Analysis and visualisation of RDF resources in Ondex

An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a distributed knowledge base which has the potential to advance biomedical research [1]. This potential, however, cannot be realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need for tools that provide data reduction, visualization and interactive analysis capabilities.
Ondex is a data integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated with ontologies. This data model conforms to the Semantic Web framework, in particular to RDF, and therefore Ondex is ideally positioned as a platform that can exploit the semantic web. 
The Ondex system offers a range of features and analysis methods of potential value to semantic web users, including:
-	An interactive graph visualization interface (Ondex user client), which provides data reduction and representation methods that leverage the ontological annotation.
-	A suite of importers from a variety of data sources to Ondex (http://ondex.org/formats.html)
-	A collection of plug-ins which implement graph analysis, graph transformation and graph-matching functions.
-	An integration toolkit (Ondex Integrator) which allows users to compose workflows from these modular components
-	In addition, all importers and plug-ins are available as web-services which can be integrated in other tools, as for instance Taverna [3].
The developments that will be presented in this demo have made this functionality interoperable with the Semantic Web framework. In particular we have developed an interactive importer, based on SPARQL that allows the query-driven construction of datasets which brings together information from different RDF data resources into Ondex.
These datasets can then be further refined, analysed and annotated both interactively using the Ondex user client and via user-defined workflows. The results of these analyses can be exported in RDF, which can be used to enrich existent knowledge bases, or to provide application-specific views of the data. Both importer and exporter only focus on a subset of the Ondex and RDF data models, which are shared between these two data representations [4].
In this demo we will show how Ondex can be used to query, analyse and visualize Semantic Web knowledge bases. In particular we will present real use cases focused, but not limited to, resources relevant to plant biology. 
We believe that Ondex can be a valid contribution to the adoption of the Semantic Web in Systems Biology research and in biomedical investigation more generally. We welcome feedback on our current import/export prototype and suggestions for the advancement of Ondex for the Semantic Web.

References

1.	Ruttenberg, A. et. al.: Advancing translational research with the Semantic Web, BMC Bioinformatics, 8 (Suppl. 3): S2 (2007).
2.	Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Ruegg, A., Rawlings, C., Verrier, P., Philippi, S.: Graph-based analysis and visualization of experimental results with Ondex. Bioinformatics 22 (11):1383-1390 (2006).
3.	Rawlings, C.: Semantic Data Integration for Systems Biology Research, Technology Track at ISMB’09, http://www.iscb.org/uploaded/css/36/11846.pdf (2009).
4.	Splendiani, A. et. al.: Ondex semantic definition, (Web document) http://ondex.svn.sourceforge.net/viewvc/ondex/trunk/doc/semantics/ (2009).
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A novel on-field training intervention improves novice goalkeeper penalty kick performance

This study developed an on-field anticipation training intervention with the aim of improving novice goalkeeper penalty kick performance. Eighteen participants were allocated to either one-player (OP); or three-player (TP) training. The OP group faced “traditional” practice, with one player running-up to execute each kick. The TP group faced three players in a form of variable practice; two players stopped their run-up approximately 1.2m from the ball with the third-player executing the kick. Following training, results revealed that TP made significantly more saves when facing non-deception kicks in comparison with OP. An implication for applied practice is that there are potential gains to be made through training anticipation skills via new on-field practices rather than the current research focus on video-based training

Hot hands, cold feet? Investigating effects of interacting constraints on place kicking performance at the 2015 Rugby Union World Cup

Place kicks in Rugby Union present valuable opportunities to score points outside the spatiotemporal dynamics of open play but are executed under varying performance constraints. We analysed effects of specific task constraints and relevant contextual factors on place kick performance in the 2015 Rugby Union World Cup. Data were collected from television broadcasts for each place kick. In addition to kick outcomes, contextual factors, including time of the kick in the match, score margin at the time of the kick, and outcome of the kicker’s previous kick, were recorded. Effects of spatial task constraints were analysed for each kick, using distance (m) and angle (°) of the kick to the goalposts. A binomial logistic regression model revealed that distance from, and angle to, the goalposts were significant predictors of place kick outcome. Furthermore, the success percentage of kickers who missed their previous kick was 7% lower than those who scored their previous kick. Place kick success percentage in the 10 minutes before half-time was 8% lower than the mean tournament success percentage, which was 75% (95% CI 71% to 78%). The highest kick success percentage was recorded when scores were level (83%; 95% CI 72% to 91%). Our data highlighted how subtle changes in task constraints and contextual factors can influence performance outcomes in elite performers in international competition. Fluctuations in place kick success suggested that individual constraints, such as thoughts, emotions, and fatigue, induced during competition, could interact with perceptions to influence emergent performance behaviours

