National Cancer Institute
caDSR
Briefing for Small Scale Harmonication
Project
Denise Warzel
Associate Director, Core Infrastructure
caCORE Product Line Manager
July 25, 2007
National Cancer Institute
NCI Center for Biomedical Informatics and
Information Technology (CBIIT)
• The CBIIT is the NCI’s strategic and tactical arm for
research information management
• We collaborate with both intramural and extramural
groups
• Mission to integrate and harmonize disparate research
data
• Production, service-oriented organization. Evaluated
based upon customer and partner satisfaction.
National Cancer Institute
caDSR and EVS 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.
National Cancer Institute
Goals of the Registry
•
Goals tools development:
– Simplify development and creation of ISO/IEC 11179 compliant
metadata by Data Element Curators and UML Modelers
– Simplify consumption of Data Elements and standard vocabularies
by end users and application developers through APIs and web
services
– Enhance reuse of Data Elements across domains
– Enable semantic consistency across research domains
– Support metadata life-cycle and governance processes
•
Created, maintained by NCI Contractors and Open Development
model
•
Available as an open-source download
* Training *
National Cancer Institute
* Training *
National Cancer Institute
Introduction to caDSR Tools
–
CDE Browser to Search for, View and Download
–
–
–
Form Builder to Create user specified collections of CDEs
• Skip patterns, repeating groups, default values
Side-by-Side Compare
UML Model Browser to View and manage UML Model metadata
–
CDE Curation Tool to Create Data Elements
–
Admin Tool to Administer caDSR and curate content - “Power Users”
–
Sentinel Tool to Generate end user ‘Alerts’ triggered by metadata changes
–
Semantic Integration Workbench – Semantic Integration/Annotation Tools, annotate, transform and
register metadata
Batch Load to import Administered Items
• Excel Loader (MS Excel)
–
•
•
•
Semantic Integration Workbench
UML Model Loader (XMI)
Case Report Form Loader (MS Excel)
Access, Develop, Manage, Consume
National Cancer Institute
Curation Tool
•
•
To Create, Edit or Version:
•
Value Domains
•
Data Elements
Construct ISO compliant Data Elements
by building up the pieces
• Builds Names and Definitions from
underlying components.
“Get Associated”
–
•
Data Element Concepts
ISO 11179 Wizard
–
•
•
Leverage ISO to retrieve related CDEs
“Block Edit”
• “shopping cart”
• Assign classification schemes
• Versioning
National Cancer Institute
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
National Cancer Institute
CDE Browser
“CONTEXT
Browsing”
•
View, Search, Download
–
•
FormBuilder to Build / Download Forms
and Data Elements
•
“Context Browsing” Tree
•
Basic Search
Shopping cart feature
–
By Classification Schemes
–
By Forms
CDE Basic Search Criteria
–
Google-like search
–
Sortable search results by clicking on
column headings
National Cancer Institute
CDE Browser
•
Advanced Search
–
Leverages ISO 11179 and Concept
semantic attributes
• Find all with “18254-3”
permissible value
• Find all with “Gene*”
• Find all with “Released”
workflow status
• Find all with “Standard”
Registration status
•
Advanced Search
Etc.
National Cancer Institute
Form Builder
•
Create and Manage Forms
–
Organize CDEs into modules
within a Form
–
Create skip patterns, default
values, repeating groups
–
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
National Cancer Institute
Form Builder
•
Create and Manage Forms
–
Organize CDEs into modules
within a Form
–
Create skip patterns, default
values, repeating groups
–
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
National Cancer Institute
CDE Side-by-Side Compare
•
CDE Side-by-Side Compare
– Build shopping cart,
compare CDE metadata
side by side
– Download to excel
spreadsheet
National Cancer Institute
UML Model Browser
•
View CDEs as part of a UML
Domain Model
• Classes
• Attributes
• Associations
•
View Contact information, like to
UML source file, documentation,
etc
National Cancer Institute
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)
• Define high level “Protocol”
National Cancer Institute
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
Semantic Integration Workbench
and UML Loader
–
XMI representation of a UML
Class Diagram
• Class Object Class
• Attribute Property
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
Gracely Pain
Unpleasantness
Scale
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
caBIG
11/18/2004
Requested by
Dianne Reeves
NCI_Concept_Code
• Enumeration Value
Domain
• Mapped EVS Concepts
• Data Element Concept,
Value Domain and Data
Element harmonized with
existing content and
created from the above
•
Excel Loaders
–
Formatted MS Worksheet
–
Administered Items
National Cancer Institute
ISO/IEC Administered Item
Administration Record and Common Attributes
•
•
•
•
•
•
•
•
•
•
Unique Identifier
•
•
•
Registration Authority (RA)
Data Identifier (within RA)
Version
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
Additional Value Domain Attributes
•
Datatype (ISO 11179)
•
•
•
•
•
•
•
•
•
Name, Description, Scheme Reference,
Annotation (ISO 11179)
Codegen compatible, Comment
Format (ISO 11179)
Maximum Characters (ISO 11179)
Unit of Measure (ISO 11179)
Minimum Characters
High Value
Low Value
Character Set
•
If Enumerated:
•
•
Permissible Values (ISO 11179)
• Value, Value Meaning, Begin Date,
End Date (ISO 11179)
• High Value, Low Value
If Non-enumerated:
•
Reference Document pointing to External
‘Top Node’ Concept
National Cancer Institute
Create For Standard Codes
National Cancer Institute
Create For Standard Code Sets
- Use this if you want everyone store the code the same way
National Cancer Institute
caDSR URLs
•
•
•
caDSR Home Page http://ncicb.nci.nih.gov/core/caDSR
–
Browser and Form Builder: http://cdebrowser.nci.nih.gov/
–
Admin Tool: http://cadsradmin.nci.nih.gov/
–
Curation Tool: http://cdecurate.nci.nih.gov/
–
Sentinel Tool: http://cadsrsentinel.nci.nih.gov/
–
Freestyle search: http://freestyle.nci.nih.gov/
–
Semantic Integration Workbech: http://cadsrsiw.nci.nih.gov/
caDSR Users, Developers ListServ
–
http://list.nih.gov to subscribe to caDSR_Users@list.nih.gov
–
http://list.nih.gov to subscribe to caDSR_Software_Developers@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@list.nih.gov
National Cancer Institute
caCORE Reading Materials
•
caCORE Homepage:
–
•
caCORE User Application Manual:
–
•
http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview
ftp://ftp1.nci.nih.gov/pub/cacore/NCICBapplications/NCICBAppManual.pdf
NCICB GFORGE
•
•
caGRID Browser
–
•
•
http://ncicb.nci.nih.gov/NCICB/training
caDSR Business Rules
–
•
ftp://ftp1.nci.nih.gov/pub/cacore/caCORE3.1_Tech_Guide.pdf – caCORE APIs
caCORE Training
–
•
http://cagrid-browser.nci.nih.gov/cagrid-browser/
caCORE Technical Guide:
–
•
http://gforge.nci.nih.gov
http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr/business_rules
caDSR_Users List serv subscribe:
–
http://list.nih.gov
–
Send Request for caDSR Account to: ncicb@pop.nci.nih.gov
caBIG home page: documentation about the Grid
–
http://cabig.nci.nih.gov
National Cancer Institute
Questions?