Results for 'semantic data annotation'

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  1. The Development of Non-Coding RNA Ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed (...)
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  2.  64
    OmniSearch: A Semantic Search System Based on the Ontology for MIcroRNA Target for microRNA-Target Gene Interaction Data.Huang Jingshan, Gutierrez Fernando, J. Strachan Harrison, Dou Dejing, Huang Weili, A. Blake Judith, Barry Smith, Eilbeck Karen, A. Natale Darren & Lin Yu - 2016 - Journal of Biomedical Semantics 7 (1):1.
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary (...)
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  3.  86
    Horizontal Integration of Warfighter Intelligence Data: A Shared Semantic Resource for the Intelligence Community.Barry Smith, Tatiana Malyuta, William S. Mandrick, Chia Fu, Kesny Parent & Milan Patel - 2012 - In Proceedings of the Conference on Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR. pp. 1-8.
    We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of (...)
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  4. Integration of Intelligence Data Through Semantic Enhancement.David Salmen, Tatiana Malyuta, Alan Hansen, Shaun Cronen & Barry Smith - 2011 - In Proceedings of the Conference on Semantic Technology in Intelligence, Defense and Security (STIDS). CEUR, Vol. 808.
    We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of (...)
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  5.  80
    No Wisdom in the Crowd: Genome Annotation at the Time of Big Data - Current Status and Future Prospects.Antoine Danchin - 2018 - Microbial Biotechnology 11 (4):588-605.
    Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential (...)
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  6. “Identifying Phrasal Connectives in Italian Using Quantitative Methods”.Edoardo Zamuner, Fabio Tamburini & Cristiana de Sanctis - 2002 - In Stefania Nuccorini (ed.), Phrases and Phraseology – Data and Descriptions. Peter Lang Verlag.
    In recent decades, the analysis of phraseology has made use of the exploration of large corpora as a source of quantitative information about language. This paper intends to present the main lines of work in progress based on this empirical approach to linguistic analysis. In particular, we focus our attention on some problems relating to the morpho-syntactic annotation of corpora. The CORIS/CODIS corpus of contemporary written Italian, developed at CILTA – University of Bologna (Rossini Favretti 2000; Rossini Favretti, Tamburini, (...)
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  7. An Ontological Architecture for Orbital Debris Data.Robert J. Rovetto - 2015 - Earth Science Informatics 9 (1):67-82.
    The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris and broader SSA domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to (I) represent general orbital debris and SSA (...)
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  8. Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are (...)
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  9. Development of FuGO: An Ontology for Functional Genomics Investigations.Patricia L. Whetzel, Ryan R. Brinkman, Helen C. Causton, Liju Fan, Dawn Field, Jennifer Fostel, Gilberto Fragoso, Tanya Gray, Mervi Heiskana, Tina Hernandez-Boussard & Barry Smith - 2006 - Omics: A Journal of Integrative Biology 10 (2):199-204.
    The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common (...)
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  10. A Domain Ontology for the Non-Coding RNA Field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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  11. The Orbital Space Environment and Space Situational Awareness Domain Ontology – Towards an International Information System for Space Data.Robert J. Rovetto - 2016 Sept - In Proceedings of The Advanced Maui Optical and Space Surveillance Technologies (AMOS) Conference.
    The orbital space environment is home to natural and artificial satellites, debris, and space weather phenomena. As the population of orbital objects grows so do the potential hazards to astronauts, space infrastructure and spaceflight capability. Orbital debris, in particular, is a universal concern. This and other hazards can be minimized by improving global space situational awareness (SSA). By sharing more data and increasing observational coverage of the space environment we stand to achieve that goal, thereby making spaceflight safer and (...)
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  12. The Role of Disagreement in Semantic Theory.Carl Baker - 2013 - Australasian Journal of Philosophy (1):1-18.
    Arguments from disagreement often take centre stage in debates between competing semantic theories. This paper explores the theoretical basis for arguments from disagreement and, in so doing, proposes methodological principles which allow us to distinguish between legitimate arguments from disagreement and dialectically ineffective arguments from disagreement. In the light of these principles, I evaluate Cappelen and Hawthorne's [2009] argument from disagreement against relativism, and show that it fails to undermine relativism since it is dialectically ineffective. Nevertheless, I argue that (...)
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  13. A Semantic Approach for Knowledge Capture of microRNA-Target Gene Interactions.Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang & Zixing Liu - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015),. pp. 975-982.
    Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In (...)
