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Ontology-based Tools to Enhance Data Curation

Ontology-based Tools to Enhance Data Curation. Trish Whetzel, PhD Outreach Coordinator December 9, 2010. BioPortal. http://bioportal.bioontology.org/. Enhancing the Curation Workflow. Data submission Ontology Widgets and Ontology Web services Ontology enrichment BioPortal Notes

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Ontology-based Tools to Enhance Data Curation

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  1. Ontology-based Tools to Enhance Data Curation Trish Whetzel, PhD Outreach Coordinator December 9, 2010

  2. BioPortal http://bioportal.bioontology.org/

  3. Enhancing the Curation Workflow • Data submission • Ontology Widgets and Ontology Web services • Ontology enrichment • BioPortal Notes • Annotation of textual metadata • NCBO Annotator

  4. Ontology Widgets • BioPortal Widgets Jump To Term-selection RSS feed

  5. Ontology Widgets • BioPortal Widgets Visualization Tree widget

  6. Ontology Views • Subset of ontology • Accessible via all BioPortal Functionality View of NCBI Taxonomy used in NeuroMorpho.org

  7. Web Services • Ontology Web services • Access to ontology content via REST services • Types • Search across all BioPortal ontologies • Get Term details • Get Term parents, children or siblings • Extract subsets of terms • Available for all ontologies in BioPortal • http://www.bioontology.org/wiki/index.php/BioPortal_REST_services

  8. Enhancing the Curation Workflow • Data submission • Ontology Widgets and Ontology Web services • Ontology enrichment • BioPortal Notes • Annotation of textual metadata • NCBO Annotator

  9. BioPortal Notes • Notes • Provide a mechanism to collect structured information • Programmatic access • Alerts – Email and RSS • Integration with ontology editing programs

  10. BioPortal Notes

  11. Enhancing the Curation Workflow • Data submission • Ontology Widgets and Ontology Web services • Ontology enrichment • BioPortal Notes • Annotation of textual metadata • NCBO Annotator

  12. Annotator: The Basic Idea • Tag textual metadata with ontology terms

  13. Tools for annotation of textual metadata • 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

  14. UIMA platform Code User Interface Excel Annotator Web service

  15. Resource Index • Ontology-based index of publicly available biomedical data

  16. 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

  17. Acknowledgements • NCBO Team • Mark Musen, Stanford Univerity • Partners: Barry Smith, University of Buffalo, Chris Chute, Mayo Clinic, and Peggy Storey, University of Victoria • Developers, Driving Biological Projects, and other Collaborators

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