Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant (...) to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable (...) strategy for the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is (...) designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of (...) the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

This is a commentary on the article by Augusto (2022; this issue) on categories and foundation ontology (FO). We agree that the notion of categories of kinds of elements to devise a FO deserves more attention than it has received to date. From a practical point of view sensu developing domain ontologies, however, it probably does not matter much as long as a FO is used and that that one was understood.

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and (...) familiarizing the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel (...) by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field. (shrink)

Words are indispensable linguistic tools for beings like us. However, there is not much philosophical work done about what words really are. In this paper, I develop a new ontology for words. I argue that words are abstract artifacts that are created to fulfill various kinds of purposes, and words are abstract in the sense that they are not located in space but they have a beginning and may have an end in time given that certain conditions are (...) met. What follows from this two-fold argument is that words, from an ontological point of view, are more like musical works, fictional characters or computer programs, than numbers or sets. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set (...) of principles learned from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Current controversies about knowledge integration reflect conflicting ideas of what it means to “take Indigenous knowledge seriously”. While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and integration failures. On (...) the one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by (...) taking account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General (...) Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational (...) modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the (...) anthropic principle of participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in (...) a variety of different domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) should be considered not as restricted to Substantial types but instead should be applied to model Endurant Types in general, including Relator types, Quality types and Mode types. We also contribute a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

This work aims to make tense logic a more robust tool for ontologists, philosophers, knowledge engineers and programmers by outlining a fusion of tense logic and ontology of time. In order to make tense logic better understandable, the central formal primitives of standard tense logic are derived as theorems from an informal and intuitive ontology of time. In order to make formulation of temporal propositions easier, temporal operators that were introduced by Georg Henrik von Wright are developed, and (...) mapped to the ontology of time. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned (...) in the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the (...) view of brands as mere marks or names and interpret them as emergent products with properties that afford branding in the sense of Gibson’s ecological psychology. Brand strength is a function of the degree to which brands occupy defensible niches in product space. Branding as a process involves changing external or internal boundaries of products. Several arguments are proposed in favor of brand realism. The fragments of an ontology of marketing are developed in a broadly Aristotelian framework. Brand realism has significant implications for a new understanding of issues ranging from the effects of advertising to financial brand valuation, the nature of trademarks, and marketing strategy in general. It permits one to treat brand equity as a real phenomenon not dependent on associations, attitudinal states such as brand loyalty, or spurious constructs such as brand character or personality. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop (...) and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

I argue that current projects in ‘naturalized metaphysics’ fail to be properly naturalistic, and thereby fail in their stated aim to take one’s metaphysics from science. I argue that naturalism must involve the idea of taking science seriously, and that this can only be spelled out in terms of taking not only the theories of science seriously, but also its practice and its socio-linguistic situatedness seriously as well. This accords with naturalism because not doing so draws an artificial (non-natural) distinction (...) between the epistemic products of science as essence, and its socio-linguistic and practical features as accidents. The picture of naturalism which falls out of this is a form of pragmatism. Once this is spelled out, the question becomes, what is the appropriate attitude for the pragmatist/naturalist to have toward ontology? It is not the same as that of traditional metaphysics, since such an attitude (that metaphysical theorizing can make positive epistemic contributions) requires a priori commitments which themselves are (1) not subject to empirical review, and (2) are anthropocentric and so potentially distorted. But the pragmatist/naturalist will not go the opposite way, and say that metaphysics is meaningless either, since (true to their pragmatic commitments) ontology does things for the scientist and the layperson. It is a mistake to reject it wholesale, since the task of asserting what there is, exposing such an ontology to criticism, both empirical and logical, and revising it, has both small-scale and large-scale consequences. On the small-scale, ontologies are a guide for thinking—scientists, engineers, and lay people can and do use models of existence to navigate occurent problems in their day-to-day lives. Whether this is posing research hypotheses, developing protocols for generating new materials, or cooling off a cup of coffee, ontology plays a role. Large-scale consequences are more weighty, and more difficult to see. These large-scale consequences have to do with the aims and values which individuals and societies possess, and their interrelation with ontology. This certainly was at the forefront of the earliest ontologies—the Epicureans and Stoics built their moral philosophy on the basis of what ontology they thought was correct. This sort of practice goes on, unabated, today, though with virtually no overt acknowledgement of this important interdependency. How, for the pragmatist, do we make sense of ontological talk, if we are to eschew traditional metaphysics? Ontology—the naturalist/pragmatist declares—is a tool. Ontology helps us do things, whether it be predict behavior, understand phenomena, blame or forgive someone, and hope or despair about a life after this one (for example). Building an ontology is about building our own concepts, and this, in turn is a negotiation between our beliefs, experiences, and commitments, and the beliefs, experiences, and commitments of with whom we’re discursively engaged. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult (...) to extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Objective – is to formulate a methodological discourse regarding the place and role of the language interconnected with the process of socialization of a person and develop a systemic idea of the corresponding functional features. -/- Materials & Methods – this discourse is formulated on the basis of a systemic idea of the personality socialization, which, in turn, is realized using the structural-ontological method of studying the subject matter field in interdisciplinary researches. This method involves the construction of special visual-graphic (...) matrices that reflect the interaction of the primary process and the material of the studied system. -/- Results. The work with the structural-ontological matrix made it possible to analyze the functions of the language in the context of such significant factors of socialization as complex psychodynamics, civilization space and the function of reflection. At the same time, reflection is considered at the level of two plans – primary (reflection-bond) and secondary (reflection-splitting). This made it possible to deduce the idea of the role of language beyond the traditional framework of working with text and analyze the place of the language in the context of activities to establish a connection between individuals, which is realized in a specific cooperative situation (Shchedrovitsky). In particular, the look at language as a specific tool of civilizational rationing, the mechanism of which is provided through reflection-communication. Thus, the language is examined through the prism of its systemic influence on the morphology of the psyche. -/- Conclusions – a structural-ontological analysis of the place and role of language in the process of personality socialization has led us to construction of a hypothesis about the phenomenon of language discontentment, as a tendency to distance away ego-consciousness in the process of individuation from linguistic ontology. The arguments were also advanced in favor of the assumption regarding the peculiarities of the influence of language discontentment on cultural activities and the psychodynamic contribution of this phenomenon in the midlife crisis (Jung). (shrink)

