Web services and the Development of Semantic Applications

• 1. Web Services and Developmentof Semantic ApplicationsTrish WhetzelOutreach CoordinatorTHE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY

2. National Center forBiomedical Ontology Mission To create software for the application ofontologies in biomedical science and clinicalcare 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-AnneStorey 3. National Centers for Biomedical Computing(http://www.ncbcs.org) 4. NCBO Key Activities We create and maintain a library ofbiomedical ontologies We build tools and Web services toenable the use of ontologies We collaborate with scientificcommunities that develop and useontologies 5. www.bioontology.org 6. Links of Interest http://bit.ly/ncbo-amia-demo 7. Outline Learning Objectives REST Web services BioPortal NCBO Web Services 8. Learning Objectives Learn what Web services are available fromNCBO Learn how to programmatically use theseWeb services Learn how to combine these Web services toperform tasks 9. REST Web Services Accessed via HTTP http://rest.bioontology.org/{parameters} Each unique URL is a representation of someobject Operations include GET, POST, PUT, DELETE Lightweight, easy to build 10. Web ServicesCodeUserInterfaceBrowser 11. Outline REST Web services BioPortal NCBO Web Services BioPortal SPARQL Endpoint 12. http://bioportal.bioontology.org 13. Outline REST Web services BioPortal NCBO Web Services BioPortal SPARQL Endpoint 14. http://http://rreesstt..bbiioooonnttoollooggyy..oorrggOntologyServicesOntologyServices Search Traverse Comment Download Search Traverse Comment DownloadMappingServicesMappingServicesWWididggeettss Create Upload Download Tree-view Auto-complete Graph-view Tree-view Auto-complete Graph-viewAAnnnnoottaattioionnDDaattaa A Acccceessss Create Upload DownloadVVieiewwssTTeerrmm r reeccooggnnititioionnFetch dataannotated with agiven termFetch dataannotated with agiven termhhttttpp::////bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg 15. Ontology Web ServicesAccessing, browsing, searching and traversing ontologies in Your application 16. Ontology Web Services List All Ontologies List all ontologies in BioPortal Documentation: http://bit.ly/sxL2Qi GoogleDoc Excel example:http://bit.ly/ncbo-list-all-ontologies 17. One ontology idhas many ontologyversion idsOntology version idOntology id 18. Ontology Web Services cont. Search Search by term or term identifier across all ontologiesin BioPortal Documentation: http://bit.ly/tMDkr6 Example clients Java: http://bit.ly/ttTb1G Perl: http://bit.ly/sPXC2X 19. Ontology Web Services cont. Term get details about a term including its definition,synonyms, URI, super- and sub-classes, and otherproperties http://bit.ly/teedbd Hierarchy get parent, children, and sibling termshttp://bit.ly/tPzm75 20. RightFieldhttp://www.sysmo-db.org/rightfield 21. ECG Gadgethttp://wiki.cvrgrid.org/iinnddeexx..pphhpp//EECCGGGGaaddggeett 22. ISAcreatorhttp://isatab.sourceforge.nneett//iissaaccrreeaattoorr..hhttmmll 23. DOG4DAG Ontology GenerationTool for OBO-Edit and Protg 24. Word Add-in 25. cgMDRhttp://ccaanncceerrggrriidd..oorrgg//iinnddeexx..pphhpp 26. openMDRhttp://citih.osumc.edu/pprroojjeeccttss//pprroojjeecctt&&rr==11003322 27. eleMaphttps://vviiccttrr..vvaannddeerrbbiilltt..eedduu//eelleeMMAAPP// 28. BioPortal Import Pluginhttp://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin 29. widgetsUsing NCBO technology on your web pages 30. Widgets Form auto-complete auto-complete functionand can return term URI, term ID or termname Jump To auto-complete function to selectterm and Jump To BioPortal to view termdetails Visualize widget view the ontology structureand relations Tree widget view the ontology treeCode for widgets is available on BioPortal 31. WidgetsForm auto-completeRSS feedJump To 32. WidgetsTree widgetVisualization 33. RedFlyhttp://redfly.ccccrr..bbuuffffaalloo..eedduu//iinnddeexx..pphhpp 34. Radiological Societyof North Americahhttttpp::////rraaddlleexx..oorrgg// 35. GMinerhhttttpp::////ggmmiinneerr..mmccww..eedduu// 36. Knowledge Egghhttttpp::////wwwwww..kkuunnnnsskkaappsseeggggeett..nnoo// 37. Notes Web ServicesPropose new terms and comment on ontologies 38. Notes Web Service Add term proposals and comments onontology terms Documentation:http://www.bioontology.org/wiki/index.php/Ontology_ 39. WebProtghttp://protegewiki.stanford.eedduu//wwiikkii//WWeebbPPrrootteeggee 40. VIEWsCustom subset of large ontologies 41. Views and Value Sets Users can submit their own derivatives ofBioPortal ontologies these which become first-class objects in BioPortal andcan be used as all other Web services 42. Views in BioPortal 43. Views and Value Sets View Extraction Web service Given a root node term, extracts all child termshttp://bit.ly/uXeh2s Access directly from Protg via the BioPortalImport pluginhttp://protegewiki.stanford.edu/wiki/BioPortal_Import_ 44. MAPPING Web ServicesUsing NCBO technology to integrate terminologies and ontologies 45. MMaappppiinnggssRootTerm-1 Term-2Term-3 Term-4Term-5Rt1 t2t4t3t5 t6 t7Term-2 t1Term-5 t5Ontology A Upload or Downloadmapping subsetsOntology B 46. UUssiinngg MMaappppiinnggss ffoorr qquueerryyffeeddeerraattiioonn 47. Mappings Mappings Web service Documentation:http://www.bioontology.org/wiki/index.php/BioPortal_ Functions Get/Download Create/Upload Example Perl client to Get mappings:http://bit.ly/tDKPQd 48. Annotator web serviceUsing Ontologies to Annotate Your Data 49. Annotator: The Basic Idea Tag textual metadata with ontology terms 50. Annotator Workflow 51. Annotator Web Service Tag free text with ontology terms Documentation:http://www.bioontology.org/wiki/index.php/Annotator_ Example clients: Perl: http://bit.ly/vKYpCP Java: http://bit.ly/rRFoKd 52. Gene WikiAnnotatorhttp://en.wikipedia.oorrgg//wwiikkii//PPoorrttaall::GGeennee__WWiikkii 53. Statistical Tracking ofOntological Phrases (STOP)http://www.mooneygroup.oorrgg//ccoonntteenntt//wweebbttoooollss 54. Ontological Discovery Environmenthttp://oonnttoollooggiiccaallddiissccoovveerryy..oorrgg// 55. STRIDE 56. Data serviceUsing Ontologies to Access Public Data 57. Resource Index: The Basic Idea The index can be used for Search Data mining 58. Resources index: Example 59. Data Access Resource Index Web service Documentation:http://www.bioontology.org/wiki/index.php/Resource_ 60. ODiSSea 61. BioPortal SPARQL Endpoint Documentation:http://www.bioontology.org/wiki/index.php/SPARQL_ Query interface: http://sparql.bioontology.org/ Example queries:http://sparql.bioontology.org/examples Sample code: https://github.com/ncbo/sparql-code-examples 62. Thank you! Web service documentation:http://www.bioontology.org/wiki/index.php/NCBO_REST_services Keep in touch NCBO Announce mailing list: http://bit.ly/osLzng Software support: [email protected] Twitter: @bioontology Facebook: http://on.fb.me/bioontology LinkedIn: http://linkd.in/ncbo-group Questions:[email protected]