample01" + }, + { + "reference": "Observation/mCODETNMClinicalRegionalNodesCategoryExample01" + }, + { + "reference": "Observation/mCODETNMClinicalDistantMetastasesCategoryExample01" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMPathologicDistantMetastasesCategoryExample01.json b/spec/Examples_mCODE_r4/mCODETNMPathologicDistantMetastasesCategoryExample01.json new file mode 100644 index 00000000..3922d959 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMPathologicDistantMetastasesCategoryExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMPathologicDistantMetastasesCategoryExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMPathologicDistantMetastasesCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Distant Metastases Category ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

M Category: pM0

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21901-4", + "display": "Distant metastases.pathology [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "pM0", + "display": "M0" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMPathologicPrimaryTumorCategoryExample01.json b/spec/Examples_mCODE_r4/mCODETNMPathologicPrimaryTumorCategoryExample01.json new file mode 100644 index 00000000..a0e4be40 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMPathologicPrimaryTumorCategoryExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMPathologicPrimaryTumorCategoryExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMPathologicPrimaryTumorCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Primary Tumor Category ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

T category: pT3

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21899-0", + "display": "Primary tumor.pathology Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "pT3", + "display": "T3" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMPathologicRegionalNodesCategoryExample01.json b/spec/Examples_mCODE_r4/mCODETNMPathologicRegionalNodesCategoryExample01.json new file mode 100644 index 00000000..a5f114a0 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMPathologicRegionalNodesCategoryExample01.json @@ -0,0 +1,56 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMPathologicRegionalNodesCategoryExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMPathologicRegionalNodesCategory" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Regional Nodes Category ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

N Category: pN3

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21900-6", + "display": "Regional lymph nodes.pathology [Class] Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "pN3", + "display": "N3" + } + ] + } +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETNMPathologicStageGroupExample01.json b/spec/Examples_mCODE_r4/mCODETNMPathologicStageGroupExample01.json new file mode 100644 index 00000000..b18d0537 --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETNMPathologicStageGroupExample01.json @@ -0,0 +1,67 @@ +{ + "resourceType": "Observation", + "id": "mCODETNMPathologicStageGroupExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMPathologicStageGroup" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: TNM Pathologic Stage Group ***

Name: John B. Anyperson

MRN: m123

Date: 04/01/19

Cancer staging system: AJCC Version 8

Stage group: IIIC

" + }, + "status": "final", + "focus": [ + { + "reference": "Condition/mCODEPrimaryCancerConditionExample01" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "method": + { + "text": "AJCC Version 8" + }, + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "21902-2", + "display": "Stage group.pathology Cancer" + } + ] + }, + "subject": { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime": "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://cancerstaging.org", + "code": "3C", + "display": "IIIC" + } + ] + }, + "hasMember": [ + { + "reference": "Observation/mCODETNMPathologicPrimaryTumorCategoryExample01" + }, + { + "reference": "Observation/mCODETNMPathologicRegionalNodesCategoryExample01" + }, + { + "reference": "Observation/mCODETNMPathologicDistantMetastasesCategoryExample01" + } + ] +} \ No newline at end of file diff --git a/spec/Examples_mCODE_r4/mCODETumorMarkerTestExample01.json b/spec/Examples_mCODE_r4/mCODETumorMarkerTestExample01.json new file mode 100644 index 00000000..7f24252c --- /dev/null +++ b/spec/Examples_mCODE_r4/mCODETumorMarkerTestExample01.json @@ -0,0 +1,49 @@ +{ + "resourceType" : "Observation", + "id": "mCODETumorMarkerTestExample01", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TumorMarkerTest" + ] + }, + "text": { + "status": "generated", + "div": "

*** mCODE Example: Tumor Marker Test Example: Epidermal growth factor receptor Ag (EGFR) ***

Patient Name: John B. Anyperson

MRN: m123

Test Date: 04/01/19

EGFR Status: Positive

" + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + } + ] + } + ], + "code" : { + "coding" : [ + { + "system" : "http://loinc.org", + "code" : "39004-7", + "display" : "Epidermal growth factor receptor Ag [Presence] in Tissue" + } + ], + "text" : "EGFR" + }, + "subject" : { + "reference": "Patient/mCODEPatientExample01", + "display": "John B. Anyperson" + }, + "effectiveDateTime" : "2019-04-01", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "10828004", + "display": "Positive (qualifier value)" + } + ] + } +} \ No newline at end of file diff --git a/spec/IndexFolder_Oncocore/CancerDxCodingSystems.png b/spec/IndexFolder_Oncocore/CancerDxCodingSystems.png index aefd4cc5..ab3e0788 100644 Binary files a/spec/IndexFolder_Oncocore/CancerDxCodingSystems.png and b/spec/IndexFolder_Oncocore/CancerDxCodingSystems.png differ diff --git a/spec/IndexFolder_Oncocore/changelog.html b/spec/IndexFolder_Oncocore/changelog.html new file mode 100644 index 00000000..5cfb0d19 --- /dev/null +++ b/spec/IndexFolder_Oncocore/changelog.html @@ -0,0 +1,57 @@ +

mCODE Release Notes / Change Log

+ +

mCODE 0.9.1 Release

+

The following are changes relative to mCODE 0.9.0.

