PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

Background  

In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools.     

CIBEX: center for information biology gene expression database

We describe the current status of the gene expression database CIBEX (Center for Information Biology gene EXpression database, http://cibex.nig.ac.jp), with a data retrieval system in compliance with MIAME, a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. CIBEX serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data.     

WiGID: wireless genome information database

WiGID, wireless genome information database, is a new application for mobile internet and can be reached through wireless application protocol (WAP). The main purpose of WiGID is to give easy access to information on completely sequenced genomes. Genome entries in WiGID can be queried by the number of open reading frames (ORFs), genus and species name and year published. Initial search results are linked to information on the full entry. AVAILABILITY: WiGID can be accessed through WAP at http://wigid.cgb.ki.se/index.wml and through the regular internet at http://wigid.cgb.ki.se.     

The MEROPS database as a protease information system

Peptidases (often termed proteases) are of great relevance to biology, medicine, and biotechnology. This practical importance creates a need for an integrated source of information about peptidases. In the MEROPS database (www.merops.ac.uk), peptidases are classified by structural similarities in the parts of the molecules responsible for their enzymatic activity. They are grouped into families on the basis of amino acid sequence homology, and the families are assembled into clans in light of evidence that they share common ancestry. The evidence for clan-level relationships usually comes from similarities in tertiary structure, but we suggest that secondary structure profiles may also be useful in the future. The classification forms a framework around which a wealth of supplementary information about the peptidases is organized. This includes images of three-dimensional structures, alignments of matching human and mouse ESTs, comments on biomedical relevance, human and other gene symbols, and literature references linked to PubMed. For each family, there is an amino acid sequence alignment and a dendrogram. There is a list of all peptidases known from each of over 1000 species, together with summary data for the distributions of the families and clans throughout the major groups of organisms. A set of online searches provides access to information about the location of peptidases on human chromosomes and peptidase substrate specificity.     

CytReD: A database collecting human cytokinome information

The cytokines/related receptors system represents a complex regulatory network that is involved in those chronic inflammatory processes which lead to many diseases as cancers. We developed a Cytokine Receptor Database (CytReD) to collect information on cytokine receptors related to their biological activity, gene data, protein structures and diseases in which these and their ligands are implicated. This large set of information may be used by researchers as well as by physicians or clinicians to identify which cytokines, reported in the literature, are important in a given disease and, therefore, useful for purposes of diagnosis or prognostic. AVAILABILITY: The database is available for free at http://www.cro-m.eu/CytReD/     

The use of information technology in improving medical performance. Part I. Information systems for medical transactions

Investment in medical information technologies reached $15 billion in 1996. However, these technologies have not had the wide impact predicted in streamlining bureaucracy, improving communications, and raising the effectiveness of care. In this series, we identify how such technologies are being used to improve quality and performance, the future directions for advancement, and the policy and research developments required to maximize public benefit from these technologies. Each of these articles focuses on a different type of information technology: (1) information systems to manage medical transactions; (2) physician-support technologies to improve medical practice; and (3) patient-focused technologies designed to change how people manage their own care. This first article of a 3-part series examines the successes of and opportunities for using advanced information systems that track and manage medical transactions for large populations to improve performance. Examples of such systems include: HEDIS, which gathers standardized data from health plans on quality of care; the USQA Health Services Research Program, which tracks treatment patterns and outcomes for 14 million insurance members; Ford's program to collect medical data for over 600,000 employees; and Harvard Pilgrim Health Care's system of computerized laboratory, pharmacy, ambulatory, and hospital admission records for its 1.5 million members. Data from these systems have led to modest improvements in knowledge and practice patterns for some diseases. Significant barriers are slowing efforts to add outcomes data to these databases and broaden the databases to cover larger populations. Nonetheless, existing data in currently evolving systems could be used to greater benefit in tracking public health and in identifying more effective treatments and causes of diseases.     

On-line integration of computer controlled diagnostic devices and medical information systems in undergraduate medical physics education for physicians

We designed and evaluated an innovative computer-aided-learning environment based on the on-line integration of computer controlled medical diagnostic devices and a medical information system for use in the preclinical medical physics education of medical students. Our learning system simulates the actual clinical environment in a hospital or primary care unit. It uses a commercial medical information system for on-line storage and processing of clinical type data acquired during physics laboratory classes. Every student adopts two roles, the role of ‘patient’ and the role of ‘physician’. As a ‘physician’ the student operates the medical devices to clinically assess ‘patient’ colleagues and records all results in an electronic ‘patient’ record. We also introduced an innovative approach to the use of supportive education materials, based on the methods of adaptive e-learning. A survey of student feedback is included and statistically evaluated.The results from the student feedback confirm the positive response of the latter to this novel implementation of medical physics and informatics in preclinical education. This approach not only significantly improves learning of medical physics and informatics skills but has the added advantage that it facilitates students’ transition from preclinical to clinical subjects.     

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

Background  

The biological information in genomic expression data can be understood, and computationally extracted, in the context of systems of interacting molecules. The automation of this information extraction requires high throughput management and analysis of genomic expression data, and integration of these data with other data types.     

An online database for genome information of agricultural plants

The integration-based genome database provides useful information through a user-friendly web interface that allows analysis of comparative genome for agricultural plants. We have concentrated on the functional bioinformatics of major agricultural resources, such as rice, Chinese cabbage, rice mutant lines, and microorganisms. The major functions are focused on functional genome analysis, including genome projects, gene expression analysis, gene markers with genetic map, analysis tools for comparative genome structure, and genome annotation in agricultural plants.

Availability

The database is available for free at http://nabic.naas.go.kr/     

ProRule: a new database containing functional and structural information on PROSITE profiles

MOTIVATION: Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. SUMMARY: We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains. AVAILABILITY: ProRule can be accessed through ScanProsite at http://www.expasy.org/tools/scanprosite. A file containing the rules will be made available under the PROSITE copyright conditions on our ftp site (ftp://www.expasy.org/databases/prosite/) by the next PROSITE release.     

Pathway information for systems biology

Pathway information is vital for successful quantitative modeling of biological systems. The almost 170 online pathway databases vary widely in coverage and representation of biological processes, making their use extremely difficult. Future pathway information systems for querying, visualization and analysis must support standard exchange formats to successfully integrate data on a large scale. Such integrated systems will greatly facilitate the constructive cycle of computational model building and experimental verification that lies at the heart of systems biology.     

GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems

Background  

The genomes of numerous cellulolytic organisms have been recently sequenced or in the pipeline of being sequenced. Analyses of these genomes as well as the recently sequenced metagenomes in a systematic manner could possibly lead to discoveries of novel biomass-degradation systems in nature.     

Repair-FunMap: a functional database of proteins of the DNA repair systems

Repair-FunMap is a functional database of the DNA repair systems. This database contains not only the proteins directly involved in DNA repair, but also the proteins that interact with the DNA repair proteins. A protein interaction network associated with the human DNA repair processes was established according to the functional relationship between proteins in the database. This network represents the current knowledge on the intrinsic signaling pathways related to DNA repair. The Repair-FunMap could become an essential resource center for cancer research, providing clues to understanding the inter-relationship between proteins in the network, and to building scientific models of the DNA repair processes. AVAILABILITY: http://astro.temple.edu/~feng/Servers/BioinformaticServers.htm