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Showing posts with label ODM. Show all posts
Showing posts with label ODM. Show all posts

Friday, October 30, 2009

CDISC Rules!

Ok, so a play on words. CDISC may rule in the field of Clinical Data standards, but, it does not rule in the standardisation of rules associated with data.


Let me expand here for those not familiar with the issue.


CDISC ODM provides a syntax for the definition of metadata (and data) used in the interchange of information between (and sometimes within) systems. CDISC ODM does not scope the definition of edit check rules that are applied to the data when it is captured. I feel that is a significant omission as the rules element of the data a) take a considerable time to develop and b). provide a context to the data.


Question - So, why do we not already have rules built into the standards?


Answer - rules are often technology or vendor specific. There are almost as many methods of implementing rules, as there are EDC products.


Question - Why not define a standard mechanism for creating rules that vendors could either comply with, or, support as part of interfacing?


Answer - Well, it all depends on what you want the rules to do. In their simplest form, rules are boolean expressions that result in the production of a Query or Discrepancy. However, many systems go well beyond simply raising queries. The boolean element of the rule may be consistent, but the activity performed in the situation that the boolean returns true, is often very vendor specific.


Lowest Common Denominator


So - lets assume that we are looking at implementing a lowest common denominator of rules and actions that the majority of systems support, and require


What can we do to standardize a syntax. Three options I think;


1) Choose a syntax from one of the leading vendors,


2). Develop a new syntax building on existing ODM conventions


3). Bring in another standard syntax, potentially already in the Health or LifeScience field


Lets look at them in order.   


No. 1 - Choosing a Leading Vendor Syntax is probably great for the chosen leading vendor, but, bad for most other vendors. A benefit though would be that it would already be proven as a means to represent rules and actions in a clinical study. Some syntaxes are based around standard tools such as Visual Basic for Applications, JavaScript or even SQL. This approach may create almost insurmountable boundaries for other vendor systems that do not, or cannot implement the technology - for example, it is not easy to interpret VBA on a non Microsoft platform. So - option 1 has some potential, but, depending on the chosen vendor, may result in closing the door to the standard for others.


No. 2 - Creating a new Syntax would result in something most vendors would be happy with, but, would require considerable effort from the contributors in order to develop a complete specification for the standard, as well as a reference implementation. The advantage of such approach would of course be that it would be seen as a common standard open to all, and not specifically biased to any one vendor company. In practice, the technology approach chosen would favor some more than others.


No. 3 - Leverage an existing Syntax may well bring the benefits of No. 2 without all the costs of designing something from scratch.


Ok, so lets say we go ahead with option 3 - what are the candidate standards for rules in the Health and/or LifeSciences are?


As far as I can tell, not many. In fact, I was only able to find one candidate that had any level of success - a syntax called ARDEN.


ARDEN has existed since 1989 as a syntax for describing Medical Logic. Similar to typical Rules in EDC, they are defined in Modules - Medical Logic Modules - and called based on the triggering of an event.


[For an accurate definition of ARDEN and its roots, check Google Books - search for ARDEN Syntax and examine Clinical knowledge management: opportunities and challenges By Rajeev K. Bali, Pages 209 --> 211]


As a syntax, it is mostly general purpose. Here is a snip from an Arden Syntax module,




logic:


if


last_creat is null and last_BUN is null
then


alert_text := "No recent serum creatinine available. Consider patient's kidney function before ordering contrast studies.";

conclude true;

elseif


last_creat > 1.5 or last_BUN > 30
then


alert_text := "Consider impaired kidney function when ordering contrast studies for this patient.";

conclude true;

else


conclude false;
endif;

;;




In the example, you can see that the syntax uses standard if/then/elseif/endif constructs. Assignments use the := combination etc.


HL7 have a section dedicated to ARDEN here. The activity appears to be limited with no Postings or Documentation since 2004. On walking through some of the presentations, some of the consumer companies such as Eclipsys were proposing extensions to the syntax - for example to add object definition support. It would appear that the take-up of the standard has been limited to those organizations that had a problem to solve in the EHR area, and wanted to re-use a syntax, instead of inventing their own.


The fact that HL7 has lended support for ARDEN may be sufficient in itself. However, we would need to dig considerably deeper to understand how ARDEN syntax would fit with a syntax such as ODM. The first challenge is the conversion to an XML form. There are plenty of articles on ARDEN XML for further reading.


RuleML is another standard that may address the need to create Rules, as well as meeting the perceived need of being XML based.


More about ARDEN and RuleML in a later posting I think. This one is quite long enough for today.



