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caBIG^®^ Architecture

and

Vocabularies and Common Data Elements (VCDE) Joint Workspace
Face-to-Face Meeting

Notes and Action Items

**Northwestern University, Evanston, Illinois**

**October 27 -- 29, 2008**

**Table of Contents**

[**Day One: October 27,
2008................................................................................3**](#section)

[Deployment
Enhancement.............................................................................................3](#session-title-deployment-enhancement)

[Deployment Adopt/Adapt
Strategies........................................................................\...\...\...\...4](#session-title-deployment-adoptadapt-strategies)

[caGrid Service Deployment: Reports from the
Field........................................................\...\...\...4](#session-title-cagrid-service-deployment)

[.NET Working
Group...................................................................................................6](#session-title-.net-working-group)

[Cross-Cutting and Tissue Banks Workspace: Dynamic
Extensions.............................................7](#session-title-cross-cutting-and-tissue-banks-workspace-dynamic-extensions)

[Break-Out Session 1: Dynamic
Extensions........................](#session-title-break-out-session-1-dynamic-extensions)..................................................8

[Break-Out Session 2:
Workflow............................................](#session-title-breakout-session-2-workflow)\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...9

[Break-Out Session 3: Security Working
Session...............................................................\....](#session-title-break-out-session-3-security-working-session)10

**\
[Day Two: October 28,
2008...............................................................................12](#day-two-october-28-2008)**

[Future of Semantic
Infrastructure....................................................................................12](#session-title-future-of-semantic-infrastructure)

[caGrid Infrastructure and Tools in the
Future...\....................................................................13](#session-title-cagrid-infrastructure-and-tools-in-the-future)

[caCORE Infrastructure and tools in the
Future........................\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...\...13](#session-title-cacore-infrastructure-and-tools-in-the-future)

[New Requirements for Semantic Infrastructure: Tooling Now and in the
Near
Future.......................14](#session-title-new-requirements-for-semantic-infrastructure)

[Gold Compatibility, Pilot Review of
gridPIR.......................................................................16](#session-title-gold-compatibility-pilot-review-of-gridpir)

[Semantic MediaWiki (CTCAE
Review).............................................................................16](#session-title-semantic-mediawiki-ctcae-review)

[CQL
2.0..................................................................................................................17](#session-title-cql-2.0)

[Ontology-based Queries in
caGrid.................................................................................\...18](#session-title-ontology-based-queries-in-cagrid)

[Portlet Development
Discussion......................................................................................19](#session-title-portlet-development-discussion)

[Compatibility Review Software
.....................................................................................20](#session-title-compatibility-review-software)

[New Requirements for Semantic Infrastructure: Infrastructure and
Tools.....................................21](#session-title-new-requirements-for-semantic-infrastructure-infrastructure-and-tools)

**\
[Day Three: October 29,
2008.............................................................................22](#day-three-october-29-2008)**

[Birds of a Feather Session 1.A: Vocabulary Knowledge
Center.................................................22](#session-title-birds-of-a-feather-session-1.a-vocabulary-knowledge-center)

[Birds of a Feather Session 1.B: caGrid Knowledge
Center......................................................
22](#session-title-birds-of-a-feather-session-1.b-cagrid-knowledge-center)

[Birds of a Feather Session 1.C: Modelng within caBIG for Imporved
Semantic
Interoperability..........23](#session-title-birds-of-a-feather-session-2.c-object-or-class-specialization)

[Birds of a Feather Session 1.D: Metadata Registry Futures: Plug-in
Modules...........................\......23](#session-title-birds-of-a-feather-session-1.d-metadata-registry-futures-plug-in-modules)

[Birds of a Feather Session 1.E: Data Provenance on the
Grid....................................................24](#session-title-birds-of-a-feather-session-1.e-data-provenance-on-the-grid)

[Birds of a Feather Session 2.A: Compatibility Review
Software................................................25](#session-title-birds-of-a-feather-session-2.a-compatibility-review-software)

[Birds of a Feather Session 2.B:
Taverna/Workflow...............................................................25](#session-title-birds-of-a-feather-session-2.b-tavernaworkflow)

[Birds of a Feather Session 2.C: Object or Class
Specialization..................................................26](#session-title-birds-of-a-feather-session-2.c-object-or-class-specialization)

[Birds of a Feather Session 2.D: Integrating an Organizational Identify
Provider with the
Grid............26](#session-title-birds-of-a-feather-session-2.d-integrating-an-organizational-identity-provider-with-the-grid)

#   {#section .unnumbered}

# Day One: October 27, 2008

## Session Title: Deployment Enhancement

**Date:** October 27, 2008

**Time (CST):** 845-945 AM\
**Speaker(s):** Avinash Shanbhag

**\
Action Items**

  -------- --------------- ------------------------------------------ -----------
  **\#**   **Assigned To** **Description**                            **Due
                                                                      Date**

  **1**    Cross-Cutting   Those interested in obtaining Knowledge    On-going
           WS Participants Center accounts should sign up at:         
                           <http://wikiutils.nci.nih.gov/KC_signup>   

  **2**                                                               
  -------- --------------- ------------------------------------------ -----------

**Notes**

> *Challenges Ahead*

-   In Utah (January 2008) we discussed Training, Getting connected,
    Knowledge Center launch

-   Supporting Bundles: The Cross-Cutting Workspaces (XCWS) are heavily
    involved in making the Bundles successful, e.g., Single sign-on
    component

-   A large effort this year was focused on Deploying a Functional Grid
    Node at various cancer centers by September 30, 2008.

-   XC WS is supplying help to Cancer Centers who need (e.g., mentors)
    are deploying caBIG^®^.

-   There are now 130+ services on the Grid: "We have deployed the
    biggest interoperable health IT network the world has ever seen"-
    George Komatsoulis

-   caGrid User community is growing (# of downloads \>1000, \#
    subscribers \>200, number of questions per day \>10)

-   How do we grow/scale to meet the needs of deployment?

-   caBIG^®^ technologies are in use by the National Health Information
    Network (NHIN), the UK National Cancer Research Institute (NCRI) and
    the National Heart Lung and Blood Institute (NHLBI) Cardio Vascular
    Research Grid (CVRG).

-   Knowledge Centers are intended to be a self-sustaining model.
    Participants are encouraged to create accounts which are open to
    everybody.

    -   Discussion forums, bug reports, feature requests and development
        of code repository

-   Support Service Providers: First set of licensed Service Providers
    on October 2, 2008.

