Why LexGrid?

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Why LexGrid?

• Existing medical records
• Various forms of coding and classification in use
  since the early 1500s
• Modern records from the 1960s to present
  include various forms of codes
• Medical records are still on a per-institution
  basis

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Why LexGrid?

• Emerging medical records
• Multiple factors forcing new levels of
  interoperability
• Economic
• Regulatory
• Technical

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Why LexGrid?

• Bioinformatics
• Large volumes of information
• Large cross sections
• Detailed what is important may not (and cannot)
  be anticipated
• Interoperability of
• Medical (Phenomics)
• Genomics
• Environmental
• GeoSpatial

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The GAP (In Western Medicine)
Terminologies Coding and Classification
ICD-10-PCS
ICD-9-CM
MGED
SNOMED-III
CPT-4
SNOMED CT
ChEBI
MESH
SNOP
...
GO
FMA
Countries
Languages
Many, many more to come
GMOD
Mime Types
Ontologies Computable DL Frameworks
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LexGridThe purpose behind LexGrid
Communication
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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.

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Ogdens Semiotic Triangle
Thought or Reference
Symbolises
Refers to
Symbol
Referent
Stands for
C.K Ogden and I. A. Richards. The Meaning of
Meaning.
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Ogdens Semiotic Triangle
Thought or Reference
Symbolises
Refers to
Symbol
Referent
Stands for
Rose, ClipArt
C.K Ogden and I. A. Richards. The Meaning of
Meaning.
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The Communication Process
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
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The Communication Process
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
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The Communication Process
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
Syntax
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The Communication Process
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
Syntax
Shared Context
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Shared Context

• Impacts how much information can be contained in
  a symbol.

Information / Symbol
No Shared Context
Shared Species
Shared Sun
Common Culture
Common Profession
Shared Universe
Common Language
Shared Planet
Similar Education
Common Specialty
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Minimum Shared Context
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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 EMC2 versus that contained in this
  presentation...

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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.

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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

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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?

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Common Forms of Contextual Formalism

• Dictionaries
• Thesauri
• Textbooks, college courses, etc.
• Operations manuals
• Data dictionaries
• Terminologies

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The Communication Process
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
Syntax
Shared Context
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Making Shared Context Explicit
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
Formal Shared Context
Terminologies
Terminologies
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Shared Context Least Common Denominator
CONCEPT
CONCEPT
I see a ClipArt image of a red flower with ...
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
... increase the symbol complexity
Reduce the Shared Context...
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Information vs. Symbol
Information
Symbol
Symbol
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
Information predicate w/ Range of
True/False/.. Symbol - predicate w/ Range
of Concept
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Ontologies serve (at least) two roles

• Symbol - Definitional
• Concept -gt Symbol
• Symbol -gt Concept
• Symbol/Symbol translation
• Symbol validation, organization and mapping
• Are axioms not verifiable

• Information - Propositional
• Statements
• True/False/Unknown
• Convey information
• Are verifiable

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Sample Description Logic

• Symbol
• A, B
• C, D
• R
• gt
• ?
• A
• C u D
• 8 R.C
• 9 R.gt

• Interpretation
• AI, BI
• CI, DI
• RI µ ?I x ?I
• ?I
• ?
• ?I n AI
• CI Å DI
• a 2 ?I 8 b.(a,b) 2 RI ! b 2 CI
• a 2 ?I 9 b.(a,b) 2 RI

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Interpretations

• An interpretation I satisfies an inclusion C v D
  if CI µ DI, and it satisfies an equality C D if
  CI DI.
• If T is a set of axioms, then I satisfies T iff I
  satisfies each element of T.
• If I satisfies an axiom (resp. a set of axioms)
  then we say that it is a model of this axiom
  (resp. set of axioms).
• Two axioms or two sets of axioms are equivalent
  if they have the same models.

