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  1. Raymond G. Beausoleil (2014). Large Scale Integrated Photonics for Twenty-First Century Information Technologies. Foundations of Physics 44 (8):856-872.
    In this paper, we will review research done by the Large-Scale Integrated Photonics group at HP Laboratories, and in particular we will discuss applications of optical resonances in dielectric microstructures and nanostructures to future classical and quantum information technologies. Our goal is to scale photonic technologies over the next decade in much the same way as electronics over the past five, thereby establishing a Moore’s Law for optics.
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  2. OIivier Bodenreider, Barry Smith & Anita Burgun (2004). The Ontology-Epistemology Divide: A Case Study in Medical Terminology. In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004),. IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...)
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  3. Werner Ceusters & Barry Smith (2010). A Unified Framework for Biomedical Terminologies and Ontologies. Studies in Health Technology and Informatics 160:1050-1054.
    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...)
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  4. Werner Ceusters & Barry Smith (2006). Strategies for Referent Tracking in Electronic Health Records. Journal of Biomedical Informatics 39 (3):362-378.
    The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...)
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  5. Werner Ceusters, Barry Smith & James Matthew Fielding (2004). LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration. In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994). Springer.
    The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...)
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  6. James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith (2004). Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration. In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning. AMIA.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  7. Albert Goldfain, Barry Smith & Lindsay G. Cowell (2011). Towards an Ontological Representation of Resistance: The Case of MRSA. Journal of Biomedical Informatics 44 (1):35-41.
    This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...)
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  8. Michael Grüninger & Christopher Menzel (2003). The Process Specification Language: Theory and Applications. AI Magazine 24 (3):63-74.
    The Process Specification Language (PSL) has been designed to facilitate correct and complete exchange of process information among manufacturing systems, such as scheduling, process modeling, process planning, production planning, simulation, project management, work flow, and business process reengineering. We given an overview of the theories with the PSL ontology, discuss some of the design principles for the ontology, and finish with examples of process specifications that are based on the ontology.
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  9. Ken Herold (2004). Introduction to The Philosophy of Information. Library Trends 52 (3):373-376.
  10. C. Maria Keet & Alessandro Artale (2008). Representing and Reasoning Over a Taxonomy of Part-Whole Relations. Applied ontology 3 (1-2):91-110.
    Many types of part-whole relations have been proposed in the literature to aid the conceptual modeller to choose the most appropriate type, but many of those relations lack a formal specification to give clear and unambiguous semantics to them. To remedy this, a formal taxonomy of types of mereological and meronymic part-whole relations is presented that distinguishes between transitive and intransitive relations and the kind of entity types that are related. The demand to use it effectively brings afore new requirements (...)
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  11. Catherine Legg (2014). “The Meaning of a Thought is Altogether Something Virtual”: Joseph Ransdell and His Legacy. Transactions of the Charles S. Peirce Society 49 (4):451-456,.
    Joseph Ransdell (1931–2010), who received his Ph.D in philosophy from Columbia University in 1966, where he was advised by Sidney Morgenbesser, and spent most of his career at Texas Tech University, offered an original and focused challenge to academic philosophy at the end of the Second Millennium. His guiding philosophical passion was understanding how communication might best encourage and support truth seeking. This introduction to a special edition of the Transactions of the Charles S. Peirce Society which is devoted to (...)
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  12. Catherine Legg (2007). Ontologies on the Semantic Web. Annual Review of Information Science and Technology 41:407-451.
    As an informational technology, the World Wide Web has enjoyed spectacular success. In just ten years it has transformed the way information is produced, stored, and shared in arenas as diverse as shopping, family photo albums, and high-level academic research. The “Semantic Web” was touted by its developers as equally revolutionary but has not yet achieved anything like the Web’s exponential uptake. This 17 000 word survey article explores why this might be so, from a perspective that bridges both philosophy (...)
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  13. Catherine Legg & Samuel Sarjant (2012). Bill Gates is Not a Parking Meter: Philosophical Quality Control in Automated Ontology Building. Proceedings of the Symposium on Computational Philosophy, AISB/IACAP World Congress 2012 (Birmingham, England, July 2-6).
    The somewhat old-fashioned concept of philosophical categories is revived and put to work in automated ontology building. We describe a project harvesting knowledge from Wikipedia’s category network in which the principled ontological structure of Cyc was leveraged to furnish an extra layer of accuracy-checking over and above more usual corrections which draw on automated measures of semantic relatedness.
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  14. Paul M. Livingston, Heidegger on Information Technology.
    My aim in this paper is to begin a discussion about how, and to what extent, Martin Heidegger’s thinking about technology offers helpful critical terms for thinking about the nature and global sway of today’s most dominant and prevalent forms of technology, namely the interrelated technologies of information, communication, and (capitalist) commerce. My suggestion will be that Heidegger’s thought does indeed have implications for critical thinking about these technologies, but that in order to see how it does, we may have (...)
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  15. Olena Medelyan & Catherine Legg (2008). Integrating Cyc and Wikipedia: Folksonomy Meets Rigorously Defined Common-Sense. Proceedings of Wikipedia and AI Workshop at the AAAI-08 Conference. Chicago, US, July 12 2008..
    Integration of ontologies begins with establishing mappings between their concept entries. We map categories from the largest manually-built ontology, Cyc, onto Wikipedia articles describing corresponding concepts. Our method draws both on Wikipedia’s rich but chaotic hyperlink structure and Cyc’s carefully defined taxonomic and common-sense knowledge. On 9,333 manual alignments by one person, we achieve an F-measure of 90%; on 100 alignments by six human subjects the average agreement of the method with the subject is close to their agreement with each (...)
