The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This analysis shows Cantor's diagonal definition in his 1891 paper was not compatible with his horizontal enumeration of the infinite set M. The diagonal sequence was a counterfeit which he used to produce an apparent exclusion of a single sequence to prove the cardinality of M is greater than the cardinality of the set of integers N.

Physics has been slowly and reluctantly beginning to address the role and fundamental basis of the ‘observer’ which has until now also been considered metaphysical and beyond the mandate empirical rigor. It is suggested that the fundamental premise of the currently dominant view of ‘Cognitive Theory’ - “Mind Equals Brain” is erroneous; and the associated belief that the ‘Planck scale, ‘the so-called basement level of reality’, as an appropriate arena from which to model psycho-physical bridging is also in error. In (...) this paper we delineate a simple, inexpensive experimental design to ‘crack the so-called cosmic egg’ thereby opening the door to largescale extra dimensions (LSXD) tantamount to the regime of the unified field and thus awareness. The methodology surmounts the quantum uncertainty principle in a manner violating Quantum Electrodynamics, (QED), a cornerstone of modern theoretical physics, by spectrographic analysis of newly theorized Tight-Bound State (TBS) Bohr orbits in ‘continuous-state’ transition frequencies of atomic hydrogen. If one wonders why QED violation in the spectra of atomic hydrogen relates to solving the mind-body (observer) problem; consider this a 1st wrench in a forthcoming tool box of Unified Field Mechanics, UF that will soon enough in retrospect cause the current tools of Classical and Quantum Mechanics to appear as stone axes. Max Planck is credited as the founder of quantum mechanics with his 1900 quantum hypothesis that energy is radiated and absorbed discretely by the formulation, E = hv. Empirically implementing this next paradigm shift utilizing parameters of the long sought associated ‘new physics’ of the 3rd regime (classical-quantum- unified) allows access to LSXD of space; thus pragmatically opening the domain of mental action for the 1st time in history. This rendering constitutes a massive paradigm shift to Unified Field Theory creating a challenge for both the writer and the reader! (shrink)

It is possible and thereby feasible to develop and implement a pragmatic methodology for a preemptive evidentiary system of ‘Paraphysical Jurisprudence’ for mediating the occurrence of massacres. A required comprehensive completion and formalizing of the tools of epistemology (theory of knowledge) already exists and has been tested both ecumenically and scientifically. The evolution of epistemology has followed the historical progression from myth and superstition to logic and reason to empiricism and now finally to the utility of ‘transcendence’ as a tool (...) in knowledge acquisition. An inspiring example from popular culture is illustrated in the 2002 Hollywood film noir “Minority Report” designed by its director to present a ‘plausible future world’ for the year 2054 wherein an elaborate ‘Precrime Unit’ is tested to prevent murder by utilizing a trio of ‘precogs’ bathed in a ‘photonic milk’ able to presciently predetermine impending occurrences of homicide for which the Precrime Police Unit then intervenes to prevent. Disdain for a putative so-called scientific metaphysics by natural philosophers is deeply rooted in modern pragmatic societies; perhaps rightly so as consistency, credibility and lack of a comprehensive theory has been heretofore emphatically lacking. In addition to the major problem of repeatability is the perceived distinction between domains of the physical and so-called ‘spiritual’ as mutually exclusive. In this work a strong case is made for the rigorous viability and near term putative implementation of a system of paraphysical jurisprudence drawing on the utility of a panoply of concepts. The remaining question is when does feasible become practical in the face of a steady increase in the heinous massacre of innocents? (shrink)

Delineating the framework for a fundamental model of long-range coherence in biological systems is said to rely on principles beyond parameters addressed by current physical science. Just as phenomena of quantum mechanics lay beyond tools of classical Newtonian mechanics we must now enter a 3rd regime of unified field, UF mechanics. In this paper we present a battery of nine empirical protocols for manipulating long-range coherence in complex self-organized living systems (SOLS) in a manner surmounting the Copenhagen Interpretation of quantum (...) uncertainty (space-quantization) thereby allowing empirical access to underlying coherent biophysical principles driving self-organization. Interestingly, while the UF is not indicative of a 5th fundamental force in the usual phenomenal sense of quantal transfer during field interactions; it does however provide an inherent ‘force of coherence’ in an energyless ontological sense by a process called ‘topological switching’ of higher dimensional (HD) brane dynamics. It is this putative inherent property that produces long-range coherence and leads to the possibility of its direct experimental mediation. (shrink)

