Terminology and metadata whys and hows
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Terminology and Metadata Whys and hows. Harold Solbrig Apelon, Inc. Outline. “Terminology” – Why does it matter? Metadata and its relationship to terminology Creating and managing terminological resources Description of Apelon and its role in all of this. Terminology – why does it matter?.

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Terminology and metadata whys and hows

Terminology and MetadataWhys and hows

Harold Solbrig

Apelon, Inc


Outline

Outline

  • “Terminology” – Why does it matter?

  • Metadata and its relationship to terminology

  • Creating and managing terminological resources

  • Description of Apelon and its role in all of this


Terminology why does it matter

Terminology – why does it matter?

  • Information technology (IT) is about _____?

  • Depending on your perspective, information:

    • Reduces uncertainty on the part of the receiver

    • IS the reduction of uncertainty on the part of the receiver

  • The transfer of information between a sender and a receiver is known as “communication”

  • The business of IT is accurate, timely and relevant communication.


Communication and language

Communication and Language

  • 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.


The semiotic triangle

The Semiotic Triangle

Thought or Reference

Refers to

Symbolises

Symbol

Referent

Stands for

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


The semiotic triangle1

The Semiotic Triangle

Thought or Reference

Refers to

Symbolises

Symbol

Referent

Stands for

“Rose”, “ClipArt”

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


Terminology and metadata whys and hows

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


Terminology and metadata whys and hows

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


Terminology and metadata whys and hows

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


Terminology and metadata whys and hows

Context

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


Shared context

Shared Context

Impacts how much information can be contained in a symbol.

Information /

Symbol

No

Shared

Context

Shared

Sun

Shared

Species

Common

Culture

Common

Profession

Shared

Universe

Shared

Planet

Common

Language

Similar

Education

Common

Specialty


Shared universe

Shared Universe

Pioneer 10 & 11

Voyager “Golden Record”


Common specialty

Common Specialty

“Interferons are a family of cytokines that exerts antiviral, antitumor and immunomodulatory actions by inducing a complex set of proteins. One of the best known IFN-induced protein is the dsRNA-dependent protein kinase (PKR), that mediates both antiviral and anticellular activities. PKR inhibits translation initiation through the phosphorylation of the alpha subunit of the initiation factor eIF-2 (eIF-2 ) and also controls the activation of several transcription factors such as NF- B, p53, or STATs. …”

Marino Estiban. Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): Mechanism of action.

Apoptosis, Springer, Volume 5, Number 2, April 2000


The impact of context on communication

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

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

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 formalism1

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?


Terminology

Terminology

  • Symbols

    • Their encoding and decoding

    • Vocabularies, Dictionaries, Enumerations, Codes, ...

  • Context

    • Recording and sharing

    • Glossaries, textbooks, college courses, operations manuals, information models


Terminology in the digital era

Terminology in the Digital Era

  • Multi-layered

    • We’ll ignore the lower layers – polarity of diodes representing bits, bits representing numbers, characters, …


Terminology in the digital era1

Terminology in the Digital Era

  • Focus is on metadata

    • What is a particular data collection about?

    • What information can be found in it?

    • How is that information recorded?

    • What are the contextual assumptions?


Terminology and metadata whys and hows

The Communication Process

Display

Form

CONCEPT

CONCEPT

Symbolises

Refers To

Refers To

Symbolises

Decode

Encode

Stands For

Stands For

Transform

Referent


Metadata and the communication process

Metadata and the Communication Process

  • Metadata describes the forms, data bases, encoding processes, etc.

  • Terminology is the component of metadata that:

    • Manages symbols and their “meanings”

      • For users (e.g. what are the possible choices for field ‘x’, and what does each of them mean)

      • For IT professionals (the Information Model)

    • Maintains context

      • What else does a given specialty, department, company, etc. assume is known in beyond the simple definition of symbols


Terminology and metadata

Terminology and Metadata

  • Standard modeling tools (UMLS, XML Schema, …) have provided a way to communicate the structure and content of data stores and messages.

  • Models, however, have to include information about their intended context and meaning to allow data sharing across domains. Terminology provides (or is, in some senses) this component.


Terminology and metadata continued

Terminology and Metadata(continued)

  • Amongst other things, ISO 11179 provides a model of how terminology and metadata go together

    • It has the advantage of being (or being in the process of becoming) a standard

    • ISO 11179 also provides astandard model of terminology content, which would provide a vehicle for interchange in the appropriate contexts.

      • There are other models of interest as well…


Terminology and metadata in 11179

Terminology and Metadatain 11179


Terminology1

Terminology

Sounds easy enough – why not just put together a set of tables and get going?