+ +

Enhancements

+ + +

Corrections and Modifications to Existing Content

+ + +
+
+ diff --git a/spec/IndexFolder_Oncocore/disease.html b/spec/IndexFolder_Oncocore/disease.html deleted file mode 100644 index e58c999b..00000000 --- a/spec/IndexFolder_Oncocore/disease.html +++ /dev/null @@ -1,56 +0,0 @@ -

Disease

- -

 

- -

The mCODE Disease grouping includes data elements specific to the diagnosis and staging of cancer.

- -

The process of diagnosing cancer consists of gathering relevant information which identifies that type of cancer as well as its characteristics and severity. At the highest level, these can be identified as the following subgroups:

- - - - - - - - - - - - - - -
Type of cancer
Identifying the type of primary cancer and secondary cancer.
Tumor characteristics
The shape (histologic type) of the tumor cell with that of a normal cell.
Staging
an assessment of the severity and extent of the cancer type. Staging calculations will leverage results from the previous two categories, along with prognostic factors relevant to the cancer type, in order to assess an overall cancer stage group.
- -

Representing Primary and Secondary Cancers

- -

Within EHRs, primary and secondary cancers are captured as structured and coded data for several purposes: problem list mangement, medical billing, and for cancer registry reporting. Each of these purposes could reference different code sets as the primary standard. These coding systems include:

- - -

Because each of these coding systems have a legitimate purpose and could be the reference terminology for a given Electronic Health Record (EHR), mCODE has modeled support for all three. An illustration of how each coding system differs is shown in the table below:

- -mCODE Logical Model - -

Implementers will need to reference the FHIR profiles PrimaryCancerCondition and SecondaryCancerCondition on how these codes bind to the model. Further FHIR example instances will be provided for further guidance.

- -

 

- -

Staging

- -

Cancer staging is the process of determining how much cancer is in the body and where it is located. Staging describes the severity of an individual's cancer based on the magnitude of the original (primary) tumor as well as on the extent cancer has spread in the body. Understanding the stage of the cancer helps doctors to develop a prognosis and design a treatment plan for individual patients. (source: AJCC).

- -

The AJCC staging system is recognized as one of the most widely-used standards for cancer staging. However, AJCC content is proprietary and cannot be shared for public use. Consequently, this guide does not include any AJCC values due to unresolved copyright issues. As such,elements related to staging may not currently include required terminology codes for assessing the cancer stage group.

- -

As part of fair use, this IG will provide very limited examples illustrating mCODE's representation of cancer diagnoses and AJCC staging values for the purposes of technical implementation guidance to FHIR developers.

- -

Representing Comorbid Conditions

-

mCODE constrains the list of comorbid conditions that are relevant to cancer, and aligns with the Elixhauer Comorbidity Index as its main source.

- -

 

- diff --git a/spec/IndexFolder_Oncocore/examples.html b/spec/IndexFolder_Oncocore/examples.html index 29add978..39e73c10 100644 --- a/spec/IndexFolder_Oncocore/examples.html +++ b/spec/IndexFolder_Oncocore/examples.html @@ -3,13 +3,21 @@

mCODE FHIR Examples

This section provides some examples how mCODE elements may be represented in a FHIR instance which conforms to this implementation guide.

diff --git a/spec/IndexFolder_Oncocore/genomics.html b/spec/IndexFolder_Oncocore/genomics.html deleted file mode 100644 index e9de90ec..00000000 --- a/spec/IndexFolder_Oncocore/genomics.html +++ /dev/null @@ -1,26 +0,0 @@ -

Genomics Reporting

- -

Genomics is the study of the totality of DNA sequence and gene expression differences between tumor cells and normal host cells. It aims to understand the genetic basis of tumor cell proliferation and the evolution of the cancer genome under mutation and selection by the body environment, the immune system and therapeutic interventions (source: Nature).

-

mCODE will only include the minimal set of genetic related elements relevant to capture in an EHR to drive treatment options. In a tiered framework of adoption noted by the HL7 Clinical Genomics Working Group (CGWG), mCODE minimally aligns with levels 1 and 2. This is illustrated in the diagram below.

- -mCODE in the Clinical Genomics Levels of Detail - -

mCODE at this time is loosely based on HL7 CGWG Clinical Genomics Reporting Implementation Guide.

