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Abstract:The Semantic Web's promise to achieve web-wide data integration requires the inclusion of legacy relational data as RDF, which, in turn, requires the execution of SPARQL queries on the legacy relational database. In this paper we explore a hypothesis: existing commercial relational databases already subsume the algorithms and optimizations needed to support effective SPARQL execution on existing relationally stored data. The experiment, embodied in a system called Ultrawrap, comprises encoding a logical representation of the database as a graph using SQL views and a simple syntactic translation of SPARQL queries to SQL queries on those views. Thus, in the course executing a SPARQL query, the SQL optimizer both instantiates a mapping of relational data to RDF and optimizes its execution. Other approaches typically implement aspects of query optimization and execution outside the SQL environment.Ultrawrap is evaluated using two benchmarks across the three major relational database management systems. We identify two important optimizations: detection of unsatisfiable conditions and self-join elimination, such that, when applied, SPARQL queries execute at nearly the same speed as semantically equivalent native SQL queries, providing strong evidence of the validity of the hypothesis.

Motivation: Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration.Results: We develop a Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar experimental conditions. Our method, MSpresso, substantially increases the number of proteins identified in an MS/MS experiment at the same error rate, e.g. in yeast, MSpresso increases the number of proteins identified by ∼40%. We apply MSpresso to data from different MS/MS instruments, experimental conditions and organisms (Escherichia coli, human), and predict 19–63% more proteins across the different datasets. MSpresso demonstrates that incorporating prior knowledge of protein presence into shotgun proteomics experiments can substantially improve protein identification scores.Availability and Implementation: Software is available upon request from the authors. Mass spectrometry datasets and supplementary information are available from http://www.marcottelab.org/MSpresso/.Contact: marcotte@icmb.utexas.edu; miranker@cs.utexas.eduSupplementary Information: Supplementary data website: http://www.marcottelab.org/MSpresso/.

Mapping relational databases to RDF is a fundamental problem for the development of the Semantic Web. We present a solution, inspired by draft methods defined by the W3C where relational databases are directly mapped to RDF and OWL. Given a relational database schema and its integrity constraints, this direct mapping produces an OWL ontology, which, provides the basis for generating RDF instances. The semantics of this mapping is defined using Datalog. Two fundamental properties are information preservation and query preservation. We prove that our mapping satisfies both conditions, even for relational databases that contain null values. We also consider two desirable properties: monotonicity and semantics preservation. We prove that our mapping is monotone and also prove that no monotone mapping, including ours, is semantic preserving. We realize that monotonicity is an obstacle for semantic preservation and thus present a non-monotone direct mapping that is semantics preserving.In this section, we define the basic terminology used in the paper. Relational databasesAssume, a countably infinite domain D and a reserved symbol NULL that is not in D. A schema R is a finite set of relation names, where for each R ∈ R, att (R) denotes the nonempty finite set of attributes names associated to R. An instance I of R assigns to each relation symbol R ∈ R a finite set R I = {t1, . . . , t ℓ } of tuples, where each tuple tj (1 ≤ j ≤ ℓ) is a function that assigns to each attribute in att (R) a value from (D ∪ {NULL}). We use notation t.A to refer to the value of a tuple t in an attribute A. Relational algebra:To define some of the concept studied in this paper, we use relational algebra as a query language for relational

Abstract. We develop a theoretical framework to characterize the hardness of indexing data sets on block-access memory devices like hard disks. We define an indexing workload by a data set and a set of potential queries. For a workload, we can construct an indexing scheme, which is a collection of fixed-sized subsets of the data. We identify two measures of efficiency for an indexing scheme on a workload: storage redundancy, r (how many times each item in the data set is stored), and access overhead, A (how many times more blocks than necessary does a query retrieve). Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or direct commercial advantage and that copies show this notice on the first page or initial screen of a display along with the full citation. Copyrights for components of this worked owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, to republish, to post on servers, to redistribute to lists, or to use any component of this work in other works requires prior specific permission and/or a fee. Permissions may be requested from Publications Dept., ACM, Inc., 1515 Broadway, New York, NY 10036 USA, fax +1 ( For many interesting families of workloads, there exists a trade-off between storage redundancy and access overhead. Given a desired access overhead A, there is a minimum redundancy that any indexing scheme must exhibit. We prove a lower-bound theorem for deriving the minimum redundancy. By applying this theorem, we show interesting upper and lower bounds and trade-offs between A and r in the case of multidimensional range queries and set queries.