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Results for “Database Management Systems”

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At least 469 records · Page 26Linked to original sources

PubMed2003

EMMA: a platform for consistent storage and efficient analysis of microarray data.

As a high throughput technique, microarray experiments produce large data sets, consisting of measured data, laboratory protocols, and experimental settings. We have implemented the open source platform EMMA to store and analyze these data. The system provides automated pipelines for data processing and has a modular architecture that can be easily extended. EMMA features detailed reports about spots and their corresponding measurements. In addition to routine data analysis algorithms, the system can be integrated with other components that contain additional data sources (e.g. genome annotation systems).

Algorithms↗

PubMed2000

Axeldb: a Xenopus laevis database focusing on gene expression.

Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos. The data are organised in a format appropriate for comprehensive analysis, and enable comparison of images of expression pattern for any given set of genes. Information on literature, cDNA clones and their availability, nucleotide sequences, expression pattern and accompanying pictures are available. Current developments are aimed toward the interconnection with other databases and the integration of data from the literature. Axeldb is implemented using an ACEDB database system, and available through the web at http://www.dkfz-heidelberg.de/abt0135/axeldb.htm

Animals↗

PubMed2005

SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.

SUMMARY: SpA is a web-accessible system for the management, visualization and statistical analysis of T-cell receptor spectratype data. Users upload data from their spectratype analyzers to SpA, which saves the raw data and user-defined supplementary covariates to a secure database. The statistical engine performs several data analyses and statistical summaries. The visualization engine displays spectratype histograms in a Java applet and in an image file suitable for download. All of these results are also saved to the database and remain accessible to the user. Additional statistical tools specific to the analysis of multiple spectratypes are also available through the SpA interface. AVAILABILITY: The service is freely accessible via the web at http://www.duke.edu/~kepler/spa.html. Additional technical support and specialized statistical analysis and consultation are available by arrangement with the authors and, depending on the service requested, may be subject to fee.

Animals↗

PubMed1991

Intelligent management of epidemiologic data.

In the lifecycle of epidemiologic data three steps can be identified: production, interpretation and exploitation for decision. Computerized support can be precious, if not indispensable, at any of the three levels, therefore several epidemiologic data management systems were developed. In this paper we focus on intelligent management of epidemiologic data, where intelligence is needed in order to analyze trends or to compare observed with reference value and possibly detect abnormalities. After having outlined the problems involved in such a task, we show the features of ADAMS, a system realized to manage aggregated data and implemented in a personal computer environment.

Artificial Intelligence↗

PubMedDate not supplied

Using an optical scanner and data base program to manage a family medicine teaching program.

This article describes the value of optically scannable forms and off-the-shelf software in improving administration of a required multi-site, third-year family medicine preceptorship. Formerly, a small preceptorship administrative staff manually handled nearly 1,000 evaluation forms per year. The process was slow, cumbersome, expensive, and inflexible. Optically scannable forms are now used and data bases are created, from which a series of administrative reports are easily generated. This system has reduced management time and cost, eliminated errors, and allowed staff to create both standardized and specialized reports as needed.

Database Management Systems↗

PubMed2006

EST2Prot: mapping EST sequences to proteins.

BACKGROUND: EST libraries are used in various biological studies, from microarray experiments to proteomic and genetic screens. These libraries usually contain many uncharacterized ESTs that are typically ignored since they cannot be mapped to known genes. Consequently, new discoveries are possibly overlooked. RESULTS: We describe a system (EST2Prot) that uses multiple elements to map EST sequences to their corresponding protein products. EST2Prot uses UniGene clusters, substring analysis, information about protein coding regions in existing DNA sequences and protein database searches to detect protein products related to a query EST sequence. Gene Ontology terms, Swiss-Prot keywords, and protein similarity data are used to map the ESTs to functional descriptors. CONCLUSION: EST2Prot extends and significantly enriches the popular UniGene mapping by utilizing multiple relations between known biological entities. It produces a mapping between ESTs and proteins in real-time through a simple web-interface. The system is part of the Biozon database and is accessible at http://biozon.org/tools/est/.

Animals↗

PubMed2006

Six degrees of separation.

A new resource allows researchers to match the gene-expression signature of their system of interest to that of well-characterized chemical compounds-a hypothesis-generation tool with a bright future.

Database Management Systems↗

PubMed2005

What makes a gene name? Named entity recognition in the biomedical literature.

