#### ICR Workspace Meeting Notes

January 9, 2008; 2-3:30 PM EDT\
Moderator: Elaine Freund

#### 

#### Key Decisions and/or Outcomes

-   Updates on workspace working groups

-   Presentation on Dynamic Extensions by Rakesh Nagarajan

#### 

#### 

#### Action Items

+----------------+--------------------------------------+-------------+
| ##             | #### Description                     | ##          |
| ## Assigned To |                                      | ## Due Date |
+----------------+--------------------------------------+-------------+
| ###            | #### T                               | #### Jan 10 |
| # Elaine/Kiran | ry to schedule interim WF WG meeting |             |
+----------------+--------------------------------------+-------------+

#### 

#### 

#### Attendees

  ------------------------- ---------------------------------------------
  Pankaj Agarwal            Duke University

  Janis Beach               IMS

  Paul Courtney             Dartmouth College

  Ian Fore                  NCI

  Robert Freimuth           Mayo Clinic

  Elaine Freund             Third Millennium

  Mervi Heiskanen           National Institute

  Daniel Kavan              Information Management Services

  Aaron Kesv                Columbia University

  Li Kramer                 Booz Allen Hamilton

  Sal Mungal                Duke University

  Rakesh Nagarajan          Washington University

  Deanna Petrochilos        Univ of Washington

  Benjamin Powers           IMS

  Gunter Schemmann          Princeton University

  Mukesh Sharma             Washington University School of Medicine

  Patty Spears              Patient Advocate

  Grace Stafford            Jackson Laboratory

  Bob Stearman              SAIC

  David Steffen             Baylor College of Medicine

  Baris Suezk               Georgetown University
  ------------------------- ---------------------------------------------

#### 

#### 

#### Meeting Notes

Agenda review

Action item review -- Interoperability discussions with CTMS are in
progress, issue is elevated at NCICB. Other action items completed.

[ANNOUNCEMENTS:]{.underline}

Beyond ICR:

-   caGrid Portal team announced the availability of the version 2.0 of
    the caGrid portal.

-   Candidate caBIG CDE Standard for Family Relationship documentation
    release There Pre-release version of caArray 2.0 application

-   Registration for the upcoming Joint Architecture and VCDE Workspace
    Face-to-Face Meeting, January 28-30, 2008, hosted by the University
    of Utah in Salt Lake City deadline is Monday, January 14^th^.

Within ICR:

-   Continuing to look at potential workspace organization and meetings
    on other WS organization and interoperability activities are
    underway.

-   F2F dates -- being discussed for end of April start of May and we
    will begin dialog on this. Think about any possible issues (e.g.
    TBPT F2F is April 23 and 24)

[WORKING GROUP UPDATES]{.underline}

Analytical Services and Best Practices -- update report presented for
Ted Liefeld

<https://gforge.nci.nih.gov/frs/download.php/3124/ASBP_ICR_UPDATE_010908.ppt>

-   VCDE responded to the Generic Parameters Proposal.

> They have asked ASBP to continue using the generic parameters, service
> loader and Introduce to create a demo service and to track development
> time. This will inform a cost/benefit analysis of development time vs
> loss of parameter semantics. Lessons learned will provide guidance for
> future developers on process/procedure.

-   Reminder to register intent on suggested deliverables for the
    working group

-   Next meeting: January 11th at 2:00 pm EST

High-throughput -- update report presented for Martin Morgan

<https://gforge.nci.nih.gov/frs/download.php/3126/ICR_WG_HTP_9_January_2008.ppt>

-   HTP wiki progress reported
    [**http://ccis1716.duhs.duke.edu/wiki/index.php?title=HTP**](http://ccis1716.duhs.duke.edu/wiki/index.php?title=HTP),
    especially on sections for Context and the GridFTP Case Study. Other
    sections include an Endpoint References Case Study, a WS-Enumeration
    Case Study, and a Summary which highlights issues and
    recommendations.

