minimal Common Oncology Data Elements (mCODE) Implementation Guide
1.16.0 - STU Release 2 (Ballot Version)

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v1.16.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Artifacts Summary

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

Behavior: Capability Statements

The following artifacts define the specific capabilities that different types of systems are expected to have in order to comply with this implementation guide. Systems conforming to this implementation guide are expected to declare conformance to one or more of the following capability statements.

mcode-receiver-cancer-conditions-then-patients

Retrieves a Bundle of Condition resources with a code in mCODE’s cancer condition value set, and allows for associated Patient resources to be retrieved in a subsequent request. Use ONLY when reverse chaining AND _include are not available on the system.

mcode-receiver-patient-bundle

Retrieves a Bundle of Condition resources with a code in mCODE’s cancer condition value set, and allows for associated Patient resources to be retrieved in a subsequent request. Use ONLY when reverse chaining AND _include are not available on the system.

mcode-receiver-patients-and-cancer-conditions

Uses _include to retrieve a Bundle of Condition resources with a code in mCODE’s cancer condition value set, along with the associated Patient resources. Use ONLY when reverse chaining is not available on the system.

mcode-receiver-patients-in-group

Capabilities for an mCODE Data Receiver where not all cancer patients conform to mCODE. Retrieves a Group of references to Patient resources that conform to mCODE, and allows for the full Patient resources to be retrieved in a subsequent request.

mcode-receiver-patients-with-cancer-condition

Uses reverse chaining to retrieve a Bundle of Patient resources with a condition code in mCODE’s cancer condition value set.

mcode-sender-cancer-conditions-then-patients

Retrieves a Bundle of Condition resources with a code in mCODE’s cancer condition value set, and allows for associated Patient resources to be retrieved in a subsequent request. Use ONLY when reverse chaining AND _include are not available on the system.

mcode-sender-patient-bundle

Retrieves a Bundle of Condition resources with a code in mCODE’s cancer condition value set, and allows for associated Patient resources to be retrieved in a subsequent request. Use ONLY when reverse chaining AND _include are not available on the system.

mcode-sender-patients-and-cancer-conditions

Uses _include to retrieve a Bundle of Condition resources with a code in mCODE’s cancer condition value set, along with the associated Patient resources. Use ONLY when reverse chaining is not available on the system.

mcode-sender-patients-in-group

Capabilities for an mCODE Data Sender where not all cancer patients conform to mCODE. Retrieves a Group of references to Patient resources that conform to mCODE, and allows for the full Patient resources to be retrieved in a subsequent request.

mcode-sender-patients-with-cancer-condition

Uses reverse chaining to retrieve a Bundle of Patient resources with a condition code in mCODE’s cancer condition value set.

Behavior: Operation Definitions

These are custom operations that can be supported by and/or invoked by systems conforming to this implementation guide

mcode-patient-everything

Gets an mCODE Patient Bundle for a specific patient that contains all of that patient’s resources that conform to mCODE Profiles.

Structures: Abstract Profiles

These are profiles on resources or data types that describe patterns used by other profiles, but cannot be instantiated directly. I.e. instances can conform to profiles based on these abstract profiles, but do not declare conformance to the abstract profiles themselves.

Comorbidities Parent

General structure for capturing comorbid conditions with respect to a primary (‘index’) condition. The specific set of comorbidities of interest in a given context are defined by slicing the components array. The same general approach can be applied to any comorbidity category checklist.

Structures: Resource Profiles

These define constraints on FHIR resources for systems conforming to this implementation guide

Brachytherapy Treatment Phase

A summary of a phase of brachytherapy treatment that has been delivered. The scope is a treatment consisting of one or multiple identical fractions. A phase ends when there is a change in the irradiated volume, treatment fraction size, modality, or treatment technique.

Cancer Disease Status

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.

Cancer Genetic Variant

Records an alteration in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation.

Cancer Genomics Report

Genetic analysis summary report. The report may include one or more tests, with two distinct test types. The first type is a targeted mutation test, where a specific mutation on a specific gene is tested for. The result is either positive or negative for that mutation. The second type is a more general test for variants. This type of test returns the identity of variants found in a certain region of the genome.

