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Terminology Curation with the Semantic MediaWiki

Terminology Curation with the Semantic MediaWiki. Harold Solbrig Informatics Architect Apelon, Inc. The Original Task. http://www.framleyexaminer.com/. The Original Task.

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Terminology Curation with the Semantic MediaWiki

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  1. Terminology Curation with the Semantic MediaWiki Harold Solbrig Informatics Architect Apelon, Inc. Terminology and the Semantic MediaWiki

  2. The Original Task http://www.framleyexaminer.com/ Terminology and the Semantic MediaWiki

  3. 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 Terminology and the Semantic MediaWiki

  4. Approach • Gather appropriate upper level ontologies (BFO, Dolce Lite, Top Bio, UMLS Semantic Net and OBO Relations Ontology) into a single, readily referenced format • Load NCI Thesaurus into same format • Multiple parties review, annotate, recommend and categorize • Publish, analyze and evaluate results 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 Terminology and the Semantic MediaWiki

  6. Terminology and the Semantic MediaWiki

  7. Terminology and the Semantic MediaWiki

  8. Terminology and the Semantic MediaWiki

  9. Internal Hyperlink to Semantic Net Curation Status Tracking External Hyperlink to OMIM Text Rendering of DL “Some” Statement Terminology and the Semantic MediaWiki

  10. Observations, Recommendations Terminology and the Semantic MediaWiki

  11. Internal Hyperlink to BFO Dump in RDF Subcategory Terminology and the Semantic MediaWiki

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

  13. The Question Could this approach be more generally applied to the task of terminology authoring /curation Terminology and the Semantic MediaWiki

  14. Clinical Terminology • Centrally curated • Central to the practice of medicine • Insurance and reporting • Regulatory • Research • Clinical Practice • Information Sharing • ICD-9, CPT-4, SNOMED, … Terminology and the Semantic MediaWiki

  15. 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 and the Semantic MediaWiki

  16. Terminology Workflow 1995 Books PDF Distribution (3) Controlled Terminology Lists and Tables (2) (1) Curation (4) Terminology and the Semantic MediaWiki

  17. Terminology Workflow 1995 Books PDF Distribution (3) Controlled Terminology ‘B’ (2) Lists and Tables (1) Curation Terminology and the Semantic MediaWiki

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

  19. Terminology Workflow 2008 (3) Controlled Terminology B Common Distribution Model Distribution Controlled Terminology (2) (4) Online Services (1) Curation (5) Terminology and the Semantic MediaWiki

  20. 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’ Terminology and the Semantic MediaWiki

  21. 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 Terminology and the Semantic MediaWiki

  22. 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 Terminology and the Semantic MediaWiki

  23. Workflow and Feedback (3) Common Distribution Model Distribution Controlled Terminology (2) (4) Online Services (1) Curation (5) Terminology and the Semantic MediaWiki

  24. The Feedback Component Curation Terminology and the Semantic MediaWiki

  25. The Feedback Component Common Distribution Model Semantic MediaWiki (++) Distribution Online Services Annotations and Change Requests Controlled Terminology Community Review Version Staging Curation Terminology and the Semantic MediaWiki

  26. 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. Terminology and the Semantic MediaWiki

  27. MediaWiki • http://en.wikipedia.org/wiki/Wiki • Base for WikiPedia and many others… • Key characteristics • Web based editing • Page links • Categories • Templates Terminology and the Semantic MediaWiki

  28. Terminology and the Semantic MediaWiki

  29. Terminology and the Semantic MediaWiki

  30. Terminology and the Semantic MediaWiki

  31. Terminology and the Semantic MediaWiki

  32. MediaWiki • Fully documented using (surprise!) MediaWiki • Rich mechanisms for discussion, curation, export, etc. Terminology and the Semantic MediaWiki

  33. Templates Terminology and the Semantic MediaWiki

  34. Templates Terminology and the Semantic MediaWiki

  35. Sample Template Extension call Parameter Terminology and the Semantic MediaWiki

  36. Terminology and the Semantic MediaWiki

  37. Semantic MediaWiki 3 Key extensions to MediaWiki • Categories == Class • PageA … [[Category:X]]  pageA rdf:Type Category:X • Category:Y … [[Category:X]]  category:Y rdfs:subClassOf category:X • Links == Role • PageA … [[PageB]]  PageA …[[hasPart::PageB]] • Attributes == DataProperty • [[population:=32,154,773]] • Includes datatypes Terminology and the Semantic MediaWiki

  38. Categories and Relations Terminology and the Semantic MediaWiki

  39. Attributes Terminology and the Semantic MediaWiki

  40. Semantic Rendering RDF (!) Relation Attribute Value Type (or superClass) Terminology and the Semantic MediaWiki

  41. Terminology and the Semantic MediaWiki

  42. Services • We don’t want to change the terminology content on the fly Terminology and the Semantic MediaWiki

  43. Terminology Workflow 1995 Books PDF Distribution (3) Controlled Terminology Lists and Tables (2) (1) Curation (4) Terminology and the Semantic MediaWiki

  44. Thesaurus Content Terminology and the Semantic MediaWiki

  45. Services XML Web Service Transform CTDE Templates Display Terminology and the Semantic MediaWiki

  46. Links to Service Service Call Terminology and the Semantic MediaWiki

  47. Service XML Terminology and the Semantic MediaWiki

  48. CTDE Templates Terminology and the Semantic MediaWiki

  49. Display Terminology and the Semantic MediaWiki

  50. Services XML Web Service DCR (!) Transform Application Specific DTS LexBIG Protégé … CTDE Templates Display Terminology and the Semantic MediaWiki

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