In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve (...) the representation of contractual obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The (...) paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products? (shrink)

In recent years, there has been an increasing interest in thedevelopment of ontologically well-founded conceptual models for Information Systems in areas such as Service Management, Accounting Information Systems and Financial Reporting. Economic exchanges are central phenomena in these areas. For this reason, they occupy a prominent position in modelling frameworks such as the REA (Resource-EventAction) ISO Standard as well as the FIBO (Financial Industry BusinessOntology). In this paper, we begin a well-founded ontological analysisof economic exchanges inspired by a recent ontological (...) view on the nature of economic transactions. According to this view, what counts asan economic transaction is based on an agreement on the actions thatthe agents are committed to perform. The agreement is in turn based on convergent preferences about the course of action to bring about. This view enables a unified treatment of economic exchanges, regardless the object of the transaction, and complies with the view that all economictransactions are about services. In this paper, we start developing our analysis in the framework of the Unified Foundational Ontology (UFO). (shrink)

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.

La communication interdisciplinaire rencontre divers problématiques : l’hétérogénéités des informations (sémantique, standardisation des formats), les confusions linguistiques (intentions dans les énoncés, polysémie des mots) ou encore épistémologiques (expertises divergentes, terminologies inadéquates). Nous proposons pour favoriser l’intercommunication entre différents domaines de spécialité, l’emploi des ontologies informatiques : des artefacts informatiques permettant une représentation des concepts au sein d’un domaine de spécialité. Autour de la notion « d’interopérabilité sémantique », la capacité pour une machine et des acteurs de communiquer ensemble, nous viserons (...) à montrer en quoi les ontologies peuvent permettre à des acteurs de différentes disciplines de clarifier les notions propres à leurs domaines en fonction d’une analyse de leurs usages des mots. Nous tâchons ici de mettre en avant la capacité des ontologies de traiter le langage selon différents niveaux du sens d’un mot (du plus concret et appliqué, au plus abstrait et conceptuel), afin de mettre en perspective ce en quoi cette analyse basée sur les textes d’un corpus, permet de rendre compte de, si ce n’est un état du réalisme d’une discipline, du moins, servir d’outils pour aider les acteurs à normaliser leurs pratiques. En ce sens, les ontologies informatiques peuvent être considérées et utilisées comme autant de bases terminologiques servant comme outils de références pour faciliter la communication interdisciplinaire. (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)

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)

Many Public Administrations structure their services around the notion of users’ need. However, there is a gap between private, subjectively perceived needs (self-attributed) and needs that are attributed by PA to citizens (heteroattributed). Because of the gap, citizens’ needs are often only partially satisfied by PAs services. This gap is in part due to the fact that the meaning of the word “need” is ambiguous and full of antinomic nuances. The purpose of this paper is to formulate a (...) definition of “need” suitable for citizens’ needs management with respect to PA’s services offering, and to provide an accurate ontological analysis of the notion of “need” and the network of concepts that relate to it. (shrink)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology (...) repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available for (...) integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. (shrink)

Governments standardly deploy a distinction between goods and services in assessing economic health and tracking national income statistics, of which medical goods and services carry significant importance. In what follows we draw on Basic Formal Ontology (BFO) to introduce a third kind of entity called patterns, which help capture the various ways in which goods and services are intertwined and help also to show how many services generate a new kind of non-goods-related products. Patterns are (...) an overlooked yet essential features of many economic sectors including medicine. Studying patterns offers new insights into various components of economic analysis, including outcomes-oriented evaluations of medical services and the value of human capital in the medical sphere. (shrink)

Developments in biological technology in the last few decades highlight the surprising and ever-expanding practical benefits of stem cells. With this progress, the possibility of combining human and nonhuman organisms is a reality, with ethical boundaries that are not readily obvious. These inter-species hybrids are of a larger class of biological entities called “chimeras.” As the concept of a human-nonhuman creature is conjured in our minds, either incredulous wonder or grotesque horror is likely to follow. This paper seeks to mitigate (...) those worries and demotivate reasonable concerns raised against chimera research, all the while pressing current ethical positions toward their plausible conclusions. -/- In service of this overall aim, first, I intend to show that chimeras are far less foreign and fantastic in light of recent research in the lab; second, I intend to show that anti-realist (so-called “constructivist”) commitments regarding species ontology render the species distinction (i.e., the divide between human and nonhuman) superfluous as a basis for ethical practice; and third, I discuss some prevailing dignity accounts regarding the practical ethics of the creation, research, and treatment of chimeras. Consequently I intend to show that the adoption of this particular set of views (constructivist ontology, capacity-based ethics) in conjunction with recent research ought to justify a parallel with what we accord to humans persons, and that trajectory allows for cases of moral permissibility. (shrink)