-   Next meeting: Wednesday, January 16 at 3pm, Eastern

Workflow -- Kiran Keshav

<https://gforge.nci.nih.gov/frs/download.php/3125/caGrid_icr_meeting_workflow_summary_January9_2008.ppt>

-   Demo creation issues

    -   Introduce tool kit package names are lower case while caArray
        uses data types with upper case, creating a disconnect. This is
        a known issue and there is a work around.

    -   caArray data sets are too large for demos, so are identifying
        the smallest one possible

    -   JAVA 1.6 not compatible with caGRID, so there is a problem
        switching to the update

-   Status

    -   Process

        -   Get experiment and extract bioassays from caArray

        -   Use converter service created for this project and pass
            output to pre-processing service in GenePattern, if
            available

        -   Pass to and do clustering and get clustered object to Ravi
            by Jan 15

    -   In progress

        -   caArray data

        -   pre-processing service

-   Next meeting: Scheduled for Jan 25 and would like to schedule for
    before the cross-cutting face-to-face.

ACTION ITEM: Interim meeting for Workflow

[PRESENTATION]{.underline}

Dynamic Extensions -- Rakesh Nagarajan

<https://gforge.nci.nih.gov/frs/download.php/3127/Dynamic_Extensions_for_ICR.ppt>

Use case

Complex diseases have data elements unique to each. Example, biomarkers
for prostrate can be different for another tumor type.

-   Building underspecified models enable generalization of pathology,
    image, patient, etc. annotations. However the data elements are not
    semantically defined sufficiently to describe what can actually be
    stored.

-   Highly specified models in the caBIG initiative require capture all
    of the elements up front. This is a very high level of effort,
    compounded by the research moving forward fast enough to need to add
    elements dynamically.

-   Would like to allow capture of associated information that is
    institution specific and isn't needed in the model (e.g. freezer
    maintenance, date frozen)

Requirements for Dynamic Extensions (DE)

-   ISO compliant and data exposed through a well defined API and not
    requiring additional coding

-   Objective is to build infrastructure to stay caBIG compatible as
    they add elements for both VCDE and ARCH without changing code

Creating DE

-   Define extensions via the user interface or XMI

-   DE generates forms for data entry or is a bridge to the API

-   It also embeds the query within the interface (a metadata based
    interface in caTissue and caCORE for example)

Actual use of DE is in TBPT with caTissue CORE and caGrid with the API.

A diagram of workflow was presented and shows a point where extensions
can go to caDSR and be submitted for compatibility.

Comments on process: Load the extension by loading the UML model into
the tool and add more classes through EA or XMI. The DE itself is
attached to/associated with a static part of the model.

Screen shots showing the form builder, defining the UI fields, and how
to see a preview, DE creation by importing XMI were presented.

Q on forms and metadata being part of a class in the UML and DSR?

Response: DE is tightly model driven and you create "forms" in the UI,
but they relate 1:1 as classes. Subforms you create in the UI correlate
directly 1:1 with classes in the main form.

Current work is to enable separation of what the form looks like in the
UI vs. what an appropriate UML model looks like. This will be in the
next version of caTissue Suite. It was noted that currently extensions
execution requires a solid understanding of the model and there is a
danger of creating problems in the model in order to create an optimal
form.

Additional screen shots displayed the UI for data entry into the
application and the ability to query the DE static data and metadata. DE
are limited to 3 classes in caTissue, where most annotations will occur.

The DE database has it's own database (meta database) used to generate
forms and query interface.

Categories:

Slides on category definition and creation in the UI were presented. The
category concept is added, and defined in the DE of any application, to
make querying friendly. Paths between classes are predefined in UML, but
most end users don't know how to connect them logically, so use cases
allow programmers who know model to build the queries. Category is for
advanced users to set up these queries.

Leveraging DE:

-   Difficult to stick to static models.

-   Noted they are working with the XC WS -- but this is still in
    negotiation; is this caBIG compatible, what are the tooling and
    processes issues?

-   There is the ability to commit any or all parts of the model for
    compatibility review. This can be done for just the parts of the
    model you want to share in the XMI export.

-   Registration in the caDSR, to allow others to use, is encouraged.

-   Policy still to be formed for use by any of the other domain
    workspaces.