> *At caBIG^®^Annual Meeting 2008:*

-   Training and outreach (e.g., tutorial by Baris Suzek)

-   Compatibility reviews & Worlds Fair demos

-   Hack-a-thon, e.g., caBIO

-   Continue our work with other Workspaces: e.g., Workflow with ICR

-   XC WS have been fulfilling mission to outreach to Domain WS and
    taking in input from Domain Workspaces

-   Training (cont) : Recent Bootcamp (China and India attendees)

-   caBIG^®^ and NCRI (UK) collaboration (grid of grids)

-   TeraGrid (won Best Technology Track Paper)

-   XC WS garnered Annual Meeting Recognition awards

-   Security is key element: Policy Analysis Framework

-   Security Working Group: LOA (Level of Assurance) 1 and 2, pilot
    efforts with University of Texas (Credentialing), enterprise
    security requirements

## Session Title: Deployment Adopt/Adapt Strategies

**Date:** October 27, 2008

**Time (CST):** 1015-1115 AM\
**Speaker(s):** Paul Courtney

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Q: In the National Health Interview Survey (NHIS), what does
    SMOKE100 stand for?

> A: The survey identifies a smoker as someone who has had 100
> cigarettes in their lifetime.

-   Q: How does one know if the data being shared is real or not?

> A: This remains an open question.

-   Q: How do we measure the use of an enterprise data warehouse?

> A: Instead of measuring how we will capture the data, how will we use
> it going forward?

-   Q: De-identified data does not mean open access; how do we bring
    people on to data sharing?

> A: This question has to do with communication issues with Center
> Deployment Leads (CDLs). We will address CDL issues in enterprise
> program year 2 by incorporating the issues in year 1 into the roles
> and responsibilities for year 2.

-   Q: Will legacy application scripts made available?

## Session Title: caGrid Service Deployment

**Date:** October 27, 2008

**Time (CST):** 1115 AM-1200 PM\
**Speaker(s):** JJ Maurer, Justin Permar, Kunal Modi

**\
Action Items**

  -------- --------------- ----------------------------------------- -----------
  **\#**   **Assigned To** **Description**                           **Due
                                                                     Date**

  1        Denise Warzel   Bring back requirements to CORE team from November
                           session.                                  2008

  2        Cross-Cutting   Request caGrid Knowledge Center wiki      November
           WS Participants accounts if interested.                   2008
  -------- --------------- ----------------------------------------- -----------

**Notes**

*caGrid Service Deployment -- JJ Maurer*

-   Test data may eventually be removed from Production Grid.

-   Labeling different kinds of data on the grid with metadata could be
    used to indicate quality (i.e., tagging data to indicate
    peer-review, etc.).

-   Users want to know "If someone wants to use my data, what
    information do they need in order to know it is usable to them?"

-   Q: Do we have the appropriate domain experts participating to
    provide that metadata?

-   Q: Is there a link between Grid services and metadata registries?

-   Denise Warzel will take back requirements to CORE team, including
    services and data quality as part of solution.

-   Q: How many systems indicated they wished to link legacy systems and
    migrate data to caTissue Suite? Were there any commonalities among
    legacy systems at different deployment sites?\
    A: These site systems were almost all home-built with a few
    commercial systems who would rather adapt than adopt. We need
    solutions for middle point to stage data through database staging
    transformation and then loading of the data.

-   Q: Have we reused transformation scripts where we could reuse
    functionality?

*caGrid Knowledge Center -- Justin Permar*

-   Participants were reminded to request caGrid Knowledge Center (KC)
    wiki accounts.

-   Guides/Mentors will provide a stream of information to the KC. This
    information will be covered further in the caGrid KC BOF session.

-   A middle ground of communication between detailed and high-level is
    needed, and the Communications Team should be plugged in to help.

-   caBIG^®^/Grid Users are not necessarily all familiar with caBIG^®^.
    The KCs will be helpful as central information centers.

-   Centers with contracts to deploy need to be able to complete their
    contracts with features currently available. Not helpful to simply
    say this feature will be in the next release.

    -   One mechanism to address this issue is to enable fixing problems
        in current releases.

    -   All bug reports and feature requests should go through the KC.
        Deployment Team should decide and communicate to grid developers
        if certain fixes/new features need to be made ASAP. A Grid
        Mentoring program with the KC is in place to voice these needs.

-   caGrid infrastructure was distinguished as the architectural
    "plumbing" and not the Enterprise application development that sits
    on top of that layer. There are some gray areas in terms of domains
    and POCs to bring the right people to the table to solve customers'
    problems.

-   The caGrid KC is routing issues to other KCs, and we must stay
    customer-oriented. The main challenge for the CDL is to know which
    forum(s) to post to.

-   The KC is intended for users with questions or for groups to get
    products on the grid. We will provide grid mentors as main POCs.

-   The Enterprise Support Network describes the KCs and corresponding
    areas of expertise for users to know where to post/start.

## Session Title: .NET Working Group

**Date:** October 27, 2008

**Time (CST):** 215-300 PM\
**Speaker(s):** Marty Humphrey

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  1                                                                 

  2                                                                 
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Q: Is there anything fundamental to what we are doing that requires
    Common Query Language (CQL) server 2005?\
    A: No, we just used CQL 2005 as a test bed.

-   The .NET client is running on the training grid.

-   Q: What are the issues with CQL processing?\
    A: There is a fairly broad language for how to trivially parse CQL
    queries, mapping to data on the back end and serving back to the
    user.

-   We can take advantage of things that Hibernate provides access to.
    Need to determine how much we could leverage Hibernate.

-   Q: What could we do regarding the Web Service Definition Language
    (WSDL)? Extensible Stylesheet Language Family (XSLT) can be used for
    tooling transparency if Java clients can consume modifications and
    have the infrastructure roll into Core deployment.

-   There are no plans in this project scope for integrating with caGrid
    security.

## Session Title: Cross Cutting and Tissue Banks Workspace: Dynamic Extensions

**Date:** October 27, 2008

**Time (CST):** 300 -- 345 PM\
**Speaker(s):** Brian Davis

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   CTMS is good at modeling their processes using Actors, Artifacts and
    Actions.

-   The next Break-Out Session for Dynamic Extensions will include going
    through the process for making Dynamic Extensions
    caBIG^®^-compatible.

-   The goal for today is to have a better description of the process.
    We should consider tool requirements to make the process more
    efficient and quicker.

-   The final deliverable for the Break-Out session is to create an
    activity diagram of the process, with more detail around the
    process.

