# ICR Workspace Teleconference

## Meeting Information

Date: November 12, 2008

Time: 2:00 pm -- 4:00 pm ET\
Moderator: Elaine Freund

#### 

## Executive Summary

Working groups ASBP and IRWG provided updates on their activities. Carl
Schaefer presented the status of the Protein Interaction Database and
the first three Service Support Providers presented their capabilities
to the ICR community.

## Action Items

Table 1: Meeting Action Item List

  ------------------------------------------------------------------------
  **Assigned To**   **Description**                         **Due Date**
  ----------------- --------------------------------------- --------------
  Baris             export EA version of the seed model to  
                    HTML for others to view                 

  ------------------------------------------------------------------------

## Meeting Notes

### ANNOUNCEMENTS

[Version 1.1 of the caBIG^®^ Clinical Trials Suite is
released. ]{.underline}

The caBIG® Clinical Trials Suite is a comprehensive set of
caGrid-enabled tools that securely support clinical trials activities,
including registering and tracking patients, managing patient activities
and calendars, reporting and tracking adverse events, reviewing
laboratory data, transferring data to between applications, capturing
and cleaning the clinical data, and analyzing and reporting on the
collected data. The components in the 1.1 bundle are:

-   Clinical Participant Registry (C3PR) (version 2.5.2) -- A tool for
    managing clinical trial patient enrollment data across multiple
    clinical trials, organizations and sites
    ([[https://cabig.nci.nih.gov/tools/c3pr]{.underline}](https://cabig.nci.nih.gov/tools/c3pr)).

-   Patient Study Calendar (PSC) (version 2.3.3) -- A tool for creating
    and editing study calendar templates, generating and viewing
    prospective calendars of patient activities, tracking activities as
    they occur, and managing patient calendars as they change during a
    study
    ([[https://cabig.nci.nih.gov/tools/PatientStudyCalendar]{.underline}](https://cabig.nci.nih.gov/tools/PatientStudyCalendar)).

-   Adverse Event Reporting System (caAERS) (version 1.5.1) -- A tool
    for collecting, managing, processing and reporting routine and
    serious adverse events that occur during clinical trials
    ([[https://cabig.nci.nih.gov/tools/caAERS]{.underline}](https://cabig.nci.nih.gov/tools/caAERS)).

-   Clinical Data Exchange (caXchange) (version 1.5.0) -- A configurable
    hub for exchanging clinical trial information between applications
    and systems.
    ([[https://cabig.nci.nih.gov/tools/LabIntegrationHub]{.underline}](https://cabig.nci.nih.gov/tools/LabIntegrationHub))

-   CTODS Lab Viewer (version 1.5.0) -- The Lab Viewer interface allows
    users to view and query laboratory data in the Clinical Trials
    Object Data System (CTODS) and select subsets of tests to be sent to
    a clinical trials database.  This release also includes the Cancer
    Center Hub Client (CCHS) for batch loading labs and converting them
    from HL7 v2 to HL7 v3
    ([[https://cabig.nci.nih.gov/inventory/infrastructure/CTODS]{.underline}](https://cabig.nci.nih.gov/inventory/infrastructure/CTODS)).

-   C3D Connector (version 1.2.0) -- A BRIDG-based adapter that allows
    applications in the caBIG® Clinical Trials Suite to share
    information with the C3D Clinical Data Management System.  It can
    also be configured to operate with other Clinical Data Management
    Systems.

The tools in the caBIG® Clinical Trials Suite are intended for use by
clinical researchers.  Each tool provides an end user-oriented graphical
user interface as well as a Java-based Application Programming Interface
(API) and a caGrid compatible Grid Service for programmatic access to
data. All of the applications are built on a common set of open-source
technologies for ease of installation and maintenance.
([[http://ncicb.nci.nih.gov/download/cctslicenseagreement.jsp]{.underline}](http://ncicb.nci.nih.gov/download/cctslicenseagreement.jsp)).

