EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

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Automation Of Making Innovative Decisions In Development Of City Infrastructure

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The main recipe component of most types of flour confectionery is wheat flour, the technological properties of which largely effect not only the quality indicators of the finished product, but also the stability of the technological flow of its production. However, today, in Russia there are no specialized requirements for the quality of wheat flour for confectionery, in contrast to the requirements for the baking wheat flour. The article lists the main problems and features of the quality of Russian wheat flour consisting in the absence of target classifications of grain and a decrease in its qualitative potential, in particular, a decrease in the amount of gluten and improvement of its quality. As part of the work, the influence of the technological properties of wheat flour on the rheological parameters of the dough and the quality of sugar cookies, which are traditionally in high demand of population groups of every age, was studied, while the share of domestic products is more than 85%. The work was performed in the laboratory of flour confectionery products of All-Russian Scientific Research Institute of Confectionery Industry. The determination of organoleptic, physical and chemical, structural and mechanical indicators of raw materials, semi-finished products and finished products was carried out by standard methods.The main recipe component of most types of flour confectionery is wheat flour, the technological properties of which largely effect not only the quality indicators of the finished product, but also the stability of the technological flow of its production. However, today, in Russia there are no specialized requirements for the quality of wheat flour for confectionery, in contrast to the requirements for the baking wheat flour. The article lists the main problems and features of the quality of Russian wheat flour consisting in the absence of target classifications of grain and a decrease in its qualitative potential, in particular, a decrease in the amount of gluten and improvement of its quality. As part of the work, the influence of the technological properties of wheat flour on the rheological parameters of the dough and the quality of sugar cookies, which are traditionally in high demand of population groups of every age, was studied, while the share of domestic products is more than 85%. The work was performed in the laboratory of flour confectionery products of All-Russian Scientific Research Institute of Confectionery Industry. The determination of organoleptic, physical and chemical, structural and mechanical indicators of raw materials, semi-finished products and finished products was carried out by standard methods

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