Results for 'Danya Ruttenberg'

55 found
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  1.  51
    The Standing of Psychoanalysis.Howard S. Ruttenberg - 1984 - Noûs 18 (3):534-541.
  2.  54
    Old Challenges or New Issues? Genetic Health Professionals’ Experiences Obtaining Informed Consent in Diagnostic Genomic Sequencing.Danya F. Vears, Pascal Borry, Julian Savulescu & Julian J. Koplin - 2021 - AJOB Empirical Bioethics 12 (1):12-23.
    Background While integrating genomic sequencing into clinical care carries clear medical benefits, it also raises difficult ethical questions. Compared to traditional sequencing technologies, genomic sequencing and analysis is more likely to identify unsolicited findings (UF) and variants that cannot be classified as benign or disease-causing (variants of uncertain significance; VUS). UF and VUS pose new challenges for genetic health professionals (GHPs) who are obtaining informed consent for genomic sequencing from patients.Methods We conducted semi-structured interviews with 31 GHPs across Europe, Australia (...)
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  3. A practical checklist for return of results from genomic research in the European context.Danya F. Vears, Signe Mežinska, Nina Hallowell, Heidi Beate Hallowell, Bridget Ellul, Therese Haugdahl Nøst, , Berge Solberg, Angeliki Kerasidou, Shona M. Kerr, Michaela Th Mayrhofer, Elizabeth Ormondroyd, Birgitte Wirum Sand & Isabelle Budin-Ljøsne - 2023 - European Journal of Human Genetics 1:1-9.
    An increasing number of European research projects return, or plan to return, individual genomic research results (IRR) to participants. While data access is a data subject’s right under the General Data Protection Regulation (GDPR), and many legal and ethical guidelines allow or require participants to receive personal data generated in research, the practice of returning results is not straightforward and raises several practical and ethical issues. Existing guidelines focusing on return of IRR are mostly project-specific, only discuss which results to (...)
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  4. Self-Developing America.H. J. RUTTENBERG - 1960
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  5.  21
    The Greeks on Pleasure. J. C. B. Gosling, C. C. W. Taylor.Howard Ruttenberg - 1985 - Ethics 95 (4):963-964.
  6.  22
    Consent for rapid genomic sequencing for critically ill children: legal and ethical issues.Danya Vears, Zornitza Stark, Fiona Lynch & Christopher Gyngell - 2021 - Monash Bioethics Review 39 (Suppl 1):117-129.
    Although rapid genomic sequencing (RGS) is improving care for critically ill children with rare disease, it also raises important ethical questions that need to be explored as its use becomes more widespread. Two such questions relate to the degree of consent that should be required for RGS to proceed and whether it might ever be appropriate to override parents’ decisions not to allow RGS to be performed in their critically ill child. To explore these questions, we first examine the legal (...)
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  7.  52
    Plato's use of the analogy between justice and health.Howard S. Ruttenberg - 1986 - Journal of Value Inquiry 20 (2):145-156.
  8. Social enterprise.Danya Sterling - 2012 - Ethos: Social Education Victoria 20 (2):18.
     
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  9. Teaching and Learning: VELS/VCE - Enterprising Solutions to Homelessness - the Big Issue.Danya Sterling - 2010 - Ethos: Social Education Victoria 18 (4):35.
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  10. Guidelines for writing definitions in ontologies.Selja Seppälä, Alan Ruttenberg & Barry Smith - 2017 - Ciência da Informação 46 (1): 73-88.
    Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...)
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  11.  26
    On the Epistemic Status of Prenatal Ultrasound: Are Ultrasound Scans Photographic Pictures?Maddalena Favaretto, Danya F. Vears & Pascal Borry - 2020 - Journal of Medicine and Philosophy 45 (2):231-250.
    Medical imaging is predominantly a visual field. In this context, prenatal ultrasound images assume intense social, ethical, and psychological significance by virtue of the subject they represent: the fetus. This feature, along with the sophistication introduced by three-dimensional ultrasound imaging that allows improved visualization of the fetus, has contributed to the common impression that prenatal ultrasound scans are like photographs of the fetus. In this article we discuss the consistency of such a comparison. First, we investigate the epistemic role of (...)
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  12. The functions of definitions in ontologies.Selja Seppälä, Alan Ruttenberg, & Barry Smith - 2016 - In Roberta Ferrario & Werner Kuhn, Formal Ontology in Information Systems. Proceedings of the Ninth International Conference (FOIS 2016). Amsterdam: IOS Pres. pp. 37-50.
    To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.
