HSR&D Cyberseminar- 17 -Department of Veterans Affairs

VINCI Data services, February 27, 2012

**VINCI Data Services**

**HSR&D Cyber Seminar**

**February 27, 2012**

Moderator:  And we are at the top of the hour, so I would like to introduce our speaker.  From VINCI speaking for us today is Hamid Saoudian.  He is a software engineer manager.  Hamid has a bachelor’s degree in both civil engineering and computer science and a master’s degree in civil engineering.  He has been with the VA for almost three years as the lead data manager of the VINCI program.  His experience includes twenty years as the software engineer manager and lead architect for Salt Lake City Corporation.  We are very thankful to have Hamid sharing his expertise with us today.  If you’re ready I would like to turn it over to you at this time.

Hamid Saoudian:  Thank you.  Good morning everybody.  Happy Monday morning.  As our host mentioned I’m—my name is Hamid Saoudian and I’m doing this presentation from Salt Lake City today.  That’s where most of the VINCI staff are located.

We... back in October we did a series of presentations on VINCI and hopefully they were helpful for you in getting to know more of VINCI and what services VINCI is able to provide you in helping you do your VA research work.

Today’s presentation we’re starting another series of presentations, hopefully to reinforce some of the ideas that we introduced back in October and also be able to build on top of those and also tell you a bit more about what has been done since that time and again, help you get to know more about VINCI and what we’re able to offer you.

So—hopefully at this point you can all see my screen.  

Moderator:  Yes.  You’re coming through just fine.  Do you have it in slideshow mode?

Hamid Saoudian:  Yes.

Moderator:  Great.  Go ahead.  Thank you.

Hamid Saoudian:  Thank you.  So VINCI—again, VINCI stands for VA Informatics and Computing Infrastructure.  And let’s take it quick look at—okay—it’s—okay.  Let’s take a look at today’s agenda for this presentation.  I’ll begin by doing a quick review of what is VINCI for those of you who may not have used VINCI in the past or not even heard of VINCI in the past.  It will let you have at least a quick understanding of what VINCI is.  From there I’ll talk briefly about VINCI data and our previous presentation—we talked in much more detail about the data that’s available to VINCI.  Today I’ll just mention the available data very quickly and from there we get into VINCI data services which is the primary topic of today’s presentation.

From there we’ll tell you a little bit about what enhancements and their new features we are planning and then we’ll take any questions that you may have at the end.

So VINCI was established to be a secure analytical workspace for VA researchers.  It is made up of many high very high performance servers.  Top of the line—for example some of the servers that we have are sixty four nodes up to two terabytes of ram and they’re basically in short—top of the line, best servers that money can buy these days.   All this hardware has been assembled to help you do your research work.  We have very large capacity for data storage.  There are a number of tools available to help you do your analysis work and all of this is available in the form of a remote desktop connection where you remotely connect something similar to a cloud computing and you remotely use these services on the servers and the storage to be able to do all your analysis work.  And all of it—and no direct cost to you—the—the VA funding using the VA funding we’ve been able to put together this program and all of this is for you to use. 

And in addition to all the hardware and software of course we have a set of staff both in Austin and Salt Lake City and other locations to assist you in utilizing VINCI.

A quick look at the data center of Vinci.  It’s located in Austin, Texas.  Like I mentioned many high performance servers, hundreds of terabytes of storage. In high performance SAN form.  We have recently improved our networking between the servers with new—with a new switch and that work is going to continue to hopefully improve some of the networking performance issues that we’ve had in recent past.

We have a dedicated set of system administrators in Austin that are in charge of keeping up these servers and maintaining them and getting the best performance out of the hardware that we have available to us.

If you work in the VINCI environment, all of your data; all of your work is regularly backed up and achieved in a safe and secure manner.  That’s another advantage that would be available to you by using VINCI.

Taking a quick look at the VINCI software, mostly focused on analysis software, of course.  Having access to large data sets.  Most of the data is stored in SQL server.  There are a number of different SQL servers available for data storage—your data that you may bring in as part of your project and data that we would be able to provide you.  There are a number of different analysis software available.  On top of the list is of course SAS which is one of the most popular data analysis software available with the SAS installation that we have which is currently on a very large server including the large server we have a unique installation of SAS grid which is made up of ten different servers and provides a very high capacity—high performance platform for doing SAS analysis work.

In addition to SAS, we have data, SPSS as a number of other analysis software.  We offer the whole suite of Microsoft office tools available in VINCI.  We have other publishing software available there so when you come in and use VINCI you can do all of your analysis work and also at the same time be able to put together documents for publishing using all the tools that are available to you.

In addition to all the third party tools that we have in VINCI.  In VINCI we have software developers that are building tools to help VA researchers.  Amongst those is the NLP setup tools and there’s currently a NLP package that is available to all VINCI users to be able to do natural language processing on the data that you have available to you in VINCI.  At the same time if you have a need for other software that we don’t currently offer and VINCI again, depend on on the availability of funding, we would be able to purchase additional software for you to be able to use as a part of your project.