Because…

  • Terminology has to be shared across multiple domains. This, after all, is its raison d'être

    • The model of the terminology itself has to be shareable.

    • The semantics of the terminology have to be shareable.

  • Terminology and knowledge management are inextricably intertwined

    • Fractal in nature – you can never stop adding

    • Boundaries are imprecise and expand

    • This means that there is no such thing as a “small terminology”

    • The components of terminology can also be viewed as declarative programs.

    • This means that the rigor of software development is applicable as well.


Terminology continued

Terminology(continued)

3)The knowledge behind terminology needs to be shared

  • Terminology resources depend on specialists (e.g. doctors, physicists, biologists, geneticists, etc…)

  • Development is expensive

  • Maintenance is often very expensive.


Prerequisites to terminology creation

Prerequisites to Terminology Creation

  • Know the standards

    • General standards (SKOS, RDF, OWL, 11179, SBVR, XML, UML, XMI, …)

    • Domain specific.

      • Example: Medical – HL7, LQS, CTS, CTS-2, UMLS, SNOMED, …

  • Know the tools

    • Development: TDE, Protégé, Obo Edit, Fact++, Racer, Jena, EVS, LexGrid…

    • Distribution: DTS, RDF, OWL, SKOS, …

  • Know the content

    • General (Dublin Core, CYC, SUMO, …)

    • Domain specific (Medical: NCIt, UMLS, ICD’s, SNOMED-CT, Gene Ontology, …)


Terminology and workflow

Terminology and Workflow

  • Terminology management includes:

    • Discovery

    • Federation

    • Authoring

    • Review

    • Distribution

    • Adoption


Process example sequencing

Process (Example Sequencing)

Import

Report

Review

Transform

Author

Translate

Approve

Extract

Load

Post-coordinate

Plan

Federate

Incorporate

Map

Version

Review in Context

Access

Customize

Maintain

Submit

Publish

Subscribe

Process Submissions

Migrate

Reevaluate

Replace


Terminology and metadata whys and hows

Content

Update

Applications

VOSER

Semantic

MediaWiki (++)

Annotations and

Change Requests

Status

Report

Core

SME

Submission

Work

Flow


Key points

Key Points

  • Terminology is a critical component for cross-discipline, cross-enterprise information sharing.

  • Terminology development is a non-trivial task – it needs to be done correctly.

  • Terminology resources need to be federated, shared and reused.

  • But… there’s help!


Apelon

Apelon

  • Largest provider of terminology products and services

  • Unique expertise


Employees

Employees

  • Internationally known terminology experts

  • Regular contributors to industry standards, publications and conferences


Mission

Mission

  • Apelon software and services support the development, maintenance, and practical deployment of structured terminologies

  • Put another way, we help our customers- create,- maintain, and- leverage

  • standard and enterprise terminologies

  • It’s all about speaking the same language


Facts

Facts

Most of the world’s standard healthcare terminology resources have been built and/or are maintained with Apelon tools, including

  • SNOMED

  • CPT

  • ICD-9-CM

  • NDF-RT

  • UMLS


Software products

Software Products

  • Terminology Development Environment (TDE)

  • Distributed Terminology System (DTS)

  • TermWorks


1 terminology authoring tde

1 – Terminology Authoring (TDE)

  • Tools to create and maintain structured terminologies

  • Improve productivity, data quality and scalability

  • Enhance the value of enterprise assets

    • Commercial product – CPT

    • Internal infrastructure – Kaiser Permanente CMT

    • Public benefit – SNOMED CT, NDF-RT, NCI Thesaurus

Author

ICD

CPT

SNOMED

NDF-RT

. . .


1 tde

1 - TDE

  • Based on Description Logic (DL)

    • Automated classification

    • Identifies redundancy

    • Provably consistent terminology

  • Collaborative features

    • Distributed authoring

    • Workflow

    • Conflict identification / resolution

  • Version control

  • Customizable interface and constraints


1 automatic classification

Body

Disease

is-a

part-of

Heart

is-a

affects

part-of

is-a

affects

1 – Automatic Classification

Cardiac Disease

Mitral Stenosis

Mitral Valve


2 terminology deployment

Terminology servers reduce costs of terminology acquisition, integration and management

Applications

EMRs and CDRs

NextGen, VA

Knowledge repositories

CDC, NCI

Healthcare information portals

HKHA

Deploy

Applications

Customize

2 – Terminology Deployment


2 what is a terminology server

2 – What is a Terminology Server?

