Saturday, September 21, 2013

Is CDISC Controlled Terminology going the wrong way? A follow up

So I made some "change requests" to the CDISC-CT ...

Here are the answers (in italic) that were send to me by the CDISC-CT team.

"The CDISC Terminiology team met to discuss your requests. Here are our decisions:

a) pH - Team agrees to remove from Unit codelist.

b) BEATS/MIN - This is a common clinical unit of measure for heart rate and pulse rate. It is classified as a unit of measure by SNOMED-CT. It is classified as a unit of measure by NCPDP (National Council for Prescription Drug Program). Therefore it will not be removed. 

 c) BAR - For CDISC, both units of measure and units of presentation are in the same codelist. It is up to the user based on the definition to select the correct term. This term is published in the FDA SPL list. We understand your concern regarding units of measure versus units of presentation. We have included units for presentation from ISO 11616 as distinguished from units of measure. If BAR for pressure is needed for clinical trial work, please submit a request to add that as a new term. Currently we will leave "BAR" as a dosing unit. 

Concerning a) thank you - there seem to be a few chemists left on this world
Concerning b) essentially says: we copy the errors of others
Concerning c) oh my God ...

How does UCUM deal with the "beats/min" issue?
From the specification I read:
"§6 curly braces 1) The full range of characters 33–126 can be used within a pair of curly braces (‘{’ and ‘}’). The material enclosed in curly braces is called annotation.
2) Annotations do not contribute to the semantics of the unit but are meaningless by definition. Therefore, any fully conformant parser must discard all annotations. Parsers of limited conformace should not value annotations in comparison of units.
3) Annotations do, however, signify the end of a unit symbol.
4) An annotation without a leading symbol implies the default unit 1 (the unity).
5) Curly braces must not be nested.
Curly braces are here because people want annotations and deeply believe that they need annotations. Especially in chemistry and biomedical sciences, there are traditional habits to write annotations at units or instead of units, such as “%vol.”, “RBC”, “CFU”, “kg(wet tis.)”, or “mL(total)”. These habits are hard to overcome. Any attempt of a coding scheme to restrict this percieved expressiveness will ultimately result in the coding scheme not being adopted, or just “half-way” adopted (which is as bad as not adopted).
Two alternative responses to this reality exist: either give in to the bad habits and blow up of the code with dimension- and meaningless unit atoms, or canalize this habit so that it does no harm. The Unified Code for Units of Measure canalizes this habit using curly braces."

So, for a heart beat frequency, the correct UCUM unit is "/min", but also ("canalized bad habit") the following would be allowed "{beats}/min".

For "units" such as "bar", "bottle", "capsule" I have now proposed the team to move these into a separate codelist, so that these are really separate from "measument units" (according to wikipedia: "standardized quantity of measurement of a physical quantity").
This would strongly improve machine-processability of SDTM records: a machine can then be explained that "units" of this codelist can NOT be used for comparisons. With the current situation (mixing up of standardized units and non-standardized units) such machine-processability is impossible (or extremely dangerous).

I will follow up as soon as I have a response from the CDISC-CT team.