@conference {ICBO_2018_24, title = {ICBO_2018_24: eXtensible ontology development (XOD) using web-based Ontoanimal tools}, 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 = {

The eXtensible ontology development (XOD) strategy proposes four principles to support interoperable and robust ontology development. These principles include ontology term reuse, semantic alignment, design pattern usage, and community extensibility. In this software demo, we show how Ontoanimal tools (e.g., Ontofox, Ontodog, Ontorat, and Ontokiwi) can be used to support the implementation of these XOD principles. The development of the Cell Line Ontology (CLO) is used for the demonstration.

}, keywords = {Cell Line Ontology, CLO, eXtensible ontology development, Ontodog, Ontofox, Ontokiwi, Ontorat, XOD}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_24.pdf }, author = {Edison Ong and Yongqun He and Jie Zheng} } @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_59, title = {ICBO_2018_59: Coordinated Evolution of Ontologies of Informed Consent}, 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 = {

Our project brings together a number of OBO Foundry ontologies related to the representation of informed consent, and expands and enriches them, so that they may provide a representation of informed consent across the informed consent (IC) life cycle. The IC lifecycle involves not only documentation of the consent when originally obtained, but actions that require clear communication of permissions from the initial acquisition of data and specimens through handoffs to, for example, secondary researchers, allowing them access to data or biospecimens referenced in the terms of the original consent. This poster details the progress we have made in representing the domain of consent, as well as the future applications that such work can make possible.

}, keywords = {informed consent, informed consent life cycle, ontology collaboration, reference ontology}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_59.pdf }, author = {J. Neil Otte and Cooper Stansbury and Jonathan Vajda and Frank Manion and Elizabeth Umberfield and Yongqun He and Marcelline Harris and Jihad Obeid and Mathias Brochhausen and William Duncan and Cui Tao} }