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  14.  76
    Ontology Based Annotation of Contextualized Vital Signs.Goldfain Albert, Xu Min, Bona Jonathan & Barry Smith - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO). Montreal: pp. 28-33.
    Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system (...)
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  15. Between Singularity and Generality: The Semantic Life of Proper Names.Laura Delgado - 2019 - Linguistics and Philosophy 42 (4):381-417.
    Although the view that sees proper names as referential singular terms is widely considered orthodoxy, there is a growing popularity to the view that proper names are predicates. This is partly because the orthodoxy faces two anomalies that Predicativism can solve: on the one hand, proper names can have multiple bearers. But multiple bearerhood is a problem to the idea that proper names have just one individual as referent. On the other hand, as Burge noted, proper names can have predicative (...)
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  16.  27
    Semantic expressivism for epistemic modals.Peter Hawke & Shane Steinert-Threlkeld - forthcoming - Linguistics and Philosophy:1-37.
    Expressivists about epistemic modals deny that ‘Jane might be late’ canonically serves to express the speaker’s acceptance of a certain propositional content. Instead, they hold that it expresses a lack of acceptance. Prominent expressivists embrace pragmatic expressivism: the doxastic property expressed by a declarative is not helpfully identified with that sentence’s compositional semantic value. Against this, we defend semantic expressivism about epistemic modals: the semantic value of a declarative from this domain is the property of doxastic attitudes (...)
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  17. How to Pull a Metaphysical Rabbit Out of an End-Relational Semantic Hat.Nicholas Laskowski - 2014 - Res Philosophica 91 (4):589-607.
    Analytic reductivism in metaethics has long been out of philosophical vogue. In Confusion of Tongues: A Theory of Normativity (2014), Stephen Finlay tries to resuscitate it by developing an analytic metaethical reductive naturalistic semantics for ‘good.’ He argues that an end-relational semantics is the simplest account that can explain all of the data concerning the term, and hence the most plausible theory of it. I argue that there are several assumptions that a reductive naturalist would need to make about (...)
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  18. Quantification, Negation, and Focus: Challenges at the Conceptual-Intentional Semantic Interface.Tista Bagchi - manuscript
    Quantification, Negation, and Focus: Challenges at the Conceptual-Intentional Semantic Interface Tista Bagchi National Institute of Science, Technology, and Development Studies (NISTADS) and the University of Delhi Since the proposal of Logical Form (LF) was put forward by Robert May in his 1977 MIT doctoral dissertation and was subsequently adopted into the overall architecture of language as conceived under Government-Binding Theory (Chomsky 1981), there has been a steady research effort to determine the nature of LF in language in light of (...)
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  19.  81
    Modeling Semantic Emotion Space Using a 3D Hypercube-Projection: An Innovative Analytical Approach for the Psychology of Emotions.Radek Trnka, Alek Lačev, Karel Balcar, Martin Kuška & Peter Tavel - 2016 - Frontiers in Psychology 7.
    The widely accepted two-dimensional circumplex model of emotions posits that most instances of human emotional experience can be understood within the two general dimensions of valence and activation. Currently, this model is facing some criticism, because complex emotions in particular are hard to define within only these two general dimensions. The present theory-driven study introduces an innovative analytical approach working in a way other than the conventional, two-dimensional paradigm. The main goal was to map and project semantic emotion space (...)
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  20. A Conceptual Investigation of the Ontological Commensurability of Spatial Data Infrastructures Among Different Cultures.D. J. Saab - 2009 - Earth Science Informatics 2 (4):283-297.
    Humans think and communicate in very flexible and schematic ways, and a Spatial Data Infrastructure (SDI) for the Amazon and associated information system ontologies should reflect this flexibility and the adaptive nature of human cognition in order to achieve semantic interoperability. In this paper I offer a conceptual investigation of SDI and explore the nature of cultural schemas as expressions of indigenous ontologies and the challenges of semantic interoperability across cultures. Cultural schemas are, in essence, our ontologies, (...)
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  21. Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation (...)
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  22. The HL7 Approach to Semantic Interoperability.Jobst Landgrebe & Barry Smith - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. pp. 139-146.
    Health Level 7 (HL7) is an international standards development organisation in the domain of healthcare information technology. Initially the mission of HL7 was to enable data exchange via the creation of syntactic standards which supported point-to-point messaging. Currently HL7 sees its mission as one of creating standards for semantic interoperability in healthcare IT on the basis of its flagship “version 3” (v3). Unfortunately, v3 has been plagued by quality and consistency issues, and it has not been able to (...)
