santosh-pingle
commented
2 years ago Started looking into it!
Closed fredhersch closed 2 years ago
santosh-pingle
commented
2 years ago Started looking into it!
santosh-pingle
commented
2 years ago @fredhersch (Starting a new screener loads the FHIR Screener Questionnaire resource) Can you please share Questionnaire resource.
santosh-pingle
commented
2 years ago As per updates received from @jingtang10, extraction of screener questionnaire response is pending for some clarifications on data modelling, therefore we will not have implementation for extraction logic as of now.
santosh-pingle
commented
2 years ago @jingtang10 @fredhersch
Below json file is used to show the screener encounter questionnaire. https://github.com/google/android-fhir/pull/627/files#R1
Once questionnaire response is submitted, next step is to extract the resource from the questionnaire. Currently ResourceMapper.extract() api is used to extract the resource, but it requires Questionnaire.item.definition and extension to extract the resource.
e.g "definition": "http://hl7.org/fhir/StructureDefinition/...
"extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { ....
Therefore requesting you please updates screener encounter json with Questionnaire.item.definition and extension.
jingtang10
commented
2 years ago Discussed offline. See this comment: https://chat.fhir.org/#narrow/stream/179255-questionnaire/topic/SDC.20Extraction.20examples/near/226341617
It seems to me that the right thing to do is to use each group as an extraction context. and everything within that group gets mapped into the resource for the group. In this questionnaire that's already how things are organized.
santosh-pingle
commented
2 years ago @jingtang10
Can you please provide your feedback/early review comments on below file changes https://github.com/google/android-fhir/compare/sp/multiple-resources-extraction?expand=1
I have updated some of the screener encounter questionnaire items and group item for definition based urls, can you please confirm those? (your input is required regarding definition urls to check whether further changes are required in resource mapper to update resource fields in existing code e.g list of values)
Remaining items still require definition url, can you please provide inputs on it?
santosh-pingle
commented
2 years ago @jingtang10
SDC library ResourceMapper was not updating multiple answers of the given question item to the resource field. Though, response had captured multiple answers, it was only showing the list of first answers in the resource field. => Support is added, it was required to update all selected answers of "symptoms " and "Medical history" in resource.
santosh-pingle
commented
2 years ago Currently, sdc library does not support the risk assessment as per feedback from Jing, therefore risk related response will not be updated to the resource fields until library supports it.
santosh-pingle
commented
2 years ago Screener encounter questionnaire json need to be updated for below question items for definition base extraction
Jing had provided some inputs on it, like adding hidden question, and code item to the questionnaire. Referring documentation for more information on it.
santosh-pingle
commented
2 years ago @jingtang10
We also need to discuss multiple resources mapping just before saving them into the application database. These multiple resources are extracted from resource mapper and returned as bundle. e.g Encounter, Observation resources, Condition.
jingtang10
commented
2 years ago @jingtang10
We also need to discuss multiple resources mapping just before saving them into the application database. These multiple resources are extracted from resource mapper and returned as bundle. e.g Encounter, Observation resources, Condition.
Great question. There're two approaches to link extracted resources with existing resources
subject field of Observation etc.subject of Observation)The first approach is more generic and probably more elegant but I'm happy for us to do 2 first and follow up with another change to implement the first one.
jingtang10
commented
2 years ago Currently, sdc library does not support the risk assessment as per feedback from Jing, therefore risk related response will not be updated to the resource fields until library supports it.
Currently, sdc library does not support the risk assessment as per feedback from Jing, therefore risk related response will not be updated to the resource fields until library supports it.
I think we can map most of the risk factor questions to observations or conditions: e.g. https://hl7.org/fhir/us/core/2017Jan/ValueSet-us-core-observation-ccdasmokingstatus.html we can borrow the codes from this profile.
Let's not use SDC extraction for RiskAssessment, let's do that as a step in the business logic following the extraction.
jingtang10
commented
2 years ago @jingtang10
SDC library ResourceMapper was not updating multiple answers of the given question item to the resource field. Though, response had captured multiple answers, it was only showing the list of first answers in the resource field. => Support is added, it was required to update all selected answers of "symptoms " and "Medical history" in resource.
can you create an issue for this please?
jingtang10
commented
2 years ago Screener encounter questionnaire json need to be updated for below question items for definition base extraction
- Covid vaccination
- Temperature
- Pulse Oximetry
Jing had provided some inputs on it, like adding hidden question, and code item to the questionnaire. Referring documentation for more information on it.
For temperature and pulse oximetry, we will need to extract Observations with a Quantity value. A Quantity value is basically a number and a unit. So if we want the user to choose a unit (in the case of fahrenheit or celsium) we need to present another question, if we don't want the user to choose a unit, then we probably need a hidden field. Example:
{
"text": "Record temperature",
"type": "decimal",
"linkId": "5.1.0",
"definition": "https://..../Observation.valueQuantity.value"
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/minValue",
"valueDecimal": 35.0
},
{
"url": "http://hl7.org/fhir/StructureDefinition/maxValue",
"valueDecimal": 45.0
}
]
},
{
"type": "drop-down",
"linkId": "5.1.0",
"definition": "https://..../Observation.valueQuantity.system"
"initial": "http://unitsofmeasure.org"
"hidden": true...
},
{
"type": "drop-down",
"linkId": "5.1.0",
"definition": "https://..../Observation.valueQuantity.code"
"answerOptions": [
"F",
"C"
]
}More info: https://hl7.org/fhir/R4/bodytemp.html
fredhersch
commented
2 years ago Screener encounter questionnaire json need to be updated for below question items for definition base extraction
- Covid vaccination
- Temperature
- Pulse Oximetry
Jing had provided some inputs on it, like adding hidden question, and code item to the questionnaire. Referring documentation for more information on it.
