EcoInformatics Initiative 04/18/2007 Terminology and the Semantic MediaWikiEcoterm IV – Vienna 17 – 18 April 2007 Terminology Curation with the Semantic MediaWiki Harold Solbrig Informatics Architect Apelon, Inc.

04/18/2007 Terminology and the Semantic MediaWiki 2

04/18/2007 Terminology and the Semantic MediaWiki 3 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.

04/18/2007 Terminology and the Semantic MediaWiki 4 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

04/18/2007 Terminology and the Semantic MediaWiki 5 Solution By using the Semantic MediaWiki (SMW), we were able to accomplish all of the goals in a (very) reasonable period of time

04/18/2007 Terminology and the Semantic MediaWiki 6 Discussion We also discovered that, with some extensions, the SMW could be useful for publishing, annotating and cross- referencing other terminological (and other..) resources.

04/18/2007 Terminology and the Semantic MediaWiki 7 Questions? … just kidding.

04/18/2007 Terminology and the Semantic MediaWiki 8 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.

04/18/2007 Terminology and the Semantic MediaWiki 9 MediaWiki Base for WikiPedia and many others… Key characteristics  Web based editing  Page links  Categories  Templates

04/18/2007 Terminology and the Semantic MediaWiki 10 MediaWiki Fully documented using (surprise!) mediawiki Rich mechanisms for discussion, curation, export, etc.

04/18/2007 Terminology and the Semantic MediaWiki 11

04/18/2007 Terminology and the Semantic MediaWiki 12 Common constructs [[Train Transport]] – hyperlink to page named “Train_Transport” ‘‘Italic’’, ‘‘‘Bold’’’ * Bullet point [ The W3C] – hyperlink … and much more

04/18/2007 Terminology and the Semantic MediaWiki 13 Templates

04/18/2007 Terminology and the Semantic MediaWiki 14 Templates

04/18/2007 Terminology and the Semantic MediaWiki 15 Sample Template Parameter Extension call

04/18/2007 Terminology and the Semantic MediaWiki 16 Semantic MediaWiki

04/18/2007 Terminology and the Semantic MediaWiki 17 Semantic MediaWiki 3 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

04/18/2007 Terminology and the Semantic MediaWiki 18 Categories and Relations

04/18/2007 Terminology and the Semantic MediaWiki 19 Attributes

04/18/2007 Terminology and the Semantic MediaWiki 20 Semantic Rendering Type (or superClass) Attribute Value Relation RDF (!)

04/18/2007 Terminology and the Semantic MediaWiki 21 Thesaurus Content

04/18/2007 Terminology and the Semantic MediaWiki 22 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…

04/18/2007 Terminology and the Semantic MediaWiki 23 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…

04/18/2007 Terminology and the Semantic MediaWiki 24 Commentary Link to another NCI comment Link to external Ontology Categorization in external Ontology

04/18/2007 Terminology and the Semantic MediaWiki 25 Computed

04/18/2007 Terminology and the Semantic MediaWiki 26 How is it Working? Very well!

04/18/2007 Terminology and the Semantic MediaWiki 27 What can we do to improve it…

04/18/2007 Terminology and the Semantic MediaWiki 28 Terminology Centrally curated Central to the practice of medicine  Insurance and reporting  Regulatory  Research  Clinical Practice  Information Sharing ICD-9, CPT-4, SNOMED, …

04/18/2007 Terminology and the Semantic MediaWiki 29 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

04/18/2007 Terminology and the Semantic MediaWiki 30 Terminology Workflow 1995 Controlled Terminology Curation (1) Distribution Books PDF Lists and Tables (2) (3) (4)

04/18/2007 Terminology and the Semantic MediaWiki 31 Terminology Workflow 1995 Controlled Terminology ‘B’ (1) (2) (3) Curation Distribution Books PDF Lists and Tables

04/18/2007 Terminology and the Semantic MediaWiki 32 Terminology Workflow 2008 Controlled Terminology Curation (1) Distribution (2) (3) (5) Common Distribution Model Online Services (4)

04/18/2007 Terminology and the Semantic MediaWiki 33 Terminology Workflow 2008 Controlled Terminology Curation (1) Distribution (2) (3) (5) Common Distribution Model Online Services (4) Controlled Terminology B

04/18/2007 Terminology and the Semantic MediaWiki 34 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’

04/18/2007 Terminology and the Semantic MediaWiki 35 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

04/18/2007 Terminology and the Semantic MediaWiki 36 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

04/18/2007 Terminology and the Semantic MediaWiki 37 Workflow and Feedback Controlled Terminology Curation (1) Distribution (2) (3) (5) Common Distribution Model Online Services (4)

04/18/2007 Terminology and the Semantic MediaWiki 38 The Feedback Component Curation

04/18/2007 Terminology and the Semantic MediaWiki 39 The Feedback Component Curation Semantic MediaWiki (++) Annotations and Change Requests Community Review Distribution Common Distribution Model Online Services Version Staging

04/18/2007 Terminology and the Semantic MediaWiki 40 Issues and Next Steps (1) SHARED Semantics  {{Definition|…}}  {{Synonym|…}}}  {{References|…}}  {{DLSome|…}}  {{DLAll|…}}  … anyone?

04/18/2007 Terminology and the Semantic MediaWiki 41 Issues and Next Steps (2) Figure out namespaces  NCI:Activity, AgroVoc:Fish, …  NCI_Activity, AgroVoc_Fish  ??? (2a) Identifiers (Activity vs. C12345) (2b) Versions (2c) URI’s (vs. URL’s)  Internal  External

04/18/2007 Terminology and the Semantic MediaWiki 42 Certification and Sanctioning Who can edit? Who can validate? Who selects updates? … (see:

04/18/2007 Terminology and the Semantic MediaWiki 43 Automatic Export Selecting sets of updates Formatting update recommendations for target curators, etc…

04/18/2007 Terminology and the Semantic MediaWiki 44 Synchronization Changes implemented in terminology  Update wiki pages  Say what changed  What changes are incorporated by value? By reference?

04/18/2007 Terminology and the Semantic MediaWiki 45 Approach and Responsible Parties Shared Semantics  Core set based on LexGrid & OWL  Post on WIKI and link on SMW site  Assigned to Apelon, Mayo, NCI, ???  Extend to OBO, SKOS (?), XMDR…  Connections to 12620

04/18/2007 Terminology and the Semantic MediaWiki 46 Time Frame and Assignments URI’s, namespaces, naming  UK NCR (CancerGrid) – looking at unAPI and servers  (Hopefully) can provide URI resolver svc.  Short term – use templates / extensions

04/18/2007 Terminology and the Semantic MediaWiki 47 Content SNOMED-CT, ICD-9-CM, many, many others are already available via. Apelon DTS Services  Available soon FMA, HL7 Version 3 Terminology, OBO Foundry (GO, PATO, etc) as time permits Others as needed (and funded…)

04/18/2007 Terminology and the Semantic MediaWiki 48 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

04/18/2007 Terminology and the Semantic MediaWiki 49 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: for access.