-   The Break-Out session will define the different terms used, like
    "owner," "create," "Dynamic Extension," and "submit." It will define
    the actors, artifacts and actions.

-   The ultimate goal is to make the Dynamic Extensions work!

-   Q: This is a use case for TBPT using caTissue Suite; does this
    activity only apply to caTissue and TBPT or is this relevant for
    other workspaces? Should we look at just caTissue or at the broader
    way to approach this since others will be working on it too, like
    caIntegrator?

> A: caBIG^®^ has always been better at focusing on real use cases, like
> caTissue rather than trying to accommodate larger scopes, and using
> the example of the real use case to broader issues.

-   Q: The actors, roles, and actions sounds similar to the HL7v3 model.
    Are you trying to harmonize it into HL7?

> A: There is nothing specific to HL7, but the need for an activity
> diagram. It is too complicated for just a small group of people to
> solve, and needs to be opened to a larger more diverse community.

-   The exercise is to describe the Compatibility Review process and
    interoperability, and how it can be applied to Dynamic Extensions.

-   There is a need for input from the Architecture and caCORE SDK teams
    to address the issues of how to add extensions and put them through
    the APIs. Dynamic Extensions need to be instantiated as a separate
    service. It is important to have discussion on how SDK and Introduce
    can help address Dynamic Extension issues.

-   It would be helpful if Ian Fore (TBPT WS Lead) and others from the
    TBPT Workspace can articulate the use cases so that the obstacles
    can be pointed out explicitly.

## Session Title: Break-Out Session #1: Dynamic Extensions

**Date:** October 27, 2008

**Time (CST):** 400 -- 530 PM\
**Speaker(s):** Brian Davis

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

*XCWS Team*

-   The process might be more similar to that of a CDE Review instead of
    a Compatibility Review.

-   Adopters would be providing the Dynamic Extensions.

-   Problem: Each user expands model with their own Dynamic Extensions.

-   Who owns the TBPT Domain Analysis Model (DAM)?

    -   Software Developers?

    -   Knowledge Centers?

-   The key is to make sure the owner of the model extensions is
    identified!

-   Assumption: XCWS, if not the owner, will be involved in
    harmonization.

-   Proposed steps for submission of dynamic extensions:

    -   Step 1 (B1): After model submitter informs the Life Science (LS)
        Composite Architecture Team (CAT)/LS DAM, then the XCWS review
        the Compatibility Review Submission Package. CRS receives the
        Compatibility Review Submission Package. TBPT will have to
        designate authority for the model.

    -   Step 2 (B2): CRS Loader loads CRS package.

    -   Step 3 (B3): Compatibility Review Team leads review

    -   Step 4 (B4): Compatibility Review team Leader
        **[assigns]{.underline}** load to CRS Loader. This step was
        removed since the CRS receives the submission package.

    -   Step 5 (B5): CRS Loader **[loads]{.underline}** Compatibility
        Submission Package to CRS. This step was moved to Step 2 (B2).

    -   Step 6 (B6): Compatibility Review team Leader **[assigns
        tasks]{.underline}** to Compatibility review team. This step is
        okay.

    -   Step 7-9 (B7-9): (B7) Compatibility Review team
        **[reviews]{.underline}** Artifacts and annotates criteria, (B8)
        Compatibility Review team Leader **[collates]{.underline}**
        individual reports and **[produces]{.underline}** full Review
        report, (B9) Compatibility Review team Leader
        **[Present]{.underline}** CRS artifacts and final review
        artifact and ppt to XC WS telecons via telecon for VOTE. There
        should be a "Delta" Review as opposed to full Compatibility
        Review. Alternatively suggested that this review process would
        be a CDE Review and not a Compatibility Review at all.

    -   Step 10 (B10): XC WS participants **[discuss and
        VOTE]{.underline}** (pass or not pass). The group discussed how
        they could shorten the review process, but ultimately the XC WS
        would need to have a final vote.

    -   Step 11 (B11): XC WS (pointperson9) **[informs]{.underline}**
        TissueBanks (pointperson10), LS_CAT, LS_DAM,
        caTissueSuiteModelOwner, caTissueSuite Developers, Owner of
        DynExt. The package should go back to the person who submitted
        the package in B1.

-   VCDE Proposal: The XCWS will only accept reviews developed against
    the latest approved version.

-   If the proposal is not accepted, there should be some "policy" in
    place stating that someone in the domain WS will be responsible for
    duplicate/similar models (standardization issue).

-   It is a content review, not an application review.

-   There is a need to "define" some type of review that may not be a
    Compatibility Review or a CDE Review. It should be a streamlined
    process.

-   LS CAT/LS DAM issue: Recommendation that in Step A3 submission team
    needs to report to LS CAT/DAM. This is a task for the TBPT.

-   LS CAT/DAM should be involved before B1 step, the process specified
    by the domain WS.

-   An added artifact for XCWS would be a statement from the TBPT WS
    that it has informed the LS CAT/LS DAM team about the model and
    which includes a response from the LS CAT/DAM team.

-   XCWS Actors: Recommendation to remove EVS content team, caDSR
    curators and Claire Wolfe.

-   TBPT Actors: Recommendation to add LS CAT/LS DAM team or other
    Domain Authority.

-   The group briefly discussed issues around just changing Value
    Domains of some CDEs and versioning issues.

-   Suggestion to have a "Diff" function within the CRS to identify
    differences in the dynamic model and the XMI (the original model
    needs to be included in the submission package).

-   VCDE Proposal: Dynamic Extensions can only be added to those
    applications that have already passed Silver Level Compatibility.

-   The group decided that a pure CDE review was not sufficient. The
    review process needs to include a review of the model as the CDEs
    are attached to the model.

-   Finally, the group asked how they could make the review process
    faster than a "normal" Compatibility Review.

There needs to be a whole section here on TBPT side

## Session Title: Breakout Session #2: Workflow

**Date:** October 27, 2008

**Time (CST):** 400-530 PM\
**Speaker(s):** Ravi Madduri

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Ravi got a real use case for workflows!

    -   The use case pulls specified phenotype out of a study in
        caTissue and send computational analysis to Gene Pattern.

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-   There was a lively discussion around syntactic interoperability and
    CDE reuse.

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-   Orchestration vs Choreography

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-   Discussion around Recommendations document from ICR Workflow working
    group

    -   Lack of Analytical Services

    -   Service Stability

    -   Services Using Older Versions of caGrid

    -   Shim/Translation Services

    -   Statistics for data-type reuse and User Experiences (when using
        services)

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-   Need tooling to find the models that are out there so the developer
    can reuse.

