the lexical grid 1/14/2005copyright © 2005 mayo clinic1

1/14/2005 Copyright © 2005 Mayo Clinic 2

Outline

• Purpose - why we built the Lexical Grid

• Function – what the Lexical Grid can do


PurposeWhy did we built the Lexical Grid?

Communication


Communication

Communication

n. 2. the imparting or interchange of thoughts, opinions, of information by speech, writing or signs.

Information

n. 2. any knowledge gained through communication, research, instruction, etc.

Random House Dictionary of the English Language, 1983


Language and the Communication Process

• Language - a “specification” that enables communication

• Semantics - the association between signs or symbols and their intended “meaning”

• Syntax - the rules for ordering and structuring the signs into phrases and sentences

• Pragmatics - the relationship between signs and symbols and the recipient. Broadly, the shared context.


Ogden’s Semiotic Triangle

C.K Ogden and I. A. Richards. The Meaning of Meaning.

Thought or Reference

Referent Symbol

SymbolisesRefers to

Stands for“Rose”, “ClipArt”


The Communication Process

CONCEPT

Referent

Refers ToSymbolises

Stands For“Rose”,“ClipArt”

Refers ToSymbolises


CONCEPT

Symbol Symbol

“I see a ClipArt image of a rose”




CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Semantics




CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Semantics

Syntax




CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Semantics

Syntax

Context Context

Shared Context



Shared Context

Impacts how much information can be contained in a symbol.

NoSharedContext

SharedUniverse

CommonLanguage

SharedSpecies

SharedPlanet

SharedSun

CommonCulture

SimilarEducation

CommonProfession

CommonSpecialty

Information / Symbol


Minimum Shared Context


Shared Culture

“It is possible to find the truth without controls, but the process has been demonstrated again and again to be notably inefficient, so that years may be required before it is appreciated that a given treatment is worthless...”


Shared Specialties

“Both ontologically and in order of explanation, the intentionality of the propositional attitudes is prior to the intentionality of natural languages; and, both ontologically and in order of explanation, the intentionality of mental representations is prior to the intentionality of propositional attitudes.”


The impact of context on communication

Shared context:• Allows information to be communicated in larger,

more succinct “chunks”.• Drug, analgesic and NSAID are all “chunks”,

yet differ markedly in conceptual complexity.• Enables specialized symbol sets:

• Contrast the amount of information contained in the formula E=MC2 versus that contained in this presentation...


Contextual Formalism

The degree of formality in a shared context can vary across a wide spectrum:

• Tacit context which is simply presumed• Contextual negotiation proceeding the

actual message• Rigorous and formal rules and documents

describing the form and possible meanings behind every message and phrase.


Factors Effecting the Degree Contextual Formalism

• Number of participating parties• Formalism needs to increase as number of

participants increase

• Geographic, cultural and temporal proximity of communicators

• The further apart communicators are, the less they can assume

• Amount of shared context• The more you have, the more important it

becomes to be organized


Factors Effecting the Degree Contextual Formalism

• The cost of imprecise communication• Poetry and literature - low cost (some may argue

actual gain)• Technical and professional - high to very high

cost• What is the cost of assuming the units of a

thrust specification?• What is the cost of assuming the dose of a

prescription?• What is the cost of assuming the century in

which the communication originated?


Common Forms of Contextual Formalism

• Dictionaries

• Thesauri

• Textbooks, college courses, etc.

• Operations manuals

• Data dictionaries

• Terminologies


Shared Context...



CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Semantics

Syntax

Context Context

Shared Context




CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Lexicon

Information Model /Data Model

Context Context

Shared Context



Making Shared Context Explicit

CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Context Context

Formal SharedContext

Terminologies Terminologies

Making Shared Context Explicit


Shared Context Least Common Denominator

CONCEPT

Referent

Refers ToSymbolises


Refers ToSymbolises


CONCEPT

Symbol Symbol


Context Context

Reduce the Shared Context...

Terminologies Terminologies

Terminologies

“I see a ClipArt image of a red flower with ...”