In the ontology of music the Aristotelian theory of musical works is the view that musical works are immanent universals. The Aristotelian theory (hereafter Musical Aristotelianism) is an attractive and serviceable hypothesis. However, it is overlooked as a genuine competitor to the more well-known theories of Musical Platonism and nominalism. Worse still, there is no detailed account in the literature of the nature of the universals that the Aristotelian identifies musical works with. In this paper, I argue that the (...) best version of Musical Aristotelianism identifies musical works with structural universals. I first motivate the view by outlining its explanatory benefits. I then argue that Musical Aristotelianism is preferable to Musical Platonism and present a novel account of musical works as structural universals by developing D. M. Armstrong’s theory of structural universals. I discuss the consequences of Musical Aristotelianism with respect to on-going issues in debates about musical works and defend the view against an influential objection, concluding that Musical Aristotelianism is a genuine competitor in debates about the nature of musical works. (shrink)

When governments collect data relating to economic activity they commonly employ a distinction between goods and services. Both goods and services have economic value. Goods (cars, houses, bottles of milk) are, very roughly, independent continuants which can be alienated (sold, gifted, rented, and so forth). Services (hairdressing, gardening, teaching) are, again very roughly, occurrents. They are occurrents which are further often said to be marked by the fact that production and consumption coincide. Social services under both (...) headings typically involve combinations of service provision. The patterns in question are primarily those of the family (where the patterns to be maintained or restored are, roughly, those characteristic of a healthy family life) and of the child (patterns characteristic of healthy development, provided by child protective services, who work to prevent child abuse). (shrink)

Social work is a contested tradition, torn between the demands of social governance and autonomy. Today, this struggle is reflected in the division between the dominant, neoliberal agenda of service provision and the resistance offered by various critical perspectives employed by disparate groups of practitioners serving diverse communities. Critical social work challenges oppressive conditions and discourses, in addition to addressing their consequences in individuals’ lives. However, very few recent critical theorists informing critical social work have advocated revolution. A challenging exception (...) can be found in the work of Cornelius Castoriadis (1922–97), whose explication of ontological underdetermination and creation evades the pitfalls of both structural determinism and post-structural relativism, enabling an understanding of society as the contested creation of collective imaginaries in action and a politics of radical transformation. On this basis, we argue that Castoriadis’s radical-democratic revisioning of revolutionary praxis can help in reimagining critical social work’s emancipatory potential. (shrink)

We describe an experimental approach toward implementing a commonsense "microtheory" for buying and selling. Our prototype system characterizes how intelligent agents hold items and money, how they buy and sell items, and the way money and items are transferred. The ontology of the system includes money (cash, check, credit card), agents (people, organizations), items (movable, real estate, service), barter, and the notions of transfer, loan, buying by installments, profit, and loss.

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)

In recent years, there has been an increasing interest in the development of well-founded conceptual models for Service Management, Accounting Information Systems and Financial Reporting. Economic ex- changes are a central notion in these areas and they occupy a prominent position in frameworks such as the Resource-Event Action (REA) ISO Standard, service core ontologies (e.g., UFO-S) as well as financial stan- dards (e.g. OMG’s Financial Industry Business Ontology - FIBO). We present a core ontology for economic exchanges inspired (...) by a recent view on this phenomenon. According to this view, economic exchanges are based on an agreement on the actions that the agents are committed to perform. This view enables a unified treatment of economic exchanges, regardless the object of the transaction. We ground our core ontology on the Unified Foundational Ontology (UFO), discussing its formal and conceptual aspects, instantiating it as a reusable OntoUML model, and confronting it with the REA standard and the UFO-S service ontology. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare (...) must be aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

