Introduction to the caDSR Presented to HL7 Vocab SIG January 24, 2005

1
Introduction to the caDSRPresented to HL7 Vocab
SIG January 24, 2005

• Denise Warzel
• National Cancer Institute, Center for
  Bioinformatics
• caDSR Project Officer, Software Development

2
Presentation Outline

• caCORE Overview
• ISO/IEC 11179 Overview
• caDSR Implementation and tooling

3
caCORE Components

• caCORE is the open-source foundation upon which
  the NCICB builds its research information
  management systems

Bioinformatics Objects
Data Standards
Enterprise Vocabulary
4
caCORE Infrastructure wiring
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Presentation Outline

• caCORE Overview
• ISO/IEC 11179 Overview
• caDSR Implementation and tooling

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Terms and Definitions for ISO/IEC 11179
Data Element
A unit of data for which the definition,
identification,
representation, and permissible values are
specified by means of a set of
attributes.
Data Element Concept
An idea
Data Element Representation
that can be represented in the

• Administered Item A registry item for which
  administrative information is recorded in an
  Administration Record
• Data Element A unit of data for which the
  definition, identification, representation, and
  permissible values are specified by means of a
  set of attributes.
• Data Element Concept An idea that can be
  represented in the form of a data element,
  described independently of any particular
  representation.
• Value Domain A set of attributes describing
  representational characteristics of instance data
  with or without enumerated permissible values.

The part of a data element having
form of a data element, described
independently of any particular
A value domain, datatype,and other
representation.
representational specifications.
Representation Class
A
classification of data
elements based upon the
type of representational
form.
Value Domain
A set of attributes
Conceptual Domain
A set
of possible value meanings
describing representational Characteristics of
instance data with or without permissible values.

of a data element expressed
without representation.
Value Meaning
A member of the
Permissible Value
An
set of finite allowed inventory of
expression of a value
notions that can be categorized
meaning in a specific
for a conceptual domain.
value domain
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What is ISO/IEC 11179?

• ISO/IEC 11179 Parts 1-6 Information technology
  Specification and Standardization of data
  elements
• A metamodel for data element metadata
• Standard by which to convey semantic, syntactic
  and lexical meaning
• Human and machine understandable
• Unambiguous

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ISO/IEC 11179 Information technology Standard

• ISO/IEC 11179 Part 1 Framework for the
  specification and standardization of data
  elements
• ISO/IEC 11179 Part 2 Classification for data
  elements
• ISO/IEC 11179 Part 3 Registry metamodel and
  basic attributes
• ISO/IEC 11179 Part 4 Rules and Guidelines for
  the Formulation of Data Elements
• ISO/IEC 11179 Part 5 Naming and Identification
  Principles for Data Elements
• ISO/IEC 11179 Part 6 Registration of data
  elements
• Publically Available from
• http//isotc.iso.ch/livelink/livelink/fetch/2000/2
  489/Ittf_Home/PubliclyAvailableStandards.htm??Redi
  rect1

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Basic Metamodel Components
Conceptual_Domain
Data_Element_Concept
Data Element Concept
Conceptual Domain
having
specifying
1..1
1..1
0..
0..
1..1
1..1
data_element_concept_conceptual_domain_relationshi
p
1..1
1..1
specified_by
represented_by
Perception
expression
specification
Representation
representing
providing_representation_to
0..
0..
0..
0..
Value_Domain
Data_Element
Value Domain
representation
Data Element
0..
0..
1..1
1..1
represented_with
providing_representation_for
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Why ISO/IEC 11179?

• What is this datum?
• Provides concrete guidance on the creation and
  maintenance of discrete data element attributes
  and metadata (semantics) enabling the formulation
  of data elements in a consistent, standard manner
  
• Metadata Repository/Registry
• Framework for Data element standardization and
  registration allow the creation of a shared data
  environment in much less time and with much less
  effort than it takes for conventional data
  management methodologies.
• Adoption of 11179 Allowed us to Get on with it

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ISO/IEC 11179 Administered Items
Derivation_Rule
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ISO/IEC Administered Item Administration Record
and Common Attributes

• Unique Identifier
• Administrative Status
• Registration Status
• Creation Date
• Administrative Note(s)
• Effective Date
• Change Date(s)
• Change Description(s)
• Origin
• Until Date

• Created By
• Modified By
• Name(s)
• Definition(s)
• Stewardship Information
• Submitter Information
• Reference Document(s)
• Classifications

