The fallacy fallacy is either the misdiagnosis of fallacy or the supposition that the conclusion of a fallacy must be a falsehood. This paper explores the relevance of these and related errors of reasoning for the appraisal of arguments, especially within virtue theories of argumentation. In particular, the fallacy fallacy exemplifies the Owl of Minerva problem, whereby tools devised to understand a norm make possible new ways of violating the norm. Fallacies are such tools and so are vices. Hence a (...) similar problem arises with argumentative vices. Fortunately, both instances of the problem have a common remedy. (shrink)

'The Last Owl' is a very singular novel built from interconnected poetic tales, culminating in an apocalyptic love. Its dense psychological symbolic plot intends to touch deep realms of the human condition. As for the title it relates to Hegel's phrase mentioning the Owl of Minerva, stating that only when civilizations are nearing their ultimate decay, their final throes, is philosophy able to utter something substantial on them, since deepest truths about history may be caught only during their agony, as (...) they leave scene during "dusk". Accordingly, Philosophers' ponderings approach human history in a analogous way to the hunting owl's gaze while flying over fields at nightfall. Would a last 'Owl of Minerva' be already flying over humankind in this 21st century so obscured by dooming signs ? (shrink)

The focus of this paper is on Kant and on a text which has often been drawn upon when talking about the present situation of philosophy at university, namely his 'The Conflict of the Faculties' of 1798. Kant’s claims, though not applicable to the contemporary situation directly, can indeed be worked out in a way which can assign a distinct and clearly identifiable role for university-based philosophy. I need to emphasize, though, that I am not suggesting that this is the (...) only way Kant’s thoughts in this respect can be adapted to and utilized for such an account. Quite the contrary, Kant’s text offers a manifold of highly important options here. In my article I will seek to establish the following claims: a) Kant, in his later years, which therefore amounts to something like his “mature” position, subscribed to a conception of a public use of reason which mainly referred to the Faculties of Philosophy at universities. b) Kant’s dismissal of philosophy according to the school conception of it must not be taken as a dismissal of academic philosophy altogether. Philosophy practiced at university by professionals is vital for Kant to build philosophy as a fully worked out discipline and to answer questions revolving around the issue of the compatibility of the theoretical standpoint and Kant’s own moral theory. c) Neither a) nor b) can be immediately applied to the contemporary situation we find ourselves in. Combining elements of a) and b), however, a possible route for the actualization of Kant’s ideas may open up. At least one of the functions for which university-based philosophy is uniquely qualified is the assessment of the implications of progress in the natural sciences for the conception of a moral standpoint in general, and as such for a core element of our self-understanding as rational beings. (shrink)

Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-level ontology that allows (...) expressing these modes. (shrink)

Axiom weakening is a technique that allows for a fine-grained repair of inconsistent ontologies. Its main advantage is that it repairs on- tologies by making axioms less restrictive rather than by deleting them, employing the use of refinement operators. In this paper, we build on pre- viously introduced axiom weakening for ALC, and make it much more irresistible by extending its definitions to deal with SROIQ, the expressive and decidable description logic underlying OWL 2 DL. We extend the definitions of (...) refinement operator to deal with SROIQ constructs, in particular with role hierarchies, cardinality constraints and nominals, and illustrate its application. Finally, we discuss the problem of termi- nation of an iterated weakening procedure. (shrink)

The expression “The owl of Minerva flies at dusk” is used to convey that philosophers are only able to identify the assumptions that are made within a period of history, a period of which they are part, when that period is coming to an end and those assumptions will soon no longer be made. In this paper, I support a rival view according to which those involved in a historical period can know their assumptions earlier, given appropriate talent and effort.

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (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.

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

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

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.

