# Presentation: 016810

## Mayo LexGrid Import Toolkit

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

## 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

## valueDomain

- systemRelease

- relation

- codedEntry

- codingScheme

- 1..*

- 0..*

- 1..*

- 1..*

- 1..*

## Schema Migration

- LexGrid
**XML Schema**

- LexGrid
**SQL**

- LexGrid
**XMI**

- LexGrid
**Java**

- LexGrid
**LDAP**

## Schema Migration

- LexGrid
**XML Schema**

- LexGrid
**Java**

**LexGrid**
**EMF**

- LexGrid
**Castor**

## Schema Migration

- LexGrid
**XML Schema**

- LexGrid
**Java**

**LexGrid**
**EMF**

- LexGrid
**Castor**

## Conversion Tools

- LexGrid
**XML Schema**

**LexGrid**
**EMF**

- LexGrid
- XML

**Editors**

**Conversion**
**Tools**

- LexGrid
- SQL

**Conversion**
**Tools**

- LexGrid
- LDAP

**Conversion**
**Tools**

## Conversion Tools XML Importing

- LexGrid
**XML Schema**

**LexGrid**
**EMF**

- LexGrid
- XML

**Editors**

**Conversion**
**Tools**

- LexGrid
- SQL

**Conversion**
**Tools**

- LexGrid
- LDAP

**Conversion**
**Tools**

## Conversion Tools XML Importing

**LexGrid**
**EMF**

- LexGrid
- XML

- X
- S
- L
- T

- XML

- Apelon
- Ontylog

- ADL
- RDF

- OWL

- SQL
- XML

- ...

## Conversion Tools

- LexGrid
**XML Schema**

- LexGrid
**SQL**

- LexGrid
**XMI**

- LexGrid
**Java**

- LexGrid
**LDAP**

**LexGrid**
**EMF**

## Conversion ToolsLDAP Import/Export

- LexGrid
**LDAP**

**LexGrid**
**EMF**

- LexGrid
- XML

## Conversion ToolsSQL Import/Export

- LexGrid
**LDAP**

**LexGrid**
**EMF**

- LexGrid
- XML

- LexGrid
- SQL

- LexGrid
- SQL
- Lite

**UMLS**
**RRF**

- Indented
- Text

**EPA**
**DTIC**
**...****.**

## Conversion ToolsJava Integration

- LexGrid
**LDAP**

**LexGrid**
**EMF**

- LexGrid
**XML**

- LexGrid
**SQL**

- Java

- Protege

**Foundational **
**Model of**
**Anatomy**

## Conversion ToolsJava Import

- LexGrid
**LDAP**

**LexGrid**
**EMF**

- LexGrid
**XML**

- LexGrid
**SQL**

**ECLIPSE**

**LexGrid Editor**

- Java

## Interfaces

- LexGrid
**LDAP**

- LexGrid
**SQL**

- Common Terminology Services

- .NET

- RMI / Corba

- SOAP

- Java

## Conversion Tools XML Exporting

**LexGrid**
**EMF**

- LexGrid
- XML

- X
- S
- L
- T

- XML

- Apelon
- Ontylog

- ADL
- RDF

- OWL

- SQL
- XML

- ...

## The Mayo Lexical Grid Architecture

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

## 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

## Approach

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

## The GridBackbone

- Node

- Node

- Node

- Node

- Node

- Node

- NCI

- CAP

- Mayo

- Stanford

**...**

**...**

## The GridShared Protocols

## The GridCommon Model

- Node

- Node

- Node

- Node

- Node

- Node

## The GridDirectory and Index Services

## The Grid“Virtual View”

## MDA and Terminologies

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

## 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?

## 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
- ...

## Terminology vs. “Knowledge Base”

- _Terminology_
- Definitions
*Must be shared*
- Defines common context

- _Knowledge Base_
- Inferences
- Frequently _*not*_ shared
- Can change across contexts

## Terminology, Knowledge Base and “Ontology” (today)

**Terminology**

**Knowledge Base**

**Ontology**

**Lexical Information**
**(Definitions,**
** ****Designations,**
**Instructions)**

## 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

## Terminology / KB / Information ModelExample

**LOINC**

**Terminology**

**UCUM**

**HL7 ObservationInterpretation**

**Knowledge Bases**

**Laboratory Management**

**Diagnostic Test Interpretation**

**Information Model**

**Routine Lab Report **

## The Communication Process

_**CONCEPT**_

- Referent

*Refers To*

*Symbolises*

*Stands For*

**“****Rose”,**
**“****ClipArt”**

*Refers To*

*Symbolises*

*Stands For*

**“****Rose”,**
**“****ClipArt”**

_**CONCEPT**_

_**Symbol**_

_**Symbol**_

**“****I see a ClipArt image of a rose”**

- Semantics

- Information
- Model

- Context

- Terminology

**KB1**

**KB2**

## Terminology and InformationModels

**Information**
**Model**

**Terminology**

## Information ModelClass Definitions

**CodedConcept**

**definedBy**

## Information ModelClass Definitions

## Slide 36

## Information ModelDefinitions

**CodedConcept**

**definedBy**

## Slide 39

## Information ModelDefinitions

**SymbolReference**

## Slide 41

## Resulting Model

## Resulting Model

**Data Element**
**Concept**

**Data Element**

**Concept**
**Domain**

**Value**
**Domain**

**Non-enumerated**
**Value Domain**

**Enumerated**
**Value Domain**

**Value Meaning**

## Slide 44

## Slide 45

## Slide 46

## Slide 47

## Slide 48

## Slide 49

## Slide 50

## Slide 51

## Slide 52

## Terminology and 11179Concepts and Relationships

**Code System**

**Coded Entry**

**Relationship**

## Terminology and 11179Concepts and Relationships

- Terminology and 11179Concepts and Relationships

**Code System**

**Coded Entry**

**Relationship**

## Terminology and 11179Concepts and Relationships

**Code System**

**Coded Entry**

**Relationship**

## Terminology and 11179Concepts and Relationships

**Code System**

## Terminology and 11179Administered Item

**Any administered item**
**has one or more names and/or**
**definitions in one or more contexts**

## Terminology and 11179Administered 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

## Additional Terminological Attributes

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