... increase the symbolcomplexity

Shared Context Least Common Denominator


Communication and Clinical Information


Clinical Information Today

• Still transitioning from paper to digital

• Existing digital records grew up in an era of scarce resources

• Maximum shared context• High information content per token

• Information is highly filtered• Only preserve what is absolutely necessary

• Context is tacit and local• Sharing information is labor intensive and

imprecise• Mapping between local contextual knowledge

and incomplete and idiosyncratic understanding of target medium



ClinicalRecord

Dictation

Notes

Direct Entry

Coding and Classification

Local Context

GlobalContext



• High degree of tacit shared context• Records require interpretation to be used

externally

• External representations are ‘lossy’• ICD-9, CPT & the like are abstractions and

classifications

• Expensive or impossible to utilize for purposes not originally envisioned by system architects

• e.g. genetics research


Bioinformatics Research

• Needs high volumes of clinical data• Statistical power requirements• May have to span more than one institution

• May need to include environmental and other factors

• Cross-institutional and regions

• Will often be searching for new information• ‘Raw’ information available to clinician or

laboratory • May not be considered clinically significant


Bioinformatics ResearchClinical Information Requirements

• High Volume

• Detailed

• Comparable

• Multi-institutional

• Multi-specialty

• Linkable with bio-, enviro-, socio- and other information types


How do we get there?

• Maximize usefulness of today’s clinical information

• Improve acquisition and recording mechanisms for future clinical information



1) Create an explicit, global shared context• Terminology – shared terms, codes, and

precise definitions• Information model – data elements,

relationships and definitional (terminological) links



2) Map existing information structures onto this grid• Local data elements and structures

common data elements• Local names and descriptions

common terminology• Local codes and classifications

defined in terms of common terminology structure



3) Define future information systems requirements in terms of a shared information model and terminology• Develop tooling to allow consistent,

granular information capture• Storage resources are no longer the issue• Clinician time and efficiency is the new

bottleneck• Create standards and resources to make

implementation practical



ClinicalRecord

Dictation

Notes

Direct Entry


Local Context

GlobalContext


Clinical Information in the Future

GlobalContext

ClinicalRecord

Dictation

Notes

Direct Entry


(Process)

Terminologies

Information Models


Future Information

• Migrate to common models and terminology• common shared terminology• well understood shared information models

• Locally enhanced, but common elements remain common

• Tooling to minimize / eliminate translation steps• (semi) structured information entry• Definitions and terminology directly available to

clinician• Entry tools that allow both precision and detail


The GAP“Terminologies”


“Ontologies”Computable DL Frameworks

ICD-9-CM

CPT-4

ICD-10-PCS

MESH

SNOMED-IIISNOMED CT

GO...

Many, many more to comeCountries

Languages

Mime Types

SNOP

FMA

ChEBI

MGED

GMOD


We want the best of both worlds

• Definitions, instructions, comments

• Access to existing clinical records

• Computability

• Dynamic and distributed evolution

• Focus on specific uses and contexts

• Ability to navigate and traverse at will


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


Synopsis

The purpose of the Lexical Grid is to provide a framework that:

• Can represent yesterday’s, today’s and tomorrow’s terminological resources as a single virtual structure

• Allow these resources to be cross-linked and indexed

• Consists of building blocks and tools that allow applications and users to take advantage of the content where and when it is needed.


FunctionWhat the Lexical Grid can do?


The Heart of the Lexical Grid

The LexGrid Model - a model of terminology that:1) Explicitly names and defines the

things that the LexGrid tools need to reference explicitly

2) Represents “non-semantic” entities as name/value pairs


The LexGrid Model


The LexGrid Model

• Source is currently maintained in XML Schema

• (Semi) automatic transformations available to

• Unified Modeling Language (UML)• XML Model Interchange (XMI)• Eclipse Modeling Framework (EMF)• Java• LDAP Schema


The LexGrid Node

• A LexGrid Node is software and a backing data store that represents terminological information in a format semantically faithful to the LexGrid Model

LexGridNode

DataStore


LexGrid Components

LexGridNode

DataStore

Services

WebClients

Java

.NET

...

Import

Editors

Browsers

Query Tools

OWL

RDFXML

CSV

Terminology

Browse andEdit

Export

Embed

...