This paper aims to evidence the meaning of “ontology of present”, a concept elaborated by Michel Foucault, and intends to elucidate the philosopher’s idea that subjectivity is historically formed. The context of the concept’s emergence will be analyzed, considering Foucault’s studies on the ancient greco-roman moral, in which he discuss the role of liberty and autonomy in the development of citizens. To the philosopher, the ontology of present consists in a critic of the domination and subjugation mechanisms, (...) produced by disciplinary and control societies. With this critic, Foucault pictures theoric tools to analyze the actuality, making possible to transform the historical processes of subjectification. Keywords: ontology of the present; subjectivity; history; Michel Foucault; actuality. (shrink)

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest (...) on a sound ontology of social interaction. We illustrate this thesis in relation to the HL7 RIM, which is one centrally important tool for communication in the healthcare domain. (shrink)

Creations of many contemporary artists indicate the emergence of technoculture. Although artistic manifestations of technoculture may appear to be a provocation, they encourage fundamental ontological questions, such as whether a person has unchanging nature; what was and is our relationship to the Other, and what it should be; to what extent can body and mind be altered before they stop being “human”; what is the future of our species. To properly understand the works of technoculture artists, it appears necessary to (...) have a thorough grasp post- and transhumanism as their key sources of inspiration. As a result, the developed tools will be employed to indicate which aspects of technoculture are a manifestation of post- and transhumanist ideas. This analysis is based primarily on the works of Stelarc and Orlan – two widely commented artists of technoculture. (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which (...) may however provide general lessons for the developers of ontologies in the future. (shrink)

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the (...) mathematical practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of “geometric judgments” from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) “space” should be revisited for the purposes of life sciences. (shrink)

This paper is concerned with certain ontological issues in the foundations of geographic representation. It sets out what these basic issues are, describes the tools needed to deal with them, and draws some implications for a general theory of spatial representation. Our approach has ramifications in the domains of mereology, topology, and the theory of location, and the question of the interaction of these three domains within a unified spatial representation theory is addressed. In the final part we also (...) consider the idea of non-standard geographies, which may be associated with geography under a classical conception in the same sense in which non-standard logics are associated with classical logic. (shrink)

Conceptual models as representations of real-world systems are based on diverse techniques in various disciplines but lack a framework that provides multidisciplinary ontological understanding of real-world phenomena. Concurrently, systems’ complexity has intensified, leading to a rise in developing models using different formalisms and diverse representations even within a single domain. Conceptual models have become larger; languages tend to acquire more features, and it is not unusual to use different modeling languages for different components. This diversity has caused problems with consistency (...) between models and incompatibly with designed systems. Two main solutions have been adopted over the last few years: (1) A currently dominant technology-based solution tries “to harmonize or unify” models, e.g., unifies EER and UML. This solution would solidify modeling achievements, reaping benefits from huge investments over the last thirty years. (2) A less prevalent solution is to pursuit deeper roots that reveal unifying modeling principles and apparatuses. An example of the second method is a “category theory”-based approach that utilizes the strengths of the graph and set theory, along with other topological tools. This manuscript is a sequel in a research venture that belongs to the second approach and uses a model called thinging machines (TMs) founded on Stoic ontology and Lupascian logic. TM modeling contests the thesis that there is no universal approach that covers all aspects of an application, and the paper demonstrates that pursuing such universality is anything but a dead-end method. This paper continues in this direction, with emphasis on TM foundation (e.g., existence and subsistence of things) and exemplifies this pursuit by proposing an alternative representation of set theory. (shrink)