Let’s take a quick look at VINCI data.  So we have hardware.  All the tools and software that you may need.  Of course, a big part of data analysis is having access to data and we believe VINCI provides the largest collection of available data sets for research work in the VA.  VINCI is a partner or a subgroup of DW, the corporate data warehouse team.  And we have access to all of the data available through CDW that we can make it favorable to a VA researchers.  The largest bit of data that’s available through CDW is their production data which includes many different domains including vitals, pharmacy, lab, and then and a long list of other domains.  CDW just recently completed basically building a—I believe it was twenty domains in eighteen months so they were recognized for that accomplishment.  And they are working every day to bring in and provide additional data domains.

In addition to the production data from CDW we also have access to what is known as CDW raw which is to be able to quickly get snapshots of other data domains that are not available in the CDW production data set.

That may—that has been very helpful to VA researchers and our teams.  One of the largest data sets out there is the TIU data set, the Text information the clinical notes and through this CDW Raw we’ve been able to so far get two different snapshots of that data and right now the CDW team is working on extracting a new snapshot of the TIU data for us.

Radiology, allergy and several other domains are also available through the CW Raw mechanism.  Again, quickly the difference between raw and production—the production data is updated nightly and the raw data is basically a snapshot of the data at the time of the extraction.  Depending on the data and the needs of the users those snapshots are updated as needed.

In addition to the data from CDW we also have DSS Data, all the DSS NDEs and they’re available in both SAS and SQL Server format.  We also have all the Med SAS in SAS and SQL server format and the vital status data again in SAS and SQL format.

That’s a quick look at all the different data that’s available to us that we can make available to the VA researchers.  With that as an introduction to VINCI and VINCI data let’s take a quick look at the rest of the data for today’s presentation which is on the VINCI Data services.  We’ll talk about the different modes available to VA researchers to ask us questions or ask for data.  All the different types of things that we can do for you that—the security of the data—the forms of the data that we can make available to you and how we can make it easier for you to work with that data and understand the data and take advantage of the data that’s available.  So at the top of the list there, is what we call data needs assessment and this is where you may have an idea about a research project that you may want to consider but you’re not sure if the data is available to you to be able to do that analysis or you may want to just take a quick peek at what maybe available and how you may be able to use it. 

As you all know, access to the data is basically controlled by national data systems.  And you would have to apply for access to the data through national data systems, but prior to that starting that process, you may just want to get a feel for if you have sufficient cohort size for your study or what types of data are available.  Maybe have somebody run a couple of queries for you on the data, get some summary information back so this is the mechanism that we can provide you that service.  You can contact VINCI and submit your question, maybe the criteria that you might want to use to select your cohort and be able to see how many patients are in the cohort criteria that selection criteria that you have in mind and if it’s sufficient to start your project.

So we can do that work for you.  You can submit your question and we can run those queries for you.  This has been an increasingly popular form for VA researchers to use VINCI and we try to do the best we can to answer all the questions and at this point, it’s our strategy to continue that service.  We believe it’s a very useful and helpful service to researchers out there.  Of course then to help you understand the data we have a bit of documents that fully describe all the data and we encourage you to refer to the documentation first before submitting your question and hopefully the documentation will be able to provide you with the answers that you need.

I should also mention that there is a great service available through VIReC and VIReC has traditionally been in charge of providing VA researchers with the help they need to get started on using VA data for research and they are going to continue that service so we also encourage you to utilize VIReC resources for answering your questions and then getting help on the data.

Aside from the data needs assessment you went through this data needs assessment and you may still have some more questions and at this point you want—before you start your actual project you want to have access to some real data and even be able to use VINCI to do some preliminary analysis for us, let’s say.  The mechanism available to you for that is what we call preparatory to research work and here you apply for that type of access through NDS which grants you basically the permission to be able to work with real data to actually work with data and also have access to summary data, aggregation data through VINCI.  So once you’re granted that type of access then we create a database for you in VINCI and you are given a complete workspace in VINCI which includes file shares and all the tools in VINCI, so you’re able to easily come in and take advantage of database services and all the analysis tools and storage services of VINCI all in one place.  At the same time the VINCI data staff will work with you to answer your questions or prepare aggregates of the data for you.  So that is a great service and several research projects have opted to use that service to date.

Moderator:  Sorry to interrupt.  I have a quick clarifying question. Somebody just wrote in and said what was that resource?  Was it VIReC?

Hamid Saoudian:  Yes.  VIReC.

Moderator:  Thank you.

Hamid Saoudian:  And they have an extensive website.  There are a lot of documents available on VIReC regarding the data and how to get started with your VA research work.  We strongly encourage folks out there to continue to use VIReC as basically to get started with their VA research work.  There are a lot of helpful documents on their website and they have staff to answer your questions as well.

