Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information

SciTech News Volume 71, No. 2 (2017)

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The Inhuman Overhang: On Differential Heterogenesis and Multi-Scalar Modeling

As a philosophical paradigm, differential heterogenesis offers us a novel descriptive vantage with which to inscribe Deleuze’s virtuality within the terrain of “differential becoming,” conjugating “pure saliences” so as to parse economies, microhistories, insurgencies, and epistemological evolutionary processes that can be conceived of independently from their representational form. Unlike Gestalt theory’s oppositional constructions, the advantage of this aperture is that it posits a dynamic context to both media and its analysis, rendering them functionally tractable and set in relation to other objects, rather than as sedentary identities. Surveying the genealogy of differential heterogenesis with particular interest in the legacy of Lautman’s dialectic, I make the case for a reading of the Deleuzean virtual that departs from an event-oriented approach, galvanizing Sarti and Citti’s dynamic a priori vis-à-vis Deleuze’s philosophy of difference. Specifically, I posit differential heterogenesis as frame with which to examine our contemporaneous epistemic shift as it relates to multi-scalar computational modeling while paying particular attention to neuro-inferential modes of inductive learning and homologous cognitive architecture. Carving a bricolage between Mark Wilson’s work on the “greediness of scales” and Deleuze’s “scales of reality”, this project threads between static ecologies and active externalism vis-à-vis endocentric frames of reference and syntactical scaffolding

Toxicity Pathways – from concepts to application in chemical safety assessment

Few would deny that the NRC report (NRC, 2007), "Toxicity Testing in the 21st Century: A Vision and Strategy”, represented a re-orientation of thinking surrounding the risk assessment of environmental chemicals. The key take-home message was that by understanding Toxicity Pathways (TP) we could profile the potential hazard and assess risks to humans and the environment using intelligent combinations of computational and in vitro methods. In theory at least, shifting to this new paradigm promises more efficient, comprehensive and cost effective testing strategies for every chemical in commerce while minimising the use of animals. For those of us who embrace the vision and the strategy proposed to achieve it, attention has increasingly focused on how we can actually practice what we preach. For a start, 21st century concepts described in the report have to be carefully interpreted and then translated into processes that essentially define and operationalize a TP framework for chemical risk assessment. In September 2011 the European Commission's Joint Research Centre (JRC) and the Hamner Institutes for Health Sciences co-organised a "Toxicity Pathways" workshop. It was hosted by the JRC and took place in Ispra, Italy. There were 23 invited participants with more or less equal representation from Europe and North America. The purpose of the meeting was to address three key questions surrounding a TP based approach to chemical risk assessment, namely – What constitutes a TP? How can we use TPs to develop in vitro assays and testing strategies? And, How can the results from TP testing be used in human health risk assessments? The meeting ran over two days and comprised a series of thought-starter presentations, breakout sessions and plenty of group discussions. The outcome was captured by rapporteurs and compiled as a workshop report which is available for download (without charge) from the JRC website. Here we expand on selected deliberations of the workshop to illustrate how TP thinking is still evolving and to indicate what pieces of the puzzle still need to fall into place before TP based risk assessment can become a reality.JRC.I.5-Systems Toxicolog

Experiments in becoming: corporeality, attunement and doing research

Human geography has become deeply interested in a range of research methods that focus on researchers’ corporeal engagement with their research sites. This interest has opened up an exciting set of research horizons, energising the discipline in a whole range of ways. Welcoming this engagement, this paper presents a series of meditations on the process of using the researcher’s corporeal learning as a research tool. Exploring two research projects, as well as the work of the photographer Nikki S Lee, it examines how the process of becoming corporeally capable might productively be framed as sets of ongoing experiments. Framing such engagements as experiments is a useful heuristic through which to think rigorously about what such research can claim as knowledge. More controversially, the paper argues that the heuristic of the experiment helps us to attend to the varying durations of becoming in ways that much existing work has discounted. Developing corporeal capacities – gaining a skill, becoming capable of doing a particular activity – involves becoming attuned to a range of thresholds, the crossing of which open up novel and frequently unexpected perspectives. Attunement to these thresholds does not arise simply through the process of mixing in and participating in a research site. It requires careful attention to the parameters of transformation involved in being able to participate. The paper explores how such parameters might be decided upon and calibrated as part of an ongoing engagement with a research site or event. Our aim is not to artificially restrict or constrain how human geographers approach their research design. Rather it is to encourage human geographers to show more courage in their use of corporeal based research methodologies

Bottom-Up Modeling of Permissions to Reuse Residual Clinical Biospecimens and Health Data

