Introduction to the caDSR
Presented to HL7 Vocab SIG
January 24, 2005
Denise Warzel
National Cancer Institute, Center for Bioinformatics
caDSR Project Officer, Software Development
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Presentation Outline
• caCORE Overview
• ISO/IEC 11179 Overview
• caDSR Implementation and tooling
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caCORE Components
• caCORE is the open-source foundation upon which the NCICB
builds its research information management systems
Bioinformatics Objects
Data Standards
Enterprise Vocabulary
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caCORE Infrastructure wiring
Public APIs
Domain object metadata
Common data
elements
(CDEs)
Common data elements
Vocabulary for
CDE specification
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Dictionary, thesaurus
services
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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
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.
Data Element Representation:
The part of a data element having
A value domain, datatype,and other
representational specifications.
Representation Class:A
classification of data
elements based upon the
type of representational
form.
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.
Conceptual Domain:A set
of possible value meanings
of a data element expressed
without representation.
Value Meaning:A member of the
set of finite allowed inventory of
notions that can be categorized
for a conceptual domain.
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Value Domain: A set of attributes
describing representational
Characteristics of instance data
with or without permissible values.
Permissible Value:An
expression of a value
meaning in a specific
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/2000/2489/Ittf_Home/PubliclyAvailableSt
andards.htm??Redirect=1
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Basic Metamodel Components
Conceptual_Domain
Data_Element_Concept
Data Element Concept
+having
0..*
+specifying
1..1
Conceptual Domain
data_element_concept_conceptual_domain_relationship
1..1
+represented_by
1..1
+specified_by
Perception
expression
specification
Representation
+representing
+providing_representation_to
0..*
0..*
Value_Domain
Data_Element
Data Element
representation
0..*
+providing_representation_for
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Value Domain
1..1
+represented_with
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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
Administered_Item
Classification_Scheme
Conceptual_Domain
Context (for administered item)
Data_Element
Data_Element_Concept
Object_Class
Property
Representation_Class
Value_Domain
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
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•
•
•
•
•
•
•
•
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
Administered_Item
Classification_Scheme
Form
Conceptual_Domain
Context (for administered item)
Concept Class
Data_Element
The Concept Class
Provides
Semantic Linkage
Data_Element_Concept
Object_Class
Property
Representation_Class
Value_Domain
Derivation_Rule
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caDSR Implementation of ISO/IEC
11179 Model
Conceptual Domain
Agent
Object
Agent
Classification Schemes
caDSRTraining
Valid Values
Data Element Concept
Chemopreventive Agent
Value Domain
Chemopreventive Agent Name
Property
Chemopreventive
Cyclooxygenase Inhibitor
Doxercalciferol
Eflornithine
…
Ursodiol
Representation
Name
Data Element
Chemopreventive Agent Name
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Context
caCORE
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NCICB Concept Class
Common 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
Curators
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Developers
General
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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
Basic Search
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– Google-like search
– Sortable search results by
clicking on column headings
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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”
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• “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
OC
caDSR DEFAULT VALUES: Workflow status = "Released" Alw ays. Version = 1.0 Alw ays. Create Date =Date loaded by Loader. Created by = EVS. Long Name = EVS Preferred nam e
EVS Preferred Nam e
Definition
Definition Source
Database
Context Preferred Nam E
effective Begin Date
Change Note
Alternate Nam e Type
VARCHAR2 (20)
Mapped to Long Name
and Preferred Name
Not Null
VARCHAR2 (2000)
PreferredDefinition
VARCHAR2 (2000)
Definition Source
VARCHAR2 (255)
Database
VARCHAR2 (20)
Requestors Context
VARCHAR2 (30)
YY.MM.B
VARCHAR2 (2000)
Text
VARCHAR2 (20)
AlternateName.Type
Not Null
Celsius Scale
The temperature
scale defined by
the values 0
degree Celsius for
the freezing point
of water and 100
degrees Celsius
for the boiling
point of water.
The Celsius
degree (C) is the
same size as a
Kelvin and equal
to (F - 32)/1.8. To
convert Celsius to
Fah
Null
NCI
Not Null
NCI Thesaurus
Not Null
caBIG
Null
11/18/2004
Null
Requested by
Dianne Reeves
Not Null
NCI_Concept_Code
HEENT
NCI
HEENT is the
Head, Ears, Eyes,
Nose and Throat,
and is referred to
as a body system
on a physical or
medical
examination. The
term is typically
used as 'HEENT'
in a physician or
caregiver notes.
NCI Thesaurus
caBIG
11/18/2004
Requested by
Dianne Reeves
NCI_Concept_Code
The Gracely Pain NCI
Unpleasantness
Scale is a visual
analog scale of 0
to 20 used by a
subject to define
their pain
unpleasantness
experience.
Together with the
intensity scale
these tools serve
to differentiate the
patient's sensory
perception of pain
inte
NCI Thesaurus
Gracely Pain
Unpleasantness
Scale
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caBIG
11/18/2004
Requested by
Dianne Reeves
NCI_Concept_Code
• 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@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@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_TrainingL@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/NCICBapplications/NCICBAppManual.pdf
•
caCORE Technical Guide:
– ftp://ftp1.nci.nih.gov/pub/cacore/caCORE2.0_Tech_Guide.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/BusinessRules
•
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@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
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• Oracle
–
–
–
–
–
–
–
Edmond Mulaire
Ram Chilukuri
Prerna Aggarwal
Dan Ladino
Christophe Ludet
Shaji Kakkodi
Jane Jiang
• SAIC
– Kathleen Gundry
– Tommie Curtis
– Brenda Maeske
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