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  23. Annotating Affective Neuroscience Data with the Emotion Ontology.Janna Hastings, Werner Ceusters, Kevin Mulligan & Barry Smith - 2012 - In Third International Conference on Biomedical Ontology. ICBO. pp. 1-5.
    The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. (...)
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  24.  59
    ARGOS Policy Brief on Semantic Interoperability.Dipak Kalra, Mark Musen, Barry Smith & Werner Ceusters - 2011 - Studies in Health Technology and Informatics 170 (1):1-15.
    Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including (...)
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  25.  55
    Semantic Interoperability in Healthcare. State of the Art in the US. A Position Paper with Background Materials.Werner Ceusters & Barry Smith - 2010 - In European Union ARGOS Project: Transatlantic Observatory for Meeting Global Health Policy Challenges through ICT-Enabled Solution.
    Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus (...)
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  26. Conceptual Atomism and the Computational Theory of Mind: A Defense of Content-Internalism and Semantic Externalism.John-Michael Kuczynski - 2007 - John Benjamins & Co.
    Contemporary philosophy and theoretical psychology are dominated by an acceptance of content-externalism: the view that the contents of one's mental states are constitutively, as opposed to causally, dependent on facts about the external world. In the present work, it is shown that content-externalism involves a failure to distinguish between semantics and pre-semantics---between, on the one hand, the literal meanings of expressions and, on the other hand, the information that one must exploit in order to ascertain their literal meanings. It is (...)
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  27. The Space Object Ontology.Robert J. Rovetto - 2016 - 2016 1.
    This paper develops the ontology of space objects for theoretical and computational ontology applied to the space (astronautical/astronomical) domain. It follows “An ontological architecture for Orbital Debris Data” (Rovetto, 2015) and “Preliminaries of a Space Situational Awareness Ontology” (Rovetto, Kelso, 2016). Important considerations for developing a space object ontology, or more broadly, a space domain ontology are presented. The main category term ‘Space Object’ is analyzed from a philosophical perspective. The ontological commitments of legal definitions for artificial space objects (...)
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  28. Preliminaries of a Space Situational Awareness Ontology.Robert J. Rovetto & T. S. Kelso - 2016 Feb - In Renato Zanetti, Ryan P. Russell, Martin T. Oximek & Angela L. Bowes (eds.), Proceedings of AAS/AIAA Spaceflight Mechanics Meeting, in Advances in the Astronautical Sciences. Univelt Inc.. pp. 4177-4192.
    Space situational awareness (SSA) is vital for international safety and security, and for the future of space travel. The sharing of SSA data and information should improve the state of global SSA for planetary defense and spaceflight safety. I take steps toward a Space Situational Awareness (SSA) Ontology, and outline some central objectives, requirements and desiderata in the ontology development process for this domain. The purpose of this ontological system is to explore the potential for the ontology research topic (...)
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  29. Ontology For Europe's Space Situational Awareness Program.Robert J. Rovetto - 2017 - In T. Flohrer & F. Schmitz (eds.), Proceedings of the 7th European Conference on Space Debris. Darmstadt, Germany: European Space Agency.
    This paper presents an ontology architecture concept for the European Space Agency‘s (ESA) Space Situational Awareness (SSA) Program. It incorporates the author‘s domain ontology, The Space Situational Awareness Ontology and related ontology work. I summarize computational ontology, discuss the segments of ESA SSA, and introduce an option for a modular ontology framework reflecting the divisionsof the SSA program. Among other things, ontologies are used for data sharing and integration. By applying ontology to ESA data, the ESA may better (...)
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  30.  59
    The Co-Ascription of Ordered Lexical Pairs: A Cognitive-Science-Based Semantic Theory of Meaning and Reference. Part 1.Tom Johnston - manuscript
    Lexical semantics has a problem. As Allesandro Lenci put it, the problem is that it cannot distinguish semantic from non-semantic relationships within its data. (2008, 2014). The data it relies on are patterns of co-occurrence of lexemes within linguistic corpora. But patterns of co-occurrence can reflect either our knowledge of what the world is like or our knowledge of what words mean -- matters of fact or matters of meaning. -/- In this essay, I develop a (...)
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  31. The Evaluation of Ontologies: Editorial Review Vs. Democratic Ranking.Barry Smith - 2008 - In Proceedings of InterOntology (Tokyo, Japan, 26-27 February 2008),. Tokyo: Keio University Press. pp. 127-138.
    Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, (...)
