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PubMed2005

ProLysED: an integrated database and meta-server of bacterial protease systems.

UNLABELLED: Bacterial proteases are an important group of enzymes that have very diverse biochemical and cellular functions. Proteases from prokaryotic sources also have a wide range of uses, either in medicine as pathogenic factors or in industry and therapeutics. ProLysED (Prokaryotic Lysis Enzymes Database), our meta-server integrated database of bacterial proteases, is a useful, albeit very niche, resource. The features include protease classification browsing and searching, organism-specific protease browsing, molecular information and visualisation of protease structures from the Protein Data Bank (PDB) as well as predicted protease structures. AVAILABILITY: ProLysED is integrated into the ProLysES (Prokaryotic Lysis Enzymes Site) website at http://genome.ukm.my/prolyses/. Access to the ProLysED database is free for academic users upon registration.

Amino Acid Sequence↗

PubMed2004

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.

MOTIVATION: Most ordinary traits are well described by multiple measurable parameters. Thus, in the course of elucidating the genes responsible for a given trait, it is necessary to conduct and integrate the genetic mapping of each parameter. However, the integration of multiple mapping results from different publications is prevented by the fact that they are conventionally published and accumulated in printed forms or graphics which are difficult for computers to reuse for further analyses. RESULTS: We have defined an XML-based schema as a container of genetic mapping results, and created a database named TraitMap containing curator-checked data records based on published papers of mapping results in Homosapiens, Mus musculus, and Arabidopsis thaliana. TraitMap is the first database of mapping charts in genetics, and is integrated in a web-based retrieval framework: termed Genome <--> Phenome Superhighway (GPS) system, where it is possible to combine and visualize multiple mapping records in a two-dimensional display. Since most traits are regulated by multiple genes, the system associates every combination of genetic loci to biomolecular networks, and thus helps us to estimate molecular-level candidate networks responsible for a given trait. It is demonstrated that a combined analysis of two diabetes-related traits (susceptibility to insulin resistance and non-HDL cholesterol level) suggests that molecular-level relationships such as the interaction among leptin receptor (Lepr), peroxisome proliferators-activated receptor-gamma (Pparg) and insulin receptor substrate 1 (Irs1), are candidate causal networks affecting the traits in a multigenic manner. AVAILABILITY: TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/

Chromosome Mapping↗

PubMed2005

Integrating relevance feedback techniques for image retrieval using reinforcement learning.

Relevance feedback (RF) is an interactive process which refines the retrievals to a particular query by utilizing the user's feedback on previously retrieved results. Most researchers strive to develop new RF techniques and ignore the advantages of existing ones. In this paper, we propose an image relevance reinforcement learning (IRRL) model for integrating existing RF techniques in a content-based image retrieval system. Various integration schemes are presented and a long-term shared memory is used to exploit the retrieval experience from multiple users. Also, a concept digesting method is proposed to reduce the complexity of storage demand. The experimental results manifest that the integration of multiple RF approaches gives better retrieval performance than using one RF technique alone, and that the sharing of relevance knowledge between multiple query sessions significantly improves the performance. Further, the storage demand is significantly reduced by the concept digesting technique. This shows the scalability of the proposed model with the increasing-size of database.

Algorithms↗

PubMed2003

GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes.

Laboratories working with draft phase genomes have specific software needs, such as the unattended processing of hundreds of single scaffolds and subsequent sequence annotation. In addition, it is critical to follow the "movement" and the manual annotation of single open reading frames (ORFs) within the successive sequence updates. Even with finished genomes, regular database updates can lead to significant changes in the annotation of single ORFs. In functional genomics it is important to mine data and identify new genetic targets rapidly and easily. Often there is no need for sophisticated relational databases (RDB) that greatly reduce the system-independent access of the results. Another aspect is the internet dependency of most software packages. If users are working with confidential data, this dependency poses a security issue. GAMOLA was designed to handle the numerous scaffolds and changing contents of draft phase genomes in an automated process and stores the results for each predicted ORF in flatfile databases. In addition, annotation transfers, ORF designation tracking, Blast comparisons, and primer design for whole genome microarrays have been implemented. The software is available under the license of North Carolina State University. A website and a downloadable example are accessible under (http://fsweb2.schaub. ncsu.edu/TRKwebsite/index.htm).

Algorithms↗

PubMed1993

Operating system components--Part II.