Standpoint epistemology has been linked with increasing calls for deference to the socially marginalized. As we understand it, deference involves recognizing someone else as better positioned than we are, either to investigate or to answer some question, and then accepting their judgment as our own. We connect contemporary calls for deference to old objections that standpoint epistemology wrongly reifies differences between groups. We also argue that while deferential epistemic norms present themselves as a solution to longstanding injustices, habitual deference prevents (...) the socially dominant from developing for themselves the skills necessary to expand their capacity for empathy, to deftly probe for evidence, and to ask critical questions. Consequently, we argue that standpoint epistemology must be understood as calling for inclusion, not deference. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, (...) agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

This monograph offers a fresh perspective on the applicability of mathematics in science. It explores what mathematics must be so that its applications to the empirical world do not constitute a mystery. In the process, readers are presented with a new version of mathematical structuralism. The author details a philosophy of mathematics in which the problem of its applicability, particularly in physics, in all its forms can be explained and justified. Chapters cover: mathematics as a formal science, mathematical ontology: (...) what does it mean to exist, mathematical structures: what are they and how do we know them, how different layers of mathematical structuring relate to each other and to perceptual structures, and how to use mathematics to find out how the world is. The book simultaneously develops along two lines, both inspired and enlightened by Edmund Husserl’s phenomenological philosophy. One line leads to the establishment of a particular version of mathematical structuralism, free of “naturalist” and empiricist bias. The other leads to a logical-epistemological explanation and justification of the applicability of mathematics carried out within a unique structuralist perspective. This second line points to the “unreasonable” effectiveness of mathematics in physics as a means of representation, a tool, and a source of not always logically justified but useful and effective heuristic strategies. (shrink)

Attempting art: an essay on intention-dependenceIt is a truism among philosophers that art is intention-dependent—that is to say, art-making is an activity that depends in some way on the maker's intentions. Not much thought has been given to just what this entails, however. For instance, most philosophers of art assume that intention-dependence entails concept-dependence—i.e. possessing a concept of art is necessary for art-making, so that what prospective artists must intend is to make art. And yet, a mounting body of anthropological (...) and art-historical evidence and philosophical argument suggests that not only is such a criterion unsatisfied by most of the art-historical canon, but it also rests on a false premise: concepts of 'art' are not shared between cultures, nor even in the same culture across time. My dissertation aims to rectify this error by first exploring what our commitment to art's intention-dependence actually entails, and then showing that, properly understood, intention-dependence sets a number of important constraints on theories of art with respect to explanatory desiderata such as the success- and failure-conditions of art-attempts, the cross-cultural identification of art, and the reference of 'art' and art-kind terms. I begin by situating art's intention-dependence in the philosophical literature on intentional action, arguing that, properly conceived, intention-dependence is a weak criterion which can be satisfied either directly or indirectly. It therefore does not necessarily entail concept-dependence. I then use this distinction to motivate a new treatment of the success- and failure-conditions for art-attempts, arguing that the extant model's emphasis on compliance with 'the manner intended' is far too restrictive to capture actual artistic practices. I go on to show that Ruth Millikan's model of linguistic conventions supplies an independently plausible explanation of art's concept-independent origins in terms of the development of a system of indirectly intention-dependent conventions called an 'artworld'. I argue that this account of artworld development supplies us with the tools we need to distinguish art-kinds from other artifactual kinds. Finally, I turn my attention to methodological issues, arguing that even though 'art' is a social kind with its roots in arbitrary and historically-contingent networks of conventions, the philosophy of art is not merely an exercise in bare conceptual analysis. In fact, there is now a great deal of evidence to show that the ways we think about 'art' are inconsistent, incomplete, imperialistic, and largely unprincipled. Yet I argue that this does not mean that the artworld data have no bearing on theories of art. Instead, I argue that our best reflective understanding of our artworld practices sets the constraints on the reference of 'art' and art-kind terms. I argue that we have no privileged epistemic access to the ontology of social kinds; our only privilege lies in our ability to determine the proper subject of our inquiries. (shrink)

