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NCBO Technology

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NCBO Technology

  1. 1. NCBO Technology Trish Whetzel Outreach Coordinator THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY
  2. 2. Outline • NCBO Overview • BioPortal and NCBO Web Services • BioPortal SPARQL Endpoint • Applications using NCBO Technology
  3. 3. 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 at Buffalo - Dr. Barry Smith – University of Victoria - Dr. Margaret-Anne Storey
  4. 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
  5. 5. National Centers for Biomedical Computing (http://www.ncbcs.org)
  6. 6. www.bioontology.or g
  7. 7. Social Media
  8. 8. Outline • NCBO Overview • BioPortal and NCBO Web Services • BioPortal SPARQL Endpoint • Applications using NCBO Technology
  9. 9. bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg
  10. 10. BioPortal • Repository of biomedical ontologies • Infrastructure is domain independent • Stores ontologies developed in OWL, Protégé frames, OBO format, and Rich Release Format • Access to ontologies via Web interface, Web services, and SPARQL • Access control for private ontologies • Supports subsets/views of ontologies
  11. 11. BioPortal Architecture Ruby on Rails Tomcat Spring Framework Hibernate ORM Protégé DB RDF Data Store LexEVS OWL, RDF, Protégé frames Restlet OBO format, UMLS RRF, LexGrid XML Third party applications SPARQL Access
  12. 12. Virtual Appliance Installations
  13. 13. Virtual Appliance User Locations
  14. 14. Outline • NCBO Overview • BioPortal and NCBO Web Services • BioPortal SPARQL Endpoint • Applications using NCBO Technology
  15. 15. 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
  16. 16. 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 TTeerrmm r reeccooggnnititioionn Search “data” annotated with a given term Search “data” annotated with a given term hhttttpp::////bbiiooppoorrttaall..bbiioooonnttoollooggyy..oorrgg
  17. 17. Ontology Web Services Accessing, browsing, searching and traversing ontologies in Your application
  18. 18. Ontology Web Services • Search – Search by term or term identifier across all ontologies in BioPortal – Results are ranked by Web page views – Parameters to expand or constrict search
  19. 19. Ontology Web Services • Term – Get details about a term including it’s definition, synonyms, URI, super- and sub-classes, and other properties
  20. 20. Ontology Web Services • Hierarchy – Get parent, children, and sibling terms
  21. 21. Notes Web Services Propose new terms and comment on ontologies
  22. 22. Notes Web Service • Add comments or terms proposals to an ontology • Maintained as metadata associated with the ontology
  23. 23. WebProtégé http://protegewiki.stanford.eedduu//wwiikkii//WWeebbPPrrootteeggee
  24. 24. VIEWs Custom subset of large ontologies
  25. 25. 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
  26. 26. Views in BioPortal
  27. 27. Views and Value Sets • View Extraction Web service – Given a root node term, extracts all child terms • Access directly from Protégé via the BioPortal Import plugin http://protegewiki.stanford.edu/wiki/BioPortal_I mport_Plugin
  28. 28. MAPPING Web Services Using NCBO technology to integrate terminologies and ontologies
  29. 29. 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
  30. 30. Mapping Access • Get a list of mappings for an ontology to all other ontologies • Get a list of mappings between two ontologies • Get a list of mappings for a single term • Get a list of mappings between two terms
  31. 31. widgets Using NCBO technology on your web pages
  32. 32. 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
  33. 33. Widgets Form auto-complete RSS feed Jump To
  34. 34. Widgets Tree widget Visualization
  35. 35. Annotator web service Using Ontologies to Annotate Your Data
  36. 36. Annotator: The Basic Idea • Tag textual metadata with ontology terms
  37. 37. Annotator Workflow
  38. 38. Data service Using Ontologies to Access Public Data
  39. 39. Resource Index: The Basic Idea • The index can be used for • Search • Data mining
  40. 40. Outline • NCBO Overview • BioPortal and NCBO Web Services • BioPortal SPARQL Endpoint • Applications using NCBO Technology
  41. 41. hhttttpp::////ssppaarrqqll..bbiioooonnttoollooggyy..oorrgg//
  42. 42. BioPortal SPARQL Data (beta) • Ontology Content • Ontology Metadata • Ontology Term Mapping Data
  43. 43. BioPortal SPARQL Data (beta) • All ontologies from BioPortal – Original ontology format transformed into RDF • OBO and OWL converted via OWL API • RRF converted via UMLS2RDF custom code – Latest version only in beta release • Statistics (as of Dec. 2012) – 415 ontologies – 4.2M terms – 2419 different predicates – 80M triples
  44. 44. BioPortal Ontology Metadata
  45. 45. BioPortal Metadata Ontology
  46. 46. Globals • Provides rdfs:subPropertyOf reasoning to enable querying over multiple ontologies while using the same predicate – http://bioportal.bioontology.org/ontologies/globals • Implemented for: – Preferred name – skos:prefLabel – Synonyms – skos:altLabel – Term definition – skos:definition – Term author – dc:author
  47. 47. Outline • NCBO Overview • BioPortal and NCBO Web Services • BioPortal SPARQL Endpoint • Applications using NCBO Technology
  48. 48. Applications using NCBO Technology
  49. 49. Applications using NCBO Technology • Ontology Development and Visualization • Data Annotation • Data Integration
  50. 50. http://protegewiki.stanford.edu/wiki/ BioPortal_Import_Plugin
  51. 51. hhttttpp::////oollss22oowwll..ssoouurrcceeffoorrggee..nneett//
  52. 52. hhttttpp::////wweebbpprrootteeggee//
  53. 53. http://www.biotec.tu-dresden.de/research/ schroeder/dog4dag/
  54. 54. hhttttpp::////rraaddlleexx..oorrgg//
  55. 55. Applications using NCBO Technology • Ontology Development and Visualization • Data Annotation • Data Integration
  56. 56. http://www.sysmo-db. org/rightfield
  57. 57. http://isatab.sourceforge.nneett//iissaaccrreeaattoorr..hhttmmll
  58. 58. http://wiki.cvrgrid.org/iinnddeexx..pphhpp//EECCGGGGaaddggeett
  59. 59. http://rreeddffllyy..ccccrr..bbuuffffaalloo..eedduu//iinnddeexx..pphhpp
  60. 60. Applications using NCBO Technology • Ontology Development and Visualization • Data Annotation • Data Integration
  61. 61. Annotator http://en.wikipedia.oorrgg//wwiikkii//PPoorrttaall::GGeennee__WWiikkii
  62. 62. KKnnoowwlleeddggee EEgggg hhttttpp::////wwwwww..kkuunnnnsskkaappsseeggggeett..nnoo//
  63. 63. http://ontologicaldiscovery.oorrgg//
  64. 64. ODiSSea hhttttpp::////wwwwww..hhuubb..sscciivveerrssee..ccoomm//
  65. 65. Thank you! • Web service documentation: http://www.bioontology.org/wiki/index.php/ NCBO_REST_services • Keep in touch – Software support: support@bioontology.org –Twitter: @bioontology – Facebook: http://on.fb.me/bioontology – LinkedIn: http://linkd.in/ncbo-group

