OMOP CDM and Clinical Trials

Vojtech_Huser · January 25, 2017, 6:14pm

@christian - I agree that trial arms are also in scope.

I also want to document that there is communication with Columbia U on how to unify some clinical trial data conventions. (possibly to be used by the phenotypeDataExtraction package) (find similar patients given an a trial NCT)

Vojtech_Huser · January 25, 2017, 7:21pm

For representing enrollment and withdrawing for a trial identified by an NCT, possible parameters would be SNOMED codes from here

OMOP vocabulary seems to have also some SNOMED national extension (for example, scottish study is represented under this concept)

Vojtech_Huser · February 10, 2017, 10:06pm

to keep the conversation going:

Here is possible representation of trial enrollment using OBSERVATION table.

entering a trial - Enrollement (start)
Observation_concept_id: http://www.ohdsi.org/web/atlas/#/concept/4163733 (Patient consented to clinical trial)
value_as_string: NCT000035135

leaving the trial early (due to a decision of a patient (no longer interested) or researcher (non compliance) (end)

*Observation_concept_id:*http://www.ohdsi.org/web/atlas/#/concept/4087907 (Patient withdrawn from trial)
value_as_string: NCT000035135

fully completing the trial (end)
Observation_concept_id: http://www.ohdsi.org/web/atlas/#/concept/40482840 Completion of clinical trial
value_as_string: NCT000035135

Eldar · October 12, 2017, 12:39pm

Please, sign me up

Vojtech_Huser · March 23, 2018, 1:31pm

I was discussing study data transformation with someone (think SDTM data transformed to ADAM data).

Here is another issue for the group to discuss:

To capture raw data as well as “for analysis” transformed data - I propose to use the same table (e.g., measurement) and use type columns to indicate raw vs. transformed. (just to put a proposal to the discussion)

Not capturing raw data is probably not an option. This would make OMOP inferior to current standards.

To capture transformation steps (captured in Define.XML), OMOP METADATA table could be used for that purpose.

Christian_Reich · March 24, 2018, 7:58am

I would start with the analysis. Because that is what the OMOP CDM is. And that’s were the use cases live. Raw data are pre-ETL in this world.

Andrew · March 25, 2018, 5:27pm

I am interested.

Josh_R · November 6, 2018, 6:44pm

@Vojtech_Huser - Since there were a few posters at the Symposium on using OMOP and RWE for Clinical Trial analysis, thought it might make sense to try and revive this thread.

I see a few levels of items to consider for being able to fully leverage the power of OMOP CDM with RCTs. I don’t think this is exhaustive per se, but thought it might help spur the discussion.

A: Data Model Interoperability:

CDISC SDTM conversion to OMOP CDM
CDISC ADaM conversion to OMOP CDM
OMOP conversion back to CDISC

B: RCT Administrative Records:

Patient Screening (not the recorded determination of eligibility, but that the screening took place)
Patient Randomization

C: RCT Visit Type (e.g., was the visit for screening, baseline, follow-up, etc.)

D: Non-standard Interventions and Outcomes (e.g., how to record and deal with investigational therapies, unvalidated PROs, etc.)

@Vojtech_Huser - I’m wondering where you’d recommend is the best place to capture the issues and lessons learned from our respective CDISC conversion efforts?

Vojtech_Huser · November 8, 2018, 2:49pm

I like your proposed topics. I focused mostly on how trial data can co-exist next to EHR data when both are ETLed into OMOP.

Some of my observations are summarized here:project/sdtm-omop at master · vojtechhuser/project · GitHub

One community effort could be to produce “SOURCE_TO_CONCEPT” map for the lab test below: (that we saw in the sample data)

github.com

vojtechhuser/project/blob/master/sdtm-omop/omop-output-csv/measurement-S-freq-with-units.csv

measurement_source_value,unit_source_value,n
Diastolic Blood Pressure~DIABP,mmHg,8205
Systolic Blood Pressure~SYSBP,mmHg,8205
Pulse Rate~PULSE,BEATS/MIN,8201
Temperature~TEMP,C,2720
Weight~WEIGHT,kg,2050
Blood Urea Nitrogen~BUN|CHEMISTRY,mmol/L,1828
Calcium~CA|CHEMISTRY,mmol/L,1828
Cholesterol~CHOL|CHEMISTRY,mmol/L,1828
Creatinine~CREAT|CHEMISTRY,umol/L,1828
Gamma Glutamyl Transferase~GGT|CHEMISTRY,U/L,1828
Protein~PROT|CHEMISTRY,g/L,1828
Urate~URATE|CHEMISTRY,umol/L,1828
Alkaline Phosphatase~ALP|CHEMISTRY,U/L,1824
Phosphate~PHOS|CHEMISTRY,mmol/L,1822
Alanine Aminotransferase~ALT|CHEMISTRY,U/L,1814
Albumin~ALB|CHEMISTRY,g/L,1814
Aspartate Aminotransferase~AST|CHEMISTRY,U/L,1814
Bilirubin~BILI|CHEMISTRY,umol/L,1814
Creatine Kinase~CK|CHEMISTRY,U/L,1814

This file has been truncated. show original

(Also tagging @Craig_Mayer in our clinical research informatics team)

