Ontology Web services for Semantic Applications
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The document describes ontology web services created by the National Center for Biomedical Ontology to facilitate the application of ontologies in biomedical science. The services provide access to ontologies and related functions like searching, term details, hierarchies and mappings. Additional services allow the creation of ontology-based annotations using tools like the annotator and ontology recommender. All services are accessible via RESTful web APIs.
Ontology Web services for Semantic Applications
- 1. Ontology Web Services for Semantic Applications Trish Whetzel, PhD Outreach Coordinator
- 2. National Center for Biomedical Ontology • Mission – To create software for the application of ontologies in biomedical science and clinical care • NCBO Partners – Stanford University - Dr. Mark A. Musen – Mayo Clinic - Dr. Christopher G. Chute – University of Buffalo - Dr. Barry Smith – University of Victoria - Dr. Margaret-Anne Storey
- 3. National Centers for Biomedical Computing (http://www.ncbcs.org)
- 4. REST Web Services • Accessed via HTTP – http://rest.bioontology.org/{parameter} • Each unique URL is a representation of some object • Operations include GET, POST, PUT, DELETE • Lightweight, easy to build
- 6. Web Services Code User Interface Browser http://bioportal.bioontology.org
- 7. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 8. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 9. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – search by term or term identifier across all ontologies in BioPortal – Term – get details about a term including it’s URI, super- and sub-classes, properties – Hierarchy – get parent or children terms – Mapping – get mappings between terms – Notes – get comments/new term proposals added to the ontology – RDF – get RDF snippet for term or entire ontology
- 10. Ontology Web Services • BioPortal Search Demo 10
- 11. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 12. Ontology Web Services • Widgets – Jump To – auto-complete function to select term and Jump To BioPortal to view term details – Term-selection widget – auto-complete function and can return term URI, term ID or term name – Visualize widget – view the ontology structure and relations – Tree widget – view the ontology tree Code for widgets is available on BioPortal
- 13. Ontology Widgets • BioPortal Widgets RSS feed Term-selection Jump To
- 14. Ontology Widgets • BioPortal Widgets Tree widget Visualization
- 15. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 16. Annotator: The Basic Idea • Tag textual metadata with ontology terms 16
- 18. Code Annotator Web service UIMA platform Excel User Interface
- 19. Annotator Addin
- 20. Annotator Addin
- 21. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator –Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 22. Ontology Recommender Clement Jonquet, Mark A. Musen and Nigam H. Shah Building a Biomedical Ontology Recommender Web Service Journal of Biomedical Semantics 2010, 1(Suppl 1):S1
- 23. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 24. Lexicon Builder www.bioontology.org/wiki/inde x.php/Lexicon_Builder
- 25. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 26. Resource Index: The Basic Idea 26
- 27. Resource Index: Use Case 27
- 28. Resource Index: Use Case 28
- 29. Resource Index: Use Case 29
- 31. Ontology Web Services • Access Ontologies and Views (Value sets or Slims) – Search – Term – Hierarchy – Mapping – Notes – RDF • Widgets – Auto-complete – Visualization • Create ontology-based annotations – Annotator – Ontology Recommender – Lexicon Builder • Access ontology-based index of annotations – Resource Index
- 32. Tools using NCBO Technology 32 http://www.bioontology.org/technology
- 33. Thank you! • Using NCBO Technology in Your Project: http://www.bioontology.org/wiki/index.php/Using_ NCBO_Technology_In_Your_Project • Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_ REST_services • Questions: support@bioontology.org