Sunday, May 29, 2005
CDISC and Last Day
On The last day of PharmaSUG, Wednesday, I saw a presentation by Thomas Cox from SAS Institute on CDISC standards. Thomas described how SAS is committed to data standards in that they are very involved in data standards organizations such as CDISC. They are also continuing to develop new tools to address these needs. Most of Thomas’s presentation used the ODM as an example, but he also touched upon the SDTM which is closer to what is used during submission. He suggests how there will be a transition from submitting SAS transport file in version 5, to the new standard DEFINE.XML. This is a “machine readable” format this is also going to replace the DEFINE.PDF. The DEFINE.XML on the surface looks like a PROC CONTENTS of the data. But as Thomas demonstrated with the new CDISC viewer, it has more information. The structure of the data is organized by clinical domains and follows standardization rules. PROC CDISC will review some of these rules and generates WARNING messages alerting you of potential non standards. There are also hyperlinks within the DEFINE.XML that allows you to drill down to code lists, and actual transport versions of your data if you want to see the contents.

The support for XML continues to be developed as SAS v9 XML engine is more robust. Besides the updated XML libname data engine, there are new formats and informats to help handle XML. The PROC CIDSC also will assist in generating the DEFINE.XML. Currently, the PROC CDISC does produce DEFINE.XML for the ODM model but the SDTM is not yet production. Here is an example as to how you use PROC CDISC:
PROC CDISC MODEL=SDTM;
SDTM SDTMversion=’3.1’;
DOMAINDATA data=conform.ae;
RUN:
It does not perform the data transformation but if your data is in the right format, it will convert it to the DEFINE.XML which can be viewed by the CDISC Viewer. One feature which I was impressed by with the CIDSC Viewer is that it has the ability to drill down to the audit history of how a particular variable is derived including the name of the programmer and text describing how they derived it. The CDISC Viewer allows you to drill down and see an audit log of all the pivotal points of the decisions for any particular dataset or variable. From a reviewer’s perspective, this metadata will be very informative during an audit. The challenge may be how you would capture and enter this information. Since the
Sy/Validate tools automatically collect this audit history information, I thought it would be a great idea for it to feed this metadata directly into the DEFINE.XML. This will definitely be a good feature to be implemented soon. I also like the fact that he CDISC viewer can link to and view SAS datasets besides transport format. It will be a versatile multipurpose viewer.
This year’s conference was the “hottest” in record. It was also the most attended with 637 attendees. Next year will be held in Bonita Springs Florida where it was boasted as having milder weather since it is close to the beaches of the Gulf of Mexico. I hope to see you there next year.
Tuesday, May 24, 2005
9.2 and Outsource
I caught up with Wayne Hester today who was a Systems Developer for the Output Delivery & Reporting of SAS Institute. Wayne specialized in the RTF. Currently, there are no plans to support the MSWord (.doc) format but there will be continued support and further development for RTF. The new features being developed for SAS 9.2 is a new ODS engine for “tagsets”. Instead of the statement:
ODS RTF
It will be:ODS TAGSETS.RTF
Many of the features of the new tagsets are similar to the old ODS RTF engine but there are some enhancements. For example, there is more support on the control over the height spacing between lines. An example:
PROC TEMPLATE
STYLE PARKSKUP from PARSKIP / FONT= (“Arial”, 72 pt);
If there are so many variables and the output wraps around into panels, the new ODS engine has a better calculation algorithm to do a best fit of the panels according to the header and footer is displayed. There are also greater control over the use of styles to control font color, super script and special character.
TITLE “test *{style for ground=red *{super *{Unicode ALPHA}”;
In this example, the asterisk is the ODS escape character signifying the instructions for the style.
I spoke to Himesh Patel who was the director of Data Visualization on some of the development of ODS Graph for 9.2. Many of the statistical procedures that were had ODS graphics experimental for 9.1 will become production for 9.2. There were also three new PROC in SAS GRAPH. This included PROC GBARLINE, SGPLOT and SGMATRIX. The SGMATRIX generates multiple paned scatter and histogram graphs without the need to do a PROC GREPLAY.
There was also a new ODS Graph Editor that allows you to edit your graph after it is produced. It is an interactive editor which you can alter titles and highlight data points. Things that you may have done in annotate can now be edited in this fashion. The graph files in this case are stored in PNG format. There was also a new GRAPH Studio Designer which is going to be experimental in version 9.2. It generates nice PROC TEMPLATE code to lay out multiple graphs on one page.