  

[5th NHIN Forum: Nationwide Health Information Network (NHIN) Trial
Implementations: A Path to Production]{.underline}

The 5th NHIN Forum will be held December 15 -- 16, 2008 in Washington,
DC.

This forum will be open to the public and will include participants in
the NHIN Trial Implementations who worked through the NHIN Cooperative,
including Health Information Exchanges and Federal agencies and other
key stakeholders, as well as ONC program offices. This forum will
showcase the work of the NHIN Cooperative, including experiences and
lessons learned from the Trial Implementations.

To register for this event:
[[www.blsmeetings.net/nhinf]{.underline}](https://webmail.hhs.gov/exchweb/bin/redir.asp?URL=http://www.blsmeetings.net/nhinf)

The newest licensed caBIG^®^ Support Service Providers have been
announced.  Semantic Bits, ScenPro, Inc. and Terrapin Systems (TerpSys)
are now each licensed by the National Cancer Institute (NCI) to market
their services as part of the caBIG^®^ Support Service Providers
Program. 

### 

### ACTION ITEM REVIEW

Support Service Provider Categories:

-   **Help Desk Support** - support for the end users and local IT
    administrators using (adoption/adaption) of the Bundle tools.

    -   [Terrapin Systems
        (TerpSys)](http://www.terpsys.com/caBIG-support-services.html)
        http://www.terpsys.com/caBIG-support-services.html

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-   **Adaptation and Enhancement of caBIG^®^ -Compatible Software
    Applications** - supports caBIG^®^ -compatible software development
    and includes adaptation of existing systems for caBIG^®^
    compatibility, custom enhancements to existing caBIG^®^ tools that
    satisfy specific user-driven requirements while maintaining caBIG^®^
    compatibility, and de novo development of caBIG^®^ -compatible
    applications and tools.

    -   [5AM Solutions, Inc.](http://cabig.5amsolutions.com/) Please see
        link below

    -   [Ekagra Software
        Technologies](http://www.ekagrasoft.com/Services.htm) Please see
        link below

    -   [ScenPro, Inc.](http://www.scenpro.com/c_cabig.html)
        http://www.scenpro.com/c_cabig.html

    -   [Semantic Bits](../Semantic%20Bits%20)
        http://www.semanticbits.com/services/cabig-service-provider

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-   **Deployment Support for caBIG^®^ Software Applications** - Includes
    onsite or offsite procurement and provisioning of hardware,
    operating systems and other software, such as application servers
    and databases, along with installation and configuration of caBIG^®^
    software, legacy data transformation and migration. Deployment
    support also includes integration of multiple caBIG^®^ tools and
    caBIG-compatible applications through open application programming
    interfaces (APIs). Possible services include data management,
    security services, hosting, performance tuning, network
    connectivity, grid enablement and maintenance of web server/database
    and application specific administrative IT tasks.

    -   [5AM Solutions, Inc.](http://cabig.5amsolutions.com/)

    -   Akaza Research
        <http://www.akazaresearch.com/about_akaza/caBIG.html>

    -   [Ekagra Software
        Technologies](http://www.ekagrasoft.com/Services.htm)

    -   Semantic Bits

    -   SRA Corporation

    -   Terrapin Systems (TerpSys)

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-   **Documentation and Training Materials and Services** - Includes
    development of documentation and training materials and the
    provision of training services for caBIG^®^software applications,
    caBIG^®^ compatibility for existing systems, and use of caCORE
    infrastructure.

    -   Akaza Research (Training Materials and Services)

    -   ScenPro, Inc.

    -   Terrapin Systems (TerpSys) (Training Materials)

 

### WORKING GROUP REPORTS

#### ASBP

> <https://gforge.nci.nih.gov/frs/download.php/5293/20081112_ASBPUpdateToICR.ppt>

-   Generic Parameters -- Pilot services status is Gene Neighbors
    service is available in the next 48 hours. PHC soon as well. The
    group still needs to define tuning parameter vs data definition.