Cancer Patient

A patient who has been diagnosed with or is receiving medical treatment for a malignant growth or tumor. The is the most essential profile in mCODE, since it is referenced by many other profiles. The only difference between the mCODE Patient profile and the US Core Patient Profile is that Patient.deceased is a must-support element in mCODE.

Cancer-Related Medication Administration

An episode of medication administration for a patient whose condition is related to a primary or secondary cancer condition. In the context of chemotherapy drugs, the medication administration in most cases is performed and documented by the provider.

Cancer-Related Medication Request

A record of a medication prescription or consumption associated with cancer treatment. The medication may reported by the prescriber, prescribing organization, or patient. It does not have to be directly observed.

Cancer-Related Surgical Procedure

A surgical action addressing a cancer condition. The scope of this profile has been narrowed to cancer-related procedures by constraining the reasonReference and reasonCode to cancer conditions, one of which is required.

Cancer Stage Group

The extent of the cancer in the body, according to a given cancer staging classification system, based on evidence such as physical examination, imaging, and/or biopsy or based on pathologic analysis of a specimen.

Comorbidities Elixhauser

Comorbid condition checklist and optional risk score, using Elixhauser comorbidity categories as defined by the Agency for Healthcare Research and Quality (AHRQ) Healthcare Cost and Utilization Project (H-CUP).

ECOG Performance Status

The Eastern Cooperative Oncology Group (ECOG) Performance Status represents the patient’s functional status and is used to determine their ability to tolerate therapies in serious illness, specifically for chemotherapy. (Definition from: LOINC)

Genetic Specimen

A small sample of blood, hair, skin, amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue which is excised from a subject for the purposes of genomics testing or analysis.

Genomic Region Studied

The area of the genome region referenced in testing for variants.

Karnofsky Performance Status

The Karnofsky Performance Status (KPS) is a tool used to measure a patient’s functional status. It can be used to compare the effectiveness of different therapies and to help assess the prognosis of certain patients, such as those with certain cancers. The KPS score ranges from 0 to 100 in intervals of 10. Higher scores are associated with better functional status, with 100 representing no symptoms or evidence of disease, and 0 representing death.

mCODE Patient Bundle

A collection of data for an mCODE cancer patient.

mCODE Patient Group

A group of patients included in the scope of mCODE, whose cancer-related resources conform to mCODE profiles.

Primary Cancer Condition

Records the the primary cancer condition, the original or first tumor in the body (Definition from: NCI Dictionary of Cancer Terms). Cancers that are not clearly secondary (i.e., of uncertain origin or behavior) should be documented as primary.

Radiotherapy Course Summary

A summary of a course of radiotherapy delivered to a patient. It records the treatment intent, termination reason, modalities, techniques, number of sessions, and doses delivered to one or more body volumes. To describe the treatment in more detail, use either TeleradiotherapyTreatmentPhase or BrachytherapyTreatmentPhase, which should reference this summary through their partOf elements. Whether the course has been fully delivered or stopped is indicated in the status element.

Radiotherapy Volume

A volume of the body used in radiotherapy planning or treatment delivery.

Secondary Cancer Condition

Records the history of secondary neoplasms, including location(s) and the date of onset of metastases. A secondary cancer results from the spread (metastasization) of cancer from its original site (Definition from: NCI Dictionary of Cancer Terms).

TNM Distant Metastases Category

Category describing the extent of a tumor metastasis in remote anatomical locations, based on evidence such as physical examination, imaging, and/or biopsy.

TNM Primary Tumor Category

Category of the primary tumor, based on its size and extent, based on evidence such as physical examination, imaging, and/or biopsy.

TNM Regional Nodes Category

Category of the presence or absence of metastases in regional lymph nodes, based on evidence such as physical examination, imaging, and/or biopsy.

Teleradiotherapy Treatment Phase

A summary of a phase of teleradiotherapy treatment that has been delivered. The scope is a treatment consisting of one or multiple identical fractions. A phase ends whenever there is a change in the irradiated volume, dose per fraction, modality, or technique.

Tumor

Identifies a tumor that has not been removed from the body. Whenever possible, a single resource conforming to this profile will be used to track a tumor over time (as opposed to creating new Tumor-conforming BodyStructure resources each time that tumor is measured). Use TumorSpecimen to represent the tumor after removal from the body.

