Terminology Curation with the Semantic MediaWiki

04/18/2007 Terminology and the Semantic MediaWiki

Terminology Curation with the

Semantic MediaWiki

Harold SolbrigInformatics Architect

Apelon, Inc.


http://www.framleyexaminer.com/

The Original Task


The Original Task

Evaluate the roles, categories and organization of the National Cancer Institute (NCI)’s Cancer Thesaurus with respect to:

• Upper Level Ontological Principles• ISO TC37 & Related principles


Approach

1. Gather appropriate upper level ontologies (BFO, Dolce Lite, Top Bio, UMLS Semantic Net and OBO Relations Ontology) into a single, readily referenced format

2. Load NCI Thesaurus into same format3. Multiple parties review, annotate, recommend

and categorize4. Publish, analyze and evaluate results


Solution

By using the Semantic MediaWiki (SMW), we were able to accomplish all of the goals in a (very) reasonable period of time





Internal Hyperlink to Semantic Net

External Hyperlink to OMIM

Text Rendering of DL “Some” Statement

Curation Status Tracking


Observations, Recommendations


Internal Hyperlink to BFO

Subcategory

Dump in RDF


Discussion

We also discovered that, with some extensions, the SMW could be useful for publishing, annotating and cross-referencing other terminological (and other..) resources.


The Question

Could this approach be more generally applied to the task of terminology authoring /curation


Clinical Terminology

• Centrally curated• Central to the practice of medicine

– Insurance and reporting– Regulatory– Research– Clinical Practice– Information Sharing

• ICD-9, CPT-4, SNOMED, …


Clinical Terminology

• Quality and content is important• Needs central vetting, integration, qa

– Central model doesn’t scale– Need input from (many) experts– Need visible, active feedback loop


Terminology Workflow 1995

ControlledTerminology

Curation

(1)

Distribution

BooksPDF

Lists andTables

(2)

(3)

(4)




‘B’

(1)

(2)

(3)

Curation

Distribution

BooksPDF

Lists andTables




Curation

(1)

Distribution

(2)

(3)

(5)

CommonDistribution

Model

OnlineServices

(4)




Curation

(1)

Distribution

(2)

(3)

(5)

CommonDistribution

Model

OnlineServices

(4)


B


Common Distribution Model

• LexGrid• (a little bit of…) OWL

– NCI Thesaurus & SNOMED CT– Still requires LexGrid-like additions– “Pushing the envelope”

• UMLS RRF– Although underspecified as a ‘model’


Online Services

• OMG Terminology Query Services– Not heavily used– Perceived (incorrectly) as CORBA specific– Perceived as too complex– Object oriented and stateful

• ANSI Common Terminology Services– Being adopted– Necessary but not sufficient– Stateless

• CTS-2– Co-development beginning w/ HL7 & OMG


Online Services

• LexBIG– LexGrid for the Bio Informatics Grid– Robust query specification– Meets many end-user (developers) requirments

• Not simple to implement – it actually adds value• Not a standard - but will be used to guide CTS-2


Workflow and Feedback


Curation

(1)

Distribution

(2)

(3)

(5)

CommonDistribution

Model

OnlineServices

(4)


The Feedback Component

Curation


The Feedback Component

Curation

SemanticMediaWiki (++)

Annotations andChange Requests

CommunityReview

Distribution

CommonDistribution

Model

OnlineServices

VersionStaging



Wiki’s

• Community developed• Collaborative• “Organic” – to the very core…• Primary focus (to date) is human

consumption• Traceable, provenance automatically

recorded, differences, undo and redo.


MediaWiki

• http://en.wikipedia.org/wiki/Wiki• Base for WikiPedia and many others…• Key characteristics

– Web based editing– Page links– Categories– Templates






MediaWiki

• Fully documented using (surprise!) MediaWiki

• Rich mechanisms for discussion, curation, export, etc.


Templates


Templates


Sample Template

ParameterExtension call



Semantic MediaWiki

3 Key extensions to MediaWiki1. Categories == Class

– PageA … [[Category:X]] pageA rdf:Type Category:X

– Category:Y … [[Category:X]] category:Y rdfs:subClassOf category:X

2. Links == Role– PageA … [[PageB]] PageA …[[hasPart::PageB]]

3. Attributes == DataProperty – [[population:=32,154,773]]– Includes datatypes


Categories and Relations


Attributes


Semantic Rendering

Type (or superClass)

Attribute Value

Relation RDF (!)



Services

• We don’t want to change the terminology content on the fly




Curation

(1)

Distribution

BooksPDF

Lists andTables

(2)

(3)

(4)


Thesaurus Content


Services

WebService

Transform

XML

CTDETemplates

Display


Links to Service

Service Call


Service XML


CTDE Templates


Display


Services

WebService

Transform

XML

CTDETemplates

Display

DTSLexBIGProtégé…

DCR (!)

ApplicationSpecific


The Next Step

WebService

Transform

XML

CTDETemplates

Display

DCR (!)

ApplicationSpecific

???


Preliminary Work


How is it Working?

Very well!


Status

• Collaboration on TCDE– Apelon w/ DTS Server / LexBIG– Mayo with Protégé Server

• Workflow– NCI / Apelon

• Identifier resolution / hyperlinks• Tools

– Semantic Templates– Ajax search and hyperlinks– Hover over– WYSWIG editing– …


Questions?

• [email protected]• http://wiktolog.org• http://wiki.ontoworld.org/index.php/Seman

tic_MediaWiki

Terminology Curation with the Semantic MediaWiki

Documents

semantic mediawikiobservations

semantic mediawikisolutionby

semantic mediawikidiscussionwe

semantic netexternal

semantic mediawiki smw

umls semantic net

terminology curation

importantneeds central