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Lung Cancer Message Support Guidance

Introduction

This guide aims to explain the process to follow in order to read and understand the message “Lung-Cancer-Message-Bundle-Example” based on Lung Excel template. More information on FHIR messages can also be found in Simplifier INCISIVE project.

Message description

In this chapter describes the message content in a table containing these columns.

Table Columns description

Column Name	Description
Tab Template	Tab name included in excel file of Lung Cancer
Variable	Variable name included in Excel file
ID resource	ID identification inside the assigned resource
FHIR message location	Attribute used to inform the variable inside the bundle
Example value	Example value used to inform the variable assigned
Required by FHIR specification	Inform the variable is mandatory/optional in XML, based on compliance with the FHIR specification
INCISIVE profile	URL of profiles created by INCISIVE
Condition	Description term condition

Table with Message description

Tab template General Info

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Patient Number	lungpatient01	Patient.identifier.value	004-000001	Optional
Gender	lungpatient01	Patient.gender	female	Optional
Age at diagnosis	lungdiagnosticReport01	DiagnosticReport.extension.valueAge.value	56	Mandatory	Extension
Ethnicity	lungpatient01	Patient.extension.valueCodeableConcept.coding.code	1	Optional	Extension
		Patient.extension.valueCodeableConcept.coding.display	White	Optional
Medical History	lungcondition01	Condition.code.text	N39.8	Optional
Emphysema	lungobservation01	Observation.component.valueBoolean	true	Optional
Smoker	lungobservation02	Observation.component.valueCodeableConcept.coding.code	2	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Ex	Optional
Years of smoking	lungobservation02	Observation.component.valueInteger	10	Optional
Number of cigarettes per day	lungobservation02	Observation.component.valueInteger	15	Optional
Age quitting smoking	lungobservation02	Observation.component.valueInteger	50	Optional
Familial Cancer History Father	lungobservation01	Observation.component.valueBoolean	true	Optional
Familial Cancer History Mother	lungobservation01	Observation.component.valueBoolean	true	Optional
Medication general info	lungmedication01	Medication.code.text	Medication therapy	Optional
Current state	lungpatient01	Patient.extension.valueCode	0	Optional	Extension
Notes general info	lungobservation01	Observation.note.text	Observation note	Mandatory
Provider	lungorganization01	Organization.identifier.type.coding.code	1	Optional	CodeSystem
		Organization.identifier.type.coding.display	AUTH	Optional
Case	-	MessageHeader.eventCoding.display	Primary malignant neoplasm of lung (disorder)	Mandatory
Delivery Time general info	-	Bundle.timestamp	2023-07-24T12:29:17.239+02:00	Optional

Tab template Baseline

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Hemoptysis baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Cough baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Dyspnea baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Weight Loss baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Other symptoms baseline	lungcondition02	Condition.evidence.code.text	Other symptoms	Optional
Performance status baseline	lungobservation03	Observation.component.valueInteger	5	Optional
Existence of Laboratory data baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Computerized axial tomography (CT) baseline	lungobservation05	Observation.component.valueBoolean	true	Optional
Annotated CT baseline	lungobservation05	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Magnetic resonance imaging (MRI) baseline	lungobservation05	Observation.component.valueBoolean	true	Optional
Annotated MRI baseline	lungobservation05	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Positron emission tomography (PET/CT) baseline	lungobservation05	Observation.component.valueBoolean	true	Optional
Annotated PET/CT baseline	lungobservation05	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Histopathology Image baseline	lungobservation05	Observation.component.valueBoolean	true	Optional
Annotated Histopathology Image baseline	lungobservation05	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Xray baseline	lungobservation05	Observation.component.valueBoolean	true	Optional
Annotated Xray baseline	lungobservation05	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Laterality	lungobservation03	Observation.component.valueCodeableConcept.coding.code	0	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Right lung	Optional
Lobe	lungobservation03	Observation.component.valueCodeableConcept.coding.code	RUL	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Right upper lobe	Optional
Max tumor diameter baseline	lungobservation03	Observation.component.valueQuantity.value	4.8	Optional
Lung Volume	lungobservation03	Observation.component.valueQuantity.value	4500000	Optional
Solidity	lungobservation03	Observation.component.valueCodeableConcept.coding.code	0	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Solid	Optional
Central Necrosis	lungobservation03	Observation.component.valueBoolean	true	Optional
Cavitation	lungobservation03	Observation.component.valueBoolean	true	Optional
Borders	lungobservation03	Observation.component.valueCodeableConcept.coding.code	0	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Irregular	Optional
Pleural Effusion baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Lymph nodes baseline	lungobservation04	Observation.component.valueBoolean	true	Optional
Lymph node stations baseline	lungobservation04	Observation.component.valueString	1	Optional
Lymph nodes max short axis diameter baseline	lungobservation04	Observation.component.valueQuantity.value	1.3	Optional
Lung nodules baseline	lungobservation04	Observation.component.valueBoolean	true	Optional
Number of nodules baseline	lungobservation04	Observation.component.valueInteger	1	Optional
Lung nodules location baseline	lungobservation04	Observation.bodySite.coding.code	1	Optional	CodeSystem
		Observation.bodySite.coding.display	Same lung	Optional
Distant metastasis baseline	lungobservation03	Observation.component.valueBoolean	true	Optional
Distant metastasis location baseline	lungobservation03	Observation.bodySite.coding.code	1	Optional	CodeSystem
		Observation.bodySite.coding.display	Liver	Optional
Stage baseline	lungobservation03	Observation.component.valueString	IA3	Optional
Ti baseline	lungobservation03	Observation.component.valueString	T0	Optional
Ni baseline	lungobservation03	Observation.component.valueString	N0	Optional
Mi baseline	lungobservation03	Observation.component.valueString	M0	Optional