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in terms (...) of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions. (shrink)

Come è emerso dall’analisi filosofica e dalla ricerca nelle scienze cogni- tive, la maggior parte dei concetti, tra cui molti concetti medici, esibisce degli “effetti prototipici” e non riesce ad essere definita nei termini di condizioni necessarie e sufficienti. Questo aspetto rappresenta un problema per la pro- gettazione di ontologie in informatica, poiché i formalismi adottati per la rap- presentazione della conoscenza (a partire da OWL – Web Ontology Langua- ge) non sono in grado di rendere conto dei concetti nei (...) termini dei loro tratti prototipici. Nel presente articolo ci concentriamo sulla classe dei disordini mentali facendo riferimento alle descrizioni che ne vengono date nel DSM-5. L’idea è quella di proporre un approccio ibrido, in cui i formalismi delle ontologie sono combinati a una rappresentazione geometrica della conoscenza basata sugli spazi concettuali. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)

Types are fundamental for conceptual modeling and knowledge representation, being an essential construct in all major modeling languages in these fields. Despite that, from an ontological and cognitive point of view, there has been a lack of theoretical support for precisely defining a consensual view on types. As a consequence, there has been a lack of precise methodological support for users when choosing the best way to model general terms representing types that appear in a domain, and for building sound (...) taxonomic structures involving them. For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. At the core of this enterprise, there has been a theory of types specially designed to address these issues. This theory is ontologically well- founded, psychologically informed, and formally characterized. These results have led to the development of a Conceptual Modelling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed on conceptual model design in a variety of domains including academic, industrial, and governmental settings. These experiences exposed improvement opportunities for both the OntoUML language and its underlying theory, UFO. In this paper, we revise the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of OntoUML’s meta-types (e.g. kind, role, phase, mixin) should be considered not as restricted to substantial types but instead should be applied to model endurant types in general, including relator types, quality types, and mode types. We also contribute with a formal characterization of this fragment of the theory, which is then used to advance a new metamodel for OntoUML (termed OntoUML 2). To demonstrate that the benefits of this approach are extended beyond OntoUML, the proposed formal theory is then employed to support the definition of UFO-based lightweight Semantic Web ontologies with ontological constraint checking in OWL. Additionally, we report on empirical evidence from the literature, mainly from cognitive psychology but also from linguistics, supporting some of the key claims made by this theory. Finally, we propose a computational support for this updated metamodel. (shrink)

In the article’s first section, the author clarifies how the metaphilosophical question can be interpreted. In the second and third sections, a Hegelian phenomenological method is applied to the diachronic theoretical development of feminist philosophies – especially two of its moments, sexual difference thought and Judith Butler’s version of queer theory – to understand whether any indications emerge from this development concerning the contents, model of rationality, identity, and methods of these philosophies. The Hegelian metaphilosophical premise is that we can (...) understand what it means to do feminist philosophy only by observing, like the Owl of Minerva, the history of its theoretical development and interpreting the indispensability of each of its moments, and, at the same time, the presence in them of elements for their dialectical sublation. At the end of this analysis, some conclusions for the future of feminist philosophies are drawn. The author argues that the evolution of feminist philosophies shows that they cannot have a defined content or method. They are intrinsically open to their destabilization and sublation, passing from questions about women to general philosophical questions. How to understand the latter – and whether to welcome this ‘sunset’ as a positive, eminently queer event – is the topic of the final reflections. (shrink)

Explanations in behavioural neuroscience are often said to be mechanistic in the sense that they explain an organism’s behaviour by describing the activities and organisation of the organism’s parts that are “constitutively relevant” to organism behaviour. Much has been said about the constitutive relevance of working parts (in debates about the so-called “mutual manipulability criterion”), but relatively little has been said about the constitutive relevance of the organising relations between working parts. Some New Mechanists seem to endorse a simple causal-linking (...) account: organising relations are constitutively relevant to organism behaviour if and only if (and because) they are causal relations that link the working parts that are constitutively relevant to organism behaviour. In this paper, I argue that the causal-linking account is inadequate because it neglects the constitutive relevance of anatomical relations that organise the working parts of a behaving organism. I demonstrate this by considering a case study where the anatomical organisation of the barn owl (Tyto alba) is constitutively relevant to their mechanism for sound localization. The anatomical organisation of this mechanism is best understood as the back-and-forth flow of task information across 7 “levels of anatomy” (a notion that I distinguish from levels of mechanism). A further implication, I conclude, is that at least some of the interlevel structure of neuroscientific explanation is accounted for by levels of anatomy, not levels of mechanism. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

