caCORE In Action: An Introduction to caDSR and EVS Browsers for End Users A Tool Demonstration from caBIG™ caCORE (Common Ontologic Representation Environment) June, 2008

The goal of this demo is to introduce you to the capabilities and benefits of a tool that is available for use from caBIG™. You can also adapt your existing tool to become caBIG™ compatible, and set up your tool to interface with the caDSR or EVS APIs for access to the content presented by these tools. Agenda and Goal Overview and Introduction to caCORE End User Tools: caDSR CDE Browser, UML Model Browser, EVS Bioportal Functionality Resources and Next Steps

caBIG™ Overview caBIG™ is an information network enabling all constituencies in the cancer community – researchers, clinicians, patients – to share data and knowledge to accelerate the discovery of new diagnostics and therapeutics, and improve patient outcomes. caBIG™ Vision Connect the cancer research community through a shareable, interoperable infrastructure Deploy and extend standard rules and a common language to more easily share information Build or adapt tools for collecting, analyzing, integrating and disseminating information associated with cancer research and care

caCORE End Users Access to caDSR Metadata Registry and EVS Ontologies

caCORE Products Overview The caCORE (cancer Common Ontologic Representation Environment) and CORE Infrastructure products and services include tools for Application Developers, Data Managers and metadata Content Curators. This demo highlights the tools aimed at Data Managers needing to share common data descriptions and terminology for data in NCI funded research and clinical trials. These tools would be used to browse and download NCI Common Data Elements (CDE) documentation and the Terminologies referenced in data descriptions. caDSR: Data Standards Registry CDE Browser - Skip to Demo SlidesCDE BrowserSkip to Demo Slides UML Model Browser – Skip to Demo SlidesUML Model BrowserSkip to Demo Slides Enterprise Vocabulary Services Overview BioPortal - Skip to Demo SlidesBioPortal Skip to Demo Slides

Using caCORE End Users Tools Who and Why? Target Users: Data Managers and Content Curators. EVS and caDSR provide the underpinnings of the semantic metadata supporting a wealth of clinical and scientific and clinical research data being created and shared on the web via web browsers and caGrid. The National Cancer Institute Center for Bioinformatics (NCICB) has developed an evolving core infrastructure designed to provide the ability to seamlessly translate and interchange semantically immutable information. this demonstration will introduce the user to the set of caCORE web based tools aimed at helping end users of semantic metadata. Core Functions / Modules: The caCORE tools in this demonstration have web interfaces to allow users to search, download and use the rich documentation available for caCORE based systems. These tools help Data Managers and Content Curators create and use the sharable data descriptions that support information exchange, regardless of source, location or format.

Demonstration of CDE Browser

A Quick Preview: Key Functions and Benefits of CDE Browser Target End User: Designed for caDSR Curators and Public Users Key Search Features Browser Tree Basic Search for Data Elements Advanced Search for Data Elements related to Other Administered Components Search Preferences Search Results Download Data Elements Compare Data Elements Adopters of CDE Browser: caBIG™

Introduction to caDSR Tools CDE Browser to Search for and Download Side-by-Side Compare Form Builder to Create user specified collections of CDEs CDE Curation Tool to Create Data Elements Admin Tool to Curate and Administer caDSR - “Power Users” Sentinel Tool (3.0) Subscription Service generates end user ‘Alerts’ triggered by metadata changes Freestyle Search API and User interface to search across all types of administered items using serach terms, concept codes, identifiers etc. UML Model Browser to view Information Models UML Class Diagrams annotated using SIW and loaded via UML Loader Semantic Integration Workbench and Batch Load to import Administered Items UML Loader (XMI) Access, Develop, Manage, Consume

CDE Browser Workflow Find Reusable Data Elements Protocol Description Identify Data Collection Requirements Obtain MetaData Descriptions Use to design new data collection Forms

What is a Data Element? Data Element Data Element Concept Person Race Race Category Code Person Race Category Code Object ClassCharacteristic Representation Term Permissible Value / Meaning / Description Value Domain

Overview of CDE Browser caDSR Search Tree: Displays all the current caDSR Contexts. Users can search for groups of CDEs by navigating the tree. Data Element Search Panel: This is the main search window. Users looking for Data Elements can enter a key word or phrase. Navigation Menu: use these buttons to navigate to the CDE cart, Form Builder, or back to Home( that is back to this page) Access to Form Builder

CDE Browser Tree The tree expands and collapses by clicking on the “+” and “-” of the folders in the tree. Click the link to expand exposing collections of data elements at that level of the tree.