Consent forms serve as evidence of permissions granted by patients for clinical procedures. As the recognized value of biospecimens and health data increases, many clinical consent forms also seek permission from patients or their legally authorized representative to reuse residual clinical biospecimens and health data for secondary purposes, such as research. Such permissions are also granted by the government, which regulates how residual clinical biospecimens may be reused with or without consent. There is a need for increasingly capable information systems to facilitate discovery, access, and responsible reuse of residual clinical biospecimens and health data in accordance with these permissions. Semantic web technologies, especially ontologies, hold great promise as infrastructure for scalable, semantically interoperable approaches in healthcare and research. While there are many published ontologies for the biomedical domain, there is not yet ontological representation of the permissions relevant for reuse of residual clinical biospecimens and health data. The Informed Consent Ontology (ICO), originally designed for representing consent in research procedures, may already contain core classes necessary for representing clinical consent processes. However, formal evaluation is needed to make this determination and to extend the ontology to cover the new domain. This dissertation focuses on identifying the necessary information required for facilitating responsible reuse of residual clinical biospecimens and health data, and evaluating its representation within ICO. The questions guiding these studies include: 1. What is the necessary information regarding permissions for facilitating responsible reuse of residual clinical biospecimens and health data? 2. How well does the Informed Consent Ontology represent the identified information regarding permissions and obligations for reuse of residual clinical biospecimens and health data? We performed three sequential studies to answer these questions. First, we conducted a scoping review to identify regulations and norms that bear authority or give guidance over reuse of residual clinical biospecimens and health data in the US, the permissions by which reuse of residual clinical biospecimens and health data may occur, and key issues that must be considered when interpreting these regulations and norms. Second, we developed and tested an annotation scheme to identify permissions within clinical consent forms. Lastly, we used these findings as source data for bottom-up modelling and evaluation of ICO for representation of this new domain. We found considerable overlap in classes already in ICO and those necessary for representing permissions to reuse residual clinical biospecimens and health data. However, we also identified more than fifty classes that should be added to or imported into ICO. These efforts provide a foundation for comprehensively representing permissions to reuse residual clinical biospecimens and health data. Such representation fills a critical gap for developing applications which safeguard biospecimen resources and enable querying based on their permissions for use. By modeling information about permissions in an ontology, the heterogeneity of these permissions at a range of levels (e.g., federal regulations, consent forms) can be richly represented using entity-relationship links and embedded rules of inference and inheritance. Furthermore, by developing this content in ICO, missing content will be added to the Open Biological and Biomedical Ontology (OBO) Foundry, enabling use alongside other widely adopted ontologies and providing a valuable resource for biospecimen and information management. These methods may also serve as a model for domain experts to interact with ontology development communities to improve ontologies and address gaps which hinder successful uptake.PHDNursingUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162937/1/eliewolf_1.pd

Defining Design and Technology in an Age of Uncertainty: The View of the Expert Practitioner.

Long standing debate surrounds the position Design and Technology holds in the English and Welsh national curriculum. Some commentators espouse alignment with Science, Technology, Engineering and Mathematics (STEM) as its natural home, whilst others argue that this stifles creativity and takes no account of the ?designerly? nature they consider to be a central tenet of the subject. Against this backdrop, the subject has undergone changes in both prescribed subject knowledge content and examination and assessment arrangements by which pupil progress and attainment are measured. Set against this background, the work presented here summarises a Delphi study which sought to canvass the opinion of established and experienced Design and Technology teachers about how they perceive the attributes, values and unique features of the subject. The results are analysed to give a view of the subject from within the classroom. Analysis reveals that participants in the study consider the ?uniqueness? of the subject to prevail over the values and attributes they collectively define it by. The study moves on to discuss the findings in relation to the values and direction which underpin policy documentation that drives and shapes the subject from a national perspective. Finally, the work concludes by highlighting several important areas worthy of further research which have emerged and could be seen as contributory to understanding the nature and essence of Design and Technology

Sport for development and transformative social change: The potential of Margaret Archer’s Morphogenetic Approach to reconceptualise a longstanding problem

Frequent calls for sport-for-development (SfD) to be re-oriented towards transformative social change reflect the extent that policies and programmes have instead focused on individualised forms of personal development. However, SfD research has yet to substantially address fundamental ontological assumptions and underlying conceptualisations of transformative social change. To addresses this gap, we consider how Margaret Archer’s Morphogenetic Approach can help explain how transformative social change might occur through SfD activities. Three conceptual contributions are brought into focus: (1) assuming a realist social ontology, (2) making distinctions between structure, culture and agency, and (3) identifying social change as happening across three temporal phases. We conclude by identifying potential benefits and implications of applying the Morphogenetic Approach to consider the potential for SfD to contribute to social change