-   HTP and Grid Transfer -- developed presentation for VCDE and ARCH
    with requirements for the next solution. They will raise issue of
    semantic and syntax correct if you use caGRID transfer

-   Draft white paper for data modeling progressing.

#### IRWG

> <https://gforge.nci.nih.gov/frs/download.php/5294/20081112_IRWG_ICR_WS_Presentation.ppt>

-   caDSR generated model will not do the trick in creating an ICR DAM,
    but it was helpful starting information

-   Developing seed model (themes/use cases) with core models

-   Built out and iterations which has led to a draft. The next
    iteration si to working on associations.

-   ACTION ITEM: Baris to export EA version of the seed model to HTML
    for others to view

-   Still to do is handling cross-references, coming to a consistent
    specification, associations and links, descriptions and permissible
    values are next topic to finalize the model

> Q. on touch points with BRIDG explored?
>
> A. Will start considering that and identify touch points and how to go
> from ICR model to the others. They may need to add helper classes
> (specimen, image, etc).

### PID

<https://gforge.nci.nih.gov/frs/download.php/5300/20081112_ICR_Protein_Interaction_Database.ppt>

-   His tool has been around since 2001 and continues to grow..

-   Publication in NAR 2008 database issue.

-   There is web site to browse

-   Objectives

    -   Represent network relations and overcome arbitrary pathway
        boundaries.

        -   Store canonical pathways but can retrieve subsets

    -   Specificity -- annotate with UniProt ids for Proteins, represent
        post translational modifications, can capture families of
        molecules (non traditional -- has to do with functionality being
        the same, allow for abstract states -- active, inactive -
        location)

    -   Dynamically built from structured data and is not comprehensive,
        and doesn't include biochemical reactions

-   Showed basic entities: molecule, interaction, role types and
    molecule use.

-   Content from manual curation and ETL of: NCI-Nature, BioCarta,
    Reactome, (KEGG - mostly metabolic)

-   Has visualization tool or you can export (XML and BioPax).

-   Data: BioPax is picked up by Pathway Commons, working on getting
    data into caBIO, import Reactome via BioPax. BioPax import/export is
    a step where there is loss of information.

Q. On amount of KEGG data being low

A. The only pull human data

Q. What about canonical pathways from KEGG?

A. PID takes them as is and doesn't deal with gaps from canonical
pathways built using orthologues

Q. Does pathway import lead to redundancies

A. They give no meaning ascribed to names, and wanted to be able to
merge data but they have strict rules of equivalence by database cross
references (some use uniprot vs EG and are thus not equivalent) and
attributes. Manual tweaks did not help the poor mapping. A long term
goal is to detect equivalence.

Q. A participant's internal interaction database numbers are quite
different compared to some of the PID numbers -- asked for
specification.

A. There is a loss of info: only take human data, and what do you count
as an interaction? For example a catalytic activity is not an
interaction in PID, you must have an output to the reaction. They are
not importing HTP data.

-   Retrieve interaction sets and assemble into connected networks.

-   Visualization tools and ability to traverse

-   Showed caBIO model

Q. Suggestion for CDE re-use (accession and PMID)

A. The term they chose is not equivalent to accession. PMID is being
reused already and is in caBIO.

-   There is high interest in pathways because we want ways to
    understand HTP molecular data (genomic neighborhood, clustering have
    problems). Pathways allow for using an existing framework but is not
    limited by linear contiguity.