- -

Genetic Test Identifiers

-

mCODE allows for different coding systems like the Logical Observation Identifiers and Names (LOINC) and local codes to specify the genomics test or panel provided that a the coding system or ID convention is specified. While Genetic Testing Registry (GTR) is currently the best source for identifying genetic tests, the user should be aware that the GTR cannot be a sole reliable source since the test data is voluntarily updated and there is no overarching data steward.

- -

Sources of Information

-

References used in the mCODE biomarker model include:

- - -

 

- diff --git a/spec/IndexFolder_Oncocore/implementation.html b/spec/IndexFolder_Oncocore/implementation.html index 78125c40..f11d8b0e 100644 --- a/spec/IndexFolder_Oncocore/implementation.html +++ b/spec/IndexFolder_Oncocore/implementation.html @@ -1,92 +1,183 @@ -

Appendix A: Technical Implementation Notes

+

Implementation Notes

+

This page contains miscellaneous information on modeling and FHIR implementation. The content is primarily directed at informaticists and implementers of mCODE. The following topics are addressed:

-

This section contains content specific for FHIR implementers. This allows for introductory and overview content to be shared among the broader community which includes clinicians, project leaders, and executive decision makers.

- -

 

- -

General Notes

- -

Data Dictionary and FHIR IG alignment

-

It is anticipated that mCODE will move to FHIR Release 4 when commercial vendors and US Core and/or Argonaut officially support the parts of R4 required by mCODE.

-

FHIR Examples

+

Conformance Requirements

+ +

Relationship to US Core

+

With one exception (see below), the profiles presented in this guide conform to US Core Implementation Guide (v3.0.0). Each mCODE Profile uses a corresponding US Core profiles as its base profile, and thus, cannot break the rules established by that profile in US Core. For example, if US Core has a required element, by virtue of profile inheritance, mCODE cannot make that element optional. However, it is not true that any instance that conforms to an mCODE profile will automatically conform to US Core. In particular, the use of extensible value sets requires caution. Extensibility is only allowed when an appropriate concept is not available in the US Core value set. Please note:

-

 

+

The one known exception to US Core compliance is in GenomicsReport, where the category attribute is set to 'GE' (Genetics), a code from the Diagnostic Service Section Codes value set. However, US Core requires the category 'LAB' in every diagnostic report containing laboratory results, and restricts the category to 1..1, thus preventing any other categorization. This is assumed to be an oversight in the US Core specifications.

-

Treatment

+

International Version of mCODE

+

Although the current version of mCODE is US-specific, there is a potential for an international version of mCODE. If interested, please contact one of the authors.

-

The following mCODE FHIR profiles are relevant to cancer treatment:

+

mCODE Roles

+

At present, two roles are defined:

-

 

+

In the future, additional roles may be defined.

-

Representing Clinical Trial Drugs

-

Given RxNorm's limitation of including only FDA approved drugs, mCODE represents the MedicationStatement ValueCodeableConcept with a binding of RxNorm (extensible). This allows for the inclusion of other coding systems like the NCI Thesaurus (NCIT) to represent clinical trial oncology drugs.

- -

Laboratory and Vital Signs

- -

Tumor Markers

-

mCODE identifies a dedicated FHIR profile called TumorMarkerTest for the identification of serum and tissue-based tumor markers.

+

"Must Support" Interpretation

+

In FHIR, the MustSupport flag indicates that implementation shall provide "meaningful support" for the element, as defined by its implementation guide. In mCODE, there are two sources of MustSupport elements: those inherited from US Core, and those defined in mCODE. To conform to US Core, the MustSupport elements inherited from US Core must follow the interpretation of MustSupport defined in US Core.

+

Elements defined as MustSupport in mCODE do not follow the US Core rules. MustSupport elements defined in mCODE shall be interpreted as follows:

+ +

Unfortunately, FHIR does not have the ability to track the source of MustSupport flags, and the only way to know where a MustSupport flag is defined is by direct comparison of US Core and mCODE profiles.

-

 

- -

Genomics Reporting

- +

Required Elements

+

An mCODE data element is required if any of the following criteria are met:

+

In other words, a data element may be 1..1, but if it is contained by an optional element, then it is not required unless its containing element is actually present in a given instance of the profile.

-

 

-

FHIR Terminology Overview

+

mCODE's rules regarding required data elements are the same as US Core's rules. To paraphrase those rules, a Data Sender must provide each required element or an explicit data absent reason for each missing data item.

-

This implementation guide supplies terminology bindings drawn primarily from LOINC for "observables", and SNOMED-CT for values, results and findings. When appropriate codes are not available in the preferred vocabulary, alternative vocabularies are used, in the following order of preference: SNOMED-CT (if the element is an observable), NCI Thesaurus and Metathesaurus, and local codes.

+

Minimum Requirement for "mCODE Conformance"

+

The mCODE IG outlines conformance requirements and expectations for individual mCODE instances in terms of structural constraints and terminology bindings. Any FHIR resources claiming to conform to mCODE must validate against the declared mCODE profile.