So after that—after you’re granted access to the data and you may and this has been our experience, some of the studies have—they come in with their own cohort list.  There are some that don’t have a cohort list.  And they basically have some inclusion exclusion criteria’s in mind to basically create the cohort for them.  And their selection criteria may involve multiple domains.  So here’s another service we provide to the research teams in basically developing that cohort list for them.  We work with you; you can submit to us the various criteria that you have in mind.  We develop queries based on that—based on your criteria to create a cohort list that you can then use in your study.  So following that process, let’s say you bring in your cohort or you develop the cohort list for you then we get to the actual data extraction.  Here we have a team that will work with you.  We assign an individual to your project that will work directly with you or your team to basically extract the data that you need and make that available to you in VINCI.  To be able to do that, we have developed a basically a communication mechanism which we call the correspondence site.  It’s basically a way for us to keep track of all the correspondence between our team and your research team.  And have a complete record of the information that you submit to us so we can use that information to extract the data for you.  And o this side, we also store all the documentation—any additional documentation that you may provide us to do that data extraction.

Here’s a quick view of that sample from the website—it’s the SharePoint site where we can submit messages in our team and your team is also able to submit messages and every time a message is submitted the other side gets an alert that a message was submitted that requires somebody to go in and take care of that message and respond to the request.  It also have the space for basically storing all the documents for that study and all the members of your study team and our VINCI data team have access to this site.

So a little bit more on the data extraction process.  We work with you and we ask you to fill out these forms basically that would help us more closely identify the data that you need—all the different primers that you need—the data sets are made up of SQL server tables.  We ask you to identify the data that you need, the fields that you need, the tables that you need.  Also the selection criteria for that data.  The ultimate goal here is to essentially provide a lean dataset to you that provides only the data that you are interested in other than additional data that may just get in your way or old data that may make your analysis work more difficult.  That’s a primary goal of course from the VA standpoint and the security standpoint it is a goal to only provide the data that’s necessary for the VA research project, not more and then thereby minimizing the some of the risk associated with basically having this data out there.  So it serves both sides, we believe.  And of course all this data will be made available to you in a SQL server database dedicated to your project and any additional analysis work that you want to do you’d be able to do that on the dataset that’s available to you.

I should, at this point mention that VINCI and all its services are available to you even if you don’t plan to use any data through VINCI.  You may have your own dataset that you want to bring in and be able to do—just utilize the hardware and the tolls available in VINCI.  We encourage you to use that—the great services.  It’s free.  It’s out there for you to use.  If you have your own data you can easily bring in all that data and take advantage of all the tools in VINCI.

So aside from all the data we’ll provide—we can provide to you—we can provide this data in various formats and I mentioned SQL server but we can also convert that data to staff if you need it and staff files or other form—file formats as needed.  We also work with you depending on how you intend to use the data to be able to add indexes to the different tables, to be able to better tune the performance of the queries that you may be run in on in the data sets and help you perform the work that you do in a more efficient manner.

And again I’m going to mention the security basically aspect of this—only your team and our VINCI data team have access to the data that’s made available to you.  All the different VINCI studies, all the different research projects, hosted on VINCI are kept totally separate from a security standpoint and there are no cross permissions between these different datasets.  Your data is fully secured and protected in VINCI.

One of the other services that the data team provides—I mentioned the raw data sets that we have access to through the Corporate Data Warehouse.  In many instances, the raw data comes in basically as raw data.  I guess that’s why the term raw is used for that dataset.  It’s basically it’s unclean.  It’s not standardized.  The data types may have been selected to facilitate the extraction process without running into any errors.  So in many instances, the data types, the data field names may not be in the form that would be suitable for end users.  So we go through this process of transforming those datasets into what we call a clean format.  We standardize the names, the data types and we also add indexes to the tables to basically make queries more efficient.  We also may add keys for joins between the table to make that process more efficient.  Another service that we provide is the data description documents.  I briefly mentioned that at the beginning of the presentation.  We have a complete set of documentation on all the different data domains that are provided through VINCI and if you like to learn more about the data that’s available through VINCI this is probably the best place to start.  These documents are available on VINCI’s website and you can go in and download those or just look at those directly online and they give you a hopefully give you a good understanding of the data that’s available and they describe each domain and each table within the domain and also a good description of the field and with the basically a reference back to the [inaudible] data that’s basically to original source of all the data available in VINCI.  Here’s a quick screen shot of the data description document that’s basically a—there’s a menu on the top where you go in and select the different domains that you want to look at and then the document itself that comes up after the selection.

The last thing that I want to mention as far as the services provided through VINCI is the new system that we’ve put in place a few weeks ago with the increasing number of projects that we have in VINCI, data request projects we needed a system to be able to track these projects so we put together a quick project tracking system to help us keep track of all the projects, the status of these projects, what data has been made available to each project and also who is working on a project, how much time do we spend on a project and this is helpful for us from a management standpoint to keep track of all the projects.  At the same time it can be a helpful source of data for the research teams.  We can make this data available to you if you have a need for it.  We can tell you how much data has been extracted for your project and which domains were used, the number of records in each domain and each dataset so we can make all that data available to you as well.  It also from a management standpoint it creates a number of reports that would help us more efficiently manage VINCI as a project as a program.  Here is a quick screen shot of a couple of the screens in that project tracking system.  And I’ll quickly show you a couple of the reports.  This one should give you a good feel for how the number of projects over time are increasing or we’re seeing an exponential increase in the number of projects that we are serving.  At the last count, I believe we’re right around 170 projects so far that we have served data to in VINCI and just looking at this bar chart should give you a good feel for how quickly the number of projects are increasing. 

