Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)
A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)
Ethical or ‘socially sustainable’ sourcing mechanisms mandating labour standards among the suppliers and subcontractors that organisations source goods and services from are becoming more common. The issue of how labour activist groups such as trade unions can encourage organisations to adopt and strengthen these mechanisms within domestic production networks is largely unexplored. Using three cases of domestic sustainable sourcing campaigns developed by unions in Britain, the strategies used by labour activists, the characteristics of the organisations targeted and the motivations of (...) lead firms for improving sourcing practices are analysed. The article makes a significant contribution by demonstrating that organisational susceptibility to reputational risk is a key factor influencing the capacity of activist groups to convince and compel their targets to improve sourcing practices. It argues that different types of organisations are susceptible to reputational damage in different ways, that risk events provide opportunities for unions to strengthen their leverage against target organisations, and that the multidimensional nature of corporate reputation needs to be better considered for understanding how campaigns are framed and executed. (shrink)
Ethical guidance from the British Medical Association about treating doctor–patients is compared and contrasted with evidence from a qualitative study of general practitioners who have been patients. Semistructured interviews were conducted with 17 GPs who had experienced a significant illness. Their experiences were discussed and issues about both being and treating doctor–patients were revealed. Interpretative phenomenological analysis was used to evaluate the data. In this article data extracts are used to illustrate and discuss three key points that summarise the BMA (...) ethical guidance, in order to develop a picture of how far experiences map onto guidance. The data illustrate and extend the complexities of the issues outlined by the BMA document. In particular, differences between experienced GPs and those who have recently completed their training are identified. This analysis will be useful for medical professionals both when they themselves are unwell and when they treat doctor–patients. It will also inform recommendations for professionals who educate medical students or trainees. (shrink)
Using Chicago as our case, this article puts forth a notion of black placemaking that privileges the creative, celebratory, playful, pleasurable, and poetic experiences of being black and being around other black people in the city. Black placemaking refers to the ways that urban black Americans create sites of endurance, belonging, and resistance through social interaction. Our framework offers a corrective to existing accounts that depict urban blacks as bounded, plagued by violence, victims and perpetrators, unproductive, and isolated from one (...) another and the city writ large. While ignoring neither the external assaults on black spaces nor the internal dangers that can make everyday life difficult, we highlight how black people make places in spite of those realities. Our four cases – the black digital commons, black public housing reunions, black lesbian and gay nightlife, and black Little League baseball – elucidate the matter of black lives across genders, sexualities, ages, classes, and politics. (shrink)
American society was transformed by the expansion of capital Westward and the explosion in opportunities for land-grabbing and agricultural and industrial investment. F.J. Turner’s frontier thesis portrays this transformation as the fulfilment of American character. The tensions between character and personality are examined following the ideas of Carl Schmitt on the significance of ‘the occasion’ in acquiring competitive advantage. Schmitt indicated the significance of a ‘vertical’ frontier in challenging social conventions and this constitutes a counterpoint to the ‘horizontal’ frontier developed (...) in the frontier thesis of Turner. The importance of the occasion and personality in developing the American way of life is presented by an examination of the vaudeville and celebrity traditions in American entertainment. (shrink)
Gilead et al. propose an ontology of abstract representations based on folk-psychological conceptions of cognitive architecture. There is, however, no evidence that the experience of cognition reveals the architecture of cognition. Scale-free architectural models propose that cognition has the same computational architecture from sub-cellular to whole-organism scales. This scale-free architecture supports representations with diverse functions and levels of abstraction.
In this response, we provide further clarification of the propositional approach to human associative learning. We explain why the empirical evidence favors the propositional approach over a dual-system approach and how the propositional approach is compatible with evolution and neuroscience. Finally, we point out aspects of the propositional approach that need further development and challenge proponents of dual-system models to specify the systems more clearly so that these models can be tested.
The past 50 years have seen an accumulation of evidence suggesting that associative learning depends on high-level cognitive processes that give rise to propositional knowledge. Yet, many learning theorists maintain a belief in a learning mechanism in which links between mental representations are formed automatically. We characterize and highlight the differences between the propositional and link approaches, and review the relevant empirical evidence. We conclude that learning is the consequence of propositional reasoning processes that cooperate with the unconscious processes involved (...) in memory retrieval and perception. We argue that this new conceptual framework allows many of the important recent advances in associative learning research to be retained, but recast in a model that provides a firmer foundation for both immediate application and future research. (shrink)