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  13.  48
    Predictive Psychiatric Genetic Testing in Minors: An Exploration of the Non-Medical Benefits.Arianna Manzini & Danya F. Vears - 2018 - Journal of Bioethical Inquiry 15 (1):111-120.
    Predictive genetic testing for susceptibility to psychiatric conditions is likely to become part of standard practice. Because the onset of most psychiatric diseases is in late adolescence or early adulthood, testing minors could lead to early identification that may prevent or delay the development of these disorders. However, due to their complex aetiology, psychiatric genetic testing does not provide the immediate medical benefits that current guidelines require for testing minors. While several authors have argued non-medical benefits may play a crucial (...)
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  14.  15
    Review of Adolf Grünbaum: The Foundations of Psychoanalysis: A Philosophical Critique[REVIEW]Howard Ruttenberg - 1987 - Ethics 97 (2):491-492.
  15.  13
    Doctor–Parent Disagreement for Preterm Infants Born in the Grey Zone: Do Ethical Frameworks Help?Alice Cavolo, Danya F. Vears, Gunnar Naulaers, Bernadette Dierckx de Casterlé, Lynn Gillam & Chris Gastmans - 2024 - Journal of Bioethical Inquiry 21 (4):723-734.
    Objective: To examine i) how ethical frameworks can be used in concrete cases of parent–doctors’ disagreements for extremely preterm infants born in the grey zone to guide such difficult decision-making; and ii) what challenges stakeholders may encounter in using these frameworks. Design: We did a case analysis of a concrete case of parent–doctor disagreement in the grey zone using two ethical frameworks: the best interest standard and the zone of parental discretion. Results: Both ethical frameworks entailed similar advantages and challenges. (...)
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  16.  14
    Correction to: Predictive Psychiatric Genetic Testing in Minors: An Exploration of the Non-Medical Benefits.Arianna Manzini & Danya F. Vears - 2018 - Journal of Bioethical Inquiry 15 (1):121-121.
    The article [Title], written by [AuthorNames], was originally published electronically on the publisher’s internet portal on [date of OnlineFirst publication] without open access.
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  17.  70
    Overcoming the ontology enrichment bottleneck with Quick Term Templates.Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan R. Brinkman, Susanna Assunta Sansone & Richard Scheuermann - 2011 - Applied ontology 6 (1):13-22.
    When developing the Ontology of Biomedical Investigations (OBI), the process of adding classes with similar patterns of logical definition is time consuming, error prone, and requires an editor to...
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  18. Definitions in ontologies.Selja Seppälä, Alan Ruttenberg, Yonatan Schreiber & Barry Smith - 2016 - Cahiers de Lexicologie 109 (2):175‐207.
    Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.
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  19.  31
    Book Review:The Standing of Psychoanalysis. B. A. Farrell. [REVIEW]Howard S. Ruttenberg - 1984 - Ethics 94 (2):350-.
  20. An Axiomatisation of Basic Formal Ontology with Projection Functions.Kerry Trentelman, Alan Ruttenberg & Barry Smith - 2010 - In Kerry Taylor, Advances in Ontologies, Proceedings of the Sixth Australasian Ontology Workshop. University of Adelaide. pp. 71-80.
    This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.
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  21. BFO: Basic Formal Ontology.J. Neil Otte, John Beverley & Alan Ruttenberg - 2022 - Applied ontology 17 (1):17-43.
    Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...)
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  22. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration.Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Nigam Shah, Patricia L. Whetzel & Suzanna Lewis - 2007 - Nature Biotechnology 25 (11):1251-1255.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...)
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  23. Freedom and History and Other Essays: An Introduction to the Thought of Richard McKeon.Zahava K. Mckeon & Howard Ruttenberg - 1991 - Transactions of the Charles S. Peirce Society 27 (1):135-140.
    This volume of essays is an important introduction to the thought of one of the twentieth century's most significant yet underappreciated philosophers, Richard McKeon. The originator of philosophical pluralism, McKeon made extraordinary contributions to philosophy, to international relations, and to theory-formation in the communication arts, aesthetics, the organization of knowledge, and the practical sciences. This collection, which includes a philosophical autobiography as well as the out-of-print title essay "Freedom and History" and a previously unpublished essay on "Philosophic Semantics and Philosophic (...)
     
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  24. The Ontology for Biomedical Investigations.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, Mark Jensen, 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 & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    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, such as adding semantic expressivity to (...)
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  25.  23
    Book Review:Plato. R. M. Hare. [REVIEW]Howard Ruttenberg - 1984 - Ethics 94 (4):724-726.