This next chart shows the number of records that we have provided to research projects and I believe that last bar in the chart is for the most recent quarter—it shows something over twenty billion records that were extracted and made available to the research projects.  Any of the research projects that we’re seeing as of late have been asking for large sets of data which VINCI at this point seems to be really well suited for that type of projects due to the high capacity that we have both in terms of data storage and analysis capability.

At the very end here, I just quickly want to mention a set of new initiatives, ideas that we’re pursuing at this point to basically add to the services that we’re currently providing or enhance those services.  We are trying to build a new knowledge base-basically a place where we can store all the information regarding the data to help researchers understand the data better and the issues that we may find that we think would be helpful for end users to know.  We would also make this knowledge base open to all of you as end users where you can share your experience and your knowledge about the data with others so that we believe this can be a great mechanism to share all that information and then we’re hoping to bring up that knowledge base online over the next few months.  

We are another initiative that we’re considering is starting to work on cleaning and standardizing the data.  Much of the data that comes through CEW is basically a copy of the data that’s in the VISTA system and CEW production is that’s the data is modeled and optimized for a data warehouse system, but still the data is can be improved and then better standardized.  Many of you may know who have worked with the data a lot of duplicates or various ways of spelling the same lab test for example so we’re hoping to be able to standardize that data and then clean that data to basically make it easier for you to use the data as we understand many of you after we provide the data to you you go through this exercise of cleaning the data, standardizing the data every time for every project you do.  So we’re hoping to be able to do this work once and make that available to you in a cleaner form and saving you some time.  The other ideas that we’re working on is creating—we’re calling it this point a “Less identifiable” data set.  

As you know the VA data includes all the patient identifiers that social security number, name, address and so forth.  For many of the projects that you do—you don’t really need that data.  You’re more interested in the clinical data and not necessarily patient identifiers so we are at least considering at this point creating a less identifiable data set and thereby making it easier for you to basically get access to the data quicker, and so hopefully—we’re hoping that that would make the data access review process quicker and be able to basically get access to the data more efficiently faster to basically reduce the time that you spend waiting to get access to the data.  Of course, with all this data, there’s an increasing need for metadata and there’s a lot of work that we can do in providing more data about the data and developing data profile reports of all the data that’s available to help you understand the data better.  Along with that we’re also considering creating some analysis cubes to help you do your analysis so you don’t’ have to spend so much time crunching through these large data sets to get what you want and then create some canned reports on top of that idea reports so you can get a quick view of the data or the trends in the data, maybe some frequency reports to help you understand and take advantage of the data easier.

Of course I mentioned VINCI’s software development initiative—that group is working on a number of various ideas to develop cohort selection tools and basically query tools and once those are—I’ve seen some basically samples of those projects and then previews of those projects and looked very promising.  Hopefully when they’re made available to you and they will help you in querying the data faster and easier.  So that brings us to the end of the presentation.  We have a poll question.  I just went over some of the ideas that we have for making enhancements and improvements for VINCI to a VINCI data services for you.  We just want to get some feedback from you on what you think are some of the things that we can do—I’ve lifted some of the items that I just mentioned for improvement.  If you think those are important for you—if they are helpful to you, please let us know.  I think with this poll question we only have the option of having five choices there, so that’s why this list is a little bit shorter than all the items that I just mentioned.  If you have any ideas of your own that can—that you think are things that we can do to help you better, please let us know.  So with that, that’s the end of our presentation. 

We’re open for question and answer at this point.

Moderator:  Thanks Hamid.  I have opened the polls and people are responding.  We’ve had about half of the attendees respond so I’m going to leave it open for a few more seconds and let everybody have a chance to give their opinions.  We do have a lot of questions that have come in.

Hamid Saoudian:  You should mention on this poll that you can—you’re free to select more than one.  You’re not bound to select one.  You can select one or more or anything else that you want to add.

Moderator:  Thank you.  The answers are still coming in.  So we’ll give it a few more seconds.  When I close the poll I will share the results with everyone and it means you can talk through it real quick or we can move on to Q&A.  We’ve had about two thirds of the people vote so I’ll give it a few more seconds.

And as the bottom choice says, if you have something else you want to specify just open up your Q&A and you can put your answer there and I’ll be sure to pass it along to the VINCI folk.

Okay the answers have stopped coming in. I’m going to close the poll.  I’m going to share the results with everybody and there you go.  You can see those, correct?

Hamid Saoudian:  No.

Moderator:  Now you should be able to see them.

Hamid Saoudian:  Okay.  Great.  Yes.

Moderator:  I’m going to turn it back over to you, Hamid and your screen and we will go ahead and start the Q&A portion now.  Do you have anyone joining you for the Q&A?

Hamid Saoudian:  Yes.  Let me take a quick moment and introduce them, the folks that are here now.  Of course from our—we have most of our data team here and these are the names.  Some of them should be familiar to you.  They’ve worked with our team.  We have Alan, [inaudible] we have Evan.  We have Suga and we have VINCI program manager Troy Barrett also present.

