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    DiseaseLink Knowledge Base and
    KnowledgeCapture

    Category  Cross-Omics>Knowledge Bases/Databases/Tools

    Abstract  DiseaseLink Knowledge Base and KnowledgeCapture are
    the two (2) main components of GulfStream Bioinformatics (GSBio’s)
    Disease-Specific Platform, which enables convenient web-based
    acquisition, retrieval and analysis of information.

    1) DiseaseLink™ Knowledge Base -- The DiseaseLink™ Knowledge
    Base reduces the complexity and resources required to gather
    requirements and design the databases relevant to particular
    applications and diseases.

    The approach leverages the value of pre-defined disease models to
    help harmonize comparable data across disparate silos and support
    the interoperability and retrieval of standard and customer-specific
    information sources.

    DiseaseLink™ models currently encode 3,000 data elements and
    7,000 data values across 75 disease groups.

    2) KnowledgeCapture™ Software Development Kit and Modeling
    Methodology -- KnowledgeCapture™ enables the customization of
    disease models, and the development of applications that support the
    entry, storage, management, retrieval and reporting of data represented
    by these disease models.

    Using the toolkit, the data specifications developed using
    DiseaseLink™ and the modeling methodology are automatically
    transformed into fully functional multi-tier web applications.

    DiseaseLink™ Knowledge Base -- The DiseaseLink™ Knowledge
    Base enables researchers to select from an extensive taxonomy of data
    elements to create a customized, disease- and research-specific
    information model with structured vocabulary to serve as the foundation
    of an integrated data environment.

    The DiseaseLink™ Knowledge Base includes 75 disease models.
    Each model defines the information requirements of corresponding
    disease-specific data collection and analysis applications, enabling
    researchers to rapidly construct customized information models.

    The DiseaseLink™ Knowledge Base was created by GSBio’s team of
    clinical researchers, molecular biologists, medical librarians and
    biomedical informatics specialists in conjunction with clinicians and
    scientists at academic medical research centers.

    GSBio’s clinical informatics development group continues to expand
    and refine the models available in the DiseaseLink™ Knowledge Base.

    KnowledgeCapture™ Modeling Methodology and Software
    Development Kit (SDK) -- The KnowledgeCapture™ modeling
    methodology provides easy to use tools for the customization of pre-
    defined disease models from the DiseaseLink™ Knowledge Base.

    In addition, it enables rapid deployment of a robust enterprise software
    system, including components to:

    1) Display, enter and query data via web-based user interfaces.
    2) Check that the data entered is valid in the context it is entered through
    server-side validation.
    3) Transform the entered information into the format to be stored in the
    associated database.
    4) Manage user work flows.
    5) Integrate such features into new or existing host applications via
    application programming interfaces (APIs).

    With KnowledgeCapture™, many of these processes are automated,
    minimizing the development effort and increasing the quality and
    reliability of the resulting system.

    Disease-Specific Platform Deployment --
    GSBio’s Disease-Specific Platforms address problems of data
    structure, standardization and integration for data annotation. As such,
    your engagement begins with discussion and analysis of your
    information needs.

    These needs are represented according to the DiseaseLink™
    Knowledge Base using well-known tools such as Microsoft Excel® and
    based on GSBio’s starter kit of pre-designed data elements. There is
    No complex modeling tool to learn - just fill in and manipulate
    spreadsheets.

    The next step is generation of your database and multi-tier web-based
    application using the KnowledgeCapture™ Software Development Kit.
    The content and metadata in spreadsheets serve as instructions to the
    toolkit, which automatically creates database schema, software classes
    and other application components.

    The final step is the administration, selection and modification of your
    suite of web-based data entry forms generated from your information
    specifications, followed by data entry.

    Standard Terminologies in the DiseaseLink™ Knowledge Base --
    1) Extensive use of structured data element and values with associated
    text note fields.
    2) SNOMED-CT CUI augmented by local extensions to fill clinical
    ontology gaps and to support tissue intake and tracking.
    3) Diagnosis concepts pre-coordinated for high degree of granularity
    and specificity.
    4) Surgical pathology based on CAP Synoptic Reports and AJCC6.
    5) Gene tests conform to HUGO Gene Nomenclature Committee.
    6) Chromosomal aberration tests conform to International System for
    Human Cytogenetic Nomenclature.
    7) Occupation and environmental exposure based on Bureau of Labor
    Statistics SOC.
    8) Disease Model elements and values proto-typed in the ISO 11179
    standard of the NCI caBIG™ Cancer Data Standards Repository.
    9) Lab tests partially mapped to LOINC and submission of concepts to
    LOINC to fill gaps.
    10) RxNorm and other systems within UMLS evaluated for inclusion in
    standards maps.

    Collaborators --
    Disease-specific information requirements that are incorporated into
    the DiseaseLink™ Knowledge Base are reviewed by an external team
    of clinical researchers representing both industry and leading research
    institutions:

    Faculty and fellows at leading research institutions --
    1) Whitehead Institute; 2) Beth Israel Deaconess Medical Center; 3)
    Massachusetts General Hospital; 4) Dana Farber Cancer Institute; M.D.
    and 5) Anderson Cancer Institute.

    Industry researchers --
    Exelixis and OSI Pharmaceuticals.

    System Requirements  

    Web-based user interface

    Manufacturer   Home office; see web site for international locations.

    GulfStream Bioinformatics
    99 Hayden Avenue
    Lexington, MA 02421
    Phone: (781) 676-7000
    E-mail: info@gulfstreambio.com

    Manufacturer's Web Site  www.ardais.com/solutions_diseaselink.htm

    Price   Contact manufacturer

    G6G Product Number  20198

    G6G Manufacturer Number 101155
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