The recognition of biomedical concepts in natural text (named entity recognition, NER) is a key technology for automatic or semi-automatic analysis of textual resources. Precise NER tools are a prerequisite for many applications working on text, such as information retrieval, information extraction or document classification. Over the past years, the problem has achieved considerable attention in the bioinformatics community and experience has shown that NER in the life sciences is a rather difficult problem. Several systems and algorithms have been devised and implemented. In this paper, the problems and resources in NER research are described, the principal algorithms underlying most systems sketched, and the current state-of-the-art in the field surveyed.

Algorithms↗

PubMed2004

SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis.

MOTIVATION: A comprehensive gene expression database is essential for computer modeling and simulation of biological phenomena, including development. Development is a four-dimensional (4D; 3D structure and time course) phenomenon. We are constructing a 4D database of gene expression for the early embryogenesis of the nematode Caenorhabditis elegans. As a framework of the 4D database, we have constructed computer graphics (CG), into which we will incorporate the expression data of a number of genes at the subcellular level. However, the assignment of 3D distribution of gene products (protein, mRNA), of embryos at various developmental stages, is both difficult and tedious. We need to automate this process. For this purpose, we developed a new system, named SPI after superimposing fluorescent confocal microscopic data onto a CG framework. RESULTS: The scheme of this system comprises the following: (1) acquirement of serial sections (40 slices) of fluorescent confocal images of three colors (4',6'-diamino-2-phenylindole (DAPI) for nuclei, indodicarbocyanine (Cy-3) for the internal marker, which is a germline-specific protein POS-1 and indocarbocyanine (Cy-5) for the gene product to be examined); (2) identification of several features of the stained embryos, such as contour, developmental stage and position of the internal marker; (3) selection of CG images of the corresponding stage for template matching; (4) superimposition of serial sections onto the CG; (5) assignment of the position of superimposed gene products. The Snakes algorithm identified the embryo contour. The detection accuracy of embryo contours was 92.1% when applied to 2- to 28-cell-stage embryos. The accuracy of the developmental stage prediction method was 81.2% for 2- to 8-cell-stage embryos. We manually judged only the later stage embryos because the accuracy for embryos at the later stages was unsatisfactory due to experimental noise effects. Finally, our system chose the optimal CG and performed the superposition and assignment of gene product distribution. We established an initial 4D gene expression database with 56 maternal gene products. AVAILABILITY: This system is available at http://anti.lab.nig.ac.jp/spi/ and http://anti.lab.nig.ac.jp/4ddb/

Animals↗

PubMed2004

Using XML technology for the ontology-based semantic integration of life science databases.

Several hundred internet accessible life science databases with constantly growing contents and varying areas of specialization are publicly available via the internet. Database integration, consequently, is a fundamental prerequisite to be able to answer complex biological questions. Due to the presence of syntactic, schematic, and semantic heterogeneities, large scale database integration at present takes considerable efforts. As there is a growing apprehension of extensible markup language (XML) as a means for data exchange in the life sciences, this article focuses on the impact of XML technology on database integration in this area. In detail, a general architecture for ontology-driven data integration based on XML technology is introduced, which overcomes some of the traditional problems in this area. As a proof of concept, a prototypical implementation of this architecture based on a native XML database and an expert system shell is described for the realization of a real world integration scenario.

Algorithms↗

PubMedDate not supplied

A clinical information system for foster care in Israel.

It is a source of great concern in Israel that children placed out of home may lose permanence and may drift in the child welfare system. One way to avoid this danger is to improve the monitoring of the children by using modern information technology as a practice aid. A clinical information system is being installed that responds to the information needs of practitioners on all levels of the foster care system. The viability of the system and its possible effects on practice and on clinical judgment are examined.

Child↗

PubMed2003

Extracting synonymous gene and protein terms from biological literature.

MOTIVATION: Genes and proteins are often associated with multiple names. More names are added as new functional or structural information is discovered. Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance. RESULTS: We have explored four complementary approaches for extracting gene and protein synonyms from text, namely the unsupervised, partially supervised, and supervised machine-learning techniques, as well as the manual knowledge-based approach. We report results of a large scale evaluation of these alternatives over an archive of biological journal articles. Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database.

Abstracting and Indexing↗

PubMed2004

Managing complex change in clinical study metadata.

