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BioPortal and NCBO Web services

BioPortal and NCBO Web services. Trish Whetzel Outreach Coordinator. National Center for Biomedical Ontology. Mission To create software for the application of ontologies in biomedical science and clinical care NCBO Partners Mark Musen, Stanford University

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BioPortal and NCBO Web services

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  1. BioPortal and NCBO Web services Trish Whetzel Outreach Coordinator

  2. National Center for Biomedical Ontology • Mission • To create software for the application of ontologies in biomedical science and clinical care • NCBO Partners • Mark Musen, Stanford University • Christopher Chute, Mayo Clinic • Barry Smith, University at Buffalo • Margaret-Anne Storey, University of Victoria

  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

  5. www.bioontology.org

  6. http://bioportal.bioontology.org

  7. Search • Traverse • Comment • Download Ontology Services Views • Create • Upload • Download Mapping Services http://rest.bioontology.org • Tree-view • Auto-complete • Graph-view Widgets Annotation Term recognition Fetch “data” annotated with a given term Data Access http://bioportal.bioontology.org

  8. Browse ontologies

  9. Search for terms

  10. Widgets Term auto-complete Visualization Tree widget

  11. Tag text with ontology terms

  12. Generation of tagged data Text clinical note BioPortal – knowledge graph Creating clean lexicons Term – 1 : : : Term – n Frequency Diseases NCBO Annotator Term recognition tool NCBO Annotator NegEx Patterns Procedures Syntactic types Drugs Terms Recognized NegEx Rules – Negation detection Further Analysis Negation detection Cohort of Interest Terms form a temporal series of tags 

  13. Adverse drug events ROR of 2.058, CI of [1.804, 2.349] PRR of 1.828, CI of [1.645, 2.032] The uncorrected X2 statistic has p-value < 10-7. ROR=1.524, CI=[0.872, 2.666] PRR=1.508, CI=[0.8768, 2.594] X2 p-value=0.06816.

  14. Search ontology-based index

  15. Who is using our Web services?

  16. BioPortal SPARQL Endpoint http://sparql.bioontology.org/

  17. Links of Interest • Web service documentation http://www.bioontology.org/wiki/index.php/NCBO_REST_services • Software questions • Software support: support@bioontology.org • Social media • Twitter: @bioontology • Facebook: http://on.fb.me/bioontology • LinkedIn: http://linkd.in/ncbo-group

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