**Vocabularies and Common Data Elements Workspace Teleconference**

November 15, 2007\
Meeting Minutes

**Teleconference Information\
**Date: November 15, 2007\
Time: 1:00 PM - 3:00 PM ET\
Moderator: Brian Davis

**Executive Summary**

The VCDE WS received Liaison Reports from the "Documentation & Training"
and "Imaging" Workspaces. The Guide to Mentors group gave a presentation
on version control of documentation, and the CDE leadership group
provided a recommendation on an Education Levels CDE Standard. A
kick-off was held for geWorkbench silver level compatibility review, and
a report was given on the caTissue Core v1.2 silver level review.
Lastly, a presentation on the NCIA project was given that demonstrated
the project's history in re-using CDEs in a software development
environment.

**Key Outcomes/Decisions**

-   The VCDE WS voted to approve the Education Levels CDE standard.

-   Kiran Keshav will compare geWorkbench with GenePattern in the next
    round of geWorkbench development.

-   Xin Zheng recommended, upon a full review, that caTissue Core v1.2
    be recognized as silver level compatible, to which the VCDE
    Workspace agreed. caTissue v1.2 has passed VCDE WS level silver
    level compatibility (Arch WS still needs to approve).

**Action Items**

+---------------+-------------------------------------------+---------+
| **Assigned    | **Description**                           | **Due   |
| To**          |                                           | Date**  |
+===============+===========================================+=========+
| Stuart Turner | > Circulate the Annotations Imaging       | Nov.    |
|               | > Markup Developer Project (AIM) Sample   | 29^th^  |
|               | > Instances to interested parties from    |         |
|               | > the VCDE Workspace                      |         |
+---------------+-------------------------------------------+---------+
| Brian Davis   | > Develop "Bundle release" versioning     | Mid     |
|               | > system to go together with              | D       |
|               | > Documentation Versioning system         | ecember |
+---------------+-------------------------------------------+---------+
| Daniela Smith | > Notify caBIG community of Education     | Nov     |
|               | > Level CDEs for 30 day comment period    | 30^th^  |
+---------------+-------------------------------------------+---------+

**Meeting Materials**

**Attendees**

  -----------------------------------------------------------------------
  **Albert Einstein**

  Quan Chen

  Xin Zheng

   

  **Duke University**

  Pankaj Agarwal

   

  **Fox Chase**

  Min Hua

   

  **Georgetown University**

  Baris Suzek

   

  **Jackson Lab**

  Grace Stafford

   

  **Mayo Clinic**

  James Buntrock

  Bob Freimuth

  Craig Stand

  Jyotishman Pathak

  **MD Anderson**

  Mike Riben

   

  **UC-Davis**

  Stuart Turner

   Cecil Lynch

  **University of Hawaii**

  Lynne Wilkens

   Mike Loomis

  **Washington University**

  Mukesh Sharma

   

  **NCICB**

  George Komatsoulis

  **SAIC**

  Tommie Curtis

  Janice Chili

   

  **TerpSys**

  Claire Wolfe

   John White

  **Gulf Stream Bioinformatics**

  David Aronow

  Kristel Dobratz

  **IMS**

  Mary McAdams

   

  **Persistent Systems**

  Srikanth Adiga

   

  **Westat**

  Shelly Niwah

   

  **3rd Millennium, Inc.**

  Brian Davis

   

  **BAH**

  Vikram Purohit

   Mike Keller

  **OTHER**

  Kiran Keshav (Columbia University)

  Pam Mayfield (Baylor)

  Alan Hogg (NCRI-UK)
  -----------------------------------------------------------------------