In highly functional metadata-driven software, the interrelationships within the metadata become complex, and maintenance becomes challenging. We describe an approach to metadata management that uses a knowledge-base subschema to store centralized information about metadata dependencies and use cases involving specific types of metadata modification. Our system borrows ideas from production-rule systems in that some of this information is a high-level specification that is interpreted and executed dynamically by a middleware engine. Our approach is implemented in TrialDB, a generic clinical study data management system. We review approaches that have been used for metadata management in other contexts and describe the features, capabilities, and limitations of our system.

Artificial Intelligence↗

PubMed1994

[The Ulm databank].

Since 1968 one of our major research efforts consists in establishing a methodology for performing psychoanalytic process research. Within this frame tape-recording of psychoanalytic long-term treatments constituted an essential methodical step inevitably leading to the production of a large collection of verbatim transcripts. We gradually and inadvertently realized the need for a major computerized databank to assist our own research. With support of the German Research Foundation we started in 1980 with the development of the Ulm Textbank Management System. While realizing the system it became obvious that such a databank would serve as well other researchers involved in process research when analyzing verbatim material. The final shape of the systems thus was strongly influenced by the orientation towards a variety of users and methodological approaches. Meanwhile this task is completed and the Ulm Textbank, as it is known, is available as a new unique tool for psychotherapy research.

Database Management Systems↗

PubMed1992

Automated therapeutic drug monitoring in an ambulatory care endocrine clinic.

OBJECTIVE: To develop and implement an automated therapeutic drug monitoring system for accessing data from endocrine clinic patients who had been prescribed insulin, oral hypoglycemic agents (OHA), or levothyroxine. DATA SOURCES: We designed a computer system to retrieve clinical data from the Medical Information System (MIS), a centralized hospital computer system, and import this information directly into a Macintosh personal computer. Physician entry of prescriptions for insulin, OHA, or levothyroxine into MIS formed the basis for a computer program to retrieve daily diagnostic and prescription information, demographics, and laboratory analyses, including blood glucose and glycosylated hemoglobin for insulin and OHA orders and free and total thyroxine, total triiodothyronine, and thyroid stimulating hormone for levothyroxine orders. The information was imported into a database program (4th Dimension). RESULTS: The system identifies laboratory values outside of predetermined therapeutic ranges, maintains an up-to-date patient profile, and edits and generates reports. Preliminary experience suggests that automation eliminates 75-90 percent of the time required to manually collect the same information, and improves the accuracy, comprehensiveness, and utility of reports. CONCLUSIONS: Automated therapeutic drug monitoring minimizes the time required to collect clinical data, alerts clinicians to potential problems, and provides a means to assess overall therapeutic management. Our methodology can be used to evaluate other medications in a variety of general or specialty clinics.

Ambulatory Care↗

PubMed2005

SuperDrug: a conformational drug database.

MOTIVATION: Different resources exist for experimentally determined and computed three-dimensional (3D)-structures of low molecular weight structures but for approved drugs, no free, publicly accessible source of 3D-structures and conformers is available. Furthermore, for selection purposes or for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemical (ATC) classification codes to each structure according to the WHO-scheme would be desirable. RESULTS: The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. To account for structural flexibility they are represented by 10(5) structural conformers. Here we present a web-query system enabling searches for drug name, synonyms, trade name, trivial name, formula, CAS-number, ATC-code etc. 2D-similarity screening (Tanimoto coefficients) and an automatic 3D-superposition procedure based on conformational representation are implemented. Drug structures above a similarity threshold as well as superimposed conformers can be retrieved in the mol- file format via a graphical interface. AVAILABILITY: For academic use the system is accessible at http://bioinf.charite.de/superdrug. The retrieval system requires the free browser-plugin 'chime' from MDL for visualization.

Computer Graphics↗

PubMed2002

Architecture of a mediator for a bioinformatics database federation.

Developments in our ability to integrate and analyze data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad hoc queries across multiple data resources and correlating data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous distributed biological databases. Our architecture makes use of the existing search capabilities and indexes of the underlying databases, without infringing on their autonomy. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation, and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in SRS.

Algorithms↗

PubMed1991

Computer systems for dental practice management. A new generation of independent dental software.

A new generation of computer programs for dental patient management eliminates total dependence on the vendor for programming support. The software design enables information collected with the dental system to be transferred to popular off-the-shelf programs designed for business. A simplified example is used to illustrate for practitioners the advantages of this type of data structure management. Programs designed on this basis offer optimum performance and expandibility for both present and future needs.

Computer Systems↗