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BFO-aligned Ontologies for Clinical and Translational Research: OGMS, IDO, and VO

BFO-aligned Ontologies for Clinical and Translational Research: OGMS, IDO, and VO. (Orlando Presentation, 2/8/2013) http:// ncorwiki.buffalo.edu/index.php/CTSA_Ontology_Workshop Yongqun “Oliver” He University of Michigan Medical School Ann Arbor, MI 48109. BFO and OBO Foundry Principles.

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BFO-aligned Ontologies for Clinical and Translational Research: OGMS, IDO, and VO

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  1. BFO-aligned Ontologies for Clinical and Translational Research: OGMS, IDO, and VO (Orlando Presentation, 2/8/2013) http://ncorwiki.buffalo.edu/index.php/CTSA_Ontology_Workshop Yongqun “Oliver” HeUniversity of Michigan Medical SchoolAnn Arbor, MI 48109

  2. BFO and OBO Foundry Principles • BFO: Basic Formal Ontology • BFO has been used a top level ontology for many ontologies associated with clinical and translational research • Examples: OGMS, IDO, VO, OBI, OAE • All OBO foundry library ontologies follow OBO Foundry principles, e.g., openness, collaboration, and use of a common shared syntax

  3. OGMS: Ontology of General Medical Science • An ontology of the major types of entities involved in a clinical encounter. • An upper ontology for clinical medicine • A mid-level ontology with respect to BFO • Includes ~100 general terms • By: • Albert Goldfain • Richard Scheuermann • Barry Smith, … https:// code.google.com /p/ogms/

  4. Wide OGMS Applications Ontologies using OGMS: • IDO • DO • SDO • AERO • OAE • VSO • OMRSE • VO • ... Courtesy: figure kindly provided by Albert Goldfain

  5. OGMS application example:Development of OAE • OAE: Ontology of Adverse Events • OAE ‘adverse event’: • = def. a OGMS: ‘pathological bodily process’ that occurs after a medical intervention. • Does not assume causality • ‘causal adverse event’ assumes causality • >1,000 specific AE terms in OAE now, mapped to MedDRA terms OAE for AE data analysis Ref: Sarntivijaiet al., 2012 PLoS ONE

  6. IDO: Infectious Disease Ontology IDO-core Central Terms: • IDO: represent the entire infectious disease domain • Interoperability with other disease and health domains • IDO-core: by Lindsay Cowell, Barry Smith, and others Courtesy: figure kindly provided by Lindsay Cowell

  7. I IDO-Sa IDO-Asp IDO- IDO- IDO-Core IDO- Bac Fun IDO- TB Cry IDO- IDO- IDO- IDO- Sch Flav Par Virus IDO-Mal IDO-Flu IDO Core-Extension Development Strategy • IDO extensions are developed by extending IDO-core OGMS CL Courtesy: figure kindly provided by Lindsay Cowell • We developed an IDO extension: Brucellosis Ontology GO BP OBI

  8. IDOBRU: Brucellosis Ontology as an IDO Extension • Focuses on the domain of zoonotic brucellosis, caused by Gram-negative bacterium Brucella. • Incorporates all IDO-core terms, has over 880 Brucella-specific terms, and imports terms from other ontologies. Citation: “Asiyah” Yu Lin, Zuoshuang Xiang, Yongqun He. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. PMID: 22041276.

  9. IDO-core is the top ontology of IDOBRU

  10. Vaccine Ontology (VO) • VO: A biomedical ontology in the domain of vaccine and vaccination • Support data integration, literature mining, and reasoning • Integrated with VIOLIN • VIOLIN: a vaccine database and analysis system, including many programs, e.g.: • ~3000 vaccines • Protegen: protective antigens. ~600 • Vaxjo: vaccine adjuvants: > 100 • Vaxign: vaccine design • Widely used by vaccine community • Funded by a NIAID R01 grant http://www.violinet.org http://www.violinet.org/vaccineontology

  11. Many Ontology Tools developed during VO development Linked ontology data server Ontology fetching tool Mass generation of new terms Ontology community view generator Ontology data analysis

  12. VO Statistics and Development • OntoFox to import external terms and axioms from other 16 ontologies • Ontorat to generate a large number of terms and axioms automatically • VO includes >1000 vaccines for >20 host spp. against various diseases

  13. VO imports OBI terms for vaccine investigation OBI/VO modeling of “vaccine protection assay” OBI: Ontology for Biomedical Investigations ~20 communities involved Reference: Brinkman et al. (2007). Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 2010, 1(Suppl 1):S7. PMID: 20626927.

  14. Example: Afluria Influenza Vaccine

  15. U of Michigan Ontology Research • UM Ontology Working Group: • Members: Marcy Harris, Alla Karnovsky, Frank Manion, Oliver He, Asiyah Yu Lin, Jeff Cowall, … • Activities: Biweekly meetings, … • Developing a Clinical and Translational Research Ontology. • UM MCubed pilot award: • Title: Ontology Development and Applications for Clinical and Translational Science • To: Alla, Marcy, and Oliver; Period: 1.5 years • UM CTSA: Michigan Institute for Clinical & Health Research (MICHR) • Ontology research needed to integrate huge datasets • Committed to collaborative community effort • One project: Informed Consent Ontology (ICO) (next slide) • Case study: Head and neck cancer biorepository

  16. Informed Consent Ontology (ICO) • ICO: A prototype, aligned with BFO. • Currently focused on research permissions • UM CTSA Project Team: • Alla Karnovsky, Frank Manion, Marcy Harris, Oliver He, Nick Steneck, Blake Roessler Patient Record Institutional Records Authority Subject Courtesy: figures kindly provided by AllaKarnovskyand Nickolas Steneck consent Information Research Permission Subject matter expert view IRB/ eResearch Protocol Informed Consent Form Reference: Development of an Informed Consent Ontology to Support Biobanking. Alla Karnovsky, Frank J. Manion, Oliver He, Terry Weymouth, V. Glenn Tarcea; Lisa Powell, Blake J. Roessler, Nicholas H. Steneck. AMIA 2012 Annual Symposium.

  17. Clinical Data Integration Required • Records of millions of patients in UM Health System (UMHS) • Ontology is needed for true clinical data integration Courtesy: figure kindly provided by Jeff Cowall

  18. Acknowledgements Barry Smith (BFO, OGMS, IDO, VO, ...) • Oliver He Group: • Zuoshuang “Allen” Xiang • “Asiyah” Yu Lin • Sirarat Sarntivijai Lindsay Cowell (IDO) • OGMS Development Team • Albert Goldfain • Richard Scheuermann, … • UM Literature Mining Collaborators: • Arzucan Özgür • JungukHur • OBI Consortium: • Bjoern Peters • Jie Zheng • Chris Stoeckert • Alan Rutternberg • Melanie Courtot, … VO Collaborators: Barry, Lindsay, Alan, Bjoern, …. UM Ontology Working Group Listed in a previous slide Funding: NIH grants R01AI081062 & U54-DA-021519 UM MCubed pilot project, MICHR (UM CTSA)

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