topic Re: Import CDISC ODM v1.3 XML in SAS Health and Life Sciences

Import CDISC ODM v1.3 XML

MichaelH_ — Tue, 19 Jan 2021 07:53:12 GMT

Can anyone help with how to read CDISC compliant ODM v1.3 XML (from and API to a clinical trials database built using Viedoc) into SAS 9.4?

I have been trying:

filename xmlinp 'F:\xml\ClinicalDataBackup.xml';

libname xmlinp xml xmltype=CDISCODM;

proc contents data=xmlinp._all_;

SAS errors:

check_ordernum has no inst

ERROR: XML describe error: Internal processing error.

From the SAS documentation, it seems there may be some issues with the XML – could you confirm:

There are separate XML files for the clinical data and the metadata; there are <itemGroupDef> elements in the metadata XML but not in the clinical data XML (I am trying to read in the clinical data); the <itemGroupDef> elements do not have attributes of “SASDatasetName” – are these show stoppers for SAS? Would these be a problem is I could get the XML in ODM v1.2 and use Proc CDISC?

Re: Import CDISC ODM v1.3 XML

Lex_SAS — Fri, 05 Feb 2021 16:01:10 GMT

Hi Michael,

The CDISCODM xmltype on the libname and PROC CDISC expect ODM 1.2. Also, both libname and PROC CDISC would expect the data and metadata to be in the same XML ODM file.

Please be aware that PROC CDISC was deprecated and replaced by the SAS Clinical Standards Toolkit (CST) quite a long time ago.

CST supports ODM 1.3 and can handle metadata and data separately. CST is at version 1.7.2, and is supported, but no longer actively developed.

For information about CST see: https://support.sas.com/en/software/sas-clinical-standards-toolkit-support.html

and also http://support.sas.com/rnd/base/cdisc/cst/

For a paper about CST and ODM, see: https://www.lexjansen.com/pharmasug/2013/HT/PharmaSUG-2013-HT06-SAS.pdf

(Using the SAS® Clinical Standards Toolkit 1.5 to import CDISC ODM files).

Lex Jansen

Principal Solutions Consultant @ SAS

Re: Import CDISC ODM v1.3 XML

MichaelH_ — Sun, 07 Feb 2021 22:19:55 GMT

Thanks Lex, that's a useful summary, and references, and it sounds like the Clinical Standards Toolkit is what I need to read in data and metadate in separate files. I understand from SAS Support that SAS 64 bit is required to use the CST, so unfortunately I am not yet able to take advantage of it.