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 (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl. (shrink)

(1994). European dimensions of Finnish culture: A survey of international and European orientation of Finnish intellectuals. World Futures: Vol. 39, The Evolution of European Identity: Surveys of the Growing Edge A Report by the European Culture Impact Research Consortium (EUROCIRCON), pp. 25-46.

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

I suggest that the transformation of an artifact from an introductory-type instrument into a viable, collectively used tool cannot be understood solely in terms of gradual adaptation of the technology and user environment, but also as a qualitatively broader integration process in which an expansion takes place. The case illustrated a constrained shift of an artifact from its first adopter, an individual pioneer user, to a more collective user in institutional medicine. The artifact, a neuromagnetometer instrument for brain research and (...) diagnostics, brings together physicists, neuroscientists, physicians as well as various practitioners from the medical imaging industry. I applied an activity-theoretical framework for analysing the adoption of the neuromagnetometer from the pioneer phase of implementation into the more established use. The case showed that the anticipated transformation of the artifact constituted a major challenge for the user organization and its practitioners. It is suggested that an expansion of the object into a shared object of implementation among the separate practitioner groups is indispensable.This expansion of the object involves for the practitioners to recognize both the different objects and requirements of the pioneer phase of the implementation and the new phase of introduction into medical practice. It is shown that this recognition does not, however, come as given, spontaneously born in the transition. The emerging new object may remain only partially shared if not made visible by deliberate effort among the practitioners. The expansion requires collective visualization of the work and reflective dialogue on it. Employing analytical tools, such as the activity-theoretical concepts used here, is one possible way of facilitating such an effort. (shrink)

This paper examines two different ways of understanding the concept of bodily integrity and their political implications. In Drucilla Cornell's use of the concept, the body cannot be separated from the mind. Protecting bodily integrity means protecting possibilities of imagining the self as whole. Martha Nussbaum's theorizing is based on a liberal way of conceptualizing subjectivity, in which the mind and the body are separate, and bodily integrity is used to refer to physical inviolability.