Last year, PharmaSUG tried out a new format of doing a panel discussion on CDISC. It was a success so there was a few more panel discussion this year. I helped host a panel today on how outsourcing will affect SAS programmers. There were some questions on how offshore companies handle the time differences. Andrew Fagan did agree that there is some challenge in having an immediate feedback on questions from the whole team when they are on a different time zone. The audience asked if there are any specific guidelines or regulations from the FDA on outsourcing. There did not seem to be any one that knew about. There were also concerns on security of data. A solution that Marty Rosenberg suggested was to have the data stored on local servers and the outsource vendors log in remotely. As a whole, there were a lot of interest in this topic but people were very filled with concerns.
Monday, May 23, 2005
PharmaSUG Monday
PharmaSUG kicked off on Monday morning under the Arizona sun. I checked out Dana Rafiee’s hands on workshop entitled “Get Experience with New SAS Drug Development Software”. There were many features for SDD so only a subset was demonstrated during the workshop. From the client’s perspective, it is rather simple in that all that was needed was a web browser. However, the architecture was rather complex including a web server, along with an application server. There were plenty of components such as the implementation of WebDAV which creates libnames and remote lettered drives on the server. This allows programs to on the client machine to access data on the server.
Some of the features and capabilities that were covered for SDDS included: esignatures for security, all files organized and stored in folders, importing and exporting data, and version control with audit trail. Dana described that the goal for the workshop was to have users log onto SDD and use the data explorer. The users then wrote and executed SAS programs and applied some data importing and exporting. This is only a subset of the capabilities but it was what was possible in the short work shop.
I saw a presentation by Mr. Benze entitled “Risk Based Approach to SAS Program Validation” that made some good points. It was noted that if your SAS programs and computer system is not validated, problems and errors found can cause delays that can be costly for the sponsor. It also creates credibility issues that are difficult to quantify. There were references to Guidelines that strongly recommends that data being analyzed should be validated. The amount of effort that goes into validating a SAS program depends on the risk assessment that the program has. This can range from a simple peer review to a more formal requirements and test plan. It was also important for the SAS programs to be controlled to ensure completeness and accuracy.
I talked to Vincent DelGobbo who is a Senior Systems Developer in the Web Tools Group at SAS Institute. He demonstrated stored processes which is part of the Integrated Technology package. This allows SAS programs to be executed via a Java Servelet in a similar way to how SAS/IntrNet utilizes CGI to execute SAS programs. There seem to be more tools however since it also generates HTML front ends for you as a template compared to SAS/IntrNet which requires you to create all your own custom interfaces. It does this through the integrated technology themes using cascading style sheets to standardize the way front ends are generated.
I got a chance to catch up with Thomas Cox who was part of the XML Integration Team. There are new developments for PROC CDISC which has been in production since SAS 8.2. The data standards established by CDISC are constantly being updated so PROC CDISC is keeping up with the changes. What was new to me was the CDISC Viewer which is only now in beta. It looked a little like the SAS viewer that is available for PC SAS but it viewed define.xml files. This will be available as a free download from the SAS website. I was very impressed with its ability to have hyperlinks that exist from the columns from the define.xml file being viewed. If the meta tags in the define.xml has the proper HREF meta tags, it will display link to an external file similar to how a hyperlink in an HTML file. This is definitely something I plan to download and check out.
The PROC CDISC has support for the ODM version 1.2. However, it appears to have limited support for SDTM and SDS. Thomas explains to me that the XML expressions and schemas has not yet been defined fully for SDTM and SDS and therefore the PROC CDISC can not yet implement these features. SAS is putting efforts into keeping on the edge of all the standards that is coming out of CDISC.
I met Sara Holshouser who was one of the developers for SAS Drug Development software. I was intrigued by some of the new features which I saw from Dana in the morning. The way it organizes your SAS programs and data is similar to how windows explorer works. This is done with a hierarchical folder structure. The data viewer was very useful with features of performing some simple summary statistics. I like how SDD define certain libnames and certain constructs that may server specific as macro variables. SDD handles the management of this by resolving these macro variables to run on its server. The process editor also seems to be more refined from the earlier versions I saw from last year. It is now at version 3.0 with 3.1 in the near future. The process editor is similar to the display manager editor with color coding and all the nice features of accessing online help in case you forget the syntax of a particular PROC. There are plenty of features of SDD which I have not fully get a chance to see so I will probably try to catch up with Sara again tomorrow to learn more.
