Validations for TUMOR.XPT ?

Hi! No validation around

Hi!

No validation around tumor.xpt data was implemented in the tool so far. I am not sure the tumor.xpt domain validation will be included in the next release.

Regards,

Sergiy 

Next release?

Hi Sergiy,

I was wondering when is the new release is scheduled. And if it will include some validation for tumor.xpt.

I'm also wondering if the config files can be extended to contain user-defined validation rules for custom domains?

Hi Amelia,  1. There is no

Hi Amelia, 

1. There is no exact plan date for new release. It will be published soon.

2. No Tumor.xpt validation in v1.4. My understanding is that this domain is temporary solution, because most info can be derived from SDTM data. 

3. I am not sure what do you mean by "use-defined val. rules for custom domains"?

Regards, 

Sergiy

Hi Sergyi, Point #3 was

Hi Sergyi,

Point #3 was referiing to the posibility of defining new validation rules in config.xml for a domain like tumor.xpt.

Regards,

Amelia

Implement validations for tumor

Hi Sergyi,

Teoretically speaking, if one would like to implement its own validations for tumor.xpt... what would be the steps?

So far I did the following:

1. config-send-3.0.xml: add ItemGroupDef entry for tumor;

2. config-send-3.0.xml: add ItemDef entries for all tumor columns;

3. SEND Metadata 3.0.csv: add entries for all tumor columns (btw, this file seems to duplicate ItemDef content from config-send-3.0.xml like label, type char or num, etc);

4. config-send-3.0.xml: added the general validation rules. Some custom ones are to be added.

My issue is the following:

My tumor .xpt is located in distinct folder and its content is not added to the main define.xml. So:

- if I run validation and specify in "Define.xml" the location of the main define.xml, I get a "Configuration Missing" message (which seems OK since no reference to tumor.xpt is done in my define.xml);

- if I run validation and don't specify in "Define.xml" any define.xml, TUMOR validation is done, but I get more CT Warnings related to the standard domains since the cross-check with define.xml is no longer done for them.

Any suggestion on how to solve this: have the tumor.xpt validations in my report and still specify in "Define.xml" the location of the main define.xml to benefit from the CT validations for the Tabulation domains?

Best regards,

Amelia

Hi Amelia,  Actually it's not

Hi Amelia, 

Actually it's not exactly as you described mostly due to changes across validator versions. E.g., #3. there are .CSV metadata files anymore.

Define file issue can be handle by introducing a new ability to work with several data sources. E.g., to ensure consistency across studies or standards.

However, as I said before, a validation of tumor.xpt file has very low value compare to other users-expected features like new versions of SDTM standard (e.g., 3.1.3, Device or therapeutic specific), enhanced ADaM validation, define.xml tool, etc.

Regards, 

Sergiy

Hi Sergyi, Thanks for the

Hi Sergyi,

Thanks for the clarifications. Looking forward to the new validator version ;)

Getting back to my issue: assuming I put together some validations for tumor.xpt, can I generate a single report to contain all the validations for the Tabulation domains and also my custom ones for tumor.xpt? Keeping in mind that I still want to make a referrence to my define.xml file for the Tabulation domains...

Regards,

Amelia

There is no cross-standards

There is no cross-standards or cross-studies validation in an open source validator. This is a feature of the commercial OpenCDISC Enterprise product only. Therefore now it's not possible to use two different define.xml files during the same validation process in a free version of a validator.

One option for you is to 1. include tumor.xpt validation in SEND/SDTM profile, 2. run it two times for each define.xml file and 3. ignore all non-related messages.

Another approach is to have a separate validation profile for tumor.xpt only and also ignore non-relative messages about SEND/SDTM data.

Neither of them are a good and clean solution. Engine modification is required for cross-data source validation. We used diffrent technology for such task in OpenCDISC Enterprise. 

Regards, 

Sergiy