Moderator:  Great.  Thank you.  Getting to our first question, Hamid, can you accept the screen share again, so I can see my question list?

Hamid Saoudian:  Did that work?  

Moderator:  No.  Go ahead and press accept.  We can get started.   The first question that came in are radiology reports and radiology orders available in CDW?

Ki Win:  This is Ki Win from data team and radiology report is available in CW Raw data and order we have radiology medicine order.  I’m not sure if this is what we asked for, but we have that in the radiology, too.

Moderator:  Thank you.  The next question that came in—is—how frequently is the data ID backed up?

Hamid Saoudian:  Data ID.  I’m not sure what the they mean by data ID, but the CW production data each record gets a data warehouse ID number but we also maintain all the original identifiers from the VISTA system both in the raw dataset and on the production data sets.  I’m not sure if that answers the callers question, but if they want to send us an e-mail, if we can answer their question—they can send us an e-mail VINCI@VA.gov and we can hopefully better answer that question.

Moderator:  Great.  Thanks.  I do just want to make a quick note before we move on all of our attendees when you exit the session at the end you will be prompted to complete a quick survey—just a little feedback.  Please do take a moment to answer those few questions as we do.  These are feedback to inform our future sessions.  The next question—will your infrastructure match that of online—on live desktop or Apple I-pad, they have a one gigabyte internet and can download 20 megabytes in a second.

Hamid Saoudian:  As I mentioned we’ve recently made some improvements to the VINCI network, amongst the VINCI servers that I should also mention that VINCI has hosted within the AIGP data center and we’re bound by some of the limitations of that data center, but the data center folks are constantly working on improving their facility and I know that is a concern for the folks running that data center and the VA as a whole.  So I guess to answer that question, VINCI as a program is going to do what it can to make improvements in the capacity and the bandwidth that we’re able to provide to the end users, but again we’re bound by the larger VA network.  Many of you are at various sites connecting to VINCI remotely and the performance that you may see depends on the connection of the local facility that you’re part of to VINCI.

Moderator:  Thank you for that response.  The next question—we have a comment that came in.  This was fairly early on in the presentation.  There is a big problem in using the lab data.  Lab values and names exist in the database just as they were created in individual VA facilities.  Researchers may want to study glucose levels for example and there are 2000 different names of glucose tests.  We’ve obtained an actual list.  Comments there.

Hamid Saoudian:  Yes.  That’s definitely a problem that we have realized and is pointed out in many research teams have to deal with this—this is where we talked about the cleaning the data and standardizing the data—the VISTA system basically was implemented as a set of independent platforms out there at each VA site and each VA clinical facility and as such there were no central coordination between the different systems.  We are working with corporate data warehouse and as far as considering ideas for doing that type of work but the VA itself is also working on initiatives to better standardize and clean up this data.  So it is definitely a problem of we’ve seen and recognize and will be working with other folks to hopefully remedy this and come up with solutions.  At the minimum, we think we can provide you with routines that will help you basically clean this data or standardize the data once it’s given to you.  So if we’re not able to clean the data for you, we’ll provide a set of routines and I know not only our team is working on that, but there’s another initiative as part of the VINCI program in trying to develop a set of routines to make analysis work easier.  And once that becomes available it should be of great help in cleaning the data and standardizing the data much beyond just cleaning up duplicates and so forth.  We’ll keep you updated on the progress of that effort as we continue to work on those.

Moderator:  Thank you for that response.  The next question, do you have End Note Software?

Hamid Saoudian:  Yes.

Moderator:  Excellent.  Next question.  What is needed for VINCI staff to develop ways to make identification of commonly used tests more convenient for researchers?  Is this possible and who should we work with.  This could help lots of investigators so each group doesn’t have to reinvent the wheel.  If you’ve covered some of these things.

Hamid Saoudian:  We’ve covered that and like I said, we’ll continue to work on that with coordination.  Hopefully we do realize that this is a very big problem and there’s a lot of time wasted by every group going through the same process.  We hope to remedy that situation.

Moderator:  Thank you.  The next question, can we have access to freeware?  Free software through VINCI?  What is the process?

Hamid Saoudian:  I—um.—Part of the some of the times that I mentioned I should mention that there’s the VINCI standard workspace and a VINCI devilment work space.  The development workspace we can make available to you a server that where you can bring in your own software, freeware.  Of course we run that through a process to make sure that it meets the security standards of the VA and VINCI and to make sure it doesn’t cause any problems for other users, but after that profits, you’re free to sell software that you develop or others have developed to do your analysis work.  You would also be able to use that environment to do actual development of new teams and software to help you with that project.  There’s a dedicated environment that would be made available to you to do that type of work.

Moderator:  Thank you for that response.  The next question that we have how do we request software purchases?  What is the timeline for these purchases?  If this isn’t your expertise, feel free.

Tory:  This is Tory.  I’m the program manager for VINCI.  We are funded to be able to provide software as needed by the research community.  The issue of course is the timeline for procurement.  They have to go through the standard procurement process that happens for everything within the VA and sometimes that can be months, but yes, the easiest way to request software is to simply send an e-mail to VINCI@va.gov and someone from the staff will contact you about the requirements on that software and what a timeline and possibility for purchase might be.