To summarize this discussion, let us look at a prototype, a capsule scenario in an OS. You make a process creation request on your local timeshare system. The long-term scheduler queues up this request, and eventually creates the corresponding process. Your process takes its turns executing, scheduled by the short-term scheduler. You request a tape drive to retrieve some archived data you need, and thus invoke the resource manager. You use the file manager to access the archived data. You use the I/O system to interact with the application program and to print the reports. The memory manager is swapping pages of your data and program between main memory and secondary memory. The dispatcher in the kernel is loading your process context into the CPU when your process is next on the execute list. The interrupt handler in the kernel is servicing interrupt requests, such as those made when you do I/O to the tape. The concurrency control in the kernel is coordinating your updating and spooled printing activities. So, your process is invoking activities throughout the various layers of the OS. Most of the time, you are unaware of these many varied activities.

Computer Systems↗

PubMed2005

Some principles of the development of a clinical database/national register of selected inflammatory rheumatic diseases in the Czech Republic.

According to the World Health Organisation, rheumatic diseases are likely to go on occupying a prominent place worldwide. As to US statistics, rheumatic diseases are currently the most frequent chronic disorders and leading cause of disability. The development of functional clinical database or rheumatic diseases represents an essential condition how to acquire necessary epidemiological and other information on disorders under study. In 1999-2003, Institute of Rheumatology in cooperation with EuroMISE have developed clinical database/national register of selected systemic inflammatory rheumatic diseases inclusive of bank of sera and DNA. Aims of this phase of the pilot research have been formulated into following relevant and time borders: to gather clinical, laboratory, genetic but also pharmaco- and socio-economic data in a representative sample of patients with systemic lupus erythematosus, systemic sclerosis, polymyositis/dermatomyositis, mixed connective tissue disease; rheumatoid arthritis, juvenile chronic arthritis, ankylosing spondylitis, psoriatic arthritis and reactive arthritis. The data about patients entering the register are differentiated according to the disease of the patient. However, many diseases have several data in common. Therefore, a simple common data structure for examination of all monitored diseases was chosen. In 2002, the preset number of over 2000 registered patients had been achieved with collaboration of 34 territorial and 20 institutional rheumatologists in the whole covering the majority of the Czech Republic. Some first acquired information inclusive comparison with German database is demonstrated.

Biomedical Research↗

PubMed2000

TRANSFAC: an integrated system for gene expression regulation.

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.

Database Management Systems↗

PubMed1997

NEXUS: an extensible file format for systematic information.

NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.

Animals↗

PubMed2004

BioBuilder as a database development and functional annotation platform for proteins.

BACKGROUND: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. RESULTS: BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. CONCLUSIONS: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.

Computational Biology↗

PubMed2004

JDotter: a Java interface to multiple dotplots generated by dotter.

UNLABELLED: Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. AVAILABILITY: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.

Computer Graphics↗

PubMed2005

A structured interface to the object-oriented genomics unified schema for XML-formatted data.

Data management systems are fast becoming required components in many biology laboratories as the role of computer-based information grows. Although the need for data management systems is on the rise, their inherent complexities can deter the full and routine use of their computational capabilities. The significant undertaking to implement a capable production system can be reduced in part by adapting an established data management system. In such a way, we are leveraging the Genomics Unified Schema (GUS) developed at the Computational Biology and Informatics Laboratory at the University of Pennsylvania as a foundation for managing and analysing DNA sequence data in centromere research projects around Arabidopsis thaliana and related species. Because GUS provides a core schema that includes support for genome sequences, mRNA and its expression, and annotated chromosomes, it is ideal for synthesising a variety of parameters to analyse these repetitive and highly dynamic portions of the genome. Despite this, production-strength data management frameworks are complex, requiring dedicated efforts to adapt and maintain. The work reported in this article addresses one component of such an effort, namely the pivotal task of marshalling data from various sources into GUS. In order to harness GUS for our project, and motivated by efficiency needs, we developed a structured framework for transferring data into GUS from outside sources. This technology is embodied in a GUS object-layer processor, XMLGUS. XMLGUS facilitates incorporating data into GUS by (i) formulating an XML interface that includes relational database key constraint definitions, (ii) regularising traversal through that XML, (iii) realising automatic processing of the XML with database key constraints and (iv) allowing for special processing of input data within the framework for automated processing. The application of XMLGUS to production pipeline processing for a sequencing project and inputting the Arabidopsis genome into GUS is discussed. XMLGUS is available from the Flora website (http://flora.ittc.ku.edu/).