Experiential knowledge of elite Rugby Union players on key performance constraints in place kicking

There has been a growing tendency in sport science research to examine the relationship between empirical knowledge developed in scientific experiments and theoretical frameworks and the experiential knowledge of elite performers and practitioners (Jones, Bezodis, & Thompson, 2009; Greenwood, Davids, & Renshaw, 2014; Phillips, Davids, Renshaw, & Portus, 2014). In this study, we investigated the experiential knowledge of elite Rugby Union place kickers to access their understanding of how to satisfy interacting constraints of competitive performance and practice environments. Place kicks in Rugby Union offer opportunities to score points outside the spatiotemporal dynamics of open play, but are typically performed under varying task and contextual constraints within a performance environment. Success percentage of place kicks can fluctuate under specific task and contextual constraints, as shown in a recent analysis of the 2015 Rugby World Cup (Pocock, Bezodis, Davids, & North, under review). For example, success percentage can drop sharply at critical thresholds of distance and angle to the goalposts and can vary depending on time elapsed, score margin and previous kick success. Interestingly, place kicks in the 10 minutes before half time were 8% less successful than the tournament average, and place kickers who had missed their previous kick were 7% less successful than place kickers who had scored their previous kick. It has therefore been speculated that emotions induced during competition can interact with perceptions and action to influence the emergent behaviours of place kickers. To develop greater understanding of how fluctuations in performance data may emerge, we interviewed professional Rugby Union place kickers and sought to explore their experiences of satisfying key interacting constraints on performance. Specifically, we aimed to investigate the key constraints that place kickers perceive to influence their emotions and perceptions of task difficulty. A secondary aim of the interviews was to identify specific details of how place kicking situations are currently practised, and why they are structured in this way. We present here the experiential knowledge of place kickers which includes their perceptions of the key constraints in performance environments and how they currently prepare for place kicks. Our findings highlighted how performance constraints can influence emotions, cognitions and perceptions during place kicking performance and the data indicated how the key constraints identified in this study, combined with the findings of previous quantitative analyses, could be represented in training environments. Initial interviews revealed that place kicking is predominantly practised individually and in isolation from game-based scenarios in training, without any form of pressure or expectation. Examples of pressure that place kickers identified in interviews included expectations of team-mates, performing in front of large crowds and closely-matched scores. This presentation will conclude by discussing how an integration of empirical and experiential knowledge can enrich understanding of sport performance and provide recommendations for coaches when designing practice environments which simulate relevant performance constraints to enhance the adaptive skills of elite and developing athletes in sport

Decision-making practices during coaching sessions in grassroots youth soccer: A mixed-methods investigation

Introduction Decision making ability in players during match-play is mostly acquired through practice activities with the same underlying structure as competition (e.g., [1]). However, researchers have not fully investigated how coaches design practice sessions at the participation level of the sport (i.e., “grassroots”) or of why they used a particular activity at a specific time point. The aim of this study was to investigate the practice activities used by youth soccer coaches working at participation level in the UK and gain insight into their intentions. Methods Altogether, 12 male soccer coaches participated working with players aged 9-11 years within 10 clubs at the participation level of soccer in London, UK. A total of 35 practice sessions were observed in situ. Sessions were analysed for the proportion of time spent in activities containing ‘non-active decision-making’ (e.g., unopposed technical skills practices, fitness training) and ‘active decision-making’ (e.g., small-sided games, skills practice with opposition). An interview with the coaches about the session purpose took place after each systematic observation. Results Coaches had players spend similar amounts of time in activities with active decision-making (M = 41%) and non-active decision-making (M = 42%) with the remainder spent transitioning between activities (M = 17%). There was more non-active decision-making activity during the first half of the session (M = 64%) when compared to active decision-making activity (M = 16%). However, there was more active decision-making activity in the second half (M = 66%) when compared to non-active (M = 20%). Therefore, the session progressed in a traditional manner from predominately non-active decision-making activity early on to mostly active decision-making activity later. Interviews revealed that the coaches believe players require frequent isolated (unopposed) ‘non-active decision-making’ practices to acquire technique initially in the session and during the season. Conclusion Our findings show that coaches had players spend nearly half of session time in non-active decision-making activities that are deemed less relevant to improving soccer match performance. Findings highlight a potential gap between science and practice in the coaching of young participation level soccer players. References [1] Roca A, Ford PR (2020). Sci Med Footb. 4, 263-268

The Tea Bag Index—UK: using citizen/community science to investigate organic matter decomposition rates in domestic gardens