Moderator:  Thank you for that response.  The next question if a researcher has access to VINCI data, does he still need to access to mainframe accounts separately?

Hamid Saoudian:  Yes.  The mainframe access and the VINCI access are basically different permissions, but they’re both handled through NDS.  As I mentioned a large set of what is available on the mainframe is now available through VINCI data, [inaudible] status, but there’s still data on the mainframe that is not available through VINCI and will continue to work in bringing in some more of that data to VINCI to make it easier to get access to more data all in one place.  The answer is yes you need two separate permissions.

Moderator:  Thank you for that response.  The next question, MEDSAS and DSS data are the same as that with AITC?

Hamid Saoudian:  No.  No.  They’re two different data sets.  DSS—most of the DSS data involves financial data and DS—or MEDSAS data is more focused on clinical data.  So even though there may be some overlaps, they are different data sets created for different purposes.

Moderator:  Thank you for that response.  The next question and I think you’ve already gone over this is please provide more information with help available with data cleaning.  This has been a big problem with us?

Hamid Saoudian:  Yes.  And I think we’ve—it’s been a big problem for us as well and all the users out there and I think we’ve covered that, but—

Moderator:  Great.

Hamid Saoudian: It’s good to know that many people are concerned about that and that will help us prioritize the where we want to spend our resources in the future.

Moderator:  Thank you.  So as we are approaching the top of the hour, I would like to ask you and your team Hamid if you are available to stay on past the top of the hour to continue answering questions, that would be great, that way we could capture them on the recording.  If not, I’m happy to send you the remaining questions off line and I can get written responses which I will then send out to our attendees.  Do you have a question?

Hamid Saoudian:  We can continue for a few more minutes and then if there are more questions you can send those to us.

Moderator:  Okay.  Great.  The next question, if I do all the work myself, create the cohort, do the data, etc, do we need to submit a DART application as well?

Hamid Saoudian:  DART application basically is the mechanism to get access to be granted access to actual data so even though you may develop your own routine for selection and so forth you still need access to the data to be able to run those selection criteria and selection routines.  So the answer is yes.

Moderator:  Thank you.  I want to make a quick note.  We do have a lot of questions asking what type of data is available in CDW and I would like to point people to a previous session we had done by VIREC and it’s on using VA CDW data—so that was recorded on March 7 of 2011.  So if you’d like to go to the seminar archives page and there’s slides and video available that may better inform our researchers and with that I’ll continue on with the questions.  Do you have any comment you’d like to make with regards to that?

Hamid Saoudian:  Just that data description page that I mentioned available from VINCI website that also provides a description of all the different data domains that are available through CDW.

Moderator:  Great.  Thank you.  Does VINCI currently support neuroimaging analysis for example structural or functional MRI?

Hamid Saoudian:  From the standpoint of providing the data, no.  But if research team has access to the data or have their own data, they’re welcome to bring that data into VINCI and use the tools that to allow VINCI to work with that data.  So—

Moderator:  Thank you.  Next question in general how long does it take to get permission from DART?

Hamid Saoudian: It varies.  It’s—it depends on the type of data access being requested so we’ve seen anywhere from maybe not too much longer than a week or two up to possibly several weeks.  Many times the all the forms are not—there are still a lot of forms to be submitted, so many times the forms are incomplete and that causes delays and Tory wants to add a few things here.

Tory: I just want to reiterate that the approval process for Data Access is not a VINCI process.  It is an NDS and VA regulation policy and process.  VINCI [inaudible] application, but we have no control over any of the application processes.

Moderator:  Thank you for that.

Hamid Saoudian:  What I should also mention is that the DART process—the DART application greatly improved that response time by making it easier to submit all the documents all in one place and creating an efficient workflow for the review of those documents and their approval process.

Moderator:  Thank you.  The next question how about researchers that only need a code book and access to VINCI.  What provisions are being made to accommodate advanced researchers?

Hamid Saoudian:  Was that a code book?  That--?

Moderator:  They asked—only need a code book and access to VINCI.

Hamid Saoudian:  Okay.  I’m not sure what they mean by codebook.  The closest I can come to for that would be what is called the dimension data in VINCI which are basically the basically the list for example the list of lab tests or lists of draws—so there’s are lists of data items that are used in conjunction with the actual domain data.  And they don’t contain any patient identifier information. That data can be made available upon request so you don’t need to go through NDS to get access to that if you need access to the dimension data and you can come in and request a VINCI workspace and you can create a database for you and make that data available for you.  Those are basically public data that anybody can look at.

Moderator:   Thank you for that response.  The next question that we have for data that is available through the SAS files in Austin, is the data available in the same format?   For data not available in SAS format through Austin, are there guides to the data formatting? 

Hamid Saoudian:  For the DSS, MEDSAS and [inaudible] data we have the data available in SAS format as well.  That can be made available to the requestor, but at the same time we are encouraging most users to store their data in a SQL server.  It is the more efficient way to store the data and provide much better performance and you’re still able to connect to that data through SAS or any of the other analysis tools and work with the data as if it was stored in SAS files?  So that’s the way we encourage users to use the data but at the same time if the user wants to store the data in SAS Files they have that option as well.  So the answer is yes, the data is available in SAS format as well.

