In the era of "big data," science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary ...fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use.After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.
Ontologies of cellular networks Arp, Robert; Smith, Barry
Science signaling,
2008-Dec-16, Volume:
1, Issue:
50
Journal Article
Peer reviewed
As part of a series of workshops on different aspects of biomedical ontology sponsored by the National Center for Biomedical Ontology (NCBO), a workshop titled "Ontologies of Cellular Networks" took ...place in Newark, New Jersey, on 27 to 28 March 2008. This workshop included more than 30 participants from various backgrounds in biomedicine and bioinformatics. The goal of the workshop was to provide an introduction to the basic tools and methods of ontology, as well as to enhance coordination between groups already working on ontologies of cellular networks. The meeting focused on three questions: What is an ontology? What is a pathway? What is a cellular network?
In the biological realm, a complete explanation of a trait seems to include an explanation in terms of function. It is natural to ask of some trait, "What is its function?" or "What purpose in the ...organism does the particular trait serve?" or "What is the goal of its activity?" There are several views concerning the appropriate definition of function for biological matters. Two popular views of function with respect to living things are Cummins' organizational account and the Griffiths/Godfrey-Smith modern history account. Whereas Cummins argues that a trait functions so as to contribute to the general organization of some organism's present structure, Griffiths, and Godfrey-Smith argue that a trait functions because of its fitness with respect to the organism's recent evolutionary history. In this paper, I show how these accounts can be made compatible and compliment one another. Given that structure, organization, operational flexibility, function, and evolutionary history are all factors to be considered in an organism's makeup, we should expect that the traits of an organism function the way they do because such traits presently contribute to the overall organization of the organism (Cummins) as well as were selected for in the organism's species' recent ancestry (Griffiths/Godfrey-Smith).
In this paper, I argue that starting with the organelles that constitute a cell--and continuing up the hierarchy of components in processes and subsystems of an organism--there are clear instances of ...emergent biological phenomena that can be considered "living" entities. These components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy. I call this view the homeostatic organization view (HO V) of biological phenomena and, as is shown, it comports well with the standard philosophical accounts of nomological (metaphysical) emergence and representational (epistemological) emergence. To proffer HO V, I describe properties of biological entities that include internal-hierarchical data exchange, data selectivity, informational integration, and environmental-organismic information exchange. Further, a distinction is drawn between particularized homeostasis and generalized homeostasis, and I argue that because the various processes and subsystems of an organism are functioning properly in their internal environments (particularized homeostasis), the organism is able to exist as a hierarchically-organized entity in some environment external to it (generalized homeostasis). Stated simply: that components of biological phenomena are organized to perform some function resulting in homeostasis marks them out to be living emergent entities distinguishable, in description and in reality, from the very physico-chemical processes of which they are composed. Keywords: Data Selectivity, Hierarchical Organization, Homeostasis, Homeostatic Organization View, Information, Informational Integration, Integration, Selectivity
PDF
