Representing and coding the knowledge embedded in texts of Health Science Web published articles

Despite the fact that electronic publishing is a common activity to scholars electronic journals are still based in the print model and do not take full advantage of the facilities offered by the Semantic Web environment. This is a report of the results of a research project with the aim of investigating the possibilities of electronic publishing journal articles both as text for human reading and in machine readable format recording the new knowledge contained in the article. This knowledge is identified with the scientific methodology elements such as problem, methodology, hypothesis, results, and conclusions. A model integrating all those elements is proposed which makes explicit and records the knowledge embedded in the text of scientific articles as an ontology. Knowledge thus represented enables its processing by intelligent software agents The proposed model aims to take advantage of these facilities enabling semantic retrieval and validation of the knowledge contained in articles. To validate and enhance the model a set of electronic journal articles were analyzed

Extending the design process into the knowledge of the world

Research initiatives throughout history have shown how a designer typically makes associations and references to a vast amount of knowledge based on experiences to make decisions. With the increasing usage of information systems in our everyday lives, one might imagine an information system that provides designers access to the ‘architectural memories’ of other architectural designers during the design process, in addition to their own physical architectural memory. In this paper, we discuss how the increased adoption of semantic web technologies might advance this idea. We briefly discuss how such a semantic web of building information can be set up, and how this can be linked to a wealth of information freely available in the Linked Open Data (LOD) cloud

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

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

Information system support in construction industry with semantic web technologies and/or autonomous reasoning agents

Information technology support is hard to find for the early design phases of the architectural design process. Many of the existing issues in such design decision support tools appear to be caused by a mismatch between the ways in which designers think and the ways in which information systems aim to give support. We therefore started an investigation of existing theories of design thinking, compared to the way in which design decision support systems provide information to the designer. We identify two main strategies towards information system support in the early design phase: (1) applications for making design try-outs, and (2) applications as autonomous reasoning agents. We outline preview implementations for both approaches and indicate to what extent these strategies can be used to improve information system support for the architectural designer

Scientific Knowledge Object Patterns

Web technology is revolutionizing the way diverse scientific knowledge is produced and disseminated. In the past few years, a handful of discourse representation models have been proposed for the externalization of the rhetoric and argumentation captured within scientific publications. However, there hasn’t been a unified interoperable pattern that is commonly used in practice by publishers and individual users yet. In this paper, we introduce the Scientific Knowledge Object Patterns (SKO Patterns) towards a general scientific discourse representation model, especially for managing knowledge in emerging social web and semantic web. © ACM, 2011. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version is going to be published in "Proceedings of 15th European Conference on Pattern Languages of Programs", (2011) http://portal.acm.org/event.cfm?id=RE197&CFID=8795862&CFTOKEN=1476113

Using Noninvasive Brain Measurement to Explore the Psychological Effects of Computer Malfunctions on Users during Human-Computer Interactions

In today’s technologically driven world, there is a need to better understand the ways that common computer malfunctions affect computer users. These malfunctions may have measurable influences on computer user’s cognitive, emotional, and behavioral responses. An experiment was conducted where participants conducted a series of web search tasks while wearing functional nearinfrared spectroscopy (fNIRS) and galvanic skin response sensors. Two computer malfunctions were introduced during the sessions which had the potential to influence correlates of user trust and suspicion. Surveys were given after each session to measure user’s perceived emotional state, cognitive load, and perceived trust. Results suggest that fNIRS can be used to measure the different cognitive and emotional responses associated with computer malfunctions. These cognitive and emotional changes were correlated with users’ self-report levels of suspicion and trust, and they in turn suggest future work that further explores the capability of fNIRS for the measurement of user experience during human-computer interactions

Increasing information feed in the process of structural steel design

Research initiatives throughout history have shown how a designer typically makes associations and references to a vast amount of knowledge based on experiences to make decisions. With the increasing usage of information systems in our everyday lives, one might imagine an information system that provides designers access to the ‘architectural memories’ of other architectural designers during the design process, in addition to their own physical architectural memory. In this paper, we discuss how the increased adoption of semantic web technologies might advance this idea. We investigate to what extent information can be described with these technologies in the context of structural steel design. This investigation indicates significant possibilities regarding information reuse in the process of structural steel design and, by extent, in other design contexts as well. However, important obstacles and question remarks can still be outlined as well

Analysis reuse exploiting taxonomical information and belief assignment in industrial problem solving

To take into account the experience feedback on solving complex problems in business is deemed as a way to improve the quality of products and processes. Only a few academic works, however, are concerned with the representation and the instrumentation of experience feedback systems. We propose, in this paper, a model of experiences and mechanisms to use these experiences. More specifically, we wish to encourage the reuse of already performed expert analysis to propose a priori analysis in the solving of a new problem. The proposal is based on a representation in the context of the experience of using a conceptual marker and an explicit representation of the analysis incorporating expert opinions and the fusion of these opinions. The experience feedback models and inference mechanisms are integrated in a commercial support tool for problem solving methodologies. The results obtained to this point have already led to the definition of the role of ‘‘Rex Manager’’ with principles of sustainable management for continuous improvement of industrial processes in companies