@conference {ICBO_2018_13, title = {ICBO_2018_13: The Identity and Mereology of Pathological Dispositions}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

Diseases, risks of pathological processes and predispositions have been formalized as dispositions. The relations between those pathological dispositions, however, remain unclear. We apply here a recently developed theory of mereology and identity among dispositions to analyze such relations. In particular, we show how a framework for the identity of disposition leads to a disease being not only a disposition to a disease course, but also to each pathological process; how it avoids risk multiplicativism; and how a predisposition can be identified with a risk whose estimated probability is higher than for the risk of a reference class. We discuss how this makes predisposition always relative to a reference class, to a time-frame and to sources of risk estimates; and we clarify the nature of risk factors.

}, keywords = {disease, disposition, identity, mereology, predisposition, risk, risk factor}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_13.pdf}, author = {Adrien Barton and Olivier Grenier and Jean-Francois Ethier} } @conference {ICBO_2018_28, title = {ICBO_2018_28: KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

Human kidney has its complex structure and diverse interactions among its cells during homeostasis and in its diseased states. To systematically classify, represent, and integrate kidney gene activity, cell types, cell states, and interstitial components, we developed a Kidney Tissue Atlas Ontology (KTAO). KTAO reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology. KTAO also generates new semantic axioms to logically link terms of entities in different domains. As a first study, KTAO represents over 200 known kidney gene markers and their profiles in different cell types in kidney patients. Such a representation supports kidney knowledge base generation, query, and data integration.

}, keywords = {AKI, atlas, CKD, disease, gene marker, Kidney, KTAO, Ontology}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_28.pdf }, author = {Yongqun He and Becky Steck and Edison Ong and Laura Mariani and Chrysta Lienczewski and Ulysses Balis and Matthias Kretzler and Jonathan Himmelfarb and John F. Bertram and Evren Azeloglu and Ravi Iyengar and Deborah Hoshizaki and Sean D. Mooney} } @conference {ICBO_2018_41, title = {ICBO_2018_41: Formalizing the Representation of Immune Exposures for Human Immunology Studies}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

Human immunology studies typically examine how immune exposures associated with vaccinations, infectious, allergic or autoimmune diseases, or transplantations perturb the immune system with the goal to develop diagnostic tools and therapeutic interventions. While there are established approaches to formally represent the experimental data generated in such studies, which often comprises gene expression data, flow cytometry data, or serology data, the description of the immune exposures themselves is not well standardized. We here present a formal approach to represent immune exposures at a high level of granularity. We capture the exposure process (e.g. {\textquoteleft}vaccination{\textquoteright} or {\textquoteleft}occurrence of allergic disease{\textquoteright}), exposure material (e.g. {\textquoteleft}Tdap vaccine{\textquoteright} or {\textquoteleft}House dust mite{\textquoteright}), and the associated disease name and stage (e.g. {\textquoteleft}allergic rhinitis{\textquoteright} and {\textquoteleft}chronic{\textquoteright}). This representation scheme has been used successfully in the IEDB and an extended version has been adopted by HIPC to capture studies in ImmPort. We are reporting here on this scheme, our ongoing attempts to map the terms used to existing ontologies, and the challenges encountered.

}, keywords = {disease, Exposure, Immunology, Standardization}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_41.pdf }, author = {Randi Vita and Bjoern Peters and James Overton and Kei-Hoi Cheung and Steven Kleinstein} }