•  120
    CIDO: The Community-Based Coronavirus Infectious Disease Ontology
    with Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, Beverley John, Asiyah Yu Lin, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey, and Barry Smith
    Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS). 2021.
    Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have init…Read more
  •  112
    Ontologies for the study of neurological disease
    with Alexander P. Cox, Mark Jensen, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith, and Alexander D. Diehl
    In Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology, . 2012.
    We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level can…Read more
  •  80
    Ontological Support for Living Plan Specification, Execution and Evaluation
    with Erik Thomsen, Fred Read, Tatiana Malyuta, and Barry Smith
    In Erik Thomsen, Fred Read, William Duncan, Tatiana Malyuta & Barry Smith (eds.), Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR vol. 1304, . pp. 10-17. 2014.
    Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force …Read more
  •  184
    Improving the Quality and Utility of Electronic Health Record Data through Ontologies
    with Asiyah Yu Lin, Sivaram Arabandi, Thomas Beale, Hicks D., Hogan Amanda, R. William, Mark Jensen, Ross Koppel, Catalina Martínez-Costa, Øystein Nytrø, Jihad S. Obeid, Jose Parente de Oliveira, Alan Ruttenberg, Selja Seppälä, Barry Smith, Dagobert Soergel, Jie Zheng, and Stefan Schulz
    Standards 3 (3). 2023.
    The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvemen…Read more
  •  99
    The Neurological Disease Ontology
    with Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti, and Alexander D. Diehl
    Journal of Biomedical Semantics 4 (42): 42. 2013.
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by…Read more
  •  183
    OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies
    with Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D. Diehl, Damion Dooley, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert, Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, and Bjoern Peters
    BioaRxiv. 2021.
    Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of ov…Read more