This article presents a newly discovered votive inscription found during the course of the 2013 survey conducted at the ancient city of Phaselis and in its territory. The inscription was found where the stairs to the acropolis from the southwest of the theatre end, in front of the west wall of the tower structure give access to the acropolis. This inscription in the Doric dialect, on a limestone block measuring 0.315 x 0.77 x 0.61 m., records a dedication to Athena (...) Polias. The letters 0.03 m. high, exhibit Late Archaic - Early Classical Period features ( - - - - ) and, consequently the inscription can be dated to the Vth century B.C. -/- Phaselis and its Chief Goddess Athena Polias From the earliest times of Athena worship, especially in the Aegean Islands and Hellas, this goddess was the protectress of cities, institutions and mythological heroes and she manifested this function in various ways. In one of the earliest recorded examples she carries the epithet ἐρυσίπτολις (guardian of the cities), and in another example, in a Linear B inscription discovered in the Palace of Knossos on Crete as Atana Potnia (a-ta-na-po-ti-ni-ja), the mistress of the palace. But perhaps the most striking myth relating to this role of Athena is undoubtedly that of the Palladion statue, the reason for the fall of Troy and for defeat in the Trojan War. In this context, Troy could resist the Achaeans for as long as it was protected by the Palladion, but after it was stolen by Odysseus and Diomedes, the city was captured by the Achaeans. Subsequently, Athens, Argos and Sparta, the most powerful Greek cities, as later the city of Rome, in order to obtain Athena’s protection and so to gain legitimization for the expansion of their empires, invented their own myths claiming that the Palladion statue from Troy was brought to their cities. In another myth the Goddess became the protectress of Tegea through giving Medusa’s hair as a protective image to a hero of the city. Athena’s frequently used epithets, Polias (Πολιάς), Poliouchos (Πολιοῦχος), and the epithet the protectress of the Athenians (Ἀθηνᾶ Ἀθηνῶν μεδέουσα), employed as a means of religious propaganda by the city of Athens when it established the Delian League which subsequently evolved into an empire, clearly indicate Athena was regarded as guardian of the cities. Particularly during the Archaic and Classical Periods, it was this aspect of Athena that, politically placed the Goddess amongst the most important of deities with Zeus and Apollo, and she is most commonly found with the epithet Polias. The epithet Polias or similar, refers in particular to the heart of these cities, to their acropoleis, where Athena Polias was usually worshipped. Her temples located on the heights of the cities made her role particularly visible as the main protecting goddess. One of the best examples of this “visibility”concerns the earliest record of the epithet Polias as, although she wasn’t the chief deity of Argos, within the sanctuary of Athena Polias located on Larisa hill an inscription was found which supplies us with the text of a cult regulation which is datable to the VIth century. B.C.. The Anatolian goddess of Malija, equal to Athena (in Lycia), was attested in Hittite texts from IInd millennium B.C.. This goddess worshipped in Lycia, close to the city of Phaselis, is similarly in a relationship with cities and acropoleis. The Inscribed Pillar of Ksanthos dating from the Vth century B.C. records that many acropoleis were seized with the help of Athena ptoliporthos (πτολίπορθος) “Sacker of Cities”. In the same inscription the city of Patara was named together with Malija and it may refer to the Patara of Malija as in the example of the Lindian Athena (Lindos, city of Athena). Moreover, the goddess Malija was named with the epithet Wedrẽñni (regional, municipal) the equivalent of the epithet Polias in Rhodiapolis. During the great colonization movements (750-550 B.C.) the colonists brought the cult of Athena Polias to many Mediterranean cities, as was the case for example for Lindos on the island of Rhodos. As a matter of fact the strongest ties between Lindos and the colonies which Rhodes founded