![](media/image1.jpeg){width="6.5in" height="0.625in"}

**caBIG Evaluation Year 2 Projects**

**Request for Proposals**

February 25, 2005

## 

## 

**caBIG Year 2 -- Request for Proposal**

**Table of Contents**

## 

[Executive Summary 3](#executive-summary)

[Project Details and Background 3](#project-details-and-background)

[Project Role Descriptions 3](#project-role-descriptions)

[Appendix I -- Sample Tools/Projects Currently Under Development
6](#appendix-i-sample-toolsprojects-currently-under-development)

[Appendix II -- Example New Projects
13](#appendix-ii-example-new-projects)

[Appendix III - Evaluation Criteria
14](#appendix-iii---evaluation-criteria)

[Appendix IV: caBIG Programmatic Goals
16](#appendix-iv-cabig-programmatic-goals)

[Appendix V: RFP Response Form 21](#appendix-v-rfp-response-form)

##   {#section-3 .unnumbered}

## Executive Summary

As the caBIG program enters its second year, there is an opportunity to
expand the scope of ongoing projects, as well as develop new
capabilities and bring new groups into the community of funded
participants. This Request for Proposal (RFP) is the mechanism by which
interested parties may submit a short proposal outlining their suggested
project/participation to the NCI for possible inclusion in caBIG and
funding. These proposals will be evaluated according to the criteria
outlined in the Request for Information (RFI) sent on January 26, 2005
as amended by the responses by Cancer Center participants. Part of this
evaluation will reflect the current Workspace and Working Group
objectives, which were developed by the community as part of the program
Strategic Planning process, and were reproduced, for comment, as part of
the RFI. Centers whose project proposals are a priority for caBIG
funding will be notified in mid-April, and then the process of
assembling a detailed statement of work and task orders can move forward
for funding during program year two.

This RFP is intended **only** for new projects for the caBIG program
and/or expanded participation in additional Workspaces/Working Groups.
Proposals in response to this RFP are due by March 28, 2005. Proposals
**are not** required for existing work that will not change in the
following year of the program. Current ongoing projects, that is, those
with tasks still being completed within existing task orders, do not
require an RFP response, nor do continuations of existing Workspace
Participant task orders.

Funding levels for specific projects will reflect the level of required
effort for a Cancer Center's participation.

## 

## Project Details and Background

The cancer Biomedical Informatics Grid, or caBIG, is an informatics
infrastructure that will connect teams of cancer and biomedical
researchers together to enable them to better develop and share tools
and data in an open environment with common standards. caBIG will create
a voluntary virtual network (or grid) that links individuals and
institutions both nationally and internationally, effectively forming a
World Wide Web of cancer research. caBIG will allow researchers to
answer research questions more rapidly and efficiently, thereby
promising to accelerate progress in all aspects of cancer research--
from etiologic research to prevention, early detection and treatment.
Ultimately, because caBIG will provide a common unifying force that
facilitates progress in cancer research, the most important
beneficiaries will be cancer patients and the public at large.

Specific biomedical research tools that are being developed as part of
caBIG activities include standards-based, components-based clinical
trial management systems, tissue banks and pathology tools, and a rich
collection of integrative cancer research applications. Related data
sets within these domain areas will also be accessible to researchers
via the caBIG grid. To ensure consistency, standards and tools will be
created to support common usage of vocabularies, data elements, and the
formation of a unifying architecture for the caBIG community.

The caBIG project has, from its inception, developed on the basis of the
activities of the participating Centers. Their work is the foundation of
caBIG's emerging community-based standards and tools, all developed
based on the discussions and proposals solicited as part of the
Cooperative Development Meetings (CDM) at the inception of the program.
After a year of caBIG, with the participants developing a more refined
sense of the needs of the program, and of their own capabilities to
deliver solutions to those needs, there are many new and existing
opportunities.

## Project Role Descriptions

There are several possible roles for participants in the caBIG project.
The roles reflect the capabilities of the Cancer Centers and individuals
participating in the project, and the requirements for execution of the
proposed project. These roles are outlined below, and any proposed
project should fit into one of them. We are particularly interested, in
project year 2, to consider Adopter funding for Centers that have unique
data resources that they are interested in making publicly available via
the standards and platforms being developed in the caBIG project.

***(1) Developer:*** An NCI-designated Cancer Center funded by NCICB to
participate in a specific Workspace to undertake software or solution
development activities. Activities include:

-   Executes pre-development tasks including but not limited to user
    requirements analysis, teleconferences, whitepapers, etc.

-   Creates, implements, modifies or extends software or solutions
    according to the specifications and schedules set forth by the
    Workspace

-   Works with the caBIG Project Team to ensure that the contract
    Statements of Work adequately reflect the deliverables desired from
    the assigned Developer teams

-   Documents software or solution development processes according to
    defined processes and directives

-   Carries out Quality Assurance and Quality Control activities, such
    as white-box and unit testing, during development process

-   Carries out software defect reporting, and responds to software
    defect reports from Adopter and testing activities at other sites

-   Provides development support activities, as required by the project,
    including hosting, systems administration, and database
    administration

-   Communicates progress with the Workspace through the established
    collaborative mechanisms, including meetings, tele- and video-
    conferences, and web sites

-   Complies with formal software change control processes, as required
    by project

-   Complies with defined Workspace and/or Working Group oversight
    processes and guidelines for project activities; Acts in accordance
    with caBIG governance requirements and the higher level goals,
    priorities and principles of the grid

***(2) Adopter:*** An NCI-designated Cancer Center funded by NCICB to
undertake formal testing, validation and application of products or
solutions developed by Workspace Developers. Adopters are expected to
make use of the software that they adopt to share post-publication data
with researchers in the grid, as a means of both testing and
demonstrating the technologies as well as providing useful and unique
data sources for researchers using the Grid infrastructure. Activities
include:

-   Creates formal software or solution Test Plans according to defined
    processes and directives