Tab template Timepoints

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Label timepoints	lungobservation06	Observation.code.coding.code	1	Mandatory	CodeSystem
		Observation.code.coding.display	After 1st Treatment	Mandatory
Define other if selected timepoints	lungobservation06	Observation.category.text	Between 1st and 2nd dose of CT	Optional
Distant metastasis location timepoints	lungobservation06	Observation.bodySite.coding.code	1	Optional	CodeSystem
		Observation.bodySite.coding.display	Liver	Optional
Distant metastasis timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Date timepoints	lungobservation06	Observation.valueInteger	2	Optional
Hemoptysis timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Cough timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Dyspnea timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Weight Loss timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Other symptoms timepoints	lungcondition03	Condition.evidence.code.text	Other symptoms	Optional
Performance status timepoints	lungobservation06	Observation.component.valueInteger	5	Optional
Existence of Laboratory data timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Computerized axial tomography (CT) timepoints	lungobservation07	Observation.component.valueBoolean	true	Optional
Annotated CT timepoints	lungobservation07	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Magnetic resonance imaging (MRI) timepoints	lungobservation07	Observation.component.valueBoolean	true	Optional
Annotated MRI timepoints	lungobservation07	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Positron emission tomography (PET/CT) timepoints	lungobservation07	Observation.component.valueBoolean	true	Optional
Annotated PET/CT timepoints	lungobservation07	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Histopathology Image timepoints	lungobservation07	Observation.component.valueBoolean	true	Optional
Annotated Histopathology Image timepoints	lungobservation07	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Xray timepoints	lungobservation07	Observation.component.valueBoolean	true	Optional
Annotated Xray timepoints	lungobservation07	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional
Max tumor diameter timepoints	lungobservation06	Observation.component.valueQuantity.value	4.8	Optional
Pleural Effusion timepoints	lungobservation06	Observation.component.valueBoolean	true	Optional
Lymph nodes timepoints	lungobservation08	Observation.component.valueBoolean	true	Optional
Lymph node stations timepoints	lungobservation08	Observation.component.valueString	1	Optional
Lymph nodes max short axis diameter timepoints	lungobservation08	Observation.component.valueQuantity.value	1.3	Optional
Lung nodules timepoints	lungobservation08	Observation.component.valueBoolean	true	Optional
Lung nodules location timepoints	lungobservation08	Observation.bodySite.coding.code	1	Optional	CodeSystem
		Observation.bodySite.coding.display	Same lung	Optional
Stage timepoints	lungobservation06	Observation.component.valueString	IA3	Optional
Response to treatment	lungobservation06	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	CR	Optional
Ti timepoints	lungobservation06	Observation.component.valueString	T0	Optional
Ni timepoints	lungobservation06	Observation.component.valueString	N0	Optional
Mi timepoints	lungobservation06	Observation.component.valueString	M0	Optional

