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Ontology-based Tools to Enhance the Curation Workflow
This document discusses tools from the National Center for Biomedical Ontology (NCBO) that can enhance the data curation workflow. It describes Ontology Widgets and web services that allow consistent annotation of data by reusing terms from ontologies. It also describes BioPortal Notes for collecting structured feedback to enrich ontologies, and the NCBO Annotator web service for annotating textual metadata with ontology terms. These tools address challenges of curating large amounts of data by facilitating data submission, ontology evolution, and metadata annotation.
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Ontology-based Tools to Enhance the Curation Workflow
- 1. Ontology-based Tools toEnhance the Curation Workflow Trish Whetzel Outreach Coordinator THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY
- 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
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- 4. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
- 5. Tools for DataSubmission • 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. Tools for DataSubmission 6
- 7. Ontology Widgets •BioPortal Widgets RRSSSS ffeeeedd AAuuttoo--ccoommpplleettee JJuummpp TToo
- 8. Ontology Widgets •BioPortal Widgets TTrreeee wwiiddggeett VViissuuaalliizzaattiioonn
- 9. Tools for DataSubmission • 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. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
- 11. Tools for OntologyEnrichment • 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. 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. 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. 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
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- 16. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
- 17. Tools for annotationof 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. Annotator: The BasicIdea • Tag textual metadata with ontology terms 18
- 19. Code Annotator Webservice UIMA platform Excel User Interface
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- 22. Enhancing the Curation Workflow • Data submission – Ontology Widgets and Ontology Web services • Ontology enrichment – BioPortal Notes • Annotation of textual metadata – NCBO Annotator
- 23. Acknowledgements • NCBOTeam – 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. 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
Editor's Notes
- #3 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
- #5 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
- #6 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
- #10 -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…
- #11 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
- #17 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
- #19 GSE12391 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12391
- #20 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
- #23 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