  26. OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies.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, William Duncan, 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 & Bjoern Peters - 2021 - BioaRxiv.
    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 overarching principles. One challenge in reaching these goals was that the (...)
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  27.  95
    Ethical sharing of health data in online platforms- which values should be considered?Brígida Riso, Aaro Tupasela, Danya F. Vears, Heike Felzmann, Julian Cockbain, Michele Loi, Nana C. H. Kongsholm, Silvia Zullo & Vojin Rakic - 2017 - Life Sciences, Society and Policy 13 (1):1-27.
    Intensified and extensive data production and data storage are characteristics of contemporary western societies. Health data sharing is increasing with the growth of Information and Communication Technology platforms devoted to the collection of personal health and genomic data. However, the sensitive and personal nature of health data poses ethical challenges when data is disclosed and shared even if for scientific research purposes. With this in mind, the Science and Values Working Group of the COST Action CHIP ME ‘Citizen's Health through (...)
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  28.  38
    The Parliamentary Inquiry into Mitochondrial Donation Law Reform (Maeve’s Law) Bill 2021 in Australia: A Qualitative Analysis.Jemima W. Allen, Christopher Gyngell, Julian J. Koplin & Danya F. Vears - 2024 - Journal of Bioethical Inquiry 21 (1):67-80.
    Recently, Australia became the second jurisdiction worldwide to legalize the use of mitochondrial donation technology. The Mitochondrial Donation Law Reform (Maeve’s Law) Bill 2021 allows individuals with a family history of mitochondrial disease to access assisted reproductive techniques that prevent the inheritance of mitochondrial disease. Using inductive content analysis, we assessed submissions sent to the Senate Committee as part of a programme of scientific inquiry and public consultation that informed drafting of the Bill. These submissions discussed a range of bioethical (...)
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  29.  36
    Moving from ‘fully’ to ‘appropriately’ informed consent in genomics: The PROMICE framework.Julian J. Koplin, Christopher Gyngell, Julian Savulescu & Danya F. Vears - 2022 - Bioethics 36 (6):655-665.
    Genomic sequencing technologies (GS) pose novel challenges not seen in older genetic technologies, making traditional standards for fully informed consent difficult or impossible to meet. This is due to factors including the complexity of the test and the broad range of results it may identify. Meaningful informed consent is even more challenging to secure in contexts involving significant time constraints and emotional distress, such as when rapid genomic testing (RGS) is performed in neonatal intensive care units. In this article, we (...)
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  30.  37
    Participation of Children in Medical Decision-Making: Challenges and Potential Solutions.Vida Jeremic, Karine Sénécal, Pascal Borry, Davit Chokoshvili & Danya F. Vears - 2016 - Journal of Bioethical Inquiry 13 (4):525-534.
    Participation in healthcare decision-making is considered to be an important right of minors, and is highlighted in both international legislation and public policies. However, despite the legal recognition of children’s rights to participation, and also the benefits that children experience by their involvement, there is evidence that legislation is not always translated into healthcare practice. There are a number of factors that may impact on the ability of the child to be involved in decisions regarding their medical care. Some of (...)
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  31. The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...)
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  32.  37
    Why genomics researchers are sometimes morally required to hunt for secondary findings.Julian J. Koplin, Julian Savulescu & Danya F. Vears - 2020 - BMC Medical Ethics 21 (1):1-11.
    Genomic research can reveal ‘unsolicited’ or ‘incidental’ findings that are of potential health or reproductive significance to participants. It is widely thought that researchers have a moral obligation, grounded in the duty of easy rescue, to return certain kinds of unsolicited findings to research participants. It is less widely thought that researchers have a moral obligation to actively look for health-related findings. This paper examines whether there is a moral obligation, grounded in the duty of easy rescue, to actively hunt (...)
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  33. ARGO: Arguments Ontology.John Beverley, Neil Otte, Francesco Franda, Brian Donohue, Alan Ruttenberg, Jean-Baptiste Guillion & Yonatan Schreiber - manuscript
    Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different (...)
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  34. Ontologies for the study of neurological disease.Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl - 2012 - In Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl, Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology. Graz:
    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 candidate OBO Foundry ontology that (...)
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  35.  70
    MIREOT: The minimum information to reference an external ontology term.Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman & Alan Ruttenberg - 2011 - Applied ontology 6 (1):23-33.
    While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. Current editing tools present challenges for working with large ontologies an...
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  36. The Neurological Disease Ontology.Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti & Alexander D. Diehl - 2013 - Journal of Biomedical Semantics 4 (42):42.
