LAB_RESULT_CM transform passes non-standard RESULT_QUAL values from i2b2fact table

[mprittie]

According to the PCORnet CDMv3 spec the expected RESULT_QUAL values in the LAB_RESULT_CM table are:

• BORDERLINE
• POSITIVE
• NEGATIVE
• UNDETERMINED
• NI = No information
• UN = Unknown
• OT = Other

While running the transform (PCORNetLoader_ora.sql) we get errors on the attempted insertion of non-standard RESULT_QUAL values which are larger than the expected 12 character width (the length of UNDETERMINED). This is due to the fact that TVal_Char values in the i2b2fact table are getting passed directly along as long as they are not NULL. It appears that the transform currently expects that the TVal_Char values of matching records contain the relevant PCORI codes, which our fact table does not.

It also looks like this is on your radar, hence the inline TODO comment, but I wanted to log it here so that it's known that this is impacting others.

[jklann]

Thanks. Any suggestions on how to do this transparently without making sites change their fact tables? I haven't yet come up with a way.

[mprittie]

Hi Jeff, if we come up with a generalizable solution before you do, I'll share our approach.