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Integrating exposure data to evaluate risk: The Exposure Ontology (ExO)

Integrating exposure data to evaluate risk: The Exposure Ontology (ExO). Carolyn Mattingly, PhD North Carolina State University. How does the environment affect our health?. Genes. Environment (chemicals). Disease. http://ctdbase.org. in vitro and in vivo controlled vocabularies

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Integrating exposure data to evaluate risk: The Exposure Ontology (ExO)

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  1. Integrating exposure data to evaluate risk: The Exposure Ontology (ExO) • Carolyn Mattingly, PhD • North Carolina State University

  2. How does the environment affect our health?

  3. Genes Environment (chemicals) Disease

  4. http://ctdbase.org

  5. in vitro and in vivo • controlled vocabularies • Entrez Gene IDs • MEDIC • marker/mechanistic qualifier • in vitro and in vivo • controlled vocabularies • MeSH chemicals and drugs • MEDIC • “causal”/therapeutic qualifier C-G interactions • vertebrates and invertebrates • controlled vocabularies • Entrez Gene IDs • MeSH chemicals and drugs • CTD action ontology C-D Relationships G-D Relationships

  6. 28 curated >1,000 inferred 1,200 Genes 59 Genes Prostate Cancer

  7. Chemicals Comparable chemical data Diseases Pathways Functional annotations How to best prioritize hypotheses?

  8. Exposure data • Grounding CTD data in “real-world” exposure data • Centralizing exposure data • Integrating exposure information with other biological data

  9. What to capture and how? Phase II Phase III Phase IV Phase I Initial pilot curation to identify major concepts Full working group evaluation of draft ontology Model relationships among data concepts Expand test data set to evaluate extensibility of conceptual model and cross -reference existing ontologies Disseminate for Public feedback Iterate data model refinement and curation

  10. Exposure Stressor Exposure Receptor Interacts with to result in via Exposure Event Exposure Outcome ExO Available on OBOFoundry & BioPortal

  11. Curation-driven ontology development • Status • ~50 data points captured • ~3,000 priority articles: 600 curated, 16,000 exposure statements, 300 unique chemicals, 100 diseases Mattingly CJ, McKone TE, Callahan MA, Blake JA, Hubal EA. Environ Sci Technol. 2012. 46(6):3046.

  12. Curation

  13. Query flexibility

  14. Integrated results

  15. Pesticides Exposure Studies Exposure Levels Basics + Exposure Summary Countries Diseases GO Biological Processes Exposure Studies +

  16. bisphenol A Exposure Studies Exposure Levels Basics The following are measured exposure levels of bisphenol A or its descendants curated from various Exposure Studies. Click on DETAILS to find more information about the measurement and conditions of the study. displays the actual measurements curated from multiple papers, providing a view of the different ranges data displayed if chemical or its descendant is in the “Stressor”or “Biomarker” column

  17. click

  18. Acknowledgements Scientific Curators Allan Peter Davis Cindy Murphy Cynthia Richards Kelley Lennon-Hopkins Daniela Sciaky Jean Lay Scientific Software Engineers Michael C. Rosenstein Thomas Wiegers Biostatistician Benjamin King, MS System Administrator Roy McMorran ExO Working Group Judith Blake, PhD Michael Callahan, PhM Elaine Cohen Hubal, PhD Robin Dodson, ScD Peter Egeghy, PhD Jane Hoppin, PhD Thomas McKone, PhD Ruthann Rudel Funding: NIEHS (curation) ACC (ExO development)

  19. >300 manuscripts using CTD data >30 public databases incorporating CTD data

  20. Integrated results Gene Ontology Pathways

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