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Ontology-based Tools to Enhance the Curation Workflow

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Ontology-based Tools to Enhance the Curation Workflow

  1. 1. Ontology-based Tools to Enhance the Curation Workflow Trish Whetzel Outreach Coordinator THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY
  2. 2. Enhancing the Curation Workflow • Curation – The activity of organizing, representing and making biological information accessible to both humans and computers1 • Constraints – Large amounts of data – Time-consuming • Components to enhance – Data submission – Ontology enrichment – Annotation of textual metadata 1Howe et al. Nature. 2008 Oct 2;455(7213):590
  3. 3. BioPortal http://bioportal.bbiioooonnttoollooggyy..oorrgg//
  4. 4. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
  5. 5. Tools for Data Submission • Ontology Widgets – Code to use in your web site – Search for and select terms from ontologies to annotate your data – Enables consistent annotation of data by re-use of the properly formatted term – Available for all ontologies in BioPortal 5
  6. 6. Tools for Data Submission 6
  7. 7. Ontology Widgets • BioPortal Widgets RRSSSS ffeeeedd AAuuttoo--ccoommpplleettee JJuummpp TToo
  8. 8. Ontology Widgets • BioPortal Widgets TTrreeee wwiiddggeett VViissuuaalliizzaattiioonn
  9. 9. Tools for Data Submission • 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/BioPorta l_REST_services 9
  10. 10. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
  11. 11. Tools for Ontology Enrichment • Ontology Enrichment – Expansion of the ontology based on user need for terms • Constraints – Existing trackers do not collect structured information – No programmatic access to tracker – Lack of integration with ontology editing software 11
  12. 12. Ontology Development Lifecycle Collect feedback from Subject Matter Experts Draft prototype ontology Collect feedback from Subject Matter Experts Develop new ontology Publish Ontology Refine Ontology Collect feedback from community EEmmaaiill EEmmaaiill EEmmaaiill
  13. 13. Ontology Development Lifecycle Collect feedback from Subject Matter Experts Draft prototype ontology Collect feedback from Subject Matter Experts Develop new ontology Publish Ontology Refine Ontology Collect feedback from community BBiiooPPoorrttaall BBiiooPPoorrttaall BBiiooPPoorrttaall
  14. 14. BioPortal Notes • Notes – Provide a mechanism to collect structured information – Programmatic access – Alerts of updates from both Email and RSS – Integration with ontology editing programs
  15. 15. BioPortal Notes
  16. 16. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
  17. 17. Tools for annotation of textual metadata • 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 17
  18. 18. Annotator: The Basic Idea • Tag textual metadata with ontology terms 18
  19. 19. Code Annotator Web service UIMA platform Excel User Interface
  20. 20. Annotator Addin
  21. 21. Annotator Addin
  22. 22. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
  23. 23. 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
  24. 24. Thank you! • Using NCBO Technology in Your Project: – http://www.bioontology.org/wiki/index.php/Usin g_NCBO_Technology_In_Your_Project • Web service documentation: – http://www.bioontology.org/wiki/index.php/NCB O_REST_services • Questions: – support@bioontology.org

Notas do Editor

  • Curation – making unstructured data, structured and searchable
    Data submission – collecting structured data ( tagged with ontology terms ) at the time of data submission
    Ontology enrichment – adding new terms to the ontology at the time of submission
    Annotation of textual metadata – tagging free text with ontology term
  • Curation – making unstructured data, structured and searchable
    Data submission – collecting structured data ( tagged with ontology terms ) at the time of data submission
    Ontology enrichment – adding new terms to the ontology at the time of submission
    Annotation of textual metadata – tagging free text with ontology term
  • SimTK - https://simtk.org/home/simtk
    --physics-based simulations of biological structures
    GMiner - http://gminer.mcw.edu/
    -Ontolgoy-indexed annotations from GEO, widget used to get more information on term (Jump To)
    aTag Generator - http://hcls.deri.org/atag/generator/
    - aTags ("associative tags") are snippets of HTML that capture the information that is most important to you in a machine-readable, interlinked format, making it easier for you and others to see the big picture.
    RNSA – various tools, e.g. RadLex viewer, propose new terms
  • -ISAcreator - http://isatab.sourceforge.net/isacreator.html
    RightField – http://www.sysmo-db.org/rightfield
    Jinx - http://ncmir.ucsd.edu/downloads/jinx.shtm
    ECG Gadget – http://wiki.cvrgrid.org/index.php/CVRG_Tool_Demonstrations
    ODIE - http://www.bioontology.org/ODIE
    Word Add-in for Ontology Recognition - http://ucsdbiolit.codeplex.com/
    and more…
  • Curation – making unstructured data, structured and searchable
    Data submission – collecting structured data ( tagged with ontology terms ) at the time of data submission
    Ontology enrichment – adding new terms to the ontology at the time of submission
    Annotation of textual metadata – tagging free text with ontology term
  • Curation – making unstructured data, structured and searchable
    Data submission – collecting structured data ( tagged with ontology terms ) at the time of data submission
    Ontology enrichment – adding new terms to the ontology at the time of submission
    Annotation of textual metadata – tagging free text with ontology term
  • GSE12391
    http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12391
  • Elsevier SciVerse
    Karen Dowell, Jackson Lab
    Shai-shen Orr, Mark Davis’s lab
    Sean Mooney’s group
    Ida Sim, UCSF
    Simon Twigger, Medical college of Wisconsin
    Nathan Baker, Washington Univ.
    Amit Seth, Wright State Univ.
    Neil Sarkar, University of Vermont
    Larry Hunter, University of Colorado, Denver
  • Curation – making unstructured data, structured and searchable
    Data submission – collecting structured data ( tagged with ontology terms ) at the time of data submission
    Ontology enrichment – adding new terms to the ontology at the time of submission
    Annotation of textual metadata – tagging free text with ontology term

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