1. How Bio-Ontologies enable Open Science Nigam Shah [email_address]

2. Ontologies By Pedro Beltrão

9. Knewco: Concept Web and Wikiprofesional

10. The SWAN discourse ontology Ciccarese P, Wu E, Clark T (2007) 'An Overview of the SWAN 1.0 Ontology of Scientific Discourse‘ at the 16th International World Wide Web Conference Banff, Canada. May 8-12, 2007.

11. Collaborative KB curation: SWAN Knowledge Workbench Copyright 2007 Alzheimer Research Forum and Massachusetts General Hospital

12. Copyright 2007 Alzheimer Research Forum and Massachusetts General Hospital

13. Copyright 2007 Alzheimer Research Forum and Massachusetts General Hospital

16. Integration of Text-mining + Curation

21. NCBO ontology services Base URL: http://rest.bioontology.org/rest Documentation: www.bioontology.org/wiki/index.php/NCBO_REST_services Description REST URL List all ontologies ./ontologies Find a specific ontology ./ontologies/{ontology version id} Download ontology file ./ontologies/download/{ontology version id} Get versions of an ontology ./ontologies/version/{ontology id} Get concept ./concepts/{ontology version id}/{concept id} Search for concepts ./search/concepts/{query}?ontologies={ids} Get latest version of an ontology ./virtual/{ontology_id} Get concept for latest ontology version ./virtual/{ontology id}/{concept id} List all ontology categories ./categories

28. Example

32. NCBO services Ontology services (OBS) UMLS services BioPortal services Data service (OBR) Annotation service (OBA) Users UCSF Laboratree CollabRx PharmGKB, JAX HGMD Users BioPortal UI PDB/PLoS I2B2 NextBio IO informatics Users “ Resources” tab Knewco IO informatics

34. BioLit web resource: automated recognition of ontology terms and database IDs after publication http://biolit.ucsd.edu

35. Automated recognition of ontology terms and database IDs before publication with manual curation by author Word 2007 add-in

36. End

38. Annotation: Laboratree

39. Annotation: CollabRx caTissue/TIES Specimen Banking Specimen management is based on ontologies developed by NCI Ontology-based integration to create a virtual specimen bank

42. Ontology Access: IO-informatics

44. Data Summarization: PharmGKB 1. CYP2C9 , 2. VKORC1 , 3. CYP2A6 , etc. 1. Hemorrhage , 2. Venous Thrombosis , etc. 1. warfarin , 2. coumarin , 3. phenoprocoumon , etc. 34 scored annotations: 5 scored annotations: 20 scored annotations:

45. Data Summarization: Knewco