-

Value sets from the FHIR specification are reused to the extent possible. In addition, Argonaut Data Query Implementation Guide, and the US Core Implementation Guide were also used when necessary.

+

At present, there are no additional conformance rules on what mCODE data is to be collected, by whom, and when, or when that data is to be exchanged. mCODE Data Senders and Data Receivers may choose the subset of mCODE resources they support, according to their business needs. For example, a Genomics Laboratory may support GenomicsReport, but not vital signs or staging.

+

FHIR capability statements describe the capabilities of actual implementation or requirements of a desired solution. This IG does not include sample capability statements. The expectation is to use implementation experience collected during the STU period to model the different types of actors (such as medical oncologist, radiologist, genomics laboratory, etc.), and define appropriate capability statements for each, including search parameters and operations.

-

There may be differences across these specifications in the value sets used, as well as binding strength. This guide addresses these discrepancies by using the lowest common denominator amongst the specifications. This approach is not without challenges, as there cases where different value sets are required by different specifications, which leaves no choice but to opt for one value set over another.

+

Terminology Preferences

-

On SNOMED extensions

-

mCODE aligns with the Systematic Nomenclature of Medicine, Clinical Terms (SNOMED CT) U.S. Edition. SNOMED CT extensions outside of the U.S. Edition (e.g.: HSPC extensions, local extensions) are not included at this time.

+

This implementation guide supplies terminology bindings drawn primarily from LOINC for "observables", and SNOMED-CT for values, results and findings. When appropriate codes are not available in the preferred vocabulary, alternative vocabularies are used, in the following order of preference: SNOMED-CT (if the element is an observable), NCI Thesaurus and Metathesaurus, and local codes.

-

The specification of SNOMED US Edition is handled within the FHIR CodeableConcept.version attribute:

+

The specification of SNOMED US Edition is handled within the FHIR CodeableConcept.version attribute:

{version: "http://snomed.info/sct/731000124108"}

-

where 731000124108 is the SNOMED namespace assigned to the National Library of Medicine (NLM), who manages the SNOMED US Edition.

-

 

+

where 731000124108 is the SNOMED namespace assigned to the National Library of Medicine (NLM), who manages the SNOMED US Edition.

-

Local Value Sets

+

Value sets from the FHIR specification and US Core were reused to the extent possible. New value sets where created only when no known existing value sets were deemed to be fit for purpose, or when existing value sets were needed to be extended.

-

This guide includes multiple value sets created specifically to support the terminology needs of the models. These value sets where created only when no known existing value sets were deemed to be fit for purpose, or when existing value needs needed to be extended.

+

Patient

+

FHIR (and mCODE) allows multiple addresses for a patient. The zip code reported in mCODE should be the one specified by Address.use of "home" and Address.type of "physical".

-

NOTE:There is a known issue with HL7's FHIR implementation guide publisher that causes an error in the expansion of local value sets in the implementation guide. While this prevents the value sets from being shown in the value set pages, the content of the value sets is correctly expanded in json and xml, which readers can access from the indivual value set pages.

- -

 

- -

Cancer Staging and Proprietary Terminologies

+

Body Locations

+

A single code is often insufficient to precisely determine a body site for the purpose of describing where a tumor is located, where a surgery is targeted, or where a radiation treatment is focused. For example, in breast cancer, the location of a tumor can be described in terms of the radial position (clock face direction) and distance relative to the left or right nipple.

+

In FHIR, Condition, Procedure, and other resources represent body sites using a single code. In addition, FHIR provides a standard extension, BodyStructure Reference that can be used when a single code is insufficient. However, this approach has not been adopted, for the following reasons:

+ +

Instead, mCODE uses an approach that defines body sites conceptually, and has the required specificity, by introducing three optional extensions on bodySite:

+ -

Several proprietary terminologies, including ICD-O-3 and the American Joint Commission on Cancer (AJCC) Staging System are widely used in the cancer domain. Others, such as Current Procedural Terminology (CPT®), while not cancer-specific, are relevant for the representation of cancer-related procedures, such as surgeries or radiation procedures. This guide does not include content from these terminologies due to licensing restrictions. The guide does, however, indicate where it is appropriate to use codes from such terminologies.

+

Vital Sign Profiles

+

The vital sign profiles defined by mCODE are consistent with the FHIR vital sign profiles, which are incorporated by reference into US Core v3. The difference between FHIR and mCODE vital signs is that mCODE provides for reporting of preconditions, body positions, blood pressure method, and blood pressure body location, with appropriate value sets. The vital signs model in mCODE is aligned with the Vital Signs Implementation Guide being developed in cooperation with the Clinical Information Modeling Initiative (CIMI) Work Group.

+

Although mCODE defines its own vital signs profiles, if and when detailed vital signs profiles are standardized in a widely-accepted FHIR IG, mCODE will likely switch over to those profiles.