Seminal work intended to found a new field of integrative Noetic Science is summarized. Until now the philosophy of Biological Mechanism has ruled medicine and psychology. Penrose claims, AA scientific world-view which does not profoundly come to terms with the problem of conscious mind can have no serious pretensions of completeness@. A noetic action principle synonymous with the historic concept of élan vital is introduced as the basis of a Continuous State Conscious Universe (CSCU). The least unit of CSCU superspace (...) defines Awareness as a fundamental physical quantity like charge in electrodynamics. This cosmological context reveals the origin of complexity in self-organized living-systems wherein the physical basis of qualia is formalized. The dynamics of this teleological action principle, mediated by a unitary noetic field pervading all biochemical species, optimizes the state of well-being through homeostasis and provides the fundamental basis for developing a Moral Psychology. (shrink)

Recalling Thomas Nagel’s discussion concerning the difficulties associated with developing a scientific explanation for the nature of experience, Nagel states that current reductionist attempts fail by filtering out any basis for consciousness and thus become meaningless since they are logically compatible with its absence. In this article we call into question the fundamental philosophy of the mind-brain identity hypothesis of Cognitive Theory: ‘What processes in the brain give rise to awareness?’ and the associated search for ‘neural correlates of consciousness’ (NCC). (...) The proper scientific manner of posing the query should simply be ‘What processes give rise to awareness?’. We begin to formalize the Eccles psychon and summarize one of fourteen empirical protocols to test this putative model. This requires a new science of Unified Field, UF Mechanics, entailing in terms of our current stage of development operationally completed forms of quantum theory, gravitation and cosmology arising from a unique derivation of the M-Theory (string theoretic) vacuum. Until now the quest for psychophysical bridging has typically been in the arena between brain and quantum geometry; and many have wondered if contemporary science is sufficient for the task. Nagel further asks ‘what would be left if one removed the viewpoint of the subjective observer’ and then suggests ‘that the remaining properties would be the physical processes themselves or states intrinsic to the experience of awareness’. We examine a new theoretical framework for introducing and experimentally testing the underlying physical cosmology of these noetic parameters. (shrink)

This physics note entails a summary of an extended form of Eccles-Cartesian Interactive Dualism mind-body-multiverse paradigm called Noetic Field Theory: The Quantization of Mind (NFT), distinguished as a paradigm because it is comprehensive and empirically testable. NFT posits not only that the brain is not the seat of awareness but also that neither classical nor quantum mechanics are sufficient to describe mind as the required regime entails the new physics associated with Unified Field, UF Mechanics. This means that the brain (...) is merely a transducer (form of quantum computer) mediating mentation, sensory data and metabolic function. The so-called ‘Hard Problem’ of cognitive science arises as a category error in philosophy of mind, i.e. an incorrect posit of the question “what processes in the brain give rise to awareness” which instead should simply be queried “what processes give rise to awareness”. In the history of science whenever a hard problem has arisen it has later been shown that the underlying principles had not been understood. NFT posits these underlying principles in a comprehensive empirically testable manner solving the ancient mind-body problem in a manner that enables breaking the 1st person 3rd person barrier able to explain Psi-phenomena. The premise is that the mind-body is a naturally occurring form of ‘conscious quantum computer’ (QC), not that the QC is conscious but that it is modelled after those principles. Such QC technologies could lead to routine telepathic effect devices. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (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)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

