Globalization is resulting in complex decisions by businesses as to where and what to produce, while free trade is resulting in a greater menu of choices for consumers, often with the blending of products and goods from various cultures, called ‘glocalization.’ This paper reviews the theories and practices behind these current happenings, which are each economic, politicaleconomic, institutional, and sociological, first by looking at the supply side of why certain countries produce the goods that they do, and then at the (...) demand side, why consumers have particular, cultural tastes and preferences for goods. It also proffers theories to explain firm location and that of intra-industry trade. This occus when countries trade similar products rather than differentiating, as economic theory would suggest. After reviewing the literature, through numerous examples of political-economy and culture, it argues somewhat normatively that differences in culture and goods are a strength to the world community, and that globalization in the end will not likely result in a singular global culture with a uniformity of exactly identical economic goods anytime in the near future. (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)

We analyze the logical form of the domain knowledge that grounds analogical inferences and generalizations from a single instance. The form of the assumptions which justify analogies is given schematically as the "determination rule", so called because it expresses the relation of one set of variables determining the values of another set. The determination relation is a logical generalization of the different types of dependency relations defined in database theory. Specifically, we define determination as a relation between schemata of first (...) order logic that have two kinds of free variables: (1) object variables and (2) what we call "polar" variables, which hold the place of truth values. Determination rules facilitate sound rule inference and valid conclusions projected by analogy from single instances, without implying what the conclusion should be prior to an inspection of the instance. They also provide a way to specify what information is sufficiently relevant to decide a question, prior to knowledge of the answer to the question. (shrink)

The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

The 2010 U. S. Religious Census: Religious Congregations and Membership Survey (RCMS) is the most comprehensive picture of U.S. religious life, county by county. How thorough is the RCMS in covering local religious groups? To answer this question, three county snapshots were performed with collected data compared to the RCMS 2010 reported numbers. Data suggest that there has been an underreport by as much as 25 percent of the number of local congregations in these counties. New and emerging religious movements (...) and denominations as well as ethnic congregations comprise much of this percentage, making it more imperative for scholars to develop methodologies and frameworks in order to capture these “others” and invisible churches in America. Recently spotlighted by Religion Watch, see link below. (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)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

There can be no doubt that discrimination based on sex, race, ethnicity, religion or beliefs should not be tolerated in academia. Surprisingly, however, in recent years, policies of Diversity, Inclusion and Equity(DIE), officially introduced to counteract discrimination, have increasingly led to quite the opposite result: the exclusion of individuals who do not share a radical 'woke' ideology on identity politics (feminism, other gender activisms, critical race theory, etc.), and to the suppression of the academic freedom to discuss such dogmas. This (...) subversion of academia ― disguised Trojan-horse style as universal human rights advocacy ― is unacceptable because academia must be politically neutral and protect freedom of speech, a cornerstone of professional scholarly activity without which universities as we know them will slowly but surely suffocate. -/- Our purpose here is to put together some particularly illustrative cases of such repression in a single book, testifying to a ubiquitous trend within western culture, irreducible to a few isolated complaints. The essays contained here illustrate the abuse of power, censorship and witch-hunts at many universities and research centres in the name of DIE. -/- List of coauthors in alphabetical order: Dorian Abbot, Tomonori Agoh, Gerhard Amendt, Ivar Arpi, David Benatar, Peter Boghossian, Civitas Research Team, David Díaz Pardo de Vera, Pedro Domingos, Janice Fiamengo, Étienne Forest, Jorge Gibert Galassi, Norman Goldstuck, José L. González Quirós, Lawrence M. Krauss, Patrick LaBelle, Martín López Corredoira, Heather Mac Donald, Martin Malmgren, Erik. J. Olsson, Jordan Peterson, Constantin Polychronakos, Philip C. Salzman, Alessandro Strumia, Tom Todd, Andrei Yafaev. (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)

Coordination is a key problem for addressing goal–action gaps in many human endeavors. We define interpersonal coordination as a type of communicative action characterized by low interpersonal belief and goal conflict. Such situations are particularly well described as having collectively “intelligent”, “common good” solutions, viz., ones that almost everyone would agree constitute social improvements. Coordination is useful across the spectrum of interpersonal communication—from isolated individuals to organizational teams. Much attention has been paid to coordination in teams and organizations. In this (...) paper we focus on the looser interpersonal structures we call active support networks, and on technology that meets their needs. We describe two needfinding investigations focused on social support, which examined four application areas for improving coordination in ASNs: academic coaching, vocational training, early learning intervention, and volunteer coordination; and existing technology relevant to ASNs. We find a thus-far unmet need for personal task management software that allows smooth integration with an individual’s active support network. Based on identified needs, we then describe an open architecture for coordination that has been developed into working software. The design includes a set of capabilities we call “social prompting”, as well as templates for accomplishing multi-task goals, and an engine that controls coordination in the network. The resulting tool is currently available and in continuing development. We explain its use in ASNs with an example. Follow-up studies are underway in which the technology is being applied in existing support networks. (shrink)

Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within this context, we present a scenario-based terrorism case study to (...) highlight the challenges of operational disaster command and response. In this article, which is based on the French emergency response doctrine, we outline a semantics-based common operational command system that is designed to guarantee an efficient information flow among ERs. Our focus is on offering to all ERs, a real-time operational picture of the situation in order to enable multilevel coordination among firefighters, police, healthcare units, public authorities, and other stakeholders. Our approach consolidates information to promote timely sharing of data among ERs. The proposed system is based on an ontology that has been developed to represent the different types of knowledge on the part of ERs, providing a shared vocabulary that covers a variety of interoperability concerns. (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)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Перевод статьи: Davies T., Chandler R. Online deliberation design: Choices, criteria, and evidence // Democracy in motion: Evaluating the practice and impact of deliberative civic engagement / Nabatchi T., Weiksner M., Gastil J., Leighninger M. (eds.). -- Oxford: Oxford univ. press, 2013. -- P. 103-131. А. Кулик. -/- Вниманию читателей предлагается обзор эмпирических исследований в области дизайна онлайн-форумов, предназначенных для вовлечения граждан в делиберацию. Размерности дизайна определены для различных характеристик делиберации: назначения, целевой аудитории, разобщенности участников в пространстве и во времени, (...) среды коммуникации и организации делиберативного процесса. После краткого обзора критериев оценки вариантов дизайна рассматриваются эмпирические данные, соотносящиеся с каждым из вариантов. Эффективность онлайн-делиберации зависит от того, насколько условия коммуникации соотносятся с заданиями делиберации. Компромиссы, как, например, между анонимным или идентифицируемым участием, предполагают различные дизайны в зависимости от цели делиберации и состава участников. Выводы исследования получены на материале существующих технологий и могут измениться по мере коэволюции технологий и пользователей. (shrink)

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)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a multicriteria decision support service, based (...) on the Analytic Hierarchy Process (AHP) method, that aims to avoid overcrowding and outpacing the capacity of a hospital to effectively provide the best care to victims by finding out the most appropriate hospital that meets the victims’ needs. The proposed approach searches for the most appropriate healthcare institution that can effectively deal with the victims’ needs by considering the availability of the needed resources in the hospital, the victim’s wait time to receive the healthcare, and the transfer time that represents the hospital proximity to the disaster site. The evaluation and validation results showed that the assignment of hospitals was done successfully considering the needs of each victim and without overwhelming any single hospital. (shrink)