For temperature and pulse oximetry, we will need to extract
Observations with aQuantityvalue. AQuantityvalue is basically a number and a unit. So if we want the user to choose a unit (in the case of fahrenheit or celsium) we need to present another question, if we don't want the user to choose a unit, then we probably need a hidden field. Example:{ "text": "Record temperature", "type": "decimal", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.value" "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.system" "initial": "http://unitsofmeasure.org" "hidden": true... }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.code" "answerOptions": [ "F", "C" ] }More info: https://hl7.org/fhir/R4/bodytemp.html
Can we add the relevant LOINC code to the code section like this:
"code": [
{
"code": "44169009",
"display": "Loss of sense of smell (finding)",
"system": "http://snomed.info/sct"
}
],So it would look like this - see the addition of code under the linkId item:
{ "text": "Record temperature", "type": "decimal", "linkId": "5.1.0", "code" : [ { "code" : "8310-5", "display" : "Temperature", "system" : "http://loinc.org" }, ], "definition": "https://..../Observation.valueQuantity.value" "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.system" "initial": "http://unitsofmeasure.org" "hidden": true... }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.code" "answerOptions": [ "F", "C" ] }
fredhersch
commented
2 years ago @santosh-pingle For the initial pass, let's leave out the vaccination status. We should revisit this next.
For Temperature, the code section can be:
"code" : [
{
"code" : "8310-5",
"display" : "Temperature",
"system" : "http://loinc.org"
},
],For Pulse Oximetry it can be:
"code" : [
{
"code" : "59408-5",
"display" : "Oxygen Saturation",
"system" : "http://loinc.org"
},
],And for heart rate (pulse)
"code" : [
{
"code" : "8867-4",
"display" : "Heart rate",
"system" : "http://loinc.org"
}
]@jingtang10 We also need to discuss multiple resources mapping just before saving them into the application database. These multiple resources are extracted from resource mapper and returned as bundle. e.g Encounter, Observation resources, Condition.
Great question. There're two approaches to link extracted resources with existing resources
- Use hidden questions and pre-population of questionnaire to set the references (in our case patient ID) as answers to the hidden questions so that they will be extracted to the
subjectfield ofObservationetc.- Handle these after extraction. This requries the application to know when resource types will be in the bundle and handle them accordingly to populate certain fields (i.e.
subjectofObservation)The first approach is more generic and probably more elegant but I'm happy for us to do 2 first and follow up with another change to implement the first one.
Implemented 2 approach. I will create separate ticket to follow up 1 approach.
santosh-pingle
commented
2 years ago Screener encounter questionnaire json need to be updated for below question items for definition base extraction
- Covid vaccination
- Temperature
- Pulse Oximetry
Jing had provided some inputs on it, like adding hidden question, and code item to the questionnaire. Referring documentation for more information on it.
For temperature and pulse oximetry, we will need to extract
Observations with aQuantityvalue. AQuantityvalue is basically a number and a unit. So if we want the user to choose a unit (in the case of fahrenheit or celsium) we need to present another question, if we don't want the user to choose a unit, then we probably need a hidden field. Example:{ "text": "Record temperature", "type": "decimal", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.value" "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.system" "initial": "http://unitsofmeasure.org" "hidden": true... }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.code" "answerOptions": [ "F", "C" ] }More info: https://hl7.org/fhir/R4/bodytemp.html
Can we add the relevant LOINC code to the code section like this:
"code": [ { "code": "44169009", "display": "Loss of sense of smell (finding)", "system": "http://snomed.info/sct" } ],So it would look like this - see the addition of code under the linkId item:
{ "text": "Record temperature", "type": "decimal", "linkId": "5.1.0", "code" : [ { "code" : "8310-5", "display" : "Temperature", "system" : "http://loinc.org" }, ], "definition": "https://..../Observation.valueQuantity.value" "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.system" "initial": "http://unitsofmeasure.org" "hidden": true... }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.code" "answerOptions": [ "F", "C" ] }
I will add definition url and code as suggested, and update you if more information is required.
santosh-pingle
commented
2 years ago @jingtang10
SDC library ResourceMapper was not updating multiple answers of the given question item to the resource field. Though, response had captured multiple answers, it was only showing the list of first answers in the resource field. => Support is added, it was required to update all selected answers of "symptoms " and "Medical history" in resource.
santosh-pingle
commented
2 years ago Screener encounter questionnaire json need to be updated for below question items for definition base extraction
- Covid vaccination
- Temperature
- Pulse Oximetry
Jing had provided some inputs on it, like adding hidden question, and code item to the questionnaire. Referring documentation for more information on it.
For temperature and pulse oximetry, we will need to extract
Observations with aQuantityvalue. AQuantityvalue is basically a number and a unit. So if we want the user to choose a unit (in the case of fahrenheit or celsium) we need to present another question, if we don't want the user to choose a unit, then we probably need a hidden field. Example:{ "text": "Record temperature", "type": "decimal", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.value" "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.system" "initial": "http://unitsofmeasure.org" "hidden": true... }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.code" "answerOptions": [ "F", "C" ] }More info: https://hl7.org/fhir/R4/bodytemp.html
Can we add the relevant LOINC code to the code section like this:
"code": [ { "code": "44169009", "display": "Loss of sense of smell (finding)", "system": "http://snomed.info/sct" } ],So it would look like this - see the addition of code under the linkId item:
{ "text": "Record temperature", "type": "decimal", "linkId": "5.1.0", "code" : [ { "code" : "8310-5", "display" : "Temperature", "system" : "http://loinc.org" }, ], "definition": "https://..../Observation.valueQuantity.value" "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.system" "initial": "http://unitsofmeasure.org" "hidden": true... }, { "type": "drop-down", "linkId": "5.1.0", "definition": "https://..../Observation.valueQuantity.code" "answerOptions": [ "F", "C" ] }I will add definition url and code as suggested, and update you if more information is required.
@jingtang10
Temperature questionnaire item : With the modification below, it requires a Quantity object per item. But observation resources can reference only a single Quantity instance unlike category. It looks like limitation with this modification.