-

 

+

Laboratory Profiles

+

Many laboratory profiles in mCODE are not shown on the main Profiles page, but are listed with the panels they are a part of. To assure naming uniqueness over thousands of LOINC laboratory tests, laboratory profile names have been formulated as a concatenation of the LOINC Component, Property, Time, System, Scale, and Method. Where the concatenation exceeds the FHIR element name length limitation of 64 characters, some additional contractions have been introduced. Although mCODE defines its own laboratory profiles, if and when detailed laboratory profiles are standardized in a widely-accepted IG, mCODE will likely switch over to those profiles. +

+

mCODE includes the following 72 laboratory profiles:

+ +
\ No newline at end of file + diff --git a/spec/IndexFolder_Oncocore/index.html b/spec/IndexFolder_Oncocore/index.html index 819947b5..fd2311d7 100644 --- a/spec/IndexFolder_Oncocore/index.html +++ b/spec/IndexFolder_Oncocore/index.html @@ -1,58 +1,251 @@ - +

Contents of this Implementation Guide

-

 

-

Background

-

According to the National Cancer Institute, 38.5 percent of men and women will be diagnosed with cancer at some point during their lifetimes. In 2014, an estimated 14.7M people were living with cancer in the United States. While numbers for cancer and other major diseases are staggering in terms of human suffering, such large figures also provide a place to look for potential solutions. The ultimate goal is to establish data models, technologies, and methods that result in research-quality real-world EHR data for every patient that drives evidence-based and data-driven treatment and analytics for high-quality health outcomes. The intent is that this research-quality real-world data would allow the information gathered from all cancer patients to contribute substantially to improving care for all future cancer patients.

+

According to the National Cancer Institute, 38.5 percent of men and women will be diagnosed with cancer at some point during their lifetimes. In 2014, an estimated 14.7M people were living with cancer in the United States. While these numbers are staggering, the silver lining in the wide prevalence of cancer is the potential to learn from treatment of millions of patients. If we had research-quality data from all cancer patients, it would enable higher quality health outcomes. Today, we lack the data models, technologies, and methods to capture that data.

-

mCODE™ —short for Minimal Common Oncology Data Elements—is an initiative intended to assemble a core set of structured data elements for oncology electronic health records (EHRs). The goal is to facilitate cancer data interoperability and improve overall cancer data quality for patient care and research by establishing a set of elements that would form the basic data that would populate all EHRs for patients with cancer. mCODE™ has been created and is being supported by the American Society of Clinical Oncology (ASCO®)in collaboration with the MITRE Corporation. +

mCODE™ (short for Minimal Common Oncology Data Elements) is an initiative intended to assemble a core set of structured data elements for oncology electronic health records (EHRs). mCODE™ is a step towards capturing research-quality data from the treatment of all cancer patients. This would enable the treatment of every cancer patient to contribute to comparative effectiveness analysis (CEA) of cancer treatments. mCODE™ has been created and is being supported by the American Society of Clinical Oncology (ASCO®)in collaboration with the MITRE Corporation.

-

In late 2018, ASCO convened committee of twenty leading clinical experts in oncology, radiology, surgery, and public health developed two use cases which drove the initial clinical data requirements for mCODE. +

In late 2018, ASCO convened committee of twenty leading clinical experts in oncology, radiology, surgery, and public health developed two use cases that drove the initial clinical data requirements for mCODE:

-

In early 2019, an open survey was conducted to validate and prioritize the data elements from these use cases. Further down-scoping was done based on whether the data would be stored or capture in an electronic health record (EHR), or if it placed undue documentation burden on the clinician.

+

While mCODE ultimately is meant to be applicable to across all types of cancer, the initial focus (and both use cases) has been on solid tumors.

-

The data elements were formally modeled, and rendered as FHIR Profiles. The results are detailed in this Implementation Guide. Clinical readers should focus on the Scope and Conceptual Model. Informaticists and FHIR implementers can reference the profiles and other technical information.

+

In addition to information obtained from subject matter experts, several pre-existing standards, nomenclatures, and guidelines were consulted in the development of this specification, including:

+ +

After initial development, in early 2019, an open survey was conducted to validate and prioritize the data elements from these use cases. Further down-scoping was done based on whether the data would be stored or capture in an electronic health record (EHR), and if it would place undue documentation burden on clinicians.

+

The data elements identified in this process were modeled using the Clinical Information Modeling and Profiling Language (CIMPL) and exported as FHIR Profiles. The profiles, related FHIR artifacts, and other technical implementation information, constitute the bulk of this IG. What follows is an overview of mCODE, directed primarily at clinical readers. Readers should also take note of the Data Dictionary (Excel download), a simplified, flattened list of mCODE elements.

