terminology curation with the semantic mediawiki

04/18/2007

Terminology and the Semantic MediaWiki

Ecoterm IV – Vienna17 – 18 April 2007

EcoInformatics InitiativeEcoInformatics Initiative

Terminology Curation with the Semantic MediaWiki

Harold SolbrigInformatics ArchitectApelon, Inc.

04/18/2007 Terminology and the Semantic MediaWiki 2


The Primary 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

As with Ontology construction, it was understood by all parties that this was a process – not a goal.


Approach

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

2. Load NCI Thesaurus into same format

3. Multiple parties review, annotate, recommend and categorize

4. 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


Discussion

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


Questions?

… just kidding.


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 editingPage linksCategoriesTemplates


MediaWiki

Fully documented using (surprise!) mediawiki

Rich mechanisms for discussion, curation, export, etc.


Common constructs

[[Train Transport]] – hyperlink to page named “Train_Transport”

‘‘Italic’’, ‘‘‘Bold’’’ * Bullet point [http://www.w3c.org/ The W3C] – hyperlink … and much more


Templates


Sample Template

ParameterExtension call


Semantic MediaWiki


Semantic MediaWiki3 Key extensions to MediaWiki

1. 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 (!)


Thesaurus Content


Templates?

; Gene_Product_Is_Biomarker_Type

: The role is used to designate the type of …

Kind: [[:Category:NCI_Kind]]

‘‘‘Semantic Type:’’’ [NCI_Semantic_Type::Category:SN_Conceptual_Entity|Conceptual Entity]

Brittle, not readily changed…


Templates?

{{OntylogDescription|ns=NCI|text=“The role is used to designate…”}}

{{Kind|ns=NCI|target=Kind}}

{{ResourceRef|name=Semantic_Type|ns=NCI|target=Conceptual_Entity|targetns=SN}}

Can readily be updated viat template…


Commentary

Link to another NCI comment

Link to external Ontology

Categorization in external Ontology


Computed


How is it Working?

Very well!


What can we do to improve it…


Terminology

Centrally curated Central to the practice of medicine

Insurance and reportingRegulatoryResearchClinical Practice Information Sharing

ICD-9, CPT-4, SNOMED, …


Clinical Terminology

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

Central model doesn’t scaleNeed input from (many) expertsNeed 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 CTStill requires LexGrid-like additions“Pushing the envelope”

UMLS RRFAlthough 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

LexBIGLexGrid for the Bio Informatics GridRobust query specificationMeets 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


Issues and Next Steps

(1) SHARED Semantics{{Definition|…}}{{Synonym|…}}}{{References|…}}{{DLSome|…}}{{DLAll|…}}…

12620 anyone?


Issues and Next Steps

(2) Figure out namespacesNCI:Activity, AgroVoc:Fish, …NCI_Activity, AgroVoc_Fish???

(2a) Identifiers (Activity vs. C12345)(2b) Versions(2c) URI’s (vs. URL’s)

InternalExternal


Certification and Sanctioning

Who can edit? Who can validate? Who selects updates? … (see:

http://en.citizendium.org/wiki/Main_Page


Automatic Export

Selecting sets of updates Formatting update recommendations for

target curators, etc…


Synchronization

Changes implemented in terminologyUpdate wiki pagesSay what changedWhat changes are incorporated by value? By

reference?


Approach and Responsible Parties

Shared SemanticsCore set based on LexGrid & OWLPost on WIKI and link on SMW siteAssigned to Apelon, Mayo, NCI, ???Extend to OBO, SKOS (?), XMDR…Connections to 12620


Time Frame and Assignments

URI’s, namespaces, namingUK NCR (CancerGrid) – looking at unAPI and

servers(Hopefully) can provide URI resolver svc.Short term – use templates / extensions


Content

SNOMED-CT, ICD-9-CM, many, many others are already available via. Apelon DTS ServicesAvailable soon

FMA, HL7 Version 3 Terminology, OBO Foundry (GO, PATO, etc) as time permits

Others as needed (and funded…)


What we’ve got to date

Apelon DTS Server Extension Includes both defined and classified view (!) Export in restful XML (currentely Apelon, soon to be

LexGrid) XMDR Export Format Protégé (Native and OWL 3.2) prototype

Done by Mayo Both import and export Still needs templates


Questions?

This time for real

Note: SMW will be made externally available (w/ simple password) once we get contract specific info cleaned up (NCI will probably publish shortly)… contact: [email protected] for access.

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