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Outline

Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science. Jiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith. Outline. Introduction Method Results and Discussion

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Outline

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  1. Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science Jiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith

  2. Outline • Introduction • Method • Results and Discussion • Conclusion and Future Directions

  3. Scope • Body fluids: liquid and gaseous portions of substance excreted or secreted from, and inside, the bodies of organisms. • Focus on the case of human organisms. • Provide a preliminary application ontology covering body fluids in both healthy and diseased human organism.

  4. Only small fraction of human body fluids in FMA:

  5. Examples of further human body fluid types, not in FMA:

  6. Development • Draw on FMA as our overarching anatomy framework . • Portion of body fluid defined: a portion of body substance that consists of a mixture of fluid, solutes and particles. • Other terms treated as children of FMA: Portion of body fluid. • Draw on other resources: SNOMED CT : Body fluid (substance), Origin of fluid (attribute), and Body fluid retention (disorder).

  7. BLO • Blood Ontology (BLO) • a controlled vocabulary designed for use in annotating and organizing data about blood, including data pertaining to: -blood transfusions (donation process control) -hematology (immunologic basis) -blood derivative products (frozen plasma) -content of regulatory documentation (regulations under FDA) -associated regulatory processes (tests of blood quality).

  8. SALO • Saliva Ontology (SALO) • a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics[PMID: 15623624, PMID: 17968930].

  9. KUPO • Kidney and Urinary Pathway Ontology (KUPO) • an ontology that describes kidney and urinary anatomy, the cells in the associated organs and tissue, and the gene products in those cells and their functional attributes and cellular components and associated pathologies.

  10. Method • Body fluids share common features: relations to biological process(GO), to proteins(PRO), to cell types(CT) • Given variety of different body fluid, common features must be specialized to each individual case. • In developing BFLO we accordingly employ a novel method :generalization and specialization.

  11. Method • BLO and SALO taken as an input, and corresponding terms aligned in light of common BFO category. • Aligned terms then joined to form a new ontology term as output: eg. portion of blood, portion of saliva → portion of body fluid. • MIREOT guidelines followed at every stage when terms imported into BFLO from other ontologies.

  12. Results and Discussion • BFLO fragment illustrating fundamental entities:

  13. Results and Discussion • BFLO help us focus on the relevant content of the reference ontologies and to conjoin the corresponding fragments together in a way that helps us address cross-domain issues. • Another potential uses of BFLO concern comparisons of the diagnostic value of different body substances where the results of tests employing one substance point to the need for tests using some other substance.

  14. Results and Discussion • For instance, similarities and differences in protein composition in plasma and saliva samples mapped[PMID: 19898684]. • Use information about known biomarkers in blood to make inferences to the presence of as yet unknown biomarkers in saliva. • Some proteins with different behaviors in special conditions -> proper functional annotation if ontology-based data to support prediction.

  15. Conclusion and Future Directions • Full understanding of body requires: data relating not merely to body fluids, but also in combination with other body fluids, and of course with other anatomical entities. • Close coordination with the OBO Foundry, consolidation of a common framework, and exploration of potential collaborations with KUPO, as well as expansion to other representative fluids, are the next steps.

  16. Conclusion and Future Directions • Demand for a resource that can accelerate the consistent representation, organization and manipulation of body fluid data. • BFLO has the opportunity to advance both basic and translational science (e.g. BFLO to aid integrated diagnostics by annotating blood, saliva, urine data).

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