{
"text": "Temperature",
"type": "group",
"linkId": "5.0.0",
"code": [
{
"code": "8310-5",
"display": "Temperature",
"system": "http://loinc.org"
}
],
"definition": "http://hl7.org/fhir/StructureDefinition/Observation",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "Observation",
"name": "temperature"
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "page",
"display": "Page"
}
],
"text": "Page"
}
}
],
"item": [
{
"text": "Add instructions for capturing temperature",
"type": "display",
"linkId": "5.0.1"
},
{
"linkId": "5.1.0",
"text": "Record temperature",
"type": "quantity",
"definition": "http://hl7.org/fhir/StructureDefinition/datatypes#Observation.value"
},
{
"text": "Unit",
"type": "choice",
"linkId": "5.2.0",
"required": true,
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.value",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "drop-down",
"display": "Drop down"
}
],
"text": "Drop down"
}
}
],
"answerOption": [
{
"valueCoding": {
"code": "F",
"display": "F"
}
},
{
"valueCoding": {
"code": "C",
"display": "C"
}
}
]
}
]
},
So I am thinking to just capture quantity as temperature value.
santosh-pingle
commented
2 years ago @jingtang10
Currently, answers does not get updated to the valueQuantity in Observation resource. valueQuantity is declared as abstract type in Observation. Resource mapper fail to use value (QuantityValue) and its nested field to update the answer.
santosh-pingle
commented
2 years ago @ekigamba
It does not set the answer to the definition field if the field type is abstract type.
santosh-pingle
commented
2 years ago Working on #674, trying to come up with generic fix for Type in hapi model
santosh-pingle
commented
2 years ago (SDC library, it does not set the answer to the definition field if the field type is choice type), I will try to create PR by eod today.Which will unblock us to add implementation for resource extraction of temperature, pulse oximetry and pulse heart rate.
santosh-pingle
commented
2 years ago It will update the answers to the choice of data types fields of extracted resources of temperature, pulse oximetry and pulse heart rate.
santosh-pingle
commented
2 years ago @fredhersch Updated screener questionnaire items with definition.
santosh-pingle
commented
2 years ago Checking whether existing vaccination questionnaire item response answers get updated to resource fields or not.
fredhersch
commented
2 years ago @santosh-pingle let's leave this for now. Want to get the observations for risk factors, symptoms and vital signs working first.
santosh-pingle
commented
2 years ago @fredhersch Extracted resources are seen in local db as like below.
Heart Rate
{"resourceType":"Observation","id":"4cff9613-c5b1-4ea3-b323-c20a05802c5f","subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":72.0}}
Pulse Rate
{"resourceType":"Observation","id":"ca74b044-8f81-4c49-9360-995b2c0901e9","subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":92.0}}
Temperature
{"resourceType":"Observation","id":"a8cd80e4-514d-4562-841e-f9180c6d5c4d","subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":36.0,"code":"C"}}
Medical History
{"resourceType":"Condition","id":"fb69a03b-4a14-45a3-bfaa-9eee30def876","category":[{"coding":[{"system":"http://snomed.info/sct","code":"161527007","display":"Asthma"}],"text":"Asthma"},{"coding":[{"system":"http://snomed.info/sct","code":"13645005","display":"Chronic Lung Disease"}],"text":"Chronic Lung Disease"},{"coding":[{"system":"http://snomed.info/sct","code":"35489007","display":"Depression"}],"text":"Depression"},{"coding":[{"system":"http://snomed.info/sct","code":"161445009","display":"Diabetes"}],"text":"Diabetes"},{"coding":[{"system":"http://snomed.info/sct","code":"161501007","display":"Hypertension"}],"text":"Hypertension"},{"coding":[{"system":"http://snomed.info/sct","code":"56265001","display":"Heart disease"}],"text":"Heart disease"},{"coding":[{"system":"http://snomed.info/sct","code":"161450003","display":"High blood lipids"}],"text":"High blood lipids"}],"subject":{"reference":"Patient/2126234"}}
Symptoms
{"resourceType":"Observation","id":"c584d404-6321-4f33-abcd-dd276112b083","category":[{"coding":[{"system":"http://snomed.info/sct","code":"386661006","display":"Fever"}],"text":"Fever"},{"coding":[{"system":"http://snomed.info/sct","code":"13645005","display":"Shortness of breath"}],"text":"Shortness of breath"},{"coding":[{"system":"http://snomed.info/sct","code":"49727002","display":"Cough"}],"text":"Cough"},{"coding":[{"system":"http://snomed.info/sct","code":"44169009","display":"Loss of smell"}],"text":"Loss of smell"}],"subject":{"reference":"Patient/2126234"}}Modifying vitalSigns questionnaire item to add code in questionnaire item.
santosh-pingle
commented
2 years ago @fredhersch @aditya-07
It seems code structure can not be used as it is in questionnaire item e.g
{
"code": "8310-5",
"display": "Temperature",
"system": "http://loinc.org"
}
] Looks like It requires to restructure code in questionnaire item as group of item so that it can be captured in response as answers. If yes, any suggestion how will it be added it to questionnaire?
Can you please confirm?
santosh-pingle
commented
2 years ago @fredhersch @aditya-07
It seems code structure can not be used as it is in questionnaire item e.g
{ "code": "8310-5", "display": "Temperature", "system": "http://loinc.org" } ]Looks like It requires to restructure code in questionnaire item as group of item so that it can be captured in response as answers. If yes, any suggestion how will it be added it to questionnaire?
Can you please confirm?
These items need be hidden in questionnaire, as it will have initial value as an answer.
santosh-pingle
commented
2 years ago @fredhersch
Updated Temperature Questionnaire item to update the code for temperature vitalSigns. Pulse Heart rate and oximetry items will also be updated for code.
Please confirm once.
{
"text": "Temperature",
"type": "group",
"linkId": "5.0.0",
"definition": "http://hl7.org/fhir/StructureDefinition/Observation",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "Observation",
"name": "temperature"
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "page",
"display": "Page"
}
],
"text": "Page"
}
}
],
"item": [
{
"text": "Add instructions for capturing temperature",
"type": "display",
"linkId": "5.1.0"
},
{
"linkId": "5.2.0",
"type": "group",
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "Quantity",
"name": "quantity"
}
}
],
"item": [
{
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.value",
"text": "Record temperature",
"type": "decimal",
"linkId": "5.2.1",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/minValue",
"valueDecimal": 35.0
},
{
"url": "http://hl7.org/fhir/StructureDefinition/maxValue",
"valueDecimal": 45.0
}
]
},
{
"text": "Unit",
"type": "choice",
"linkId": "5.2.2",
"required": true,
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.code",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "drop-down",
"display": "Drop down"
}
],
"text": "Drop down"
}
}
],
"answerOption": [
{
"valueCoding": {
"code": "F",
"display": "F"
}
},
{
"valueCoding": {
"code": "C",
"display": "C"
}
}
]
}
]
},
{
"linkId": "5.3.0",
"type": "group",
"enableWhen": [
{
"question": "5.1.0",
"operator": "=",
"answerBoolean": "true"
}
],
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "CodeableConcept",
"name": "code"
}
}
],
"item": [
{
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding",
"type": "group",
"linkId": "5.3.1",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "Coding",
"name": "coding"
}
}
],
"item": [
{
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding.code",
"type": "string",
"linkId": "5.3.1.1",
"initial": [
{
"valueString": "8310-5"
}
]
},
{
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding.system",
"type": "string",
"linkId": "5.3.1.2",
"initial": [
{
"valueString": "http://loinc.org"
}
]
},
{
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding.display",
"type": "string",
"linkId": "5.3.1.3",
"initial": [
{
"valueString": "Temperature"
}
]
}
]
}
]
}
]
},
@fredhersch
Updated Temperature Questionnaire item to update the
codefor temperature vitalSigns. Pulse Heart rate and oximetry items will also be updated for code.Please confirm once.