+ +

Scope and Conceptual Model

+

mCODE consists of data elements divided into six groups, illustrated in the following diagram:

+ + +mCODE Logical Model

 

-

Disclaimers

-

+

Patient Group

+

The mCODE Patient group contains the following basic information about the patient:

+ +

Patient is the most essential FHIR profile, as all other mCODE major elements reference it. The mCODE Patient profile differs only slightly from the US Core Patient Profile. Most significantly, Patient.deceased is a must-support element in mCODE.

+ +

Disease Characterization Group

+ +

The mCODE Disease Characterization group includes data elements specific to the diagnosis and staging of cancer. This includes:

+ + +

Representing Cancer Diagnosis

+

The cancer diagnosis combines the type, site, and certain characteristics of the cancer. Depending on the EHR and provider organization, different code systems may be used, such as:

+ + +

Because each of these coding systems are found "in the wild", mCODE supports all three. Implementers should be aware, however, that how the cancer diagnosis is coded can affect compliance with US Core (see Implementation Notes for details). Two attributes and one FHIR extension of the FHIR Condition Resource are involved with coding the cancer diagnosis: the Code, the HistologyMorphologyBehavior extension, and the Body Site. How these attributes are used, depending on the coding system, is captured in the table below:

+ + +mCODE Logical Model + +

Implementers should reference the PrimaryCancerCondition and Secondary Cancer Condition profiles for details on the use of these terminologies and associated value sets.

+ +

Representing Cancer Staging Information

+

Cancer stage information is contained in a set of profiles, representing clinical stage group and pathologic stage group panels with members representing the primary tumor (T) category, the regional nodes (N) category, and the distant metastases (M) category. Non-TNM staging systems are not currently represented in mCODE, reflecting mCODE's current focus on solid tumors. In mCODE, a single patient may have more than one staging panel, although this is not common in practice.

+

Clinical applications vary in their representation of T, N, and M staging category values, falling into one of two naming conventions:

+ + + +

mCODE recommends that the implementer align with AJCC's convention of representing the staging category value with the prepended classification in both TNMClinicalStageGroup and TNMPathologicStageGroup profiles. This code convention is aligned with the AJCC's digital data and clearly distinguishes the staging classification as clinical, pathologic, or neoadjuvant without having to retrieve further context from the model. Nonetheless, separate profiles for clinical and pathological staging were developed, with an eye toward future extensibility, in particular, the ability to additional prognostic factors relevant to particular types of cancers in the TNMPathologicStageGroup.

+ + +

Laboratory Results and Vital Signs Group

+

Core Laboratory Results

+

Many laboratory tests could be relevant to an individual with cancer. The initial mCODE release includes only two core laboratory tests:

+ +

These core diagnostic labs are modeled separately from cancer-specific serum and tissue-based prognostic factors.

+ +

Tumor Marker Tests

+

Tumor markers are key prognostic factors in calculating cancer staging, identifying treatment options, and monitoring progression of disease. For example, an abnormal increase in prostate-specific antigen (PSA) levels is a prognostic factor for prostate cancer. Other tumor markers include estrogen receptor (ER) status, progresterone receptor (PR) status, carcinoembryonic antigen (CEA) levels, among others. See the profile TumorMarkerTest for full details.

+ +

We distinguish Tumor Marker Tests from genetic tests that are measured at the DNA, RNA, or chromosomal level, addressed in the Genomics section. +

+ +

Vital Signs

+

Vital signs are measurements of the most essential, or "vital" body functions. Traditionally, vital signs include blood pressure, heart rate, respiratory rate, and temperature. More recently, height and weight have been included. Only BP, body height and body weight are included in mCode because they are believed to be the most critical to assessment and treatment.

+ +

The vital sign profiles defined by mCODE are consistent with the FHIR vital sign profiles, which are incorporated by reference into US Core v3. The difference between FHIR and mCODE vital signs is that mCODE provides for reporting of preconditions, body positions, blood pressure method, and blood pressure body location, with appropriate value sets. The vital signs model in mCODE is aligned with the Vital Signs Implementation Guide being developed in cooperation with the Clinical Information Modeling Initiative (CIMI) Work Group. Although mCODE defines its own vital signs profiles, if and when detailed vital signs profiles are standardized in a widely-accepted FHIR IG, mCODE will likely switch over to those profiles.

+ +

Treatments Group

+

The Treatment group includes reporting of procedures and medications used to treat a cancer patient, or relevant to that treatment. Treatments are captured using the following profiles:

+ +

Like US Core, mCODE gives preference to representing medications using the National Library of Medicine (NLM) RxNorm terminology - a coding standard established by the Office of the National Coordinator (ONC) for the exchange of drugs. However, RxNorm is restricted to FDA-approved drugs and does not include clinical trial drugs. To address this limitation, mCODE allows for the inclusion of other coding systems like the NCI Thesaurus (NCIT) to represent clinical trial oncology drugs.