Hinweis der Redaktion

  • "Like" NCBO on Facebook: http://on.fb.me/bioontology
    Follow NCBO on Twitter: http://twitter.com/#!/bioontology
    Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
  • http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceontology=1009&targetontology=1032&pagesize=10&pagenum=1&apikey=24e037b6-54e0-11e0-9d7b-005056aa3316
  • GSE12391
  • Documentation at http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal#Preferred_Label.2C_Synonyms_and_other_common_predicates
  • BioPortal Import Plugin – enables term re-use by being able to select ontology terms from BioPortal for use in your own ontology project
  • The plugin was developed as part of the Open architecture for Accessible Services Integration and Standardization (OASIS) project, which facilitates interoperability across service providers, mobile devices (wearable devices, phones, palm, etc.) smart home technology, and medical care providers for elderly and disabled population. Utilizes key technologies in order to provide holistic services to older people to support their physical and psychological independence, stimulate their social or psychological engagement and foster their emotional well being.
    The plugin designed to aid ontology developers during the knowledge elicitation stage and allows ontology developers to search for terms from a repository of ontologies and compare similar classes, properties, and instances.
    OASIS – Open architecture for Accessible Services Integration and Standardization project
    It is an Integrated Project with the scope to revolutionise the interoperability, quality, breadth and usability of services for all daily activities of older people.
    Brings together a consortium of 33 partners across 11 countries.
  • Notes (comments and term proposals) submitted in BioPortal are accessible in Web Protégé
  • DOG4DAG - Ontology Generation Tool for OBO-Edit and Protégé
    generates ontology terms, definitions, and relationships based on natural language text found in PubMed, the Web, or PDF documents and therefore supports the extension of existing ontologies with terms from resources commonly used in biocuration
  • Custom view of RadLex ontology implemented using the NCBO Web services. Therefore, the ontology is stored and managed in BioPortal, but the display is customized by using the Web services to access the content of RadLex and format as the community prefers
  • RightField – data annotation with fields limited to selected ontologies
  • ISACreator - 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.
    New – OntoMaton, ISAcreator functionality in GoogleDocs
  • 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.
  • RedFly – database of transcription regulatory elements in Drosophila
  • GeneWiki - Structured annotations enable pathway analysis, statistical analyses, cross-species comparisons
  • Knowledge Egg - Uses Jump To widget to access information from BioPortal and then search through databases
  • GeneWeaver, developed by the Jackson Laboratory, uses the Annotator to identify ontology terms from metadata descriptions and uses these in analysis of gene relationships
  • ODiSSea – application within SciVerse Hub that uses the NCBO Annotator to identify ontology terms in SciVerse content and also links these to data records via the NCBO Resource Index