Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

© 2013 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes

Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

Non Adiabatic Centrifugal Compressor Gas Dynamic Performance Definition

Most centrifugal compressors operate in conditions with negligible heat transfer (adiabatic compression). Their plant tests conditions are similar or close to adiabatic conditions. Test regulations establish measures to diminish influence of a heat transfer “compressor body – atmospheric air” to an exit temperature. Therefore a temperature rise in a compressor is used to calculate a work input coefficient and efficiency. Unlike it high pressure centrifugal compressors of gas turbines and superchargers operate in conditions with very active heat transfer with ambience, lubricant and hot turbine parts. Non adiabatic compression process evidently influence on temperatures inside a flow path, gas density, velocity triangles. But this aspect of a problem is out of the discussed problem. This problem is how to define gas dynamic performance of a compressor. The author has at his disposal hot test data of a small turbocharger compressor with the impeller diameter 48mm. Data were provided by the colleague Prof. J. Seume (Institute of Turbo machines, Hanover University, Germany): mass flow rate, total pressures and four total temperatures: directly at compressor borders and on a distance of them. The difference of values demonstrates strong heat transfer in inlet and exit pipes. The detailed study in the Institute of Turbo machines, Hanover University has shown that compression process is sufficiently non adiabatic. Unrealistic influence of rotation speed on efficiency points on it indirectly. The author applied the Universal modeling method of Prof. Y. Galerkin to reduce test data firstly. The 5-th generation computer programs were developed recently and successfully applied to model gas dynamic performances of subsonic compressors. The German colleagues made a supposition that measured temperature difference is very close to an adiabatic process at design RPM 202000. This performance was modeled with the standard complex of empirical coefficients. The roughness of cast surfaces was taken into account. Test data of TU SPb show that work input coefficient is linear function of a flow coefficient at an impeller exit independent of Mach number in subsonic area. The linear supposition was applied for transonic and supersonic flows as well. This procedure was applied with 6-th generation of computer programs. The 6-th generation program takes into account shocks and calculates losses in 3-D impellers in quasi-3-D mode. In result the modeling of performances in range of RPM 104000-202000 is more satisfactory. The set of empirical coefficients for calculation of head losses and work input coefficient can be applied for test data reducing of other small turbocharger compressor performances

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

Copyright @ 2014 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), 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.Over the 16 years, the Bio-Ontologies SIG at ISMB has provided a forum for vibrant discussions of the latest and most innovative advances in the research area of bio-ontologies, its applications to biomedicine and more generally in the organisation, sharing and re-use of knowledge in biomedicine and the life sciences. The six papers selected for this supplement span a wide range of topics including: ontology-based data integration, ontology-based annotation of scientific literature, ontology and data model development, representation of scientific results and gene candidate prediction

Broadening the Scope of Nanopublications

In this paper, we present an approach for extending the existing concept of nanopublications --- tiny entities of scientific results in RDF representation --- to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications.Comment: To appear in the Proceedings of the 10th Extended Semantic Web Conference (ESWC 2013

Evaluation of the perspective need in staffing of the Donetsk region economy

Досліджено тенденції перспективного розвитку промисловості Донецького регіону в контексті кадрового забезпечення економіки області. На основі прогнозованих даних розвитку виробництва, наведених у Стратегії розвитку Донецької області, та розрахунків, що ґрунтуються на динаміці зміни показників середньооблікової чисельності промислово-виробничого персоналу, обсягів виробленої продукції та продуктивності праці в основних галузях промисловості за десятиріччя, розраховано додаткову потребу в промислово-виробничому персоналі в Донецькому регіоні в 2017 р. Розкрито проблему дисбалансу ринку праці. Доказано необхідність створення комплексного підходу до проблеми регулювання ринку праці, що повинен охоплювати створення системи моніторингу, прогнозування показників розвитку, а також побудову на даній основі відповідної системи освіти і підготовки кадрів.The trends of perspective development of the Donetsk region industry in the context of need in staffing of the regional economy are researched in the article. For providing more complete information that will help to forecast the labor market development the research of demand and supply should be conducted taking into account the factors which significantly affect the dynamics of mentioned indices. So it is necessary to develop a well developed technique of the labor force demand and supply identification. Calculation and determination of the perspective need in staffing by professional qualifications should become an economic foundation of professional orientation of population and its professional education, distribution and use of labor. The key principle of the planning and forecasting system of sizes and structure of the personnel training should be a firm’s focus on the quantity of specialists trained and companies demanding such specialists. The additional need in the industrial personnel in the Donetsk region for 2017 was calculated on the basis of industry development forecasts according to the data declared in the Strategy of Development of the Donetsk region and on the basis of the dynamics of average number of industrial personnel, quantity of output and labor productivity in key industries during the past decade. The problem of the labor market imbalance was disclosed. The necessity of a system approach to the problem of the labor market regulation, a monitoring system creation, forecasting the growth rates, establishment of an appropriate education system and personnel training was proven. The conclusions about the necessity of investments into industry aimed at the technical re-equipment of production and replacement of manual labor and about the necessity of modernization of education system concerning the personnel training for the regional economy needs for covering the detected shortage of personnel are drawn