We study imagination as reality-oriented mental simulation : the activity of simulating nonactual scenarios in one’s mind, to investigate what would happen if they were realized. Three connected questions concerning ROMS are: What is the logic, if there is one, of such an activity? How can we gain new knowledge via it? What is voluntary in it and what is not? We address them by building a list of core features of imagination as ROMS, drawing on research in cognitive psychology (...) and the philosophy of mind. We then provide a logic of imagination as ROMS which models such features, combining techniques from epistemic logic, action logic, and subject matter semantics. Our logic comprises a modal propositional language with non-monotonic imagination operators, a formal semantics, and an axiomatization. (shrink)

It is well known that systems of action deontic logic emerging from a standard analysis of permission in terms of possibility of doing an action without incurring in a violation of the law are subject to paradoxes. In general, paradoxes are acknowledged as such if we have intuitions telling us that things should be different. The aim of this paper is to introduce a paradox-free deontic action system by (i) identifying the basic intuitions leading to the emergence of the paradoxes (...) and (ii) exploiting these intuitions in order to develop a consistent deontic framework, where it can be shown why some phenomena seem to be paradoxical and why they are not so if interpreted in a correct way. (shrink)

Currently available systems of action deontic logic are not designed to model procedures to assess the conduct of an agent which take into account the intentions of the agent and the circumstances in which she is acting. Yet, procedures of this kind are essential to determine what counts as culpable not doing. In light of this, we design an action logic, AL, in which it is possible to distinguish actions that are objectively possible for an agent, viz. there are no (...) objective impediments for the agent to do them, and actions that, besides being objectively possible, are compatible with the setting or intentions of the agent. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Intentionality is traditionally defined as the property of a mental state to be directed at something presented in a particular way. The fact that we can think about objects which do not exist makes this definition problematic: what kind of things are those objects? The aim of this paper is to analyse the definition of intentionality as a relation in theories which do not admit non-existent special entities. In particular, I consider John R. Searle and Tim Crane’s theories of intentionality (...) and I argue that neither Searle’s notion of a non-ordinary relation between the intentional state and the intentional object nor Crane’s idea of a relation between the intentional state and the intentional content succeed in holding together the traditional definition of intentionality and the purpose to not be committed to some kind of special entities. This intent seems finally hardly compatible with the traditional definition of intentionality. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

A famous programmatic phrase from the Soliloquia shows how the young Augustine, in his thirties, had a clear idea of what one had to investigate in order to attain a knowledge of God: “Deum et animam scire cupio”. Here, Augustine established a link between two objects of research. Starting from this relation, this article explores Augustine’s anthropological doctrine, and focuses on four images used by Augustine to illustrate the human condition: (1) the lamp (lucerna), symbolizing the man composed by a (...) body, which is the container, and by a soul enclosed in the body, which is the flame. (2) The knight (eques), where although it is the horse (equus) that gives the name to the compound and defines the characteristics of its rider, the term ‘eques’ does not in any way designate the horse. (3) The centaur (centaurus), which expresses the inseparable unity of the two natures but also their distinction. (4) The chariot (biga), which perfectly symbolizes the union between body and soul, by the horses, and introduces a reference to God, by the figure of the charioteer. (shrink)

The aim of this paper is to introduce a system of dynamic deontic logic in which the main problems related to the de finition of deontic concepts, especially those emerging from a standard analysis of permission in terms of possibility of doing an action without incurring in a violation of the law, are solved. The basic idea is to introduce two crucial distinctions allowing us to differentiate (i) what is ideal with respect to a given code, which fixes the types (...) of action that are abstractly prescribed, and what is ideal with respect to the specific situation in which the agent acts, and (ii) the transitions associated with actions and the results of actions, which can obtain even without the action being performed. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Semiotics has been making progressively inroads into marketing research over the past thirty years. Despite the amply demonstrated conceptual appeal and empirical pertinence of semiotic perspectives in various marketing research streams, spanning consumer research, brand communications, branding and consumer cultural studies, there has been a marked deficit in terms of consolidating semiotic brand-related research under a coherent disciplinary umbrella with identifiable boundaries and research agenda. -/- The Handbook of Brand Semiotics furnishes a compass for the perplexed, a set of anchors (...) for the inquisitive and a solid corpus for scholars, while highlighting the conceptual richness and methodological diversity of semiotic perspectives. -/- Written by a team of expert scholars in various semiotics and branding related fields, such as John A. Bateman, David Machin, Xavier Ruiz Collantes, Kay L. O’Halloran, Dario Mangano, George Rossolatos, Merce Oliva, Per Ledin, Gianfranco Marrone, Francesco Mangiapane, Jennie Mazur, Carlos Scolari, Ilaria Ventura, and edited by George Rossolatos, Chief Editor of the International Journal of Marketing Semiotics, the Handbook is intended as a point of reference for researchers who wish to enter the ‘House of Brand Semiotics’ and explore its marvels. -/- The Handbook of Brand Semiotics, actively geared towards an inter-disciplinary dialogue between perspectives from marketing and semiotics, features the state-of-the-art, but also offers directions for future research in key streams, such as: -/- · Analyzing and designing brand language across media · Brand image, brand symbols, brand icons vs. iconicity · The contribution of semiotics to transmedia storytelling · Narrativity and rhetorical approaches to branding · Semiotic roadmap for designing brand identity · Semiotic roadmap for designing logos and packaging · Sociosemiotic accounts of building brand identity online · Multimodality and Multimodal critical discourse analysis · Challenging the omnipotence of cognitivism in brand- related research · Semiotics and (inter)cultural branding · Brand equity semiotics Comparative readings of structuralist, Peircean and sociosemiotic approaches to brandcomms . (shrink)