{ "text": "Temperature", "type": "group", "linkId": "5.0.0", "definition": "http://hl7.org/fhir/StructureDefinition/Observation", "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { "language": "application/x-fhir-query", "expression": "Observation", "name": "temperature" } }, { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "page", "display": "Page" } ], "text": "Page" } } ], "item": [ { "text": "Add instructions for capturing temperature", "type": "display", "linkId": "5.1.0" }, { "linkId": "5.2.0", "type": "group", "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity", "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { "language": "application/x-fhir-query", "expression": "Quantity", "name": "quantity" } } ], "item": [ { "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.value", "text": "Record temperature", "type": "decimal", "linkId": "5.2.1", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "text": "Unit", "type": "choice", "linkId": "5.2.2", "required": true, "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.code", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "drop-down", "display": "Drop down" } ], "text": "Drop down" } } ], "answerOption": [ { "valueCoding": { "code": "F", "display": "F" } }, { "valueCoding": { "code": "C", "display": "C" } } ] } ] }, { "linkId": "5.3.0", "type": "group", "enableWhen": [ { "question": "5.1.0", "operator": "=", "answerBoolean": "true" } ], "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code", "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { "language": "application/x-fhir-query", "expression": "CodeableConcept", "name": "code" } } ], "item": [ { "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding", "type": "group", "linkId": "5.3.1", "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { "language": "application/x-fhir-query", "expression": "Coding", "name": "coding" } } ], "item": [ { "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding.code", "type": "string", "linkId": "5.3.1.1", "initial": [ { "valueString": "8310-5" } ] }, { "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding.system", "type": "string", "linkId": "5.3.1.2", "initial": [ { "valueString": "http://loinc.org" } ] }, { "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.code.coding.display", "type": "string", "linkId": "5.3.1.3", "initial": [ { "valueString": "Temperature" } ] } ] } ] } ] },
With this change code is seen as below for temperature.
{"resourceType":"Observation","id":"15e1944b-d2e1-4feb-b0c0-f521b026c098","code":{"coding":[{"system":"http://loinc.org","code":"8310-5","display":"Temperature"}]},"subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":36.0,"code":"C"}}
Thanks @santosh-pingle the output looks right to me. I do wonder whether we can work on the Questionnaire component so as not have to split up all of the different items. Let me think about this further
fredhersch
commented
2 years ago @santosh-pingle For observations there are two scenarios:
I would recommend that we add an observation.category of 'vital-signs' - to all observations that represent vital-signs. We can aim to address this at a later stage. Could we just add this to the Questionnaire json for the relevant group of items?
NOTE: This is the same pattern we would follow for laboratory type data that would be stored as Observation but with the observation.category of laboratory
The Observation.code is also expressed in a way that does not specify the observation action but indicates a statement about findings reduced to a single name (or term), as in the above item. In this example, the Observation.value is present and "qualifies" the finding typically confirming or refuting it. For example:
code=[Abdominal tenderness]
value=[found/true]There are three scenarios:
A) When there can be multiple choices each leading to the generation of an individual resource - for example, we use the repeats:true for a drop-down itemControl to generate a list of checkboxes with the question: Do you have any of the following symptoms
"item": [
{
"text": "In the past two weeks have you experienced ANY of these symptoms?",
"type": "choice",
"linkId": "1.1.0",
"required": true,
"repeats": true,
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "drop-down",
"display": "Drop down"
}
],
"text": "Drop down"
}
}
],
"answerOption": [
{
"valueCoding": {
"code": "386661006",
"display": "Fever",
"system": "http://snomed.info/sct"
}
},
{
"valueCoding": {
"code": "13645005",
"display": "Shortness of breath",
"system": "http://snomed.info/sct"
}
},
{
"valueCoding": {
"code": "49727002",
"display": "Cough",
"system": "http://snomed.info/sct"
}
},
{
"valueCoding": {
"code": "44169009",
"display": "Loss of smell",
"system": "http://snomed.info/sct"
}
}
]
}
]
},
Selected Fever and Cough would generate TWO Observation resources with:
For non-selected options, we would NOT extract resources
An example observation would look like:
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00",
"versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"
},
"status": "final",
"category": [
{
"coding": [
{
"code": "exam",
"display": "symptoms",
"system": "http://terminology.hl7.org/CodeSystem/observation-category"
}
]
}
],
"code": {
"coding": [
{
"code": "386661006",
"display": "Fever (finding)",
"system": "http://loinc.org"
}
],
"text": "Fever (finding)"
},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"
},
"subject": {
"reference": "Patient/<patient_id>"
},
"valueBoolean": {
"value" : "true"
}
}And for the Cough observation:
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00",
"versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"
},
"status": "final",
"category": [
{
"coding": [
{
"code": "exam",
"display": "symptoms",
"system": "http://terminology.hl7.org/CodeSystem/observation-category"
}
]
}
],
"code": {
"coding": [
{
"code": "49727002",
"display": "Cough",
"system": "http://loinc.org"
}
],
"text": "Cough"
},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"
},
"subject": {
"reference": "Patient/<patient_id>"
},
"valueBoolean": {
"value" : "true"
}
}
B) When each question is a boolean response e.g. "Do you have fever"? Yes / No / Don't know | "Do you have cough" "Yes / No / Don't know"
{
"type": "group",
"required": true,
"linkId": "S",
"text": "Symptoms",
"item": [
{
"type": "choice",
"required": true,
"linkId": "S0",
"code": [
{
"code": "386661006",
"display": "Fever (finding)",
"system": "http://snomed.info/sct"
}
],
"text": "Have you had a fever (over 38°C) in the past 24 hours?",
"answerValueSet": "http://fhir.data4life.care/covid-19/r4/ValueSet/yesno"
},
In this scenario the relevant observation.code comes from the item.code section and the observation.value is the boolean. The resulting observation would look like:
Selecting Yes would generate a single Observation resource with:
For non-selected options, we would NOT extract resources
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00",
"versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"
},
"status": "final",
"category": [
{
"coding": [
{
"code": "exam",
"display": "symptoms",
"system": "http://terminology.hl7.org/CodeSystem/observation-category"
}
]
}
],
"code": {
"coding": [
{
"code": "386661006",
"display": "Fever (finding)",
"system": "http://loinc.org"
}
],
"text": "Fever (finding)"
},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"
},
"subject": {
"reference": "Patient/<patient_id>"
},
"valueBoolean": {
"value" : "true"
}
}
C) For handling riskfactors like smoking status the preferred approach would be a hybrid:
"item": [
{
"text": "Do you smoke cigarettes?",
"type": "choice",
"linkId": "2.1.0",
"required": true,
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "drop-down",
"display": "Drop down"
}
],
"text": "Drop down"
}
}
],
"code": [
{
"code": "72166-2",
"display": "Tobacco smoking status NHIS",
"system": "http://loinc.org"
}
],
"answerOption": [
{
"valueCoding": {
"code": "77176002",
"display": "Current smoker",
"system" : "http://snomed.info/sct"
}
},
{
"valueCoding": {
"code": "8517006",
"display": "Ex-smoker",
"system" : "http://snomed.info/sct"
}
},
{
"valueCoding": {
"code": "8392000",
"display": "Non-smoker",
"system" : "http://snomed.info/sct"
}
}
]
},
Here the resulting Observation which should ideally be observation.category = 'social-history' would look like:
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00",
"versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"
},
"status": "final",
"category": [
{
"coding": [
{
"code": "social-history",
"display": "social history",
"system": "http://terminology.hl7.org/CodeSystem/observation-category"
}
]
}
],
"code": {
"coding": [
{
"code": "72166-2",
"display": "Tobacco smoking status NHIS",
"system": "http://loinc.org"
}
],
"text": "Tobacco smoking status NHIS"
},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"
},
"subject": {
"reference": "Patient/<patient_id>"
},
"valueCodeableConcept": {
"coding": [
{
"code": "8392000",
"display": "Non smoker",
"system": "http://snomed.info/sct"
}
],
"text": "Non smoker"
}
}@santosh-pingle can you review this please. Thanks
santosh-pingle
commented
2 years ago Sure, please give me sometime, I will review it.
fredhersch
commented
2 years ago @santosh-pingle In response to your earlier comment for extracting the Temperature observation, I'm sharing an edited version of the Questionnaire here. I have put the code in the root item and removed the itemId 5.3.0
What I think we should have is a single group with: Item for the code: Observation.code = item.code (codeableConcept values) Item for the valueQuantity:
I don't think the expression is quite right yet ...
{
"text": "Temperature",
"type": "group",
"linkId": "5.0.0",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "Observation",
"name": "temperature"
}
},
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#observation.code",
"code" : [
{
"code" : "8310-5",
"display" : "Temperature",
"system" : "http://loinc.org"
}
],
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "page",
"display": "Page"
}
],
"text": "Page"
}
}
],
"item": [
{
"text": "Add instructions for capturing temperature",
"type": "display",
"linkId": "5.1.0"
},
{
"linkId": "5.2.0",
"type": "group",
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity",
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
"valueExpression": {
"language": "application/x-fhir-query",
"expression": "Quantity",
"name": "quantity"
}
}
],
"item": [
{
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.value",
"text": "Record temperature",
"type": "decimal",
"linkId": "5.2.1",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/minValue",
"valueDecimal": 35.0
},
{
"url": "http://hl7.org/fhir/StructureDefinition/maxValue",
"valueDecimal": 45.0
}
]
},
{
"text": "Unit",
"type": "choice",
"linkId": "5.2.2",
"required": true,
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.code",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "drop-down",
"display": "Drop down"
}
],
"text": "Drop down"
}
}
],
"answerOption": [
{
"valueCoding": {
"code": "F",
"display": "F"
}
},
{
"valueCoding": {
"code": "C",
"display": "C"
}
}
]
}
]
},
]
},
@santosh-pingle In response to your earlier comment for extracting the Temperature observation, I'm sharing an edited version of the Questionnaire here. I have put the code in the root item and removed the itemId 5.3.0
What I think we should have is a single group with: Item for the code: Observation.code = item.code (codeableConcept values) Item for the valueQuantity:
- Observation.valueQuantity.value = value
- Observation.valueQuantity.code = code
- Observation.valueQuantity.system = http://unitsofmeasure.org (hidden field)
- Observation.valueQuantity.unit = F or C (as per earlier thread these could either be hidden or if they are user selected then they need to be an additional item)
I don't think the expression is quite right yet ...
{ "text": "Temperature", "type": "group", "linkId": "5.0.0", "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { "language": "application/x-fhir-query", "expression": "Observation", "name": "temperature" } }, "definition": "http://hl7.org/fhir/StructureDefinition/Observation#observation.code", "code" : [ { "code" : "8310-5", "display" : "Temperature", "system" : "http://loinc.org" } ], { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "page", "display": "Page" } ], "text": "Page" } } ], "item": [ { "text": "Add instructions for capturing temperature", "type": "display", "linkId": "5.1.0" }, { "linkId": "5.2.0", "type": "group", "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity", "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext", "valueExpression": { "language": "application/x-fhir-query", "expression": "Quantity", "name": "quantity" } } ], "item": [ { "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.value", "text": "Record temperature", "type": "decimal", "linkId": "5.2.1", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/minValue", "valueDecimal": 35.0 }, { "url": "http://hl7.org/fhir/StructureDefinition/maxValue", "valueDecimal": 45.0 } ] }, { "text": "Unit", "type": "choice", "linkId": "5.2.2", "required": true, "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueQuantity.code", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "drop-down", "display": "Drop down" } ], "text": "Drop down" } } ], "answerOption": [ { "valueCoding": { "code": "F", "display": "F" } }, { "valueCoding": { "code": "C", "display": "C" } } ] } ] }, ] },
Not sure, whether we can add code and definition to the extension and then extract it with definition based approach. Does extension have definition element?
santosh-pingle
commented
2 years ago VitalSigns saved in local db as below.