In the quest for a new social turn in philosophy of science, exploring the prospects of a Vygotskian perspective could be of significant interest, especially due to his emphasis on the role of culture and socialisation in the development of cognitive functions. However, a philosophical reassessment of Vygotsky's ideas in general has yet to be done. As a step towards this direction, I attempt to elaborate an approach on scientific representations by drawing inspirations from Vygotsky. Specifically, I work upon (...) Vygotsky’s understanding on the nature and function of concepts, mediation and zone of proximal development. -/- I maintain that scientific representations mediate scientific cognition in a tool-like fashion (like Vygotsky’s signs). Scientific representations are consciously acquired through deliberate inquiry in a specific context, where it turns to be part of a whole system, reflecting the social practices related to scientific inquiry, just scientific concepts do in Vygotsky’s understanding. They surrogate the real processes or effects under study, by conveying some of the features of the represented systems. Vygotsky’s solution to the problem of the ontological status of concepts points to an analogous understanding for abstract models, which should be regarded neither as fictions nor as abstract objects. -/- I elucidate these views by using the examples of the double-helix model of DNA structure and the development of our understanding of the photoelectric effect. (shrink)

Developing tools is a crucial aspect of experimental practice, yet most discussions of scientific change traditionally emphasize theoretical over technological change. To elaborate on the role of tools in scientific change, I offer an account that shows how scientists use tools in exploratory experiments to form novel concepts. I apply this account to two cases in neuroscience and show how tool development and concept formation are often intertwined in episodes of tool-driven change. I support this view (...) by proposing common normative principles that specify when exploratory concept formation and tool development succeed to initiate scientific change. (shrink)

This paper presents a diagrammatic notation for visualizing epistemic entities and relations. The notation was created during the Visualizing Worldviews project funded by the University of Toronto’s Jackman Humanities Institute and has been further developed by the scholars participating in the university’s Research Opportunity Program. Since any systematic diagrammatic notation should be based on a solid ontology of the respective domain, we first outline the current state of the scientonomic ontology. We then proceed to providing diagrammatic tools (...) for visualizing the epistemic entities and relations of this ontology. These basic diagramming techniques allow us to construct diagrams of various types for both synchronic and diachronic visualizations. The paper concludes by highlighting some future research directions. As the notation presented here is de facto accepted and used in scientonomy, the paper suggests no modifications. (shrink)

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, sequence, expression, (...) boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics. (shrink)