was the cult of Athena. In consequence, these cities offered precious gifts to the Temple of Athena in Lindos as a demonstration of both their veneration of the goddess and of loyalty. According to myth, the city of Phaselis was colonized in 691/690 B.C. by a group under the leadership of Lakios from Lindos and the Athena cult of the mother city was brought to Phaselis. Thereafter the Phaselitai dedicated the helmets and sickles to Athena Lindia upon which was inscribed, “Having taken them from the Solymoi, the Phaselitai offered them to Athena Lindia, when Lakios was the leader of the colonists”. In addition to this, the other evidence concerning the presence of Athena in the city confirms that this deity was the chief goddess of Phaselis. During the Classical, and especially in the Hellenistic Period, depictions of Athena’s owl, of her Palladion and of Athena Promachos are found. As mentioned above, the epithet Polias usually draws attention to a city’s acropolis with the temple of Athena Polias located there. In the case of Phaselis, the find spot of these votive inscriptions, reused in a wall of a tower that was built in defense of the acropolis, provides an additional indication for the localization of Athena’s temple to the acropolis. This temple most probably was on the acropolis where there are the ruins of a columned building and large ashlar blocks possibly indicating the site of a temple; however, due to the dense vegetation and in the absence of excavations, at present this localisation cannot be stated with certainty. Another reference indicating that Athena Polias was the chief deity of the city was the presence of a holy relic in the Temple of Athena, the spear of the hero of the Trojan War Achilles. During his campaign against the Persians, Alexander the Great stayed in Phaselis in the winter of 334/333 B.C. and he left Achilles’ spear in the Temple of Athena at Phaselis. During the Hellenistic Period, Hellenistic Kings were mentioned with the chief deities of the Archaic and Classical periods as were the emperors in Roman Imperial Period. And according with this practice, the boule and demos of Phaselis worshipped Athena Polias together with the deified emperors, known from an honorific inscription for a certain Ptolemaios. Evidence from the Late Roman Period, especially from the IIIrd century A.D., records the Palladeios agons (ἀγὼν Παλλάδειος) were held in the city in honour of the Goddess Athena. Consequently, philological, epigraphic as well as numismatic evidence shows the Goddess Athena was the chief deity of the city of Phaselis from the Archaic Period into the Late Roman Period. As the epithet Polias on this votive inscription indicates, the goddess had a temple which should be located on the acropolis where the holy relic (Achilles’ spear) was kept and where the officials of the goddess conducted their functions. This new votive inscription provides record of the role Athena occupied in this early post-colonisation period of the city’s political and socio-cultural history. Further, it is also a physical document dating from the city’s Late Archaic-Early Classical Period, aiding in the evaluation of both Phaselis and of the wider region’s history of settlement. (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 volume includes topics from political philosophy and normative ethics on the one hand to philosophy of science and the philosophical underpinnings of water management policy on the other. It contains reflections on ecological nationalism, the legacy of Grey Owl, the meaning of ‘outside’ to Canadians, the paradigm shift from mechanism to ecology in our understanding of nature, the meaning of the concept of the Anthropocene, the importance of humans self-identifying as ‘earthlings’, the challenges of biodiversity protection and the status (...) of cross-bred species, how to ground the moral considerability of ecosystems, the collapse of the Newfoundland and Labrador cod fishery, and much more. It covers metaphysics, ontology, ethics, political philosophy, critical history, and environmental policy. The range of topics and frames is as diverse and challenging as the land itself. (shrink)