**[Meeting Notes]{.smallcaps}**

**1. Liaison Reports -- D&T, Imaging Workspaces**

***CTMS --*** The CTMS Workspace liaison report will be postponed until
the November 29, 2007 VCDE teleconference.

***Documentation & Training --*** Bob Freimuth provided the
Documentation & Training Workspace liaison report. The focus of the last
4-6 weeks of meetings in the D&T workspace has been the work going on
with the caBIG Essentials Package (scheduled to be public by the end of
this week), which is being developed to support the caBIG Deployment
Program . This package will be presented to cancer center leads and
institution leads, with topics including deployment self assessment,
information on tools, applications present in the CTMS & life sciences
bundles, DSIC workspace practices and the level of participation
required of the cancer centers for the DSIC workspace, understanding the
grid and how it works (tutorials), how to make caBIG tools adhere to
established guidelines, and criteria for modules. Sal Mungal and Bob
Freimuth have been assigned (as members of the Training WS) the task of
making the "Closer Look at Compatibility" module, which will be
different from the other caBIG modules, as this module will discuss
criteria not at the lowest possible level, but at a more middle level;
it will be targeted towards developers and technical leads, and will
talk about criteria for each of the four levels of compatibility. In
addition, this content is being extended with two modules called "From
Theory to Practice," which will focus on semantic annotation and CDE
re-use. All these modules will be a part of the 1^st^ release scheduled
to come out by the end of this month. Once the gold level criteria has
been worked out, there will be one more addition to the package called
"Path to Gold Level Compatibility," for applications going from silver
to gold. The D&T workspace wants a Wiki environment running to capture
the lessons learned from the enterprise adoption program going on with
caTissue Core. Additionally, training tools to support audio and movie
recording to help people better understand and take a tour of the
applications are being worked on -- by adding movies and audio
components, people can more effectively learn what the tools do and how
to use them.

***Imaging*** -- Stuart Turner provided the Imaging Workspace liaison
report. Recent work has revolved around obtaining feedback and
debriefing community members from the October 11^th^ -- 12^th^
face-to-face meeting. Also, preparations for the RSNA 2007 Annual
Meeting are underway. There is inherent difficulty into getting data
into the "soup to nuts" imaging clinical trial project that was planned,
so this project has been changed to be "soup" without the nuts. A
portion of an image based clinical trial will be demonstrated through
the Imaging Workspace's presence at RSNA 2007. David Channin recently
released some sample instances of AIM annotations, allowing the
community to see what is emerging from the AIM (Annotations and Imaging
Markup Developer) Project. The AIM team is now able to generate DICOM
structured reports from AIM XML data. The AVT team is at the beginning
of their project, and is currently doing a gap analysis. Work is
underway on a number of projects that are being developed in the IVI
Workspace-- AIM, NCIA, XIP and Middleware; the VCDE workspace will be
reviewing all for compatibility. Silver level compatibility review has
been kicked off for the NCIA. The RadLex Research Playbook Developer is
radiological lexicon in Protégé that attempts to capture procedures and
protocols used in radiology -- it is available in GForge for those who
want to review it. A meeting was held on November 14^th^, 2007 between
VCDE and Imaging to help VCDE understand how all the imaging projects
work together.

**2. Guides to Mentors Update**

***Version Control of Documentation --** Bob Freimuth*

This version control of documentation effort will show how the guides
are handling document versioning. This version numbering system is
consistent and allows the guides to interpret the documents in a similar
fashion. A white paper describing this is available on the GForge site
in the SCM repository. This version numbering system was decided on
after studying many available systems -- this one allowed the retention
of the most advantages while excluding as many disadvantages as possible
of the systems studied. Each component of the system signifies a
different level of maturity. The minor components are intended to be
incremented only after the VCDE and Architecture Workspaces approve the
changes in those documents, which is intended to happen on a quarterly
basis. A few of the advantages of using this system are:

-   Similar visually and functionally to existing systems, so it will be
    easy to pick up on

-   The use of a rational number provides intuitive sorting

-   A decision was made to leave out the delimiter between the item and
    patch component to eliminate the need of customized knowledge of
    sorting routines

-   A lack of alphanumeric identifiers makes interpreting the number
    more intuitive

    Practical advantages of this system are that :

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-   Using a fixed number of digits eliminates ambiguity in how each of
    those components is incremented

-   Truncating of trailing zeros does not change the interpretation

    This numbering system has been implemented on the "Guides to
    Documents" available on GForge -- these will maintain the version
    numbering system to establish uniformity and help the public
    understand what the current version of the document is.

    *Feedback / Discussion*

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-   The question was asked to see if the obvious thing is to now turn
    this into a data standard, to which it was noted that the version
    number system being described here is for documents, while in
    actuality the workspace may want to create "bundles" of documents.