Tab template Treatment

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Label treatment	lungobservation09	Observation.code.coding.code	1	Mandatory	CodeSystem
		Observation.code.coding.display	After 1st Treatment-1st FollowUp	Mandatory
Define other if selected treatment	lungobservation09	Observation.category.text	Between 1st and 2nd dose of CT	Optional
Surgery treatment	If = true
Type of surgery	lungprocedure01	Procedure.category.text	Pneumonectomy	Optional		If Surgery treatment =true, else delete all lungprocedure01 and component Lymphadenectomy of lungobservation09
Date of surgery	lungprocedure01	Procedure.performedString	2	Optional
Location of Surgery	lungprocedure01	Procedure.bodySite.text	RUL	Optional
Lymphadenectomy	lungobservation09	Observation.component.valueBoolean	true	Optional
Chemotherapy (CTX)	If = true
Type of CTX	lungprocedure02	Procedure.code.text	Cisplatino	Optional		If CTX=true, else delete all lungprocedure02
Date of last CTX	lungprocedure02	Procedure.performedString	2	Optional
Chemoradiotherapy (CRT)	If = true
Type of CRT	lungprocedure03	Procedure.code.text	Crizotinib	Optional		If CRT=true, else delete all lungprocedure03
Date of last CRT	lungprocedure03	Procedure.performedString	2	Optional
Chemoimmunotherapy (CIT)	If = true
Type of CIT	lungprocedure04	Procedure.code.text	Crizotinib	Optional		If CIT=true, else delete all lungprocedure04
Date of last CIT	lungprocedure04	Procedure.performedString	2	Optional
Targeted therapy (TT)	If = true
Type of TT	lungprocedure05	Procedure.code.text	Crizotinib	Optional		If TT=true, else delete all lungprocedure05
Date of last TT	lungprocedure05	Procedure.performedString	2	Optional
Immune therapy (IT)	If = true
Type of IT	lungprocedure06	Procedure.code.text	Alectinib	Optional		If IT=true, else delete all lungprocedure06
Date of last IT	lungprocedure06	Procedure.performedString	2	Optional
Radiation therapy (RT)	If = true
Date of last RT	lungprocedure07	Procedure.performedString	2	Optional		If RT=true, else delete all lungprocedure07
Delivered dose of RT	lungmedicationAdministration01	MedicationAdministration.dosage.dose.value	50.4	Optional
Number of fractions RT	lungmedicationAdministration01	MedicationAdministration.dosage.rateQuantity.value	28	Optional
Post-treatment surgery	If = true
Type of post-treatment surgery	lungprocedure08	Procedure.category.text	Pneumonectomy	Optional		If Post-treatment surgery=true, else delete all lungprocedure08
Date of post-treatment surgery	lungprocedure08	Procedure.performedString	2	Optional

Tab template Histology - Mutations

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Biopsy	If = true
Biopsy label	lungprocedure09	Procedure.statusReason.coding.code	1	Optional	CodeSystem	If Biopsy=true, else delete all lungprocedure09
		Procedure.statusReason.coding.display	After 1st Treatment	Optional
Define other if selected histology-mutations	lungprocedure09	Procedure.category.text	Between 1st and 2nd dose of CT	Optional
Date of Biopsy	lungprocedure09	Procedure.performedString	2	Optional
Surgery histology-mutations	If = true
Surgery date	lungprocedure10	Procedure.performedString	2	Optional		If Surgery histology-mutations=true, else delete all lungprocedure10
Lung Cancer Type	lungobservation12	Observation.category.coding.code	1	Optional	CodeSystem
	lungobservation12	Observation.category.coding.display	Adenocarcinoma	Optional
Lung Cancer Grade	lungobservation12	Observation.component.valueInteger	1	Optional
PD-L1	lungobservation10	Observation.component.valueBoolean	true	Optional
BRAF	lungobservation10	Observation.component.valueBoolean	true	Optional
ALK	lungobservation10	Observation.component.valueBoolean	true	Optional
EGFR	lungobservation10	Observation.component.valueQuantity.value	10	Optional
HER2	lungobservation10	Observation.component.valueBoolean	true	Optional
MET	lungobservation10	Observation.component.valueBoolean	true	Optional
RET	lungobservation10	Observation.component.valueBoolean	true	Optional
ROS1	lungobservation10	Observation.component.valueBoolean	true	Optional
IGF1R	lungobservation10	Observation.component.valueBoolean	true	Optional
ERBB2	lungobservation10	Observation.component.valueBoolean	true	Optional
PIK3CA	lungobservation10	Observation.component.valueBoolean	true	Optional
KRAS	lungobservation10	Observation.component.valueBoolean	true	Optional
Sampling	lungobservation11	Observation.component.valueString	Light microscopy	Optional
Staining/type of assay performed	lungobservation11	Observation.component.valueString	Hematoxylin	Optional
Magnification	lungobservation11	Observation.component.valueString	x10	Optional
Other sample-related information	lungobservation11	Observation.component.valueString	example	Optional

