Results for 'Natale Darren'

41 found
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  1. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
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  2. 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 our (...)
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  3. Framework for a Protein Ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...)
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  4. 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 niche in semantic annotation of (...)
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  5.  97
    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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  6.  37
    The Representation of Protein Complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...)
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  7.  99
    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 data set (...)
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  8.  52
    Protein-Centric Connection of Biomedical Knowledge: Protein Ontology Research and Annotation Tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  9.  37
    Protein Ontology: Enhancing and Scaling Up the Representation of Protein Entities.Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross & Alan Ruttenberg - 2017 - Nucleic Acids Research 45 (D1):D339-D346.
    The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...)
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  10.  67
    TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...)
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  11.  98
    Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
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  12.  46
    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 for the (...)
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  13.  38
    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 for the (...)
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  14. Are There Indefeasible Epistemic Rules?Darren Bradley - 2019 - Philosophers' Imprint 19.
    What if your peers tell you that you should disregard your perceptions? Worse, what if your peers tell you to disregard the testimony of your peers? How should we respond if we get evidence that seems to undermine our epistemic rules? Several philosophers have argued that some epistemic rules are indefeasible. I will argue that all epistemic rules are defeasible. The result is a kind of epistemic particularism, according to which there are no simple rules connecting descriptive and normative facts. (...)
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  15. Naturalness as a Constraint on Priors.Darren Bradley - forthcoming - Mind:fzz027.
    I argue that epistemologists should borrow the metaphysician’s concept of naturalness and assign higher priors to more natural hypotheses.
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  16. Self-Location is No Problem for Conditionalization.Darren Bradley - 2011 - Synthese 182 (3):393-411.
    How do temporal and eternal beliefs interact? I argue that acquiring a temporal belief should have no effect on eternal beliefs for an important range of cases. Thus, I oppose the popular view that new norms of belief change must be introduced for cases where the only change is the passing of time. I defend this position from the purported counter-examples of the Prisoner and Sleeping Beauty. I distinguish two importantly different ways in which temporal beliefs can be acquired and (...)
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  17. When Betting Odds and Credences Come Apart: More Worries for Dutch Book Arguments.Darren Bradley & Hannes Leitgeb - 2006 - Analysis 66 (2):119-127.
    If an agent believes that the probability of E being true is 1/2, should she accept a bet on E at even odds or better? Yes, but only given certain conditions. This paper is about what those conditions are. In particular, we think that there is a condition that has been overlooked so far in the literature. We discovered it in response to a paper by Hitchcock (2004) in which he argues for the 1/3 answer to the Sleeping Beauty problem. (...)
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  18. Confirmation in a Branching World: The Everett Interpretation and Sleeping Beauty.Darren Bradley - 2011 - British Journal for the Philosophy of Science 62 (2):323-342.
    Sometimes we learn what the world is like, and sometimes we learn where in the world we are. Are there any interesting differences between the two kinds of cases? The main aim of this article is to argue that learning where we are in the world brings into view the same kind of observation selection effects that operate when sampling from a population. I will first explain what observation selection effects are ( Section 1 ) and how they are relevant (...)
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  19. Multiple Universes and Observation Selection Effects.Darren Bradley - 2009 - American Philosophical Quarterly 46 (1):72.
    The fine-tuning argument can be used to support the Many Universe hypothesis. The Inverse Gambler’s Fallacy objection seeks to undercut the support for the Many Universe hypothesis. The objection is that although the evidence that there is life somewhere confirms Many Universes, the specific evidence that there is life in this universe does not. I will argue that the Inverse Gambler’s Fallacy is not committed by the fine-tuning argument. The key issue is the procedure by which the universe with life (...)
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  20. Should Explanations Omit the Details?Darren Bradley - forthcoming - British Journal for the Philosophy of Science.
    There is a widely shared belief that the higher level sciences can provide better explanations than lower level sciences. But there is little agreement about exactly why this is so. It is often suggested that higher level explanations are better because they omit details. I will argue instead that the preference for higher level explanations is just a special case of our general preference for informative, logically strong, beliefs. I argue that our preference for informative beliefs entirely accounts for why (...)
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  21. Functionalism and The Independence Problems.Darren Bradley - 2013 - Noûs 47 (1):545-557.
    The independence problems for functionalism stem from the worry that if functional properties are defined in terms of their causes and effects then such functional properties seem to be too intimately connected to these purported causes and effects. I distinguish three different ways the independence problems can be filled out – in terms of necessary connections, analytic connections and vacuous explanations. I argue that none of these present serious problems. Instead, they bring out some important and over-looked features of functionalism.
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  22. Self-Locating Belief and Updating on Learning.Darren Bradley - forthcoming - Mind:fzy046.
    Beliefs that locate you in space or time are self-locating beliefs. These cause a problem for Bayesian models of belief. Miriam Schoenfield (2016) offers a solution – that on learning x, agents should update on the fact that they learned x. I will argue that Schoenfield’s suggestion does not solve the problem.