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-   Local view vs Global view for the developer

    -   Processes and governance for Shim services

    -   Shim service -- does someone have a responsibility to "fix" to
        make "interoperability" without Shim?

    -   Might this be a "CRS" function to detect "Shims?"

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-   Joel suggested a bottom up approach to observe the patterns of reuse
    in ad hoc integration/workflows and the other would be a top down
    approach to look at research projects like The Cancer Genome Atlas
    (TCGA) and I-SPY2 for reusable models and recommend them.

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-   Q: When you have a "Service Failure" in the middle of a workflow, do
    you lose all the previous work you have done?

> A: No

-   Q: In Taverna Workflows does the data always have to come back to
    the program you are using?

> A: Yes

-   Q: Can you also integrate standard Web services?

> A: Yes

## Session Title: Break-Out Session #3: Security Working Session

**Date:** October 27, 2008

**Time (CST):** 400-530 PM\
**Speaker(s):** Steve Langella, Kunal Modi

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  1        Steve          Contact the University of Texas           December
           Langella,      federation (i.e., Clare Goldsmith) around 2008
           Kunal Modi     having Shibboleth as a Grid API for       
                          authentication services.                  

  2                                                                 
  -------- -------------- ----------------------------------------- -----------

**Notes**

> *caGrid 1.3 Security - Steve Langella*

-   Presentation:

-   GAARDS Overview

-   caGrid 1.3 Security Features

-   Project Information

-   Discussion:

-   How do we "sell" caBIG security to cancer centers? They may view our
    authentication/authorization systems as an extra layer on top of
    their own.

-   There may be a change in philosophy for centers in terms of
    federation as we move to using other types of certificates.

-   There are subsets within institutions seeking Level of Assurance
    (LOA) 2 access (for low to medium sensitivity data).

-   We need to talk to the University of Texas federation (i.e., Clare
    Goldsmith) around having Shibboleth as a Grid API for authentication
    services.

-   Anyone operating at LOA3 is essentially operating at Levels 1 and 2
    by inclusion.

-   Review of proxy versus short term certificates -- the protocol and
    infrastructure are largely the same but there are certain
    differences. Proxies can be used for delegation.

-   Auditing:

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-   Requirement for Identity Providers to be sent auditing reports (to
    view own information on authentication).

-   Are there any auditing ties to the Portal?

> *caGrid Security: A Deployment Perspective - Kunal Modi*

-   Presentation:

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-   Security -- Current Perspective, Ground Reality, Deployment
    Perspective

-   Firewall Issues

-   Tech Stack Concerns

-   Securing a Container

-   Physical Access

-   Application Security

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-   Discussion:

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-   Center Deployment Leads and Center Directors need education on
    security issues and upgrades. We need data about identity management
    systems delivered to the deployment centers.

-   Regarding security vulnerabilities, we need a well-defined procedure
    with roles and responsibilities for reporting patches and upgrades
    (procedure development in progress).

-   There are no standard ratings for levels of vulnerability.

-   There are many advantages to using existing commercial standards for
    authorization instead of creating our own.

-   Applications have their own identity providers and credentials;
    institutions need help in migrating their local security to the
    grid. This migration may work for the majority of applications that
    are built on caCORE but it may not work for all applications.

# Day Two: October 28, 2008

## Session Title: Future of Semantic Infrastructure

**Date:** October 28, 2008

**Time (CST): 815-830 AM**\
**Speaker(s):** Frank Hartel

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**    Frank Hartel   Give PPT version of presentation to       October 29,
                          Brian/Summy to be posted.                 2008

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Frank discussed some ideas of what to do in the future regarding
    semantic infrastructure from feedback received from others.

-   Defined "data semantics" and the challenges faced in past years to
    do this. There is a need to make information explicit as opposed to
    traditionally implied formats.

-   Q: When you talk about payload, is it your vision that metadata
    about the actual content will reside within the payload, or is it
    external from the payload and the structure of the message?

> A: We know how to do metadata now, we can anticipate what needs to be
> described and how to store it. We are not currently using it to
> dictate how it behaves and how routing occurs. There may be some
> things we are not using. This would be above the metadata. We do not
> know how to analyze the meaning of the content of a message payload.
> If we could do that, it would supplement the messaging.

-   Q: In a particular string, do the XML tags correspond to a specific
    class?

> A: It could do that. It could explain how tags relate to other
> classes. Because you can create and maintain with automated tools
> covering all the important aspects of your operation. The tags can be
> fine-grained and detailed.

-   C: It can be challenging for binary data.

> R: This is true but Gittens' theory was more targeted to data that
> could be parsable, but it is possible to look at doing this with
> binary data.

-   Q: Is this different than notions of content-driven data? Like EA
    and SOA.

> A: No it is not different.

## Session Title: caGrid Infrastructure and Tools in the Future

**Date:** October 28, 2008

**Time (CST):** 830-900 AM\
**Speaker(s):** Larry Brem, Scott Oster

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  1                                                                 

  2                                                                 
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   The challenge of the KCs is to work together to build and support
    the community.

-   The KCs are addressing user needs and feeding back into caGrid
    timelines.

-   Building high-order APIs; application teams need to contribute to
    this effort in addition to development. The Google team published
    their SDK. APIs have been built that combine different grid
    components that they might publish to community to use as well. The
    KCs should support this open-source activity -- i.e., making code
    available such that users can look at the code and use it for
    development. The Incubator platform of the Grid KC is available for
    this purpose.

-   Need to support reusable infrastructure, APIs and tooling.

## Session Title: caCORE Infrastructure and Tools in the Future

**Date:** October 28, 2008

**Time (CST):** 900-930 AM\
**Speaker(s):** Denise Warzel

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   There are new tools that perform user interface analysis.

-   It is important to be able to explain how to interface with these
    tools to clinicians.

## Session Title: New Requirements for Semantic Infrastructure

**Date:** October 28, 2008

**Time (CST):** 1000-1100 AM\
**Speaker(s):** Panel (Individual names below)

**\
Action Items**

  -------- --------------- ----------------------------------------- -----------
  **\#**   **Assigned To** **Description**                           **Due
                                                                     Date**

  1        Cross-Cutting   Contact Ravi Madduri with further use     On-going
           WS Participants cases for workflow.                       

  2        Ravi Madduri    Follow up with Satish Patel around gene   End
                           pathology querying based on ICR Workflow  November
                           WG (for gRAVI)                            

  3        Cross-Cutting   Participants with further questions       On-going
           WS Participants around new requirements for tooling       
                           should contact the individual speakers.   
  -------- --------------- ----------------------------------------- -----------

**Notes**

> *caDSR -- Bilal Elahi*

-   Clinician as Community Physician not just researcher

-   Q: When will training be available?

