•  613
    Representing Mental Functioning: Ontologies for Mental Health and Disease
    with Janna Hastings, Werner Ceusters, Kevin Mulligan, and Barry Smith
    In Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop), Ceur. 2012.
    Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based…Read more
  •  599
    The Ontology for Biomedical Investigations
    with Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, and Jie Zheng
    PLoS ONE 11 (4). 2016.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, …Read more
  •  545
    The Neurological Disease Ontology
    with Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, 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
  •  286
    Towards an Ontology of Mental Functioning (ICBO Workshop)
    with Janna Hastings, Werner Ceusters, Kevin Mulligan, and Barry Smith
    In Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Proceeedings of the Third International Conference on Biomedical Ontology, . 2012.
  •  222
    Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych
    with Joanna Hastings, Gwen A. Frishkoff, Barry Smith, Russell A. Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner, and Maryann E. Martone
    Avant: Trends in Interdisciplinary Studies 7 (3): 101-117. 2016.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for…Read more
  •  214
    The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and …Read more
  •  209
    Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych
    with Janna Hastings, Gwen Frishkoff, Barry Smith, Russell Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica Turner, Maryann Martone, and Przemysław Nowakowski
    Avant: Trends in Interdisciplinary Studies 7 (3): 101-117. 2016.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for…Read more
  •  190
    A number of researchers have begun to demonstrate that the widely discussed ?Knobe effect? (wherein participants are more likely to think that actions with bad side-effects are brought about intentionally than actions with good or neutral side-effects) can be found in theory of mind judgments that do not involve the concept of intentional action. In this article we report experimental results that show that attributions of knowledge can be influenced by the kinds of (non-epistemic) concerns that…Read more
  •  142
    Improving the Quality and Utility of Electronic Health Record Data through Ontologies
    with Asiyah Yu Lin, Sivaram Arabandi, Thomas Beale, William Duncan, Hicks D., Hogan Amanda, R. William, 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
  •  8
    Call for Papers: Building as Service
    with Carolyn Fahey and Tom Spector
    Architecture Philosophy 2 (2). 2017.