Results for 'semantic data annotation'

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  1.  87
    OmniSearch: A Semantic Search System Based on the Ontology 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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  2.  65
    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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. SNOMED CT Standard Ontology Based on the Ontology for General Medical Science.Shaker El-Sappagh, Francesco Franda, Ali Farman & Kyung-Sup Kwak - 2018 - BMC Medical Informatics and Decision Making 76 (18):1-19.
    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 (...)
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  10.  22
    Methodology for Semantic Enhancement of Intelligence Data.Barry Smith, Tatiana Malyuta & William Mandrick - 2013 - CUBRC Report.
    What follows is a contribution to the horizontal integration of warfighter intelligence data as defined in Chairman of the Joint Chiefs of Staff Instruction J2 CJCSI 3340.02AL: -/- Horizontally integrating warfighter intelligence data improves the consumers’ production, analysis and dissemination capabilities. HI requires access (including discovery, search, retrieval, and display) to intelligence data among the warfighters and other producers and consumers via standardized services and architectures. These consumers include, but are not limited to, the combatant commands, Services, (...)
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  11.  53
    Semantic expressivism for epistemic modals.Peter Hawke & Shane Steinert-Threlkeld - 2021 - Linguistics and Philosophy 44 (2):475-511.
    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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  12. The Semantics of Slurs: A Refutation of Coreferentialism.Adam M. Croom - 2015 - Ampersand: An International Journal of General and Applied Linguistics 2:30-38.
    Coreferentialism refers to the common assumption in the literature that slurs and descriptors are coreferential expressions with precisely the same extension. For instance, Vallee recently writes that “If S is an ethnic slur in language L, then there is a non-derogatory expression G in L such that G and S have the same extension”. The non-derogatory expression G is commonly considered the nonpejorative correlate of the slur expression S and it is widely thought that every S has a coreferring G (...)
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  13. 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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  14. 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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  15. 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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  16. Semantics in Support of Biodiversity: An Introduction to the Biological Collections Ontology and Related Ontologies.Ramona L. Walls, John Deck, Robert Guralnik, Steve Baskauf, Reed Beaman, Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Barry Smith & Others - 2014 - PLoS ONE 9 (3):1-13.
    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in (...)
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  17. 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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  18. 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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  19. The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
    The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project (...)
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  20. Survey-Based Naming Conventions for Use in OBO Foundry Ontology Development.Schober Daniel, Barry Smith, Lewis Suzanna, E. Kusnierczyk, Waclaw Lomax, Jane Mungall, Chris Taylor, F. Chris, Rocca-Serra Philippe & Sansone Susanna-Assunta - 2009 - BMC Bioinformatics 10 (1):125.
    A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...)
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  21. 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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  22. 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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  23. 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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  24.  41
    Principles Behind Semantic Relation Between Common Abbreviations and Their Expansions on Instagram.Andi Kaharuddin - 2020 - International Journal of Criminology and Sociology 9:2270-2276.
    The phenomenon of abbreviation used on Instagram is an interesting thing since the users modify the abbreviation form of expansion words making deviation from the original meaning. The principle of meaning relation between abbreviations and their expansions is used to make a change to the purposes of Instagram users. This research was aimed to describe the principle of abbreviation used in Instagram. An exploitation method was used by the technique of making screenshots and recording the abbreviation data. The results (...)
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  25. 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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  26. 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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  27.  75
    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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  28. 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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  29. 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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  30. 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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  31. Translating the Idiom of Oppression: A Genealogical Deconstruction of FIlipinization and the 19th Century Construction of the Modern Philippine Nation.Michael Roland Hernandez - 2019 - Dissertation, Ateneo de Manila University
    This doctoral thesis examines the phenomenon of Filipinization, specifically understood as the ideological construction of a “Filipino identity” or ‘Filipino subject-consciousness” within the highly determinate context provided by the Filipino ilustrado nationalists such as José Rizal, Marcelo H. del Pilar and their fellow propagandists inasmuch as it leads to the nineteenth (19th) century construction of the modern Philippine nation. Utilizing Jacques Derrida’s deconstructive thinking, this study undertakes a genealogical critique engaged on the concrete historical examination of what is meant by (...)