Thursday, November 13, 2008

CDISC SDTM versus ODM?

I have read with great interest an article posted in ClinPage - The Future of ODM, SDTM and CDISC.   These discussions relate primarily to the proposed requirement from the FDA for data submissions to be made in XML format rather than SAS Transport file format.   I don't think we will see many arguments around this point - XML is now the accepted extensible method of describing the combined data and metadata.  What is more contentious is that it is requested that data be provided in the HL7 v3 Message format.  FDA Docket No. FDA-2008-N-0428 from August 2008 elaborates on where the FDA are in the process.

In addition to the move to an HL7 Message format rather than SAS XPT, commentary exists on a suggestion that a move to ODM rather than SDTM would be considered.   This point is also put forward by Jozef Aerts of xml4pharma.

I would like to comment on a comparison of SDTM versus ODM.

Operational Data Model

ODM was the first CDISC standard to successfully go through the authoring process.  It was aimed as a means to represent data in to context of data capture. Data was indexed to Visits and Forms. The syntax was designed to describe data not from an effective storage format, but from a source to destination format.  You could get data from System A by Visit and Form to System B by Visit and Form.   This is great where the presentation of the data has importance and meaning.

Submission Data Tabulation Model

SDTM, unlike ODM, focuses on groupings of data - not by CRF Form - but by the use of data.  All Demographics information appears on the same record for example.  The SDTM structure has now also become the basis for data delivery and storage within many organizations.  A number of large PharmaBio companies based internal cross company standards on SDTM.

Modelling from Data Captured

The format of data will differ depending on the medium used to capture the data.  Some form factors might have 30 questions on a form, others such as Patient Diaries, might only have 1 or 2 question per form. In addition, when designing a CRF for ease of use, it may not make sense to apply the content of each SDTM domain as the basis for deciding what does and does not go onto a single form. Whether the data appeared on one form, or across many forms is not important when it comes to the value of the data.  Many EDC vendors have gone down the route of designing the database for data capture according to EAV rules - Entity-Attribute-Value form - where each value captured on any form is dropped into a single table. Once captured, data is then re-modelling into a relation structure that may or may not model the layout of the page. (xForms is a generic technology touted as being a potential means of addressing this challenge - I will leave further discussion on this to a later article).

Based on the above, it would seem logical that SDTM is of greater value when used as the method of delivery of data for submission or analysis than ODM.

However, that is not the only reason why SDTM makes sense over ODM when developing and executing eClinical studies.  The primary reason related to metadata re-use.

ODM is not a suitable format for modelling studies because it does not lend itself to ensuring that similar studies are able to effectively re-use metadata.  Sure - I can take a study, copy the metadata, and I have another study... easy... but what about changes.   What if I remove a few fields, add a few fields, change the visit structure. That will of course change the data outputs format if ODM was the format- an issue - see above, but, more importantly it will greatly impact any rules that might exist on the forms.  Rules that use some form of wildcarding mechanism may, or may not work.   Anyway, this is not a posting on metadata architecture, so I will leave it at that.

Bringing together SDTM and HL7 v3

So back to SDTM and HL7.  Is this the right way to go?   I can understand the logic behind this.  Being able to bring EHR and Clinical Trial data together within a common standard could be very useful.  However, at what cost?  

I am not aware of any eClinical application that automatically creates SDTM compliant data sets - regardless of transport layer.  The mapping of proprietary metadata to SDTM is quiet involved with varying degrees of software development required from the various system vendors.  Typically, either SAS macro transformations are used, or, some form of ETL (Extract, Transform and Load) Tool.  This is all complicated enough. Creating a tool that creates SDTM datasets in HL7 v3 is considerably more complicated. Even for large companies it will be a major development under taking.  The complexity is such that smaller companies will simply fail to manage to effectively deliver the data in a cost effective way.

Tools providers may step in - they may offer a means to convert a basic SDTM ASCII file with additional information into a SDTM HL7 v3 file. XML4Pharma as based on recent critique of the approach do not appear to be wishing to jump into supporting this, but, if this becomes a mandate, some companies will.

Playing on the other side of the argument - one of the principles of XML is that the data is also human readable.  In reality, once you add all of the 'overhead', especially with a complicate syntax such as HL7 v3, you end up with something that is only readable by technical gurus.  But then, maybe it shouldn't be people that interpret these files, maybe the complexity has got to the point where it only makes sense that a computer application interprets the files and then presents the appropriate information to the user.  Modern eClinical systems offer views on data. Maybe the presentation of the Submission data is managed in the same way - through an application that presents a view based on purpose.