-   Executes formal software or solution Test Plans, and documents the
    results, submitting defect reports into systems established for that
    purpose

-   Creates and documents formal software or solution Validation
    (IQ/OQ/PQ) Plans, as required by project

-   Executes formal software or solution Validation Plans (IQ/OQ/PQ), as
    required by project

-   Integrates software or solutions into existing informatics systems
    at Adopter site

-   Imports data sets from actual practice, both from Adopter site and
    elsewhere

-   Submits formal software or solution defect reports into systems
    established for that purpose

-   Exports processed data where appropriate into systems and processes
    that reflect the use of the adopted software or solution in actual
    practice

-   Creates End-User Documentation for finalized versions of software or
    solutions, according to caBIG documentation standards and templates

-   Complies with defined Workspace oversight processes and guidelines
    for project activities; Acts in accordance with caBIG governance
    requirements and the higher level goals, priorities and principles
    of the grid

***(3) Workspace or Working Group Participant:*** A group of
NCI-designated Cancer Center members (and other invited stakeholders)
funded to provide guidance and support for Workspace and/or Working
Group activities. Participants include representatives from the
Developer and Adopter teams.

-   Defines, within the scope of the Workspace and/or Working Group, the
    specific vision, goals and priorities of that Workspace and/or
    Working Group

-   Prioritizes the defined Workspace and/or Working Group goals, in
    terms of specific software, solution and tool deliverables, creating
    a working plan

-   Schedules the initial working plan, based on the established
    development process

-   Work with other Working Group members to create formal software or
    solution specifications for the assigned deliverables. These
    specifications are likely to take the form of use-cases, UML
    diagrams, and other high-level representations of the problem

-   Provides for interactive Quality Control and Quality Assurance
    processes to ensure that the software or solutions developed by the
    Developers accurately reflects the intent of the Workspace and/or
    Working Group

-   Creates near- and medium-term strategies for general activities
    which reflect the overall goals of the Workspace and/or Working
    Group

-   Creates documentation around the adoption and implementation of
    standards within the context of the Workspace and/or Working Group
    area, including formal Standards Documentation, White Papers, and
    general caBIG policy documents

-   Participates in discussions with outside experts and groups focused
    on areas of similar interest and research germane to the Workspace
    area

-   Complies with defined Workspace and/or Working Group oversight
    processes and guidelines for Workspace and/or Working Group
    activities; Acts in accordance with caBIG governance requirements
    and the higher level goals, priorities and principles of the grid

-   Communicates and shares information with other Workspaces and
    Working Groups to enhance the congruence and consistency of
    activities and priorities across the caBIG initiative as a whole

## Appendix I -- Sample Tools/Projects Currently Under Development

**[Clinical Trial Management Systems Workspace]{.smallcaps}**

> ***Structured Protocol Representation Prototype***
>
> Software that represents clinical trial protocols in a structured,
> computable fashion.
>
> ***Adverse Events Reporting Tool (Requirements 1 -- 4)***
>
> An open source software tool that is used to collect, process and
> report adverse events that occur during clinical trials.
>
> ***caBIG Compatibility Grading Prototype***
>
> A document that evaluates software and modules for compatibility at
> the Bronze, Silver, and Gold level as defined by the caBIG community.
>
> ***Harmonization of UML Representations, Ontological Representations
> and Data Elements***
>
> A white paper that recommends approaches for ensuring seamless
> representation between UML representations, ontological
> representations and data elements, based on the Adverse Events domain,
> NCI Thesaurus and data elements for adverse events. The white paper
> will include a review of the existing relationships and role names in
> the NCI Thesaurus.
>
> ***Metadata Harmonization***
>
> A standardization of CTMS models using common vocabularies and data
> elements.
>
> ***CTMS/CDUS Reporting Tool***
>
> A reporting interface that electronically translates data from various
> systems into required formats and submits to CDUS and CTMS.
>
> ***Financial Billing Tool***
>
> Software that manages and monitors clinical trials expenditures and
> financial billing compliance.
>
> ***Laboratory Interface***
>
> An interface that enables laboratory data across multiple systems and
> in multiple formats to be translated into common standards.
>
> ***C3D***
>
> Database designed to provide critical functionality needed for an
> efficient web-based clinical trials information management system such
> as protection of patient confidentiality, maintaining audit trails,
> and integration with information systems. C3D also provides an array
> of informatics tools to support data standardization, validation, and
> quality assurance.
>
> ***C3PR***
>
> A tool that is used to manage relationships between participants and
> trials to increase patient accruals and to integrate clinical research
> to cancer research.

**[Tissue Banks & Pathology Tools Workspace]{.smallcaps}**

> ***caTISSUE***
>
> An enterprise suite that manages, queries, retrieves, and harnesses
> tissue specimen data and annotations across a federated
> infrastructure.
>
> ***caTISSUE High Level Architecture***
>
> A document that outlines a high level architecture of the caTISSUE
> system.
>
> ***caTISSUE Lite Prototype***
>
> A model that demonstrates the functionality of the database and
> specimen tracking system within caTISSUE.
>
> ***caTISSUE Prototype***
>
> A model that demonstrates the functionality of the annotation systems
> and mapping tools within caTISSUE.
>
> ***Requirements Specifications Survey and Results***
>
> A comprehensive survey that gathers information about all Tissue Banks
> from each TBPT institution. Now available at:
> http://cabig.nci.nih.gov/workspaces/TBPT/FinalTBPTWSSurveyv3.pdf
>
> ***Federated Tissue Data Set White Paper***
>
> A whitepaper that details how to establish a federated dataset (across
> the Cancer Centers) of paraffin embedded tumor tissues.
>
> ***De-identification Tool***
>
> A tool that de-identifies any free text report, based on the HIPAA
> "Safe-Harbor" algorithm. De-identification is required for caTIES and
> caTISSUE to handle electronic medical information.
>
> ***caTIES***
>
> An information extraction tool designed to automate the process of
> coding, storing, and retrieving data from free-text Pathology Reports.
>
> ***Data Sharing Federation DRAFT Concept of Operations (CONOPS)***
>
> A document that aids in the process of sharing pathology data over the
> grid.