We investigate a speci c model of knowledge and beliefs and their dynamics. The model is inspired by public announcement logic and the approach to puzzles concerning knowledge using that logic. In the model epistemic considerations are based on ontology. The main notion that constitutes a bridge between these two disciplines is the notion of epistemic capacities. Within the model we study scenarios in which agents can receive false announcements and can have incomplete or improper views about other agent's epistemic (...) capacities. Moreover, we try to express the description of problem speci cation using the tools from applied ontology { RDF format for information and the Protege editor. (shrink)

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

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will (...) support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

Canadian Environmental Philosophy is the first collection of essays to take up theoretical and practical issues in environmental philosophy today, from a Canadian perspective. The essays cover various subjects, including ecological nationalism, the legacy of Grey Owl, the meaning of “outside” to Canadians, the paradigm shift from mechanism to ecology in our understanding of nature, the meaning and significance of the Anthropocene, the challenges of biodiversity protection in Canada, the conservation status of crossbred species in the age of climate change, (...) and the moral status of ecosystems. This wide range of topics is as diverse and challenging as the Canadian landscape itself. Given the extent of humanity's current impact on the biosphere – especially evident with anthropogenic climate change and the ongoing mass extinction – it has never been more urgent for us to confront these environmental challenges as Canadian citizens and citizens of the world. Canadian Environmental Philosophy galvanizes this conversation from the perspective of this place. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)

The article aims to substantiate the philosophy of synthesis, which is built on the basis of analysis, but gives it a constructive direction. The turning point from analysis to synthesis is the problematization of the elements identified in the analysis, their criticism, replacement, or rearrangement, leading to the construction of alternative concepts and propositions that expand the field of the thinkable and innovate the categorical apparatus of philosophy. This article provides examples of philosophical synthesis at different levels: alternative terms and (...) concepts (“infinition”), postulates (the “diamond rule” in ethics), and disciplines (“horrology” as the study of the self-destructive mechanisms of civilization). Next, we consider the transition from the philosophy of synthesis to the synthesis of philosophy itself with contemporary scientific and technical practices. Technology of the 21st century is no longer instrumental/utilitarian, but a fundamental technology ("onto–technology"), which, thanks to science’s penetration into the micro- and macrocosm, can change the foundational parameters of being, thereby acquiring a philosophical dimension. Accordingly, philosophy as a study of the most general principles of the universe becomes a practical requirement in any “world-forming,” synthesizing acts of technology, including the design of computer games and multi-populated virtual worlds (e.g., “Second Life”), that involve a new ontology, logic, ethics, and axiology. The vocation of philosophy in the 21st century is not just to comprehend our unique world, but to lay the foundations for new world-forming practices, to initiate and design the ontology of possible worlds, and to pave the way for alternative forms of synthetic life and artificial intelligence. Contrary to Hegel, philosophy is no longer the “owl of Minerva” taking flight at dusk, but a skylark proclaiming the dawn of a new creative day. -/- . (shrink)

I begin my comment on Westphal’s study by exploring briefly his refutation of “the arbitrariness thesis,” and then focusing on the “conditio humanae,” i.e. the conditions of life as freedom realized in common life. As I understand it, coordination and cooperation among persons are required because employing freedom in the presence of others presupposes an act of recognition that acknowledges a priori the necessity of universal respect. The right to use and possess things within the institution of property is an (...) illustrative example of this necessity. Justice requires possession not in the form of some equal distribution but as a normative requirement that “everyone shall have property.” One must have property in order to enter the world of inter-subjectivity and become a person. This has important implications for determining how poverty is related to the validity of laws, which depends on the joint legislative will of all persons. (shrink)

The purpose of the present essay is to explicate the basic movement which the Understanding exercises upon itself at the end of the chapter on “Force and the Understanding” in Hegel’s Phenomenology of Spirit. Unlike many other commentators on the Phenomenology, I hope to show how Hegel’s argumentation in this chapter applies not merely to the Newtonian paradigm (to which Hegel makes explicit reference), but to any paradigm which involves the objectivistic presuppositions of the Understanding.