The high-profile debate between John Milbank and Slavoj Žižek in The Monstrosity of Christ comprises an immensely important work in the contemporary intersection of Church dogmatics and ontology. This study consists of an indirect commentary on this debate, using Milbank and Žižek’s dispute as a foil for mobilizing an ontology favorable to Eastern Orthodox dogmatics. The starting point here is that Orthodoxy simply bypasses Neo-Platonism as the definitive philosophical expression of its dogmatic theology, and, on this score, Žižek’s (...) powerful criticisms of theurgic Neo-Platonism can be embraced and redirected in support of an ontology of the Orthodox dogma of synergy. It will be shown that Milbank’s position that there is a “Catholic Žižek” who embraces theurgy—that is, analogical, Neo-Platonist ontology—is mistaken; the dismantling of the “suspended middle” is necessary for the Žižekian and that, therefore, a Catholic version of this figure does not exist. But it will be suggested that, instead, there is a latent Orthodox Žižek whose criticism of analogical ontology can pave the way for a more profitable dialogue between Žižek and Orthodoxy. The conclusion will provide a playful reading of an Orthodox Žižek—an entirely fictional but ontologically serviceable character—who can begin new conversations between ontology and dogmatic theology. The upshot of the study is the extension of Terry Eagleton’s claim that the historical materialist, but not the dialectical materialist, can legitimately venerate the Virgin Mary—to the surprising suggestion that even the dialectical materialist can justifiably venerate her, too. (shrink)

What are economic exchanges? The received view has it that exchanges are mutual transfers of goods motivated by inverse valuations thereof. As a corollary, the standard approach treats exchanges of services as a subspecies of exchanges of goods. We raise two objections against this standard approach. First, it is incomplete, as it fails to take into account, among other things, the offers and acceptances that lie at the core of even the simplest cases of exchanges. Second, it ultimately fails (...) to generalize to exchanges of services, in which neither inverse preferences nor mutual transfers hold true. We propose an alternative definition of exchanges, which treats exchanges of goods as a special case of exchanges of services and which builds in offers and acceptances. According to this theory: (i) The valuations motivating exchanges are propositional and convergent rather than objectual and inverse; (ii) All exchanges of goods involve exchanges of services/actions, but not the reverse; (iii) Offers and acceptances, together with the contractual obligations and claims they bring about, lie at the heart of all cases of exchange. (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)

Nonostante la pervasività della nozione di servizio e le recenti proposte per una Scienza dei Servizi unificata, esistono ancora parecchie inconsistenze tra le varie definizioni di servizio in uso nelle diverse discipline (e spesso anche all'interno della stessa disciplina). In particolare, a dispetto del fatto che l'obiettivo generale di questa scienza dovrebbe essere di permettere a persone e calcolatori di interagire agevolmente con i servizi nella vita di tutti i giorni, molti approcci alla modellazione dei servizi in informatica (specialmente quelli (...) centrati sui servizi web) sembrano focalizzarsi principalmente sugli aspetti connessi al flusso dati, per cui i servizi sono considerati come scatole nere che trasformano un ingresso in un’uscita, e che interoperano tra loro secondo modalità predefinite. Questo modello a scatola nera ha sicuramente i suoi vantaggi ma, stando a quanto dicono Petrie e Bussler, sembra funzionare bene sono all'interno di contesti omogenei, i cosiddetti parchi di servizi, dove l'interoperabilità è tecnicamente possibile solo perché i contenuti e le modalità di erogazione di ogni servizio sono predefiniti e condivisi da tutti i soggetti coinvolti. (shrink)

According to modal realism formulated by David Lewis, there exist concrete possible worlds. As he argues the hypothesis is serviceable and that is a sufficient reason to think it is true. On the other side, Lewis does not consider the pragmatic reasons to be conclusive. He admits that the theoretical benefits of modal realism can be illusory or that the acceptance of controversial ontology for the sake of theoretical benefits might be misguided in the first place. In the first (...) part of the paper, I consider the worry and conclude that although the worry is justified, there can be an epistemological justification for his theory. Next, I outline the so-called indispensability argument for the legitimacy of mathematical Platonism. Finally, I argue that the argument, if accepted, can be applied to metaphysics in general, to the arguing for the existence of concrete (im)possibilia in particular. (shrink)

Vietnamese scientists on the list of "100.000 influential scientists" this year increased sharply in number and rank. -/- The ranking was selected by a group of scientists led by Professor John PA Ioannidis and colleagues from Stanford University (USA) on the Scopus database and published by Elsevier Publishing House.