> A: Generally training comes out with the release, based on release
> date.

-   Q: Are you talking about the caCORE curriculum?

> A: It will be available with the CORE release scheduled for January
> 2009.
>
> *SIW/UML Loader -- Christophe Ludet*

-   4.0.0.1 release -- Late November

-   4.0.0.2 release -- Early 2009

-   Multi-dimensional arrays (Check with Baris)

> *LexEVS -- Tom Johnson*

-   The LexEVS developers are interested in knowing how many are
    actually using the old API. There is a forum on the Vocabulary KC
    site to "poll" this. They requested that the community to go to the
    site and register and let them know if they are using the old API.

-   Q: Is there anything on the Vocabulary KC site under LexEVS?

> A: Currently there is nothing there. It will be the same API and could
> applied to connecting to the Grid.
>
> *caGrid Core -- Scott Oster*

-   Q: Do you have to rewrite the second pass through, or will Globus
    figure out that you already have data 1, 3, 5, etc.?

> A: It will be able to identify which services the different data came
> from.

-   When a re-query is done, it would be able to know which data
    services were down and the data could be mapped back to its source.
    Query execution control associating new metadata with results;
    remove, wait and try 10 min later, 5 times.

-   Q: Is channel comprehension available to help reduce data transfer
    in Globus?

> A: Channel compression with Globus Tool Kit: Can do with transfer
> missing uniform. Transfer is per application issue right now depending
> on how you are going to use it. Can specify compressing on this end
> and decompressing on the other end.
>
> *caGrid Portal -- Josh Phillips*

-   Q: How will ontology-based querying plug into the portal?

> A: People involved in ontology based queries will be integrated into
> this work, but not sure when/how.

-   Q: What is the possibility of exposing other information and
    querying on similar things, like CDEs called different things by
    different groups?

> A: Part of this issue will be addressed by caDSR team.

-   caDSR for 4.0.0.2 will surface data on the Grid, which can be
    queried through the Portal. Ontology Query work -- Construct user
    interface to use ontology to build query. Search on alternate names
    of data element.

> *caCORE SDK -- Satish Patel*

-   An overview of caCORE SDK 4.1 new features was given, followed by a
    description of the future direction of the SDK.

-   The caCORE SDK 4.1 release date is November 14, 2008.

> *caGrid Workflow -- Ravi Madduri*

-   Please continue to submit use cases for workflow. Cross-cutting use
    cases for translational science will help define what can be
    satisfied by our tools today and help identify the gaps to address.

-   Workflows stored on Portal.

-   Need Translational Enterprise Use Cases

> *gRAVI -- Ravi Madduri*

-   gRAVI can be used to invoke services as part of workflow to get
    queried results.

-   This team is working with the UK myGrid team to expose myGrid
    analytics as grid services.

-   Ravi Madduri should follow up with Satish Patel around gene
    pathology query feedback based on ICR Workflow WG work.

-   Can use gRAVI as part of Taverna. GeneConnect/caBIO/Chromosome
    increase/decrease expression.

> *Introduce -- Shannon Hastings*

-   Introduce 1.3 enhancement review, including security, service
    development, and future enhancements.

-   Q: In using Globus, is there any plan for movement to a SAX-based
    parser?\
    A: The integrity of messages with security is hard to ensure, due to
    security breaks from service reassembly. This parsing can be
    facilitated by a spring security framework. There will be an
    evolution of Globus in the next few years (i.e., new design on top
    of SOAP stack), and the Introduce team will be keeping up with this
    evolution to adopt its tools.

## Session Title: Gold Compatibility, Pilot Review of gridPIR

**Date:** October 28, 2008

**Time (CST):** 1100 AM-1215 PM\
**Speaker(s):** Scott Oster, Bob Freimuth, Sal Mungal, Lynne Wilkens,
Lewis Frey, Pankaj Agarwal

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Interface model provide?

-   For analytical service, so for data services (SQL queries)

## Session Title: Semantic MediaWiki (CTCAE Review)

**Date:** October 28, 2008

**Time (CST):** 130-200 PM\
**Speaker(s):** Traci St. Martin, Ann Setser, Lewis Frey

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   In the Medical Dictionary for Regulatory Activities (MedDRA) the
    lower level term is the level which will be the adverse event (AE)
    term in the Common Terminology Criteria for Adverse Events (CTCAE)
    version 4.0.

-   MedDRA has 5 levels of hierarchy and CTCAE has 2 levels.

-   In 1994 the Common Toxicity Criteria (CTC) started mapping to
    MedDRA, but this mapping has been imprecise

-   The Cancer Therapy Evaluation Program (CTEP) decides when its
    necessary to revise CTCAE.

-   There was a comment that recording physicians are using the CTCAE
    revision technology in order to better support their needs.

-   Q: Having hundreds of people submitting proposals at a time, how did
    you handle the difficulty in curating this terminology?

> A: Single members of working groups were entering information into the
> Wiki.

## Session Title: CQL 2.0

**Date:** October 28, 2008

**Time (CST):** 230-300 PM\
**Speaker(s):** David Ervin and John Eisenschmidt

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes:**

-   Current query capability (1.0)

-   Simple, arbitrary data source

-   Path based query, driven by domain model

-   Logical grouping capability

> *Issues:*

-   Often too simple

-   Can be confusing (flexible, but confusing)

-   Binary and Unitary attributes hard to distinguish

> *Changes to make in 2.0*

-   From users, e.g., IMG and TBPT

-   Populate associations

-   Add in strong Value Types

-   More aggregating function

> *Association Population:*

-   Typed attribute values

-   Query Modifiers

-   Technology preview process

-   Continuous Feedback process

-   Survey Process

-   Resources

-   Q: Can you use the technology preview to teach domain specialists
    interested in technologies to use the tooling (e.g., clinicians)?

> A: Not in scope for this effort.

## Session Title: Ontology-Based Queries in caGrid

**Date:** October 2, 2008

**Time (CST):** 315-345 PM\
**Speaker(s):** Josh Phillips, John Carter, & Alejandra Gonzalez-Beltran

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   It is a great idea to adopt modularity ontology approaches
    (IBM/Cimino Paper).

-   Reasoning on instance data in full-blown Grid can be an issue. How
    can we adopt modular ontology for instance data? Microsoft has an
    application doing an A Box summarization that could address instance
    level data.