{"resourceType":"Observation","id":"633cfdc9-061e-4462-97d3-6f13fa967e6d","code":{"coding":[{"system":"http://loinc.org","code":"8310-5","display":"Temperature"}]},"subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":36.0,"system":"http://unitsofmeasure.org","code":"C"}}
{"resourceType":"Observation","id":"42d0314e-1948-454e-9ef8-5a08041a8d17","code":{"coding":[{"system":"http://loinc.org","code":"8867-4","display":"Heart rate"}]},"subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":76.0,"system":"http://unitsofmeasure.org","code":"/min"}}
{"resourceType":"Observation","id":"5e44c47a-2b52-4b56-8abc-9937eac7ee62","code":{"coding":[{"system":"http://loinc.org","code":"59408-5","display":"Oxygen Saturation"}]},"subject":{"reference":"Patient/2126234"},"valueQuantity":{"value":99.0,"system":"http://unitsofmeasure.org","code":"%"}}
@santosh-pingle For observations there are two scenarios:
- For vital-signs: we use observation.code from the item and then set the observation.value using the valueQuantity (type Quantity) with hidden fields for the units coding system. This has been well documented by @jingtang10 in the thread above
I would recommend that we add an observation.category of 'vital-signs' - to all observations that represent vital-signs. We can aim to address this at a later stage. Could we just add this to the Questionnaire json for the relevant group of items?
NOTE: This is the same pattern we would follow for laboratory type data that would be stored as Observation but with the observation.category of laboratory
- For other observations e.g. symptoms, risk-factors the specification offers 4 approaches - see here
- For our base implementation we are proposing to support 'option 3'
The Observation.code is also expressed in a way that does not specify the observation action but indicates a statement about findings reduced to a single name (or term), as in the above item. In this example, the Observation.value is present and "qualifies" the finding typically confirming or refuting it. For example: code=[Abdominal tenderness] value=[found/true]There are three scenarios:
A) When there can be multiple choices each leading to the generation of an individual resource - for example, we use the repeats:true for a drop-down itemControl to generate a list of checkboxes with the question: Do you have any of the following symptoms
"item": [ { "text": "In the past two weeks have you experienced ANY of these symptoms?", "type": "choice", "linkId": "1.1.0", "required": true, "repeats": true, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "drop-down", "display": "Drop down" } ], "text": "Drop down" } } ], "answerOption": [ { "valueCoding": { "code": "386661006", "display": "Fever", "system": "http://snomed.info/sct" } }, { "valueCoding": { "code": "13645005", "display": "Shortness of breath", "system": "http://snomed.info/sct" } }, { "valueCoding": { "code": "49727002", "display": "Cough", "system": "http://snomed.info/sct" } }, { "valueCoding": { "code": "44169009", "display": "Loss of smell", "system": "http://snomed.info/sct" } } ] } ] },Selected Fever and Cough would generate TWO Observation resources with:
- Observation.code is a Codeable Concept with values from the valueCoding result
- Observation.value is a boolean of true
For non-selected options, we would NOT extract resources
An example observation would look like:
{ "resourceType": "Observation", "id": "78354025-1059-4f0f-8b04-8478d696d234", "issued": "1990-03-12T09:04:10.192-05:00", "meta": { "lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA" }, "status": "final", "category": [ { "coding": [ { "code": "exam", "display": "symptoms", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } ], "code": { "coding": [ { "code": "386661006", "display": "Fever (finding)", "system": "http://loinc.org" } ], "text": "Fever (finding)" }, "effectiveDateTime": "1990-03-12T09:04:10-05:00", "encounter": { "reference": "Encounter/<encounter_id>" }, "subject": { "reference": "Patient/<patient_id>" }, "valueBoolean": { "value" : "true" } }And for the Cough observation:
{ "resourceType": "Observation", "id": "78354025-1059-4f0f-8b04-8478d696d234", "issued": "1990-03-12T09:04:10.192-05:00", "meta": { "lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA" }, "status": "final", "category": [ { "coding": [ { "code": "exam", "display": "symptoms", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } ], "code": { "coding": [ { "code": "49727002", "display": "Cough", "system": "http://loinc.org" } ], "text": "Cough" }, "effectiveDateTime": "1990-03-12T09:04:10-05:00", "encounter": { "reference": "Encounter/<encounter_id>" }, "subject": { "reference": "Patient/<patient_id>" }, "valueBoolean": { "value" : "true" } }B) When each question is a boolean response e.g. "Do you have fever"? Yes / No / Don't know | "Do you have cough" "Yes / No / Don't know"
{ "type": "group", "required": true, "linkId": "S", "text": "Symptoms", "item": [ { "type": "choice", "required": true, "linkId": "S0", "code": [ { "code": "386661006", "display": "Fever (finding)", "system": "http://snomed.info/sct" } ], "text": "Have you had a fever (over 38°C) in the past 24 hours?", "answerValueSet": "http://fhir.data4life.care/covid-19/r4/ValueSet/yesno" },In this scenario the relevant observation.code comes from the item.code section and the observation.value is the boolean. The resulting observation would look like:
Selecting Yes would generate a single Observation resource with:
- Observation.code is a Codeable Concept with values from the code section
- Observation.category = 'exam' (ideally)
- Observation.value is a boolean of true - TBC
For non-selected options, we would NOT extract resources
{ "resourceType": "Observation", "id": "78354025-1059-4f0f-8b04-8478d696d234", "issued": "1990-03-12T09:04:10.192-05:00", "meta": { "lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA" }, "status": "final", "category": [ { "coding": [ { "code": "exam", "display": "symptoms", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } ], "code": { "coding": [ { "code": "386661006", "display": "Fever (finding)", "system": "http://loinc.org" } ], "text": "Fever (finding)" }, "effectiveDateTime": "1990-03-12T09:04:10-05:00", "encounter": { "reference": "Encounter/<encounter_id>" }, "subject": { "reference": "Patient/<patient_id>" }, "valueBoolean": { "value" : "true" } }C) For handling riskfactors like smoking status the preferred approach would be a hybrid:
"item": [ { "text": "Do you smoke cigarettes?", "type": "choice", "linkId": "2.1.0", "required": true, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "drop-down", "display": "Drop down" } ], "text": "Drop down" } } ], "code": [ { "code": "72166-2", "display": "Tobacco smoking status NHIS", "system": "http://loinc.org" } ], "answerOption": [ { "valueCoding": { "code": "77176002", "display": "Current smoker", "system" : "http://snomed.info/sct" } }, { "valueCoding": { "code": "8517006", "display": "Ex-smoker", "system" : "http://snomed.info/sct" } }, { "valueCoding": { "code": "8392000", "display": "Non-smoker", "system" : "http://snomed.info/sct" } } ] },Here the resulting Observation which should ideally be observation.category = 'social-history' would look like:
{ "resourceType": "Observation", "id": "78354025-1059-4f0f-8b04-8478d696d234", "issued": "1990-03-12T09:04:10.192-05:00", "meta": { "lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA" }, "status": "final", "category": [ { "coding": [ { "code": "social-history", "display": "social history", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } ], "code": { "coding": [ { "code": "72166-2", "display": "Tobacco smoking status NHIS", "system": "http://loinc.org" } ], "text": "Tobacco smoking status NHIS" }, "effectiveDateTime": "1990-03-12T09:04:10-05:00", "encounter": { "reference": "Encounter/<encounter_id>" }, "subject": { "reference": "Patient/<patient_id>" }, "valueCodeableConcept": { "coding": [ { "code": "8392000", "display": "Non smoker", "system": "http://snomed.info/sct" } ], "text": "Non smoker" } }
Thanks!
Reviewing it.
@fredhersch Do you want me to restructure questionnaire json to support definition based extraction for above questionnaire items ? or will it be shared with me? Thanks!
fredhersch
commented
2 years ago If you can propose the correct way that would be great. Thanks
On Thu, 5 Aug 2021, 1:03 pm santosh-pingle, @.***> wrote:
@santosh-pingle https://github.com/santosh-pingle For observations there are two scenarios:
- For vital-signs: we use observation.code from the item and then set the observation.value using the valueQuantity (type Quantity) with hidden fields for the units coding system. This has been well documented by @jingtang10 https://github.com/jingtang10 in the thread above
I would recommend that we add an observation.category of 'vital-signs' - to all observations that represent vital-signs. We can aim to address this at a later stage. Could we just add this to the Questionnaire json for the relevant group of items?
NOTE: This is the same pattern we would follow for laboratory type data that would be stored as Observation but with the observation.category of laboratory
For other observations e.g. symptoms, risk-factors the specification offers 4 approaches - see here https://www.hl7.org/fhir/observation.html#code-interopl
- For our base implementation we are proposing to support 'option 3'
The Observation.code is also expressed in a way that does not specify the observation action but indicates a statement about findings reduced to a single name (or term), as in the above item. In this example, the Observation.value is present and "qualifies" the finding typically confirming or refuting it. For example:
code=[Abdominal tenderness]
value=[found/true]
There are three scenarios:
A) When there can be multiple choices each leading to the generation of an individual resource - for example, we use the repeats:true for a drop-down itemControl to generate a list of checkboxes with the question: Do you have any of the following symptoms
"item": [
{ "text": "In the past two weeks have you experienced ANY of these symptoms?", "type": "choice", "linkId": "1.1.0", "required": true, "repeats": true, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "drop-down", "display": "Drop down" } ], "text": "Drop down" } } ], "answerOption": [ { "valueCoding": { "code": "386661006", "display": "Fever", "system": "http://snomed.info/sct" } }, { "valueCoding": { "code": "13645005", "display": "Shortness of breath", "system": "http://snomed.info/sct" } }, { "valueCoding": { "code": "49727002", "display": "Cough", "system": "http://snomed.info/sct" } }, { "valueCoding": { "code": "44169009", "display": "Loss of smell", "system": "http://snomed.info/sct" } } ] } ] },Selected Fever and Cough would generate TWO Observation resources with:
- Observation.code is a Codeable Concept with values from the valueCoding result
- Observation.value is a boolean of true
For non-selected options, we would NOT extract resources
An example observation would look like:
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"},
"status": "final",
"category": [
{ "coding": [ { "code": "exam", "display": "symptoms", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] }],
"code": {
"coding": [ { "code": "386661006", "display": "Fever (finding)", "system": "http://loinc.org" } ], "text": "Fever (finding)"},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"},
"subject": {
"reference": "Patient/<patient_id>"},
"valueBoolean": {
"value" : "true"
}
}
And for the Cough observation:
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"},
"status": "final",
"category": [
{ "coding": [ { "code": "exam", "display": "symptoms", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] }],
"code": {
"coding": [ { "code": "49727002", "display": "Cough", "system": "http://loinc.org" } ], "text": "Cough"},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"},
"subject": {
"reference": "Patient/<patient_id>"},
"valueBoolean": {
"value" : "true"
}
}
B) When each question is a boolean response e.g. "Do you have fever"? Yes / No / Don't know | "Do you have cough" "Yes / No / Don't know"
{ "type": "group", "required": true, "linkId": "S", "text": "Symptoms", "item": [ { "type": "choice", "required": true, "linkId": "S0", "code": [ { "code": "386661006", "display": "Fever (finding)", "system": "http://snomed.info/sct" } ], "text": "Have you had a fever (over 38°C) in the past 24 hours?", "answerValueSet": "http://fhir.data4life.care/covid-19/r4/ValueSet/yesno" },In this scenario the relevant observation.code comes from the item.code section and the observation.value is the boolean. The resulting observation would look like:
Selecting Yes would generate a single Observation resource with:
- Observation.code is a Codeable Concept with values from the code section
- Observation.category = 'exam' (ideally)
- Observation.value is a boolean of true - TBC
For non-selected options, we would NOT extract resources
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"},
"status": "final",
"category": [
{ "coding": [ { "code": "exam", "display": "symptoms", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] }],
"code": {
"coding": [ { "code": "386661006", "display": "Fever (finding)", "system": "http://loinc.org" } ], "text": "Fever (finding)"},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"},
"subject": {
"reference": "Patient/<patient_id>"},
"valueBoolean": {
"value" : "true"
}
}
C) For handling riskfactors like smoking status the preferred approach would be a hybrid:
"item": [
{ "text": "Do you smoke cigarettes?", "type": "choice", "linkId": "2.1.0", "required": true, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/questionnaire-item-control", "code": "drop-down", "display": "Drop down" } ], "text": "Drop down" } } ], "code": [ { "code": "72166-2", "display": "Tobacco smoking status NHIS", "system": "http://loinc.org" } ], "answerOption": [ { "valueCoding": { "code": "77176002", "display": "Current smoker", "system" : "http://snomed.info/sct" } }, { "valueCoding": { "code": "8517006", "display": "Ex-smoker", "system" : "http://snomed.info/sct" } }, { "valueCoding": { "code": "8392000", "display": "Non-smoker", "system" : "http://snomed.info/sct" } } ] },Here the resulting Observation which should ideally be observation.category = 'social-history' would look like:
{
"resourceType": "Observation",
"id": "78354025-1059-4f0f-8b04-8478d696d234",
"issued": "1990-03-12T09:04:10.192-05:00",
"meta": {
"lastUpdated": "2021-04-01T12:45:31.338652+00:00", "versionId": "MTYxNzI4MTEzMTMzODY1MjAwMA"},
"status": "final",
"category": [
{ "coding": [ { "code": "social-history", "display": "social history", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] }],
"code": {
"coding": [ { "code": "72166-2", "display": "Tobacco smoking status NHIS", "system": "http://loinc.org" } ], "text": "Tobacco smoking status NHIS"},
"effectiveDateTime": "1990-03-12T09:04:10-05:00",
"encounter": {
"reference": "Encounter/<encounter_id>"},
"subject": {
"reference": "Patient/<patient_id>"},
"valueCodeableConcept": {
"coding": [ { "code": "8392000", "display": "Non smoker", "system": "http://snomed.info/sct" } ], "text": "Non smoker"}
}
Reviewing it.
@fredhersch https://github.com/fredhersch Do you want me to restructure questionnaire json to support definition based extraction for above questionnaire items ? or you are going to share it with me?
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santosh-pingle
commented
2 years ago Working on symptoms to extract each answer as single observation resource.
santosh-pingle
commented
2 years ago Yesterday, @fredhersch and we discussed offline, we can choose option 3 or 4. Updating symptoms questionnaire item json with definition based extraction.
santosh-pingle
commented
2 years ago Below observations were extracted for selected symptoms.
{"resourceType":"Observation","id":"4dd0f662-9a5a-4631-90c5-3ea225ecd78c","code":{"coding":[{"system":"http://snomed.info/sct","code":"386661006","display":"Fever"}],"text":"Fever"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/7f030a5d-8036-48fc-8e09-facbf595ac79"}}
{"resourceType":"Observation","id":"4dc0c628-d48c-4e96-9d29-ab3b6165870f","code":{"coding":[{"system":"http://snomed.info/sct","code":"13645005","display":"Shortness of breath"}],"text":"Shortness of breath"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/7f030a5d-8036-48fc-8e09-facbf595ac79"}}
{"resourceType":"Observation","id":"def92e59-cb77-4c36-b985-59d9c4cfe0e7","code":{"coding":[{"system":"http://snomed.info/sct","code":"49727002","display":"Cough"}],"text":"Cough"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/3df329b6-d81b-4cd2-8854-0ac6e2e19d7c"}}
{"resourceType":"Observation","id":"36b7951c-097e-4405-8f68-fd609840c1cc","code":{"coding":[{"system":"http://snomed.info/sct","code":"44169009","display":"Loss of smell"}],"text":"Loss of smell"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/3df329b6-d81b-4cd2-8854-0ac6e2e19d7c"}}
Working on medical history (conditions) to extract each answer as single observation resource.
santosh-pingle
commented
2 years ago Extracted medical history resources for selected answers.
{"resourceType":"Condition","id":"01ba55e1-b1e9-4591-a688-b4cf440ab8dd","code":{"coding":[{"system":"http://snomed.info/sct","code":"161450003","display":"High blood lipids"}],"text":"High blood lipids"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}
{"resourceType":"Condition","id":"3482634b-9c12-4e45-85fb-898b5418ee75","code":{"coding":[{"system":"http://snomed.info/sct","code":"56265001","display":"Heart disease"}],"text":"Heart disease"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}
{"resourceType":"Condition","id":"2214ce35-16fd-4ffb-a888-7dde96a8fa20","code":{"coding":[{"system":"http://snomed.info/sct","code":"161501007","display":"Hypertension"}],"text":"Hypertension"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}
{"resourceType":"Condition","id":"796fc950-9162-42b9-bab6-e8943b909556","code":{"coding":[{"system":"http://snomed.info/sct","code":"161445009","display":"Diabetes"}],"text":"Diabetes"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}
{"resourceType":"Condition","id":"3c9834bd-e0be-4d3a-9111-6d74b4e6c447","code":{"coding":[{"system":"http://snomed.info/sct","code":"35489007","display":"Depression"}],"text":"Depression"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}
{"resourceType":"Condition","id":"b7cd02d4-a91d-459c-9b16-cc35b0e534e2","code":{"coding":[{"system":"http://snomed.info/sct","code":"13645005","display":"Chronic Lung Disease"}],"text":"Chronic Lung Disease"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}
{"resourceType":"Condition","id":"cede860d-7f7f-4f4c-bdaa-a649546057ab","code":{"coding":[{"system":"http://snomed.info/sct","code":"161527007","display":"Asthma"}],"text":"Asthma"},"subject":{"reference":"Patient/2126234"},"encounter":{"reference":"Encounter/59b08660-ec85-4026-a4f2-327220a43b71"}}Looking into #626
User story As a HCW I can select to initiate a new sceener for a patient generating a new encounter and relevant observations
Steps:
Alt path:
Additional information