Opening Session
I flew into Phoenix Arizona this afternoon to attend PharmaSUG 2005. The Southwest captain said it was 104 degrees and climbing. We just happen to be catching Phoenix at record temperatures. The Pointe South Mountain Resort is quite a nice resort where the conference is being held. The opening session opened today at 6:30 and was presented by Nancy Brucken, Academic Chair and Susan Fehrer, Operations Chair. They shared the fact that PharmaSUG had a record number of registrations this year at 635 attendees. Andrew Fagan gave the key note speech tonight referencing a paper that was publishing on the FDA website regarding the FDA’s critical path initiatives. The paper is available on the FDA’s website published March of 2004. It outlined some of the problems which the FDA is seeing. It tried to identify solutions by changing both the process and technologies. There were no specific instructions on how things can should be fixed but it did recommend that vendors work together to come up with solutions.

One of the problems that the FDA has identified is that there was a dip in the number of drugs in the pipeline in recent years. It then identifies some of the potential causes to this problem. New technologies such as Genomics are too new and have not yet fully met its potential. The recent mergers and business developments also has an effect the number of drugs being developed. All the easy target for disease is taken and has been developed. The chronic diseases are harder to implement. There is also a focus on drugs that are block busters. The failure rate of drugs has not improved. Only 8% of drugs being developed ever reach to market. For Phase III trials, the failure rate is now at 50%. Andrew also stressed the point that standards are lacking and this is having an affect on the success of drug development. The FDA realizes that even they themselves are lacking standards within their own organization. This is internal to the FDA, not to mention throughout the industry. The FDA still does not have the ability to look across all studies they have reviewed. This is referred to as lack of “institutional memory”.
SAS is trying to address some of these challenges that the FDA has identified. They have solutions in the areas such as Micro arrays, involvement in standards such as CDISC. SAS is a corporate sponsor and is on the board of director. SAS is also involved in working with the ODM, AdaM and define.xml. SAS views that standards groups such as CDISC and HL7 to be critical to the re-engineering push at the FDA. Among some of the other tools that SAS is working on includes: PROC CDISC, CDISC Viewer, XML Engine, XML Map Extension, new SAS formats, CDISC SDTM metadata templates for ETL studio and SAS Drug development. SAS Drug development forms a frame work to provide a solution for a compliant environment.
Most of the problems which the FDA has identified can not be solved by technology alone. There has to be corporation between vendors and FDA. Other solutions involve further development and evolution of technology.
Nancy and Susan concluded the opening session by pointing out some themes for this year’s conference. Validation is a definite theme. Other themes include CDISC, standards and electronic submissions. It was a great opening session with lots of interesting information. It is getting late so I will sign off and will report more tomorrow… actually it is already Monday morning… later today.
Wednesday, May 18, 2005
CDISC SDS 3.1
I am looking forward to learning more about the development and implementation of CDISC at PharmaSUG this year. I was working on a client and was reviewing the standards for SDS version 3.1 right now. I recently updated my %cdisc tool (
http://meta-x.com/sydata/cdisc.html) which verifies data against the CDISC standards.
I decided to try to run my integrity check against the CDISC structure itself to see how consistently they are following their own rules. In most cases, they are adhering to their own recommendations. However, my check did reveal some inconsistencies. The report makes recommendations that CDISC may want to consider. However, I am not sure who to send these to. Last time, I posted on their website discussion but got no response. Let me know who at CDISC to bring these suggestions to.
You can find the report of my recommendations as a result of the %cdisc tool at:
http://meta-x.com/sydata/demo/cdisc.html
Saturday, May 14, 2005
PharmaSUG in one week
It is only a week out before PharmaSUG 2005 in Pheonix Arizona. I enjoy writing so it is always fun to write about what I learn at conferences like PharmaSUG. In past years, I gather all my notes and write on the conference a week after it is all over. This allows me to let all the information soak in and for me to share with friends what I found useful. You can find some of previous "Sy/Notes" located at:
http://meta-x.com/synotes/I thought I would try something new this year. I would write an blog instead. This will be more immediate in a sense that the moment I learn something new at PharmaSUG, I will post it right away. That way, you will beable to learn about the conference as it is happening. I will bring my digital camera too to see if I can upload anything interesting.
I hope there is good internet connection there in Pheonix so I can do a daily (if not more) posting. Blogs can be more interactive too in that you can add comments and forward to other friends. Please send me or add comments on the blog. This is the first year I am trying this out so any feedback you may have is appreciated.
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