BibSonomy publications for /tag/dlSat May 14 12:24:09 CEST 2011Software Engineering, 2009. WCSE '09. WRI World Congress onmay113 -116Reasoning with Inconsistent OWL Ontologies for Software Reuse22009DL OWL Java A framework for reasoning with inconsistent OWL ontologies is presented with the aim to support the design of Software design patterns. The priority information between axioms are given explicitly, allowing for the use of pieces of information having various levels of confidence, a preferential semantics is then defined for reasoning with prioritized ontology, the property of the method is studied, and the reasoning algorithms is given.Fri Feb 11 11:26:32 CET 2011Journal of Web Semantics1{From SHIQ and RDF to OWL: The Making of a Web Ontology Language }12003DL ontology owl Wed Sep 08 10:39:14 CEST 2010Artificial Intelligence141275 - 1309Representing ontologies using description logics, description graphs, and rules1732009DL OWL descriptionlogics Description logics (DLs) are a family of state-of-the-art knowledge representation languages, and their expressive power has been carefully crafted to provide useful knowledge modeling primitives while allowing for practically effective decision procedures for the basic reasoning problems. Recent experience with DLs, however, has shown that their expressivity is often insufficient to accurately describe structured objects--objects whose parts are interconnected in arbitrary, rather than tree-like ways. DL knowledge bases describing structured objects are therefore usually underconstrained, which precludes the entailment of certain consequences and causes performance problems during reasoning. To address this problem, we propose an extension of DL languages with description graphs--a knowledge modeling construct that can accurately describe objects with parts connected in arbitrary ways. Furthermore, to enable modeling the conditional aspects of structured objects, we also extend DLs with rules. We present an in-depth study of the computational properties of such a formalism. In particular, we first identify the sources of undecidability of the general, unrestricted formalism. Based on that analysis, we then investigate several restrictions of the general formalism that make reasoning decidable. We present practical evidence that such a logic can be used to model nontrivial structured objects. Finally, we present a practical decision procedure for our formalism, as well as tight complexity bounds.Wed Jun 30 10:40:21 CEST 2010Berlin/HeidelbergConcept Lattices261--286Lecture Notes in Computer ScienceApplying Formal Concept Analysis to Description Logics.29612004analysis concept description dl fca formal logic logics Given a finite set $\mathcal{C} := \{ C_1, \ldots, C_n\}$ of description logic concepts, we are interested in computing the subsumption hierarchy of all least common subsumers of subsets of $\mathcal{C}$ as well as the hierarchy of all conjunctions of subsets of $\mathcal{C}$. These hierarchies can be used to support the bottom-up construction of description logic knowledge bases. The point is to compute the first hierarchy without having to compute the least common subsumer for all subsets of $\mathcal{C}$, and the second hierarchy without having to check all possible pairs of such conjunctions explicitly for subsumption. We will show that methods from formal concept analysis developed for computing concept lattices can be employed for this purpose.Sat May 15 23:53:06 CEST 2010The Description Logic Handbook: Theoryand Implementationand and Applications359-381{Conceptual Modeling with Description Logics}2003conceptual dl modeling ontology proj:o4p Sun Apr 25 09:31:29 CEST 2010ICFCAconf/icfca/200751-65Lecture Notes in Computer ScienceA Proposal for Combining Formal Concept Analysis and Description Logics for Mining Relational Data.43902007dl fca mining relation Sat Apr 17 22:32:00 CEST 2010Named Graphs as a Mechanism for Reasoning about Provenance2006dl namedgraph owl proj:o4p reasoning toread Named Graphs is a simple, compatible extension to the RDF abstract syntax that enables statements to be made about RDF graphs. This approach is in contrast to earlier attempts such as RDF reification, or knowledge-base specific extensions including quads and contexts. In this paper we demonstrate the use of Named Graphs and our experiences developing new kinds of semantic web application that build on Named Graphs for digital signatures, provenance, and semantic reasoning. We present a working example based on the Named Graphs for Jena (NG4J) API, from which we developed a semantic version control system for Software Engineering capable of reasoning about Named Graph-based provenance. We go on to discuss the implications of Named Graphs for Description Logics and semantic inference strategies.Fri Mar 05 16:10:41 CET 2010ECAIconf/ecai/1996323-327CARIN: A Representation Language Combining