Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the Saccharomyces Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford.edu/Saccharomyces/.

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins

The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam and ProDom. Links to the InterPro graphical interface allow users to see at a glance whether proteins from the cluster share particular functional sites. CluSTr also provides cross-references to HSSP and PDB. The database is available for querying and browsing at http://www.ebi.ac.uk/clustr.

The Stanford Microarray Database

The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77–80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73–76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10–14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332–333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45–48] and can be accessed at http://genome-www.stanford.edu/microarray.

HC Forum®: a web site based on an international human cytogenetic database

Familial structural rearrangements of chromosomes represent a factor of malformation risk that could vary over a large range, making genetic counseling difficult. However, they also represent a powerful tool for increasing knowledge of the genome, particularly by studying breakpoints and viable imbalances of the genome. We have developed a collaborative database that now includes data on more than 4100 families, from which we have developed a web site called HC Forum® (http://HCForum.imag.fr). It offers geneticists assistance in diagnosis and in genetic counseling by assessing the malformation risk with statistical models. For researchers, interactive interfaces exhibit the distribution of chromosomal breakpoints and of the genome regions observed at birth in trisomy or in monosomy. Dedicated tools including an interactive pedigree allow electronic submission of data, which will be anonymously shown in a forum for discussions. After validation, data are definitively registered in the database with the email of the sender, allowing direct location of biological material. Thus HC Forum® constitutes a link between diagnosis laboratories and genome research centers, and after 1 year, more than 700 users from about 40 different countries already exist.

A unification-based natural language interface to a database.

An implementation of a Lexical Functional Grammar (LFG) natural language front-end to a database is presented, and its capabilities demonstrated by reference to a set of queries used in the Chat-80 system. The potential of LFG for such applications is explored. Other grammars previously used for this purpose are briefly reviewed and contrasted with LFG. The basic LFG formalism is fully described, both as to its syntax and semantics, and the deficiencies of the latter for database access application shown. Other current LFG implementations are reviewed and contrasted with the LFG implementation developed here specifically for database access. The implementation described here allows a natural language interface to a specific Prolog database to be produced from a set of grammar rule and lexical specifications in an LFG-like notation. In addition to this the interface system uses a simple database description to compile metadata about the database for later use in planning the execution of queries. Extensions to LFG's semantic component are shown to be necessary to produce a satisfactory functional analysis and semantic output for querying a database. A diverse set of natural language constructs are analysed using LFG and the derivation of Prolog queries from the F-structure output of LFG is illustrated. The functional description produced from LFG is proposed as sufficient for resolving many problems of quantification and attachment.

Is question answering fit for the semantic web? A survey

With the recent rapid growth of the Semantic Web (SW), the processes of searching and querying content that is both massive in scale and heterogeneous have become increasingly challenging. User-friendly interfaces, which can support end users in querying and exploring this novel and diverse, structured information space, are needed to make the vision of the SW a reality. We present a survey on ontology-based Question Answering (QA), which has emerged in recent years to exploit the opportunities offered by structured semantic information on the Web. First, we provide a comprehensive perspective by analyzing the general background and history of the QA research field, from influential works from the artificial intelligence and database communities developed in the 70s and later decades, through open domain QA stimulated by the QA track in TREC since 1999, to the latest commercial semantic QA solutions, before tacking the current state of the art in open user-friendly interfaces for the SW. Second, we examine the potential of this technology to go beyond the current state of the art to support end-users in reusing and querying the SW content. We conclude our review with an outlook for this novel research area, focusing in particular on the R&D directions that need to be pursued to realize the goal of efficient and competent retrieval and integration of answers from large scale, heterogeneous, and continuously evolving semantic sources.