-

 

+

Genomics Group

+

mCODE includes the minimal set of genetic related elements relevant to capture in an EHR to inform cancer assessment and treatment options. The approach is based on the HL7 CGWG Clinical Genomics Reporting Implementation Guide. However, mCODE simplifies genomics reporting to single discrete variants or to variants that were found in a given DNA region. Three profiles relate to the capture of clinical genomics data:

+ +

The identity of non-genomic laboratory tests is typically represented by a Logical Observation Identifiers and Names (LOINC) code. However, many genetic tests and panels do not have LOINC codes, although some might have an identifier in the NCBI Genetic Testing Registry (GTR), a central location for voluntary submission of genetic test information by providers. While GTR is currently the best source for identifying many genetic tests, the user should be aware that the GTR may not be reliable source since the test data is voluntarily updated and there is no overarching data steward. Standardization of codes for genetic tests is essential to facilitate data analysis of genetic tests, and should be a priority for the genomics testing community in the near future. Implementers should also note that, to conform to the requirements of the US Core Laboratory Result Profile, LOINC must be used, if a suitable code is available. If there is no suitable code in LOINC, then a code from an alternative code system (such as GTR) can be used.

+ + +

Outcomes Group

+

Recording outcomes of cancer treatment in mCODE involves two data elements: disease status and date of death. Other common outcome measures, such as progression-free survival, time to recurrence, and overall survival, can be derived from time-indexed observations of disease status. The date of diagnosis is also required for some derived measures (see Disease Characterization). At this time, mCODE does not include patient reported outcomes.

+ +

Disease Status

+

Formal recording of disease status is often limited to clinical trials, involving precise criteria such as RECIST. The lack of outcome data outside of trials greatly limits the application of real-world data. Disease status information is rarely found in structured form in EHRs. If recorded at all, the information is found in clinical notes, which is of limited usefulness.

+

mCODE asks for disease progression to be recorded in structured form as part of patient encounters. In mCODE, disease status is defined as "A clinician's qualitative judgment on the current trend of the cancer, e.g., whether it is stable, worsening (progressing), or improving (responding). The judgment may be based a single type or multiple kinds of evidence, such as imaging data, assessment of symptoms, tumor markers, laboratory data, etc." In other words, the disease status is an assessment by the oncologist that synthesizes all currently available information about the patient. The ICAREdata™ Project is conducting a study in association with a randomized controlled trial (RCT), which aims to demonstrate the ability to calculate equivalent clinical trial endpoints using computable clinical treatment data. +

+ +

Date of Death

+

Date of death data can be obtained from several sources outside of the clinical setting. If available in the EHR, it can be reported through via mCODE, but more likely, it will be filled in from vital records, after the last clinical interaction.

+ + + +

Disclaimers and Known Limitations

+

+

Credits

-

Domain content was provided by the ASCO/CancerLinQ team with additional research from the MITRE Corporation. Help, guidance, and wisdom was generously provided by all members of the ASCO/CancerLinQ team, especially the Dr. Robert Miller and Dr. Wendy Rubenstein.

-

This IG was authored by the MITRE Corporation using the Clinical Information Modeling and Profiling Language (CIMPL), a free, open source toolchain from MITRE Corporation.

+

The authors recognize the leadership and sponsorship of Dr. Monica Bertagnolli, President, ASCO and Dr. Jay Schnitzer, MITRE Chief Technology Officer. Dr. Steven Piantadosi and the Alliance for Clinical Trials in Oncology coordinated real-world data collection in clinical trials, as part of this project. The ASCO/CancerLinQ team was led by Dr. Robert Miller and Dr. Wendy Rubinstein. Lead MITRE contributors were Mark Kramer, Rute Martins, Chris Moesel, and May Terry. Andre Quina and Dr. Brian Anderson guide the overall mCODE effort at MITRE. HL7 sponsorship and input from Clinical Interoperability Council and Clinical Information Modeling Initiative is gratefully acknowledged, with special thanks to Richard Esmond and Laura Heermann Langford.

+

This IG was authored by the MITRE Corporation using the Clinical Information Modeling and Profiling Language (CIMPL), a free, open source toolchain from MITRE Corporation.

+ +

Contact Information

+ + + + + + + + + + + + + + + +
+

General Inquiries:

+
+

mcode-info@asco.org

+
+

Co-Editor:

+
+

Dr. Robert Miller

+

ASCO CancerLinQ

+

robert.miller@asco.org

+
+

Co-Editor:

+
+

Mark Kramer

+

MITRE Corporation

+

mkramer@mitre.org

+

 

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Laboratory Results and Vital Signs

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Core Laboratory Results

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Laboratory panels and results encompass a breadth of diagnostics across many different subspecialties. Given the need for greater scoping, we identify mCODE™ are scoped to the core set of labs ordered as part of an initial diagnostic workup, regardless of disease type.