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  32. 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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  33. 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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  34. “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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  35. The Perception of Material Qualities and the Internal Semantics of the Perceptual System.Rainer Mausfeld - 2010 - In Albertazzi Liliana, Tonder Gert & Vishwanath Dhanraj (eds.), Perception beyond Inference. The Information Content of Visual Processes. MIT Press.
    The chapter outlines an abstract theoretical framework that is currently (re-)emerging in the course of a theoretical convergence of several disciplines. In the first section, the fundamental problem of perception theory is formulated, namely, the generation, by the perceptual system, of meaningful categories from physicogeometric energy patterns. In the second section, it deals with basic intuitions and assumptions underlying what can be regarded as the current Standard Model of Perceptual Psychology and points out why this model is profoundly inadequate for (...)
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  36. The Environment Ontology: Contextualising Biological and Biomedical Entities.Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis - 2013 - Journal of Biomedical Semantics 4 (43):1-9.
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s (...)
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  37. The Role of Ontologies for Sustainable, Semantically Interoperable and Trustworthy EHR Solutions.Bernd Blobel, Dipak Kalra, Marc Koehn, Ken Lunn, Peter Pharow, Pekka Ruotsalainen, Stefan Schulz & Barry Smith - 2009 - Studies in Health Technology and Informatics 150:953-957.
    As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...)
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  38.  99
    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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  39. 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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  40. 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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  41. 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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  42.  53
    Moral Realism and Semantic Accounts of Moral Vagueness.Ali Abasnezhad - forthcoming - Inquiry: An Interdisciplinary Journal of Philosophy:1-13.
    Miriam Schoenfield argues that moral realism and moral vagueness imply ontic vagueness. In particular, she argues that neither shifty nor rigid semantic accounts of vagueness can provide a satisfactory explanation of moral vagueness for moral realists. This paper constitutes a response. I argue that Schoenfield's argument against the shifty semantic account presupposes that moral indeterminacies can, in fact, be resolved determinately by crunching through linguistic data. I provide different reasons for rejecting this assumption. Furthermore, I argue that (...)
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  43.  73
    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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  44. 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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  45. 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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  46. 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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  47.  22
    Introduction to CAT4. Part 3. Semantics.Andrew Thomas Holster - manuscript
    CAT4 is proposed as a general method for representing information, enabling a powerful programming method for large-scale information systems. It enables generalised machine learning, software automation and novel AI capabilities. This is Part 3 of a five-part introduction. The focus here is on explaining the semantic model for CAT4. Points in CAT4 graphs represent facts. We introduce all the formal (data) elements used in the classic semantic model: sense or intension (1st and 2nd joins), reference (3rd join), (...)
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  48.  86
    An Ontological Investigation Over Human Relations in Linked Data.Miroslav Vacura, Vojtěch Svátek & Aldo Gangemi - 2016 - Applied Ontology 11 (3):227-254.
    The research presented in this article is motivated by the increasing importance of complex human relations in linked data, either extracted from social networks, or found in existing databases. The FOAF vocabulary, targeted in our research, plays a central role in those data, and is a model for lightweight ontologies largely used in linked data, such as the DBpedia ontology and schema-org. We provide an overview of FOAF and other approaches for describing human relations, followed by a (...)
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  49.  73
    PROMES: An Ontology‐Based Messaging Service for Semantically Interoperable Information Exchange During Disaster Response.Linda Elmhadhbi, Mohamed‐Hedi Karray, Bernard Archimède, J. Neil Otte & Barry Smith - 2020 - Journal of Contingencies and Crisis Management 28 (3):324-338.
    Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and inefficient (...)
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  50.  84
    The Non-Coding RNA Ontology : A Comprehensive Resource for the Unification of Non-Coding RNA Biology.Huang Jingshan, Eilbeck Karen, Barry Smith, A. Blake Judith, Dou Dejing, Huang Weili, A. Natale Darren, Ruttenberg Alan, Huan Jun & T. Zimmermann Michael - 2016 - Journal of Biomedical Semantics 7 (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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