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How to store Psychiatric Scale into OMOP data base?

(Wang Man) #1

1.which domain should I choose,observation、procedure or measurement?
2.Whether each scale has a total score ID,for example “PHQ-9 - Patient health questionnaire 9” (concept id 44804610)/“Patient Health Questionnaire 9 item (PHQ-9) total score [Reported]”(concept id 3042932)? If I can not find corresponding total score ID,how can I deal with it?
3.whether it is correct or not if i store every question of the scale as the same way like the total score?
4.what does “class” mean in the athena?For example,a concept name has two kinds of class,but they have same domain.How should i choose?

(Dmytry Dymshyts) #2

This allows you to connect questions to a questionnaire using SURVEY_CONDUCT table.

For the PHQ-9 case you can use Patient Health Questionnaire 9 item (PHQ-9) total score [Reported] to represent the total score (put in Observation table),
and you put in the OBSERVATION table related questions and answers (if you have this information):
Feeling down, depressed, or hopeless in last 2 weeks [Reported.PHQ]
Feeling tired or having little energy in last 2 weeks [Reported.PHQ]

If you can’t find some scales among standard OHDSI concepts, please report, and we consider adding them.

Concept_class identifies distinct semantic group of concepts. Nothing to do with CDM building, so disregard it.

(Wang Man) #3

Thanks a lot!You are a star!

(Wang Man) #4

1.How can i find a SURVEY_CONDUCT_ID?Should i use SURVEY_CONCEPT_ID,or use a Procedure_ID like “Assessment using Young mania rating scale36684932”?
2.As we have a question / answer record in the observation table,why should i link it to the patient questionnaire?What does the patient questionnaire mean?Which table should i put it in?

(Dmytry Dymshyts) #5
  1. SURVEY_CONDUCT_ID is just a number of a row in the table.
    There’s no domain specified for SURVEY_CONCEPT_ID, so you can use Procedure concept (“Assessment using Young mania rating scale36684932” or Measurement concept_id 458501000124102 Young mania rating scale
  2. “Young mania rating scale” is a given questionnaire.
    I suppose the idea of SURVEY_CONDUCT is to help to track which questions belong to which Scale (questionnaire).

So, if you connect OBSERVATION entries
Feeling down, depressed…
Feeling tired or having…
to the PHQ9 survey_concept_id you’ll know which questions make PHQ9.
(Not concepts but event_ids as said in the documentation).

And SURVEY_CONDUCT allows you to add additional information such as RESPONDENT_TYPE_CONCEPT_ID, so you can indicate whether it was done by patient or by caregiver, doctor, or someone else.
TIMING_CONCEPT_ID - so you indicate the follow-up period.
and other.

As far as I know there are not so many use cases of SURVEY_CONDUCT usage yet, so you’re welcome to share your thougths.

Anyway, I suppose, the main focus during studies would be on total scores, so people will just query Observation table for this purpose.

(Wang Man) #6

We have several scales:“Young mania rating scale”,“Quick inventory of depressive symptomatology”,and “Sheehan disability scale”.They have not got a total score id like " Patient Health Questionnaire 9 item (PHQ-9) total score [Reported]".How do I store their scores into OMOP?

(Dmytry Dymshyts) #7

You can use “Young mania rating scale” as MEASUREMENT.measurement_concept_id with total score in value_as_number.
We can make a convention: The scale stays in MEASUREMENT and even its description doesn’t have “total score” we keep total score in mind.

Let it be temporal solution until we collect more information about Psychiatric scales to make more mature decision

(Dmytry Dymshyts) #8

There’s a Psychiatry Working Group

You can make a list of questions and possible solutions (if present) and present in the one of the meetings.

(Thomas White, MD, MS, MA, CHIE) #9

There are a (growing?) number of standardized assessment and diagnostic survey instruments encoded in LOINC. There are LOINC Panels for the entire survey, LOINC codes for each question within the survey, and enumerated value choices (answer options) for those questions. For some of the answers, there are mappings to SNOMED to represent the clinical meaning.

Should surveys encoded in LOINC be stored in the MEASUREMENT table? If you have surveys with results stored across the MEASUREMENT and OBSERVATION tables, does that complicate querying for the presence of a survey administration and/or the scored result of survey scales?

(Wang Man) #10

Thanks a lot!