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  32.  65
    Orbital Space Environment and Space Situational Awareness Domain Ontology.Robert J. Rovetto - 2016 - In Stefano Borgo, Jean-Rémi Bourguet & Adrien Barton (eds.), CEUR workshop proceedings of The Joint Ontology Workshops, with the 9th International Conference of Formal Ontology for Information Systems (FOIS), Early Career Symposium. CEUR Scientific Workshops.
    A short summary paper of my Orbital Space Domain Ontology project (purl.org/space-ontology), originally conceived in 2011. Since then I've sought (without success) opportunities to realize it (either as a PhD or other degree thesis; or in an employment position) toward my original passion of entering the space sector and gaining further space education. Since then persons in the relevant space disciplines have seen the potential in it, and unfortunately some have taken advantage of my ideas yet excluded me from work. (...)
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  33. Monsters and the Theoretical Role of Context.Brian Rabern & Derek Ball - 2019 - Philosophy and Phenomenological Research 98 (2):392-416.
    Kaplan (1989) famously claimed that monsters--operators that shift the context--do not exist in English and "could not be added to it". Several recent theorists have pointed out a range of data that seem to refute Kaplan's claim, but others (most explicitly Stalnaker 2014) have offered a principled argument that monsters are impossible. This paper interprets and resolves the dispute. Contra appearances, this is no dry, technical matter: it cuts to the heart of a deep disagreement about the fundamental structure (...)
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  34. Updating Data Semantics.Anthony S. Gillies - 2020 - Mind 129 (513):1-41.
    This paper has three main goals. First, to motivate a puzzle about how ignorance-expressing terms like maybe and if interact: they iterate, and when they do they exhibit scopelessness. Second, to argue that there is an ambiguity in our theoretical toolbox, and that exposing that opens the door to a solution to the puzzle. And third, to explore the reach of that solution. Along the way, the paper highlights a number of pleasing properties of two elegant semantic theories, explores (...)
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  35. Modality and Expressibility.Matthew Mandelkern - 2019 - Review of Symbolic Logic 12 (4):768-805.
    When embedding data are used to argue against semantic theory A and in favor of semantic theory B, it is important to ask whether A could make sense of those data. It is possible to ask that question on a case-by-case basis. But suppose we could show that A can make sense of all the embedding data which B can possibly make sense of. This would, on the one hand, undermine arguments in favor of B (...)
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  36. Identifying Virtues and Values Through Obituary Data-Mining.Mark Alfano, Andrew Higgins & Jacob Levernier - 2018 - Journal of Value Inquiry 52 (1).
    Because obituaries are succinct and explicitly intended to summarize their subjects’ lives, they may be expected to include only the features that the author finds most salient but also to signal to others in the community the socially-recognized aspects of the deceased’s character. We begin by reviewing studies 1 and 2, in which obituaries were carefully read and labeled. We then report study 3, which further develops these results with a semi-automated, large-scale semantic analysis of several thousand obituaries. Geography, (...)
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  37. The Lying Test.Eliot Michaelson - 2016 - Mind and Language 31 (4):470-499.
    As an empirical inquiry into the nature of meaning, semantics must rely on data. Unfortunately, the primary data to which philosophers and linguists have traditionally appealed—judgments on the truth and falsity of sentences—have long been known to vary widely between competent speakers in a number of interesting cases. The present article constitutes an experiment in how to obtain some more consistent data for the enterprise of semantics. Specifically, it argues from some widely accepted Gricean premises to the (...)
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  38. The Ontology of Command and Control.Barry Smith, Mietinnin Kristo & Mandrick William - 2009 - In Proceedings of the 14th International Command and Control Research and Technology Symposium (ICCRTS).
    The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within (...)
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  39. Natural Language Processing and Semantic Network Visualization for Philosophers.Mark Alfano & Andrew Higgins - forthcoming - In Eugen Fischer & Mark Curtis (eds.), Methodological Advances in Experimental Philosophy. Bloomsbury.
    Progress in philosophy is difficult to achieve because our methods are evidentially and rhetorically weak. In the last two decades, experimental philosophers have begun to employ the methods of the social sciences to address philosophical questions. However, the adequacy of these methods has been called into question by repeated failures of replication. Experimental philosophers need to incorporate more robust methods to achieve a multi-modal perspective. In this chapter, we describe and showcase cutting-edge methods for data-mining and visualization. Big (...) is a useful investigatory tool for moral psychology, and it fits well with the Ramsification method the first author advances in a series of recent papers. The guiding insight of these papers is that we can infer the meaning and structure of concepts from patterns of assertions and inferential associations in natural language. (shrink)
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  40. Mapping Human Values: Enhancing Social Marketing Through Obituary Data-Mining.Mark Alfano, Andrew Higgins & Jacob Levernier - forthcoming - In Eda Gurel-Atay & Lynn Kahle (eds.), Social and Cultural Values in a Global and Digital Age. Routledge.