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  23. Monty Hall, Doomsday and Confirmation.Darren Bradley & Branden Fitelson - 2003 - Analysis 63 (1):23–31.
    We give an analysis of the Monty Hall problem purely in terms of confirmation, without making any lottery assumptions about priors. Along the way, we show the Monty Hall problem is structurally identical to the Doomsday Argument.
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  24. Everettian Confirmation and Sleeping Beauty: Reply to Wilson: Figure 1.Darren Bradley - 2015 - British Journal for the Philosophy of Science 66 (3):683-693.
    In Bradley, I offered an analysis of Sleeping Beauty and the Everettian interpretation of quantum mechanics. I argued that one can avoid a kind of easy confirmation of EQM by paying attention to observation selection effects, that halfers are right about Sleeping Beauty, and that thirders cannot avoid easy confirmation for the truth of EQM. Wilson agrees with my analysis of observation selection effects in EQM, but goes on to, first, defend Elga’s thirder argument on Sleeping Beauty and, second, argue (...)
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  25. Weisberg on Design: What Fine-Tuning's Got to Do with It.Darren Bradley - 2012 - Erkenntnis 77 (3):435-438.
    Jonathan Weisberg (2010 ) argues that, given that life exists, the fact that the universe is fine-tuned for life does not confirm the design hypothesis. And if the fact that life exists confirms the design hypothesis, fine-tuning is irrelevant. So either way, fine-tuning has nothing to do with it. I will defend a design argument that survives Weisberg’s critique — the fact that life exists supports the design hypothesis, but it only does so given fine-tuning.
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  26. Philosophers Should Prefer Simpler Theories.Darren Bradley - 2018 - Philosophical Studies 175 (12):3049-3067.
    Should philosophers prefer simpler theories? Huemer (Philos Q 59:216–236, 2009) argues that the reasons to prefer simpler theories in science do not apply in philosophy. I will argue that Huemer is mistaken—the arguments he marshals for preferring simpler theories in science can also be applied in philosophy. Like Huemer, I will focus on the philosophy of mind and the nominalism/Platonism debate. But I want to engage with the broader issue of whether simplicity is relevant to philosophy.
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  27. Sleeping Beauty: A Note on Dorr's Argument for 1/3.Darren Bradley - 2003 - Analysis 63 (3):266–268.
    Cian Dorr (2002) gives an argument for the 1/3 position in Sleeping Beauty. I argue this is based on a mistake about Sleeping Beauty's epistemic position.
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  28. Porous Memory and the Cognitive Life of Things.John Sutton - 2002 - In D. Tofts, A. Jonson & A. Cavallaro (eds.), Prefiguring Cyberculture: An Intellectual History. Cambridge: MIT Press. pp. 130--141.
    Published in Darren Tofts, Annemarie Jonson, and Alessio Cavallaro (eds), _Prefiguring Cyberculture: an intellectual history_ (MIT Press and Power Publications, December 2002). Please do send comments: email me. Back to my main publications page . Back to my home page.
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  29. Carnap’s Epistemological Critique of Metaphysics.Darren Bradley - 2018 - Synthese 195 (5):2247-2265.
    Many who take a dismissive attitude towards metaphysics trace their view back to Carnap’s ‘Empiricism, Semantics and Ontology’. But the reason Carnap takes a dismissive attitude to metaphysics is a matter of controversy. I will argue that no reason is given in ‘Empiricism, Semantics and Ontology’, and this is because his reason for rejecting metaphysical debates was given in ‘Pseudo-Problems in Philosophy’. The argument there assumes verificationism, but I will argue that his argument survives the rejection of verificationism. The root (...)
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  30. Justified Concepts and the Limits of the Conceptual Approach to the A Priori.Darren Bradley - 2011 - Croatian Journal of Philosophy 11 (3):267-274.
    Carrie Jenkins (2005, 2008) has developed a theory of the a priori that she claims solves the problem of how justification regarding our concepts can give us justification regarding the world. She claims that concepts themselves can be justified, and that beliefs formed by examining such concepts can be justified a priori. I object that we can have a priori justified beliefs with unjustified concepts if those beliefs have no existential import. I then argue that only beliefs without existential import (...)
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  31. Philosophy of Mind Is (in Part) Philosophy of Computer Science.Darren Abramson - 2011 - Minds and Machines 21 (2):203-219.
    In this paper I argue that whether or not a computer can be built that passes the Turing test is a central question in the philosophy of mind. Then I show that the possibility of building such a computer depends on open questions in the philosophy of computer science: the physical Church-Turing thesis and the extended Church-Turing thesis. I use the link between the issues identified in philosophy of mind and philosophy of computer science to respond to a prominent argument (...)
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  32. Conditionalization and Belief De Se.Darren Bradley - 2010 - Dialectica 64 (2):247-250.