**[Integrative Cancer Research Workspace]{.smallcaps}**

> ***Distance-Weighted Discrimination***
>
> A tool that performs statistical corrections to reduce systematic
> biases resulting from different sources of RNA, batches of
> microarrays, and particularly different microarray platforms. This
> tool will be ported to an open-source, caBIG compliant platform this
> year.
>
> ***GenePattern***
>
> An analysis platform that supports multidisciplinary genomic research
> programs. Its architecture and environment are expressly designed to
> allow rapid prototyping and integration of new technologies. For
> caBIG, an adapter to GenePattern will be created to allow the
> application to read data directly from caBIO/caArray.
>
> ***Magellan***
>
> A web-based system that allows biologists to perform complex analyses
> on heterogeneous data. Stored data and annotations are treated as
> abstract entities such that arbitrary, user-defined types of
> information can be stored. Magellan will consume data from
> caBIO/caArray and adapt its architecture to Silver-level compliance.
>
> ***Visual and Statistical Data Analyzer (VISDA)***
>
> This tool will be ported to an open-source, caBIG compliant platform
> this year.
>
> ***Cancer Molecular Pages Prototype***
>
> A database and automated annotation system that combines automated
> computer-based annotations and automated data collection from
> experimental stations and a set of web-based visualization tools. This
> system will consume data from caArray.
>
> ***FunctionExpress***
>
> An environment that analyzes and visualizes complementary data sets.
> The system provides a mechanism for regular updates of integrated
> annotation data that can be readily associated with probes on
> microarrays. The application allows for plotting of raw and
> transformed microarray data, for viewing orthologous probe sets from
> other experiments, and for creating literature-based gene networks.
> This tool will be ported to an open-source, caBIG compliant platform
> this year.
>
> ***Gene Ontology Miner (GOMiner)***
>
> An application that leverages the Gene Ontology (GO) to identify the
> biological processes, functions, and components represented in gene
> lists. GOMiner classifies genes into biologically coherent categories
> and assesses these categories. GOMiner will be made available as a web
> service.
>
> ***HapMap, PromoterDB***
>
> HapMap is a database that stores human SNPs, their genotypes, and the
> linkage disequilibrium relationships among them. PromoterDB is a
> curated resource for the vertebrate transcription factor that binds
> sites and their corresponding regulatory regions. Both datasets will
> be made available through caBIO.
>
> ***Protein Information Resource (PIR)***
>
> An integrated public bioinformatics resource that maintains the
> Protein Sequence Database (PSD), an annotated protein database
> containing over 283,000 sequences covering the entire taxonomic range.
> Individual involved with PIR are also members of the UniProt
> consortium, the central international resource of protein sequence and
> function that unifies the PIR, Swiss-Prot, and TrEMBL databases. PIR
> will be made available as a web service for caBIG.
>
> ***SEED***
>
> A framework that supports peer-to-peer annotation of genomes.
> Investigators work independently on their instances of the SEED
> database and synchronize their work when desired, or update code
> versions quickly via the network. SEED will be made available as a web
> service for caBIG.
>
> ***caArray***
>
> A microarray data repository that contains the following: MIAME 1.1
> compliance; support for MAGE-ML import and export; utilities for the
> submission and retrieval of Affymetrix and GenePix native file
> formats; controlled vocabularies; and accessibility through a MAGE-OM
> API.
>
> ***NCI-60 Data Sharing***
>
> Sixty diverse human cancer cell lines used by the NCI Developmental
> Therapeutics Program since 1990 to screen more than 100,000 chemical
> compounds for anticancer activity. Laboratories have assessed
> potential molecular targets and modulators of activity in these cells,
> resulting in a broad range of datasets. These datasets will be made
> available through caArray.
>
> ***Zebrafish Microarray Data Sharing***
>
> A service that provides microarray data generation services for the
> community of scientists using zebrafish as a model organism for the
> study of cancer. Through this caBIG project, Thomas Jefferson will
> make datasets from this repository available to the research community
> by identifying sharable datasets and making these datasets available
> via a caBIG-defined exchange format.
>
> ***Pathways Tool Development***
>
> A set of tools that leverage current resources, allowing users to view
> pathway data in the context of caBIG annotation and expression data.
> These resources include: BioPAX, a common exchange format for pathways
> data; cPath, a database focused on protein-protein interactions; and
> Cytoscape, a bioinformatics software platform for visualizing
> molecular interaction networks and integrating these interactions with
> gene expression profiles and other stat data. These existing resources
> will be leveraged to create a set of tools that will allow users to
> view pathway data in the context of caBIG annotation and expression
> data.
>
> ***Quantitative Pathway Analysis in Cancer (QPACA)***
>
> A pathway modeling and analysis system that supports exploration of
> quantitative biological data in the context of a pathway description.
> At the center of the system is a pathway representation that enables
> visualization and computational analysis of pathway structure. QPACA
> will be interoperable with Magellan and the pathways exchange standard
> identified by caBIG.
>
> ***Reactome (GKB) Data***
>
> A curated database of fundamental biological pathways in humans that
> uses strict rules of assertion and evidence tracking to ensure a
> consistent high quality product. This database will be made compatible
> with the pathways exchanges standard identified by caBIG.
>
> ***Proteomics Laboratory Information Management System Prototype
> (LIMS) Prototype***
>
> A system that is used to track the lab processes relevant to 2D-gel
> electrophoresis, with a schema to support the addition of new data
> types as they emerge. The availability of an open-source proteomics
> LIMS will ultimately allow a distributed development model in which
> additional modules can be contributed by other centers.
>
> ***Q5***
>
> An algorithm that supports probabilistic disease classification of
> expression-dependent proteomic data from mass spectrometry of human
> serum. The algorithm employs Principal Components Analysis (PCA)
> followed by Linear Discriminant Analysis (LDA) on whole spectrum
> Surface-Enhanced Laser Desorption/Ionization Time of Flight
> (SELDI-TOF) Mass Spectrometry (MS) data. This tool will be ported to
> an open -- source, caBIG compliant platform this year.
>
> ***RProteomics***
>
> A system that aids cancer researchers in the processing of MALDI-TOF
> data. These R libraries will be developed, and incorporated into a
> caBIG-compliant system that will aid cancer researchers in
> post-processing of their mass spectrometry data.
>
> ***TrAPSS***
>
> A system of several tools that aid scientists in searching for the
> genetic mutation or mutations that cause a defect or disease. The
> system offers support for almost all areas of a mutation discovery
> project from the creation and prioritization of a large candidate gene
> list, to the selection, ordering, and managing of primer pairs, and
> even support for secondary structural content prediction assay
> results. TrAPSS will be adapted to the caBIG architecture this year.