Tumor Marker Test

The result of a tumor marker test. Tumor marker tests are generally used to guide cancer treatment decisions and monitor treatment, as well as to predict the chance of recovery and cancer recurrence.

Tumor Size

Records the dimensions of a tumor

Tumor Specimen

Represents a tumor after it has been removed from the body. Prior to excision, use Tumor (a BodyStructure) instead. If this tumor was represented by Tumor while still in the body, use identifier to associate with that resource.

Structures: Data Type Profiles

These define constraints on FHIR data types for systems conforming to this implementation guide

Body Structure Identifier

An identifier that designates a body structure such as a tumor and can be used for tracking the structure over time.

Structures: Extension Definitions

These define constraints on FHIR data types for systems conforming to this implementation guide

Specific Condition Code for Comorbidity

An extension for representing a specific condition code corresponding to the comorbid condition category.

Specific Condition Reference for Comorbidity

An extension for representing a reference to a condition resource corresponding to the comorbid condition category.

Condition related to resource

The resource has an unspecified relationship with a Condition.

Evidence Type

Categorization of the kind of evidence used as input to the clinical judgment. This corresponds to both the S and O in SOAP.

Histology-Morphology-Behavior

An extension describing the morphologic and behavioral characteristics of the cancer.

Location Qualifier

Qualifier to refine an body location. These include qualifiers for laterality, relative location, directionality, number, and plane.

Radiotherapy Dose Delivered To Body Volume

Dose parameters for one radiotherapy volume.

Radiotherapy Fractions Delivered

The total number of fractions (treatment divisions) actually delivered for this volume.

Radiotherapy Modality

Extension capturing a modality of external beam or brachytherapy radiation procedures.

Radiotherapy Number of Sessions

The number of sessions in a course of radiotherapy.

Radiotherapy Technique

Extension capturing a technique of external beam or brachytherapy radiation procedures.

Treatment Intent

The purpose of a treatment.

Termination Reason

A code explaining an unplanned or premature termination of a plan of treatment, course of medication, or research study.

Terminology: Value Sets

These define sets of codes used by systems conforming to this implementation guide

Location Qualifier Value Set

Qualifiers to refine a body structure or location. These include qualifiers for laterality, relative location, directionality, number, and plane.

Brachytherapy Modality Value Set

Codes describing the modalities of brachytherapy procedures.

Brachytherapy Technique Value Set

Codes describing the techniques of brachytherapy (internal or surface radiation) procedures.

Cancer Body Location Value Set

Codes describing the location(s) of primary or secondary cancer. The value set includes all codes from the SNOMED CT body structure hierarchy (codes descending from 123037004 ‘Body Structure’). The cancer body location may also be expressed using ICD-O-3 topography codes, however, those codes are not included here due to intellectual property restrictions. These topography terms have four-character codes that run from C00.0 to C80.9 ref. Only SNOMED CT and ICD-O-3 are considered conformant.

Cancer Disease Status Evidence Type Value Set

The type of evidence backing up the clinical determination of cancer progression.

Cancer Disorder Value Set

A broad cancer-related value set containing both primary and secondary tumor types, with codes from ICD-10 and SNOMED CT, including both diagnosis and histology/morphology/behavior codes. ICD-O-3 morphology codes may also be used and are considered conformant to the specification. For SNOMED, the value set includes all codes descending from 363346000 ‘Malignant neoplastic disease (disorder)’ and 108369006 ‘Neoplasm (morphologic abnormality)’.

Cancer-Related Surgical Procedure Value Set

Includes surgical procedure codes from SNOMED CT, ICD-10-PCS and CPT. The value set may be a superset of cancer surgery codes, but narrowing the set further risks eliminating potentially useful and relevant codes.

Stage Group Value Set

This value set is intended to contain allowable values for Stage Group, according to TNM staging rules. AJCC codes (preferably, version 8 for current cancers) SHOULD be used.

Cancer Staging System Value Set

System used for staging.

ClinVar Value Set

Value set of human genetic variants, drawn from ClinVar. The codes in this value set refer to the ClinVar Variation ID, or the identifier for the variant or set of variants that were interpreted. Source: NCBI ClinVar Data Dictionary

Condition Status Trend Value Set

How patient’s given disease, condition, or ability is trending.