Can new technology enhance purpose-driven, democratic dialogue in groups, governments, and societies? Online Deliberation: Design, Research, and Practice is the first book that attempts to sample the full range of work on online deliberation, forging new connections between academic research, technology designers, and practitioners. Since some of the most exciting innovations have occurred outside of traditional institutions, and those involved have often worked in relative isolation from each other, work in this growing field has often failed to reflect the full (...) set of perspectives on online deliberation. This volume is aimed at those working at the crossroads of information/communication technology and social science, and documents early findings in, and perspectives on, this new field by many of its pioneers. -/- CONTENTS: -/- Introduction: The Blossoming Field of Online Deliberation (Todd Davies, pp. 1-19) -/- Part I - Prospects for Online Civic Engagement -/- Chapter 1: Virtual Public Consultation: Prospects for Internet Deliberative Democracy (James S. Fishkin, pp. 23-35) -/- Chapter 2: Citizens Deliberating Online: Theory and Some Evidence (Vincent Price, pp. 37-58) -/- Chapter 3: Can Online Deliberation Improve Politics? Scientific Foundations for Success (Arthur Lupia, pp. 59-69) -/- Chapter 4: Deliberative Democracy, Online Discussion, and Project PICOLA (Public Informed Citizen Online Assembly) (Robert Cavalier with Miso Kim and Zachary Sam Zaiss, pp. 71-79) -/- Part II - Online Dialogue in the Wild -/- Chapter 5: Friends, Foes, and Fringe: Norms and Structure in Political Discussion Networks (John Kelly, Danyel Fisher, and Marc Smith, pp. 83-93) -/- Chapter 6: Searching the Net for Differences of Opinion (Warren Sack, John Kelly, and Michael Dale, pp. 95-104) -/- Chapter 7: Happy Accidents: Deliberation and Online Exposure to Opposing Views (Azi Lev-On and Bernard Manin, pp. 105-122) -/- Chapter 8: Rethinking Local Conversations on the Web (Sameer Ahuja, Manuel Pérez-Quiñones, and Andrea Kavanaugh, pp. 123-129) -/- Part III - Online Public Consultation -/- Chapter 9: Deliberation in E-Rulemaking? The Problem of Mass Participation (David Schlosberg, Steve Zavestoski, and Stuart Shulman, pp. 133-148) -/- Chapter 10: Turning GOLD into EPG: Lessons from Low-Tech Democratic Experimentalism for Electronic Rulemaking and Other Ventures in Cyberdemocracy (Peter M. Shane, pp. 149-162) -/- Chapter 11: Baudrillard and the Virtual Cow: Simulation Games and Citizen Participation (Hélène Michel and Dominique Kreziak, pp. 163-166) -/- Chapter 12: Using Web-Based Group Support Systems to Enhance Procedural Fairness in Administrative Decision Making in South Africa (Hossana Twinomurinzi and Jackie Phahlamohlaka, pp. 167-169) -/- Chapter 13: Citizen Participation Is Critical: An Example from Sweden (Tomas Ohlin, pp. 171-173) -/- Part IV - Online Deliberation in Organizations -/- Chapter 14: Online Deliberation in the Government of Canada: Organizing the Back Office (Elisabeth Richard, pp. 177-191) -/- Chapter 15: Political Action and Organization Building: An Internet-Based Engagement Model (Mark Cooper, pp. 193-202) -/- Chapter 16: Wiki Collaboration Within Political Parties: Benefits and Challenges (Kate Raynes-Goldie and David Fono, pp. 203-205) -/- Chapter 17: Debian’s Democracy (Gunnar Ristroph, pp. 207-211) -/- Chapter 18: Software Support for Face-to-Face Parliamentary Procedure (Dana Dahlstrom and Bayle Shanks, pp. 213-220) -/- Part V - Online Facilitation -/- Chapter 19: Deliberation on the Net: Lessons from a Field Experiment (June Woong Rhee and Eun-mee Kim, pp. 223-232) -/- Chapter 20: The Role of the Moderator: Problems and Possibilities for Government-Run Online Discussion Forums (Scott Wright, pp. 233-242) -/- Chapter 21: Silencing the Clatter: Removing Anonymity from a Corporate Online Community (Gilly Leshed, pp. 243-251) -/- Chapter 22: Facilitation and Inclusive Deliberation (Matthias Trénel, pp. 253-257) -/- Chapter 23: Rethinking the ‘Informed’ Participant: Precautions and Recommendations for the Design of Online Deliberation (Kevin S. Ramsey and Matthew W. Wilson, pp. 259-267) -/- Chapter 24: PerlNomic: Rule Making and Enforcement in Digital Shared Spaces (Mark E. Phair and Adam Bliss, pp. 269-271) -/- Part VI - Design of Deliberation Tools -/- Chapter 25: An Online Environment for Democratic Deliberation: Motivations, Principles, and Design (Todd Davies, Brendan O’Connor, Alex Cochran, Jonathan J. Effrat, Andrew Parker, Benjamin Newman, and Aaron Tam, pp. 275-292) -/- Chapter 26: Online Civic Deliberation with E-Liberate (Douglas Schuler, pp. 293-302) -/- Chapter 27: Parliament: A Module for Parliamentary Procedure Software (Bayle Shanks and Dana Dahlstrom, pp. 303-307) -/- Chapter 28: Decision Structure: A New Approach to Three Problems in Deliberation (Raymond J. Pingree, pp. 309-316) -/- Chapter 29: Design Requirements of Argument Mapping Software for Teaching Deliberation (Matthew W. Easterday, Jordan S. Kanarek, and Maralee Harrell, pp. 317-323) -/- Chapter 30: Email-Embedded Voting with eVote/Clerk (Marilyn Davis, pp. 325-327) -/- Epilogue: Understanding Diversity in the Field of Online Deliberation (Seeta Peña Gangadharan, pp. 329-358). -/- For individual chapter downloads, go to odbook.stanford.edu. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)

The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our cognitive acts (for example, (...) the planet Earth, its exterior surface); and those which exist only in virtue of such acts (for example: the equator, the North Sea). The visual field, too, can be conceived as an example of an extended entity that is dependent in the sense at issue. The paper suggests extending this analogy by postulating entities which would stand to true judgments as the visual field stands to acts of visual perception. The judgment field is defined more precisely as that complex extended entity which comprehends all entities which are relevant to the truth of a given (true) judgment. The work of cognitive linguists such as Talmy and Langacker, when properly interpreted, can be shown to yield a detailed account of the structures of the judgment fields corresponding to sentences of different sorts. A new sort of correspondence-theoretic definition of truth for sentences of natural language can then be formulated on this basis. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and inefficient (...) exchange of data and information among those involved, which can impede the response process and slow decision making. We, therefore, hypothesize that promoting semantic interoperability across ERO information systems might improve information exchange among stakeholders and thereby allow a more coherent response to the disaster. We propose an ontology‐based messaging service on the basis of the Emergency Data Exchange Language (EDXL) standards. The parties involved will continue to use the terminologies to which they are accustomed, but the system will resolve inconsistencies and thereby enhance mutual understanding among EROs by ensuring semantic translation of the exchanged information. The evaluation of the semantic translation demonstrated the effectiveness and accuracy of the proposed service. (shrink)

Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary (...) resolves inconsistent terminologies and promotes semantic interoperability among ERs. In this work, we discuss developing POLARISCO as an extension of Basic Formal Ontology and the Common Core Ontologies. We conclude by presenting a real use-case to check the efficiency and applicability of the proposed ontology. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

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)

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)

Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation (...) of the FGM Ontology (FGMO) in 2016. Here, we present a revised and expanded version of the FGM Ontology, which includes enrichments along four dimensions: (1) documenting recent FGMs applications; (2) reorganising the framework to incorporate an updated representation of types of manufacturing processes; (3) enriching the axioms of the ontology; and (4) importing mid-level ontologies from the Common Core Ontologies (CCO) and Product Life Cycle (PLC) Ontologies. The work is being carried out within the framework of the Industry Ontology Foundry (IOF), and the ontology is conformant to Basic Formal Ontology (BFO). (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)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The project of a 'naive physics' has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as K hler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from (...) a knowledge of these historical roots of their discipline, which are shown to imply above alla critique of the set-theory-based models of reality typically presupposed by contemporary work in common-sense ontology [1]. (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 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)

While contemporary philosophers have devoted vast amounts of attention to the language we use in describing and finding our way about the world of everyday experience, they have, with few exceptions, refused to see this world itself as a fitting object of theoretical concern. In what follows I shall seek to show how the commonsensical world might be treated ontologically as an object of investigation in its own right. At the same time I shall seek to establish how such a (...) treatment might help us better philosophically to understand the structures of both physical reality and cognition. (shrink)

What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas were (...) developed prior to the scientific discoveries of the modern era, he approached the objects and relations of everyday reality with the same ontological seriousness with which scientists today approach the objects of physics. We shall seek to show that what Aristotle has to say about these commonsensical objects and relations can, when translated into more formal terms, be of use also to contemporary ontologists. More precisely, we shall argue that his ideas can contribute to the development of a rigorous theory of those social and institutional components of everyday reality – the settings of human behavior – which are the subject of this volume. When modern-day philosophers turn their attentions to ontology they begin not with Aristotle but rather, in almost every case, with a set-theoretic ontology of the sort which is employed in standard model-theoretic semantics. Set-theoretic ontology sees the world in atomistic terms: it postulates a lowest level of atoms or urelements, from out of which successively higher levels of set-theoretic objects are then constructed. The approach to ontology to be defended here, in contrast, starts not with atoms but with the mesoscopic objects by which we are surrounded in our normal day-to-day.. (shrink)

Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artificial (...) intelligence encouraged by these successes, especially in the domain of language processing. We then show an alternative approach to language-centric AI, in which we identify a role for philosophy. (shrink)

Values exist not in isolation, but in complex wholes. Values are what they are because of the complex wholes in which they are situated. To do justice to this thesis will require a holistic ontology, a theory according to which many types of entities exist only as inseparable parts or moments of wider contexts or environments. An ontological theory of environments -- with roots in Gestalt psychology and the ecological psychology of J. J. Gibson and Roger Barker, and which is (...) related also to the theory of motivation sketched by Edmund Husserl as part of his theory of the lifeworld or Lebenswelt -- will help us to understand the ontology of values. It will help us to understand what values are. It will not, however, tell us what is good or bad. From facts of ontology, no value propositions follow. (shrink)

If mind is a creature of adaptation, then our standard theories of intentionality and of mental representation are in need of considerable revision. For such theories, deriving under Cartesian inspiration from the work of Brentano, Husserl and their followers, are context-free. They conceive the subject of mental experience in isolation from any surrounding physico-biological environment. Husserl sought in his later writings to find room for the surrounding world of human practical experience, and a similar expansion of concerns can be detected (...) also in the writings of other later phenomenologists such as Heidegger, Sartre, and Merleau-Ponty. But in none of these authors do we find sustained attempts to grapple with the intervolvements of the world of human thought, feeling and action with the environment of human behavior as this is described by physics and biology. Their work can, however, be seen in a new light when conjoined with the ideas on perception and action of J. J. Gibson and Roger Barker, both of whom (independently) conceived their work under the banner of 'ecological psychology.' It is against this background that the term 'Husserlian ecology' is to be understood in this essay. (shrink)

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

The paper relates classical treatments of physics and metaphysics to contemporary work on common sense in the field of artificial intelligence (J. Hobbs, P. Hayes, et al.). It defends the universality (and truth) of certain basic principles of common-sense physics and shows why these basic principles must leave certain issues undetermined.

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.