lexgrid philosophy, model and interfaces harold r solbrig division of biomedical statistics and...
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LexGridPhilosophy, Model and Interfaces
Harold R Solbrig
Division of Biomedical Statistics and Informatics
Mayo Clinic
05/01/2009 LexGrid - Philosophy and Model 2
Outline
• Why the LexGrid model was created
• LexGrid approach and principles
• Key aspects of the LexGrid model
05/01/2009 LexGrid - Philosophy and Model 3
Why LexGrid?
The situation in the late 1990’s:
• Multiple “terminologies” available• SNOMED-3 and SNOMED-RT• READ Codes• HCDA (ICD-8 w/ Mayo Extensions)• ICD-9-CM• ...
05/01/2009 LexGrid - Philosophy and Model 4
Why LexGrid?
The situation in the late 1990’s:
• DL was on the horizon• SNOMED-RT• GALEN• DAML+OIL beginning to emerge
05/01/2009 LexGrid - Philosophy and Model 5
Why LexGrid?
Mayo Health Sciences Research • Multiple experiments and projects
involving NLP, semi-automated record coding and classification, terminology-driven record retrieval, coded medical records, etc.
05/01/2009 LexGrid - Philosophy and Model 6
Why LexGrid?
Mayo recognized the need for re-use• Terminologies have common
characteristics• Software should be reusable
• Search and indexing• Query• Tree traversal• ...
05/01/2009 LexGrid - Philosophy and Model 7
Why LexGrid?
Part of the solution was the service oriented model:
• Aka “Breadboard”
• API specifications (OMG’s LQS was primary example)
05/01/2009 LexGrid - Philosophy and Model 8
Why LexGrid?
Service Oriented Model:
Application performs search against server using a SNOMED-RT database. Referred to as API specification. An Interface specification may include a server connected to a collection of ICD9CM tables.
Application
Find designations matching “Myocard Infarct”
Client
Server
SNOMED-RT ICD-9-CM
Server
API Specification
Interface Specification
05/01/2009 LexGrid - Philosophy and Model 9
Why LexGrid?API/Interface Specification
Provides a common semantics• What is a “definition”,
“designation”, “relationship”, ...• Provides a common interface
Allows implementation to be specific to the terminology...
05/01/2009 LexGrid - Philosophy and Model 10
Single databases load by an import module. Semantic mapping occurs within the individual server.
Server
SNOMED-RT
ICD-9-CM
Import Import
...
Import
SemanticMapping
SemanticMapping
SemanticMapping
Why LexGridAPI/Interface Specification
05/01/2009 LexGrid - Philosophy and Model 11
Why LexGrid?Harmonization on the model level
There are three different import modules, but they now connect to the common data model. The semantic mapping occurs during the import rather than within the server.
CommonServer
Common Data Model
Import Import Import
SemanticMapping
SemanticMapping Semantic
Mapping
05/01/2009 LexGrid - Philosophy and Model 12
Why LexGrid?
LexGrid:
A Common Terminology Data Model
Descriptive not Prescriptive
05/01/2009 LexGrid - Philosophy and Model 13
LexGridDesign Principles
Must span spectrum of “terminology”• Code/value lists• Thesauri (BT/NT)• Classification Schemes • Ontology & DL
05/01/2009 LexGrid - Philosophy and Model 14
LexGridDesign Principles
Must provide common semantics for elements that are used in service API:
• (Textual) Definitions• Designations• Comments
• Language / context / character set• Hierarchies• Relationships
05/01/2009 LexGrid - Philosophy and Model 15
LexGridDesign Principles
Must support non-API components as tag/value pairs.
Must map ALL internal semantics to external (terminological) definitions.
• A property is useless if you don’t know the meaning of the tag
• A relation is useless if you don’t know its definition
05/01/2009 LexGrid - Philosophy and Model 16
LexGridDesign Principles
Focus should be in information model vs. implementation:
• Originally implemented in LDAP• XML Schema Model• (Multiple) SQL Renderings to meet
different user requirements• Both Castor and Eclipse EMF
renderings
05/01/2009 LexGrid - Philosophy and Model 17
LexGrid ModelService Layer becomes secondary!
The common data model where semantic mapping occurs in the import modules. Additional services can also run off of the same data model, such as REST (read) or Hybernate
Common Data Model
Import
Services
Import
SemanticMapping
SemanticMapping
Service
Import
SemanticMapping
REST (read)Hybernate
...
05/01/2009 LexGrid - Philosophy and Model 18
LexGridKey Components
Key components coding schemes include code and associations. Code for definitions, designations, comments and instructions. All of which have defined properties. Associations include Relation, Source and Target.
Properties
Coding Scheme
Code
Definitions
Designations
Comments
Instructions
Associations
Relation
Source
Target
1..*
1..*
1..*
05/01/2009 LexGrid - Philosophy and Model 19
LexGridKey Components
Mappings• supportedCodingScheme• supportedSource• supportedProperty• supportedAssociation• supportedPropertyQualifier• .....
Transform a “local name” to a URI• supportedAssociation localId=“hasPart”
URI=“http://www.obofoundry.org/ro/ro.owl#part_of”>
05/01/2009 LexGrid - Philosophy and Model 20
LexGridFuture and Next Steps
Many loaders, interfaces available today
• OBO, OWL, RDF, UMLS, CSV, Ontylog, custom...
Several service API’s and implementations
• CTS, LexEVS (core of caBIG), LexWiki (sort of “implementation”)
05/01/2009 LexGrid - Philosophy and Model 21
LexGridFuture and Next Steps
LexRDF
• OWL (2.0), DC, FOAF, SKOS (2008), RDF, RDFS, RO (to an extent) together now provide a reasonable overlay to LexGrid semantics
• Next step is to absorb and integrate• Mappings can now reference these• RDF import/export form that maintains
model while using appropriate tags
05/01/2009 LexGrid - Philosophy and Model 22
More Information
http://LexGrid.org/
https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page