DNA Change Type Value Set

DNA Change Type of a variant

Elixhauser Comorbid Condition Value Set for HIV-AIDS

Elixhauser Comorbid Condition Value Set for HIV-AIDS. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Alcohol Abuse

Elixhauser Comorbid Condition Value Set for Alcohol Abuse. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Blood Loss Anemia

Elixhauser Comorbid Condition Value Set for Blood Loss Anemia. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Leukemia

Elixhauser Comorbid Condition Value Set for Leukemia. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Lymphoma

Elixhauser Comorbid Condition Value Set for Lymphoma. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Metastatic cancer

Elixhauser Comorbid Condition Value Set for Metastatic cancer. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for malignant solid tumors in situ

Elixhauser Comorbid Condition Value Set for malignant solid tumors in situ. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for malignant solid tumors without metastases

Elixhauser Comorbid Condition Value Set for malignant solid tumors without metastases. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Cerebrovascular Disease

Elixhauser Comorbid Condition Value Set for cerebrovascular disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Chronic Pulmonary Disease

Elixhauser Comorbid Condition Value Set for Chronic Pulmonary Disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Coagulation Deficiency

Elixhauser Comorbid Condition Value Set for Coagulation Deficiency. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Congestive Heart Failure

Elixhauser Comorbid Condition Value Set for CongestiveHeartFailure. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Deficiency Anemia

Elixhauser Comorbid Condition Value Set for Deficiency Anemia. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Dementia

Elixhauser Comorbid Condition Value Set for Dementia. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Depression

Elixhauser Comorbid Condition Value Set for Depression. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for diabetes with chronic complications

Elixhauser Comorbid Condition Value Set for diabetes with chronic complications. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for diabetes without chronic complications

Elixhauser Comorbid Condition Value Set for diabetes without chronic complications. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for drug abuse

Elixhauser Comorbid Condition Value Set for drug abuse. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Hypertension, Complicated

Elixhauser Comorbid Condition Value Set for Hypertension, Complicated. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Hypertension, Uncomplicated

Elixhauser Comorbid Condition Value Set for Hypertension, Uncomplicated. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Hypothyroidism

Elixhauser Comorbid Condition Value Set for Hypothyroidism. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Mild Liver Disease

Elixhauser Comorbid Condition Value Set for Mild Liver Disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Moderate to Severe Liver Disease

Elixhauser Comorbid Condition Value Set for Moderate to Severe Liver Disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Neurological Movement Disorders

Elixhauser Comorbid Condition Value Set for Neurological Movement Disorders. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Neurological Seizure Disorders

Elixhauser Comorbid Condition Value Set for Neurological Seizure Disorders. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Obesity

Elixhauser Comorbid Condition Value Set for Obesity. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Other Neurological Disorders

Elixhauser Comorbid Condition Value Set for Other Neurological Disorders. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Other Thyroid Disorder

Elixhauser Comorbid Condition Value Set for Other Thyroid Disorder. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Paralysis

Elixhauser Comorbid Condition Value Set for Paralysis. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Peripheral vascular disease

Elixhauser Comorbid Condition Value Set for Peripheral vascular disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Psychosis

Elixhauser Comorbid Condition Value Set for Psychosis. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Pulmonary circulation disorders

Elixhauser Comorbid Condition Value Set for Pulmonary circulation disorders. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Moderate Renal Failure

Elixhauser Comorbid Condition Value Set for Moderate Renal Failure. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Severe Renal Failure

Elixhauser Comorbid Condition Value Set for Severe Renal Failure. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Rheumatoid Arthritis and collagen vascular diseases.

Elixhauser Comorbid Condition Value Set for Rheumatoid Arthritis and collagen vascular diseases. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Chronic peptic ulcer disease.

Elixhauser Comorbid Condition Value Set for Chronic peptic ulcer disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Valvular disease

Elixhauser Comorbid Condition Value Set for Valvular disease. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Elixhauser Comorbid Condition Value Set for Weight loss

Elixhauser Comorbid Condition Value Set for Weight loss. ICD-10 codes are drawn from https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp, version 2021.1

Genetic Specimen Type Value Set

The type of specimen analyzed in a genetic test. The values are taken from code system http://terminology.hl7.org/CodeSystem/v2-0487, and represent a subset of HL7 Version 2 Table 0487 (http://hl7.org/fhir/v2/0487).