Abstract: The study aimed to determine the quality of services and its role in enhancing strategic flexibility, from the point of view of the internal beneficiary in non-governmental hospitals in Gaza Strip. The study relied on the descriptive and analytical approach, and the questionnaire was designed as a tool to collect data and consisted of (39) items, and the researchers used the comprehensive survey method, and the number of the study population was (536) individuals, where (434) questionnaires were retrieved, (...) and the recovery rate was (80.97%). The study revealed many results, the most important of which were: the existence of a high degree of approval by the study sample regarding the quality of services, as it was evident through the field of service quality obtaining a relative weight (79.90%), and the results of the study indicated that there is a moderate degree of approval by the members of the study sample. On the strategic flexibility, as it was evident by obtaining the area of strategic flexibility as a whole on a relative weight (60.44%). The results of the study revealed a statistically significant relationship between the quality of services and the strategic flexibility in non-governmental hospitals in Gaza Strip, with a correlation coefficient of 0.490). The results of the study also revealed a statistically significant effect of the quality of services on the strategic flexibility in non-governmental hospitals in Gaza Strip. The study reached many recommendations, the most important of which were: Establishing an effective system to receive patients' complaints in a manner that ensures rapid response and treatment, to achieve continuous communication between patients and the hospital administration, to notify patients of dealing with the complaints they submit, and to work to provide all medical and health specialties in hospitals in place. The study, by making use of medical delegations visiting Gaza Strip, involving them in therapeutic operations, bringing in doctors and specialists from abroad, updating the criteria for measuring services provided to patients on an ongoing basis, based on patients' suggestions and complaints, developing facilities in hospitals, as well as updating medical devices and equipment Used in hospitals periodically and the need to work on appointing young people and people of energy, for vacancies in the hospitals under study, and the need to seek the help of an administrative staff that is distinguished by scientific and practical qualifications, and to work on updating information systems, archiving and networks through which data and information are transferred between departments, and finding mechanisms to be done from During which the information stored can be used to enhance the decision-making process. (shrink)

This text is an English translation of those several sections of the original paper in Russian, where collection-related issues are considered. The full citation of the original paper is as following: Pavlinov I.Ya. 2016. [Bioraznoobrazie i biokollektsii: problema sootvetstvia]. In: Pavlinov I.Ya. (comp.). Aspects of Biodiversity. Archives of Zoological Museum of Lomonosov Moscow State University, Vol. 54, Pр. 733–786. -/- Orientation of biology, as a natural science, on the study and explanation of the similarities and differences between organisms led in (...) the second half of the 20th century to the recognition of a specifi c subject area of biological explorations, viz. biodiversity (BD). One of the important general scientifi c prerequisites for this shift was understanding that (at the level of ontology) the structured diversity of the living nature is its fundamental property equivocal to subjecting of some of its manifestations to certain laws. At the level of epistemology, this led to acknowledging that the “diversifi cationary” approach to description of the living beings is as justifi able as the before dominated “unifi cationary” one. This general trend has led to a signifi cant increase in the attention to BD. From a pragmatic perspective, its leitmotif was conservation of BD as a renewable resource, while from a scientifi c perspective the leitmotif was studying it was studying BD as a specifi c natural phenomenon. These two points of view are united by recognition of the need for scientific substantiation of BD conservation strategy, which implies the need for a detailed study of BD itself. At the level of ontology, one of the key problems in the study of BD (leaving aside the question of its genesis) is determination of its structure, which is interpreted as a manifestation of the structure of the Earth’s biota itself. With this, it is acknowledged that the subject area of empirical explorations is not the BD as a whole ( “Umgebung”) but its particular manifestations (“Umwelts”). It is proposed herewith to recognized, within the latter: fragments of BD (especially taxa and ecosystems), hierarchical levels of BD (primarily within- and interorganismal ones), and aspects of BD (before all taxonomic and meronomic ones). Attention is drawn to a new interpretation of bioinformatics as a discipline that studies the information support of BD explorations. An important fraction of this support are biocollections. The scientifi c value of collections means that they make it possible both empirical inferring and testing (verification) of the knowledge about BD. This makes biocollections, in their epistemological status, equivalent to experiments, and so makes studies of BD quite scientific. It is emphasized that the natural objects (naturalia), which are permanently kept in collections, contain primary (objective) information about BD, while information retrieved somehow from them is a secondary (subjective) one. Collection, as an information resource, serves as a research sample in the studies of BD. Collection pool, as the totality of all collection materials kept in repositories according to certain standards, can be treated as a general sample, and every single collection as a local sample. The main characteristic of collection-as-sample is its representativeness; so the basic strategy of development of the collection pool is to maximize its representativeness as a means to ensure correspondence of structure of biocollection pool to that of BD itself. The most fundamental characteristic of collection, as an information resource, is its scientific signifi cance. The following three main groups of more particular characteristics are distinguished: — the “proper” characteristics of every collection are its meaningfulness, informativeness, reliability, adequacy, documenting, systematicity, volume, structure, uniqueness, stability, lability; — the “external” characteristics of collection are resolution, usability, ethic constituent; — the “service” characteristics of collection are its museofication, storage system security, inclusion in metastructure, cost. In the contemporary world, development of the biocollection pool, as a specific resource for BD research, requires considerable organizational efforts, including work on their “information support” aimed at demonstrating the necessity of existence of the biocollections. (shrink)

