Is I2B2DEMODATA.CONCEPT_DIMENSION.CONCEPT_CD supposed to be unique?

[AFB]

If I understand correctly, the only thing linking I2B2DEMODATA.OBSERVATION_FACT to I2B2DEMODATA.CONCEPT_DIMENSION is the CONCEPT_CD column, is that correct?

Therefore, there must be a unique constraint on the CONCEPT_CD column in CONCEPT_DIMENSION, otherwise there would be exploding joins. Is that also correct?

Thanks.

[AFB]

Okay, looks like in the actual I2B2DEMODATA content, CONCEPT_CD is not unique:

select count(*) from(
select concept_cd,count(*) N from concept_dimension
group by concept_cd)
where n>1
union all
select count(*) from(
select concept_cd,count(*) N from concept_dimension
group by concept_cd)
where n=1;

/*
non unique    1671
unique    70130
*/

...but then, I2B2 devs, what's the point of even having a CONCEPT_DIMENSION? The many-to-many relationship between paths and actual physical, non-redundant observations is already served by the ontology tables in I2B2METADATA. CONCEPT_DIMENSION could be a mapping to a set of reference paths and descriptions chosen so that starting from a set of observations (e.g. "show me what the most frequent diagnoses were between these dates for these patients") there would always be available a human-readable set of annotations. But, when CONCEPT_CD is permitted to be non-unique, such joins cannot will give redundant observations.

So, my question becomes this: what, if anything, in I2B2 actually relies on there being this many-to-many relationship between entries in CONCEPT_DIMENSION and OBSERVATION_FACT?

If nothing, then this suggests I can work around this problem by altering CONCEPT_DIMENSION to only have unique CONCEPT_CDs without impacting anything else. Thoughts?

[Murphy, Shawn N.]

The primary key of the concept dimension is the concept_path.   The logical interpretation is that a singled coded item (such as the medication “aspirin”) could exist under multiple classification paths,  such as an anti inflammatory medication and a cardiac medication.

 

Thanks,

Shawn.

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[AFB]

Hi, Shawn, long time no see and thanks for your response.

Aren't multiple concept paths already provided by the ontologies in the I2B2METADATA schema?

For the aspirin example, if you use CONCEPT_PATH search for encounters where aspirin was prescribed as a cardiac medication, you will also get all visits associated with anti-inflammatory prescriptions and vice-versa.

If CONCEPT_PATHs encode actual data rather than metadata, that information is lost once that observation is imported into OBSERVATION_FACT because of this ambiguity in the mapping between CONCEPT_CD and CONCEPT_PATH. So, it logically follows that either OBSERVATION_FACT should contain a CONCEPT_PATH column or a uniqueness constraint should be enforced on CONCEPT_CD.

I'm guessing that it's probably easier to implement the latter fix at my end. I'm just wondering what components of I2B2 query CONCEPT_DIMENSION.CONCEPT_PATH to find concept codes instead of querying e.g. I2B2METADATA.I2B2.C_FULLNAME

[Murphy, Shawn N.]

If you are looking to go from the fact table to identifying a concept with the fact table code, c_name should be unique and is probably what you are looking for.  A real world problem is that the classification paths can be multiple for each item and that is what the concept path deals with.

 

Thanks,

Shawn.

 

From: i2b2-ins...@googlegroups.com [mailto:i2b2-ins...@googlegroups.com] On Behalf Of AFB
Sent: Tuesday, September 23, 2014 10:47 AM
To: i2b2-ins...@googlegroups.com
Subject: Re: Is I2B2DEMODATA.CONCEPT_DIMENSION.CONCEPT_CD supposed to be unique?

 

Hi, Shawn, long time no see and thanks for your response.

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