Web services and the Development of Semantic Applications
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NCBO Technology Tutorial AMIA TBI 2012.
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Web services and the Development of Semantic Applications
- 1. Web Services and Development of Semantic Applications Trish Whetzel Outreach Coordinator THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY
- 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. NCBO Key Activities • We create and maintain a library of biomedical ontologies • We build tools and Web services to enable the use of ontologies • We collaborate with scientific communities that develop and use ontologies
- 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 from NCBO • Learn how to programmatically use these Web services • Learn how to combine these Web services to perform tasks
- 9. REST Web Services • Accessed via HTTP – http://rest.bioontology.org/{parameters} • Each unique URL is a representation of some object • Operations include GET, POST, PUT, DELETE • Lightweight, easy to build
- 10. Web Services Code User Interface Browser
- 11. Outline • REST Web services • BioPortal • NCBO Web Services • BioPortal SPARQL Endpoint
- 13. Outline • REST Web services • BioPortal • NCBO Web Services • BioPortal SPARQL Endpoint
- 14. http://http://rreesstt..bbiioooonnttoollooggyy..oorrgg Ontology Services Ontology Services • Search • Traverse • Comment • Download • Search • Traverse • Comment • Download Mapping Services Mapping Services WWididggeettss • Create • Upload • Download • Tree-view • Auto-complete • Graph-view • Tree-view • Auto-complete • Graph-view AAnnnnoottaattioionn DDaattaa A Acccceessss • Create • Upload • Download VVieiewwss TTeerrmm r reeccooggnnititioionn Fetch “data” annotated with a given term Fetch “data” annotated with a given term hhttttpp::////bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg
- 15. Ontology Web Services Accessing, 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 id has many ontology version ids Ontology version id Ontology id
- 18. Ontology Web Services cont. • Search – Search by term or term identifier across all ontologies in 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 it’s definition, synonyms, URI, super- and sub-classes, and other properties http://bit.ly/teedbd • Hierarchy – get parent, children, and sibling terms http://bit.ly/tPzm75
- 23. DOG4DAG Ontology Generation Tool for OBO-Edit and Protégé
- 24. Word Add-in
- 28. BioPortal Import Plugin http://protegewiki.stanford.edu/wiki/ BioPortal_Import_Plugin
- 29. widgets Using NCBO technology on your web pages
- 30. Widgets • Form auto-complete – auto-complete function and can return term URI, term ID or term name • Jump To – auto-complete function to select term and Jump To BioPortal to view term details • Visualize widget – view the ontology structure and relations • Tree widget – view the ontology tree Code for widgets is available on BioPortal
- 31. Widgets Form auto-complete RSS feed Jump To
- 32. Widgets Tree widget Visualization
- 34. Radiological Society of North America hhttttpp::////rraaddlleexx..oorrgg//
- 37. Notes Web Services Propose new terms and comment on ontologies
- 38. Notes Web Service • Add term proposals and comments on ontology terms • Documentation: http://www.bioontology.org/wiki/index.php/Ontology_
- 41. VIEWs Custom subset of large ontologies
- 42. Views and Value Sets • Users can submit their own derivatives of BioPortal ontologies – these which become first-class objects in BioPortal and can be used as all other Web services
- 44. Views and Value Sets • View Extraction Web service – Given a root node term, extracts all child terms http://bit.ly/uXeh2s • Access directly from Protégé via the BioPortal Import plugin http://protegewiki.stanford.edu/wiki/BioPortal_Import_
- 45. MAPPING Web Services Using NCBO technology to integrate terminologies and ontologies
- 46. MMaappppiinnggss Root Term-1 Term-2 Term-3 Term-4 Term-5 R t1 t2 t4 t3 t5 t6 t7 Term-2 t1 Term-5 t5 Ontology A Upload or Download mapping subsets Ontology B
- 47. UUssiinngg MMaappppiinnggss ffoorr qquueerryy ffeeddeerraattiioonn
- 48. 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
- 49. Annotator web service Using Ontologies to Annotate Your Data
- 50. Annotator: The Basic Idea • Tag textual metadata with ontology terms
- 52. 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
- 53. Gene Wiki Annotator http://en.wikipedia.oorrgg//wwiikkii//PPoorrttaall::GGeennee__WWiikkii
- 54. Statistical Tracking of Ontological Phrases (STOP) http://www.mooneygroup.oorrgg//ccoonntteenntt//wweebbttoooollss
- 55. Ontological Discovery Environment http://oonnttoollooggiiccaallddiissccoovveerryy..oorrgg//
- 56. STRIDE
- 57. Data service Using Ontologies to Access Public Data
- 58. Resource Index: The Basic Idea • The index can be used for • Search • Data mining
- 60. Data Access • Resource Index Web service – Documentation: http://www.bioontology.org/wiki/index.php/Resource_
- 61. ODiSSea
- 62. 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
- 63. Thank you! • Web service documentation: http://www.bioontology.org/wiki/index.php/NC BO_REST_services • Keep in touch – NCBO Announce mailing list: http://bit.ly/osLzng – Software support: support@bioontology.org – Twitter: @bioontology – Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group • Questions: support@bioontology.org
Notes de l'éditeur
- The CVRG ECG Gadget is a Web 2.0 mashup application built using the GoogleWeb Toolkit and Visualization API. †It integrates the CVRG ECG Storage &Analysis Workflows with ECG Visualization/Annotation using REST services available from the NCBO Bioportal. †The application can be executed using an Apache Tomcat server, allowing the application to be run locally and/or remotely. †The application has been tested in Internet Explorer 7 & 8.Questions and feedback on the tool itself are welcome.
- A ‘user-friendly’ standalone Java application that assists the experimentalists to annotate the experimental metadata. Depending on the configuration (set via the ISAconfigurator tool), certain fields prompt a pop-up browser to search and select terms from ontologies that are accessed in real time via the Ontology Lookup Service and BioPortal.
- Ontology Generation Tool for OBO-Edit and Protégé (NEW)
- cgMDR is developed by Steve Harris’ group at the University of Oxford. It is an Excel Add-in that allows users to annotate data elements with terms from BioPortal.
- The screenshots: Main screen from where a user chooses to add conceptual reference to a registry item User can select a specific Terminology from the drop down list – Bioportal-SNOMEDCT, Bioportal-HL7, etc Shows the results of query for a specific term in a specific terminology from Bioportal – some basic information and link back to parent source URL.
- eMERGE - a national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. This allows researchers to harmonize their local phenotype data dictionaries to existing metadata and terminology standards such as the caDSR (Cancer Data Standards Registry and Repository), NCIT (NCI Thesaurus) and SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms). Use this tool to search/browse metadata related to different studies, create new study & its related metadata, users can also export metadata in excel format.
- http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceontology=1009&targetontology=1032&pagesize=10&pagenum=1&apikey=24e037b6-54e0-11e0-9d7b-005056aa3316
- GSE12391 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12391
- Structured annotations enable pathway analysis, statistical analyses, cross-species comparisons
- Indexing an element from GEO. The GEO element GDS1989 is annotated according to its title and its description, as well as by the ontology elements that comprise the transitive closure over the parent–child relationships subsumed by the direct annotations.