Kant’s “transcendental” or “critical” philosophy is an instance of what can be called the “critique of immediacy.” As part of his critical project, Kant argues that one cannot merely assume that there is a reestablished harmony between thought and being. Instead, one must effect a “return to the subject” and examine the forms of thought themselves, in order to determine the extent to which thought and being are commensurable. As a result of his “transcendental turn,” Kant concludes that what at (...) first appears as immediately given to thought is always already (at least partly) the result of some kind of activity or mediation on the part of the thought itself. Hegel approves of Kant’s critical orientation: Kant correctly demanded to know “how far the forms of thought were capable of leading to the knowledge of truth,” and correctly concluded that “the forms of thought must be made into an object of investigation.” However, for Hegel, the problem with Kant was that he aimed to examine the forms of thought as if they were necessarily separated from being itself. Thus the Kantian strategy, for Hegel, led to a twofold absurdly. (shrink)

I discuss this collection of essays on Hegel and the sciences while stressing the interest of Hegel's philosophy of nature in the light of later non-mainstream developments in the life-sciences and medicine. I compare then the chapters dedicated to Hegel's logic with recent literature on para-consistent logic and re-interpretations of Hegel's own logic.

Abstract: This essay traces the relationship between Hegel and some common portrayals of modern philosophy in the nineteenth century. I explain much of the rationale behind the neo-Kantian narrative of modern philosophy, and argue that the common division of modern philosophers into rationalists and empiricists executed a principally anti-Hegelian agenda. I then trace some failed attempts by anglophone philosophers to reconcile Hegel with the neo-Kantian history, in the interest of explaining Hegel’s subsequent unpopularity in England and America. Finally, I argue (...) that recent attempts to read Hegel in Kantian terms often rest on a misguided appropriation of an anti-Hegelian historical narrative. (shrink)

Frederick Neuhouser's The Foundations of Hegel's Social Theory expertly answers many standard objections to Hegel's theory, and offers a careful reading of its basic principles. However, questions remain whether Neuhouser can successfully reconstruct Hegel's theory while avoiding its links to Hegel's logic. Hegel's normative conclusions depend on logical principles about the self that are not adequately translated into Neuhouser's normative and consequentialist arguments.

Hegel congratulated himself on noticing that the German verb aufheben embodied a speculative dialectic in the interrelation of its multiple meanings. Translators have been hard put to find an equivalent English word. I think I have found a similar word in English, which, if not exactly a translation, still shows a similar interaction among the contrasting motions of its different meanings.

Stephen Houlgate has written an introduction to Hegel that is more than historical. For him, “Hegel’s is still a viable philosophical endeavour with extremely important things to contribute to modern debates, particularly the debates about historical relativism, poverty and social alienation, the nature of freedom and political legitimacy, the future of art, and the character of the Christian faith”. This ambitious book is clearly written and very thoughtful. By concentrating on a number of central themes, Houlgate avoids giving us another (...) numbing summary of the whole Hegelian system, yet he conveys a general idea and feel for the overall project. He also provides fresh looks at areas of Hegel’s thought not usually treated by those in his wing of Hegel interpretation. (shrink)

This provocative book questions whether contemporary humanity can face death in any of the traditional ways, since the events of our century have created a new selfhood and a new death. Wyschogrod describes the “death event” and the “death world”; these refer to the Holocaust but also to the destructive bombings in World War II, and most importantly to the death-in-life of the Nazi and Stalinist concentration and labor camps. Her thesis is.

