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 (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Over the past decade or so, a new interdisciplinary field has emerged in the ground between, on the one hand, computer science – and artificial intelligence in particular – and, on the other, the area of philosophy concentrating on the language and structure of argument. There are now hundreds of researchers worldwide who would consider themselves a part of this nascent community. Various terms have been proposed for the area, including "Computational Dialectics," "Argumentation Technology," and "Argument-based Computing," but the term (...) that has stuck is simply Argument & Computation. It encompasses several specific strands of research, such as: . the use of theories of argument, and dialectic in particular, in the design and implementation of protocols for multi-agent action and communication; . the application of theories of argument and rhetoric in natural language processing and affective computing; . the use of argument-based structures for autonomous reasoning in artificial intelligence, and in particular, for defeasible reasoning; . computer-supported collaborative argumentation – the implementation of software tools for enabling online argument in domains such as education and e-government. These strands come together to form the core of a research field that covers parts of artificial intelligence (AI), philosophy, linguistics, and cognitive science, but, increasingly, is building an identity of its own. (shrink)