BUG: Missing smoking information

BobanL commented 1 month ago

Description

Missing smoking information in the social history section when it's only available in table. FHIR conversion work will be required to convert from table elements to proper FHIR elements.

Steps to reproduce

List out the steps in detail to reproduce the bug

Missing tobacco use (not a smoker):

Visit ffa9550f-9a88-4348-9da3-4ca4a1e5f554 OR 7f02b35a-b172-4845-af55-d173574e5579)
Social History -> Tobacco Use

Missing additional information:

Visit 0aa7a9c2-87e4-4115-876e-b0253bb8dabf (smoker)
Social History -> Tobacco Use

Expected Result

Explain how it should function if the bug was fixed. Attach screenshot if applicable

Actual result

Explain what's happening now when the bug is present. Attach screenshot if applicable

Missing additional information on how they smoke:

Priority

Provide an estimate for level of impact the bug has today by placing an X in the applicable bracket

Priority

[ ] Low priority The bug does not have to be fixed immediately. High and medium priority bugs should be addressed first.
[x] Medium priority Typically, medium-priority bugs do not affect customers directly and therefore can be fixed in the normal course of testing and development.
[ ] High priority High priority bugs must be addressed immediately. They often affect the app’s functionality and impact customers and their user experience. They must take priority.

Notes

Include any additional context or information here that doesn't fit into other parts of the template

Example of one that works - http://localhost:3000/view-data?id=1.2.840.114350.1.13.202.3.7.8.688883.486

sarahtress commented 1 month ago

@BobanL this one is a little trickier. do you know which of the fields we could convert to FHIR out of what is shown?

BobanL commented 1 month ago

@BobanL this one is a little trickier. do you know which of the fields we could convert to FHIR out of what is shown?

I believe all of the data can be converted to FHIR, but most of the eICR examples we have only have that First "Smoking Status" column.

This is the XML that we have to convert in the detailed example:

                    <entry>
                        <observation classCode="OBS" moodCode="EVN">
                            <templateId root="2.16.840.1.113883.10.20.22.4.85"/>
                            <templateId extension="2014-06-09" root="2.16.840.1.113883.10.20.22.4.85"/>
                            <id extension="Z251^^449868002" root="1.2.840.114350.1.13.202.3.7.1.1040.2"/>
                            <code code="11367-0" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="History of tobacco use"/>
                            <text>
                                <reference value="#sochist31"/>
                            </text>
                            <statusCode code="completed"/>
                            <effectiveTime>
                                <low nullFlavor="UNK"/>
                                <high nullFlavor="NA"/>
                            </effectiveTime>
                            <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" code="449868002" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Smokes tobacco daily" xsi:type="CD"/>
                            <author>
                                <templateId root="2.16.840.1.113883.10.20.22.4.119"/>
                                <templateId extension="2019-10-01" root="2.16.840.1.113883.10.20.22.5.6"/>
                                <time value="20220722"/>
                                <assignedAuthor>
                                    <id extension="261930222" root="1.2.840.114350.1.13.202.3.7.1.1133"/>
                                    <id extension="TANGCX" root="1.2.840.114350.1.13.202.3.7.2.697780"/>
                                    <id nullFlavor="UNK" root="2.16.840.1.113883.4.6"/>
                                </assignedAuthor>
                            </author>
                        </observation>
                    </entry>

                    <entry>
                        <observation classCode="OBS" moodCode="EVN">
                            <templateId root="2.16.840.1.113883.10.20.22.4.38"/>
                            <templateId extension="2015-08-01" root="2.16.840.1.113883.10.20.22.4.38"/>
                            <id extension="Z251^^8663-7" root="1.2.840.114350.1.13.202.3.7.1.1040.3"/>
                            <code code="8663-7" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Cigarettes smoked current (pack per day) - Reported"/>
                            <text>
                                <reference value="#sochist31packsperday"/>
                            </text>
                            <statusCode code="completed"/>
                            <effectiveTime value="20220722"/>
                            <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" value="3" xsi:type="REAL"/>
                        </observation>
                    </entry>

                    <entry>
                        <observation classCode="OBS" moodCode="EVN">
                            <templateId root="2.16.840.1.113883.10.20.22.4.85"/>
                            <templateId extension="2014-06-09" root="2.16.840.1.113883.10.20.22.4.85"/>
                            <id extension="Z251^^65568007" root="1.2.840.114350.1.13.202.3.7.1.1040.2"/>
                            <code code="11367-0" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="History of tobacco use"/>
                            <text>
                                <reference value="#sochist31"/>
                            </text>
                            <statusCode code="completed"/>
                            <effectiveTime>
                                <low nullFlavor="UNK"/>
                                <high nullFlavor="NA"/>
                            </effectiveTime>
                            <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" code="65568007" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Cigarette Smoker" xsi:type="CD"/>
                            <author>
                                <templateId root="2.16.840.1.113883.10.20.22.4.119"/>
                                <templateId extension="2019-10-01" root="2.16.840.1.113883.10.20.22.5.6"/>
                                <time value="20220722"/>
                                <assignedAuthor>
                                    <id extension="261930222" root="1.2.840.114350.1.13.202.3.7.1.1133"/>
                                    <id extension="TANGCX" root="1.2.840.114350.1.13.202.3.7.2.697780"/>
                                    <id nullFlavor="UNK" root="2.16.840.1.113883.4.6"/>
                                </assignedAuthor>
                            </author>
                        </observation>
                    </entry>

                    <entry>
                        <observation classCode="OBS" moodCode="EVN">
                            <templateId root="2.16.840.1.113883.10.20.22.4.38"/>
                            <templateId extension="2015-08-01" root="2.16.840.1.113883.10.20.22.4.38"/>
                            <id extension="Z251^^401201003" root="1.2.840.114350.1.13.202.3.7.1.1040.4"/>
                            <code code="401201003" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED-CT" displayName="Cigarette pack-years">
                                <translation nullFlavor="UNK"/>
                            </code>
                            <statusCode code="completed"/>
                            <effectiveTime value="20220722"/>
                            <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" value="90" xsi:type="REAL"/>
                        </observation>
                    </entry>

(This is just packs x years)

sarahtress commented 1 month ago

@BobanL can we make a table with the following columns:

Smoking Status
Duration
Type
Amount
Observation Date

where:

duration is calculated from start date to end date, or just total number of years.
type would be cigarettes, etc
amount is # of packs per day, or whatever else could be a possible data input there
and observation date is just the date is was added to the medical record

mcmcgrath13 commented 2 weeks ago

I've split off the request to make a table with more data to #2883, while this ticket will just address the missing smoking status data

CDCgov / phdi