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Description Logic
Much study (DAMLOIL, OWL, CL, )

• Symbol
• A, B
• C, D
• R
• gt
• ?
• A
• C u D
• 8 R.C
• 9 R.gt

• Interpretation
• AI, BI
• CI, DI
• RI µ ?I x ?I
• ?I
• ?
• ?I n AI
• CI Å DI
• a 2 ?I 8 b.(a,b) 2 RI ! b 2 CI
• a 2 ?I 9 b.(a,b) 2 RI

But what of this????
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Interpretation and OWL

• OWLAnnotationProperty
• in OWL DL one cannot define subproperties or
  domain/range constraints for annotation
  properties
• Five annotation properties are predefined by OWL
• owlversionInfo
• rdfslabel
• rdfscomment
• rdfsseeAlso
• rdfsisDefinedBy

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A Rose in OWL?

• ltowlClass rdfIDRosegt
• ltrdfssubClassOf rdfresourceFloweringPlant/gt
• ltrdfssubClassOfgt
• ltowlrestrictiongt
• ltowlonProperty rdfresourcehasRisk/gt
• ltowlsomeValuesFrom rdfresourceThorn/gt
• lt/owlrestrictiongt
• lt/rdfssubClassOfgt
• lt/owlClassgt

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A Rose in OWL?

• ltowlClass rdfIDCgt
• ltrdfssubClassOf rdfresourceA/gt
• ltrdfssubClassOfgt
• ltowlrestrictiongt
• ltowlonProperty rdfresourceR/gt
• ltowlsomeValuesFrom rdfresourceD/gt
• lt/owlrestrictiongt
• lt/rdfssubClassOfgt
• lt/owlClassgt

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The Communication Process

CONCEPT
CONCEPT
Symbolises
Refers To
Refers To
Symbolises
rose
floweringPlant, hasRisk thorn
Stands For
Stands For
Referent
Symbol
Context
x 2 ?I 9 thorn.(x, thorn) 2 hasRiskI Å x 2
floweringPlantI
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The Communication Process
A101I flower
A102I sharp spine

R1I possible misfortune
A101I rose
CONCEPT
CONCEPT
Symbolises
Refers To
Refers To
Symbolises
A101
A102, R1 A103
Stands For
Stands For
Referent
Symbol
Context
x 2 ?I 9 A102.(x, A102) 2 R1I Å x 2 A103\cI

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Definitions vs. Propositions

• Is this
• The thing that is defined as a procedure that
  involves an excision of a structure of lobe of
  lung? (Axiom)

2. A statement saying All procedures that
involve an excision of the structure of lobe of
lung are pulmonary lobectomy? (Falsifiable
proposition)
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LexGrid Focus

• Definitional Aspects of Ontologies
• Making sure that the information (axioms) that
  are the basis of propositions are accurate,
  complete and reproducible
• Making sure that resulting propositions are
  verifiable that the terms that come out match
  the terms that go in

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(Reference) Ontologies

• Reference ontologies are not designed to be nice
  - they are designed to be big, boring and true.
• Barry Smith

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LexGrid Goal

• 1) Combine
• Lexical Semantics
• Names
• (Textual) Definitions
• Comments
• Other non-classification property
• Context
• Languages and dialects
• Communities and specialties
• Localizations
• Logical Semantics
• Roles and Relations

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LexGrid Goal

• 2) Use these to integrate, reason about and
  report
• Existing data codes
• Special contexts
• Need formalization
• New information
• New screens
• Metadata

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The LexGrid 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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LexGrid Three-Pronged Approach
LexGrid Model
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The Heart of the Lexical Grid

• The LexGrid Model - a model of terminology that
• Explicitly names and defines the things that the
  LexGrid tools need to reference explicitly
• Represents non-semantic entities as name/value
  pairs

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Modeling Extremes
hyperNormalized
hyperSpecified
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hyperNormalized Model

• Incredibly flexible
• - Doesnt say a heck of a lot about a given
  domain.
• Specialization is possible
• Entity Patient
• Attribute Name/String
• Relationship hasName
• Many hyperNormalized models already exist ER1 /
  UML / SQL /

hyperNormalized
hyperSpecified
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hyperSpecified Model
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hyperSpecified Model

• Incredibly precise you know exactly what
  youve got
• Unwieldy and inflexible
• Difficult to understand

hyperNormalized
hyperSpecified
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Modeling Pragmatics