-   Q: Where should the reasoning services exist? LexBIG, LexEVS
    services infrastructure?

> A: Could model an interface so that someone could request modeling a
> reasoning service. Not sure if we can have them in LexBIG. It is a
> black box right now.

-   Q: Are you converting the entire Grid response to an RDF output, or
    is it only relevant to existing components of the OWL model?

> A: Alejandra is working on this with OWL ontologies.

-   Q: Are you asking for instance data or model data? I am asking about
    response data (from the query). Is the data coming back as Grid
    data, or semantically integrated data?

> A: You should be able to request/query OWL instance data and get OWL
> instance data back.

-   Query Translation (DMR, SPARQL)

-   Where is "reasoner" functionality?

## Session Title: Portlet Development Discussion

**Date:** October 28, 2008

**Time (CST):** 415-445 PM\
**Speaker(s):** Konrad Rokicki, Manav Kher, Josh Phillips

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  1                                                                 

  2                                                                 
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   A caBIO Portlet demo with the training grid was given to show a
    microarray annotation query by gene.

-   The Liferay Portal is a good tool for web application developers,
    but the caGrid Portal has sufficient functionality on its own.

-   It was suggested that Tapestry be considered for built-in portlet
    support.

-   The caBIO portlet was developed in two months with a full-time FTE.

-   Q: Are there plans to communicate over the Grid through the Portal
    rather than through a back-end API (i.e., move a portlet to talk to
    caBIO over the Grid)?\
    A: No, this is not part of the plan; current grid APIs were used for
    greater efficiency (i.e., HQL, AJAX) to query the grid directly.

-   Q: Can you comment on the performance of the applications as
    stand-alone versus integrated?\
    A: The response time is comparable, but will be uncertain as more
    portlets are added.

-   There may be plans to develop another portal for portlet to portlet
    communication.

## Session Title: Compatibility Review Software

**Date:** October 28, 2008

**Time (CST):** 500 -- 530 PM\
**Speaker(s):** Bob Freimuth

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Q: Are primary concepts ordered?

> A: Yes they are.

-   Q: Do you get the last one (CDE Reuse) from caDSR?

> A: It comes from the caDSR. When we do the query we look at workflow
> status, and pull it out from there.

-   Q: Will it still turn pink if there is something wrong with it?

> A: All the things that are wrong, for example, those things which you
> said "no" to as a reviewer, will be in the report.

-   Q: Can you make it easier to load?

> A: Yes, it is on the future functionality list.

-   Q: Is there going to be a keyboard navigation function for those who
    use their keyboard more than the mouse?

> A: We can talk about it.

-   Q: If an incremental review of a project was done on a project that
    was already reviewed would you have to submit both XMIs?

> A: If the first review was done by CRS, then no, but if not then yes.

-   Q: Some are color blind; is there a way to put a checkbox?

> A: Yes, there is a way to filter for anything unanswered and it will
> be color coded.

-   Q: There are Y/N questions in individual reports, will you include
    color coding in that report?

> A: We do not have this feature currently, but we could consider it.

-   We have to be aware of 508 Compliance.

-   Q: Would hidden associations be shown?

> A: They should be.

-   Requirements:

    -   Easier load (not BOB FREIMUTH, developers should eventually do
        it)

    -   Keyboard navigation

    -   To see what has been reviewed -- check box instead/in addition
        to color

    -   Color review in individual reports

    -   508 Compliance requirements

## Session Title: New Requirements for Semantic Infrastructure: Infrastructure and Tools

**Date:** October 28, 2008

**Time (CST):** 530-545 PM\
**Speaker(s):** Larry Brem

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   *Knowledge Centers*

    -   Should be the user advocate, not shuffle users around

    -   caGrid KC will be helping with Deployment

-   *Deployment*

    -   Need to have really simple deployment packages

    -   Make available legacy application scripts

-   *.NET*

    -   The infrastructure can support .NET applications with minimal
        additional work (14 minutes)

    -   For a client there were 6 lines that needed to be edited (they
        are buried in the Axis system and may be hard to fix)

-   *Security*

    -   Technology and Policy need to be better aligned

    -   How do we "sell" caBIG security to Cancer Centers

```{=html}
<!-- -->
```
-   *Workflow*

    -   We got another use-case!

    -   Service Stability is very important

    -   Shim services mean lack-of-interoperability, but are sometimes
        necessary

        -   Who maintains shim services?

        -   If a shim is necessary, someone should look *real* close at
            it

-   *Dynamic Extensions*

    -   Tissue Banks KC will be instrumental

    -   Review of XMI comparison

    -   We really need a Life Sciences Domain Analysis Model

    -   Cross-Cutting and Domain Workspaces will need to figure out how
        to deal with them

-   *Gold Compliance*

    -   Tooling needs

    -   Requires Automation

-   *CQL 2.0*

    -   Take into account associations

    -   More aggregation functions

    -   Have a new technology Preview Process

-   *Ontology Based Queries*

    -   See Josh Phillip's slide

    -   SQL to SPARQL translation

-   *COPPA*

    -   ISO Datatypes its own project?

    -   Behavioral and functional semantics will be important going
        forward

    -   Should we do semantics by contract?

# Day Three: October 29, 2008

## Session Title: Birds of a Feather Session 1.A: Vocabulary Knowledge Center

**Date:** October 29, 2008

**Time (CST):** 900-1030 AM\
**Speaker(s):** Cheryl Nintemann

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

Questions for the Vocabulary Knowledge Center team:

[Content:]{.underline}

-   Would you consider expanding information on the Vocabulary Knowledge
    Center to include information on terminology, vocabulary and
    ontologies for people who are not familiar how they work or can
    help?

    -   there is already some content related to vocabulary and

> terminology within the wiki; however, we will continue to
>
> address this need and add content that is appropriate for
>
> potential users to assist them in their needs

[Code Repository]{.underline}

-   Is the Vocabulary Knowledge Center looking at other types of data to
    store within the repository that does not relate specifically to the
    tools within our scope but more towards vocabulary and terminology
    in general?

    -   this is a possibility to address the needs of users

> wanting information on vocabulary and terminology; will
>
> have to look at what is available for migration and
>
> appropriateness for our customers

## Session Title: Birds of a Feather Session 1.B: caGrid Knowledge Center

**Date:** October 29, 2008

**Time (CST):** 900-1030 AM\
**Speaker(s):** Justin Permar

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Additional user track: systems administrators

    -   Mobile applications for iPhone, etc., especially to get updates
        about changes on the Grid (status, etc.), e.g., Google widgets

-   Need information comparing and contrasting Grid vs. other enterprise
    options such as ESB, SOA, etc.