**[Architecture Workspace]{.smallcaps}**

> ***caBIG Compatibility Guidelines***
>
> A document that provides guidelines for producing software and tools
> that are caBIG compatible. This document also provides a set of
> definitions caBIG participants can use to measure the maturity level
> of potential caBIG applications. This is a living document that will
> evolve with the emerging caBIG compatibility guidelines and
> definitions as determined by the caBIG community. Now available at:
>
> http://cabig.nci.nih.gov/guidelines_documentation/caBIG_Compatibility_Document
>
> ***caGRID -- Phase I White Paper***
>
> A white paper that documents the evaluation of caGRID, a system
> created to facilitate data and system integration across the caBIG
> network. Development of the system was based on The Globus Tool Kit
> and the Open Grid Services Architecture-Data Access Integration
> (OGSA-DAI). Based on this evaluation, the white paper was used to
> inform the caBIG community. Now available at:
>
> http://cabig.nci.nih.gov/workspaces/Architecture/Documents/caGRID/caGRID_Whitepaper.pdf/view
>
> ***Mentoring Assignments Across Workspaces***
>
> A document that illustrates the pairings between the Architecture
> Workspace Mentoring Team Members and each of the developer projects
> within caBIG. Each developer project is assigned an Architecture
> Workspace representative to provide support and guidance regarding
> Architecture related matters.
>
> ***Workflow White Paper***
>
> A white paper that documents the evaluation of various workflow
> technologies and articulates the need for workflow within the caBIG
> community. Based on the evaluation, the white paper will present
> findings, recommendations and a final design to the caBIG community.
>
> ***ID Management White Paper***
>
> A white paper that documents the evaluation of the LSID specification
> and additional add-ons necessary to satisfy use cases within caBIG.
> Based on the evaluation, the white paper will present findings,
> recommendations, and a final design to the caBIG community.
>
> ***Security White Paper***
>
> A white paper that documents the evaluation of security standards and
> architectures needed to support caBIG. Based on the evaluation, the
> white paper will present findings, recommendations, and a final design
> to the caBIG community.
>
> ***Common Query Language White Paper***
>
> A white paper that documents the evaluation of query languages that
> can be leveraged and standardized across all the data grid services
> within caBIG. Based on this evaluation, the white paper will present
> findings, recommendations and a final design to the caBIG community.

**[Vocabularies & Common Data Elements]{.smallcaps}**

> ***CDE Governance Model***
>
> A model that manages the development and administration of CDEs in the
> Domain Workspaces of caBIG. This model represents the VCDE Workspace
> consensus on the most optimal and relevant governance model for the
> creation, collection and curation of CDEs, within the caBIG context.
> Now available at:
> http://cabig.nci.nih.gov/workspaces/VCDE/CDE%20development%20models.pdf
>
> ***VCDE Guidance Mentoring Teams***
>
> VCDE Mentoring Teams that meet the CDE needs of the Domain Workspaces,
> as well as, initiate and maintain the CDE governance model with the
> Workspaces. Each Mentoring Team, consisting of VCDE Cancer Center
> participants, has been assigned a NCI subject matter expert to advise
> in vocabulary and CDE related matters.
>
> ***Mentoring Assignments Across Workspaces***
>
> A document that illustrates the pairings between the VCDE Workspace
> Mentoring Team Members and each of the developer projects within
> caBIG. Each developer project is assigned a VCDE Workspace
> representative to provide support and guidance with regard to VCDE
> related matters.
>
> ***Vocabularies Deployment Document***
>
> A document that outlines vocabulary standards consistent with
> compatibility requirements among the many existing legacy systems in
> the cancer research community.
>
> ***CDE Harmonization within caDSR Contexts***
>
> The process by which the VCDE Workspace facilitates communication
> across contexts within caDSR. The VCDE Workspace serves as the final
> review board for CDE harmonization.
>
> ***Procedures for the Review and Approval of New VCDE Content***
>
> A document that outlines the procedures for reviewing and approving
> new VCDE content. This document will provide for overall
> standardization of CDEs within caBIG.
>
> ***Data Standards Approval Guidelines***
>
> A document that outlines the procedures for reviewing and approving
> data standards. The VCDE Workspace will serve as the final review
> board for both NCI and caBIG-generated data standards.