PHILOSOPHY OF HUMAN RIGHTS: HUMAN RIGHTS IN LIGHT OF THEIR INTERNATIONAL PROTECTION Summary The book consists of two main parts: in the first, on the basis of an analysis of international law, elements of the contemporary conception of human rights and its positive legal protection are identified; in the second - in light of the first part -a philosophical theory of law based on the tradition leading from Plato, Aristotle, and St. Thomas Aquinas is constructed. The conclusion contains an application (...) of the results of the analysis conducted in the second part. The first part comprises four chapters. The first aims at revealing characteristics of human rights on the basis of an analysis of historical conditioning of the inter-national law of human rights and its development. The historical context displays the practical, vindicative, and critical character of the positive legal protection of human rights. Moreover, the process of change of positive human rights law is distinguished from the process of change of human rights as such. In the second chapter the content of human rights - a topic which is only auxiliary to the conducted analysis - is discussed. Basic typology and catalogues of rights proclaimed in the Universal Declaration of Human Rights and protected in the International Covenants of Human Rights are presented. The review of the content of rights aims at a more precise limitation of the field of research. The examination shows a diversity of rights which poses a serious challenge to the coherence of every philosophical theory of human rights. In the third chapter, central in the first part, international law is analyzed with regard to the characteristics of rights and the foundations of them. The analysis of documents shows a number of solutions referring to the anthropological foundations of rights. The inherent dignity of the human person is the source of all human rights. Each human being is recognized as free, and endowed with both reason and conscience. In the propounded conception of man individuals are not rivals but create a community which is a condition for their development. International law characterizes the rights as universal, inherent, inalienable and inviolable. The reconstructed conception also comprises the following basic elements: on the level of the structure of rights, a recognition of their equality, interdependence, and comprehensiveness; in the grounding of these rights, a recognition of the anthropological foundations of law; in the conception of positive law, a recognition of the secondariness of the positive law of human rights to human rights themselves, and a recognition of human rights and justice as the basis for legal order; in the conception of state, a recognition of the well-being of the individual as the fundamental aim of actions undertaken by political institutions, and recogni¬tion of rights which form an impassable boundary to the power of the state, includ¬ing its legislative actions. The characterization of the international legal paradigm serving for the under¬standing of human rights is supplemented by analyses of the structure of their posi¬tive legal protection. Various meanings of the terms "right" and "freedom" are distinguished. Subjective right, as basic structure of the positive legal protection of human rights, is understood as a complex relation formed by various legal situations of the subject of a right which create a functional whole in respect of the subordi-nation of human person to its good. Subordinating person to a good proper for it, expressed usually in a proclamatory norm, is the central element of particular rights around which further elements aiming at the realization of this good are built. In the second part of the book a philosophical theory is developed which allows for the location of a coherent foundation for the presented characterization of human rights and their positive legal protection. This part consists of two chapters. The first includes a review of some - not entirely satisfactory - means of founding of human rights; the second presents philosophical conceptions of law and man which may form a basis for the constructed theory. The review of arguments contained in the first chapter does not aim at a detailed analysis of various specific ways of argumentation encountered in works on this subject but rather at a concise presentation of the main possible lines of argumentation. These analyses also serve to emphasize the positive solutions which are pro¬posed later and to underscore the explanatory power of the elaborated theory. This theory, retaining accurate intuitions contained in the presented types of argumenta¬tion, helps in avoiding their consequences which are difficult to reconcile with the reconstructed paradigm of human rights. Efforts to base human rights on the norms of international law rightly take into account the necessity of determining the content of the rights and their positive legal protection as a means for the realization of man's good. These attempts, how¬ever, do not properly take into account the inherent character of human rights, which are independent of positive law and provide grounds for applying specific legislative measures and not others. Founding human rights on freedom accurately points at the freedom of an indi¬vidual as a constitutive element of some rights; however, absolutization of freedom leads, to a loss of an important element of the contemporary paradigm of under¬standing human rights. This foundation undermines recognition of the fact that human rights may set limits to both the freedom of others and the freedom of the subject of rights itself. Additionally, attempts at the so-called axiological justification of human rights are discussed. This type of justification has a few variants depending on the as¬sumed conception of value. Subjectivistic conceptions have similar advantages and disadvantages to the conceptions basing human rights on freedom; objectivistic conceptions while providing for the universality of human rights place, the fundamental aim of human rights protection beyond the individual human being - in the idealistically existing world of values; finally, conceptions rooting values and human rights in culture, while accurately noting that human rights are learned through the medium of culture, place the source of human rights beyond a concrete individual - in culture and processes which take place in it - which leads to difficulties in finding a basis for the universality of rights. Furthermore, attempts to ground human rights in specific characteristics of the human being are presented. This type of approach points to an important problem of dependence of the content of rights on what man is. However, recognition of specific characteristics of a human being as an ontic foundation of the existence of rights poses a danger to their universality since one has to accept that it is not enough to be a man to be a subject of rights, but a man possessing specific charac¬teristics. The second chapter aims at outlining solutions worked out by Saint Thomas Aquinas. For a fuller understanding of his propositions selected elements of Plato's and Aristotle's philosophy are presented. It was them who formulated the founda¬tions for reflection on law and justice in the ontological context. A qualification is made that Stoicism is not be analysed in depth. Although Thomas' concept of law was undoubtedly developed under the influence of the Stoic doctrine as well, it is not in this that one should look for the tools to understand the ontic foundations of human rights and law in general since the Stoic moral philosophy and philosophy of law were developed in the context of a theory of being which assumed monistic and pantheistic premises as foundations, leading to the recognition of a total subor¬dination of the human individual to a larger unity of which man is only a part. The analysis of Plato's and Aristotle's texts concentrates on problems of justice. Plato seems to be the first philosopher who reflected on the formula basic in the history of European thought: to render to each his due. It appears that justice as both a characteristic of man and his acts is understood in the perspective of that which is just, that which is a good for another man - the recipient of the act. The basis for determining what is just is the relation of correspondence between some¬one and something. While in the case of Plato this relation is based on something beyond its terms, namely on ideas, in the case of Aristotle the relation occurs on account of the elements of the relation itself. Something is just when it contributes to the develop¬ment of the recipient of an act realizing that which is just. At the same time, the realization of that which is just is a good for the agent. In the analysis of the just two types of relation are revealed: the relation of due-to-recipient occurring on account of the compatibility of that which is due, with the recipient of the act; and - a "superstructure" - a relation of obligation-of-subject occurring on account of the compatibility of the acting subject with the thing which should be done. The basis for being that which is due is formed by various potentialities of development of man - the recipient of agency; the basis of being that which is an obligation is the possibility