Challenging Ubiquitous Inverted Files

Stand-alone ranking systems based on highly optimized inverted file structures are generally considered ‘the’ solution for building search engines. Observing various developments in software and hardware, we argue however that IR research faces a complex engineering problem in the quest for more flexible yet efficient retrieval systems. We propose to base the development of retrieval systems on ‘the database approach’: mapping high-level declarative specifications of the retrieval process into efficient query plans. We present the Mirror DBMS as a prototype implementation of a retrieval system based on this approach

SoK: Cryptographically Protected Database Search

Protected database search systems cryptographically isolate the roles of reading from, writing to, and administering the database. This separation limits unnecessary administrator access and protects data in the case of system breaches. Since protected search was introduced in 2000, the area has grown rapidly; systems are offered by academia, start-ups, and established companies. However, there is no best protected search system or set of techniques. Design of such systems is a balancing act between security, functionality, performance, and usability. This challenge is made more difficult by ongoing database specialization, as some users will want the functionality of SQL, NoSQL, or NewSQL databases. This database evolution will continue, and the protected search community should be able to quickly provide functionality consistent with newly invented databases. At the same time, the community must accurately and clearly characterize the tradeoffs between different approaches. To address these challenges, we provide the following contributions: 1) An identification of the important primitive operations across database paradigms. We find there are a small number of base operations that can be used and combined to support a large number of database paradigms. 2) An evaluation of the current state of protected search systems in implementing these base operations. This evaluation describes the main approaches and tradeoffs for each base operation. Furthermore, it puts protected search in the context of unprotected search, identifying key gaps in functionality. 3) An analysis of attacks against protected search for different base queries. 4) A roadmap and tools for transforming a protected search system into a protected database, including an open-source performance evaluation platform and initial user opinions of protected search.Comment: 20 pages, to appear to IEEE Security and Privac

BioWarehouse: a bioinformatics database warehouse toolkit

BACKGROUND: This article addresses the problem of interoperation of heterogeneous bioinformatics databases. RESULTS: We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. CONCLUSION: BioWarehouse embodies significant progress on the database integration problem for bioinformatics

The exploration of a category theory-based virtual Geometrical product specification system for design and manufacturing

In order to ensure quality of products and to facilitate global outsourcing, almost all the so-called “world-class” manufacturing companies nowadays are applying various tools and methods to maintain the consistency of a product’s characteristics throughout its manufacturing life cycle. Among these, for ensuring the consistency of the geometric characteristics, a tolerancing language − the Geometrical Product Specification (GPS) has been widely adopted to precisely transform the functional requirements from customers into manufactured workpieces expressed as tolerance notes in technical drawings. Although commonly acknowledged by industrial users as one of the most successful efforts in integrating existing manufacturing life-cycle standards, current GPS implementations and software packages suffer from several drawbacks in their practical use, possibly the most significant, the difficulties in inferring the data for the “best” solutions. The problem stemmed from the foundation of data structures and knowledge-based system design. This indicates that there need to be a “new” software system to facilitate GPS applications. The presented thesis introduced an innovative knowledge-based system − the VirtualGPS − that provides an integrated GPS knowledge platform based on a stable and efficient database structure with knowledge generation and accessing facilities. The system focuses on solving the intrinsic product design and production problems by acting as a virtual domain expert through translating GPS standards and rules into the forms of computerized expert advices and warnings. Furthermore, this system can be used as a training tool for young and new engineers to understand the huge amount of GPS standards in a relative “quicker” manner. The thesis started with a detailed discussion of the proposed categorical modelling mechanism, which has been devised based on the Category Theory. It provided a unified mechanism for knowledge acquisition and representation, knowledge-based system design, and database schema modelling. As a core part for assessing this knowledge-based system, the implementation of the categorical Database Management System (DBMS) is also presented in this thesis. The focus then moved on to demonstrate the design and implementation of the proposed VirtualGPS system. The tests and evaluations of this system were illustrated in Chapter 6. Finally, the thesis summarized the contributions to knowledge in Chapter 7. After thoroughly reviewing the project, the conclusions reached construe that the III entire VirtualGPS system was designed and implemented to conform to Category Theory and object-oriented programming rules. The initial tests and performance analyses show that the system facilitates the geometric product manufacturing operations and benefits the manufacturers and engineers alike from function designs, to a manufacturing and verification