    Obituaries are an especially rich resource for identifying people’s values. Because obituaries are succinct and explicitly intended to summarize their subjects’ lives, they may be expected to include only the features that the author(s) find most salient, not only for themselves as relatives or friends of the deceased, but also to signal to others in the community the socially-recognized aspects of the deceased’s character. We report three approaches to the scientific study of virtue and value through obituaries. We begin by (...)
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  41. The Neurological Disease Ontology.Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti & Alexander D. Diehl - 2013 - Journal of Biomedical Semantics 4 (42):42.
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical (...)
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  42. Ontology for the Intelligence Analyst.Barry Smith - 2012 - CrossTalk 14 (Nov/Dec):18-25.
    As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case (...)
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  43. Definite Descriptions and Semantic Pluralism.Brendan Murday - 2014 - Philosophical Papers 43 (2):255-284.
    We pose two arguments for the view that sentences containing definite descriptions semantically express multiple propositions: a general proposition as Russell suggested, and a singular proposition featuring the individual who uniquely satisfies the description at the world-time of utterance. One argument mirrors David Kaplan's arguments that indexicals express singular propositions through a context-sensitive character. The second argument mirrors Kent Bach's and Stephen Neale's arguments for pluralist views about terms putatively triggering conventional implicatures, appositive, and nonrestrictive relative clauses. After presenting these (...)
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  44. Why Fuss About These Quirks of the Vernacular? Propositional Attitude Sentences in Prior’s Nachlass.Giulia Felappi - 2016 - Synthese 193 (11):3521-3534.
    In English, in order to speak about Arthur’s attitudes, we use sentences like “Arthur believes that natural language is messy”. For sentences of this kind we have a standard theory, according to which the ‘that’-clause ‘that natural language is messy’ denotes a proposition. As Prior showed for the first time, the standard theory appears to be at odds with some linguistic data. Geach and Prior both assumed that linguistic data are to be taken as reliable guides to a (...)
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  45.  46
    Biomedical Terminologies and Ontologies: Enabling Biomedical Semantic Interoperability and Standards in Europe.Bernard de Bono, Mathias Brochhausen, Sybo Dijkstra, Dipak Kalra, Stephan Keifer & Barry Smith - 2009 - In European Large-Scale Action on Electronic Health.
    In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular (...)
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  46. Concepts and Reference: Defending a Dual Theory of Natural Kind Concepts.Jussi Jylkkä - 2008 - Dissertation, University of Turku
    In this thesis I argue that the psychological study of concepts and categorisation, and the philosophical study of reference are deeply intertwined. I propose that semantic intuitions are a variety of categorisation judgements, determined by concepts, and that because of this, concepts determine reference. I defend a dual theory of natural kind concepts, according to which natural kind concepts have distinct semantic cores and non-semantic identification procedures. Drawing on psychological essentialism, I suggest that the cores consist of (...)
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  47. Data, Privacy, and the Individual.Carissa Véliz - 2020 - Center for the Governance of Change.
    The first few years of the 21st century were characterised by a progressive loss of privacy. Two phenomena converged to give rise to the data economy: the realisation that data trails from users interacting with technology could be used to develop personalised advertising, and a concern for security that led authorities to use such personal data for the purposes of intelligence and policing. In contrast to the early days of the data economy and internet surveillance, the (...)
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  48. Privacy, Autonomy, and Personalised Targeting: Rethinking How Personal Data is Used.Karina Vold & Jessica Whittlestone - 2019 - In Carissa Véliz (ed.), Report on Data, Privacy, and the Individual in the Digital Age.
    Technological advances are bringing new light to privacy issues and changing the reasons for why privacy is important. These advances have changed not only the kind of personal data that is available to be collected, but also how that personal data can be used by those who have access to it. We are particularly concerned with how information about personal attributes inferred from collected data (such as online behaviour), can be used to tailor messages and services to (...)
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  49. Ontological Support for Living Plan Specification, Execution and Evaluation.Erik Thomsen, Fred Read, William Duncan, Tatiana Malyuta & Barry Smith - 2014 - In Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR vol. 1304. pp. 10-17.
    Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...)
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  50.  69
    An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method (...)
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