    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 the Ontology for General Medical Science (OGMS) (...)
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  37. Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problem.Metin Gurcan, Tomaszewski N., Overton John, A. James, Scott Doyle, Alan Ruttenberg & Barry Smith - 2017 - Journal of Biomedical Informatics 66:129-135.
    Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...)
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  38. Ontology and the Future of Dental Research Informatics.Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick - 2010 - Journal of the American Dental Association 141 (10):1173-75.
    How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...)
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  39. Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology.Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl (eds.) - 2012 - Graz:
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  40.  22
    Storing paediatric genomic data for sequential interrogation across the lifespan.Christopher Gyngell, Fiona Lynch, Danya Vears, Hilary Bowman-Smart, Julian Savulescu & John Christodoulou - 2025 - Journal of Medical Ethics 51 (3):205-211.
    Genomic sequencing (GS) is increasingly used in paediatric medicine to aid in screening, research and treatment. Some health systems are trialling GS as a first-line test in newborn screening programmes. Questions about what to do with genomic data after it has been generated are becoming more pertinent. While other research has outlined the ethical reasons for storing deidentified genomic data to be used in research, the ethical case for storing data for future clinical use has not been explicated. In this (...)
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  41.  22
    Offering and Returning Secondary Findings in the Context of Exome Sequencing for Hearing Loss: Clinicians’ Views and Experiences.Lauren Notini, Clara Gaff, Julian Savulescu & Danya F. Vears - 2023 - AJOB Empirical Bioethics 14 (2):74-83.
    Background There is ongoing debate regarding whether and under which circumstances secondary findings (SF) should be offered in the pediatric context. Although studies have examined patient perspectives on receiving SF, little research has been conducted examining the experiences of clinicians offering SF to parents of newborns receiving genomic sequencing for a recently diagnosed medical condition.Methods To address this, we conducted qualitative interviews exploring the views and experiences of 12 clinicians who offered SF to parents of infants who had diagnostic exome (...)
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  42. Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...)
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  43.  33
    The social shaping of a diagnosis in Next Generation Sequencing.Janneke M. L. Kuiper, Pascal Borry, Danya F. Vears & Ine Van Hoyweghen - 2021 - New Genetics and Society 40 (4):425-448.
    Although Next Generation Sequencing (NGS) has increased our ability to test and diagnose, its results are often not clear-cut and require a complex interpretation and negotiation process by both healthcare professionals and patients involved. In this paper, we explore how diagnoses identified through NGS are socially shaped under influence of the broader social context. Using an analytical framework stemming from the sociology of health and illness and science and technology studies, with a focus on the construction of diagnosis and the (...)
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  44. More about ontology: Response.Barry Smith, Louis Goldberg, Michael Glick & Alan Ruttenberg - 2011 - Journal of the American Dental Association 142 (3):252-254.
    Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.
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  45.  36
    Pre- and post-testing counseling considerations for the provision of expanded carrier screening: exploration of European geneticists’ views.Sandra Janssens, Davit Chokoshvili, Danya F. Vears, Anne De Paepe & Pascal Borry - 2017 - BMC Medical Ethics 18 (1):46.
    BackgroundCarrier screening is generally performed with the aim of identifying healthy couples at risk of having a child affected with a monogenic disorder to provide them with reproductive options. Expanded carrier screening, which provides the opportunity for multiple conditions to be screened in one test, offers a more cost-effective and comprehensive option than screening for single disorders. However, implementation of ECS at a population level would have implications for genetic counseling practice.MethodsWe conducted semi-structured interviews with sixteen European clinical and molecular (...)
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  46. The ImmPort Antibody Ontology.William Duncan, Travis Allen, Jonathan Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg & Alexander D. Diehl - 2016 - Proceedings of the International Conference on Biological Ontology 1747.
    Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...)
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  47. The development of non-coding RNA ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...)
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  48. VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In Barry Smith, ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo: NCOR.
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...)
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  49. Improving the Quality and Utility of Electronic Health Record Data through Ontologies.Asiyah Yu Lin, Sivaram Arabandi, Thomas Beale, William Duncan, 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 & Stefan Schulz - 2023 - Standards 3 (3):316–340.
    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 improvement, and translational research. Analogous limitations to sharing objective data in (...)
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  50. A domain ontology for the non-coding RNA field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In Huang Jingshan, Eilbeck Karen, Blake Judith A., Dou Dejing, Natale Darren A., Ruttenberg Alan, Smith Barry, Zimmermann Michael T., Jiang Guoqian & Lin Yu, IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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