Communicating Cuneiform:The Evolution of a Multimedia Cuneiform Database

Our paper presents the work of the Cuneiform Digital Forensic Project (CDFP), an interdisciplinary project at The University of Birmingham, concerned with the development of a multimedia database to support scholarly research into cuneiform, wedge-shaped writing imprinted onto clay tablets and indeed the earliest real form of writing. We describe the evolutionary design process and dynamic research and developmental cycles associated with the database. Unlike traditional publications, the electronic publication of resources offers the possibility of almost continuous revisions with the integration and support of new media and interfaces. However, if on-line resources are to win the favor and confidence of their respective communities there must be a clear distinction between published and maintainable resources, and, developmental content. Published material should, ideally, be supported via standard web-browser interfaces with fully integrated tools so that users receive a reliable, homogenous and intuitive flow of information and media relevant to their needs. We discuss the inherent dynamics of the design and publication of our on-line resource, starting with the basic design and maintenance aspects of the electronic database, which includes photographic instances of cuneiform signs, and shows how the continuous review process identifies areas for further research and development, for example, the “sign processor” graphical search tool and three-dimensional content, the results of which then feedback into the maintained resource.

Teallach - a flexible user - interface development environment for object database applications

The Teallach project has adapted model-based user-interface development techniques to the systematic creation of user-interfaces for object-oriented database applications. Model-based approaches aim to provide designers with a more principled approach to user-interface development using a variety of underlying models, and tools which manipulate these models. Here we present the results of the Teallach project, describing the tools developed and the flexible design method supported. Distinctive features of the Teallach system include provision of database-specific constructs, comprehensive facilities for relating the different models, and support for a flexible design method in which models can be constructed and related by designers in different orders and in different ways, to suit their particular design rationales. The system then creates the desired user-interface as an independent, fully functional Java application, with automatically generated help facilities.

A semantic paradigm for intelligent data access

An implementation of Sem-ODB—a database management system based on the Semantic Binary Model is presented. A metaschema of Sem-ODB database as well as the top-level architecture of the database engine is defined. A new benchmarking technique is proposed which allows databases built on different database models to compete fairly. This technique is applied to show that Sem-ODB has excellent efficiency comparing to a relational database on a certain class of database applications. A new semantic benchmark is designed which allows evaluation of the performance of the features characteristic of semantic database applications. An application used in the benchmark represents a class of problems requiring databases with sparse data, complex inheritances and many-to-many relations. Such databases can be naturally accommodated by semantic model. A fixed predefined implementation is not enforced allowing the database designer to choose the most efficient structures available in the DBMS tested. The results of the benchmark are analyzed. ^ A new high-level querying model for semantic databases is defined. It is proven adequate to serve as an efficient native semantic database interface, and has several advantages over the existing interfaces. It is optimizable and parallelizable, supports the definition of semantic userviews and the interoperability of semantic databases with other data sources such as World Wide Web, relational, and object-oriented databases. The query is structured as a semantic database schema graph with interlinking conditionals. The query result is a mini-database, accessible in the same way as the original database. The paradigm supports and utilizes the rich semantics and inherent ergonomics of semantic databases. ^ The analysis and high-level design of a system that exploits the superiority of the Semantic Database Model to other data models in expressive power and ease of use to allow uniform access to heterogeneous data sources such as semantic databases, relational databases, web sites, ASCII files, and others via a common query interface is presented. The Sem-ODB engine is used to control all the data sources combined under a unified semantic schema. A particular application of the system to provide an ODBC interface to the WWW as a data source is discussed. ^

Data structures for highly efficient querying of spatial data

The virtual quadrilateral is the coalescence of novel data structures that reduces the storage requirements of spatial data without jeopardizing the quality and operability of the inherent information. The data representative of the observed area is parsed to ascertain the necessary contiguous measures that, when contained, implicitly define a quadrilateral. The virtual quadrilateral then represents a geolocated area of the observed space where all of the measures are the same. The area, contoured as a rectangle, is pseudo-delimited by the opposite coordinates of the bounding area. Once defined, the virtual quadrilateral is representative of an area in the observed space and is represented in a database by the attributes of its bounding coordinates and measure of its contiguous space. Virtual quadrilaterals have been found to ensure a lossless reduction of the physical storage, maintain the implied features of the data, facilitate the rapid retrieval of vast amount of the represented spatial data and accommodate complex queries. The methods presented herein demonstrate that virtual quadrilaterals are created quite easily, are stable and versatile objects in a database and have proven to be beneficial to exigent spatial data applications such as geographic information systems. ^