HUGO Gene Nomenclature Committee Gene Names Value Set

HUGO Gene Nomenclature Committee Gene Names Value Set

Human Genome Variation Society Sequence Variant Nomenclature Value Set

HGVS nomenclature is used to report and exchange information regarding variants found in DNA, RNA, and protein sequences.

Histology Morphology Behavior Value Set

Codes representing the structure, arrangement, and behavioral characteristics of malignant neoplasms, and cancer cells. Inclusion criteria: in situ neoplasms and malignant neoplasms. Exclusion criteria: benign neoplasms and neoplasms of unspecified behavior. Note: ICD-O-3 morphology codes are referenced in the logical definition but not expanded in the value set for intellectual property reasons. For primary cancers, the ICD-O-3 behavior suffix should be /1, /2, or /3. For secondary cancers, the ICD-O-3 behavior suffix should be /6.

Observation Codes for Distant Metastases Category

Identifying codes based on the timing of classification for distant metastases (M) staging observations.

Observation Codes for Primary Tumor Category

Identifying codes based on the timing of classification for primary tumor (T) staging observations.

Observation Codes for Regional Node Category

Identifying codes based on the timing of classification for regional node (N) staging observations.

Observation Codes for Stage Group Category

Identifying codes based on the timing of classification for stage group observations.

Present-Absent-Unknown

Value set used in association with phenomena that can be observed as being present or absent, such as a finding, organism, or physical object.

Primary or Uncertain Behavior Cancer Disorder Value Set

Types of primary malignant neoplastic disease, coded in SNOMED CT or ICD-10-CM.

For SNOMED CT coding, use a code from the disorder hierarchy under SNOMED CT 363346000 ‘Malignant neoplastic disease (disorder)’ excluding codes descending from SNOMED CT 128462008 ‘Secondary malignant neoplastic disease (disorder)’. If body location is not precoordinated (i.e., implied by the code), the site of the primary tumor should be specified in the body site attribute.

For ICD-10-CM coding, use one of the codes given in this value set representing primary malignant neoplasms and neoplasms of uncertain or unspecified behavior.

Note that ICD-O-3 specifies morphology and topography, not disorder. If ICD-O-3 is used, the primary cancer disorder code must be specifically be SNOMED CT 363346000  ’Malignant neoplastic disease (disorder)’. The ICD-O-3 morphology and topography codes should be entered in the HistologyMorphologyBehavior and body location fields, respectively.

Radiotherapy Modality Value Set

Codes describing the modalities of external beam and brachytherapy radiation procedures, for use with radiotherapy summaries. This value set is the union of the EBRT and brachytherapy modality value sets.

Radiotherapy Technique Value Set

Codes describing the techniques of external beam and brachytherapy radiation procedures, for use with radiotherapy summaries. This is the union of the EBRT and brachytherapy technique value sets.

Radiotherapy Treatment Location Qualifier Value Set

Various modifiers that can be applied to body locations where radiotherapy treatments can be directed.

Radiotherapy Treatment Location Value Set

Codes describing the body locations where radiotherapy treatments can be directed.

Radiotherapy Volume Type Value Set

Codes describing the types of body volumes used in radiotherapy planning and treatment. The value set includes the most common codes from DICOM CID 9534 Radiotherapy Targets (UID 1.2.840.10008.6.1.1244) and adds a code for Organs at Risk (OAR).

Secondary Cancer Disorder Value Set

Types of secondary malignant neoplastic disease, coded in SNOMED CT or ICD-10-CM.

  • SNOMED CT coding: Use a code from the disorder hierarchy under secondary malignant neoplastic disease (SNOMED CT 128462008).
  • ICD-10-CM coding: Use one of the codes given in this value set representing secondary malignant neoplasms and neoplasms of uncertain or unspecified behavior. If body site is not precoordinated (implied by the code), it should be specified separately using the body location.