-   Need to link data sharing plans to Grid security implementation

-   Fostering the caGrid community

    -   KC hosts open conference call / chat room for any and all
        questions/topics

    -   Potentially host users group call, inviting users (e.g.,
        incubator project reps) to present

    -   caGrid announce list for community to announce/advertise
        projects, services, contributions

    -   Tag cloud on the wikis: most popular pages are easiest to find

    -   Portlet displaying statistics on models to facilitate re-use

**Session Title: Birds of a Feather Session 1.C: Modeling within caBIG®
for Improved Semantic** Interoperability

**Date:** October 29, 2008

**Time (CST):** 900-1030 AM\
**Speaker(s):** Stuart Turner

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Need to add notes here.

## Session Title: Birds of a Feather Session 1.D: Metadata Registry Futures: Plug-in Modules

**Date:** October 29, 2008

**Time (CST):** 900-1030 AM\
**Speaker(s):** Denise Warzel

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Summary: Idea of taking content from the caDSR and local registry
    and using XML transformers to map them to models.

-   SAWSDL: link it to ontology (a standard tag name for XML schema and
    WSDL).

-   Q: What is the purpose? Are you writing SPARQL queries?

> A: Concepts are linked to ontology references.

-   Currently, when writing queries against these things, the person
    querying needs to have a deep understanding of ontologies.

-   In order to map ontologies to data models, SPARQL code needs to be
    written for each database. It is no small task.

-   Layering the different languages on top of each other results in
    more specificity (UML, RDF, OWL).

-   CQL is much harder than SQL. We should look at an end product with
    simple query language and starting with that end product, work
    backwards.

-   The question is: where's your market? Will the next market already
    know CQL and it won't be as difficult?

-   End users should not have to know about the model. From the use case
    backwards, you can identify the ontologies that would need to be
    used.

-   Q: what is eXist (LGPL = public license)?

> A: It is a type of database that would use a specific language.

-   The ID has 3 parts: name of source, public id, and version.

-   Q: Is it .NET based?

> A: It is a combination of technologies, but it goes through .NET
> framework.

-   Q: Can you make it into a virtual server?

> A: You can make your desktop available to others if that is a virtual
> server.

-   Q: Can you open others' registries?

> A: Yes, if you know the address. You can make yours available to
> others.

-   It is not a distributed registry, but a decentralized registry
    (extract and load).

-   Q: Can you do federated queries?

> A: No, you can only query one registry at a time.

-   Linking tags will probably be a future function.

-   It uses the same API that the Semantic Integration Workbench (SIW)
    uses.

-   Can currently look up data elements and concept codes, but not value
    domains.

-   Can create own CDE as well as search for existing CDEs to use.

-   Creates element in the local metadata registry (MDR).

## Session Title: Birds of a Feather Session 1.E: Data Provenance on the Grid

**Date:** October 29, 2008

**Time (CST):** 900-1030 AM\
**Speaker(s):** Jim McCusker

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Need to add notes here.

## Session Title: Birds of a Feather Session 2.A: Compatibility Review Software

**Date:** October 29, 2008

**Time (CST):** 1100 AM-1230 PM\
**Speaker(s):** Bob Freimuth

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

> 1)      URLs on GFORGE. Add the URL and the description to the gforge.
> Also, add the URL for 3.0 on 2.1 webpage and vice versa (Brian);
>
> 2)      Easier access to people to review data (Brian). Discuss
> specific use cases.
>
> 3)      Tables where we double click right now; make it like a URL
> (underline/highlight/mouseover) and activate at single click (Brian).
>
> 4)      Tag that says whether it is a Silver level or gold level
> review-once you are on the actual review page (Avinash).
>
> 5)      Able to resize the left hand panel. (Brian)
>
> 6)      Also add the button save, reset to the top of the page
> (Brian).
>
> 7)      Move finish review away from save and reset buttons (Mukesh,
> Brian)---people might hit finish by mistake.
>
> 8)      In Submission package, when you load the required files---if
> you have not provided all the files at one time, the link to the other
> files gets lost when the error is generated. This is after admin
> approves the initial package.
>
> 9)      The wording all classes and attributes --need to be change to
> this class or this attribute (Mike).
>
> 10)   For non-enumerated value domain the check list items related to
> the enumerated VD should be defaulted to No applicable or not shown
> (Mike).
>
> 11)   Error in loading the roundtrip XMI. Not clear what error,
> explicit message.
>
> 12)   Add CDE public ID on the description page so you can go directly
> go to the relevant CDE.

## Session Title: Birds of a Feather Session 2.B: Taverna/Workflow

**Date:** October 29, 2008

**Time (CST):** 1100 AM-1230 PM\
**Speaker(s):** Ravi Madduri

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**    Ravi Madduri   Determine if new business requirements    November
                          for CPAS been communicated by Workflow    2008
                          WG?                                       

  **2**    Ravi Madduri   Determine if ICR can map their use cases  November
                          to tools                                  2008

  **3**    Ravi Madduri   Follow up to make workflow use cases      November
                          received more concrete                    2008
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Ravi reviewed history to use Taverna.

```{=html}
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```
-   Saltz tool is used to tie ontologies into caGrid. They haven't
    looked at LexBIG and EVS yet.

-   There is sufficient information to create a workflow but there is a
    gap in services and content. The potential is there to create tool
    for users for reusable pipelines and the "My Experiment" website is
    where users publish their workflows. You can boot strap workflows.

-   A realistic representation of tool capabilities is needed to create
    something meaningful.

Use case from Lewis Frey:

-   Model mapping into CDEs -- Web services for NLP for automated
    mapping and searching between models and CDEs.

```{=html}
<!-- -->
```
-   Input is domain model -- define objects -- and tie it into what is
    existing -- get objects return and give dev the models.

-   Services exist but have to be stood up.