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ISO/IEC 11179 NCICB Extensions
Form
Concept Class
The Concept Class Provides Semantic Linkage
Derivation_Rule
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caDSR Implementation of ISO/IEC 11179 Model
Conceptual Domain Agent
Object Agent
Valid Values Cyclooxygenase Inhibitor Doxercalcife
rol Eflornithine Ursodiol
Data Element Concept Chemopreventive Agent
Value Domain Chemopreventive Agent Name
Property Chemopreventive
Classification Schemes caDSRTraining
Representation Name
Data Element Chemopreventive Agent Name
Context caCORE
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NCICB Concept ClassCommon Attributes

• Concept Class
• Administered Item attributes
• Concept Unique Identifier
• Pointer to an externally defined concept
• Concept Definition Source
• Names the source terminology/ontology/vocabulary
• Concept Relationship
• Semantic Order of the concepts
• NOTE ISO describes a Concept Relationship as a
  semantic link among two or more concepts. There
  is a subtlety in our implementation. In caDSR
  use the concept relationships as more of a
  derivation rule, naming the order of the concepts
  - not semantic relationships in an ontologic or
  object model sense of relationship.
• Object Class, Property, Representation term,
  Qualifier terms, Value Domains

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Why vocabularies/ontology important?

• Goal Semantically unambiguous,
  interoperability
• Data Element curators are not necessarily
  vocabulary experts
• NCI had a terminology and vocabulary services
  group EVS
• Semantic integration is achieved by tying
  Standard vocabulary identifier codes to the caDSR
  metadata
• The ISO 11179 provides the framework we were
  looking for something that could be computed
  without a human having to read and interpret
  definitions
• By abstracting the curation of concepts in caDSR
  and instead relying on external vocabularies

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EVS and caDSR Distinctions

• caDSR is a metadata repository
• maintains metadata to permit a user to locate the
  correct data element defining the characteristics
  of a piece of datum, an instance of a specific
  concept, in sufficient detail to be collected and
  stored on a computer
• EVS is a terminology server
• provides services for synonymy, mapping between
  vocabularies, hierarchical structures,
  Subconcepts, Superconcepts, Roles, Semantic type,
  etc.

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Presentation Outline

• caCORE Overview
• ISO/IEC 11179 Overview
• caDSR Implementation and tooling

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caDSR Overview

• NCI Data Element Metadata repository and registry
• Based on the ISO/IEC 11179
• Designed to integrate caCORE infrastructure
• Supports the development and deployment of Data
  Elements that are used as metadata descriptors,
  primarily for NCI-sponsored research, with an
  ever widening girth of end users
• Available as an open-source download

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caDSR Tools

• Goals of caDSR Tools development
• Simplify development and creation of ISO/IEC
  11179 compliant metadata by Data Element Curators
  and UML Modelers
• Simplify consumption of Data Elements by end
  users and application developers
• Enhance reuse of Data Elements for all
• Enable semantic consistency across research
  domains
• Support metadata life-cycle and governance
  processes

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caDSR Home Page
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Introduction to caDSR Tools

• CDE Browser to Search for and Download
• Form Builder to Create user specified collections
  of CDEs
• Side-by-Side Compare
• CDE Curation Tool to Create Data Elements
• Admin Tool to Curate and Administer caDSR -
  Power Users
• Sentinel Tool (3.0)
• Generates end user Alerts triggered by metadata
  changes
• Batch Load to import Administered Items
• Excel Loader (MS Excel)
• UML Loader (XMI)
• Case Report Form Loader (MS Excel)

Access, Develop, Manage, Consume
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CDE Browser
CONTEXT Browsing

• View, Search, Download
• Shopping cart feature
• FormBuilder to Build / Download Forms and Data
  Elements
• Context Browsing Tree
• By Classification Schemes
• By Forms
• CDE Basic Search Criteria
• Google-like search
• Sortable search results by clicking on column
  headings

Basic Search
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CDE Browser

• Advanced Search Criteria
• Leverages ISO attributes
• Find all with 18254-3 permissible value
• Find all with Gene
• Find all with Released workflow status
• Find all with Standard Registration status
• Etc.

Advanced Search
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Form Builder

• Create and Manage Forms
• Organize CDEs into modules within a Form
• Attach pdf or word format
• Classify Forms into groupings for specific end
  user communities
• Publish Un-Publish for Browser Catalog
  visibility
• Printer Friendly version
• Download CDEs

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CDE Side-by-Side Compare

• CDE Side-by-Side Compare
• Build shopping cart, compare CDE metadata side by
  side
• Download to excel spreadsheet

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Curation Tool

• To Create, Edit or Version
• Data Element Concepts
• Value Domains
• Data Elements
• ISO 11179 Wizard
• Construct ISO compliant Data Elements by building
  up the pieces
• Builds Names and Definitions from underlying
  components.
• Get Associated
• Leverage ISO to retrieve related CDEs
• Block Edit
• shopping cart
• Assign classification schemes
• Versioning

