Relationship options for fact_relationship table

[MPhilofsky (Melanie Philofsky)]

@Dymshyts,

I am hoping you can help me find an appropriate concept_id for the fact_relationship table to link two tobacco use concepts together. Filtering on concept_class_id = Relationship or filtering on vocabulary_id = Relationship gives me the same 402 concepts. Only 10 of those concepts are standard concepts. None are appropriate for linking together two social history facts. What standard relationship_concept_id should I use? I also have use cases to link sexual activity and contraception type; alcohol intake and start/stop/quit dates; illicit drug use concepts.

Thanks!
Melanie

[Dymshyts (Dmytry Dymshyts)]

It’s a good question,
looks kinda similar

Storing note data from radiology, coronary angiography, and pathology report

I converted coronary angiography report into note table of OMOP-CDM ver 5.0.2. I want to convert all reports from radiology and pathology into CDM, too. But I'm wonder how I can set relationship between these notes with primary procedure or measurements or specimens. (How can I know where the coronary angiography report comes from, when the patient has multiple coronary angiography in the same day? Current note table has visit_occurrence_id, so I can tag it. But I don't find any room for proc…

And the final idea was to propose to extend the Note table with addtional related events fields.

@MPhilofsky, according to your use case, do you think, instead of using fact_relationship table, it would be better to have related_event_id, related_domain_id fields in Observation table where you can put your additional concepts?

@Christian_Reich, is it possible to extend Measurement, Observation, Condition, Procedure tables with related_event_id, related_domain_id fields?

[MPhilofsky (Melanie Philofsky)]

better to have related_event_id, related_domain_id fields in Observation table where you can put your additional concepts?

@Dymshyts I like the idea, however, I will have many related_event_ids. Person uses tobacco, person is light cigarette smoker, person started smoking 19500101, person has 100 year pack history, etc. How would we relate them all together?

This is also similar to the cultures conversation. Another use case we are about to embark upon.

[Christian_Reich]

@Dymshyts, @MPhilofsky:

This is for THEMS and the CDM WG. Create a list of options, and let’s discuss the pros and cons. You mentioned two:

1. A predefined list of relationship concept for FACT_RELATIONSHIP (I am not a fan, as you know)
2. Adding fields for those linkages.

What else?

[MPhilofsky (Melanie Philofsky)]

@Christian_Reich,

This is for THEMS and the CDM WG.

I know! I am the one that volunteered to take on social history modeling. I am researching the options.

A predefined list of relationship concept for FACT_RELATIONSHIP

@Dymshyts - Do you know of any SNOMEDCT codes (or any standardized codes/code system) that would work for connecting social history “facts” I mention above?

@OHDSI community - How have others added social history concepts to OMOP? Or how would you add it?

Cheers,
Melanie

[Christian_Reich]

I know! I am the one that volunteered to take on social history modeling.

Hahahaha. It called “sending on a circular goose chase”.