Moderator:  Thank you.  Next question, does a project need to have a well defined cohort criteria from the beginning of the data abstraction?  Can a cohort be modified over time?

Hamid Saoudian:  Yes.  The answer is yes.  We have worked with a number of different project teams in basically providing—they provide us initial criteria and then we do some work in developing queries to create a cohort list and they review that and they come back with they want to add additional criteria or modify criteria that will affect the cohort list and the new collaborate with teams in developing that and creating the cohort list in multiple steps.

Moderator:  Thank you for that response.  The next question has a privacy offer evaluated whether the VINCI data has been de-identified with respect to HIPPA regulations?

Hamid Saoudian:  The answer is VINCI at this point does not provide de-identified data.  And in many cases it is difficult to completely de-identify data of an example the TIU data contains a lot of names, social security numbers and so forth.  In text data, many of you may know it’s [inaudible] to remove all the identifiers.  So we do not provide de-identified data.  The future idea that I mentioned for providing it less identifiable data sets that’s basically—it’s not a complete de-identified data set that we’re considering.  So no.  We are not attempting to provide or we don’t at this point and don’t intend to provide de-identified data set in the future.

Moderator:  Thank you for that response.  Can NLP be used on radiology notes?

Hamid Saoudian:  The NLP tools that the VINCI software development software has created I believe it can be used. You can connect it to your VINCI database and if you have radiology text information you can run an LP process against that data, so the answer is yes.

Moderator:  Thank you.  What application do we need to submit in order to use VINCI to store and analyze our own data and not VINCI data?

Hamid Saoudian:  For that you don’t need to go through NDS.  You’re not requesting any data.  All you need to do is basically submit a request on the VINCI’s website. You can also use if you want to use e-mail you can send an e-mail to VINCI@VA.gov and they will respond to you to the process that we can basically register your study of the process—it’s called study registration.  It happens very quickly within a few days.  You would be able to get access to use VINCI and be given a VINCI workspace and database to start importing your data and working with that data.  That’s a much quicker process than if you were asking for data.

Moderator:  Great.  Thank you.  Is it—next question—can you review what a typical timeline might be for getting data from VINCI?

Hamid Saoudian:  Um.  I’m assuming this is after the NDS approval.  As we mentioned before the NDS –approval process is independent of VINCI.  It’s a separate process but once you are approved for that data access you will hear form us immediately.  We’ll contact you and set up our correspondence site and we’ll start corresponding with you back and forth on basically understanding the specifics of your data needs and start working on that immediately.  So the work begins basically immediately within a day or two of the approval of your project—normally you’d hear from us and we’d start working with you.  The actual extraction of the data depends on the complexity of your data extraction needs and the criteria.  In many cases, it happens within days.  If it’s more complex, and requires you to review basically a partial data set that we provide to you and firm up your selection criteria, of course it would take longer.  In many cases we start working on the project immediately and are able to provide the data in a week or ten days.  Many projects are completed within that type of time period.  Some take longer depending on the needs.

Moderator:  Thanks for that response.  Somebody has a clarifying question.  You encourage storage of data.  Where?

Hamid Saoudian:  VINCI provides both database—a database for your project where you can store the data that’s made available to you—of course the data that we extract for you we place in that database and any drive data that you create you can still store that data in the same database—of course we mentioned that you can bring in your own data depending on the form of the data you can either store it in the database or on the file system that’s made available to your project within VINCI.  So you have the option of both storing your data in databases that you provide you or file system.  So and that’s all open to you depending upon the format of your data.

Moderator:  Thank you for that response.  I will give you guys the opportunity.  Are you still available or do you need to wrap things up.  

Hamid Saoudian:  We can take a couple of more and if you’d like to send us the rest of the questions, we’ll be happy to respond to those.

Moderator:  Great.  This was a very hot topic.  We have dozens of questions.  All right. And some of these—like I said, they came in early so you might have covered it already.  Will the data manager extract the cohort data in SAS format or SQL format?

Hamid Saoudian:  It—most of the work that we do is done in SQL format.  Of course, as I mentioned we can make that available in SASA format if that’s the desired format, but again we like to encourage users to store most of their data in SQL.  It’s much more efficient and they would be able to connect to it seamlessly from SAS and work with the data that was stored in basic SAS Files.

Moderator:  Thank you.  We have the exact same question but with regard to STATA instead of SAS?

Hamid Saoudian:  Again, the same thing.  You’re able to connect from STATA directly from SQL server and work with the data if you have a specific need to have the data stored in STATA file format, we can make that available as well.

Moderator:  Thanks.  What are the steps for getting NDS approval?  Is there a website with forms?  Etc?

Hamid Saoudian:  Yes.  NDS—NDS website provides complete instructions on how to get started with that process, with the DART process and they have staff to answer questions but their website should be a very good place to get started with their data request process.