-   The issue was raised that if this method will be encouraged, it must
    be standardized.

-   The question was posed with regard to how do we make sure that
    people are able to find the latest version. A proposed solution was
    to have an area of the GForge site where a link to the latest
    version could be kept and updated.

-   What was discussed in this presentation is only a first step, and
    deals with how these documents will be kept track of internally

    **3. CDE Leadership Group Update**

    ***Education Level CDE Standard Recommendation* --** Janice Chilli

    This discussion will include final recommendations for educational
    level CDE standards. The VCDE Small Group that reviewed the
    standards is hoping to get a recommendation to go out for the 30 day
    review. Daniela, Lynn, Michael, and Janice comprise the VCDE Small
    Group. This group focuses on what's common within the communities --
    they look to harmonize standards. When looking at the combined set
    of values among all the CDEs, they covered everything from
    pre-school level to doctorate degrees. The US Bureaus of Census,
    Labor and Statistics; HL7, and own EVS information were looked at.
    Studying the existing CDEs it was found that the CDEs were being
    used on case report forms, form applications, and models, including
    the BRIDG model. The review of existing CDEs was narrowed to those
    that had an enumerated value domain -- in this list it is apparent
    that the most common terminology use of CDEs depended on level of
    college education completed. One comment that came back from the
    population sciences community was that the inclusion of highest and
    most complete was redundant, because the EVS definitions already
    said that they were the highest completed. Five enumerated lists of
    CDEs have been looked at; there was no single value domain that
    could be promoted that would meet the needs of everyone, so there
    were different groupings that occurred.

    There was a discussion on how to handle different situations, and
    the decision was made that breaking down the standard in the value
    domain into the most finite carts to allow the applications and
    specific studies to group the data as they felt best was most
    appropriate. United Nations, US Departments of Census, Labor, and
    Education, and the HL7 RIM standards were looked at (HL7 provided
    very high level groups -- associate, bachelors, etc. -- and did not
    meet existing needs of CDEs). The components recommended for
    standardization were to create a new DEC:

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```
-   Person's education level

-   To create a new enumerated VD -- education level type

-   To create a new data element - person education level type

-   The UML guidance for this CDE is fairly straightforward -- the goal
    is to provide available and searchable use data

**Key Decision:** The VCDE WS voted to [approve]{.underline} the Person
Education Level Type CDE standard.

**4. Compatibility Review Kick-off for geWorkbench --** Kiran Keshav

The geWorkbench framework has several visualization features. One of the
tasks given to the geWorkbench team last year was to take the components
and grid enable them -- to create service components. To grid enable the
algorithms, the process was broken into 4 steps. The mage model was
already in the caDSR, and this model was used as the input for the
geWorkbench service. StatML (Model) was also used for a similar purpose.
The outputs were more customized because the types needed did not exist
in the caDSR. The hierarchical clustering CDEs used are in caDSR now.

*Feedback / Discussion*

-   Since GenePattern has a clustering implementation like geWorkbench,
    in terms of the cluster, what are the differences / similarities
    between the two cluster algorithms? This depends on what type of
    clusters are in the algorithms. On a higher level though, even if
    the clusters are different, commonalities may be able to found (for
    Modeling).

-   The geWorkbench team assumed that the outputs for GenePattern and
    geWorkbench would be quite different, which is why they have not yet
    studied the differences between the two applications. The
    compatibility review teams team will now study the possible
    commonalities at a high level.

-   The "Introduce" program can be used to deploy this service. TeraGrid
    is a proof of concept project that will allow binaries to be staged
    on the Teragrid, have geWorkbench linked to the TeraGrid, and allow
    all computation to be run on the TeraGrid.

-   GenePattern also has an implementation of hierarchical clusters, but
    likely has a completely different sort of cluster from geWorkbench.

-   No studies have been done with regard to performance and scalability
    because it is not appropriate to send huge data sets across the wire
    in geWorkbench, as this would be too strenuous on the receiving end.

-   Quan, Sal Mungal, and Mukesh will be the review team for
    geWorkbench.