Horn Rules and Description Logics.1996DL InfromationIntegration Wed Feb 24 22:55:14 CET 2010Proceedings of the Twentieth International Joint Conference on Artificial Intelligence (IJCAI'07)230--235Description Logic Knowledge Bases using Formal Concept Analysis2007dl fca knowledge Wed Jan 27 07:00:16 CET 2010OTM Workshopsconf/otm/2009-w49-58Lecture Notes in Computer ScienceMerging Expressive Ontologies Using Formal Concept Analysis.58722009dl fca merging ontologies Tue Jan 26 15:49:55 CET 2010to appear in SMT WorkshopExpressive Description Logics via SAT: The Story so Far2009DL SAT, SMT, Thu Jan 14 23:06:39 CET 2010OWLEDconf/owled/2007CEUR Workshop ProceedingsCompleting Description Logic Knowledge Bases using Formal Concept Analysis.2582007dl fca Fri Jan 08 09:25:07 CET 2010ICFCA46-61Lecture Notes in Computer ScienceA Finite Basis for the Set of EL-Implications Holding in a Finite Model.49332008dl exploration fca Mon Dec 14 11:54:57 CET 2009ICFCAconf/icfca/2009146-161Lecture Notes in Computer ScienceExploring Finite Models in the Description Logic .55482009AttributeExploration dl ontology Wed Nov 25 16:02:33 CET 2009Computational Logic: Logic Programming and Beyond41--60Lecture Notes in Computer ScienceDescription Logics for Information Integration24082002DL InformationIntegration integration Information integration is the problem of combining the data residing at different, heterogeneous sources, and providing the user with a unified view of these data, called mediated schema. The mediated schema is therefore a reconciled view of the information, which can be queried by the user. It is the task of the system to free the user from the knowledge on where data are, and how data are structured at the sources.Wed Nov 11 00:12:51 CET 2009The Description Logic Handbook: Theory, Implementation and Applications2003book dl Wed Nov 11 00:12:51 CET 2009Journal of Web Semantics251--53Pellet: A practical {OWL-DL} reasoner52007dl reasoner {SemanticWeb} Sun Sep 20 21:04:15 CEST 2009Nature Reviews GeneticsOct10715-724The evolutionary consequences of erroneous protein synthesis102009dl evolution imported molecular review Error s in protein synthesis disrupt cellular fitness, cause disease phenotypes and shape gene and genome evolution. Experimental and theoretical results on this topic have accumulated rapidly in disparate fields, such as neurobiology, protein biosynthesis and degradation and molecular evolution, but with limited communication among disciplines. Here, we review studies of error frequencies, the cellular and organismal consequences of errors and the attendant long-range evolutionary responses to errors. We emphasize major areas in which little is known, such as the failure rates of protein folding, in addition to areas in which technological innovations may enable imminent gains, such as the elucidation of translational missense error frequencies. Evolutionary responses to errors fall into two broad categories: adaptations that minimize errors and their attendant costs and adaptations that exploit errors for the organism's benefit.Wed Sep 16 21:44:06 CEST 2009Molecular Biology and EvolutionJan1143-153Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence262009BEAST Bayesian coalescent coevolution dl hc imported lab_meeting phylogenetics zoonotic Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores they infect since these mammals last shared a common ancestor, approximately 100 million years ago. We tested this hypothesis of host-virus codivergence in two ways: 1) we used cophylogenetic reconciliation analysis to assess the fit of the virus tree onto that of the host and 2) we estimated the evolutionary rates and divergence times for the Hantavirus genus using a Bayesian Markov Chain Monte Carlo method and similarly compared these with those of their hosts. Our reconciliation analysis provided no evidence for a history of codivergence between hantaviruses and their hosts. Further, the divergence times for the Hantavirus genus were many orders of magnitude too recent to correspond with the timescale of their hosts' speciation. We therefore propose that apparent similarities between the phylogenies of hantaviruses and their mammalian hosts are the result of a more recent history of preferential host switching and local adaptation. Based on the presence of clade-defining amino acids in all genomic segments, we propose that the patterns of amino acid replacement in these viruses are also compatible with a history of host-specific adaptation.Wed Sep 16 04:21:11 CEST 2009EvolutionSep91959-1972Perspective: Evolution and detection of genetic robustness572003dl evolution imported robustness Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness--genetic robustness--and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness: and (3) exploring the implications of genetic robustness for future evolution.dlCommunity for tag(s) dl