CDE Browser – Basic Search Search by exact phrase and word(s). By default the basic search screen allows for a search by name. You may also search by public id. Start your search.

CDE Browser – Advanced Search by Attributes Search for Alternate Names Filter Data Elements that contain a specific Permissible Value Wildcard searching is supported. Search using EVS concept name or code. Set Search Preferences here.

CDE Browser- Search Preferences Exclude or include the Test and Training contexts. Include or exclude certain Workflow or Registration statuses. SAVE your preferences.

CDE Browser – View Details Select link to view details of the Data Element Default Sort Order RE-sort by selecting any column heading. Export Data Element metadata in Excel or XML

CDE Browser – Data Element Details Detail pages are available for all Data Element descriptive information

CDE Browser – Data Element Details (Other Versions) Including all prior version of the Data Element and details about which projects are using them.

CDE Browser – Data Element Concept Details - Object Class, Concepts, Inheritance, Associations, etc.

CDE Browser – Permissible Values (Value Domain) Details Value Domains describe attributes of the instance values such as maximum and minimum length, datatype, unit of measure and display format.

CDE Browser- Value Domain Details Representation and Value Meaning EVS Concept References

CDE Browser Compare Feature A text based search may result in results including CDEs that appear to be similar In these cases, it is helpful to be able to view the details of each CDE side-by-side in order to assess how the similar CDEs are different. Users can add Data Elements to a Cart for downloading to Excel or XML Or, add to a “Compare” matrix, to view CDEs side-by- side within the CDE Browser user interface The CDE Compare feature allows you to view a selected set of Data Elements in a convenient, side-by-side format.

CDE Browser- Compare Feature Compare descriptions and all caDSR metadata for Similar Data Elements

CDE Browser- Compare Feature compare Permissible Values for Similar Data Elements

A Quick Review: Key Functions and Benefits of CDE Browser Search for Data Elements Basic Search Advanced Search View Details of Data Elements Download Data Elements Put Data Elements into a Shopping Cart fo ruse with Form Builder Compare Data Element Details Key Functionality Clarifying Tool Boundaries. No tool meets all user expectations. Here are some functions that are outside the scope of this tool. Displays ALL Data Elements, not just the NCI Standards Does not provide browsing of other types of ISO/IEC items such as Object Classes, Data Element Concepts or Value Domain except.

The Next Step: Accessing Online Resources for CDE Browser CDE Browser Online Tool Landing PageN/A Access to Training for CDE and UML Model Browser Course 1020: Using the CDE Browser and UML Browser ng/CourseOffering Software Development Project Site CDE Browser On-line Users Guide n/help/cdeBrowserHelp.html NCI Center for Bioinformatics Applications Support

Demonstration of UML Model Browser

A Quick Preview: Key Functions and Benefits of UML Model Browser Adopters of CDE Browser: caBIG™ Target End Users: Designed for UML model owners, reviewers and information model analysts Search for and view registered UML Domain Model components in caDSR UML Model Project Information and Contacts Classes Class attributes Associations between Classes and attributes ISO Components (metadata) related to those classes and attributes Download UML Model Project’s Common Data Elements (metadata) in XML format

Introduction to caDSR Tools CDE Browser to Search for and Download Side-by-Side Compare Form Builder to Create user specified collections of CDEs CDE Curation Tool to Create Data Elements Admin Tool to Curate and Administer caDSR - “Power Users” Sentinel Tool Subscription Service generates end user ‘Alerts’ triggered by metadata changes Freestyle Search API and User interface to search across all types of administered items using serach terms, concept codes, identifiers etc. UML Model Browser to view Information Models UML Class Diagrams annotated using SIW and loaded via UML Loader Semantic Integration Workbench and Batch Load to import Administered Items UML Loader (XMI) Access, Develop, Manage, Consume

UML Model Browser Workflow View and Find Reusable Models and Data Elements Develop Information Model Register Information Model in caDSR Obtain MetaData Descriptions Use to Design New Information Models

UML Model Browser Interface UML Model Search Tree: Search for model components. Navigation Menu: Access other caDSR and EVS tools and on- line help. Basic Class/Attribute Search Pane: Users looking for classes and attributes can enter search criteria here. Search Criteria Based Search: Users are presented with a drop down list from which to narrow their search by UML Project, subProject and Package.

UML Model Browser Navigation Tree Displays current caDSR Contexts For each Context, lists all the UML classes grouped by project, subproject and package Search for classes by navigating the tree and clicking on a context, project, subproject or package Search for attributes by clicking on a class project subproject package class

UML Basic Class / Attribute Search Panel Clear existing search criteria and prepare for a new search. Enter a class or attribute name (or fragment - the asterisk (*) can be used as a wild card character). Click the Class or Attribute Search button to start the search based on the selected/entered criteria.