• Make the differences that are important explicit
• Use terminology to carry the rest

hyperNormalized
hyperSpecified
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The Heart of the Lexical Grid

• The LexGrid Model - a formal model of terminology
  that
• Explicitly names and defines the entities and
  objects used in the LexGrid tooling
• Supports as many non-semantic entities (from
  the toolkit perspective) as possible via.
  Name/value pairs

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The LexGrid Model
Computation
Interpretation
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The LexGrid Model
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(Short Rave)
This is not a model of a concept!!! It is a
model of a symbol!!!
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(Short Rave)
Concept
Thought or Reference
Symbolises
Refers to
Symbol
Symbol
Referent
Stands for
Rose, ClipArt
C.K Ogden and I. A. Richards. The Meaning of
Meaning.
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Concept, Symbol and Meaning
Human Being
Human / Symbol Interaction
The focus of LexGrid
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Concept vs. Symbol

• A thing that is a flower and has thorns

Symbolizes a concept NOT a concept.
Symbol
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(short rave)

• Calling a symbol a concept in a model
• Confuses everyone
• Makes a mess of the resulting model
• Everything is a concept
• And (almost) everything is NOT in anyones
  database
• Symbols, can be modeled, carried in databases,
  reasoned with, etc.

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(end rave)
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The LexGrid Model

• Source is currently maintained in XML Schema
• First incarnation was LDAP Schema
• (Semi) automatic transformations available to
• Unified Modeling Language (UML)
• XML Model Interchange (XMI)
• Eclipse Modeling Framework (EMF)
• Java
• LDAP Schema

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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

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FunctionalityVirtual Nodes
Stanford
UCSF
Mayo
NCI
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FunctionalityVirtual Nodes

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

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FunctionalityVirtual Nodes Cross Node Search
ICD-9
FMA
MeSH
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FunctionalityReplication / Update
Update
Change Log
Subscribe
Push
Pull
Change Log
Change Log
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FunctionalityIndices
Update
Subscribe
Subscribe
Push
Push
Reasoning Service
Index Service
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FunctionalityCross References
ConceptCode C222 entityDescription
Alkylsulfonate Compound Semantic_Type
SemNetT123 UMLS_CUI C0002072
Semantic_Type URNISO2.16.840.1.113883.6.56.1T
123
UMLS_CUI URNISO2.16.840.1.113883.6.56C0002072
T123 Biologically Active Substance
C0002702 Alkanesufonates
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FunctionalityNode Directory
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LexGrid Components
SKOS
Editors
UMLS
Browsers
OWL
Browse and Edit
Import
Query Tools
OBO
Protege
(custom)
LexGrid Node
S e r v i c e s
Export
DataStore
Web Clients
Java
Embed
Protege
.NET
...
CSV
OWL
...
RDF
XML
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LexGrid Components
Swoop Protégé DagEdit XMDRp
SKOS OWL UMLS
SPARQL Prolog ..
Editors
Terminology
Browsers
Query Tools
MDA
MMFI ODM
20944
LexGrid Node
S e r v i c e s
DataStore
Web Clients
Java
.NET
...
CSV
OWL
XMDR RDF DBs
...
RDF
XML
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LexGrid and Metadata
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Different Data Forms, Same Information
Tag/Value Pair
A code in a table
Free text
Column Heading
Female Research Clinic
Table Name
Database Names
Table 17 Female Patients
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Different Vocabulary Same Information
Desired Granularity
Too Coarse
Too Fine
Coupled With Other Information
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Terminology and the Information Model
Information Model
Terminology
?
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Terminology and the Information Model
Information Model
Terminology
Terminology and structure must be coordinated to
achieve consistency and an integrated whole in
HL7 standards.
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Active Application Work

• SNOMED CMWG
• HL7 Terminfo

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LexGrid Collaborations

• NCI
• LexBIG LexGrid for caGRID
• National Center for Biomedical Ontology
• LexBIO LexGrid for NCBO
• Health Level Seven (HL7)
• Tooling
• National Library of Medicine
• ISO JTC1/SC32 (NCITS-L8) - XMDR

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Acnowledgements

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

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