1. Semantic Media Wiki Open Terminology Development - Initial Steps - Frank Hartel, Ph.D. Associate Director, Enterprise Vocabulary Services National Cancer Institute, Center for Biomedical Informatics 10th Open Forum on Metadata Registries July 10, 2007

2. 2 Biomedical Grid Terminology ( BiomedGT© ) BiomedGT© is a project of the National Cancer Institute Initially an effort of the NCI Center for Biomedical Informatics and Information Technology Transition rapidly to biomedical community partnership BiomedGT© features Open content development by biomedical community volunteers Federated ontology structure Infrastructure support by NCI Free, open license Coverage of translational research domain Clear distinction between ontology and thesaurus components

3. 3 Why Open Content Development ? Open content development by members of the community using the terminology has been proven to work, maturing rapidly Gene Ontology (GO) http://www.geneontology.org/http://www.geneontology.org/ Ontology for Biomedical Investigations (OBI) http://obi.sourceforge.net/http://obi.sourceforge.net/ And many others – see Open Biomedical Ontologies Organization http://obofoundry.org/http://obofoundry.org/ National Center for Biomedical Ontology http://bioontology.org/http://bioontology.org/ Advantages Community acceptance, content is relevant to community needs Fast publication cycle Disadvantages Development tools vs representational sophistication Long term viability of purely voluntary efforts

4. 4 Why Federation? Biomedicine is a huge domain Coverage in a single ontology isn’t in the cards Overwhelms tools, editorial and production techniques Slows production cycles, runs up costs (partially due to redundant modeling) Complexity, size overwhelm users Federation should help Ontologies scoped reflect scientific domains Scales better to tools, editorial and production techniques Easier to structure and extent, easier for users to understand More attractive to subject matter experts (SMEs) Many fine ontologies exist: reuse should help control costs Easier to federate (in theory) Federation is an active area of research and development OBO Foundry has one approachOBO Foundry Alan Rector and the Manchester Group has anotherAlan Rector W3C Health Care and Life Sciences Special Interest Group (HCLSIG) is working on another

5. 5 Open Content Development in BiomedGT Semantic Media Wiki and NCI Protégé/OWL Wiki supports biomedical SMEs Easy to learn tool Registration for SMEs who wish to edit View current BiomedGT content (from LexBIG) Make changes that are stored in Wiki database Anonymous read only access for others Protégé used by ontologists Renders SME input as OWL DL 1.1 Protégé Workflow is it the touch point SME input “harvested” from Wiki database Incorporated into work assignments to ontologists Wiki and BiomedGT GForge Project supports SME, ontologist dialogGForge Project Publication via caCORE/LexBIG services NCBO Portal-based NCI Portal supports download & interactive search/displayNCBO Portal-basedNCI Portal

6. 6 Open Collaboration Infrastructure and Process

7. 7 Context of Open Development – NCI Enterprise Vocabulary Services

8. 8 BiomedGT Collaborators and Preparations All biomedical communities will be welcome Initial collaboration is with UK Cancer Grid (Clinical Trials Ontology) Additional early collaborations within the cancer Biomedical Informatics Grid Completion of ongoing development of collaboration infrastructure will precede large scale open development Semantic Media Wiki modifications Protégé Workflow Integration of Wiki database and workflow tool Meanwhile preliminary conversion of NCI Thesaurus data are occurring Provides structural basis for subject matter domains within BiomedGT Provides basis to distinguish ontological (class representing real-world entity/process) from thesaurus classes (class provides browsing/navigation support)

9. 9 Initial Construction of BiomedGT timeline NCIT Seed BiomedGT Beta - upper level ontology - initial binning of NCIT top concepts - initial tagging: thesaurus vs ontology publish to Media Wiki worklists to Protégé Community developmentDL Modeling baselines...... BiomedGT

10. 10 Reusing Terminology Components – Federation in Protégé 3.x owl:imports of both terminologies into the Protégé editor GO NCIT

11. 11 DL Modeling in BiomedGT with Gene Ontology Terms/Concepts

12. 12 DL Modeling in BiomedGT with Gene Ontology Terms/Concepts

13. 13 Q & A