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Administration Tool

• System Administration
• User Accounts and Security
• Lists of Values (LOVs) used in content creation
• Create Framework
• Conceptual Domains
• Classification Schemes (basis for organizing CDEs
  in Browser)
• Protocols

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Sentinel Tool

• Create Alerts
• User defined triggers based on data element
  metadata attributes
• notify me of any change to the Value Domain for
  any CDE on the Adverse Event Form
• Generates and emails a report of changes matching
  Alert criteria

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Batch Loading

• Excel Loaders
• Formatted MS Worksheet
• Administered Item
• Form
• UML Loader
• XMI representation of a UML Class Diagram
• Class ?Object Class
• Attribute ?Property
• Data Element Concept, Value Domain and Data
  Element derived from the above

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Current User Base

• Cancer Biomedical Informatics Grid (caBIG)
  820/466/180/ 61
• Center for Cancer Research (CCR) 821/573/506/
  12
• Clinical Data Interchange Standard Consortium
  (CDISC) - 3/0
• Center for Cancer Imaging (CIP) - 238/151/148/ 2
• Cancer Therapy Evaluation Program (CTEP)
  8029/2432/2428/ .1
• Division of Cancer Prevention (DCP)
  427/321/286/ 11
• National Heart Lung and Blood Institute (NHLBI)
  0/0
• Early Detection Research Network (EDRN)
  121/1/1/ 100
• Divisions of Population Sciences and Cancer
  Control (PS CC) 85/9
• Specialized Programs of Research Excellence
  (SPOREs) 719/197/120/ 39
• Cancer Ontologic Research Environment (caCORE)
  1028/810/810 0
• Total CDEs in this Context / Released
  workflow status / Released and developed by
  this context / Reused from other contexts

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Exploring

• National Institute of Neurological and Disorders
  and Syndromes (NINDS)
• National Icelandic Center for Oncology
• Cancergrid UK

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Operating Environments

• Database Repository
• Oracle 9i
• Administration Tool
• Oracle PL/SQL, Oracle 9i Application Server
• CDE Browser
• Java, Oracle 9i Application Server
• CDE Curation Tool
• Jakarta Tomcat

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Support

• NCICB Help Desk
• ncicb_at_pop.nci.nih.gov and telephone support
• Bi-weekly Software meetings
• Hosted by Denise Warzel
• Telconference and web-cast
• Bi-weekly Content Development Meetings
• Hostd by George Komasoulis
• Telconference and web-cast
• Open end user requirements meetings, design
  reviews and prototyping/feedback sessions
• Training
• Web-cast and telconference

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Contact Information

• caDSR Home Page
• http//ncicb.nci.nih.gov/core/caDSR
• caDSR Users ListServ
• http//list.nih.gov to subscribe to
  caDSR_Users_at_list.nih.gov
• caDSR Training Home Page
• http//ncicb.nci.nih.gov/NCICB/core/caDSR/Training
  
• caDSR Training ListServe
• http//list.nih.gov to subscribe to
  caDSR_Training-L_at_list.nih.gov

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Documentation/Recommended Reading Materials

• caDSR Homepage
• http//ncicb.nci.nih.gov/core/caDSR
• caCORE User Application Manual
• ftp//ftp1.nci.nih.gov/pub/cacore/NCICBapplication
  s/NCICBAppManual.pdf
• caCORE Technical Guide
• ftp//ftp1.nci.nih.gov/pub/cacore/caCORE2.0_Tech_G
  uide.pdf caDSR APIs
• caDSR API Guide
• ftp//ftp1.nci.nih.gov/pub/cacore/caDSR/caCORE2.0_
  caDSR_API.pdf
• caDSR Business Rules
• http//ncicb.nci.nih.gov/NCICB/core/caDSR/Business
  Rules
• caDSR Content Meetings
• http//ncicb.nci.nih.gov/NCICB/core/caDSR/Content
• caDSR_Users List serv subscribe
• http//list.nih.gov
• Send Request for caDSR Account to
  ncicb_at_pop.nci.nih.gov

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caDSR Tools Team

• NCICB
• Peter Covitz
• Denise Warzel
• ScenPro
• Bill McCurry
• Tom Phillips
• Robert Harding
• Jennifer Brush
• Larry Hebel
• Smita Hastak

• Oracle
• Edmond Mulaire
• Ram Chilukuri
• Prerna Aggarwal
• Dan Ladino
• Christophe Ludet
• Shaji Kakkodi
• Jane Jiang
• SAIC
• Kathleen Gundry
• Tommie Curtis
• Brenda Maeske