**[Data Sharing & Intellectual Capital Strategic Level Working
Group]{.smallcaps}**

> ***Draft Data Sharing Survey***
>
> Assessment of data sharing capabilities among Cancer Centers. An early
> draft is now available at:
> <http://cabig.nci.nih.gov/working_groups/DSIC_SLWG/Documents/DSIC_Questionnaire/caBIG_DSIC_DatasharingsurveyDraft_20040720.pdf>
>
> ***Draft Security Administration Recommendation***
>
> A document that proposes a standard for addressing issues of security
> administration, including authorization, authentication, access
> control, provenance, and usage auditing of caBIG systems and
> resources.
>
> ***Draft Publications Policy***
>
> A document outlining the policies and procedures surrounding the
> publication of caBIG related documentation.
>
> ***Model Open Source Software License Agreement***
>
> A template agreement that can be used by caBIG participant'
> institutions to share software and related documentation.
>
> ***Data Sharing Best Practices***
>
> A document that describes best practices with respect to the sharing
> of data, software, biospecimens, reagents and other materials.
>
> ***Position Paper -- The Impact of Privacy and Security Regulations on
> the collection of Clinical Trials Data***
>
> A document that describes the impact of IRB/Patient Consent/HIPAA
> privacy and security rules on the aggregation, storage, and analysis
> of specimens and data from clinical trials.
>
> ***Position Paper -- Federated Data Software Requirements***
>
> A document that recommends software specifications to be included in
> systems providing federated data to the community.

**[Strategic Planning Strategic Level Working Group]{.smallcaps}**

> ***Strategic Plan Subcommittee Recommendations***
>
> A document that provides guidance to caBIG Workspaces and Working
> Groups regarding strategic goals.
>
> Now available at:
>
> http://cabig.nci.nih.gov/working_groups/SP_SLWG/Meetings/Subgroups/Strategic_Plan_Subcommittee/2004-05-21_Strategic_Plan_Subcommittee_Recommendations.pdf
>
> ***caBIG Position Paper***
>
> A document that defines caBIG, describes caBIG goals and objectives,
> and outlines the one, three, and five year plans for caBIG.
>
> ***Strategic Goals and Objectives***
>
> A document outlining the strategic goals for the overall caBIG
> project, as well as strategic goals for each individual Workspace and
> Working Group.

**[Training Working Group]{.smallcaps}**

> ***Application Training Template***
>
> A standard package for use by all software application designers to
> meet various training obligations. The package will include virtual
> classroom templates to overview the application, virtual classroom
> templates to highlight specific uses of the application, and
> supporting workbooks.
>
> ***Virtual Classroom/Centra Sessions***
>
> Tools, including needs gathering, marketing, scheduling, and templates
> that conduct fast turn-around, virtual classroom sessions to meet
> spontaneous community needs.
>
> ***Software Evaluation Template***
>
> Templates that are used to standardize all documentation relating to
> software evaluation within caBIG.
>
> ***caCORE Curriculum***
>
> A framework that organizes lessons designed to train caBIG
> participants on the operation and functionality of the EVS, caDSR, and
> caBIO applications.
>
> ***Open Source Environment***
>
> A framework that facilitates the creating, posting, and reviewing of
> training content to support the caBIG community.

## Appendix II -- Example New Projects

Listed below are sample projects in which interest has been shown within
the caBIG community. Projects appropriate for submission under this RFP
are not limited to these examples, nor are these examples necessarily
more likely candidates for funding than other subjects or other project
proposals which may be submitted during the RFP process. These examples
do, however, represent the topics of discussion within the Workspaces,
Working Group and caBIG Program Management that highlight areas
currently underserved by the existing portfolio of activities.

**[Clinical Trials Management Systems:]{.smallcaps}**

-   Systems which provide a mechanism with which to match patients with
    clinical trials, incorporating developers of federated systems at
    community sites to provide the capability.

-   Systems which provide a general mechanism for translating legacy
    messages in use in the Cancer Center community into HL7v3 messages.

-   Projects extending and integrating the capability of existing open
    source clinical trials modules into caBIG compliance

-   Integrating the participation of practioners into the caBIG
    activity, including physicians, nurses, clinical researchers, etc.

-   Structured protocol inclusion/exclusion criteria

**[Integrative Cancer Research:]{.smallcaps}**

-   Platform for distributed general identifier mapping service,
    allowing mapping of identifiers such as SwissProt, Entrez, uniprot,
    etc., into single standardized grid-wide identifier

-   Proteomics tools, such as:

    -   Systems for protein identification from mass spectrometry

    -   Proteomics data repositories, perhaps similar to caARRAY for
        proteomics data

-   General caBIG-compliant laboratory information management systems
    (LIMS)

**[Tissue Banks and Pathology Tools:]{.smallcaps}**

-   Validated and open source de-identification tool based on caBIG
    platform technologies, fully modularized and suitable for
    integration with other caBIG systems

-   Tools and data sources for the collection storage and analysis of
    tissue microarray data

-   Systems which can provide for automated inclusion criteria of tissue
    and pathology specimens into retrospective trials. This system is
    likely to be similar to work ongoing in the CTMS space.

-   Systems which can provide an ability to link caBIG-platform
    annotated biospecimen repositories to the related clinical/pathology
    data

-   Adopters for caTISSUE who have data sources that can be shared with
    the caBIG community

-   Image management capability for histology slides and other pathology
    images

**[Architecture:]{.smallcaps}**

-   Systems based on caBIG Architecture Workspace reference
    implementations:

    -   Deployable software implementation of a caBIG-compliant LSID
        resolver

    -   caBIG compliant, standards-based Workflow management system

    -   Grid-deployed query tools based on caBIG standard query
        mechanisms

-   Grid portal, including a user interface design for a web portal to
    the caBIG Grid resources, allowing for the user side of provided
    services

-   Additional Workspace participants with expertise in Architecture

**[Vocabularies and Common Data Elements:]{.smallcaps}**

-   Systems or mechanisms for mapping of SNOMED to and from MedDRA

-   Mechanisms for mapping between humans and model organisms other than
    the mouse

-   Additional participants in the VCDE Workspace

-   Mechanisms for training caBIG project participants quickly on
    vocabularies, common data elements, shared data models, and other
    aspects of the caBIG VCDE Workspace scope of activity

-   Patient-centered vocabularies

-   Additional Workspace participants with expertise in Vocabularies &
    Common Data Elements

## Appendix III - Evaluation Criteria

As part of the proposal process, the caBIG Project Team intends to
review all actively-participating Cancer Centers this year. The
evaluation process will be appropriately scaled for the first year, and
will be scaled appropriately to Cancer Center size and capabilities.
Both past participation and project merit will influence project
selection. For Cancer Centers which have been strong participants in the
past will have an advantage to those who have been less responsive, or
for whom there is not yet an established history.