Because climate change can be seen as the blind spot of contemporary philosophy of technology, while the destructive side effects of technological progress are no longer deniable, this article reflects on the role of technologies in the constitution of the (post)Anthropocene world. Our first hypothesis is that humanity is not the primary agent involved in world-production, but concrete technologies. Our second hypothesis is that technological inventions at an ontic level have an ontological impact and constitutes world. As we object to (...) classical philosophers of technology like Ihde and Heidegger, we will sketch the progressive contribution of our conceptuality to understand the role of technology in the Anthropocene world. Our third hypothesis is that technology has emancipatory potential and in this respect, can inaugurate a post-Anthropocene World. We consider these three hypotheses to develop a philosophical account of the ontology of technology beyond an abstract and deterministic understanding. This concept enables us to philosophically reflect on the role of technology in the Anthropocene World in general, and its contribution to the transition to the post-Anthropocene World in particular. (shrink)

Schelling and Deleuze are polarised respectively as philosopher of identity and philosopher of difference par excellence. Schelling grounds reason in his early Naturphilosophie in the a priori identity deduced from the abstraction of the proposition A=A. Deleuze, however, reworks the Platonic Idea and Nietzsche’s Eternal Return in the service of an a priori ‘problematic being’, an ontological difference-in-itself, which precedes metaphysical identity. Despite their apparently polarised metaphysical groundwork, they stumble across a similar consequence: the distinction between subject and object, and (...) any problematic derived thereof, is in consequence of the ontological constitution of the object itself. The paradox of objectivity as indifference to an a priori difference or identity is presented, and preliminarily suggested to be due to the Deleuze-Schelling opposition not being a difference-identity opposition, but an opposition between difference and a ‘blind act’ which retroactively precedes the making-identical to itself of the one as distinguished from the many. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our (...) best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed (...) theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure. (shrink)

The paper points out that the modern formulation of Bohm’s quantum theory known as Bohmian mechanics is committed only to particles’ positions and a law of motion. We explain how this view can avoid the open questions that the traditional view faces according to which Bohm’s theory is committed to a wave-function that is a physical entity over and above the particles, although it is defined on configuration space instead of three-dimensional space. We then enquire into the status of the (...) law of motion, elaborating on how the main philosophical options to ground a law of motion, namely Humeanism and dispositionalism, can be applied to Bohmian mechanics. In conclusion, we sketch out how these options apply to primitive ontology approaches to quantum mechanics in general. (shrink)

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

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

Part of a special issue, Ontologies of Living Beings, guest-edited by A. M. Ferner and Thomas Pradeu.

