THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY Ontology-based Tools to Enhance Data Curation Trish Whetzel, PhD Outreach Coordinator December 9, 2010.

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Presentation transcript:

THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY Ontology-based Tools to Enhance Data Curation Trish Whetzel, PhD Outreach Coordinator December 9, 2010

BioPortal

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

Ontology Widgets BioPortal Widgets RSS feed Term-selection Jump To

Ontology Widgets BioPortal Widgets Tree widget Visualization

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

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 – _REST_services _REST_services 7

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

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

BioPortal Notes

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

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

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 13

Code Annotator Web service Excel UIMA platform User Interface

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

Thank you! Using NCBO Technology in Your Project: – g_NCBO_Technology_In_Your_Project g_NCBO_Technology_In_Your_Project Web service documentation: – O_REST_services O_REST_services Questions: –

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