Using Provenance for Quality Assessment and Repair in Linked Open Data

As the number of data sources publishing their data on the Web of Data is growing, we are experiencing an immense growth of the Linked Open Data cloud. The lack of control on the published sources, which could be untrustworthy or unreliable, along with their dynamic nature that often invalidates links and causes conflicts or other discrepancies, could lead to poor quality data. In order to judge data quality, a number of quality indicators have been proposed, coupled with quality metrics that quantify the “quality level” of a dataset. In addition to the above, some approaches address how to improve the quality of the datasets through a repair process that focuses on how to correct invalidities caused by constraint violations by either removing or adding triples. In this paper we argue that provenance is a critical factor that should be taken into account during repairs to ensure that the most reliable data is kept. Based on this idea, we propose quality metrics that take into account provenance and evaluate their applicability as repair guidelines in a particular data fusion setting

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

Remanufacturing and product design: designing for the 7th generation

The following is taken directly from the research report. This report investigates Design for Remanufacture in terms of both detailed product design and the business context in which Design for Remanufacture may operate. Key Study Objectives • To understand the link between design and remanufacture • To understand how Design for Remanufacture can lead to increased innovation and Sustainable Development (SD) • To identify proactive strategies to further Design for Remanufactur

Compatibility of Breeding Techniques in Organic Systems

Introduction The rapid development of genetic engineering techniques is leading to a level of genetic disruption never experienced before. In order to safeguard organic integrity and to ensure organic food will continue to meet the highest consumer expectations in this challenging situation, IFOAM - Organics International is proposing a number of measures to be put in place to further fortify and enhance the organic sector’s available genetic resources. This position paper provides clarity and transparency on the criteria used by the organic sector as to what breeding techniques are compatible with organic systems, which techniques to exclude, and definitions on what should be considered as genetic engineering and genetically modified organisms (GMOs). We further differentiate between the criteria relevant for organic breeding as defined in the IFOAM – Organics International norms, versus the criteria for cultivars and breeds derived from nonorganic breeding programs regarding their compatibility for the use in commercial organic production and processing. The following experts are members of the IFOAM Working Group on New Plant Breeding Techniques: Michael Glos, Monika Messmer, Gebhard Rossmanith, Gunter Backes, Michael Sligh, Adrian Rodriguez-Burruezo, Heli Matilainen, Andre Leu, Louise Luttikholt, Helen Jensen, Eric Gall, Chito Medina, Krishna Prasad, Kirsten Arp

A qualitative exploration of the effect of visual field loss on daily life in home-dwelling stroke survivors

Objective: To explore the effect of visual field loss on the daily life of community-dwelling stroke survivors. Design: A qualitative interview study. Participants: Adult stroke survivors with visual field loss of at least six months’ duration. Methods: Semi-structured interviews were conducted with a non-purposive sample of 12 stroke survivors in their own homes. These were recorded, transcribed verbatim and analyzed with the framework method, using an inductive approach. Results: Two key analytical themes emerged. ‘Perception, experience and knowledge’ describes participant’s conflicted experience of having knowledge of their impaired vision but lacking perception of that visual field loss and operating under the assumption that they were viewing an intact visual scene when engaged in activities. Inability to recognize and deal with visual difficulties, and experiencing the consequences, contributed to their fear and loss of self-confidence. ‘Avoidance and adaptation’ were two typologies of participant response to visual field loss. Initially, all participants consciously avoided activities. Some later adapted to vision loss using self-directed head and eye scanning techniques. Conclusions: Visual field loss has a marked impact on stroke survivors. Stroke survivors lack perception of their visual loss in everyday life, resulting in fear and loss of confidence. Activity avoidance is a common response, but in some, it is replaced by self-initiated adaptive techniques

Engineering Agile Big-Data Systems

To be effective, data-intensive systems require extensive ongoing customisation to reflect changing user requirements, organisational policies, and the structure and interpretation of the data they hold. Manual customisation is expensive, time-consuming, and error-prone. In large complex systems, the value of the data can be such that exhaustive testing is necessary before any new feature can be added to the existing design. In most cases, the precise details of requirements, policies and data will change during the lifetime of the system, forcing a choice between expensive modification and continued operation with an inefficient design.Engineering Agile Big-Data Systems outlines an approach to dealing with these problems in software and data engineering, describing a methodology for aligning these processes throughout product lifecycles. It discusses tools which can be used to achieve these goals, and, in a number of case studies, shows how the tools and methodology have been used to improve a variety of academic and business systems

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

abstract: Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.The article is published at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.011824

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.Comment: 30 pages, 16 figure