Chromosome Mapping↗

PubMed2004

Retrieval for color artistry concepts.

This paper presents a work on the retrieval of artworks for color artistry concepts. First we affirm the view that the Query-by-Example paradigm fundamental to the current content-based retrieval systems is able to extend only limited usefulness. We then propose a concept-based retrieval engine based on the generative grammar of elemental concepts methodology. In the latter, the language by which color artistry concepts are communicated in artworks is used to operate semantic searches. The color artistry language is explicated into elemental concepts and the associated generative grammar. The elemental concepts are used to index the artworks, while the generative grammar is used to facilitate post-coordinate expression of color artistry concept queries by using the elemental concepts.

Abstracting and Indexing↗

PubMed2003

Pathways database system: an integrated system for biological pathways.

MOTIVATION: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. RESULTS: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data. AVAILABILITY: Available on request from the authors.

Database Management Systems↗

PubMed2004

An integrated content and metadata based retrieval system for art.

A new approach to image retrieval is presented in the domain of museum and gallery image collections. Specialist algorithms, developed to address specific retrieval tasks, are combined with more conventional content and metadata retrieval approaches, and implemented within a distributed architecture to provide cross-collection searching and navigation in a seamless way. External systems can access the different collections using interoperability protocols and open standards, which were extended to accommodate content based as well as text based retrieval paradigms. After a brief overview of the complete system, we describe the novel design and evaluation of some of the specialist image analysis algorithms including a method for image retrieval based on sub-image queries, retrievals based on very low quality images and retrieval using canvas crack patterns. We show how effective retrieval results can be achieved by real end-users consisting of major museums and galleries, accessing the distributed but integrated digital collections.

Abstracting and Indexing↗

PubMed2006

Web-based analysis of the mouse transcriptome using Genevestigator.

BACKGROUND: Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from prior knowledge or experimentation. Knowledge obtained from meta-analyzing compendia of expression data with annotation libraries can provide significant clues in understanding gene and network function, resulting in better hypotheses that can be tested in the laboratory. DESCRIPTION: Genevestigator is a microarray database and analysis system allowing context-driven queries. Simple but powerful tools allow biologists with little computational background to retrieve information about when, where and how genes are expressed. We manually curated and quality-controlled 3110 mouse Affymetrix arrays from public repositories. Data queries can be run against an annotation library comprising 160 anatomy categories, 12 developmental stage groups, 80 stimuli, and 182 genetic backgrounds or modifications. The quality of results obtained through Genevestigator is illustrated by a number of biological scenarios that are substantiated by other types of experimentation in the literature. CONCLUSION: The Genevestigator-Mouse database effectively provides biologically meaningful results and can be accessed at https://www.genevestigator.ethz.ch.

Animals↗

PubMed2004

A proposed framework for the description of plant metabolomics experiments and their results.

The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis. Such formal data descriptions, which specify the full experimental context, enable principled comparison of data sets, allow proper interpretation of experimental results, permit the repetition of experiments and provide a basis for the design of systems for data storage and transmission. The current design and example implementations are freely available (http://www.armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data.

Database Management Systems↗

PubMed2004

The Los Alamos hepatitis C sequence database.

MOTIVATION: The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. RESULTS: The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. AVAILABILITY: The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org.

Amino Acid Sequence↗

PubMed2004

Databases in use at the individual monitoring service of ITN-DPRSN.

In this work, the databases developed for routine use at the Individual Monitoring for External Radiation Service (IMS) of the Radiological Protection and Nuclear Safety Department (DPRSN) at the Nuclear and Technological Institute (ITN) in Portugal are presented. At the IMS there are two dosimetry systems running simultaneously, one based on film and the other one on thermoluminescent detectors (TLD). Two databases were initially and independently home-developed in order to meet each service's needs. A few modifications were introduced and while each service's requirements were maintained where needed, the databases were adapted in order to store the same type of information relative to the facilities and monitored workers, as well as to produce similar shaped reports and technical information. The necessary administrative features of the services were considered in the database development, made user-friendly and welcomed by the ordinary users. The improvements allowed a more direct analysis of the annual doses and an easy identification of professions and practices associated with higher dose values.

Academies and Institutes↗