A Common Terminology Services (CTS) Back-end to Protg Harold R - - PowerPoint PPT Presentation

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A Common Terminology Services (CTS) Back-end to Protg Harold R - - PowerPoint PPT Presentation

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A Common Terminology Services (CTS) Back-end to Protg Harold R Solbrig Christopher G Chute, M.D., Dr. P.H. Division of Biomedical Informatics Mayo Clinic Outline Purpose of the project Characteristics of Terminology Links The

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A Common Terminology Services (CTS) Back-end to Protégé

Harold R Solbrig Christopher G Chute, M.D., Dr. P.H.

Division of Biomedical Informatics Mayo Clinic

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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Purpose of the Project

1) Use Protégé to create an interface

between terminology and the information model

2) Use Protégé to extend standard

terminologies and (potentially) author new content.

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Terminology

  • An integrated collection of terms,

definitions, annotations, and relationships

  • Defines the specialized language of a

discipline or subject area

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Terminology and Ontology

Terminology - Define the language / tokens used in a given domain Ontology - Describes domain knowledge in a generic way and provides understanding of a domain*

*Asunción Gómez-Pérez – Tutorial on Ontological Engineering: IJCAI’99

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Information Model

  • Describes what information is

required to accomplish a particular task or process

  • Consists of named collections of data

elements and their relationships

  • Typically includes definitions of each
  • f the elements, how they are used,

possible values (at least on a conceptual level)

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Ogden’s Semiotic Triangle

Thought or Reference Symbolises Refers to Symbol Stands for Referent C.K Ogden and I. A. Richards. The Meaning of Meaning.

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Ogden’s Semiotic Triangle

Thought or Reference Referent Symbol Symbolises Refers to Stands for

“Rose”, “ClipArt”

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

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The Communication Process

CONCEPT Referent

Refers To Symbolises Stands For

“Rose”, “ClipArt” “Red”

Refers To Symbolises Stands For

CONCEPT Symbol Symbol “I see an ClipArt image of a red rose” “Rose”, “ClipArt” “Red”

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The Communication Process

CONCEPT Referent

Refers To Symbolises Stands For

“Rose”, “ClipArt” “Red”

Refers To Symbolises Stands For

CONCEPT Symbol Symbol “I see an ClipArt image of a red rose” “Rose”, “ClipArt” “Red”

Information Model Terminology – tokens and definitions

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The Communication Process

CONCEPT Referent

Refers To Symbolises Stands For

“Rose”, “ClipArt” “Red”

Refers To Symbolises Stands For

CONCEPT Symbol Symbol “I see an ClipArt image of a red rose” “Rose”, “ClipArt” “Red”

Information Model

Red roses can be used to signify love

(Part of) Ontology

Terminology – tokens and definitions

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Terminology and Information Models

  • There can be many information

models that reference the same terminology

  • It is the shared terminological

references that allows information to be searched, compared and aggregated

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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Terminology Links

Classes Slots Possible Values

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Concept References

Classes Slots Possible Values

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Concept References

  • Concept resources can include
  • Existing taxonomies
  • Trade and specialty nomenclature
  • Standardized code sets (e.g.

country codes)

  • Reporting and classification

schemes

  • Ontologies
  • ...
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Concept References

  • Resource characteristics
  • Format and structure can vary

widely

  • Availability can vary from simple

ASCII lists of code value pairs to complex ontology services such as the Apelon DTS or DIG

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Referencing Concepts

  • Creating a manageable solution
  • Create a generic model of

terminology content

  • Define an interface layer that

allows queries to be posed in terms of the generic model

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Concept Code URI

URI:ISO:2.16.840.1.113883.6.94#en

2.16.840.1.113883.6.94 Code System en Concept Code

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Concept References

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ConceptReference Example

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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Why Terminology Services?

Terminology Resources are Heterogeneous

  • Structure - varies from code/value

pairs to complex formalisms such as NCI Thesaurus or SNOMED-CT

  • Size – varies from 3 or 4 entries to

well over half a million

  • Format – can be CSV’s, SQL

Tables, XML Documents, OWL

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Why Terminology Services?

Terminology = content + software

  • Sophisticated text search

algorithms

  • DL style inference
  • Distribution, authoring,

performance...

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The Common Terminology Services (CTS) API

  • (Relatively) Simple API
  • Read-only
  • A specification on how to do things like
  • List supported code systems
  • Get code system information
  • Search coded concepts by text
  • Traverse relationships
  • Draft HL7 / ANSI Standard
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CTS Example

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CTS Interface Specification

Client Server Interface

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CTS Interface Specification

Client LDAP Service Interface HL7 Messaging Decision Logic CTS Demo SOAP Service LexGrid “Lit” ...

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SOAP Server SOAP Client

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LDAP Server Java Client

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SQL Server Java Client

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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Protégé as a CTS Client

Protégé LDAP Service Interface SOAP Service LexGrid “Lit” ...

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Protégé as a CTS Client

Need to create a terminology model

  • Code System
  • Concept Code
  • Designation
  • Description
  • Annotation
  • Relationship
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Terminology Model Code System

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Terminology Model Code System

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Terminology Model Code System - Example

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Terminology Model Terms & Designations

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Terminology Model Terms

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Terminology Model Terms - Example

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Terminology Model Designations

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Terminology Model Designations - Example

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Terminology Model Definitions, Annotations, etc.

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Terminology Model Definitions, Annotations, etc.

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Terminology Model Relations

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Terminology Model Relations

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CTS Client New File Dialog

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CTS Backend

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CTS Client Connect Dialog

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CTS Client Preferences

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CTS Client Coding Scheme Selection

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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Protégé as a CTS Service

Client Interface HL7 Messaging Decision Logic CTS Demo Protégé

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Outline

  • Purpose of the project
  • Characteristics of Terminology Links
  • The Common Terminology Services

(CTS) specification

  • Protégé as a CTS Client
  • Protégé as a CTS Server
  • Issues, discussion and next steps
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Issues, etc.

  • Slow load time
  • Appears comparable w/ OWL
  • Partially resolved w/ lazy loading
  • Need a SymbolReference
  • Dynamically resolved Symbol
  • Ties in w/ DirectedBinaryRelation
  • Relations
  • Need to reconcile w/ DirectedBinaryRelation
  • Need to make CTS Server a Protégé Server
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Protégé (client) CTS Demo Protégé Server Protégé Client

Protégé as CTS Server

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Issues, etc. (continued)

  • Need to flesh out lazy loading
  • References occur all over
  • Need to implement a hierarchy

trimmer

  • Only keep references
  • Only keep graph branch points
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Credits

  • Deepak Sharma – author
  • Dan Armbrust - CTS author

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