J. David Lewis and Richard L. Smith provide a history of pragmatism and Chicago sociology based on the positions of realism and nominalism. This issue is indeed the key to understanding pragmatism’s foundations in Charles Peirce’s original formulation. Lewis and Smith claim that there are two pragmatisms, a realistic one characterized by Peirce and Mead and a nominalistic one (which Lewis and Smith claim has no value) illustrated by James and Dewey. They argue that Chicago sociology, (...) including Herbert Blumer, was under the influence of the nominalistic pragmatism, and that Mead exercised little influence during his lifetime. The argument is based on an ahistorical, a priori "metatheoretical" realism-nominalism distinction that claims to be based on Peirce's discussions of realism and nominalism. Yet the authors support their understanding of realism by appealing to Mead’s discussion of “contact experience,” and claim that Peirce’s realism must be based in non-symbolic “pure resistance.” Ironically, such a view represents the main tenet of nominalism, that only individual particulars are real, and amounts to a denial of Peirce’s category of Thirdness as reducible to the “pure resistance” of Secondness. Lewis and Smith attempt to correct the subjectivist tendencies of symbolic interactionism yet would problematically replace them with an equally subjective view of what constitutes objectivity: individual reaction with an object. American Sociology and Pragmatism tends to present a monistic universe hinging on a nominalistic interpretation of realism, a single-visioned view that places more emphasis on labels than on the substance and pragmatic import of a theorist's thoughts, resulting in serious distortions pro and con. Yet it also has opened up for serious questioning the whole foundations of symbolic interactionism and Mead's place within pragmatism and Chicago sociology. Though the authors claim to be "revisionists," it seems to me that they are also "fundamentalists" in safely preserving Mead at the center of a history they claim he did not significantly influence. In my opinion the ongoing controversy will result in a broader understanding of the antecedents of contemporary symbolic interactionism, one that will call for Mead's now dominating role as the sole representative of pragmatism for many American sociologists to be reevaluated and placed within the context of the quite substantial contributions of Peirce, James, and Dewey. (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)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...) pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (shrink)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

First published in 1995. Routledge is an imprint of Taylor & Francis, an informa company.

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

Richard Rorty's rejection of prevailing interior-mirror understandings of the presumed relationship between “minds” and “nature,” along with his promotion of nonrepresentational accounts of knowledge, truth, and science, participates in a rich tradition of jointly pragmatist and constructivist views that spans the twentieth century. This contribution to the symposium “Whatever Happened to Richard Rorty?” considers Rorty's complex and ambivalent relation to that tradition, particularly to the work of his American pragmatist predecessors, William James and John Dewey, and to subsequent (...) pragmatist-constructivist antirepresentationalism in contemporary science and technology studies (STS) and “4E” (embodied, embedded, extended, enactive) cognitive theory. A final section on Nicholas Gaskill's contribution to the symposium questions his sense of Rorty's rhetorical recklessness and suggests that his worries over relativism, in Rorty's texts and more generally, are misplaced. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a banks computers, however, the formula fails, (...) because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to this model can be seen at (...) work today in Quebec and in Ireland, it underpins much of the rhetoric of the P.L.O., and was certainly to some degree involved as a motivating factor in much of the ethnic cleansing which took place in Bosnia in recent times. The question to be addressed in what follows is: to what extent could inter-group disputes be more peacefully resolved, and ethnic cleansing avoided, if political leaders, diplomats and others involved in the resolution of such disputes could be brought to accept weaker geometrical constraints on the shapes of nations? A number of associated questions then present themselves: What sorts of administrative and logistical problems have been encountered by existing non contiguous nations and by perforated nations, and by other nations deviating in different ways from the received geometrical ideal? To what degree is the desire for continuity and simple connectedness a rational desire, and to what degree does it rest on species of political rhetoric which might be countered by, for example, philosophical argument? These and a series of related questions will form the subject- matter of the present essay. (shrink)

The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it is not Austria which is the (...) special case when seen against the background of contemporary mainstream philosophy, but rather Germany and France. (shrink)

Artificial intelligence is man's attempt to use software to emulate the intelligence of human beings. But the complexity of the human neurological system formed in the course of evolution is impossible to replicate: "Human languages and societies are complex systems, indeed complex systems of many complex systems," so much so that their mathematical modeling is impossible. Barry Smith, philosopher and professor at the University at Buffalo. shows no uncertainty about this. His latest book written with Jobst Landgrebe, a mathematician (...) and entrepreneur in the AI field, leaves no doubt – starting with the title: Why machines will never rule the world (Routledge 2023). The book was presented in Turin during an evening organized by the Fondazione CRT and the Bruno Leoni Institute, in which Smith was interviewed based on questions developed by generative Ai. We have accepted the challenge to conduct an interview parallel to the one done with GPT4. (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)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

