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Developing General Models and Theories of Addiction
Published in Hanna Pickard, Serge H. Ahmed, The Routledge Handbook of Philosophy and Science of Addiction, 2019
Robert West, Simon Christmas, Janna Hastings, Susan Michie
What might this look like in practice? One approach to creating a general theory of addiction would be to establish an ontology of addiction with the option for those contributing to the ontology to create their own sub-ontologies with specified namespaces. Thus one might start with a medically based ontology elaborating the Mental Functioning and Mental Disease ontologies within one namespace and build others with other namespaces, adopting the principles of the OBO Foundry to maintain discipline and efficient working within the enterprise. This ontology would define entities relevant to addiction and their relationships, relate these to entities in other fields of study in multiple disciplines, and link these with empirical findings and measures.
Machine intelligence for radiation science: summary of the Radiation Research Society 67th annual meeting symposium
Published in International Journal of Radiation Biology, 2023
Lydia J. Wilson, Frederico C. Kiffer, Daniel C. Berrios, Abigail Bryce-Atkinson, Sylvain V. Costes, Olivier Gevaert, Bruno F. E. Matarèse, Jack Miller, Pritam Mukherjee, Kristen Peach, Paul N. Schofield, Luke T. Slater, Britta Langen
The ontology was developed with open-source software (the Ontology Development Kit, Protégé and WebProtégé) as recommended by the Open Biological and Biomedical (OBO) Foundry (Jackson et al. 2021), which also requires that OBO ontologies implement a set of development principles and practices for ontology consistency, uniformity, and accountability. The content coverage for the RBO was largely driven by two diverse use cases; the need to annotate data deposited in the STORE database (https://www.storedb.org/) for the European Commission–funded RadoNorm project (https://www.radonorm.eu/), which has a very broad frame of reference including both medical and environmental radiation exposure, and NASA’s GeneLab ‘omics database (https://genelab.nasa.gov), which contains data from experiments and measurements conducted in space and terrestrial space-like environments (Berrios et al. 2021). We have previously used versions of the mouse pathology (MPATH (Schofield et al. 2013)) and adult mouse anatomy (MA; (Hayamizu et al. 2015)) ontologies for annotations of the legacy datasets in the European Radiobiological Archive (ERA) containing legacy data from the JANUS and other US, European and Japanese programs (Birschwilks et al. 2011). This initial phase of concept modeling has yielded an RBO that defines more than 300 concepts, with another >3500 concepts imported from other OBO Foundry ontologies to provide critical, meaningful context.
Ontology: A Bridge between Bioethics and Data-Driven Inquiry
Published in The American Journal of Bioethics, 2021
Eric C. Merrell, Peter Maloy Koch, David Gordon Limbaugh
The first benefit that realist ontology offers design bioethics is the establishment of explicit semantic standards for data collection, which help ensure clarity and consistency in the use, organization, and sharing of information. The standards offered by realist ontologies help to ensure that data is organized in a way that maximizes discoverability, scalability, and interoperability. In recent years, the positive impact of realist ontologies has become widely recognized in a variety of disciplines. For example, the Open Biomedical Ontologies (OBO) Foundry ontologies have been successful in providing semantic standards for central, multi-disciplinary terms such as gene, cell, cell process, disease, and function, which are classes named and defined based on the best scientific evidence available (Kamdar, Tania, and Musen 2017; Smith et al. 2007). A key to the success of the OBO Foundry ontologies is an agreed upon set of ontological standards, a set of principles; adhering to these principles has allowed OBO ontologies to assert these terms but then also be curated by a community and to change as the science changes, in a consistent and uniform way.