I argue that the most promising approach to understanding J.J. Gibson's "affordances" takes affordances themselves as ontological primitives, instead of treating them as dispositional properties of more primitive things, events, surfaces, or substances. These latter are best treated as coalescences of affordances present in the environment (or "coalescences of use-potential," as in Sanders (1994) and Hilditch (1995)). On this view, even the ecological approach's stress on the complementary organism/environment pair is seen as expressing a particular affordance relation between the world (...) and the analyst. That the world is parsed in any way among events and objects, perceivers and worlds, etc., reflects equally features of certain real or possible perspectives on the world and features of the world itself. In section 1, I begin by contending that, contrary to the apparent expectations of some in the field, the bare existence of affordances is surely quite uncontroversial. In section 2, I argue that the most reasonable approach to foundational ontology is a relativistic one. In section 3, I address the claim that affordances must be ontologically complemented by effectivities for the sake of completeness, and I shall argue against that claim on grounds that I take to reflect some of Gibson's most important insights. This work will help to clarify the way affordances are to be used in the fourth and final section, where I argue that ontological work, even within special sciences, should not be merely "regional," and that the most attractive general approach to ontological questions is one that is based on affordances, rather than upon things, events, surfaces, and the like. (shrink)

I discuss the ontological assumptions and implications of General Relativity. I maintain that General Relativity is a theory about gravitational fields, not about space-time. The latter is a more basic ontological category, that emerges from physical relations among all existents. I also argue that there are no physical singularities in space-time. Singular space-time models do not belong to the ontology of the world: they are not things but concepts, i.e. defective solutions of Einstein’s field equations. I briefly discuss the (...) actual implication of the so-called singularity theorems in General Relativity and some problems related to ontological assumptions of Quantum Gravity. (shrink)

The ontology of Local Quantum Physics, Rudolf Haag’s framework for relativistic quantum theory, is reviewed and discussed. It is one of spatiotemporally localized events and unlocalized causal intermediaries, including the elementary particles, which come progressively into existence in accordance with a fundamental arrow of time. Haag’s conception of quantum theory is distinguished from others in which events are also central, especially those of Niels Bohr and John Wheeler, with which it has been compared.

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

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

Biologists explain organisms’ behavior not only as having been programmed by genes and shaped by natural selection, but also as the result of an organism’s agency: the capacity to react to environmental changes in goal-driven ways. The use of such ‘agential explanations’ reopens old questions about how justified it is to ascribe agency to entities like bacteria or plants that obviously lack rationality and even a nervous system. Is organismic agency genuinely ‘real’ or is it just a useful fiction? In (...) this paper we focus on two questions: whether agential explanations are to be interpreted ontically, and whether they can be reduced to non-agential explanations (thereby dispensing with agency). The Kantian approach we identify interprets agential explanations non-ontically, yet holds agency to be indispensable. Attributing agency to organisms is not to be taken literally in the way we attribute physical properties such as mass or acceleration, but nor is it a mere heuristic or predictive tool. Rather, it is an inevitable consequence of our own rational capacity: as long as we are rational agents ourselves, we cannot avoid seeing agency in organisms. (shrink)

In this paper I will argue that critical theory needs to make its socio-ontological commitments explicit, whilst on the other hand I will posit that contemporary social ontology needs to amend its formalistic approach by embodying a critical theory perspective. In the first part of my paper I will discuss how the question was posed in Horkheimer’s essays of the 1930s, which leave open two options: (1) a constructive inclusion of social ontology within social philosophy, or else (2) (...) a program of social philosophy that excludes social ontology. Option (2) corresponds to Adorno’s position, which I argue is forced to recur to a hidden social ontology. Following option (1), I first develop a metacritical analysis of Searle, arguing that his social ontology presupposes a notion of 'recognition' which it cannot account for. Furthermore, by means of a critical reading of Honneth, I argue that critical theory could incorporate a socioontological approach, giving value to the constitutive socio-ontological role of recognition and to the socio-ontological role of objectification. I will finish with a proposal for a socio-ontological characterization of reification which involves that the basic occurrence of recognition is to be grasped at the level of background practices. (shrink)

We present an ontological analysis of the notion of group agency developed by Christian List and Philip Pettit. We focus on this notion as it allows us to neatly distinguish groups, organizations, corporations – to which we may ascribe agency – from mere aggregates of individuals. We develop a module for group agency within a foundational ontology and we apply it to organizations.