La ricerca medica è afflitta da un problema di comunicazione. Comunità distinte di ricercatori si servono di terminologie diverse e spesso incompatibili per esprimere i risultati del loro lavoro, generando in questo modo problemi di integrazione tra database ogniqualvolta si presenti la necessità di inserire i dati medici nei computer. In un primo momento i problemi di integrazione tra database venivano risolti caso per caso, in seguito si è fatta strada l’idea di realizzare un’unica tassonomia di riferimento in cui tradurre, (...) una volta soltanto, tutti i vari sistemi di classificazione. Funzionando come una sorta di lingua franca, questa tassonomia di riferimento avrebbe automaticamente garantito ad ogni database calibrato su di essa la compatibilità con tutti gli altri. È curioso come gli informatici abbiano chiamato il sistema centrale di classificazione che stavano proponendo un’ontologia, riconoscendo così l’esistenza di più di un’affinità tra il lavoro di costruzione che un simile sistema comportava e la vecchia metafisica. Il presente articolo descrive un tentativo di sfruttare le risorse della filosofia per risolvere problemi che sorgono, in particolar modo, nel campo dell’integrazione delle terminologie mediche. Vengono delineati in particolare i contorni di un’iniziativa che è il frutto della collaborazione tra l’Istituto di Ontologia Formale e Informatica Medica e la società di software belga Language and Computing, iniziativa che prevede la messa alla prova di un’ontologia fondata su solidi principi filosofici nel contesto di potenti strumenti software per l’elaborazione di testo medico. (shrink)

The most obvious varieties of mental phenomena directed to non- existent objects occur in our experiences of works of art. The task of applying the Meinongian ontology of the non-existent to the working out of a theory of aesthetic phenomena was however carried out not by Meinong by his disciple Stephan Witasek in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows in detail how our feelings undergo certain sorts of structural modifications when they are directed towards what does not (...) exist. He draws a distinction between genuine mental phenomena and what he calls `phantasy-material', asserting that `the job of the aesthetic object, whether it is a work of art or a product of nature, is to excite and support the actualisation of phantasy-material in the experiencing subject'. We might think of such phantasy-material as a matter of Ersatz-emotions or emotional `slop'. We could then see Witasek's aesthetics as an elaborate taxonomy of the various different sorts of Ersatz-emotions which the subject allows to be stimulated within himself in his intercourse with works of art, and see works of art themselves as machines for the production of ever more subtle varieties of such phantasy-material in the perceiving subject. (shrink)

This paper is part of a book symposium for L. A. Paul (2014) Transformative Experience (OUP).

to appear in Lambert, E. and J. Schwenkler (eds.) Transformative Experience (OUP) -/- L. A. Paul (2014, 2015) argues that the possibility of epistemically transformative experiences poses serious and novel problems for the orthodox theory of rational choice, namely, expected utility theory — I call her argument the Utility Ignorance Objection. In a pair of earlier papers, I responded to Paul’s challenge (Pettigrew 2015, 2016), and a number of other philosophers have responded in similar ways (Dougherty, et al. 2015, Harman (...) 2015) — I call our argument the Fine-Graining Response. Paul has her own reply to this response, which we might call the Authenticity Reply. But Sarah Moss has recently offered an alternative reply to the Fine-Graining Response on Paul’s behalf (Moss 2017) — we’ll call it the No Knowledge Reply. This appeals to the knowledge norm of action, together with Moss’ novel and intriguing account of probabilistic knowledge. In this paper, I consider Moss’ reply and argue that it fails. I argue first that it fails as a reply made on Paul’s behalf, since it forces us to abandon many of the features of Paul’s challenge that make it distinctive and with which Paul herself is particularly concerned. Then I argue that it fails as a reply independent of its fidelity to Paul’s intentions. (shrink)

La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...) existent indépendamment de nos actes cognitifs (par exemple: la planète Terre, sa surface extérieure); et des objets qui existent seulement grâce à ces actes (par exemple: l'équateur, la Mer du Nord). Le champ visuel, lui aussi, peut être conçu comme un exemple d'une entité à extension spatiale qui est dépendante dans le sens proposé ci-dessus. L'étude présente suggère une extension de cette analogie en postulant les entités qui, pour les vrais jugements, seraient ce que le champ visuel est pour les actes de perception visuelle. Le champ de jugement est défini plus précisément comme une entité étendue complexe, contenant toutes les entités essentielles pour la vérité d'un (vrai) jugement donné. Il est possible de démontrer que le travail des linguistes cognitifs tel Talmy ou Langacker, si l'on l'interprète convenablement, produit une explication détaillée des structures des champs de jugement correspondant aux phrases de sortes différentes. Un genre nouveau de définition de la vérité en tant que correspondance pour les expressions de la langue naturelle peut donc être formulé sur cette base. (shrink)