**5. Silver Level Review Recommendation of caTissue Core v1.2** -- Xin
Zheng

Reviews have been finished, and were presented at the last meeting.
During the last week there was a meeting to address issues that had
arisen with the developers, which have now been resolved. The caTissue
Core 1.2 was developed with SDK. From the VCDE point of view, Xin Zheng
stated that the VCDE WS should approve this tool to be silver level
compatible.

*Feedback / Discussion*

-   Although not visible in the spreadsheet, (no vocabulary tab),
    vocabulary was checked for during the review.

-   There were a few concerns that CDE reuse could have been undertaken
    but was not, but the decision was made to not punish an application
    for using for example "participant" instead of "patient," because
    there may be valid reasons for using one (instead of the standard).
    This is probably an issue that is resolved at the GOLD level of
    compatibility.

-   Concepts and value domains were re-used.

**6. The NCIA CDE Re-use Story** -- Stuart Turner

NCIA was able to re-use numerous CDEs within the caDSR. NCIA is a
pre-BRIDG model, and was modeled not in light of what is happening
today, which should be kept in mind. In the tool, users query and
retrieve images and put them into their "shopping cart" (similar to
Amazon.com) to be viewed later. The archive is comprised of two imaging
data sets -- RIDER and LIDC. The goal of the Imaging Workspace is to
harmonize DICOM into the VCDE workspace -- to this goal, AIM will
provide the metadata to package into the images that go into NCIA.

*Feedback / Discussion*

-   Although AIM and NCIA could be the UML model start for the Imaging
    Workspace, and be a good enough start for capturing an image, having
    Middleware and XIP included may prove to be a better start.

-   From November 2006 to April 2007, the NCIA silver level review was
    to begin. However, in Spring of 2007 VCDE stepped back because it
    was obvious that there were issues with the modeling and CDE re-use.

-   There have been many lessons learned, and perspective has played an
    important role in the process.

-   This year, harmonization of the DICOM standard has been the focus.

-   There were attributes that should not have been in the patient
    demographic class that were. There are legacy classes that still
    exist, which AIM will replace; the target release date for AIM may
    be spring or summer of 2008.

-   Early this year, about 10 of the 74 CDEs could be mapped, and the
    rest could not be because of semantic conflicts; there are candidate
    CDEs, but due to their granularity they cannot be shared.

-   Basic outcomes and lessons learned -- NCIA enjoys 90% CDE re-use,
    vs. 8% a year ago. NCIA project has had some turnover of staff, but
    NCIA has been eager to work with VCDE to resolve previous problems,
    and VCDE is doing a good job with training and tutorials to support
    this effort.

-   Questions to keep in mind are:

    -   Can metrics be developed?

    -   Can the developed metrics be leveraged to do a meta-analysis of
        Imaging Workspace projects as time progresses?

-   Has this project been a special case where there was a standard that
    had to be used because that's what the user community needed
    (instead of vice versa), and had to be fit into the caBIG framework,
    or do the lessons learned extend beyond that?

    -   Answer: Setting all parts against DICOM was the need and was a
        best practice, but the overall lessons learned extend beyond
        this.

-   The lessening of the dependency on personal interaction will happen
    automatically in response to the rapid growth of caBIG; the
    community will have to scale in reaction to this reduction in
    dependency.

-   Amount of re-use will depend on whether it is the properties or
    attributes versus the class of CDEs; there are four attributes in
    the UML model, and in the end 3 object classes were created with
    four CDEs.

-   DICOM has three different classes, and it is possible to re-use the
    existing CDEs because things were broken down into the appropriate
    classes; the CDEs were pulled into the appropriate model.

-   In the end, the four CDEs obtained 100% re-use.

-   A before and after view of the model, and how the two models map to
    CDEs, would be useful for the community.

-   It is difficult to engage CDE re-use because finding the CDEs and
    where the UML model is on GForge and on caDSR is laborious; this
    information needs to be streamlined for the TBPT workspace to group
    together classes often used in the WS.

    -   The Imaging Workspace did this in Fall of 2006 -- they have a
        superset area that sits in the CDE browser, which when opened
        can provide all CDEs associated with this project.

    -   UML Model Projects need more context.

**Next Meeting:** Thursday, November 29, 2007, 1:00 PM -- 3:00 PM ET