Mayo LexGrid Import Toolkit

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Mayo LexGrid Import Toolkit

• Presentation to XMDR Quarterly MeetingPart 1
• March 14, 2005
• Berkeley, CA

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LexGrid Schema

• Purpose
• Capture the semantics that need to be shared in a
  standardized consistent fashion
• Capture as much of the rest as makes sense
• No promises of 100
• Outliers may have to rely on external services
  to recover the rest

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1..
1..
1..
valueDomain
systemRelease
codingScheme
1..
0..
relation
codedEntry
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Schema Migration
LexGrid XML Schema
LexGrid LDAP
LexGrid Java
LexGrid SQL
LexGrid XMI
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Schema Migration
LexGrid XML Schema
LexGrid Java
LexGrid EMF
LexGrid Castor
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Schema Migration
LexGrid XML Schema
LexGrid Java
LexGrid EMF
LexGrid Castor
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Conversion Tools
Editors
LexGrid XML Schema
LexGrid XML
LexGrid EMF
Conversion Tools
Conversion Tools
Conversion Tools
LexGrid SQL
LexGrid LDAP
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Conversion Tools XML Importing
Editors
LexGrid XML Schema
LexGrid XML
LexGrid EMF
Conversion Tools
Conversion Tools
Conversion Tools
LexGrid SQL
LexGrid LDAP
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Conversion Tools XML Importing
XML
Apelon Ontylog
X S L T
ADL RDF
LexGrid XML
OWL
LexGrid EMF
SQL XML

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Conversion Tools
LexGrid XML Schema
LexGrid LDAP
LexGrid Java
LexGrid EMF
LexGrid SQL
LexGrid XMI
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Conversion ToolsLDAP Import/Export
LexGrid LDAP
LexGrid XML
LexGrid EMF
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Conversion ToolsSQL Import/Export
LexGrid SQL
UMLS RRF
LexGrid LDAP
LexGrid XML
LexGrid EMF
LexGrid SQL Lite
Indented Text
EPA DTIC .
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Conversion ToolsJava Integration
LexGrid LDAP
LexGrid XML
LexGrid SQL
LexGrid EMF
Java
Protege
Foundational Model of Anatomy
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Conversion ToolsJava Import
LexGrid LDAP
LexGrid XML
LexGrid SQL
LexGrid EMF
Java
ECLIPSE
LexGrid Editor
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Interfaces
LexGrid SQL
LexGrid LDAP
Common Terminology Services
.NET
RMI / Corba
SOAP
Java
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Conversion Tools XML Exporting
XML
Apelon Ontylog
X S L T
ADL RDF
LexGrid XML
OWL
LexGrid EMF
SQL XML

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The Mayo Lexical Grid Architecture

• Presentation to XMDR Quarterly MeetingPart 2
• March 14, 2005
• Berkeley, CA

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The Ultimate Goal

• Terminology as a commodity resource
• Available whenever and wherever it is needed
• Online or downloadable
• Push or pull update mechanism
• Available 24x7
• Revised and updated in real-time
• Cross-linked and indexed

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Approach

• Use the internet model
• Backbone
• Protocol(s)
• Model
• Directory services
• Tools

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The GridBackbone
NCI
Node
CAP
...
Node
Node
Mayo
Node
Node
Node
...
Stanford
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The GridShared Protocols
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The GridCommon Model
Node
Node
Node
Node
Node
Node
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The GridDirectory and Index Services
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The GridVirtual View
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MDA and Terminologies

• Presentation to XMDR Quarterly MeetingPart 3
• March 14, 2005
• Berkeley, CA

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Terminology vs. Knowledge Base

• Terminology is used to encode and decode symbols
• Which symbols most accurately encode the
  concept(s) that I need to communicate in a
  specific context?
• What are the intended concept(s) represented by
  the set of symbols that were communicated in a
  specific context?

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Terminology vs. Knowledge Base

• Knowledge base defines additional information
  that might be inferred or deduced from the
  symbols used in a communication
• Causes / may cause
• Co occurrence
• Indicates
• Used for
• ...

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Terminology vs. Knowledge Base

• Terminology
• Definitions
• Must be shared
• Defines common context

• Knowledge Base
• Inferences
• Frequently not shared
• Can change across contexts

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Terminology, Knowledge Base and Ontology (today)
Knowledge Base
Lexical Information (Definitions,
Designations, Instructions)
Terminology
Ontology
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Terminology vs. Information Model

• Terminology
• An organized collection of symbols or tokens that
  represent reality as perceived in a given
  context or specialty
• Information Model
• Describes the information constants and
  variables of a particular communication act or
  set of acts

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Terminology / KB / Information ModelExample
Information Model
Terminology
Routine Lab Report
LOINC
UCUM
HL7 ObservationInterpretation
Knowledge Bases
Laboratory Management
Diagnostic Test Interpretation
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The Communication Process
KB2
KB1
Semantics
CONCEPT
CONCEPT
Symbolises
Refers To
Refers To
Symbolises
I see a ClipArt image of a rose
Rose, ClipArt
Rose, ClipArt
Stands For
Stands For
Referent
Symbol
Symbol
Context
Information Model
Terminology
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Terminology and InformationModels
Terminology
Information Model
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Information ModelClass Definitions
definedBy
CodedConcept
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Information ModelClass Definitions
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Information ModelDefinitions
definedBy
CodedConcept
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Information ModelDefinitions
SymbolReference
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Resulting Model
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Resulting Model
Data Element Concept
Concept Domain
Value Meaning
Non-enumerated Value Domain
Enumerated Value Domain
Data Element
Value Domain
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Terminology and 11179Concepts and Relationships
Code System
Coded Entry
Relationship
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Terminology and 11179Concepts and Relationships
Code System
Coded Entry
Relationship
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Terminology and 11179Concepts and Relationships
Code System
Relationship
Coded Entry
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Terminology and 11179Concepts and Relationships
Code System
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Terminology and 11179Administered Item
Any administered item has one or more names
and/or definitions in one or more contexts
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Terminology and 11179Administered Item

• Value Domain
• Enumerated_Value_Domain
• Non_enumerated_Value_Domain
• Representation Class
• Property
• Object Class
• Concept
• Concept Relationship
• Derivation Rule
• Data Element Concept
• Data Element
• Context
• Conceptual Domain
• Enumerated_Conceptual_Domain
• Non_enumerated_Conceptual_Domain
• Classification Scheme

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Additional Terminological Attributes

• _description
• non_enumerated_conceptual_domain
• value_meaning
• non_enumerated_value_domain
• context (includes language)