UML Class - Model Tree Search Results for BRIDG UML Model Project 50 Classes ‘crumb trail’ Class Search Results Package Name Click for Project Details

UML Project Details for BRIDG Reference Documents Project Contacts Project Description

UML Class - Search Result Details Displays the number of matching UML components. 1. Click on a “Class name” to view its attributes for the specific UML Project.

UML Class - Search Result Details Displays the number of matching UML components. Or 2. Select the Public ID to view class details in the caDSR Object Class browser.

UML Model Browser – Class Details, Concepts, Inheritance, Associations, etc.

UML Model Browser – Other projects using the “Participant” class. Other Projects using the Participant class

UML Model Browser – “Participant” Class Associations Navigate to associations

UML Model Browser – Navigate to an association Instance Unique Identifier Class detail is displayed Instance Unique Identifier Class detail is displayed

UML Attribute – Model Tree Search Results for “Participant” class in BRIDG Project # Matches ‘crumb trail’ Attribute Search Results Class

UML Attribute - Search Results Details Click on the Data Element (DE) Name to view DE details in the CDE Browser Download the Data Elements (DE) as XML

A Quick Review: Key Functions and Benefits of UML Model Browser Browse UML Model Project Information and Contacts Classes Class attributes Associations between Classes and attributes ISO Components (metadata) related to those classes and attributes Links to project Documentation Download Data Elements in XML Clarifying Tool Boundaries. No tool meets all user expectations. Here are some functions that are outside the scope of this tool. Does not display the classes in the model graphically (text base ‘view’) Not all models have documentation and contanct information loaded in caDSR

The Next Step: Accessing Online Resources for UML Model Browser UML Model Browser Online ser/ Tool Landing PageN/A Access to TrainingCourse 1020: CDE and UML Model Browser ng/CourseOffering ng/CourseOffering UML Model Browser Software Development GForge Project Site er/ UML Model Projects Source/Artifacts Archive NCI Center for Bioinformatics Applications Support

Demonstration of EVS BioPortal

A Quick Preview: Key Functions and Benefits of EVS BioPortal End Users of BioPortal: Target Audience: provides caBIG™ researchers, clinicians, data managers and application developers with a comprehensive source of terminology underpinning the semantic components of Data. Uses the LexGrid model for storing ontological and terminological data and the Lex server and Lex APIs BioPortal provides end users with the ability to Browse, Search, Visualize, Request New Terminology NCI Thesaurus, NCI Metathesaurus, Gene Ontology (GO), LOINC, SNOMED, MedDRA, MGED, Zebrafish

EVS BioPortal Home Page Left Navigation Bar Additional Browse Link Browse and Search Library Statistics On-Line Help

Browse Ontology Ontology Name Ontology Format Ontology Version Download, Visualize, Search

Quick Search Ontology Select Ontology from List Enter Search term Number of Search Results Item Identifier Highlighted search term in each result: “oncogene”

Advanced Search Ontology Advanced Search Feature/FunctionAction RolesSelect a role from the list to filter results. AssociationsSelect an association from the list to filter results. Include Obsolete Classes/Types Check this box if you want to include retired classes in the search results.

Visualize Ontology Class/Type Details Graph View Options: - Local Neighborhood - Sub Class Only - All Relationships Tree View

A Quick Review: Key Functions and Benefits of BioPortal Browse Ontology Search Ontology Visualize Ontology Concept Associations Clarifying Tool Boundaries. No tool meets all user expectations. Here are some functions that are outside the scope of this tool. Up-loading ontologies and meta data about ontologies is not supported Does not find implicit associations across ontologies Does not display Concept History

The Next Step: Accessing Online Resources for EVS BioPortal BioPortal Onlinehttp://bioportal.nci.nih.gov Tool Landing PageN/A Access to TrainingCourse 1050: BioPortal Training ng/CourseOffering ng/CourseOffering Software Development Project Site EVS Users LISTSERV Signup EVS Onlinehttp://ncicb.nci.nih.gov/NCICB/infrastructure/cacor e_overview/vocabulary NCI Center for Bioinformatics Applications Support

Resources and Next Steps

Two Pathways: Adopt or Adapt Interested organizations are not required to adopt this caBIG™ application to connect with caBIG™ There are other ways to share data and use common data elements and controlled vocabularies by adapting current or non-caBIG™ applications

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