1. THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY BioPortal Updates and Planned Features Trish Whetzel May 3, 2012

2. New Functionality in Last Year Allow BioPortal configuration – My Bioportal, Slices Improved support for Notes – Provisional ids for new terms, archiving, email notification Allow private and licensed ontologies Flag obsolete terms “Productionized” Ontology Recommender Automated handling of OWL2 ontologies Created beta version of triple-store architecture

3. Systemic Improvements Solidified core system Monthly release schedule Many long-standing bugs fixed Established regular VM release cycle (3x/year) Reworked entire UI to be simpler and more consistent Improved Annotator performance by 5-10x Improved user-tracking with API Key mechanism

4. Home Page Recommender Tab

5. Browse Page Custom display of selected ontologies Custom display of selected ontologies

6. Search

7. Ontology Recommender

8. Annotator

9. Slice

10. Resource Index

12. ODiSSea – Elsevier SciVerse

13. Who is using our Web services?

14. Technical Aims 1.Develop, enhance, and deploy software services and tools that allow investigators to use ontologies. 2.Integrate ontology publishing and peer review with ontology authoring. 3.Create a comprehensive ontology-based index for publicly available biomedical resources. 4.Develop analytic methods to summarize and profile biomedical data sets.

15. Plans for Coming Year Move RDF triple-store from beta to production release* Synchronize Annotator and Mappings to ontology submission and update Re-implement Annotator and Resource Index to be more reliable, better performing, and more scalable Add additional resources in Resource Index Provide improved support for projects and views Implement CTS2 API for BioPortal* Replace FlexViz Ontology Visualization with BioMixer* * Beta version of feature

16. BioPortal Architecture Updates RDF LexEVSProtégé DB Hibernate ORM Spring Framework Restlet Tomcat OWL RDF Protégé frames Ruby on Rails OBO format UMLS RRF LexGrid XML Transform Server CTS2

17. BioPortal SPARQL Endpoint http://sparql.bioontology.org/

18. Concluded Driving Biological Projects Candidate Gene Discovery through Ontological Indexing – Medical College of Wisconsin; Simon Twigger Annotation of Biomedical Data in CVRG – Johns Hopkins; Rai Winslow Cancer Nanotechnology Knowledge Base – Stanford/PNNL; David Paik & Nathan Baker

19. New Driving Biological Projects Ontology-driven analysis of high-throughput data – European Bioinformatics Institute; Helen Parkinson Using ontologies and data fusion approaches to understand organismal aging – Buck Institute for Research on Aging; Sean Mooney Synapse: A precondition space for integrative genomics – Sage Bionetworks; Michael Kellen

20. Collaborative R01 Projects Active – Integrative Tools for Protozoan Parasite Research - Chris Stoeckert, UPenn Completed (2011-2012) – Reference Ontologies for the Semantic Web - Jim Brinkley, University of Washington – Neuroscience Information Framework - Maryann Martone, UCSD – Ontologies and Biomedical Language Processing - Larry Hunter, University of Colorado – Ontology Development Information Extraction - Rebecca Crowley, University of Pittsburgh – Context-based Ontology Integration - Gil Alterovitz, Brigham and Women’s Hospital – Semantics and Services Enabled Problem Solving Environment for T. cruzi - Amit Sheth, Wright State

21. Other NCBO collaborations Informatics for Integrating Biology and the Bedside (i2b2) BioSitemaps UCSF Clinical and Translational Sciences Institute BioSharing (including Minimal Information for Biological and Biomedical Investigations) BioDBCore initiative of the International Society for Biocuration

22. Links of Interest Web service documentation http://www.bioontology.org/wiki/index.php/NCBO_R EST_services Release Notes – http://www.bioontology.org/wiki/index.php/BioPortal_Rel ease_Notes http://www.bioontology.org/wiki/index.php/BioPortal_Rel ease_Notes Software questions – Software support: support@bioontology.orgsupport@bioontology.org Social media – Twitter: @bioontology – Facebook: http://on.fb.me/bioontologyhttp://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-grouphttp://linkd.in/ncbo-group