Gardening has the potential to influence several ecosystem services, including soil carbon dynamics, and shape progression towards the UN Sustainable Development Goals, (e.g., SDG 13). There are very few citizen/community science projects that have been set up to test an explicit hypothesis. However, citizen/community science allows collection of countrywide observations on ecosystem services in domestic gardens to inform us on the effects of gardening on SDGs. The geographical spread of samples that can be collected by citizen/community science would not be possible with a team of professional science researchers alone. Members of the general public across the UK submitted soil samples and buried standardised litter bags (tea bags) as part of the Tea Bag Index—UK citizen/community science project. Participants returned 511 samples from across the UK from areas in their garden where soil organic amendments were and were not applied. The project examined the effects of application of soil amendments on decomposition rates and stabilisation of litter, and in turn, effects on soil carbon and nitrogen concentrations. This was in response to a call for contributions to a global map of decomposition in the Teatime4Science campaign. Results suggested that application of amendments significantly increased decomposition rate and soil carbon, nitrogen, and carbon: nitrogen ratios within each garden. So much so that amendment application had more influence than geographic location. Furthermore, there were no significant interactions between location and amendment application. We therefore conclude that management in gardens has similar effects on soil carbon and decomposition, regardless of the location of the garden in question. Stabilisation factor was influenced more prominently by location than amendment application. Gardening management decisions can influence a number of SDGs and a citizen/community science project can aid in both the monitoring of SDGs, and involvement of the public in delivery of SDG

Understanding key constraints and practice design in Rugby Union place kicking : experiential knowledge of professional kickers and experienced coaches

Place kicks present valuable opportunities to score points in Rugby Union, which are typically performed under varying constraints in competitive performance environments. Previous quantitative studies suggest these interacting constraints can influence fluctuations in place kick success. To further the understanding of how fluctuations in place kicking success emerge, our aim was twofold: i) to explore and identify the key constraints that professional place kickers and experienced place kicking coaches perceive to influence the difficulty of a place kick and ii) to understand the level to which current place kicking practice environments represent these key constraints experienced in performance environments. Six professional place kickers and six experienced place kicking coaches were interviewed. Using a deductive thematic analysis, 11 key constraints were identified: individual constraints of expectation for success and fatigue, task constraints of angle and distance to goalposts, environmental constraints of wind, weather, pitch, and crowd, and situational constraints of previous kicking performance, time remaining and current score margin. Place kicking is typically practised individually or with a small number of place kickers in isolation from team sessions. Where possible, coaches should be encouraged to include place kicking in simulated game scenarios during practice to represent key constraints from performance environments. Our study demonstrates how experiential knowledge can enrich the understanding of sport performance and inform the design of practice environments which simulate relevant constraints of competitive performance to enhance skill adaptation of athletes

libSBOLj 2.0: A Java Library to Support SBOL 2.0

The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic desig

Immunochemotherapy and Maintenance With Obinutuzumab or Rituximab in Patients With Previously Untreated Marginal Zone Lymphoma in the Randomized GALLIUM Trial

The aim of this study was to explore the efficacy and safety of obinutuzumab (G)- versus rituximab (R)-chemotherapy in a subgroup of patients with previously untreated marginal zone lymphoma (MZL) in the phase III GALLIUM trial (NCT01332968). Patients had stage III/IV (or stage II with bulky disease), splenic, nodal, or extranodal MZL requiring treatment. Patients were randomized 1:1 to receive G- or R-chemotherapy (cyclophosphamide, doxorubicin, vincristine, and prednisone; cyclophosphamide, vincristine, and prednisone; or bendamustine, allocated at patient level). Patients with complete/partial response at the end of induction (EOI) received G/R maintenance. Investigator-assessed progression-free survival (PFS), other time-to-event endpoints, response, and safety were assessed. Overall, 195 patients with MZL were included in this analysis: G-chemotherapy (n = 99), R-chemotherapy (n = 96). Median observation time: 59.3 months. No meaningful difference was observed between arms for PFS (4-y PFS rates: G-chemotherapy, 72.6%; R-chemotherapy, 64.1%), other time-to-event endpoints, or EOI response rates (by computed tomography [CT; G-chemotherapy, 81.8%; R-chemotherapy, 81.3%] and positron emission tomography CT [G-chemotherapy, 79.2%; R-chemotherapy, 87.5%]). All patients experienced ≥1 adverse event (AE). G-chemotherapy was associated with a higher incidence of grade 3–5 (86.1% versus 77.4%), grade 5 (14.9% versus 9.7%), and serious (66.3% versus 51.6%) AEs versus R-chemotherapy. Both arms had a higher incidence of grade 3–5 and serious AEs than patients with follicular lymphoma (GALLIUM), with G-chemotherapy being less tolerable than R-chemotherapy. Based on the observed tolerability of G-chemotherapy versus R-chemotherapy, and the comparable efficacy of G-chemotherapy and R-chemotherapy in this analysis, G-chemotherapy cannot be recommended as first-line treatment for MZL