of development of the subject of action. Aristotle distinguishes various types of freedom and points to the necessity of taking them into account in the discussion of justice. Among other things, as the core of man's freedom, he considers life for its own sake, which can be seen as his expression of the basic indices of the autotelic character of man - which is funda¬mental for later conceptions of dignity. The freedom which is described by him is not, however, inherent and inalienable; being free is conditioned by a factual possi¬bility of undertaking actions, which are not solely means to the realization of aims set by others. Thomas Aquinas takes over the Aristotelian research perspective both in his conception of man and of law. At the same time, however, he significantly enriches it. In anthropology he develops a conception of personal being. Drawing upon his distinction between existence ("that something is") and essence ("what something is"), he sees the basis for being a person in the dignity of personal being which is a certain way of existence of a rational being more perfect than that of non-personal beings. The person is a being which, by virtue of its act of existence, is individual¬ized in a specific way. It is an aim in itself. Expressing it in a negative way, one may say that it does not exist as a means for the realization of the aims of others and, in this sense, that it is free. As distinct from Aristotelian conclusions, being a person is not conditioned by the specific actions of a being. Dignity is inherent, based on that which is the foundation of the factual existence of every rational being. Although freedom requires that a being is rational, dignity still encompasses all being, all its properties and potentialities. Thus an act conforming with dignity has to take into account a whole human being. Among different types of that which is just, ius, the first place, from the point of view of understanding law, falls to "the just thing itself ("ipsa res justa"), which is right in the full meaning of the word. On the one hand, it is that which is due; on the other hand, it determines the way of acting in the utmost degree, since the course of every act is determined in the fullest extent by its aim. The content of ius may be determined both by elements independent of free decisions - ius naturale - and by free decisions taking into account the state of things - ius positivum. Recognition of the objective structure of being as the basis of law does not entail that it is possible or desirable to determine unequivocally "the only right" patterns of conduct. This concept is very well justified within the system proposed by Saint Thomas. Individualization of being is a significant element of the develop¬ment of a person as a person. It is attained by the realization of individual aims which are not unequivocally determined by circumstances and the nature common to all people. By virtue of free choices made in the sphere of that which is not by its nature unjust, the object of action becomes ius. Since in the realization of the person the individualization of human being is central, Aquinas clearly sees the need for the protection of the sphere of "dominion of will". This sphere itself constitutes ius naturale, something which is due to man independently of the acts of will. Therefore "law should forbid nothing which is not unjust" ("nihil debet lege prohiberi quod licite fieri potest", In 3 Sent., dist. 40, q. I, a. 1, 3). Besides the relation of due-to-recipient, ius also includes the relation of obligation-of-subject which is superimposed on the relation of due-to-recipient. As far as the ontic foundations of obligation are concerned, in explaining why man is subordinated to realization of the good of others, Aquinas generally follows Aristotle in accepting that this basis is the subordination to moral good - to actions conforming with the learned truth about reality. Aquinas' systemic solutions allow, however, to reach deeper and understand why moral development is also a development of the whole human being. This was difficult within Aristotle's system, since he was reluc¬tant to decide whether precedence should be given to intellectual or moral develop¬ment. The inclination to realise good of another appears to be a transcendental characteristic of being, based on its very existence. Morality understood as rational and free subordination to realize the good of another is a specifically personal way of the realization of this inclination. Thus just actions contribute to the actualization of being in the aspect of its existence and therefore to the actualization of being as a whole. Thomas' conception of natural law (lex naturalis) as participation in eternal law (lex aeterna), offers possibilities for grasping that which is just as something which is basically accessible cognition, independently of Revelation and independently of faith in God, and at the same time as something based in eternal law, understood as a design of God's wisdom. Eternal law, embracing all particular actions, is not, from the human perspective, accessible cognition directly. It is enacted in the struc-ture of the created being and - in case of human beings - in free choices taking this structure into account. In the concluding remarks, the results obtained earlier are applied directly to the contemporary conception of human rights. Human rights are understood in the first place as "just things" - concrete goods of man; as that which is due because of subordination, based on dignity, to the personal development of man. That which is just is understood as a relational - actual or potential - state of things, which exists by virtue of existing relations. Evaluations referring to that which is right are true when respective relations of due-to-recipient take place; norms of conduct are true when respective relations of obligation-of-subject take place. Examples of the application of the sketched theory outside the field of human rights are also presented. Procedural consequences of the developed theory are shown, such as the discrimination of two types of legislative procedures which differ significantly in the structure of argumentation: the first aims at recognition of that which is just independently of the will of the legislator, and the second, at making individual or collective "projects" of development compatible. Finally the possibilities of applying the theory to the increasingly important problems of the protection of the environment and the "rights" of animals are mentioned. The central issue is a philosophical conception of man and his freedom and a conception of law. It is also indispensable to turn to a general theory of being. The search for a comprehensive theory of human rights requires attention to the Abso¬lute Being - God - as well. This is important for at least two reasons. First, a conception of the Absolute Being is integral to philosophy of the systemic type -of which the present book is a piece. A conception of the Absolute Being is signifi¬cant for understanding all being, including, first of all, man as a personal being. Second, every theory of human rights which does not comprise the problem of the Absolute may be questioned as to whether solutions adopted in it do not lead, in consequence, to eliminating God from the perspective of the understanding of law. It is desirable that a philosophical theory should deal with this problem directly. A theory which eliminates God from the perspective of the understanding of rights will be unacceptable for all those who, for philosophical reasons or relying on faith, consider God as the author of inherent rights. Nevertheless, a theoretical approach to rights from the perspective of the Absolute Being should only be a possible extension of a philosophical approach which bases rights on something which is cognizable independently of the acceptance of the existence of God so that the theory is also acceptable for those who reject the existence of God or suspend their judgment on this subject. The pursued theory should therefore contain, on the one hand, reference to natural, faith-independent foundations of human rights, but on the other hand, point to a possible extension accounting for the Absolute Being. The analyses contained in this chapter have undoubtedly some historical value since they are based on source texts. Nevertheless, the use of these texts and not critical works was dictated, first of all, by a conviction that analyses embrace a given theory in the aspect selected by the interests of the researcher. Therefore to find out what past thinkers say on the subject characterized in the first part it is simpler to reach to the sources than to adopt the existing critical works. The pre¬sented reconstruction of Aquinas' views on philosophy of law incorporates proposi¬tions of supplementing and developing some of the ideas undertaken by him. Obligation to act in this and not an other way arises because human actions are subordinated to the conformity, on the one hand, of aims realized by these actions and, on the one hand, the order of being determining that which is favourable to man or destroys him. The content of the order of being is, on the one hand, determined by the structure of being independent from man's will and, on the other, by free decisions of man. (shrink)