Moderator:  Thank you.  Next question.  We will have—will we have direct access to the MEDSAS, vital status, DSS and [inaudible] data.  Right now we go directly to those files in the mainframe to develop our own cohorts.  Will we be able to do that or will we have to go through a VINCI analyst to get the data for us.  Our concern is for the extra time and complexity in adding another time and layer of people to our projects.

Hamid Saoudian:  Um.  Again, I mentioned there are two goals here; basically provide only the data that’s needed by your project thereby minimizing basically the need to provide more data that’s than needed by your project and also making the data sets that is being made available to you leaner and more suitable for efficient analysis work.  So depending upon the criteria that you may have in mind for selecting a subset of the ND files or the NSAF files we can work with you in some cases we have provided the entire NDE table to users depending upon their needs.  And I guess the answer is can be yes, depending on the needs.

Moderator:  Thank you for that response.  If we load our own data into VINCI are we allowed to download the data back to our personal computers?

Hamid Saoudian:  Um.  at this point VINCI’s policy is that any data that you work with within VINCI whether you bring it in or we extract for you needs to stay within VINCI—of course you’re able to download aggregate information and any reports and that you may create using that data, but the data itself remains in VINCI unless you get you’re able to get permission from HSRD director to download that data.

The goal here is to not to make it more difficult for users to work with the data but the VA as a whole is very much concerned about data security and I believe that the future trend is to basically concentrate data processing capabilities into more secure centers rather than spread out—data on desktops and local servers and so forth.  So VINCI is sort of the front runner in that effort, so our emphasis is in trying to keep the data in a secure environment and still make it easy for approved users to get to the data but do it in a secure and safe manner.

Moderator:  Thank you.  Would we be allowed to download CDW data from VINCI into our computers if we originally requested to have the CDW data downloaded into our computer?

Hamid Saoudian:  Um.

Moderator:  I think you may just have answered that.

Hamid Saoudian:  That in the—I guess the way to answer that is up to this point, we have that—that has been a mode of data approval process for NDS has approved data requests for CDW data that can be downloaded and not used within VINCI but that is again being reviewed.  There are some discussions between CDW and NDS and some others in reviewing that mode of data provision and there may be some changes to that so we encourage people to just contact NDS and they will be able to provide them with the latest in the data approval process and the modes that are available to you.

Moderator:  Thank you for that response.  This is a good general question, who are VINCI data managers and how can we contact them?

Hamid Saoudian:  At this point the best mechanism for contacting us is through the VINCI@VA.gov e-mail address just submit your question to that e-mail address and this is our mission to filter all of the different questions or requests that come in and the folks responsible for manning that e-mail address they forward us questions or requests that are involving data.  so that’s the best mode and from there depending upon we do work on multiple projects at the same time we assign your request to different data managers and at that point they would contact you and work with you directly.  So that—that would be the way to contact us through the VA.gov—VINCI@VA.gov. Email address.

Moderator:  Excellent.  Thank you.  Okay.  In the cohort identification process—I’m sorry—in the cohort identification process, is too possible to reconstruct a consort figure?

Hamid Saoudian:  Um.  I’m looking around the room.  None of us are familiar with what consort figure means, so—

Moderator:  They may have misspelled cohort figure but I’m not sure—

Hamid Saoudian:  If it involves a cohort size or sample size the answer is yes.  If the question involves something else, please just send us a quick e-mail and we’ll research that and get back to you very quickly.

Moderator:  Thanks.  If I don’t have access to the VA Intranet, can I still see the data descriptions?

Hamid Saoudian:  No.  At this point the VINCI site and the data descriptions are only available if you are on the VA network.  But the data descriptions are basically general purpose documents so if you have a specific need, if you want any of the data description documents and you’re not on the VA network, since it’s public information, just send us an e-mail and we’ll send you an e-mail with the portion of the document that you want to know more about.

Moderator:  Thank you.  We do still have eleven remaining questions.  Do you want me to send you those offline?

Hamid Saoudian:  Sure.  Sure.  Yes.  Since we’re twenty five minutes past the hour, just to be more efficient, I think it would be better to send those to us and we’d be happy to answer those.

Female;  Thank you so much to the remaining attendees who are still here, I will send you an—I will post the written responses with the archive of this video and audio and I would like to very much thank Hamid and the rest of the VINCI team for providing your expertise and presenting for us.  Thanks for our attendees for coming.  Do you guys have any final comments you’d like to make before we wrap things up?

Hamid Saoudian:  We appreciate everybody’s time as well and look forward to serving you with your data needs and also we ask you to look forward to attending other sessions by VINCI and learning much more about the services that we provide.  We appreciate everybody’s time and the opportunity to do this presentation.

Moderator:  Excellent.  I would like to reiterate that we do have another VINCI session coming up in April on April 11 and that will be an introduction to the SAS grid by Mark Eso and we’ll have another session coming up on April 30 which will be new natural language processing tools available on VINCI and that will be conducted presented by Ryan Cornia.  Please go to the HS [inaudible] website and look through our catalog and sign up for those future sessions and be sure to answer the survey questions as you exit the session.  Thank you everyone for joining us and this does conclude today’s HSR&D Research Seminar.

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**[End of Recording]**