On pense généralement que l'impossibilité, l'incomplétdulité, la paracohérence, l'indécidabilité, le hasard, la calcul, le paradoxe, l'incertitude et les limites de la raison sont des questions scientifiques physiques ou mathématiques disparates ayant peu ou rien dans terrain d'entente. Je suggère qu'ils sont en grande partie des problèmes philosophiques standard (c.-à-d., jeux de langue) qui ont été la plupart du temps résolus par Wittgenstein plus de 80 ans. Je fournis un bref résumé de quelques-unes des principales conclusions de deux des plus éminents (...) étudiants du comportement des temps modernes, Ludwig Wittgenstein et John Searle, sur la structure logique de l'intentionnalité (esprit, langue, comportement), en prenant comme point de départ La découverte fondamentale de Wittgenstein, à savoir que tous les problèmes véritablement « philosophiques » sont les mêmes, les confusions sur la façon d'utiliser la langue dans un contexte particulier, et donc toutes les solutions sont les mêmes— en regardant comment la langue peut être utilisée dans le contexte en cause afin que sa vérité (Conditions de satisfaction ou COS) sont claires. Le problème fondamental est que l'on peut dire n'importe quoi, mais on ne peut pas signifier (état clair COS pour) toute déclaration arbitraire et le sens n'est possible que dans un contexte très spécifique. Je dissé que quelques écrits de quelques-uns des principaux commentateurs sur ces questions d'un point de vue wittgensteinien dans le cadre de la perspective moderne des deux systèmes de pensée (popularisé comme «penser vite, penser lentement»), en utilisant une nouvelle table de intentionnalité et la nomenclature de nouveaux systèmes doubles. Je montre qu'il s'agit d'un puissant heuristique pour décrire la vraie nature de ces questions scientifiques, physiques ou mathématiques putatives qui sont vraiment mieux abordés comme des problèmes philosophiques standard de la façon dont la langue doit être utilisée (jeux de langue dans Wittgenstein terminologie). (shrink)

It is now generally recognized that figures such as Reid, Peirce, and Reinach formulated theories of speech acts avant la lettre of Austin and Searle, in Reid and Reinach’s cases under the heading ‘theory of social acts’. Here we address the question as to what conditions would have to be satisfied for such theories to count as ‘theories of speech acts’ in the now familiar sense.

Una breve rassegna della vita e dell'autobiografia spirituale dell'unico mistico americano Adi Da (Franklin Jones). L'adesivo sulla copertina di alcune edizioni dice 'L'autobiografia spirituale più profonda di tutti i tempi' e questo potrebbe essere vero. Ho 70 anni e ho letto molti libri di insegnanti spirituali e sulla spiritualità, e questo è uno dei più grandi. Certamente, è by lontano il resoconto più completo e piùchiaro del processo di illuminazione che abbia mai visto. Anche se non hai alcun interesse nel (...) più affascinante di tutti i processi psicologici umani, è un documento incredibile che rivela molto sulla religione, lo yoga e la psicologia umana e sonda le profondità e i limiti delle possibilità umane. Lo descrivo in dettaglio e paragono il suo insegnamento a quello del mistico indiano contemporaneo Osho. Coloro che desiderano un quadro aggiornato completo per il comportamento umano dalla moderna vista a due systems possono consultare il mio libro 'La struttura logica dellafilosofia, psicologia, Mind e il linguaggio in Ludwig Wittgenstein e John Searle' 2nd ed (2019). Coloro che sono interessati a più dei miei scritti possono vedere 'TalkingMonkeys--Filosofia, Psicologia, Scienza, Religione e Politica su un Pianeta Condannato--Articoli e Recensioni 2006-2019 3rd ed (2019) e Suicidal Utopian Delusions in the 21st Century 4th ed (2019) . (shrink)