Building conceptual spaces for exploring and linking biomedical resources

The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this paper we present our contribution to the community in the form of an infrastructure to annotate information resources, to discover relationships among them, and to represent and visualize the new discovered knowledge. Furthermore, we have also implemented a Web-based prototype tool which integrates the proposed infrastructure

Exploring and linking biomedical resources through multidimensional semantic spaces

Background The semantic integration of biomedical resources is still a challenging issue which is required for effective information processing and data analysis. The availability of comprehensive knowledge resources such as biomedical ontologies and integrated thesauri greatly facilitates this integration effort by means of semantic annotation, which allows disparate data formats and contents to be expressed under a common semantic space. In this paper, we propose a multidimensional representation for such a semantic space, where dimensions regard the different perspectives in biomedical research (e.g., population, disease, anatomy and protein/genes). Results This paper presents a novel method for building multidimensional semantic spaces from semantically annotated biomedical data collections. This method consists of two main processes: knowledge and data normalization. The former one arranges the concepts provided by a reference knowledge resource (e.g., biomedical ontologies and thesauri) into a set of hierarchical dimensions for analysis purposes. The latter one reduces the annotation set associated to each collection item into a set of points of the multidimensional space. Additionally, we have developed a visual tool, called 3D-Browser, which implements OLAP-like operators over the generated multidimensional space. The method and the tool have been tested and evaluated in the context of the Health-e-Child (HeC) project. Automatic semantic annotation was applied to tag three collections of abstracts taken from PubMed, one for each target disease of the project, the Uniprot database, and the HeC patient record database. We adopted the UMLS Meta-thesaurus 2010AA as the reference knowledge resource. Conclusions Current knowledge resources and semantic-aware technology make possible the integration of biomedical resources. Such an integration is performed through semantic annotation of the intended biomedical data resources. This paper shows how these annotations can be exploited for integration, exploration, and analysis tasks. Results over a real scenario demonstrate the viability and usefulness of the approach, as well as the quality of the generated multidimensional semantic spaces

Exploring over the Presumed Identity of Emerging Technology

While scientists are stepping up their efforts to develop new technologies, the ability of firms to determine the value of their technologies by identifying potential applications has become a major challenge. This article focuses on a particular phase of technology development: the emergence phase. When a promising new technology first sees the light of day in a fundamental research laboratory, its target markets often seem plentiful but are ill-defined. The inability to produce prototypes or to identify potential users makes it difficult to explore potential commercial applications. On the basis of four micro-nanotechnologies case-studies conducted within a multi-partner innovation project, this article aims to theoretically explain why the identification of applications from emerging technologies is not a trivial problem. That research analyses how technologists and non-experts interact during creative investigations on new applications. It shows that the technologists are victims of a form of cognitive fixation effect. Indeed, their beliefs and activities are guided by a stable cognitive representation of their technology: the presumed identity of technology. Based on a recent design framework, C-K Design Theory, the technological exploration process followed in our four case-studies is modeled and mechanisms to dismantle the presumed identity and to design an extended identity of technology are provided.management of emerging technology; technological exploration; identity of technology; C-K Design Theory, presumed identity; technology-push; technological innovation

Conceptualising schools as a source of social capital for HIV affected children in southern Africa

Many AIDS-affected African children lack forms of adult support and guidance traditionally provided by families. There is growing policy attention to the role schools might play in caring for children in extreme adversity in ways that go far beyond traditional education. We use the concept of the “HIV competent school,” which incorporates bonding, bridging and linking social capital, to frame a selective review of the literature on school responses to HIV/AIDS in southern African countries, and an in-depth case study of indigenous school responses in eastern Zimbabwe. We call for greater attention to the ethic of care emerging from the interaction between AIDS-affected children and relevant peers and adults in the school setting and the way in which this is limited or enabled in particular social settings

Knowledge Representation for Web Navigation

Representations of domain knowledge range from those that are ontologically formal, semantically rich to those that are ontologically informal and semantically weak. Representations of knowledge are important in many tasks, one of which is the support of travel around information spaces through the identification and linking of concepts in a field. In this paper we explore how representations of ontologically informal, semantically weak domain knowledge as captured by the Simple Knowledge Organisation System (SKOS) can enable a system to take advantage of the large number of existing ontological representations to support semantic linking of Web based information and thus facilitate information travel

Community mental health competencies: A new vision for global mental health

As part of the Movement for Global Mental Health’s efforts to scale up services, attention has shifted to the level of communities, with community engagement recognised as a key locus of action to promote treatment and rehabilitation. Communities have long been viewed as key mediators in the management of health. However, the multifarious nature of what we mean by the term ‘community’ makes the promotion of mental health through action at this level a process that is endlessly complex and demands further exploration. This chapter aims to elaborate on the validity of community mental health competency (Campbell and Burgess 2012) as a conceptual framework to guide community engagement for global mental health practice. The chapter draws on case studies from two different settings each pointing to the value of various dimensions highlighted by the approach. The studies highlight that through a focus on promoting constructive partnerships, critical dialogue, valuing local knowledge, and promoting safe spaces, mental health services can be brought in line with the varied local realities that shape communities around the world

Assembling the Healthopolis: Competitive city‐regionalism and policy boosterism pushing Greater Manchester further, faster

Health and care policy is increasingly promoted within visions of the competitive city‐region. This paper examines the importance of policy boosterism within the political construction of city‐regions in the context of English devolution. Based on a two‐year case study of health and social care devolution in Greater Manchester, England, we trace the relational and territorial geographies of policy across and through new “devolved” city‐regional arrangements. Contributing to geographical debates on policy assemblages and city‐regionalism, we advance a conceptual framework linking crisis and opportunity, emulation and exceptionalism, and evidence and experimentation. The paper makes two key contributions. First, we argue health and care policy is increasingly drawn towards the logic of global competitiveness without being wholly defined by neoliberal political agendas. Fostering transnational policy networks helped embed global “best practice” policies while simultaneously hailing Greater Manchester as a place beyond compare. Second, we caution against positioning the city‐region solely at the receiving end of devolutionary austerity. Rather, we illustrate how the urgency of devolution was conditioned by crisis, yet concomitantly framed as a unique opportunity by the local state harnessing policy to negotiate a more fluid politics of scale. In doing so, the paper demonstrates how attempts to resolve the “local problem” of governing health and care under austerity were rearticulated as a “global opportunity” to forge new connections between place, health, and economy. Consequently, we foreground the multiple tensions and contradictions accumulating through turning to health and care to push Greater Manchester further, faster. The paper concludes by asking what the present crisis might mean for city‐regions in good health and turbulent times

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table