Import Toolkit

LexGridNode

DataStore

Services

WebClients

Java

.NET

...

Import

Editors

Browsers

Query Tools

OWL

RDFXML

CSV

Terminology

Browse andEdit

Export

Embed

...


Import ToolkitUMLS / SQL / SQL Lite

The lexgrid model currently has three different server-based data storage formats. LDAP, SQL Lite and SQL. The converter package is the tooling that we have written to allow you to move data from one format to another. The converter package also allows you to import terminologies directly from a local image of the UMLS database.


Import ToolkitUMLS / SQL / SQL Lite


Import ToolkitHL7 Version 3


Import ToolkitExcel Import


Import ToolkitNative Protege


Import ComponentsOWL


Import ComponentsCustom Formats as Needed

• PDF

• HTML

• CSV

• SQL

• XML (arbitrary flavor)

• ...


Functional Components

LexGridNode

DataStore

Services

WebClients

Java

.NET

...

Import

Editors

Browsers

Query Tools

OWL

RDFXML

CSV

Terminology

Browse andEdit

Export

Embed

...


Browse and EditLexGrid Editor

• Eclipse Based

• Multi Terminology Query and Browsing

• Can co-exist w/ Protege

• Logging and Audit Trail

• Much more – needs a presentation by itself!


Browse and EditCTS Plugin for Protege


Functional Components

LexGridNode

Data Store

Services

WebClients

Java

.NET

...

Import

Editors

Browsers

Query Tools

OWL

RDFXML

CSV

Terminology

Browse andEdit

Export

Embed

...


ServicesCommon Terminology Services


ServicesSOAP


Services.NET


Services


Functionality

LexGridNode

DataStore

Services

WebClients

Java

.NET

...

Import

Editors

Browsers

Query Tools

OWL

RDFXML

CSV

Terminology

Browse andEdit

Export

Embed

...


ExportLexGrid XML Format


ExportOWL Format

UMLS Semantic Netrendered in OWL


Export

• Other XML’s

• CSV

• Parameterized queries

• ...


FunctionalityVirtual Nodes

LexGridNode

DataStoreLexGridNode

DataStore

LexGridNode

DataStore

LexGridNode

DataStore

Mayo

Stanford

UCSF

NCI


FunctionalityVirtual Nodes

• Virtual Node Toolkit• Create and load a local node• Publish in web space• Node is treated as part of the larger

grid


FunctionalityVirtual Nodes – Cross Node Search

ICD-9

FMA

MeSH


FunctionalityReplication / Update

NCIReplica

DataStore

Mayo

NCIReplica

DataStore

Stanford

NCI

DataStore

NCI

Update

Subscribe

ChangeLog

ChangeLog

ChangeLog

“Push”“Pull”


FunctionalityIndices

NCI

DataStore

NCI

Update

IndexService

Subscribe

“Push”

ReasoningService

Subscribe

“Push”


FunctionalityCross References

NCI

DataStore

UMLS

DataStore

SemanticNET

DataStoreUMLS_CUI = URN:ISO:2.16.840.1.113883.6.56:C0002072

Semantic_Type = URN:ISO:2.16.840.1.113883.6.56.1:T123

T123 – “Biologically Active Substance”

ConceptCode: C222 entityDescription: Alkylsulfonate Compound Semantic_Type: SemNet:T123 UMLS_CUI: C0002072

C0002702 – “Alkanesufonates”


FunctionalityNode Directory


Acknowledgements

• Dr. Christopher Chute – visionary and enabler

• James Buntrock – administrative enabler

• Daniel Armbrust – programmer extraordinaire

• Thomas Johnson – architect / programmer extraordinaire

• Deepak Sharma – programmer extraordinaire


Acnowledgements

This work was supported in part by a grant from the US National Library of Medicine: LM07319.


LexGrid home page

https://cabig-kc.nci.nih.gov/Vocab/KC

the lexical grid 1/14/2005copyright © 2005 mayo clinic1

Documents

mayo clinic1142005copyright

communication processcopyright

communication processlanguage

shared cultureit

shared specialtiesboth

shared contextimpacts

impact of context

tacit context