Thursday, February 12, 2015

Rule FDAC084 is just damned wrong

The FDA has recently published a set of "SDTM rules", unfortunately in Excel format, which is not machine-executable. So I started working on an XQuery representation, which will soon be available through a set of web services. You can already find some examples in my previous blog entries.

When working on these rules, I found that:
  • about 10% of them is just damned wrong
  • another about 10% is ununderstandable, even for people with a lot of experience in SDTM and define.xml
 The most notorious of the "just damned wrong" rules is surely rule FDAC0154: "Missing value for --ORRESU, when --ORRES is provided".
As we all know, there are so many tests for which there are no units for the results, just to name a few:
  • pH is dimensionless
  • all qualitative tests have no units. For example: presence of Ketones in Urine by Test strip (LOINC 24356-8)
 Today, I want to discuss another rule however, which is a consequence of the SDTM myth that the combination of LBTESTCD, LBCAT, LBSPEC, and LBMETHOD uniquely describes a lab test.

The rule FDAC084 sounds: "Standard Units (--STRESU) must be consistent for all records with same Short Name of Measurement, Test or Examination (--TESTCD), Category (--CAT), Specimen Type (--SPEC) and Method of Test or Examination (--METHOD)"

A quick search trough the LOINC database shows that this rule is just damned wrong.

Just take the following combination:

One quickly finds following tests for this combination:
  • LOINC=25428-4  Glucose [Presence] in Urine by test strip
    and the designation "ordinal".
    So this test has no units
  • LOINC=50555-2 Glucose [Presence] in Urine by automated test strip
    with typical values being 1+ to 4+ and "negative".
    So again: no units
  • LOINC=5792-7  Glucose [Mass/​volume] in Urine by test strip
    with as typical unit: mg/dL
  • LOINC=22705-8 Glucose [Moles/volume] in Urine by test strip
    with as typical unit: mmol/L
 So essentially 4 different tests, all with the same combination of LBTESTCD, LBCAT, LBSPEC and  LBMETHOD.
2 of these tests have no units at all (25284-4 and 50555-2), with the two others having different units.

So what can we learn from these examples?
  • The combination of CDISC LBTESTCD, LBCAT, LBSPEC and  LBMETHOD does not uniquely describe a lab test
  • Even worse, when looking at other LB variables that are at least expected, there is no combination that can possibly ever uniquely describe lab tests
  • The rule FDAC084 is nonsense
  • The only method to uniquely identify lab tests is the LOINC code. Unfortunately LBLOINC is "permissible", with the consequence that you almost never find it in real submissions, and putting the LOINC code itself in LBTESTCD is not allowed.