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

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

Distribution

BooksPDF

Lists andTables

‘B’

Curation

Distribution

BooksPDF

Lists andTables

Curation

Distribution

CommonDistribution

OnlineServices

Curation

Distribution

CommonDistribution

OnlineServices

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

Distribution

CommonDistribution

OnlineServices

The Feedback Component

Curation

The Feedback Component

Curation

SemanticMediaWiki (++)

Annotations andChange Requests

CommunityReview

Distribution

CommonDistribution

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

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

Distribution

BooksPDF

Lists andTables

Thesaurus Content

Services

WebService

Transform

CTDETemplates

Display

Links to Service

Service Call

Service XML

CTDE Templates

Display

Services

WebService

Transform

CTDETemplates

Display

DTSLexBIGProtégé…

DCR (!)

ApplicationSpecific

The Next Step

WebService

Transform

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?

• hsolbrig@apelon.com• http://wiktolog.org• http://wiki.ontoworld.org/index.php/Seman

tic_MediaWiki

Terminology Curation with the Semantic MediaWiki

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IBIS Conversations with MediaWiki

Semantic MediaWikinkos.slis.kent.edu/2008workshop/HaroldSolbrig.pdf · Outline • MediaWiki – what it is, how it works • Semantic MediaWiki – MediaWiki meets the Semantic Web

Curation for systemization of authentic content for ... · Curation • Rosenbaum (2011). Curation Nation • Curation is the future of online content • Curation: collection and

Presentasi CMS mediawiki

MediaWiki Cooperation - The MediaWiki User Group

MediaWiki Grammar Recovery

Hacking MediaWiki (For Users)

MediaWiki Quick Start Guide

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Pushing MediaWiki Internationalization

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Data Curation Malcolm Crowe, UWS. Digital Curation Curation techniques are for archives Curation techniques are for archives Librarians, to preserve documentsLibrarians,

La Curation qu'es aquòekladata.com/.../GG-Curation-Janvier2014.pdf · La curation ou le retour de l’humain •Les dimensions de la « curation » / du « curateur » – L’expertise

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