Note that ICD-O-3 specifies morphology and topography, not disorder; in this case that the disorder code must be SNOMED CT 128462008 (Secondary malignant neoplastic disease). The ICD-O-3 morphology and topography codes should be entered in the HistologyMorphologyBehavior and bodySite fields, respectively.

TNM Distant Metastases Category Value Set

This value set is intended to contain allowable values for the M category, according to TNM staging rules. AJCC codes (preferably, version 8 for current cancers) SHOULD be used.

TNM Primary Tumor Category Value Set

This value set is intended to contain allowable values for the T category, according to TNM staging rules. AJCC codes (preferably, version 8 for current cancers) SHOULD be used.

TNM Regional Nodes Category Value Set

This value set is intended to contain allowable values for the N category, according to TNM staging rules. AJCC codes (preferably, version 8 for current cancers) SHOULD be used.

Teleradiotherapy Modality Value Set

Codes describing the modalities of teleradiotherapy (external beam) procedures.

Teleradiotherapy Technique Value Set

Codes describing the techniques of teleradiotherapy (external beam) procedures.

Treatment Intent Value Set

The purpose of a treatment.

Treatment Termination Reason Value Set

Values used to describe the reasons for stopping a treatment or episode of care. Includes code for ‘treatment completed’ as well as codes for unplanned (early) stoppage. Applies to medications and other treatments that take place over a period of time, such as radiation treatments.

Tumor Marker Test Value Set

Codes representing tests for tumor markers. This value set of LOINC codes is not comprehensive and can be extended. Other vocabularies can be used only if the test of interest is not covered by LOINC. Tumor marker tests differ from genetic tests in that they measure levels of protein or other substances produced downstream from RNA protein synthesis.

Methods for measuring tumor size

Code for methods of measuring tumor size, including physical examination, pathology, and imaging.

Units of tumor size value set

Acceptable units for measuring tumor size

Terminology: Code Systems

These define new code systems used by systems conforming to this implementation guide

mCODE Catch Codes

Codes needed for positive identification of certain types of instances, more specifically, to uniquely associate instances with slices when they are used in bundles. The codes in this code system are used when a concept falls outside of the defined set of codes. They make it possible to use ‘required’ bindings where ‘extensible’ bindings would result an instance matching multiple slices and thus trigger validation errors.

Elixhauser Comorbidity Categories

A set of codes representing the comorbidity categories originally defined by Elixhauser, and updated by the Agency for Healthcare Research and Quality (AHRQ) Healthcare Cost and Utilization Project (H-CUP).

Radiotherapy Code System

Concepts used in association with radiotherapy profiles in mCODE, where terms could not be found in standard sources such as SNOMED CT.

mCODE Resource Identifier Code System

Concepts describing instance types, to be used in the code element of instances. These codes were created because no appropriate concept could be found in established vocabularies. These concepts are analogous to LOINC codes for laboratory observations: they identify the type of thing an instance represents.

Please note that while these codes may imply conformance to the profiles that use them, they are not synonymous with profiles and do not serve the same purpose in a FHIR resource for several reasons:

  1. An instance of a resource like Group, Observation, or Procedure may conform to multiple profiles, but may only have one ‘type of thing’ as determined by the value of code (which has a maximum cardinality of 1).
  2. Procedure.code, Observation.code, and Group.code elements require a CodeableConcept data type, which can be satisfied with a code from this code system. In contrast, a profile is identified with a canonical URL, which is represented by a URI data type. In other words, a profile’s canonical URL belongs in the meta.profile element, whereas the codes in this code system belong in Resource.code elements.
  3. The same code can correspond to more than one profile (although not the case here).

Example: Example Instances

These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like

Search by code:in in Conditions

This SearchParameter enables query of conditions by code with the in modifier.