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  16. Christopher Menzel, Basic Semantic Integration. Semantic Interoperability and Integration, Proceedings of Dagstuhl Seminar 04391.
    The use of highly abstract mathematical frameworks is essential for building the sort of theoretical foundation for semantic integration needed to bring it to the level of a genuine engineering discipline. At the same time, much of the work that has been done by means of these frameworks assumes a certain amount of background knowledge in mathematics that a lot of people working in ontology, even at a fairly high theoretical level, lack. The major purpose of this short paper is (...)
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  17. Christopher Menzel, Formal Ontology and Philosophical Content on the Semantic Web.
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  18. Christopher Menzel & Michael Grüninger (2001). A Formal Foundation for Process Modeling. In C. Welty B. Smith (ed.), Formal Ontology and Information  Systems. ACM Press.
    Process modeling is ubiquitous in business and industry. While a great deal of effort has been devoted to the formal and philosophical investigation of processes, surprisingly little research connects this work to real world process modeling. The purpose of this paper is to begin making such a connection. To do so, we first develop a simple mathematical model of activities and their instances based upon the model theory for the NIST Process Specification Language (PSL), a simple language for describing these (...)
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  19. Christopher Menzel & Patrick Hayes, SCL: A Logic Standard for Semantic Integration. Semantic Integration, CEUR Workshop Proceedings, Vol. 82 (2003).
    The Knowledge Interchange Format (KIF) [2] is an ASCII- based framework for use in exchanging of declarative knowledge among disparate computer systems. KIF has been widely used in the fields of knowledge engineering and artificial intelligence. Due to its growing importance, there arose a renewed push to make KIF an offi- cial international standard. A central motivation behind KIF standardization is the wide variation in quality, style, and content — of logic-based frameworks being used for knowledge representation. Variations of all (...)
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  20. David Milne, Catherine Legg, Medelyan Olena & Witten Ian (2009). Mining Meaning From Wikipedia. International Journal of Human-Computer Interactions 67 (9):716-754.
    Wikipedia is a goldmine of information; not just for its many readers, but also for the growing community of researchers who recognize it as a resource of exceptional scale and utility. It represents a vast investment of manual effort and judgment: a huge, constantly evolving tapestry of concepts and relations that is being applied to a host of tasks. This article provides a comprehensive description of this work. It focuses on research that extracts and makes use of the concepts, relations, (...)
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  21. Leo Obrst, Werner Ceusters, Inderjeet Mani, Steve Ray & Barry Smith (2006). The Evaluation of Ontologies: Toward Improved Semantic Interoperability. In Chris Baker & Kei H. Cheung (eds.), Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer. 139-158.
    Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...)
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  22. Samuel Sarjant, Catherine Legg, Olena Medelyan & Michael Robinson (2009). “All You Can Eat” Ontology-Building: Feeding Wikipedia to Cyc. IEEE/WIC/ACM International Conference on Web Intelligence (WI-09), 15 – 18 September 2009 Università Degli Studi di Milano Bicocca, Milano, Italy.
    In order to achieve genuine web intelligence, building some kind of large general machine-readable conceptual scheme (i.e. ontology) seems inescapable. Yet the past 20 years have shown that manual ontology-building is not practicable. The recent explosion of free user-supplied knowledge on the Web has led to great strides in automatic ontology building, but quality-control is still a major issue. Ideally one should automatically build onto an already intelligent base. We suggest that the long-running Cyc project is able to assist here. (...)
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  23. Andrea Scarantino & Gualtiero Piccinini (2010). Information Without Truth. Metaphilosophy 41 (3):313-330.
    Abstract: According to the Veridicality Thesis, information requires truth. On this view, smoke carries information about there being a fire only if there is a fire, the proposition that the earth has two moons carries information about the earth having two moons only if the earth has two moons, and so on. We reject this Veridicality Thesis. We argue that the main notions of information used in cognitive science and computer science allow A to have information about the obtaining of (...)
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  24. Barry Smith (2005). Wüsteria. Studies in Health Technology and Informatic 116:647–652.
    The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...)
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  25. Barry Smith & Mathias Brochhausen (2008). Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment. Studies in Health, Technology and Informatics 134:219-234.
    Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in (...)
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  26. Barry Smith, Pierre Grenon & Louis Goldberg (2004). Biodynamic Ontology: Applying BFO in the Biomedical Domain. Studies in Health and Technology Informatics 102:20–38.
    Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are (...)
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  27. Barry Smith, Tatiana Malyuta, Ron Rudnicki, William Mandrick, David Salmen, Peter Morosoff, Danielle K. Duff, James Schoening & Kesny Parent (2013). IAO-Intel. CEUR 1097:33-40.
    We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...)
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  28. Stefan Wintein (2012). Assertoric Semantics and the Computational Power of Self-Referential Truth. Journal of Philosophical Logic 41 (2):317-345.
    There is no consensus as to whether a Liar sentence is meaningful or not. Still, a widespread conviction with respect to Liar sentences (and other ungrounded sentences) is that, whether or not they are meaningful, they are useless . The philosophical contribution of this paper is to put this conviction into question. Using the framework of assertoric semantics , which is a semantic valuation method for languages of self-referential truth that has been developed by the author, we show that certain (...)
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