```{=html}
<!-- -->
```
-   How to get Taverna used?

-   Who are you marketing to? How does the new generation of researcher
    work (dealing with learning curve though)? Is it the
    bioinformatician as end user of Taverna? Or is the goal to have the
    ultimate end-user (information consumer/bench scientist) use it?

Discussion of who really is the end user and their skill set and use of
technology. Thoughts are:

-   Bioinformatician technologists as intermediates (service to those
    who just want the result and the right technology and platform
    aren't a concern)

-   Bioinformatics as a discipline where the bioinformatician drives the
    research questions

-   Tech savvy researchers. Is this a next gen researcher issue? It is a
    paradigm shift for users to think about objects. Lewis will think
    this will happen but traditional researchers will lag. Show how it
    can quickly create a workflow.

-   Bench researcher/scientist to build their own workflows.

Agreement that it is likely the full continuum.

Ravi is frustrated they couldn't do the workflow of interest.
RProteomics is not using current grid version and CPAS went through a
"special review." You have to make right contact at the right time to
figure out the technical details to get at the queries required to get
info of interest (from CPAS). This means there are new business
requirements for CPAS.

ACTION ITEM: Have requirements been communicated by Workflow WG?

There is unstructured data that you can't get out in the recommended
manner.

Without the structured data you can't get this all to work and to do the
science. Need to have:

1\. Services (analytics and data) out there that is of interest. What
are there real and useful data/services in caBIG? Should this be shown
in caGrid Portal?

2\. A model to expose data in a structured to make semantic and
syntactic connections

Reference implementation time has decreased from 1 month down to 1 day.

Lessons learned:

-   for VCDE to be more rigid and look at usage of structured
    identifiers

-   VCDE is tied into the Grid which ARCH is working in parallel so you
    can stand up a node. They are tied together by policy but there is
    nothing to enforce making the connections or to make the queries
    automatically aware (to catch issues).

Discussion:

-   Why service developers are interested in making service useful

```{=html}
<!-- -->
```
-   They have their own problem to solve

```{=html}
<!-- -->
```
-   Data sharing

    -   Automatic way to draw in collaborators and/or build a research
        community to work with.

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-   Is there a true understanding of federated queries.

-   Perception and status of caBIG

    -   Evolution to understand a SOA where a true discrete services
        that each do one thing really well are chained together

    -   Concern with progress

        -   Perception that caBIG is done. Some stake holders are in the
            trough of disillusion.

        -   Discussion of perception of ICR. Suggest funding projects
            that already have users (BioConductor vs upgrading
            RProteomics)

        -   Major issue is to start sharing data. Recommend funding a
            workflow user.

-   How to market Taverna.

    -   Message is there is useful method to create a workflow and now
        there is a value in how you expose data and services. Technology
        is now useful.

    -   Fosters collaboration with a goal of getting a paper. Note the
        motivation is when discoveries are being made with this
        infrastructure where you can't do it elsewhere or it would have
        taken much longer.

    -   Ability to work with previously siloed data.

    -   Previously researchers used one to a few genes in relationship
        to cancer. It is a new world with 50K things being measured, so
        the hope is to show how caBIG facilitates work in the new
        domain.

Ravi's Mantra:

WANTED: Use Cases with the intent of enabling discovery

Discussion of use cases.

-   ICR implementation shows the need for technology fixes.

-   Other issue is what functionality is actually available (ICR use
    cases "futuristic." The use cases real but can't be done due to tool
    gaps). ACTION ITEM: ICR map use cases to tools?

New Use cases:

-   TCGA -- has the data and is caBIG compatible. For a given phenotype,
    you can use the information to predict a response. Suggest TCGA as a
    reference set to compare their own data. (Lewis)

-   There are 5 ways to do normalize microarray with different ways to
    do the calls and see which one works with my information. You can
    make an incremental model of treatment to build a protocol. Workflow
    allows for standardization of data generation to analysis. Make the
    whole workflow and all algorithms available and people can duplicate
    it exactly. This would be novel. (Warren)

-   Taverna can tie into provenance info to publish data time and sets.
    Pulling in and freezing data is another application. (Warren
    extension and led to discussion of similar applications)

ACTION ITEM: Ravi pleased to have workflows and he will follow up to
make them more concrete.

Discussion:

gRAVI uses BLAST CHARM and others. They created a set of services,
freeze the resources and run the workflow including establishing the
parameters to do analysis. Then they freeze the data set which can be
used to reproduce the results.

Discussion on future directions:

-   Publishing 2.0 is making science publishing more interactive
    Publishing side is moving forward and requiring data posting.

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-   Even with all the pieces working, there are still syntactic issues.

-   Don't want proliferation of shims and the fragility of connections
    that work was noted.

-   Funding is low and so VCDE/ARCH will not go back and revisit prior
    reviewed.

-   Sustainable infrastructure point is a concern and explored the use
    of social networking tools to find what works.

-   Length of caBIG is a 15 year life cycle and some are encouraged by
    progress. Revolution and evolution goes on for a while and it is not
    all that long since this was rolled out.

## Session Title: Birds of a Feather Session 2.C: Object or Class Specialization

**Date:** October 29, 2008

**Time (CST):** 1100 AM-1230 PM\
**Speaker(s):** Stuart Turner

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   Need to add notes here.

## Session Title: Birds of a Feather Session 2.D: Integrating an Organizational Identity Provider with the Grid

**Date:** October 29, 2008

**Time (CST):** 1100 AM-1230 PM

**Speaker(s):** Steve Langella, Jim McCusker, Kunal Modi

**\
Action Items**

  -------- -------------- ----------------------------------------- -----------
  **\#**   **Assigned     **Description**                           **Due
           To**                                                     Date**

  **1**                                                             

  **2**                                                             
  -------- -------------- ----------------------------------------- -----------

**Notes**

-   This Birds of a Feather session focused on the operational aspects
    of authentication/authorization on the Grid, presentation of a
    custom authentication service at Yale (Kerberos service), and the
    process for naming groups through Grid Grouper.

-   Yale's authentication service is aiming to be NIST Level of
    Assurance 2 (for low to medium sensitivity data) compliant but needs
    policies from the Security Working Group for approval to move to
    production at LOA2.

-   Q: Is there an "Everyone" or "All User" group in Grid Grouper?\
    A: No, but caGrid 1.3 will have an "Everybody" group capability
    including authentication and authorization enforcement (when you do
    not care what group someone is in -- forces authentication with
    credentials).

-   There are two options for administrative control: 1) the institution
    can name and have administrative control over a stem or 2) the NCI
    can name the stem and then pass administrative rights to the
    institution.

-   There is a need for standardized institutional names for harmonized
    group creation.

-   There is an operational Grouper naming procedure in place, and we
    will soon have the corresponding operational policy in place.

-   A suggestion was given to use DNS for institutional domains.

-   Feedback on policy for stem name administration:

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-   Institutions should have some responsibility for group
    administration or control.

-   Best practices should be published for institutional administration
    of a stem that can be shared among other institutions.

-   A one-page instruction sheet should be provided around the
    procedures and policy for group control.