(observations also pasted for those who do not click the link)

Sample data conversion results

sample CDISC data differes in format from trial RWD (3 trials)
- person identifier used (SUBJID, RSUBJID,RUSUBJID))
  - large sample needed but not available; must also be recent (trial started and finished in the last 5 years)
SDTM manual is very long, in PDF format (this should change with CDISC SHARE initaitive)
Demographic (DM) domain does not contain year of birth. It is not clear at what time age is calculated. (at first visit of the subject?; day 1 of the trial) (convention)
trial data may be organized by visit number (not absolute date)
Demographic (DM) domain data on screen failure or arm: missing suitable concept_id (issue) (tentatively using LOINC 68839-0| Research Note) (todo new concept)
LOINC codes will be used in SDTM (in 2018, FDA clarified a LOINC strategy) so detailed mapping is not pursued.
Assignment into arms can be in COHORT table or as OBSERVATION or other table (convention).
Vital Signs (VS) domain is very similar to Laboratory (LB) domain. Both have standard units and original value and numeric value. LB has exact datetime, whereas VS has only date (issue).
_source_value columns were sometimes overloaded with multiple elements separated by delimiters (issue)
Medical History (MH) domain captures a condition at a given visit (date1) but
records onset date (date2). Date2 can be null (not known) (convention) (issue)

update: the trial arm term will be in SNOMED CT in Jan 2019 !
(I submitted it)

Vojtech_Huser · November 27, 2018, 4:57pm

Please vote/comment on this proposed high priority convention for study data Convention for representiong assignment of person to a clinical trial · Issue #37 · OHDSI/Themis · GitHub

Also, we would need row in METADATA for date.

MaximMoinat · February 6, 2019, 1:08pm

@Vojtech_Huser What is the status of this proposal? Is there an agreement on the convention within Themis?

A next step would be to also capture the details on the study in OMOP, like name, inclusion criteria and arms. A new Study domain/table might be necessary. Or has the assumption been so far that one dataset represents the data from one clinical trial?

Vojtech_Huser · April 12, 2019, 3:03pm

To complement today’s discussion in the trial WG. Here are the links I pasted during the chat

https://github.com/vojtechhuser/project/tree/master/sdtm-omop/omop-output-csv
https://github.com/vojtechhuser/project/tree/master/sdtm-omop/sdtm-input-csv

Summary of the meeting also coming soon.

One question was trial vocabulary domain or whether trial visit type should live in the existing visit type vocabulary domain.

MaximMoinat · April 12, 2019, 3:10pm

I have just written a small overview in this thread: New working group: Clinical Trials

Vojtech_Huser · August 23, 2019, 2:30pm

OMOP currently captures visits. Where a patient AND provider interact.

If a patient logs into PHR or provider mails a letter to the patient, it is a one sided event. Just patient does something or just provider does something.

From patient care and research point of view (e.g., on PHR side, ability to recruit into a applicable research study via PHR), such events matter and can be important for research.

For the clinical study WG - that could be an interesting topic to discuss. You can also post your ideas here: https://github.com/OHDSI/CommonDataModel/issues/287

julie_kohler · August 27, 2019, 7:04pm

Not just for clinical research–I would imagine for some treatment programs of the public health variety, this would be important to capture (I’m thinking of things like TB and HIV, where outreach is a routine part of clinical care). I’m working with a team to develop a EMR in Eswatini that’s pretty HIV-focused, and we are looking to build out an “outreach” module because that’s a critical part of our care program that we get evaluated on.

Agota_Meszaros · November 11, 2024, 9:28am

Dear all,

I have read a lot of things I could find online about how to capture trial data in CDM 5.4, but I am still not sure about the final solution.
It seems here Proposal: Clinical trial data conventions for OMOP CDM · Issue #196 · OHDSI/Themis · GitHub that there is a convention, but I was not able to find it in the documentation.
If we only have data on the trial number (as a procedure), should we use “Patient consented to clinical trial, 4163733”?

Thank you, if someone has info on this.

Philip_Solovyev · November 11, 2024, 10:26am

Dear @Agota_Meszaros
The conventions for clinical trials in the OMOP CDM can be found here: Home · OHDSI/ClinicalTrialsWGETL Wiki · GitHub
However, keep in mind that they were developed for version 5.3 and have not been updated for version 5.4. Although the majority of the conventions are applicable to version 5.4, some recommended concepts might become invalid or non-standard, so you need to check Athena for their substitutes.

Regarding your question about the trial number: yes, I believe it can be stored as an Observation with concept id 4163733, and the trial identifier can be entered into the value_as_string field.

Agota_Meszaros · November 11, 2024, 3:00pm

Hi @Philip_Solovyev,

thank you! Okay, we will look into the concepts before we use them, to see if they are valid.

MPhilofsky · November 12, 2024, 5:06pm

@Philip_Solovyev,

We should incorporate the Clinical Trials conventions into the Themis convention library. So, when collaborators go looking for the conventions, they will be able to easily find them. Should I reach out to you to work on adding these to the convention library?

Philip_Solovyev · November 13, 2024, 2:38pm

@MPhilofsky
I think it’s better to reach out to @mike_hamidi