The History of Ideas is presently enjoying a certain renaissance after a long period of disrepute. Increasing quantities of digitally available historical texts and the availability of computational tools for the exploration of such masses of sources, it is suggested, can be of invaluable help to historians of ideas. The question is: how exactly? In this paper, we argue that a computational history of ideas is possible if the following two conditions are satisfied: (i) Sound Method . A computational (...) history of ideas must be built upon a sound theoretical foundation for its methodology, and the only such foundation is given by the use of models , i.e., fully explicit and revisable interpretive frameworks or networks of concepts developed by the historians of ideas themselves. (ii) Data Organisation. Interpretive models in our sense must be seen as topic-specific knowledge organisation systems (KOS) implementable (i.e. formalisable) as e.g. computer science ontologies. We thus require historians of ideas to provide explicitly structured semantic framing of domain knowledge before investigating texts computationally, and to constantly re-input findings from the interpretive point of view. In this way, a computational history of ideas maximally profits from computer methods while also keeping humanities experts in the loop. We elucidate our proposal with reference to a model of the notion of axiomatic science in 18th -19th century Europe. (shrink)

Consciousness has been the bone of contention for philosophers throughout centuries. Indian philosophy largely adopted lived experience as the starting point for its explorations of consciousness. For this reason, from the very beginning, experience was an integral way of grasping consciousness, whose validity as a tool was considered self-evident. Thus, in Indian philosophy, the question was not to move from the brain to mind but to understand experience of an individual and how such an experience is determined through mental structures (...) (and secondarily, the preoccupation with the brain and its relation to the mind). In contrast, cognitive science (the study of mind and cognition through 1 interdisciplinary methods, with emphasis on computational methods) found its debates soaked in discussion which primarily involved the brain and mind. Experience was not considered a primary source of information and its validity had to be established to consider it a source of information of mind. With the rise of physicalism and realization that mental states are correlative to brain states, the body was virtually neglected from involvement in understanding the mind and the attempts to reduce mind to the brain were rampant. The inability to explain subjective experience of an individual through neuroscientific findings alone has urged philosophers to explore other ways of understanding the ontology of mind. Over the last few years, embodied cognition and enactive approach have brought back the body as a central participant in this debate, providing fertile grounds to explain the relation of brain, body and mind. This paper proposes that we understand the brain as a complex system from which the mind emerges. This emergence is marked by the development of novel property of self-consciousness in human beings. The mind is a process which is embedded throughout the body and thus, the body acts as an actualizing medium for the individual. Thus, the brain is a necessary condition for the mind to be while the mind is embedded throughout the body. The brain and mind are in reciprocal causal relationship with one another, as is the body and environment with one another. In this paper, embodied cognition is understood through principles of Merleau Ponty's idea of embodiment, than through Andy Clark and Francis Varela's alone. (shrink)

Formal ontology as it is presented in Husserl`s Third Logical Investigation can be interpreted as a fundamental tool to describe objects in a formal sense. It is presented one of the main sources: chapter five of Carl Stumpf`s Ûber den psycholoogischen Ursprung der Raumovorstellung (1873), and then it is described how Husserlian Formal Ontology is applied in Fifth Logical Investigation. Finally, it is applied to dramatic structures, in the spirit of Roman Ingarden.

