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NCBO Tools and Web services
The document describes tools and web services from the National Center for Biomedical Ontology (NCBO) including the Ontology Web Services, Ontology Widgets, NCBO Annotator, NCBO Resource Index, and Ontology Recommender. The NCBO Annotator is an open access web service that annotates text with terms from ontologies in BioPortal and includes a variety of customization parameters. The NCBO Resource Index provides an ontology-based search across publicly available biomedical resources.
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NCBO Tools and Web services
- 1. NCBO Tools andWeb Services Trish Whetzel Outreach Coordinator
- 2. Outline • NCBOBackground • Ontology Web Services • Ontology Widgets • NCBO Annotator • NCBO Resource Index • Ontology Recommender • Lexicon Builder
- 3. National Centers forBiomedical Computing
- 4. 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
- 5. RESTful Web Services • Accessed via HTTP – http://rest.bioontology.org/bioportal/ • Each unique URL is a representation of some object • Operations include GET, POST, PUT, DELETE • Lightweight, easy to build
- 6. Web Services Code UI Browser
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- 9. Ontology Widgets •See BioPortal ( http://bioportal.bioontology.org/ontologies/42490#widgets) – Term selection - autocomplete widget – Jump To - view term details in BioPortal – Visualization - view ontology – RSS feed - track updates to ontology, e.g. upload of new versions, notes, mappings
- 10. Ontology Web Services • Ontology Metadata - get information about an ontology • Term - get details about a term • Search - find term in any ontology • Hierarchy - traverse ontology hierarchy • Notes - get contents of notes • Mappings - get mapped terms http://www.bioontology.org/wiki/index.php/NCBO_REST_services
- 11. Applications Using NCBOWeb Services • Microsoft Word 2007 Add-in for Ontology Recognition • BioLit • ISAcreator • For full list, see http://www.bioontology.org/tools
- 12. Microsoft Word 2007Add-in Automated recognition of ontology terms and database IDs before publication with manual curation by author http://ucsdbiolit.codeplex.com/
- 13. BioLit Automated recognitionof ontology terms and database IDs after publication with manual curation by author http://biolit.ucsd.edu
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- 15. NCBO Annotator •Open access, ontology-based Web service that annotates or “tags” textual metadata • Annotation is done using ontologies from BioPortal, which includes OBO Foundry and Unified Medical Language System ontologies • Variety of parameters that can be customized
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- 17. Access to Annotator • BioPortal – User-friendly interface to test Annotator • Web service (REST) – Direct programmatic access • User Guide and Sample Client Code – http://www.bioontology.org/wiki/index.php/Annotator_Web_service
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- 19. Annotator Usage •Production release – April 2009 • Data processed – 66 million calls – more than 259 gigabytes of data
- 20. Annotator Users •Rat Genome Database - example use case • See http://www.bioontology.org/wiki/index.php/ NCBO_Annotator_community for additional use cases from the Annotator user community
- 21. Rat Genome Database • Use case – Are any of these genes associated with my disease or phenotype? – Is this candidate gene expressed in my tissue of interest? • Annotate Gene Expression Omnibus (GEO) records with the Annotator using – Mouse Gross Adult anatomy ontology, Rat strain ontology, Medical Subject Headings (MeSH), NCI Thesaurus – Pilot test to annotate 30 GEO datasets and associated sample records
- 22. Rat Genome Database • Results – Rat Strain ontology • High number of false positives due to short length of many rat strains (2-3 letters) and similarity to common words and variety of words used to describe strains that were not included as synonyms – Mouse adult gross anatomy • Low number of false positives • Annotation of 192 datasets resulted in precision and recall of 84.0% and 94.8% • Ability to link expression results of a gene (based on Affymetrix probe set) to anatomical location – Manual curation of results needed, but much less burdensome by the initial automated results
- 23. NCBO Resource Index • Ontology-based index of publicly available biomedical resources • Provides a mechanism to search across resources by ontology terms
- 24. Ontology Recommender •Identify ontology relevant to annotate data
- 25. Lexicon Builder http://www.bioontology.org/wiki/index.php/ Lexicon_Builder
- 26. Acknowledgements • AnnotatorDevelopment – Nigam Shah – Clement Jonquet – Fan Meng – Mark Musen • Feedback – Simon Twigger – Karen Dowell – Robin Smith
- 27. References • BioPortal – http://bioportal.bioontology.org • NCBO REST Web services – http://www.bioontology.org/wiki/index.php/NCBO_REST_ services • NCBO Annotator Web Service – http://www.bioontology.org/wiki/index.php/Annotator_ Web_service • NCBO Resource Index Web Service – http://www.bioontology.org/wiki/index.php/Resource_In dex