A terminology server is

  • a networked software component

  • that centralizes terminology content and reasoning

  • to provide (complete, consistent and effective) terminology services for other network applications


2 how is a terminology server used

2 – How is a Terminology Server Used?

  • By informaticists

    to create, maintain, localize and map terminologies

  • By clinical applications and their users

    to select and record standardized data

  • By integration engines

    to map data elements between applications


2 examples of terminology services

Term/name normalization:

What is the SNOMED CT name for heart attack?

Code translation:

What is the ICD-9 code for Myocardial Infarction?

Grouping and aggregation:

Is Myocardial Infarction a Cardiac Disease?

Clinical knowledge:

What drug treats Myocardial Infarction?

Local information:

Add L227 as the local code for Serum Calcium.

Myocardial Infarction

410.9

Yes

Streptokinase

OK

2 - Examples of Terminology Services


2 apelon s dts product

2 – Apelon’s DTS Product

  • Integrated repository for all terminologies

    • Varying release cycles regular releases

    • Inconsistent data models common object model

    • Independent views  integrated view with mappings

    • Current snapshot  version management

  • Extensible with local terminology and maps

  • Subsets

  • Easy subscription updates (with exception reports)

  • Desktop editor and webtop browser

  • Workflow support

  • Flexible import, export and integration

  • Open source


Terminology server standards

Terminology Server Standards

  • OMG’s Lexicon Query Services (LQS)

    • AKA TQS

  • Health Level Seven (and ANSI) Common Terminology Services (CTS)

    • In ISO Standardization as well

  • CTS-II

    • In process

    • Led by Apelon


Dts and standards

DTS and Standards

CTS wrapper for DTS is available

INTEL Healthcare SOA using DTS for CTS extensions

  • Currently ahead of CTS-II

  • Will be fed back into CTS-II


2 knowledge base kb

2 – Knowledge Base (KB)

  • Clinical (SNOMED CT)

  • Reimbursement (ICD, CPT, HCPCS)

  • Pharmaceuticals (Multum, NDF-RT)

  • Labs (LOINC)

  • Nursing (NIC, NOC, and NANDA)

  • Adverse events (MedDRA, COSTART, WHOART)

  • Extensive crosswalks

  • Mappings to MeSH and UMLS CUIs

  • Local additions


2 software architecture

DTS Server

Tomcat

(DTS Client)

DTS

Editor

DTS

Browser

DTS Client

Application

2 - Software Architecture

DTS

Database


3 termworks

3 - TermWorks

  • Terminology web service

  • Easy, low cost, rapid mapping solution

  • Web services standards ( SOAP / WSDL )

  • Powerful matching capabilities

  • Comprehensive set of terminologies

  • Deployment via MS Office applications

  • Examples

    • Charge master management

    • Laboratory data integration

    • Legacy data mapping


3 easy to use excel plug in

Apelon

TermWorks

Database

And Tools

Web

Services

Content Expert

3 - Easy to Use Excel Plug-in

Excelfront end


Terminology consulting

Terminology Consulting

  • Longstanding experience

  • Broad range of engagements

    • Project planning and management

    • Terminology modeling

    • Mapping of current code sets

    • Custom product additions

    • Tailored terminology applications

  • Field proven principles and practices


Representative engagements

Representative Engagements

  • Department of Veterans Affairs

    • Enterprise reference terminology and software; extensive consulting

  • SNOMED International

    • Authoring software and custom enhancements for SNOMED CT

  • National Cancer Institute

    • Authoring and deployment software; extensive consulting

  • Department of Defense

    • Enterprise medication mediation server

  • Food and Drug Administration

    • Data element standardization of Structured Product Label

  • Accenture

    • Comprehensive data standardization for a National Health Information Network (NHIN) prototype

  • Department of Health and Human Services

    • Data element standardization

  • Kaiser Permanente

    • Authoring software for the Convergent Medical Terminology (CMT)

  • Care Science / Quovadx

    • Terminology server; consulting


Recent engagements

Recent Engagements

  • National Cancer Institute

    • Restructuring the NCI Thesaurus for federation and integration with Open Biomedical Ontologies (OBO) and other resources

    • Development of a Semantic Mediawiki based collaboration environment

  • Cancer Bioinformatics Grid

    • Using terminology / metadata links for scientific reasoning.

  • Mayo Clinic (via NCI)

    • ICD 11 terminology development environment


Apelon advantages

Apelon Advantages

  • Deep understanding of terminology

  • Extensive practical experience

  • Well known, well connected, well informed

  • Stable organization

  • GSA listed


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