The starting point of this article is the observation that the emergence of the Anthropocene rehabilitates the need for philosophical reflections on the ontology of technology. In particular, if technological innovations on an ontic level of beings in the world are created, but these innovations at the same time _create_ the Anthropocene World at an ontological level, this raises the question how World creation has to be understood. We first identify four problems with the traditional concept of creation: the (...) anthropocentric, ontic and outcome orientation of traditional concepts of creation, as well as its orientation of material fabrication. We subsequently develop a progressive concept of World creation with four characteristics that move beyond the traditional conceptuality: (1) a materialistic concept of creation that accounts for (2) the ontogenetic process and (3) the ontic and ontological nature of creation, and (4) is conceptualized as semantic creation of the World in which we live and act. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...) In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

In the first part of the paper I argue that an ontology of events is precise, flexible and general enough so as to cover the three main alternative formulations of quantum mechanics as well as theories advocating an antirealistic view of the wave function. Since these formulations advocate a primitive ontology of entities living in four-dimensional spacetime, they are good candidates to connect that quantum image with the manifest image of the world. However, to the extent that some (...) form of realism about the wave function is also necessary, one needs to endorse also the idea that the wave function refers to some kind of power. In the second part, I discuss some difficulties raised by the recent proposal that in Bohmian mechanics this power is holistically possessed by all the particles in the universe. (shrink)

What is the ontology of collective action? I have in mind three connected questions. 1. Do the truth conditions of action sentences about groups require there to be group agents over and above individual agents? 2. Is there a difference, in this connection, between action sentences about informal groups that use plural noun phrases, such as ‘We pushed the car’ and ‘The women left the party early’, and action sentences about formal or institutional groups that use singular noun phrases, (...) such as ‘The United States declared war on Japan on December 8th, 1941’ and ‘The Supreme Court ruled that segregation is unconstitutional in 1954 in Brown vs. Board of Education’? 3. Under what conditions does it make sense to speak of a group doing something together, and what, if anything, is a collective action? In this paper, I argue that a) understanding action sentences about groups does not commit us to the existence of group agents per se, but only to the existence of individual agents; b) there is no difference in this regard between sentences which attribute actions to informal groups on the one hand and institutional groups on the other; c) collective action can be both intentional and unintentional; d) any random group of agents each of whom does something is also a group which does something together; e) while there is a sense in which groups per se perform no primitive collective actions, and therefore no actions at all, f) there is a sensible extension of talk of actions to groups, though it should be treated strictly speaking, like talk of group agents, as a façon de parler, for g) the only agents per se are individuals and the only actions are theirs. -/-. (shrink)

The descriptions and theoretical laws scientists write down when they model a system are often false of any real system. And yet we commonly talk as if there were objects that satisfy the scientists’ assumptions and as if we may learn about their properties. Many attempt to make sense of this by taking the scientists’ descriptions and theoretical laws to define abstract or fictional entities. In this paper, I propose an alternative account of theoretical modelling that draws upon Kendall Walton’s (...) ‘make-believe’ theory of representation in art. I argue that this account allows us to understand theoretical modelling without positing any object of which scientists’ modelling assumptions are true. (shrink)

The main purpose of the paper is to outline the formal-logical, general theory of language treated as a particular ontological being. The theory itself is called the ontology of language, because it is motivated by the fact that the language plays a special role: it reflects ontology and ontology reflects the world. Language expressions are considered to have a dual ontological status. They are understood as either concretes, that is tokens – material, physical objects, or types – (...) classes of tokens, which are abstract objects. Such a duality is taken into account in the presented logical theory of syntax, semantics and pragmatics. We point to the possibility of building it on two different levels; one which stems from concretes, language tokens of expressions, whereas the other one – from their classes, types conceived as abstract, ideal beings. The aim of this work is not only to outline this theory as taking into account the functional approach to language, with respect to the dual ontological nature of its expressions, but also to show that the logic based on it is ontologically neutral in the sense that it abstracts from accepting some existential assumptions, related with the ontological nature of these linguistic expressions and their extra-linguistic ontological counterparts (objects). (shrink)