Updating DL-Lite ontologies through first-order queries

In this paper we study instance-level update in DL-LiteA, the description logic underlying the OWL 2 QL standard. In particular we focus on formula-based approaches to ABox insertion and deletion. We show that DL-LiteA, which is well-known for enjoying first-order rewritability of query answering, enjoys a first-order rewritability property also for updates. That is, every update can be reformulated into a set of insertion and deletion instructions computable through a nonrecursive datalog program. Such a program is readily translatable into a first-order query over the ABox considered as a database, and hence into SQL. By exploiting this result, we implement an update component for DLLiteA-based systems and perform some experiments showing that the approach works in practice.Peer ReviewedPostprint (author's final draft

Discovering Cooperative Relationships of Chromatin Modifications in Human T Cells Based on a Proposed Closeness Measure

BACKGROUND: Eukaryotic transcription is accompanied by combinatorial chromatin modifications that serve as functional epigenetic markers. Composition of chromatin modifications specifies histone codes that regulate the associated gene. Discovering novel chromatin regulatory relationships are of general interest. METHODOLOGY/PRINCIPAL FINDINGS: Based on the premise that the interaction of chromatin modifications is hypothesized to influence CpG methylation, we present a closeness measure to characterize the regulatory interactions of epigenomic features. The closeness measure is applied to genome-wide CpG methylation and histone modification datasets in human CD4+T cells to select a subset of potential features. To uncover epigenomic and genomic patterns, CpG loci are clustered into nine modules associated with distinct chromatin and genomic signatures based on terms of biological function. We then performed Bayesian network inference to uncover inherent regulatory relationships from the feature selected closeness measure profile and all nine module-specific profiles respectively. The global and module-specific network exhibits topological proximity and modularity. We found that the regulatory patterns of chromatin modifications differ significantly across modules and that distinct patterns are related to specific transcriptional levels and biological function. DNA methylation and genomic features are found to have little regulatory function. The regulatory relationships were partly validated by literature reviews. We also used partial correlation analysis in other cells to verify novel regulatory relationships. CONCLUSIONS/SIGNIFICANCE: The interactions among chromatin modifications and genomic elements characterized by a closeness measure help elucidate cooperative patterns of chromatin modification in transcriptional regulation and help decipher complex histone codes

Energy efficiency of machining operations: A review

Manufacturing processes are among the most energy intensive on earth. As negative ecological and economic impacts increase, reducing energy consumption is becoming critically important. In this article, a comprehensive overview of energy-saving strategies and opportunities for increasing energy efficiency in manufacturing operations is presented, with a focus on metal cutting processes. The issues and approaches involved in energy efficiency of machine tools and machining operations are reported in the literature and a structured research methodology is proposed for this purpose including prediction and modelling of machine energy consumption, determining the relationship between process energy consumption and process variables for material removal processes and optimization of cutting parameters in order to reduce energy consumption. Numerous techniques for increasing energy efficiency in manufacturing processes are identified and summarized, strengths and weaknesses of previous studies are discussed and potential avenues for future research are suggested.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This study was funded by SAN-TEZ Project No. 00979.stz.2011-12 of the Turkish Ministry of Science, Technology and Industry

Temporal ontology-mediated queries and first-order rewritability: A short course

We discuss recent attempts to extend the ontology-based data access (aka virtual knowledge graph) paradigm to the temporal setting. Our main aim is to understand when answering temporal ontology mediated queries can be reduced to evaluating standard first-order queries over timestamped data and what numeric predicates and operators are required in such reductions. We consider two ways of introducing a temporal dimension in ontologies and queries: using linear temporal logic LTL over discrete time and using metric temporal logic MTL over dense time