Reproduced below are the current evaluation criteria for project review.

  -----------------------------------------------------------------------
  **Evaluation Area**

  **Project merit**

  Is there value and utility in what this project is producing for the
  cancer research community?

  The project follows caBIG standards, including data standards,
  information model standards, metadata standards, architectural
  standards, and development process standards

  Proposed project is in alignment with caBIG core values and principles,
  and is consistent with the overall philosophy of the project. (the
  caBIG Core Values include: Open Source, Open Development, Open Access
  and Federation.)

  Willingness and action taken to openly share data with the community

  Project should be realistic, practical, and sustainable

  Products of project activity are valuable and useful to the Cancer
  Center community

  Are the products in alignment with the current priorities and needs of
  the parent workspace, and the overall caBIG project?

  Projects are proposed with demonstrable processes that lead to working
  products.

  Cost-effectiveness of the proposal and institutional commitment

  Real-world applicability to clinicians, patients, and researchers

  **Center History**

  Has the participant delivered products that have been well documented
  and deployable?

  Does the participant have a history of building working, usable
  systems?

  Are the current work products consistent with the originally proposed
  scope and vision, and with any documented modifications that have been
  presented in face-to-face meetings and teleconferences?

  Quality of participation in an unfunded role in project Workspace

  Level of improvement of caBIG capabilities at participating Center

  caBIG community orientation of Center

  Were work products, documents and reports generally accurate, clear,
  and consistent to requirements?

  Were work products, documents and reports completed according to the
  agreed-upon timelines?

  Did the participating Center effectively control project management and
  progress reporting of their participation and projects?

  Consistently and positively participated in teleconferences and
  face-to-face meetings?

  Takes responsibility for project activities, actively provides support
  for Workspace/Working Group when needed

  Satisfactory Business/Contractual Relations
  -----------------------------------------------------------------------

## Appendix IV: caBIG Programmatic Goals

*\* Note: Same as goals for Strategic Planning Strategic Level Working
Group*

***1 Year (End of 2005)***

-   Develop first generation caBIG compliant tools and data sets and
    supporting data & architecture standards

-   Establish a mechanism for engaging the private sector (pharma,
    software vendors, etc.), additional cancer research organizations,
    and other Federal agencies/divisions

***3 Year (Summer 2008)***

-   caBIG tools and data sources have a demonstrable positive impact on
    the cancer research community

-   All Developer projects will be operating under Gold standard

-   Adoption and use of caBIG interoperable tools and data sets within
    the caBIG Community

-   Develop mechanisms for engaging and promoting the use of these
    technologies and data sets for not just research but to include
    clinical treatment activities

***5 Year (Summer 2010)***

-   Wide spread adoption, dissemination and use of caBIG interoperable
    tools and data sets within the Cancer Community at large including
    pharma, non-NCI Cancer Centers, etc

***Guiding Principals***

-   All software products must be optimized for change rather than
    trying to get it perfect the first time out. The ability to easily
    adapt our software products to future changes and external
    influences is essential

-   We must have a bias for action and not get bogged down in
    deliberation

-   Always retain a patient centric focus in conceptualizing and
    developing our solutions

-   Create standards, tools and data sources that support the NCI goal
    to reduce suffering and death due to cancer

**Workspace/Working Group Project Priorities & Participation**

***All Workspaces:***

-   Development of open source software and adherence to caBIG
    vocabularies, common data elements, and architecture standards

> **3 Year**

-   All Workspaces will provide appropriate input to the Training
    working group to enable the development of training for the software
    the Workspace produces

-   All Workspaces will explicitly address the data sharing hierarchy
    principles that are being developed by the DSIC working group

***Clinical Trial Management Systems (CTMS) Workspace***

> **Overall Goals:**

-   CTMS software developed for caBIG will initially be silver-level
    compliant; Software will reach gold-level compliance once the Grid
    infrastructure is available and tested and the metadata management
    tools and processes are fully defined

-   Consideration of existing CTMS, both commercial and home-grown, when
    generating use cases

-   Commitment to modular software design in CTMS Workspace products

-   Provide a system to which data elements from legacy CTMS systems can
    be mapped

> **1 Year**

-   **Financial**:

    -   Financial glossary, functional requirements, SOW with focus on
        Clinical Trial Financial Ledger software module

-   **Laboratory**:

    -   Identify CDISC modifications, HL7 V3 messages, and produce an
        interface to the software produced by the Adverse Events Special
        Interest Group

-   **Adverse Events:**

    -   The caBIG functional prototype for Adverse Events Software
        Modules 1-4 (Adverse Event Data Capture; Interface Between AE
        Capture/Reporting Tool & Local CT Databases; Vocabulary Mapping
        Service; and External Agency Reporting) tested at adopter sites

    -   Work with the Laboratory SIG to provide a mechanism for software
        interface with the software from that group

-   **CTMS/CDUS:**

    -   Develop and deliver use cases, establish improvements to CTEP
        reporting process

-   **caBIG Compatibility:**

    -   Develop caBIG compatibility assessment methods, gap analyses for
        several systems, create refined guidelines for assessment of
        caBIG compatibility

-   **Structured Protocol**:

    -   Create core data elements (CDISC-based) for protocol
        registration & internal tracking

    -   (Year 2) Demonstrate the use of the Structured Protocol
        Representation in a prototype

> **3 Year**

-   **Financial:**

    -   Document, deploy software to users

-   **Laboratory:**

    -   Transfer data from 2 vendor systems, transfer into Clinical
        Trials databases

-   **Adverse Events:**

    -   All 12 modules in place with interfaces to vendors and agencies

-   **CTMS/CDUS**:

    -   caBIG module for CTMS/CDUS reporting, adverse event denominator
        data

-   **Structured Protocol:**

    -   Clinical trial registry, patient eligibility, patient
        registration, treatment calendar, CRFs, Summary 4, and SIG
        components

> **5 Year**

-   **Laboratory:**

    -   The Grid, Toolkit to transfer any lab data

-   **Structured Protocol:**

    -   Complete PI authoring, custom report generation, data mining,
        results repository, and statistical analysis components

***Integrative Cancer Research (ICR) Workspace***

> **1 Year**

-   A number of the Year 1 projects in ICR will reach a
    proof-of-concept, or prototype stage at the end of Year 1.

