Software Tools and Algorithms for Biological Systems

From Ontology Selection and Semantic Web to an Integrated Information System for Food-Borne Diseases and Food Safety

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Several factors have hindered effective use of information and resources related to food safety due to inconsistency among semantically heterogeneous data resources, lack of knowledge on profiling of food-borne pathogens, and knowledge gaps among research communities, government risk assessors/managers, and end users of the information. This paper discusses technical aspects in the establishment of a comprehensive food safety information system consisting of the following steps: a) computational collection and compiling publicly available information, including published pathogen genomic, proteomic, and metabolomic data; b) development of ontology libraries on food-borne pathogens and design automatic algorithms with formal inference and fuzzy and probabilistic reasoning to address the consistency and accuracy of distributed information resources (e.g., PulseNet, FoodNet, OutbreakNet, PubMed, NCBI, EMBL, and other online genetic databases and information); c) integration of collected pathogen profiling data, (, PMP, Combase, and other relevant information into a user-friendly, searchable, “homogeneous” information system available to scientists in academia, the food industry, and government agencies; and d) development of a computational model in semantic web for greater adaptability and robustness.

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