Search by _id in Patients with multipleOr

This SearchParameter enables query of patients by _id with mutlipleOr enabled.

binet-stage-group-A

Example of a non-TNM Stage Group (Binet staging for CLL)

bodyheight-jenny-m-2018-03-06

Extended example: example of body height vital sign

bodyweight-jenny-m-2018-03-16

Extended example: example of body weight vital sign

bodyweight-jenny-m-2018-04-22

Extended example: body weight vital sign at the time of chemotherapy administration

brachytherapy-treatment-phase-low-dose-rate-temporary

Example of a brachytherapy therapy phase.

cancer-disease-status-improved

Example of Cancer Disease Status

cancer-disease-status-jenny-m

Extended example: example showing disease status (patient’s condition improved)

cancer-genetic-variant-germline-deletion

mCODE Example for Cancer Genetic Variant

cancer-genetic-variant-jenny-m

Extended example: example showing genetic variant found by breast cancer genomics panel

cancer-genetic-variant-somatic-single-nucleotide

mCODE Example for Cancer Genetic Variant

cancer-genomics-report-jenny-m

Extended example: example of gene panel report

cancer-genomics-report-john-anyperson

mCODE Example for Cancer Genomics Report

cancer-patient-adam-everyman

Example of Patient

cancer-patient-eve-anyperson

Example of Patient

cancer-patient-jenny-m

Extended example: example cancer patient

cancer-patient-john-anyperson

Example of Patient

cancer-related-mcode-comorbidities-elixhauser-jenny-m

mCODE Example for Cancer-Related Comorbidities

cancer-related-mcode-comorbidities-elixhauser-john-anyperson

Example of Cancer-Related Comorbidities

cancer-related-medication-administration-doxorubicin-jenny-m

Extended example: example showing chemotherapy medication

cancer-related-medication-request-anastrozole-jenny-m

Extended example: example showing chemotherapy medication

cancer-related-medication-request-cisplatin

Example of CancerRelatedMedicationRequest - Chemo Infusion

cancer-related-medication-request-cyclophosphamide-jenny-m

Extended example: example showing chemotherapy medication

cancer-related-medication-request-doxorubicin-jenny-m

Extended example: example showing chemotherapy medication

cancer-related-medication-request-gefitinib

Example of CancerRelatedMedicationRequest

cancer-related-medication-request-paclitaxel-jenny-m

Extended example: example showing chemotherapy medication

cancer-related-surgical-procedure-jenny-m

Extended example: example showing partial mastectomy surgical procedure

cancer-related-surgical-procedure-lobectomy

Example of Cancer Related Surgical Procedure

ecog-performance-status-fully-active

Example of ECOG Performance Status

ecog-performance-status-jenny-m

Extended example: example showing ECOG performance status

family-member-history-aunt-jenny-m

Extended example: example showing family member history of cancer

family-member-history-sister-jenny-m

Extended example: example showing family member history of cancer

family-member-history-uncle-jenny-m

Extended example: example showing family member history of cancer

genetic-specimen-left-breast-jenny-m

Extended example: example showing genetic specimen for sequencing

genetic-specimen-lung

mCODE Example for Genetic Specimen

genomic-region-studied-jenny-m

Extended example: example showing which regions were included in the genomics panel

genomic-region-studied-stk11

mCODE Example for Genomic Region Studied

mCODE Patient Group Example

Example of a Group identifying mCODE Patients

jenny-m-chest-wall-lymph-nodes-treatment-volume

Anatomic volume 2 for Jenny M’s teleradiotherapy.

jenny-m-chest-wall-treatment-volume

Anatomic volume 1 for Jenny M’s teleradiotherapy.

john-anyperson-treatment-volume

Anatomic volume for John Anyperson’s brachytherapy.

karnofsky-performance-status-normal-activity

Example of Karnofsky Performance Status

lab-result-observation-hemoglobin

Hemoglobin lab result to support CancerStageGroup example

mcode-patient-bundle-jenny-m

Extended example as a mCODE Patient Bundle

observation-smoking-history-jenny-m

Extended example: example showing smoking history

primary-cancer-condition-breast

mCODE Example for Primary Cancer Condition (breast). The example shows post-coordinated coding using SNOMED-CT, with separate codes for morphology and bodySite.