-   Projects will target Silver Level compliance, as outlined in the
    caBIG Compatibility Guidelines document.

-   A few projects will be selected as reference implementations of the
    Grid architecture.

-   All projects will comply with the caBIG principles of open source,
    open access, open development and federation.

-   For projects that reach Silver-level compliance in Year 1 and are of
    significant interest to the caBIG community, funding will be
    allocated to bring them into the grid architecture (Gold-level
    compliance)

-   **Integration/Scientific Proof-of-Concept**

    -   This was identified as the highest priority in ICR for Year 2.

    -   The goal of such a project would be to employ tools and datasets
        developed in caBIG in Year 1 (either within ICR or across
        workspaces) toward a real scientific problem

-   **Completion of Year 1 Projects** - A number of the Year 1 projects
    in ICR will reach a proof-of-concept, or prototype stage at the end
    of the year. For those in which there is significant interest,
    additional funding will need to be allocated to bring them to
    maturity

> **3 Year**

-   Bring more selected data sources and applications into Gold-level
    compliance, i.e. make them grid resources

-   Show how a federated set of resources that are syntactically and
    semantically compatible can be used to perform powerful analyses
    across the cancer research community

> **5 year**

-   Connect the ICR data and applications to resources in the Tissue
    Banks and Pathology Tools Workspace as well as the Clinical Trials
    Management System Workspace

***Tissue Banks & Pathology Tools (TBPT) Workspace***

> **1 Year**

-   Complete first iteration of caTISSUE Core / caTISSUE Lite and deploy
    to adopter sites for testing

-   Complete caTIES module and deploy to adopter sites for testing

-   (Year 2) WS Common Data Model for all TBPT applications

> **3 Year**

-   Complete development cycle for caTISSUE Lite / caTISSUE Core

-   Complete and deploy presentation / grid layer for caTISSUE

-   Further development of clinical annotation module

-   Development of 'second party' modules

```{=html}
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```
-   Billing / shipping

-   Request

-   Experimental annotation

```{=html}
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```
-   Addition of other caTISSUE modules based on ranking in
    prioritization matrix.

-   Explore the integration with other specimen bank systems (e.g. EDRN,
    cooperative group banks, CHTN) with caTISSUE

> **caTIES goals and Objectives**
>
> **1 Year**

-   (Year 2) Complete first version of caTIES - standalone repository
    for coded pathology reports -- and deploy to Adopters. Prototype
    Grid services. Begin CAP Protocol CDE development

> **3 Year**

-   Integrate caTIES fully with caGRID; Add new adopters each year; Add
    annotation source module to caTISSUE; Further enhance NLP
    capabilities; Further develop use of CAP protocols and NCI Thesaurus
    for extraction by inference

-   Demonstrate exchange of data between caBIG and other collaborative
    efforts; e.g. Shared Pathology Informatics Network

> **caTISSUE and caTISSUE Lite goals and objectives**

-   Open source architecture and adherence to "caBIG compatibility"
    guidelines with regard to architecture, controlled vocabularies and
    common data elements. caTISSUE Lite will be "Silver Level" and
    eventually, "Gold Level", when grid architecture is integrated into
    the design

-   Utilization of current specimen banking systems to generate use
    cases for model design. This will ensure that the design process
    does not "reinvent the wheel" and that caTISSUE Lite will handle all
    basic functionalities associated with the operation of a biospecimen
    bank

-   Modular design. It is recognized that all desired functionality can
    not be built immediately into caTISSUE (hence the designation for
    this project, caTISSUE Lite). However, caTISSUE Lite will be
    designed so that additional functionality (e.g. Clinical Annotation
    Module, Biological Annotation Module, Billing and Financial Module,
    Specimen Request Module) can be added to the Core system without any
    architectural redesign

-   A basic system that can be rapidly deployed to institutions with
    little or no specimen banking informatics. The first iteration of
    caTISSUE will be developed quickly and deployed to sites who are
    currently utilizing spreadsheets or highly customized databases
    (Access, FoxPro, File Maker) for tracking biospecimens. Rapid
    adoption of caTISSUE Lite will allow these institutions to expand
    their system with additional caBIG compliant modules over time

-   A system to which objects and data elements can be mapped from
    legacy biospecimen informatics system. It is clearly recognized that
    not all sites can or will adopt caTISSUE Lite as their sole solution
    for specimen banking informatics. Although not within the scope of
    this proposal, adopters will have the ability to map data from their
    own systems to objects and data elements in caTISSUE Lite, so that
    they can maintain their existing systems while participating in
    caBIG

***Vocabularies & Common Data Elements (VCDE) Workspace***

> **1 Year**

-   Plan for governance of new vocabulary and common data element
    content including establishment of review boards within VCDE WS for
    standards review and establishment of vocabulary governance model

-   Establish VCDE Mentoring Teams for domain Workspace pilot projects
    and finalize guidelines

-   Recommendation of external data standards

-   Convene regular Face to Face Meetings of the VCDE Workspace and
    joint meetings with the Architecture Workspace to address caBIG
    cross cutting issues

-   Implement VCDE Workspace developer projects

-   (Year 2) Clarify the caBIG compatibility guidelines with respect to
    vocabulary, metadata and information models and discussion with the
    domain workspace members about the resulting guidelines

