For Comment: NCPI Condition need to accomadate dbGaP Phenotype Data

[mingward]

Link to Profile

https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition-ncpi-condition.html

Feedback Submission

The documentation at NCPI FHIR IG Module: Phenotype Condition states that "is used to represent a condition or phenotype linked to a patient in a study. This means that the patient must have an assertion (status) for the given diagnosis." However, it does not mention other important measurements, such as the FEV1/FVC z-score used in the ICAC study.

Please see an example Dataset below. We see some issues of representing the following data in NCPI Condition. For example, NCPI Condition requries "assertion". For many of the dbGaP variable, those will all be "unknown". In fact, majority of dbGaP phenotype dataset data will not have "assertion" and will all be "unknown" for this field. Seemed less than idea to be represented this way. Currently, we are using Observation to represent the data.

The NCPI Condition needs to accommodate datasets similar to the one from the ICAC study (available at NCBI):

Variable Accession	Variable Name	Variable Description
phv00508492.v1.p1	SUBJECT_ID	Subject ID
phv00508493.v1.p1	STUDY	Name of study
phv00508494.v1.p1	ASTHMA	Asthma status
phv00508495.v1.p1	SEX	Sex
phv00508496.v1.p1	RACE	Race by parent report
phv00508497.v1.p1	SITE	Site
phv00508498.v1.p1	FEV1_PRED_SCR	FEV1 % predicted
phv00508499.v1.p1	INT_RESID_FEV1_PRED_SCR	FEV1 % predicted (adjusted, normalized)
phv00508500.v1.p1	AGE_FEV1_PRED_SCR	Age when FEV1 % predicted collected
phv00508501.v1.p1	FEVFVC_Z	FEV1/FVC z-score
phv00508502.v1.p1	INT_RESID_FEVFVC_Z	FEV1/FVC (adjusted, normalized)
phv00508503.v1.p1	AGE_FEVFVC_Z	Age when FEV1/FVC collected
phv00508504.v1.p1	NICALERT_RESULT_SCR	Nicalert test result of cotinine equivalents (urine)
phv00508505.v1.p1	AGE_NICALERT_RESULT_SCR	Age when Nicalert test collected
phv00508506.v1.p1	PC1	PC1
phv00508507.v1.p1	PC2	PC2
phv00508508.v1.p1	PC3	PC3
phv00508509.v1.p1	PC4	PC4
phv00508510.v1.p1	PC5	PC5
phv00508511.v1.p1	PC6	PC6

Is this feedback implementation-blocking?

Yes, this issue will block implementation.