Bioinformatics and the politics of innovation in the life sciences: Science and the state in the United Kingdom, China, and India

The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation

HSLIC Annual Report FY2014-15

https://digitalrepository.unm.edu/hslic-annual-reports/1017/thumbnail.jp

Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

HSLIC Annual Report FY2015-16

https://digitalrepository.unm.edu/hslic-annual-reports/1018/thumbnail.jp

The Function Biomedical Informatics Research Network Data Repository

The Function Biomedical Informatics Research Network (FBIRN) developed methods and tools for conducting multi-scanner functional magnetic resonance imaging (fMRI) studies. Method and tool development were based on two major goals: 1) to assess the major sources of variation in fMRI studies conducted across scanners, including instrumentation, acquisition protocols, challenge tasks, and analysis methods, and 2) to provide a distributed network infrastructure and an associated federated database to host and query large, multi-site, fMRI and clinical datasets. In the process of achieving these goals the FBIRN test bed generated several multi-scanner brain imaging data sets to be shared with the wider scientific community via the BIRN Data Repository (BDR). The FBIRN Phase 1 dataset consists of a traveling subject study of 5 healthy subjects, each scanned on 10 different 1.5 to 4 Tesla scanners. The FBIRN Phase 2 and Phase 3 datasets consist of subjects with schizophrenia or schizoaffective disorder along with healthy comparison subjects scanned at multiple sites. In this paper, we provide concise descriptions of FBIRN’s multi-scanner brain imaging data sets and details about the BIRN Data Repository instance of the Human Imaging Database (HID) used to publicly share the data

Medical informatics in an undergraduate curriculum: a qualitative study

BACKGROUND: There is strong support for educating physicians in medical informatics, and the benefits of such education have been clearly identified. Despite this, North American medical schools do not routinely provide education in medical informatics. METHODS: We conducted a qualitative study to identify issues facing the introduction of medical informatics into an undergraduate medical curriculum. Nine key informants at the University of Toronto medical school were interviewed, and their responses were transcribed and analyzed to identify consistent themes. RESULTS: The field of medical informatics was not clearly understood by participants. There was, however, strong support for medical informatics education, and the benefits of such education were consistently identified. In the curriculum we examined, medical informatics education was delivered informally and inconsistently through mainly optional activities. Issues facing the introduction of medical informatics education included: an unclear understanding of the discipline; faculty and administrative detractors and, the dense nature of the existing undergraduate medical curriculum. CONCLUSIONS: The identified issues may present serious obstacles to the introduction of medical informatics education into an undergraduate medicine curriculum, and we present some possible strategies for addressing these issues

A black art: Ontology, data, and the Tower of Babel problem

Computational ontologies are a new type of emerging scientific media (Smith, 2016) that process large quantities of heterogeneous data about portions of reality. Applied computational ontologies are used for semantically integrating (Heiler, 1995; Pileggi & Fernandez-Llatas, 2012) divergent data to represent reality and in so doing applied computational ontologies alter conceptions of materiality and produce new realities based on levels of informational granularity and abstraction (Floridi, 2011), resulting in a new type of informational ontology (Iliadis, 2013) the critical analysis of which requires new methods and frameworks. Currently, there is a lack of literature addressing the theoretical, social, and critical dimensions of such informational ontologies, applied computational ontologies, and the interdisciplinary communities of practice (Brown & Duguid, 1991; Wenger, 1998) that produce them. This dissertation fills a lacuna in communicative work in an emerging subfield of Science and Technology Studies (Latour & Woolgar, 1979) known as Critical Data Studies (boyd & Crawford, 2012; Dalton & Thatcher, 2014; Kitchin & Lauriault, 2014) by adopting a critical framework to analyze the systems of thought that inform applied computational ontology while offering insight into its realism-based methods and philosophical frameworks to gauge their ethical import. Since the early 1990s, computational ontologies have been used to organize massive amounts of heterogeneous data by individuating reality into computable parts, attributes, and relations. This dissertation provides a theory of computational ontologies as technologies of individuation (Simondon, 2005) that translate disparate data to produce informational cohesion. By technologies of individuation I mean engineered artifacts whose purpose is to partition portions of reality into computable informational objects. I argue that data are metastable entities and that computational ontologies restrain heterogeneous data via a process of translation to produce semantic interoperability. In this way, I show that computational ontologies effectively re-ontologize (Floridi, 2013) and produce reality and thus that have ethical consequences, specifically in terms of their application to social reality and social ontology (Searle, 2006). I use the Basic Formal Ontology (Arp, Smith, & Spear, 2015)—the world’s most widely used upper-level ontology—as a case study and analyze its methods and ensuing ethical issues concerning its social application in the Military Ontology before recommending an ethical framework. “Ontology” is a term that is used in philosophy and computer science in related but different ways—philosophical ontology typically concerns metaphysics while computational ontology typically concerns databases. This dissertation provides a critical history and theory of ontology and the interdisciplinary teams of researchers that came to adopt methods from philosophical ontology to build, persuade, and reason with applied computational ontology. Following a critical communication approach, I define applied computational ontology construction as a solution to a communication problem among scientists who seek to create semantic interoperability among data and argue that applied ontology is philosophical, informational in nature, and communicatively constituted (McPhee & Zaug, 2000). The primary aim is to explain how philosophy informs applied computational ontology while showing how such ontologies became instantiated in material organizations, how to study them, and describe their ethical implications