    Colin Howson (1995 ) offers a counter-example to the rule of conditionalization. I will argue that the counter-example doesn't hit its target. The problem is that Howson mis-describes the total evidence the agent has. In particular, Howson overlooks how the restriction that the agent learn 'E and nothing else' interacts with the de se evidence 'I have learnt E'.
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  33.  51
    Review of 'Theoretical Virtues in Science' by Samuel Schindler. [REVIEW]Darren Bradley - manuscript
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  34. Decision Theory, Philosophical Perspectives.Darren Bradley - 2013 - In Hal Pashler (ed.), Encyclopedia of the Mind. Sage Publications.
    Decision theory is concerned with how agents should act when the consequences of their actions are uncertain. The central principle of contemporary decision theory is that the rational choice is the choice that maximizes subjective expected utility. This entry explains what this means, and discusses the philosophical motivations and consequences of the theory. The entry will consider some of the main problems and paradoxes that decision theory faces, and some of responses that can be given. Finally the entry will briefly (...)
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  35. Descartes' Influence on Turing.Darren Abramson - 2011 - Studies in History and Philosophy of Science Part A 42 (4):544-551.
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  36. A Relevant Alternatives Solution to the Bootstrapping and Self-Knowledge Problems.Darren Bradley - 2014 - Journal of Philosophy 111 (7):379-393.
    The main argument given for relevant alternatives theories of knowledge has been that they answer scepticism about the external world. I will argue that relevant alternatives also solve two other problems that have been much discussed in recent years, a) the bootstrapping problem and b) the apparent conflict between semantic externalism and armchair self-knowledge. Furthermore, I will argue that scepticism and Mooreanism can be embedded within the relevant alternatives framework.
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  37. A Priori Causal Laws.Darren Bradley - 2017 - Inquiry: An Interdisciplinary Journal of Philosophy 60 (4):358-370.
    Sober and Elgin defend the claim that there are a priori causal laws in biology. Lange and Rosenberg take issue with this on Humean grounds, among others. I will argue that Sober and Elgin don’t go far enough – there are a priori causal laws in many sciences. Furthermore, I will argue that this thesis is compatible with a Humean metaphysics and an empiricist epistemology.
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  38. Dynamic Beliefs and the Passage of Time.Darren Bradley - 2013 - In A. Capone & N. Feit (eds.), Attitudes De Se. University of Chicago.
    How should our beliefs change over time? Much has been written about how our beliefs should change in the light of new evidence. But that is not the question I’m asking. Sometimes our beliefs change without new evidence. I previously believed it was Sunday. I now believe it’s Monday. In this paper I discuss the implications of such beliefs for philosophy of language. I will argue that we need to allow for ‘dynamic’ beliefs, that we need new norms of belief (...)
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  39.  80
    Review of 'Ontology After Carnap' Edited by Stephan Blatti and Sandra Lapointe. [REVIEW]Darren Bradley - 2017 - Analysis 77 (4):858-861.
    © The Author 2017. Published by Oxford University Press on behalf of The Analysis Trust. All rights reserved. For Permissions, please email: journals.permissions@oup.com‘Carnap is not completely unknown to us’ comments Richard Creath in his contribution to this book. ‘We often know just enough to be baffled’. It will be no surprise to anyone when I say that this book will not unbaffle us. But it does give us a collection of rewarding papers that each wrestle with the legacy Carnap has (...)
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  40. Bayesianism And Self-Locating Beliefs.Darren Bradley - 2007 - Dissertation, Stanford University
    How should we update our beliefs when we learn new evidence? Bayesian confirmation theory provides a widely accepted and well understood answer – we should conditionalize. But this theory has a problem with self-locating beliefs, beliefs that tell you where you are in the world, as opposed to what the world is like. To see the problem, consider your current belief that it is January. You might be absolutely, 100%, sure that it is January. But you will soon believe it (...)
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  41.  17
    Paolo Barbò da Soncino: Questioni di Metafisica Introduzione alla vita ed al pensiero di un tomista rinascimentale con l’edizione critica del IV libro delle sue Acutissimae Quaestiones Metaphysicales.Efrem Jindracek - 2017 - Řím, Itálie: Angelicum University Press.
    Paolo Barbò da Soncino conosciuto anche come il „Soncinas" (Soncinate) fu un domenicano italiano, filosofo e teologo tomista. Visse durante il periodo del rinascimento italiano nel XV secolo tra Bologna e Milano, morto a Cremona nel 1495. La suo apiù importante opera è proprio il commento alla Metafisica di Aristotele (Acutissimae quaestiones metaphysicales, 1 ed. Venezia 1498) che rappresenta una particolare sintesi del commentatore arabo Averrè, Tommaso d'Aquino, Erveo Natale († 1323) e Giovanni Capreolo († 1444). L'opera filosofica del (...)
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