primary-cancer-condition-cll

Example of Primary Cancer Condition - hematologic cancer

primary-cancer-condition-jenny-m

Extended example: example showing primary cancer condition

primary-cancer-condition-nsclc

Example of Primary Cancer Condition

radiotherapy-treatment-summary-chest-wall-jenny-m

Example of radiotherapy treatment summary involving external beam radiation to chest wall and regional node radiation with a chest wall boost

secondary-cancer-condition-brain-mets

Example of Secondary Cancer Condition

teleradiotherapy-treatment-phase-boost-jenny-m

Example of teleradiotherapy treatment boost phase

teleradiotherapy-treatment-phase-chest-wall-jenny-m

Example of teleradiotherapy treatment phase involving external beam radiation to chest wall and regional node radiation

tnm-clinical-distant-metastases-category-cM0

Example of TNM Clinical Distant Metastases Category

tnm-clinical-distant-metastases-category-jenny-m

Extended example: example showing TNM staging (M)

tnm-clinical-primary-tumor-category-cT3

Example of TNM Clinical Primary Tumor Category

tnm-clinical-primary-tumor-category-jenny-m

Extended example: example showing TNM staging (T)

tnm-clinical-regional-nodes-category-cN3

Example of TNM Clinical Regional Nodes Category

tnm-clinical-regional-nodes-category-jenny-m

Extended example: example showing TNM staging (N)

tnm-clinical-stage-group-3c

Example of TNM Clinical Stage Group

tnm-clinical-stage-group-jenny-m

Extended example: example showing TNM staging (stage group)

tnm-pathologic-distant-metastases-category-jenny-m

Extended example: example showing TNM staging (M)

tnm-pathologic-primary-tumor-category-jenny-m

Extended example: example showing TNM staging (T)

tnm-pathologic-regional-nodes-category-jenny-m

Extended example: example showing TNM staging (N)

tnm-pathologic-stage-group-jenny-m

Extended example: example showing TNM staging (stage group)

tumor-lobular-carcinoma-left-breast

Example of a resource conforming to the tumor profile.

tumor-marker-test-egf

mCODE Example for Tumor Marker Test

tumor-marker-test-er-jenny-m

Extended example: example showing ER status

tumor-marker-test-her2-jenny-m

Extended example: example showing HER2 status

tumor-marker-test-oncotype-dx-jenny-m

Extended example: example showing Oncotype DX breast recurrence score. Note that this test has no assigned LOINC code, so GTR is being used as a backup. Only the score from the Oncotype DX panel (as opposed to variant data from the genes in the panel) is represented here.

tumor-marker-test-pr-jenny-m

Extended example: example showing PR status

tumor-size-jenny-m

Extended example: example showing tumor size

tumor-size-pathology

Example of a resource conforming to the tumor size profile.

tumor-specimen-left-breast-jenny-m

Extended example: example tumor specimen

tumor-specimen-lobular-carcinoma-left-breast

Example of a TumorSpecimen linked to this Tumor via identifier.

us-core-condition-anxiety-jenny-m

Extended example: example showing comorbid condition (anxiety)

us-core-condition-depression-jenny-m

Extended example: example showing comorbid condition (depression)

us-core-condition-hypertension-jenny-m

Extended example: example showing comorbid condition (hypertension)

us-core-diagnosticreport-lab-jenny-m

Extended example: example of pathology findings represented as a DiagnosticReport resource.

us-core-observation-lab-neutrophils-jenny-m

Extended example: neutrophils lab test

us-core-observation-lab-sentinel-nodes-jenny-m

Extended example: example showing 3 sentinel lymph nodes were examined

us-core-observation-lab-tumor-dcis-jenny-m

Extended example: example showing DCIS diagnosis

us-core-observation-lab-tumor-invasion-jenny-m

Extended example: example showing negative invasion for the removed tumor

us-core-observation-lab-tumor-margins-jenny-m

Extended example: example showing negative margins for the removed tumor

us-core-organization-bedrock-medicine

Example of US Core Organization

us-core-organization-physician-services-inc

Extended example: example organization

us-core-practitioner-jane-radiotech

Extended example: example PCP practitioner

us-core-practitioner-kyle-anydoc

Example of Practitioner

us-core-practitioner-mary-obgyn

Extended example: example PCP practitioner

us-core-practitioner-nancy-oncology-nurse

Extended example: example RN practitioner

us-core-practitioner-owen-oncologist

Extended example: example practitioner

us-core-practitioner-peter-pathologist

Extended example: example practitioner (pathologist)

us-core-procedure-biopsy-jenny-m

Extended example: example biopsy procedure

us-core-procedure-mammogram-jenny-m

Extended example: example mammogram

us-core-smokingstatus-jenny-m

Extended example: example showing smoking status