Tag Archives: XML

The Only Three (3) [Programming] Languages You Should Learn Right Now (eClinical Speaking)

On a previous article that I wrote in 2012, I mentioned 4 programming languages that you should be learning when it comes to the development of clinical trials. Why is this important, you may ask? Clinical Trials is a method to determine if a new drug or treatment will work on disease or will it be beneficial to patients. Anayansi Gamboa - Clinical Data Management Process If you have never written a line of code in your life, you are in the right place. If you have some programming experience, but interesting in learning clinical programming, this information can be helpful.

But shouldn’t I be Learning ________?

Here are the latest eClinical programming languages you should learn:

1. SAS®: Data analysis and result reporting are two major tasks to SAS® programers. Currently, SAS is offering certifications as a Clinical Trials Programmer. Some of the skills you should learned are:

  • clinical trials process
  • accessing, managing, and transforming clinical trials data
  • statistical procedures and macro programming
  • reporting clinical trials results
  • validating clinical trial data reporting

2. ODM/XML: Operational Data Modeling or ODM uses XML to build the standard data exchange models that are being developed to support the data acquisition, exchange and archiving of operational data.

3. CDISC Language: Yes. This is not just any code. This is the standard language on clinical trials and you should be learning it right now. The future is here now. The EDC code as we know it will eventually go away as more and more vendors try to adapt their systems and technologies to meet rules and regulations. Some of the skills you should learn:

  • Annotation of variables and variable values – SDTM aCRF
  • Define XML – CDISC SDTM datasets
  • ADaM datasets – CDISC ADaM datasets

CDISC has established data standards to speed-up data review and FDA is now suggesting that soon this will become the norm. Pharmaceuticals, bio-technologies companies and many sponsors within clinical research are now better equipped to improve CDISC implementation.

Everyone should learn to code

Therefore, SAS® and XML are now cooperating. XML Engine in SAS® v9.0 is built up so one can import a wide variety of XML documentation. SAS® does what is does best – statistics, and XML does what it does best – creating reportquality tables by taking advantage of the full feature set of the publishing software. This conversation can produce report-quality tables in an automated hands-off/light out process.

Standards are more than just CDISC

If you are looking for your next career in Clinical Data Management, then SAS and CDISC SDTM should land you into the right path of career development and job security.

Conclusion: Learn the basics and advanced SAS clinical programming concepts such as reading and manipulating clinical data. Using the clinical features and basic SAS programming concepts of clinical trials, you will be able to import ADAM, CDISC or other standards for domain structure and contents into the metadata, build clinical domain target table metadata from those standards, create jobs to load clinical domains, validate the structure and content of the clinical domains based on the standards, and to generate CDISC standard define.xml files that describes the domain tables for clinical submissions.

Anayansi Gamboa has an extensive background in clinical data management as well as experience with different EDC systems including Oracle InForm, InForm Architect, Central Designer, CIS, Clintrial, Medidata Rave, Central Coding, OpenClinica – Open Source and Oracle Clinical.

Disclaimer: The legal entity on this blog is registered as Doing Business As (DBA) – Trade Name – Fictitious Name – Assumed Name as “GAMBOA”.

Source:

SAS Institute
CDISC

How to Manage Sites and Users in InForm Trial?

So you created your first InForm Trial and now what? Before you can actually enter data into your trial, you need to set up a user management system which assigns permissions to different users in your system depending on their job “role”.

In InForm, this is accomplished by using a tool called ‘User Management Tool’ or simple UMT. This tool allows sponsor to manage sites and users once the trial have gone live. There may be many different user groups with different levels and ranges of permissions.

Creating an InForm Trial – UMT:

  1. Create your InForm trial in the UMT. I won’t go into details on how to actually do this and depend upon the contract agreement with the vendor (i.e. Oracle/PhaseForward); they will perform this task for you.
  2. Select Trial Version = latest InForm version (i.e. 5.0)
  3. Select Countries where this trial will take place
  4. Select Status. Each InForm trial has 4 main statuses.
    1. Fast Start = Pre-Go Live
    2. Fast Forward = Trial is now live
    3. Fast Lock = Trial is lock
    4. Decommission = Trial is completed/archived

Managing users and groups can be a tedious task but tools such as UMT makes them easier to manage.

Roles: Roles (e.g. CRA, PI, System Administrator, etc) are used to assign specific permissions to individual users or groups, typically to perform specific functions in the InForm system.

The system allows you to either manually enter a role or import using a template called ‘MUL’ or Masters Users List. If you decided to upload your rights and roles via MUL, the system will generate a log file. It is imperative that you check this file and check any errors before proceeding.

Once the roles have been added to the UMT, you need to approved them before you build your clinical trial. The system also comes with defaulted and approved rights and roles.

Another option available is to create what is called as ‘signature groups’. If you are familiar with Medidata Rave system, this is equivalent to checking the ‘Signature required’ box and setting the investigator signature in Architect project main page.

Common use of Signatures in clinical trials are at the form level (i.e. 1 signature per form or at the subject level or studybook = 1 signature per subject).

Item Groups: Items groups is used to overrides or restrict a particular user access to a form or field. This is equivalent to ‘Restrictions – View/Entry’ in Medidata Rave.

One good example of display override usage is the coding fields restrictions. If only Clinical Coders are allowed to view / entry data on those items, you will limit access to all roles but the coders role.

Here’s a snippet of the code in .XML:

<!–?xml version=”1.0″?>–>
<MEDMLDATA xmlns=”PhaseForward-MedML-Inform4″>
/*some other code goes here*/
<ITEMGROUP
GROUPNAME=”Hidden Coding Items”
GROUPDESCRIPTION=”Hidden Coding Items”>
<!– Insert ItemRef Names –>
<ITEMREF REFNAME=”PT_NAME”/>
<ITEMREF REFNAME=”HLGT_NAME”/>
<ITEMREF REFNAME=”HLT_NAME”/>
<ITEMREF REFNAME=”LLT_NAME”/>
<ITEMREF REFNAME=”SOC_NAME”/>
</ITEMGROUP>
</MEDMLDATA>

Two other important groups that you need to be aware of is the Query and the Report Groups. The former, as the name entails, allows a user to open, answer, reissue and close queries during the course of a clinical trial. The latter, allows a particular user to run reports.

For example, an Ad Hoc User can access Ad Hoc reports via Cognos. The roles associated to this group could be your project manager, Clinical Research Associate (CRA) or your Lead Data Manager (LDM/CDM).

Once you have completed your basic setup, you will need to prepare or cook those xmls files onto your clinical trial. The rights/roles we discussed needs to be in an approved status. You also want to make sure you ‘lock for QC’ or lock the trial to prevent anyone from making changes to already added sites/users.

Sites and Users marked for upload to InForm will automatically be cooked into your trial.

Last step we need to take is to generate the XML files by selecting the link ‘Generate InFormXML.’ Now, your UAT trial is created, your URL is set up and you are ready to perform User Acceptance Testing.

Remember to validate your XML files, especially if your clinical trial is running across several countries. I have found issues with foreign languages symbols or special characters entered in the UMT system. Avoid at all cost any special characters.

Source: User Management Tool Reference Guide from PhaseFoward

Your comments and questions are valued and encouraged.
Anayansi Gamboa has an extensive background in clinical data management as well as experience with different EDC systems including Oracle InForm, InForm Architect, Central Designer, CIS, Clintrial, Medidata Rave, Central Coding, OpenClinica, Open Source and Oracle Clinical.