Multi-purpose adaptable business tier components based on Call Level Interfaces

Call Level Interfaces (CLI) play a key role in business tiers of relational and on some NoSQL database applications whenever a fine tune control between application tiers and the host databases is a key requirement. Unfortunately, in spite of this significant advantage, CLI are low level API, this way not addressing high level architectural requirements. Among the examples we emphasize two situations: a) the need to decouple or not to decouple the development process of business tiers from the development process of application tiers and b) the need to automatically adapt business tiers to new business and/or security needs at runtime. To tackle these CLI drawbacks, and simultaneously keep their advantages, this paper proposes an architecture relying on CLI from which multi-purpose business tiers components are built, herein referred to as Adaptable Business Tier Components (ABTC). Beyond the reference architecture, this paper presents a proof of concept based on Java and Java Database Connectivity (an example of CLI).

Endowing NoSQL DBMS with SQL features through standard Call Level Interfaces

To store, update and retrieve data from database management systems (DBMS), software architects use tools, like call-level interfaces (CLI), which provide standard functionalities to interact with DBMS. However, the emerging of NoSQL paradigm, and particularly new NoSQL DBMS providers, lead to situations where some of the standard functionalities provided by CLI are not supported, very often due to their distance from the relational model or due to design constraints. As such, when a system architect needs to evolve, namely from a relational DBMS to a NoSQL DBMS, he must overcome the difficulties conveyed by the features not provided by NoSQL DBMS. Choosing the wrong NoSQL DBMS risks major issues with components requesting non-supported features. This paper focuses on how to deploy features that are not so commonly supported by NoSQL DBMS (like Stored Procedures, Transactions, Save Points and interactions with local memory structures) by implementing them in standard CLI.

ABTC: multi-purpose adaptable business tier components based on Call Level Interfaces

Call Level Interfaces (CLI) are low level API that play a key role in database applications whenever a fine tune control between application tiers and the host databases is a key requirement. Unfortunately, in spite of this significant advantage, CLI were not designed to address organizational requirements and contextual runtime requirements. Among the examples we emphasize the need to decouple or not to decouple the development process of business tiers from the development process of application tiers and also the need to automatically adapt to new business and/or security needs at runtime. To tackle these CLI drawbacks, and simultaneously keep their advantages, this paper proposes an architecture relying on CLI from which multi-purpose business tiers components are built, herein referred to as Adaptable Business Tier Components (ABTC). This paper presents the reference architecture for those components and a proof of concept based on Java and Java Database Connectivity (an example of CLI).

Bipolar Tribocharging Signal During Friction Force Fluctuations At Metal-insulator Interfaces.

Friction and triboelectrification of materials show a strong correlation during sliding contacts. Friction force fluctuations are always accompanied by two tribocharging events at metal-insulator [e.g., polytetrafluoroethylene (PTFE)] interfaces: injection of charged species from the metal into PTFE followed by the flow of charges from PTFE to the metal surface. Adhesion maps that were obtained by atomic force microscopy (AFM) show that the region of contact increases the pull-off force from 10 to 150 nN, reflecting on a resilient electrostatic adhesion between PTFE and the metallic surface. The reported results suggest that friction and triboelectrification have a common origin that must be associated with the occurrence of strong electrostatic interactions at the interface.

Clustering Of Water Bodies In Unpolluted And Polluted Environments Based On Escherichia Coli Phylogroup Abundance Using A Simple Interaction Database.

Different types of water bodies, including lakes, streams, and coastal marine waters, are often susceptible to fecal contamination from a range of point and nonpoint sources, and have been evaluated using fecal indicator microorganisms. The most commonly used fecal indicator is Escherichia coli, but traditional cultivation methods do not allow discrimination of the source of pollution. The use of triplex PCR offers an approach that is fast and inexpensive, and here enabled the identification of phylogroups. The phylogenetic distribution of E. coli subgroups isolated from water samples revealed higher frequencies of subgroups A1 and B23 in rivers impacted by human pollution sources, while subgroups D1 and D2 were associated with pristine sites, and subgroup B1 with domesticated animal sources, suggesting their use as a first screening for pollution source identification. A simple classification is also proposed based on phylogenetic subgroup distribution using the w-clique metric, enabling differentiation of polluted and unpolluted sites.