Tab template Lab Results

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Exam label	lungobservation13	Observation.code.coding.code	1	Mandatory	CodeSystem
		Observation.code.coding.display	After 1st Treatment	Mandatory
Define other if selected lab results	lungobservation13	Observation.category.text	Between 1st and 2nd dose of CT	Optional
Date Laboratory	lungobservation13	Observation.valueInteger	2	Optional
Leukocytes	lungobservation13	Observation.component.valueQuantity.value	15.8	Optional
Hemoglobin (Hb)	lungobservation13	Observation.component.valueQuantity.value	16.7	Optional
Hematocrit (HCT)	lungobservation13	Observation.component.valueQuantity.value	47.4	Optional
Platelets (PLT)	lungobservation13	Observation.component.valueQuantity.value	287	Optional
Blood sugar levels	lungobservation13	Observation.component.valueQuantity.value	87	Optional
Insulin	lungobservation13	Observation.component.valueQuantity.value	4	Optional
Urea	lungobservation13	Observation.component.valueQuantity.value	36	Optional
Creatinine	lungobservation13	Observation.component.valueQuantity.value	0.72	Optional
Uric acid	lungobservation13	Observation.component.valueQuantity.value	3.5	Optional
Potassium	lungobservation13	Observation.component.valueQuantity.value	4.8	Optional
Sodium	lungobservation13	Observation.component.valueQuantity.value	142	Optional
Calcium	lungobservation13	Observation.component.valueQuantity.value	9.31	Optional
Cholesterol	lungobservation13	Observation.component.valueQuantity.value	197	Optional
Triglycerides	lungobservation13	Observation.component.valueQuantity.value	59	Optional
HDL	lungobservation13	Observation.component.valueQuantity.value	60	Optional
LDL	lungobservation13	Observation.component.valueQuantity.value	120	Optional
SGOT	lungobservation13	Observation.component.valueQuantity.value	19	Optional
SGPT	lungobservation13	Observation.component.valueQuantity.value	33	Optional
y-GT	lungobservation13	Observation.component.valueQuantity.value	14	Optional
ALP	lungobservation13	Observation.component.valueQuantity.value	227	Optional
LDH	lungobservation13	Observation.component.valueQuantity.value	270	Optional
TSH	lungobservation13	Observation.component.valueQuantity.value	0.73	Optional
Cortisol	lungobservation13	Observation.component.valueQuantity.value	22	Optional
CRP	lungobservation13	Observation.component.valueQuantity.value	0.5	Optional
BNP	lungobservation13	Observation.component.valueQuantity.value	120	Optional
HbA1c	lungobservation13	Observation.component.valueQuantity.value	5.1	Optional
Total protein in urine	lungobservation13	Observation.component.valueQuantity.value	80	Optional
Creatinine urine	lungobservation13	Observation.component.valueQuantity.value	100	Optional

In order to build the message for each patient, and to report the variables in the table above, the following steps must be followed:

1. Search inside the message text with the same word that appears in the “Variable” column.
2. Check that the resource to which it redirects us has the same id as in the “ID resource” column.
3. Enter the desired value in the double quoted space of the attribute indicated in the “Fhirmessage location” column.
4. Do not delete any part of the message, the whole structure must be the same, just change the example value, for the value you want to report. Do not change the order.
5. If you don’t have the information of the element, you can delete the node, but validate XML to ensure the structure of the XML FHIR is still correct and has no errors (you can omit the warnings in the validation). The entire message structure is static except for the values given for the attributes in the “Fhir message location” column and the timestamp which is the current datatime.
   

Description mandatory/optional of term

There will be mandatory/optional for different scenarios, according to different scenarios corresponding to different rules. These scenarios are described separately below.

• If the attribute is mandatory, all attribute structure information for this column must be reported. It cannot be deleted.

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Notes general info	colorectalobservation01	Observation.note.text	Observation note	Mandatory

• If the attribute is mandatory with a comment reporting the condition of this variable, all attribute structure information for this column must be reported, unless the variable has not value for report, all resources must be deleted.

• If an optional attribute needs to be deleted, all attribute structures except for the primary resource (e.g., observation, procedure, condition, etc.) must be deleted if that primary resource has another variable. For example, for the variable Gender, you can delete the attribute gender from the resource Patient, while other attributes such as identifier have values and do not have to be deleted.

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Gender	colorectalpatient01	Patient.gender	female	Optional

• If the attribute is optional, this happens in observation.component because Observation.component has two parts inside, Observation.component.code and Observation.component.value (this value can be valueCodeableConcept, ValueBoolean, ValueSrting, valueInteger, valueQuantity, etc.). If the variable has a value that needs to be informed, then code is mandatory, that code is mostly the SNOMED CT code or LOINC code for that variable. This means that if you need to delete variable, then you need to delete all Observation.component and cannot delete the whole Observation resource, unless there are no other elements in the same Observation, then you can delete the whole Observation resource.

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Annotated CT baseline	breastobservation05	Observation.component.valueCodeableConcept.coding.code	1	Optional	CodeSystem
		Observation.component.valueCodeableConcept.coding.display	Positive annotation	Optional

• If the attribute is optional with a comment reporting the condition of this variable, you can delete all resource if the variable has not value for report.

Variable	ID resource	FHIR message location	Example Value	Required by FHIR specification	INCISVE Profile	Condition
Surgery date	colorectalprocedure10	Procedure.performedString	2	Optional		If Surgery histology-mutations=true, else delete all colorectalprocedure10