BFO and DOLCE: So Far, So Close…

A survey of the similarities and differences between BFO and DOLCE, and of the mutual interactions between Nicola Guarino and Barry Smit

Social Objects

One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psychological environments of cognitive subjects and the different sorts of external (physical, geographical, social) environments which they inhabit. The present essay addresses this environmental version of the problem of intentionality. It draws not only on the work of Husserl and Scheler but also on the Gestalt psychological writings of Kurt Koffka and Kurt Lewin. It considers the influential subjective idealist theory of animal environments put forward by J. von Uexküll and contrasts this with a realist theory of organism-environment interaction based on the work of the ecological psychologists J. J. Gibson and Roger Barker. This realist theory is then exploited as a basis for an ontology of social objects of a range of different sorts. (This is the English original of the French translation.

The Foundational Model of Anatomy Ontology

Anatomy is the structure of biological organisms. The term also denotes the scientific discipline devoted to the study of anatomical entities and the structural and developmental relations that obtain among these entities during the lifespan of an organism. Anatomical entities are the independent continuants of biomedical reality on which physiological and disease processes depend, and which, in response to etiological agents, can transform themselves into pathological entities. For these reasons, hard copy and in silico information resources in virtually all fields of biology and medicine, as a rule, make extensive reference to anatomical entities. Because of the lack of a generalizable, computable representation of anatomy, developers of computable terminologies and ontologies in clinical medicine and biomedical research represented anatomy from their own more or less divergent viewpoints. The resulting heterogeneity presents a formidable impediment to correlating human anatomy not only across computational resources but also with the anatomy of model organisms used in biomedical experimentation. The Foundational Model of Anatomy (FMA) is being developed to fill the need for a generalizable anatomy ontology, which can be used and adapted by any computer-based application that requires anatomical information. Moreover it is evolving into a standard reference for divergent views of anatomy and a template for representing the anatomy of animals. A distinction is made between the FMA ontology as a theory of anatomy and the implementation of this theory as the FMA artifact. In either sense of the term, the FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Making use of explicit ontological principles and sound methods, it is designed to be understandable by human beings and navigable by computers. The FMA’s ontological structure provides for machine-based inference, enabling powerful computational tools of the future to reason with biomedical data

Stratification Economics and Identity Economics

Stratification economics represents an important new approach devoted to explaining economic inequality in terms of how social groups are separated or stratified along economic lines. This paper combines stratification economics with identity economics to address complications that the phenomenon of intersectionality – people having multiple social group identities – creates for stratification economics. It distinguishes two types of social identities recognized by social psychologists, categorical and relational social identities, and uses this distinction to explain how individuals’ personal identities, understood as ordered sets of social identities, can be seen to be both socially and self-constructed. Individuals order and rank their categorical social identities according to weights they assign to them in interactive social settings in which their role-based relational social identities combine different categorical social identities. Recent research in social psychology in the stigma identity threat literature is then reviewed to distinguish two different ways in which individuals respond to others’ stigmatization of their social groups in interactive settings. The paper argues that individuals respond to stigma by assigning weights to their categorical social group identities in ways that reflect both functional power relationships and stigmatization in a way that on balance tend to reinforce social stratification

On perception and ontology in the context of subjectivity and modern physics

I argue that our direct experience and some physical facts do not go well with an understanding of perception as a mechanism producing a representation of a ''truly'' outer world. Instead, it is much more coherent to treat what is traditionally considered an image in this context as a closed structure equipped in its own ontology, replacing the ''truly'' outer one from the point of view of an agent possessing it. In such a framework, the notion of existence is taken to be defined by consciousness in a way similar to qualia, making it subjective on the one hand, and reducing it to a tool on the other. This implies, in turn, that we need a form of mind-brain dualism; the best we can do in such circumstances about explaining consciousness as an epistemic device - a role intuitively imposing itself in a variety of situations - is to embed it in an abstract ontology merely serving the purpose of a ''true'' reality with the help of the mind-brain link. Obviously, the approach favors subjectivity as a foundation in the ontological sense. Objectivity is considered here only as a suitably understood product from an ''observer's'' point of view, although a functional and useful one. The paper is addressed to readers with interest in both the mind-body problem and ontological foundations of present-day physics, specifically quantum theory. The main conclusion can be absorbed without the quantum part, although it is a bit less convincing then

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

Normalized Affymetrix expression data are biased by G-quadruplex formation

Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure. This is most likely caused by the formation of G-quadruplexes, where inter-probe guanines form Hoogsteen hydrogen bonds, which probes with G-stacks are capable of forming. We demonstrate that for a specific microarray data set using the Human HG-U133A Affymetrix GeneChip and RMA normalization there is significant bias in the expression levels, the fold change and the correlations between expression levels. These effects grow more pronounced as the number of G-stack probes in a probe set increases. Approximately 14 of the probe sets are directly affected. The analysis was repeated for a number of other normalization pipelines and two, FARMS and PLIER, minimized the bias to some extent. We estimate that ∼15 of the data sets deposited in the GEO database are susceptible to the effect. The inclusion of G-stack probes in the affected data sets can bias key parameters used in the selection and clustering of genes. The elimination of these probes from any analysis in such affected data sets outweighs the increase of noise in the signal. © 2011 The Author(s)

Harvesting information from the Internet to construct ontologies

The paper evaluates the effectiveness of harvesting information from the internet to aid in the lowcost construction of an ontology. The paper describes how a proof-of-concept called OntoRanch was built, to harvest information and its relationships to construct an ontology. A systems development methodology was adopted which recognises three main stages: concept development, system building, and system evaluation. The evaluation took an interpretive hybrid approach of using both a focus group and a questionnaire to evaluate the proof-of-concept OntoRanch. The findings show that the approach of reusing information by harvesting it from the internet can provide an effective self-sustaining process that enables ontologies to be constructed in a reduced amount of time and cost