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Condition_occurrence, Death diagnoses

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#14

@dymshyts:

Hang on here. I think you are mixing things up a bit:

Concepts that can be used as cause of death don’t have to explicitely have death in their description. A good old congestive heart failure is fully compatible with life, but can be cause of death.

The problem @tbanokina is mentioning is that if a pre-coordinated code maps to more than one Standard Concept, we don’t know which of them should be considered the cause of death. If the mapping is one-to-one we don’t have to worry, since a singleton “Loss of consciousness” will not be in the original data as cause of death.

#15

@Christian_Reich, Yes, I mixed up
there are multiple questions:

  1. how to define death using condition concepts
  • should be a separate topic
  1. how to define cause of death if there are multiply mappings from one source_code
    and here I said “just ignore these loss of consciousness”

You can take a look:
http://chfs.ky.gov/NR/rdonlyres/BDE088FB-D08E-4008-B0A7-3B11890C532F/0/CausedeathcodesICD10.pdf

#16

@Christian_Reich
A solution with a new relationship between standard concepts seems to be optimal. Unfortunately, I don’t have any better ideas.

#17

Hi Everyone,

I am generating DEATH Table and I am having One subject more than once in my raw data.

Should I mention all three instance of the same subject in table.
cause of death is given like (Meddra Coding Preferred Term) in raw data or only one?.

1.ATRIAL FIBRILLATION (10003658)
2.HYPOTENSION (10021097)
3.INTERSTITIAL PULMONARY FIBROSIS (10022611)

start date and end date both are same for each observation.

Also, Kindly guide me that should i put Meddra PT Code (10003658) in CAUSE_SOURCE_VALUE and CAUSE_SOURCE_CONCEPT_ID would be the corresponding Concept ID of MedDra?
What should be the CAUSE_CONCEPT_ID in this case ? Would it be the SNOMED Concept ID From Vocab?

Please guide me as I am not sure of the same…

Regards,
Nitish

#18

Let me clarify:
patient has 3 different causes of death in a raw data?

And anyway, you use “MedDRA - SNOMED eq” to get SNOMED concepts and put into CDM Standard concepts only.

#19

Same here.

#20

I continue this chat, because it’s a principal question - how to choose the one cause of death?
@TBanokina, have you ever meet such a case when it was different Source_concepts as a cause of death?
@Christian_Reich, any advice: what to do, whom to ask?
@nitishkjha, so the person has 3 causes of death in the raw data,
and we need to pick up only one
http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:death
“Each Person may have more than one record of death in the source data. It is the task of the ETL to pick the most plausible or most accurate records to be aggregated and stored as a single record in the DEATH table.”
and I don’t know how automatically choose which one among ATRIAL FIBRILLATION, INTERSTITIAL PULMONARY FIBROSIS, HYPOTENSION should be chosen.

@Olena, as a pathologist, which one you’d choose as a cause of death?

#21

@Dymshyts.

I am not sure why this is necessary. Look:

  1. The source data (the physician declaring death of a patient) define the cause of death. We don’t have to second guess.
  2. Only where we have more than one mapping from one of these choices we have a problem, which is very rarely. because we cannot have mroe than one cause of death, but suddenly we got two or three. And for those cases we need a mechanism to choose.

So, if you could be so kind, take all the multiple mappings of ICD codes and pick one as a potential cause of death and we are done.

#22

@nitishkjha sent me an example where
ATRIAL FIBRILLATION,
INTERSTITIAL PULMONARY FIBROSIS
HYPOTENSION
were mentioned as a cause of death
@nitishkjha, Am I right?

#23

@Dymshyts:

Were they mapped from a single code? Then it is our problem. But if Nitish’s source gives him three reasons than he has to figure that out on his end.

To be honest with you, neither atrial fibrillation, nor pulmonary fibrosis, nor hypotension are acute causes of death. They are the foundation for an acute phenomenon (like a stroke). If anything, the fibrosis could wear you out.

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#24

No

probably in his data there are underlying conditions, but not an actual cause of death.

#25

@Dymshyts @Christian_Reich

I have an example. We have one project where cause of death is identified by a special flag (specific for this particular project only). For one event date and one patient there are 4 causes of death:

G3…13 (IHD - Ischaemic heart disease)
B22z.11 (Lung cancer)
G581.00 (Left ventricular failure)
H25…00 (Bronchopneumonia due to unspecified organism)

So,

  1. should we choose just one cause of death or create 4 records in cdm death table for that patient?
  2. if we have to choose one cause of death, how should we take the right cause of death?
#26

@Oksana:

That’s an interesting problem. Right now, you have only one cause of death. Clinically, this case sounds like the pneumonia did the patient in, but clearly the other diseases have contributed. Can we do more than one death record?

#27

According to this list every condition from the list will be cause of death.
And if we talk about actual cause of death, it we’ll be not a pneumonia but a respiratory failure.
So if in a raw data we have underlying conditions leading to death instead of “actual cause of death”,
thus if we display this in a CDM, we need to allow to put there several causes of death.

#28

@Christian_Reich, @Dymshyts

I am not a medical expert, so just from my understanding: if this is according to medical standards to record several causes of death when a patient dies (actual, main, leading, contributing etc causes of death), in other words if multiple causes of death for a patient in source data is not a mistake, then ETL folks should not try to guess which one should go to cdm table. I would create multiple records in cdm death table for each cause of death.

Another question is multiple death dates for a patient. Here, in my opinion, it makes sense to choose one death date “up to ETL”, “the best approximation” etc. Because it is humanly impossible to die in different dates.

However, according to CDM V.5 conventions a person can have only one record in death table: “A person can have up to one record if the source system contains evidence about the Death”, “Each Person may have more than one record of death in the source data. It is the task of the ETL to pick the most plausible or most accurate records to be aggregated and stored as a single record in the DEATH table”.

And, as I see, it was not a case in CDM V.4 conventions for death table “Each Person may have more than one record in the Death table if there is available information for multiple contributing causes of death”.

I can be wrong in my assumptions, so I just want to make it clear for me about “only one record in CDM V.5 death table for a patient”.

Thank you very much for making it clear!

#29

Just out of curiosity, the causes of death (as it relates to diagnosis codes) will be recorded in CONDITION_OCCURRENCE, correct? After thinking on what people are writing about the cause of death, we don’t need to look both in the DEATH table and CONDITION_OCCURRENCE table to find diagnosis codes for a patient, do we? IE: a person who dies of sudden heart failure (with no prior history of it), would the diagnosis code for that condition only be found in DEATH because it was a cause of death, or would it be found in CONDITION_OCCURENCE on the same date as they died?

-Chris

#30

@Oksana:

That could be a solution. We would have to officially change the Data Model back to how it was in V4, where you could have more than one record. The CDM WG does these kind of things.

However, you should not have more than one date. You got to figure out which date is the right one.

Yes, all those Conditions, including the actual killer, are in the Condition table. But only one should go into the Death table. But Oxana is saying she can’t pick and there is more than one.

#31

@Christian_Reich,
Can we start creating multiple records in cdm death table for each cause of death now or we should wait for new version of omop spec?

#32

I’d say yes. The documentation can be fixed momentarily. But only one death_date please.

#33

thats a breaking change to our model conventions, so i think we should
discuss it on the cdm workgroup to make sure we have community consensus.

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