Two stories have dominated the historiography of early modern philosophy: one in which a seventeenth century Age of Reason spawned the Enlightenment, and another in which a skeptical crisis cast a shadow over subsequent philosophy, resulting in ever narrower "limits to knowledge." I combine certain elements common to both into a third narrative, one that begins by taking seriously seventeenth-century conceptions of the topics and methods central to the rise of a "new" philosophy. In this revisionist story, differing approaches to (...) the central subject matter of early modern metaphysics--knowledge of substances through their essences and causal powers--arise as a result of disagreements about the powers of the human cognitive faculties. Methodological writings are seen as attempts to direct readers in the proper use of their cognitive faculties. The early modern rejection of the Aristotelian theory of cognition ranks equally in importance with rejection of Aristotelian doctrines about nature. Skepticism is more often than not a tool to be used in teaching the reader the proper use of the cognitive faculties, or indeed in convincing the reader of the existence or inexistence of certain cognitive faculties or powers. Instead of early modern "epistemology" or "theory of knowledge," one speaks, with seventeenth century writers, of theories of the cognitive faculties and their implications for the possibility of human knowledge. The early modern rejection of Aristotelian logic can then be seen as reflecting a negative assessment about the fit between syllogistic reasoning and logic as an art of reasoning or thinking which refines the use of the cognitive faculties. -/- Central to this new historiography is the story of the relation between the intellect and senses as cognitive faculties or powers. The development of philosophy from Descartes to Kant can be portrayed as a series of claims about the power of the intellect to know the essences of things, with resulting consequences for ontology and the foundations of natural philosophy. I illustrate this revised narrative by comparing three conceptions of the intellect in three philosophical settings, provided by several late scholastic Aristotelians, Descartes, and Locke. I have two aims: first, to exhibit the central role played by the conception of intellect or understanding in these authors, and, second, to locate their discussions of the cognitive faculties in relation to recent understandings of psychology, epistemology, logic, mind, and their relations. Early modern writings do not easily fit into the modern categories of epistemology and psychology; more generally, the early modern concern with the workings of mind does not coincide with recent conceptions of naturalism. These findings can help us to see problems with our current categories. (shrink)

What’s important about ‘coming out’? Why do we wear business suits or Star Trek pins? Part of the answer, we think, has to do with what we call agential identity. Social metaphysics has given us tools for understanding what it is to be socially positioned as a member of a particular group and what it means to self-identify with a group. But there is little exploration of the general relationship between self-identity and social position. We take up this exploration, (...) developing an account of agential identity—the self-identities we make available to others. Agential identities are the bridge between what we take ourselves to be and what others take us to be. Understanding agential identity not only fills an important gap in the literature, but also helps us explain politically important phenomena concerning discrimination, malicious identities, passing, and code-switching. These phenomena, we argue, cannot be understood solely in terms of self-identity or social position. (shrink)

Is the Smartphone (SP) an extension of consciousness or just an (other) externalization of the mind and an extension of the social? The concept of externalizing the mind more appropriately describes a series of processes that tend to be considered extensions of the mind. The human mind has evolved concurrently with various externalizations, such as utensils and language, as contributions to the development of the common environment of humanity: culture and civilization. Externalizations indicate the appearance of the human mind (...) while the extensions take into account the possibility of passing to another level (the singularity of consciousness). SP is a handy tool that mediates the personal relationship with the world, benefiting from a level of integration into the global workspace of the mind. Externalization called the SP could be a bridge from the externalization of the mind to its extensions, making the ontological leap from the utensil status to that of "part of the mind". SP is a mediator of an environment: it mediates between the mind and a special social environment called the Internet (mediates access to cognitive support provided by society through the virtual world), which is gradually becoming another reality. SP is part of the extension of human society by introducing tools into the network of personal relationships. Not the mind is expanded, but the social network, increasing the number of entities with which the human can create and maintain relationships. SP may be an extension of the social rather than an extension of the mind because it mediates an increase in the complexity of social relations that can lead to the emergence of "collective minds" (causing a change in the ontological status of society). Changing cognitive demands is a feature of the world's progress. Progress brings along with it cognitive costs of integration, technical solutions like SP, aimed at reducing these costs, generating an evolutionary advantage in the new social context. From an evolutionist perspective, the world means precisely this kind of modification of cognitive demands necessary for survival, SP joining the set of tools that mediate the cognitive progress of the world in which the human is inserted. We propose the use of an evolutionary cognitive economy principle, based on avoiding unnecessary costs, reducing losses and optimizing cognitive gains. (shrink)