An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Extending a geo-catalogue with matching capabilities

To achieve semantic interoperability, geo-spatial applications need to be equipped with tools able to understand user terminology that is typically different from the one enforced by standards. In this paper we summarize our experience in providing a semantic extension to the geo-catalogue of the Autonomous Province of Trento (PAT) in Italy. The semantic extension is based on the adoption of the S-Match semantic matching tool and on the use of a specifically designed faceted ontology codifying domain specific knowledge. We also briefly report our experience in the integration of the ontology with the geo-spatial ontology GeoWordNet

bdbms -- A Database Management System for Biological Data

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

A framework for improving the performance of verification algorithms with a low false positive rate requirement and limited training data

In this paper we address the problem of matching patterns in the so-called verification setting in which a novel, query pattern is verified against a single training pattern: the decision sought is whether the two match (i.e. belong to the same class) or not. Unlike previous work which has universally focused on the development of more discriminative distance functions between patterns, here we consider the equally important and pervasive task of selecting a distance threshold which fits a particular operational requirement - specifically, the target false positive rate (FPR). First, we argue on theoretical grounds that a data-driven approach is inherently ill-conditioned when the desired FPR is low, because by the very nature of the challenge only a small portion of training data affects or is affected by the desired threshold. This leads us to propose a general, statistical model-based method instead. Our approach is based on the interpretation of an inter-pattern distance as implicitly defining a pattern embedding which approximately distributes patterns according to an isotropic multi-variate normal distribution in some space. This interpretation is then used to show that the distribution of training inter-pattern distances is the non-central chi2 distribution, differently parameterized for each class. Thus, to make the class-specific threshold choice we propose a novel analysis-by-synthesis iterative algorithm which estimates the three free parameters of the model (for each class) using task-specific constraints. The validity of the premises of our work and the effectiveness of the proposed method are demonstrated by applying the method to the task of set-based face verification on a large database of pseudo-random head motion videos.Comment: IEEE/IAPR International Joint Conference on Biometrics, 201

Forecasting the cost of processing multi-join queries via hashing for main-memory databases (Extended version)

Database management systems (DBMSs) carefully optimize complex multi-join queries to avoid expensive disk I/O. As servers today feature tens or hundreds of gigabytes of RAM, a significant fraction of many analytic databases becomes memory-resident. Even after careful tuning for an in-memory environment, a linear disk I/O model such as the one implemented in PostgreSQL may make query response time predictions that are up to 2X slower than the optimal multi-join query plan over memory-resident data. This paper introduces a memory I/O cost model to identify good evaluation strategies for complex query plans with multiple hash-based equi-joins over memory-resident data. The proposed cost model is carefully validated for accuracy using three different systems, including an Amazon EC2 instance, to control for hardware-specific differences. Prior work in parallel query evaluation has advocated right-deep and bushy trees for multi-join queries due to their greater parallelization and pipelining potential. A surprising finding is that the conventional wisdom from shared-nothing disk-based systems does not directly apply to the modern shared-everything memory hierarchy. As corroborated by our model, the performance gap between the optimal left-deep and right-deep query plan can grow to about 10X as the number of joins in the query increases.Comment: 15 pages, 8 figures, extended version of the paper to appear in SoCC'1

FishMark: A Linked Data Application Benchmark

Abstract. FishBase is an important species data collection produced by the FishBase Information and Research Group Inc (FIN), a not-forprofit NGO with the aim of collecting comprehensive information (from the taxonomic to the ecological) about all the world’s finned fish species. FishBase is exposed as a MySQL backed website (supporting a range of canned, although complex queries) and serves over 33 million hits per month. FishDelish is a transformation of FishBase into LinkedData weighing in at 1.38 billion triples. We have ported a substantial number of FishBase SQL queries to FishDelish SPARQL query which form the basis of a new linked data application benchmark (using our derivative of the Berlin SPARQL Benchmark harness). We use this benchmarking framework to compare the performance of the native MySQL application, the Virtuoso RDF triple store, and the Quest OBDA system on a fishbase.org like application.