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The initial mCODE release includes:

- -

These core diagnostic labs are modeled separately from cancer-specific serum and tissue-based prognostic factors which in some cases, are essential for cancer diagnosis and staging. These prognostic factors are modeled as a dedicated FHIR profile for tumor marker observations.

- -

Tumor Markers

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Tumor markers are key prognostic factors in calculating cancer staging, identifying treatment options, and monitoring progression of disease. This IG distinguishes tumor markers from genetic markers as follows:

- - -

 

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Vital Signs

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By definition, vital signs are measurements of the most essential, or "vital" body functions. Traditionally, the essential vital signs are temperature, heart rate, breathing rate, blood pressure. Both definition and the inclusion of measurements included in a vital signs panel have evolved over time to loosely include a set of measurements performed directly on a patient and help inform assessment and treatment options, sometimes including height, weight, and pain scales.

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mCODE limits the list of vital signs to those which drive the calculation of a body mass index (BMI) to determine an absolute dose in a given treatment and at the time of administration. For the initial mCODE release, these include:

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Conceptual Model Overview

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Scoping and prioritization work resulted in identification of data elements in six areas:

- - -

The results are shown in the following diagram:

- -mCODE Logical Model - -

 

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Major sources of information

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Specifications consulted for the development of this IG include:

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TBD.

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Patient

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The mCODE Patient grouping contains a mix of demographics, comorbid conditions, and performance statuses which could influence a cancer diagnosis and treatment option.

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The list of elements include the following:

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The Patient is the most essential FHIR profile as all of the other mCODE major elements will reference the mCODE Patient identifier.

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mCODE Release Notes

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-
- -

mCODE 0.9.1 Errata

- - - - - - - - - - - - -
Change typeIG locationChange description
Bug fixHome pageRestored URLs so users can access mCODE use case documents.
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Treatment

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The Treatment domain includes procedures and medications administered in the treatment of a cancer patient.

- -

Procedures

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Procedures are further categorized as:

- -mCODE does not currently constrain surgical, radiation, and imaging procedures to cancer-specific therapies. Extensible value sets for each are being considered for a future release, pending further requirements from clinical subject matter experts. - -

 

- -

Medication Therapies

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Medication therapies in mCODE are further categorized as:

- - -

Chemotherapy and hormone therapy agents are not specified as constraints within the profile. Rather, we provide a means of deriving the list of relevant drug integredients pertaining to the therapeutic drug class (as Rxnorm RXCUIs) on-demand using RXCLASS.

- - -

Clinical Trial Drugs

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The mCODE model gives preference to representing medications using the National Library of Medicine (NLM) RxNorm terminology - a coding standard established by the Office of the National Coordinator (ONC) for the exchange of drugs. RxNorm however is restricted to FDA-approved drugs and does not include clinical trial drugs.

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To address this limitation, mCODE allows for the inclusion of other coding systems like the NCI Thesaurus (NCIT) to represent clinical trial oncology drugs.

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HL7 FHIR Profile: Occupational Data for Health (ODH), Release 1.1 (Standard for Trial Use)

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+

This Implementation Guide is a reconciled version, containing changes in response to comments received in the Sept. 2018 ballot. It has been updated to FHIR R4.0.0.

+

Occupational Data for Health Implementation Guide

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Reconciled Version based on Sept. 2018 Ballot

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- This Implementation Guide contains logical models and profiles to implement support for Occupational Data for Health (ODH). ODH is primarily designed to facilitate clinical care, including population health; ODH also can be used to support public health reporting, population health, and similar value-based care. ODH is not designed to support billing activities. This STU Ballot for the Occupational Data for Health (ODH) Implementation Guide (IG) is sponsored by the National Institute of Occupational Safety and Health (NIOSH), a federal agency responsible for conducting research and making recommendations for the prevention of work-related injury and illness. NIOSH is a part of the Centers for Disease and Prevention (CDC). The project to define ODH was done with a group representing a variety of stakeholders including NIOSH subject matter experts, epidemiologists, occupational health providers, and vendors. +

+ This Implementation Guide contains profiles to implement support for Occupational Data for Health (ODH). ODH is primarily designed to facilitate clinical care, including population health; ODH also can be used to support public health reporting, population health, and similar value-based care. ODH is not designed to support billing activities. This STU Ballot for the Occupational Data for Health (ODH) Implementation Guide (IG) is sponsored by the National Institute of Occupational Safety and Health (NIOSH), a federal agency responsible for conducting research and making recommendations for the prevention of work-related injury and illness. NIOSH is a part of the Centers for Disease and Prevention (CDC). The project to define ODH was done with a group representing a variety of stakeholders including NIOSH subject matter experts, epidemiologists, occupational health providers, and vendors.

Background

@@ -18,12 +18,12 @@

Scope

  • Employment Status
  • Retirement Date
  • Combat Zone Period
  • -
  • Past or Present Job for the patient or a household member which includes +
  • Past or Present Job for the patient or a household member, which includes: