Populous: A Tool For Populating OWL Ontologies From Templates

We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity attribute.
Populated tables are mapped to patterns that can then be used to automatically generate the ontology's content. Populous's contribution is in the knowledge gathering stage of ontology development. It separates knowledge gathering from the conceptualisation and also separates the user from the standard ontology authoring environments. As a result, Populous can allow knowledge to be gathered in a straight-forward manner that can then be used to do mass production of ontology content

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL

MOTIVATION: Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in particular the Open Biomedical Ontologies (OBO) community, have provided many other ontologies and an increasingly large volume of annotations of gene products that can be exploited in query and analysis. As many annotations with different ontologies centre upon gene products, there is a possibility to explore gene products through multiple ontological perspectives at the same time. Questions could be asked that link a gene product’s function, process, cellular location, phenotype and disease. Current tools, such as AmiGO, allow exploration of genes based on their GO annotations, but not through multiple ontological perspectives. In addition, the semantics of these ontology’s representations should be able to, through automated reasoning, afford richer query opportunities of the gene product annotations than is currently possible. RESULTS: To do this multi-perspective, richer querying of gene product annotations, we have created the Logical Gene Ontology, or GOAL ontology, in OWL that combines the Gene Ontology, Human Disease Ontology and the Mammalian Phenotype Ontology, together with classes that represent the annotations with these ontologies for mouse gene products. Each mouse gene product is represented as a class, with the appropriate relationships to the GO aspects, phenotype and disease with which it has been annotated. We then use defined classes to query these protein classes through automated reasoning, and to build a complex hierarchy of gene products. We have presented this through a Web interface that allows arbitrary queries to be constructed and the results displayed. CONCLUSION: This standard use of OWL affords a rich interaction with Gene Ontology, Human Disease Ontology and Mammalian Phenotype Ontology annotations for the mouse, to give a fine partitioning of the gene products in the GOAL ontology. OWL in combination with automated reasoning can be effectively used to query across ontologies to ask biologically rich questions. We have demonstrated that automated reasoning can be used to deliver practical on-line querying support for the ontology annotations available for the mouse. AVAILABILITY: The GOAL Web page is to be found at http://owl.cs.manchester.ac.uk/goal

The impact of housing features relative location on a turbocharger compressor flow

This work presents an investigation on a flow phenomenon marked by in-plane velocity non-uniformity associated with a ported shroud turbocharger compressor observed upstream of the compressor inlet at lower operating speeds. The effect of structural struts in the ported shroud (PS) cavity and the location of the volute tongue on velocity non-uniformity is studied in this paper by numerically modelling the complete compressor stage using a (Un)steady Reynolds Averaged Navier-Stokes (RANS & URANS) approach. The results show that the amplitude of in-plane velocity non-uniformity is reduced by removing the struts from the PS cavity. Furthermore, the change in location of the volute tongue is shown to either substantially diminish or enhance the amplitude of velocity non-uniformity based on the relative position of the volute tongue and the struts. The study concludes that the velocity non-uniformity is dependent on the coupled effect of volute tongue and the strut position in the PS cavity

Fundamental modelling of friction during the hot rolling of steel.

Friction is one of the most significant physical phenomena influencing metal forming, yet in comparison with metallurgy, heat transfer and mechanics it remains the least understood. The goal of this project was to develop, on as fundamental a level as possible, a friction model based upon the physics of the process to be applied to the hot rolling of steel. A fundamental friction model was developed based upon the simplified approach to the adhesion theory by Straffelini (Wear, 249, 79-85, 2001), which is an extension of Bowden and Tabor's original adhesion theory. In this work, the simplified approach's dependence on the thermodynamic work of adhesion was exploited to apply it over a wide range of temperatures. The thermodynamic work of adhesion describes the work required to form a new surface and is a function of the surface energy of the contacting materials was estimated using two approaches: Rabinowicz's and the geometric mean rule. Since high temperature surface energy data is not generally available the relative change in Young's modulus with temperature was used to estimate a material's surface energy at a desired temperature. Reciprocating friction experiments, which provided a controlled environment in which to investigate friction, were conducted to verify the application of this theory to high temperature conditions and metal-oxide contacting materials. The fundamental model describing friction was applied to the hot rolling of steel via a friction algorithm using the commercial finite element (FE) code MARC. Simply described the friction algorithm calculated a friction coefficient using material properties, defined by the user, and contact temperatures, taken from the rolling model. This resulted in the friction coefficient predicted throughout the roll bite, compared to an average friction coefficient typically employed in rolling models. The combined friction algorithm-rolling model was validated against laboratory rolling experiments. One of the assumptions of the finite element rolling model is the presence of a thin, continuous and adherent scale layer. To achieve this in the laboratory a two pass rolling schedule was employed; the first pass to remove the furnace scale and the second pass to input the desired deformation. The success of the friction algorithm was determined by comparing the experimental torques and loads to the predictions of the finite element model. The FE model with the friction algorithm predicted the friction coefficient to vary in the roll gap between approximately 0.25 and 0.35 and was able to predict the measured rolling torque with an average error of 15%, which was considered acceptable and the accuracy was increased after the bearing torque was considered. The error in the load predictions compared to the measured loads was 13.5% on average, which was also acceptable

Populous: A tool for populating ontology templates

We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity attribute. Populated tables are mapped to patterns that can then be used to automatically generate the ontology's content. Populous's contribution is in the knowledge gathering stage of ontology development. It separates knowledge gathering from the conceptualisation and also separates the user from the standard ontology authoring environments. As a result, Populous can allow knowledge to be gathered in a straight-forward manner that can then be used to do mass production of ontology content.Comment: in Adrian Paschke, Albert Burger begin_of_the_skype_highlighting end_of_the_skype_highlighting, Andrea Splendiani, M. Scott Marshall, Paolo Romano: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10, 201

Developing a kidney and urinary pathway knowledge base

<p>Abstract</p> <p>Background</p> <p>Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration.</p> <p>Results</p> <p>We present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney.</p> <p>Conclusions</p> <p>The KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain’s ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself.</p> <p>Availability</p> <p>The KUPKB may be accessed via <url>http://www.e-lico.eu/kupkb</url>.</p

Corporate Governance and the Cost of Debt of Large European Firms

This paper examines the effects of different corporate governance mechanisms on the cost of debt for large European firms and documents a novel interaction effect between shareholder rights and disclosure. Improved disclosure leads to a lower credit spread only if shareholder rights are low. A possible explanation for this finding is the ‘share rights or disclose’ hypothesis. If shareholders have sufficient rights to monitor and influence management decisions, debt providers can rely upon shareholders to mitigate agency costs. Otherwise, bondholders require a premium to compensate for the information risk due to uncertainty about the true value of the firm

The potential for dietary factors to prevent or treat osteoarthritis

Osteoarthritis (OA) is a degenerative joint disease for which there are no disease-modifying drugs. It is a leading cause of disability in the UK. Increasing age and obesity are both major risk factors for OA and the health and economic burden of this disease will increase in the future. Focusing on compounds from the habitual diet that may prevent the onset or slow the progression of OA is a strategy that has been under-investigated to date. An approach that relies on dietary modification is clearly attractive in terms of risk/benefit and more likely to be implementable at the population level. However, before undertaking a full clinical trial to examine potential efficacy, detailed molecular studies are required in order to optimise the design. This review focuses on potential dietary factors that may reduce the risk or progression of OA, including micronutrients, fatty acids, flavonoids and other phytochemicals. It therefore ignores data coming from classical inflammatory arthritides and nutraceuticals such as glucosamine and chondroitin. In conclusion, diet offers a route by which the health of the joint can be protected and OA incidence or progression decreased. In a chronic disease, with risk factors increasing in the population and with no pharmaceutical cure, an understanding of this will be crucial

OLS Client and OLS Dialog: Open source tools to annotate public omics datasets

The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open‐source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog.publishedVersio