-   Example is to map both TCGA amplifications and TCGA mutations to
    networks

### SUPPORT SERVICE PROVIDERS 

-   5AM Solutions -- Brent Gendlemen (Pres and CEO)

    -   Adapt, enhance, deploy

    -   <https://gforge.nci.nih.gov/frs/download.php/5297/service_provider_5am_intro.ppt>

-   Ekagra -- JJ Maurer

    -   Adapt, enhance, deploy

    -   <https://gforge.nci.nih.gov/frs/download.php/5298/Ekagra_SSP_ICR_11_12_2008.ppt>

-   SRA -- John Greene

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-   Deploy

-   <https://gforge.nci.nih.gov/frs/download.php/5299/ICW_caBIG-SSP_111208.ppt>

## Next Meeting

**Next Regular Meeting is Cancelled -- the next time is December 10**

Call in: 800-593-0616

Passcode: 2927756

<http://ncicb.centra.com/>

Event ID: ICR_WS

## Attendees

Table 2: List of Meeting Attendees

  -------------------- -------------------- ---------------- --------------
  **Institution**      **Participant**      **Present**      **Required**

  3rd Millennium, Inc. Elaine Freund        Y                Y

  5AM Solutions        Brent Gendleman      Y                N

  5AM Solutions        Joe Croghan          Y                N

  Argonne National Lab Ravi Madduri         Y                Y

  Booz Allen Hamilton  Li Kramer            Y                N

  Booz Allen Hamilton  Patti Kwong          Y                Y

  Baylor College of    David Steffen        Y                Y
  Medicine                                                   

  Broad Institute      Ted Liefeld          Y                Y

  Broad Institute      Jared Nedzel         Y                Y

  Columbia University  Kiran Keshav         N                Y

  Columbia University  Zhong Li             N Vacation       Y

  Dana Farber          Deven Atnoor         N Travel         Y

  Dana Farber          Jomol Mathew         N                Y

  Duke University      Sal Mungal           Y                N

  Duke University      Pankaj Argawal       N                N

  Feinstein Kean       Frank (Trey) White   Y                N
  Healthcare                                                 

  Fred Hutch           Martin Morgan        Y                Y

  Georgetown           Baris Suzek          Y                Y

  IMS                  Mary McAdams         Y                N

  Jackson Laboratory   Grace Stafford       N Hospital       Y

  Johns Hopkins        Bruce Trock          N                Y

  Mass General         Stanley Shaw         Y                Y
  Hospital                                                   

  Mayo Clinic          Bob Freimuth         N                Y

  Mayo Clinic          Brian Wilson         Y                Y

  Nartech              Tom Boals            Y                N

  NCI                  Juli Klemm           Y                Y

  NCI                  Carl Schaefer        Y                

  NCI                  Jenny Kelley         Y                N

  NCI                  Mervi Herksame       N                Y

  NCI                  Denise Warzel        N                N

  NCI \[C\]            Konrad Rokicki       N                Y

  NCI \[C\]            Sue Pan              N                Y

  NCI \[C\]            Jim Sun              Y                N

  NCI \[C\]            Lalitha Viswanath    N                N

  Patient Advocate     Patty Spears         N                Y

  Princeton            Gunter Schemmann     N                N

  SAIC                 Kevin Groch          N                Y

  SAIC                 Donna Messersmith    Y                Y

  Sapient              Stephen Goldstein    Y                N

  Stanford             Samira Guccione      N                Y

  Stanford             David Paik           Y                Y

  Stanford             Daniel Rubin         N Travel         Y

  U of Alabama         John Sandefuer       Y                N

  UCLA                 Buddy Dennis         N                Y

  UCSD                 Hannes Neidner       Y                N

  University of North  Leonard McMillan     Y                Y
  Carolina                                                   

  University of North  Wei Wang             Y                Y
  Carolina                                                   

  University of        Uma Chandran         Y                Y
  Pittsburgh                                                 

  Washington           Nathan Baker         N                Y
  University                                                 

  Washington           Rohit Pappu          N Travel         Y
  University                                                 

  Washington           J. Shaik             Y                Y
  University                                                 

  Washington           Mukesh Sharma        Y                Y
  University                                                 

  Ekagra               JJ Maurer                             

  Ekagra               Kalpesh Patel                         

  SRA                  John Greene                           

  SRA                  David Kane                            
  -------------------- -------------------- ---------------- --------------

Janis

Minh

Raghu

Roger day