-   (By End of Year 2) Provide complete Gold-Level Vocabulary/CDE
    specification

> **3 Year**

-   LexGrid Development

-   Mouse/Human Anatomy Development

***Architecture Workspace***

> **1 Year**

-   Develop and deploy the core Data Grid infrastructure. This
    infrastructure will form the nucleus architecture on which
    end-to-end, production level infrastructure will be built in year
    from years 2 through 5. It will support the minimum required
    functionality for distributed, collaborative basic research

-   (Year 2) Clarify the caBIG compatibility guidelines with respect to
    vocabulary, metadata and information models and discussion with the
    domain workspace members about the resulting guidelines

-   (By End of Year 2) Provide complete Gold-Level Architectural
    specification

> **3 Year**

-   Develop and deploy the core support for Grid-enabled,
    multi-institutional translational studies. This infrastructure will
    support the integration and analysis of clinical data with high
    throughput molecular data including gene array, proteomic, SNP,
    methylation and image data. The infrastructure will also support
    Grid-enabled sharing of de-identified clinical information and
    clinical trials protocols

> **5 Year**

-   Develop and deploy the full, production-level support for
    Grid-enabled, multi-institutional translational studies. This
    infrastructure will implement extended support for Grid-enabled
    clinical trials protocols and extensions to facilitate querying and
    integration of streaming sensor data (imaging, lab, other types of
    sensors) with other types of data. With this infrastructure, data
    generated at all levels of basic and clinical research can be
    captured, managed, and analyzed

***Data Sharing & Intellectual Capital (DSIC) Strategic Level Working
Group***

> **1 Year**

-   Develop key data sharing associated use cases for each of the caBIG
    workspaces

-   Collect and compile existing "best practices" related to proprietary
    and regulatory issues for data sharing

-   Where no "best practices" exist, seek out needed expertise to
    formulate such policies for caBIG activities

-   Prepare position papers on assigned topics relevant to each team
    focus.

> **3 Year**

-   Publish white papers (consensus documents) based on summation of
    group's position papers

-   Continue interaction with Architecture WS to develop test documents

-   Create caBIG compliant document templates that can be used by
    participating institutions to ensure compliances with data sharing
    polices

> **5 Year**

-   Serve as liaison between policy changes and system design

-   Troubleshoot remaining institutional impediments to implementing
    data sharing across the grid

***Training Strategic Level Working Group***

> **1 Year**

-   Develop caCORE training (EVS,caDSR, caBIO)

-   Develop Training for tools currently being developed starting with

```{=html}
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```
-   CTMS - Structured Protocol Development

-   ICR -- caARRAY, TrAPPS

-   TBPT -- caTIES

```{=html}
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```
-   Develop templates & standards for caBIG Software Documentation

-   Develop common standards for the evaluation of caBIG tools

> **3 Year**

-   Provide an open source electronic learning environment

-   Define Training Modalities

-   Produce "Gold" level training materials

-   Provide a common look and feel for caBIG training materials

-   Provide end user & tech support

***Strategic Planning (SP) Strategic Level Working Group***

> *\* Please see caBIG Programmatic Goals*

##  

## Appendix V: RFP Response Form

**[Instructions for submitting a response to this RFP]{.smallcaps}**

In order to submit a response to this RFP you may download the
electronic version of this response form at
<http://caBIG.nci.nih.gov/Year_2/RFP>, fill it out, and send via email
to
[cabig_year2@bah.com](mailto:cabig_year2@bah.com?subject=RFI_Response).

**[The deadline for submission of a response to this solicitation is
March 28, 2005.]{.underline}**

The responses to this RFP will be reviewed by the caBIG project team,
and awards will be announced in mid-April.

For inquiries about this RFP, please contact the caBIG Project Manager,
Mark Adams (<adams_mark@bah.com>) or via phone at (301) 998-6934.

**Cancer Biomedical Informatics Grid (caBIG)**

**Pilot Project Summary Proposal**

  ------------- ------------------ -------- ---------- -------- ----------------
  Center Name:                                         State:   

  Pilot Project                                                 
  Contact:                                                      

  Telephone:                       Email:                       

  Pilot Project                                                 
  Title:                                                        
  ------------- ------------------ -------- ---------- -------- ----------------

## 

**[I. Current Role]{.smallcaps}**

*List your **current funded** Workspace and/or Working Group membership
in the table below. Put an "X" in the box corresponding to your funded
role. If you need more space, TAB through the bottom row to add
additional lines.*

  ------------------- ----------------- ----------------- -----------------
  Workspace/Working   Developer         Adopter           Participant
  Group                                                   

                                                          

                                                          

                                                          

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

**[II. Current Tools/Projects Involvement:]{.smallcaps}**

*Please use the space below to detail your current involvement. Please
note that there are no word or page limitations, but please keep the
description succinct.*

**[III. Proposed Role]{.smallcaps}**

*If your **desired funded role** within caBIG is different than what is
marked above, please indicate your total desired role in the table
below. If you need more space, TAB through the bottom row to add
additional lines.*

  ------------------- ----------------- ----------------- -----------------
  Workspace/Working   Developer         Adopter           Participant
  Group                                                   

                                                          

                                                          

                                                          

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

**[IV. Proposed Year 2 Involvement]{.smallcaps}**

*Please use the space below to detail your proposed involvement in caBIG
including any new projects. Please note that there are no word or page
limitations, but the intent is for a succinct description of the
proposed project.*

**[V. Cancer Center Background]{.smallcaps}**

*Please use the space below to detail any background on your Cancer
Center that you feel would be helpful to the caBIG Project Team. Please
note that there are no word or page limitations, but please be
succinct.*

**[VI. Other:]{.smallcaps}**

*Please use the space below for any other information you'd like to
include in this proposal. Please note that there is no word or page
limitations, but please be succinct.*