Hegel's interpretation of Sophocles' play Antigone is central to an understanding of woman's role in the Hegelian system. Hegel is fascinated by this play and uses it in both the Phenomenology and the Philosophy of Right to demonstrate that familial ethical life is woman's unique responsibility. Antigone is revealed as the paradigmatic figure of womanhood and family life in both the ancient and modern worlds, although there are fundamental differences between these two worlds for Hegel. Through an immanent critique of (...) both the Phenomenology and the Philosophy of Right which focuses on the role of woman as presented by Hegel in the figure of Antigone, my analysis reveals the limitations of Hegel’s dialectical theory. (shrink)

In this response I first address the criticisms of omission by discussing some of the elements of the original project that were excluded in the final version (section 1). In section 2 I respond to Howard’s criticism that I assume too much transparency in conscience. In section 3 I discuss the problem of evil and the transition in the Phenomenology of Spirit from conscience to religion. I focus here especially on the distinction between Objective and Absolute Spirit, and on how (...) that distinction plays out differently in the Phenomenology and the Philosophy of Right. In section 4 I take up the specifically political issues of conscience, responding to Speight’s suggestion that conscience should have a transformative role and to De Nys’s query about the State’s relationship to dissenting moral and religious views. Finally, in section 5 I take up the issues of whether I and Hegel do justice to the range of uses of conscience and whether or not the Hegelian view is too optimistic about modernity. (shrink)

In this summary I introduce the interpretive framework for Hegel's Conscience and then provide an overview of the book’s six chapters.

This paper criticizes the assumptions behind Robert Brandom’s reading of Hegel’s Phenomenology, contending that Hegel’s concern with the rational structure of experience, his valorization of reflection over ordinary experience and his idea of the necessit y of progress in knowledge cannot be accommodated within the framework of semantic pragmatism. The central contentions are that Brandom’s pragmatism never comes to terms with Hegel’s idea of truth as a result, leading to a historicist distortion, and also that Brandom’s failure to deal with (...) Hegel’s distinction between natural consciousness and the phenomenological observer collapses Hegel’s phenomenology into a philosophy restricted to the level of natural consciousness. (shrink)

This paper examines the Hegelian moment of the for-another in its negative relation to the other moment of particularity: the for-itself. I identify the dissolving, fluidifying action of the for-another by examining figures within the Philosophy of Nature, particularly comets and moons, but also Hegel’s physics of light and sound. The dissolution of the lunar for-itself at the hands of the cometary for-another illustrates how the dynamic relation between the two moments of particularity participates in the presentation of essence, within (...) the Hegelian syllogism, i.e. as mediating between the universal and the singular. The dynamic action of cometary negativity occurs throughout the Philosophy of Nature and therefore should be pivotal to how the work is read. (shrink)

The creation of the University of Berlin in 1810 was the result of interaction between the state and philosophy, two human expressions whose relationship, at least since Socrates' death and Aristotle's exile, has tended to be problematical. That university, which became an important model for North American institutions of higher learning, was from the outset a state university; it was designed and run by the state, as opposed to what was previously the rule: institutions dependent on the Church or princes. (...) The bind, of course, is that this idea of a modern university, defined by its independence with regard to ecclesiastical and private interests, must henceforth depend on the state to guarantee its independence. This dilemma is already apparent in the philosophical ideas at work in the University of Berlin's early evolution. (shrink)

In the Philosophy of Nature, Hegel describes at length and in detail the particular workings of animal digestion and excretion, referring to the empirical research of his day (Berzelius, Spallanzani, Traviranus). By becoming engaged in the scientific disputes and insights of the time—regarding, for example, the mechanical versus chemical nature of digestion, immediate digestive assimilation and the chemical composition of feces—Hegel arrives at the novel idea that what the animal excretes as superfluous is its own particular entanglement with inorganic otherness. (...) The animal’s subsequent feeling of triumph and satisfaction constitutes the affirmation of individual purposiveness, a form of immediate ideality that Hegel presents as animal subjectivity. (shrink)

A primary fault line in the analytic philosophy of action is the debate between causal/Davidsonian and interpretivist/Anscombian theories of action. The fundamental problem of the former is producing a criterion for distinguishing intentional from non-intentional causal chains; the fundamental problem of the latter is producing an account of the relation between reasons and actions that is represented by the ‘because’ in the claim that the agent acted because she had the reason. It is argued that Hegel’s conception of teleology can (...) be used to develop the interpretivist position by solving both its and the causal theory’s fundamental problems. (shrink)