CT0085

Pinnacle 21 Support SDTM
1

Hi Dongsun,

Unfortunately I can not reproduce your case. Everything looks fine for me. CT00085 check is not firing for extendent CDISC CT terms including your example values.

Could you provide more details?

Thank you,

Sergiy

2

I ran open CDISC today and recieved same error message for EG(CT0085), LB(CT0083) and VS(CT0082) for bunch of tests. Could u plese look into this.

3

Hi Nitin,

Could you provide examples of your --TEST/–TESTCD values which generated false-positive messages?

Thank you,

Sergiy

4
EGALL, ECG All
PR, PR Interval
QRS, QRS Interval
QT, QT Interval
QTC, QTC Interval
QTCB, QTC Interval - Bazett’s Correction
QTCF, QTC Interval - Fridericia’s Correction
RRCALC, RR Interval (Calculated)
VRATE, Ventricular Rate
AMYLAS, Amylase
BANDS, Bands
FIBRIN, Fibrinogen
LBALL, Labs All
LIPASE, Lipase
PHOS, Phosphorus
PTTBLD, PTT (blood)
SEGS, SEGS
VSALL, Vital Signs All
5

Thank you, Nitin for your examples! Now I see what’s wrong.

Fisrt, please note, that some records in your example are actually incorrect. E.g.,

  • “AMYLAS, Amylase” should be “AMYLASE, Amylase”
  • “LIPASE, Lipase” should be “LIPASE, Triacylglycerol Lipase”
  • “FIBRIN, Fibrinogen” should be “FIBRINO, Fibrinogen”
  • PHOS, Phosphorus" should be “PHOS, Phosphate”

However other examples for Lab Test Codes/Names generate false-positive messages. There is bug in CT0082 check in specifications available on website. An attribute WhereFailure=“Ignore” is missing. Actually this bug was identified a while ago and all relevant checks were already corrected. We are using a more recent version of validation specifications and the engine. That’s why I could not found the cause without your helpful examples.

As a temporary solution until a new release of the validator, you can modify specifications files (e.g., config-sdtm-3.1.2.xml) in “config” folder by adding WhereFailure=“Ignore” into CT0082-CT0085 checks. See an example bellow.

Kind Regards,

Sergiy

<val:Lookup ID=“CT0082” Variable=“VAL:DECODE == LBTESTCD” From=“FILE:CDISC:%System.ConfigDirectory%/data/CDISC/SDTM/%System.CDISC.Version%/SDTM Terminology.txt” Where=“CodelistCode == ‘C67154’ @and CDISCSubmissionValue == [LBTEST]” When=“LBTEST != ‘’ @and LBTESTCD != ‘’” ActiveUnless=“%Variables[LBTEST].Define.WithCodeList%” WhereFailure=“Ignore” Message=“LBTEST and LBTESTCD values do not have the same Code in CDISC CT” Description=“Values for Lab Test or Examination Short Name (LBTESTCD) and Lab Test or Examination Name (LBTEST) variables must be populated using terms with the same Code value in CDISC control terminology. There is one-to-one relationship between LBTESTCD and LBTEST values defined in CDISC control terminilogy by Code value.” Category=“Terminology” Type=“Error”/>

6
CHAMENL, CHAMBER ENLARGEMENT CT0085 EGTEST and EGTESTCD values do not have the same Code in CDISC CT

The code list is extensible for EGTESTCD. Why does ct0085 check against code SDTM code list?

is this a bug?