NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies. It also can be customized to fit the needs of different scenarios. Ontology Recommender 2.0 combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available.Comment: 29 pages, 8 figures, 11 table

Adaptive System for Collaborative Online Laboratories

International audienceIn the last decade, researchers in the Online Engineering field have attempted to provide hands-on, web-based approaches for Distance Learning. The primary goal of this research is to produce online laboratories that serve as the educational substitute for in situ laboratories. A limitation of existing online laboratories, however, is that they generally only allow a single user to be connected at a time. Since group learning activities, such as peer assistance, peer emulation, and collaborative experimental setup, are core dimensions of the traditional laboratory experience, this shortcoming is a significant pedagogical bottleneck. Recent research has focused on creating Collaborative Online Laboratories (COL) which attempt to address this shortcoming by focusing on the group awareness aspect of the laboratory learning experience. This paper discusses how group awareness can serve as a key component in replicating the collaborative aspect of learning in local laboratories. We discuss strategies for describing group awareness and how these strategies are associated both with a tutor's pedagogical objectives and in the management of the group of collaborating students. We describe an experimental system that we have developed that uses Semantic Web technologies to define a knowledge-driven system that allows researchers to describe and execute a variety of collaborative strategies for online laboratories

Alcohol consumption among university students: a typology of consumption to aid the tailoring of effective public health policy

Objective: Elevated levels of alcohol consumption among university students are well documented. Policymakers have attempted to combat this issue at a university, national and international level. Tailoring public health policy to effectively tackle alcohol use is crucial. Using Q-methodology, the current study aims to develop a typology of alcohol consumption in the Irish university student population. Setting: A large Irish university. Participants Hundreds of possible statements on types of consumption were generated from a systematic review and a set of one-on-one interviews. These were reduced to 36 statements, 6 statements which define each of the 6 previously defined consumption types. Participants were advised to scan through the 36 statements and fill the statements into a ‘forced choice, standardised distribution’. Following this, a 45–90 min interview was conducted with students to illuminate subjectivity surrounding alcohol consumption. Analysis was conducted using PQ Method and NVivo software. Principal component analysis, followed by varimax rotation, was conducted to uncover the final factor information. Results: In total, 43 students completed the Q-study: 19 men and 24 women. A typology describing 4 distinct groupings of alcohol consumer was uncovered: the guarded drinker, the calculated hedonist, the peer-influenced drinker and the inevitable binger. Factor loadings of each of the consumer groupings were noted for type description. Conclusions: This is the first study to propose ideal types of alcohol consumption among a university student population. Further research is required to investigate the degree to which each of these ideal types is subscribed. However, this typology, in addition to informing public policy and strategies, will be a valuable analytic tool in future research

Mitigation of large-scale organic waste damage incorporating a demonstration of a closed loop conversion of poultry waste to energy at the point of source (2000-LS-1-M2) Final Report

peer-reviewedThe increase in the world population and urbanisation, have changed the way the world produces food. As the demand for cheap and readily available food in the developed world increases, high-density, intensive farming practices have replaced subsistence farming to allow for the mass production of food. An unavoidable consequence of these farming\ud practices is the generation of significant quantities of organic waste

Probing the fuzzy sphere regularisation in simulations of the 3d \lambda \phi^4 model

We regularise the 3d \lambda \phi^4 model by discretising the Euclidean time and representing the spatial part on a fuzzy sphere. The latter involves a truncated expansion of the field in spherical harmonics. This yields a numerically tractable formulation, which constitutes an unconventional alternative to the lattice. In contrast to the 2d version, the radius R plays an independent r\^{o}le. We explore the phase diagram in terms of R and the cutoff, as well as the parameters m^2 and \lambda. Thus we identify the phases of disorder, uniform order and non-uniform order. We compare the result to the phase diagrams of the 3d model on a non-commutative torus, and of the 2d model on a fuzzy sphere. Our data at strong coupling reproduce accurately the behaviour of a matrix chain, which corresponds to the c=1-model in string theory. This observation enables a conjecture about the thermodynamic limit.Comment: 31 pages, 15 figure

Exploring women's sensory experiences of undergoing colposcopy and related procedures: implications for preparatory sensory information provision

INTRODUCTION: Some women experience distress during colposcopy examinations which is partly related to women's fear, or experience, of pain during the procedure. However, little is known about women's sensory experiences of colposcopy (other than pain) or what might impact on these experiences. The aim of this study was to explore women's sensory experiences of colposcopy and related procedures and identify factors which influenced negative sensory experiences. METHODS: In-depth interviews were conducted with 23 women who had undergone, for the first time, a colposcopy (some with related procedures, including punch biopsies and loop excision) as part of follow-up for abnormal cervical cytology. Interviews were analysed thematically using the Framework Approach to organise the data and identify emerging higher-order themes. RESULTS: Women described a range of sensory experiences including pain or discomfort, cramping, stinging and cold sensations (due to the application of acetic acid to the cervix). Four key themes emerged as important aspects of the overall sensory experience: levels of pain, treatment-specific sensations, anaesthetic-specific sensations and solution-specific sensations. Factors that may influence women having a negative sensory experience were sensory expectations of the procedure(s) and lack of preparatory sensory information. DISCUSSION: Our study provides unique in-depth insight into women's sensory experiences of colposcopy and related procedures and suggests women require more preparatory sensory information. The issues identified as contributing to women having a negative sensory experience may help inform the development of pre-colposcopy information which may better prepare women with abnormal cervical cytology for follow-up examinations

Noncommutative vector bundles over fuzzy CP^N and their covariant derivatives

We generalise the construction of fuzzy CP^N in a manner that allows us to access all noncommutative equivariant complex vector bundles over this space. We give a simplified construction of polarization tensors on S^2 that generalizes to complex projective space, identify Laplacians and natural noncommutative covariant derivative operators that map between the modules that describe noncommuative sections. In the process we find a natural generalization of the Schwinger-Jordan construction to su(n) and identify composite oscillators that obey a Heisenberg algebra on an appropriate Fock space.Comment: 34 pages, v2 contains minor corrections to the published versio

'Schwinger Model' on the Fuzzy Sphere

In this paper, we construct a model of spinor fields interacting with specific gauge fields on fuzzy sphere and analyze the chiral symmetry of this 'Schwinger model'. In constructing the theory of gauge fields interacting with spinors on fuzzy sphere, we take the approach that the Dirac operator $D_q$ on q-deformed fuzzy sphere $S_{qF}^2$ is the gauged Dirac operator on fuzzy sphere. This introduces interaction between spinors and specific one parameter family of gauge fields. We also show how to express the field strength for this gauge field in terms of the Dirac operators $D_q$ and $D$ alone. Using the path integral method, we have calculated the $2n-$point functions of this model and show that, in general, they do not vanish, reflecting the chiral non-invariance of the partition function.Comment: Minor changes, typos corrected, 18 pages, to appear in Mod. Phys. Lett.