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PubMed2000

Laboratory database to manage electrophoresis and chromatography separations and the associated samples.

A database was developed to store, organize, and retrieve the data associated with electrophoresis and chromatography separations. It allows laboratories to store extensive data on separation techniques (analytical and preparative). The data for gel electrophoresis includes gel composition, staining methods, electric fields, analysis, and samples loaded. The database stores data on chromatography conditions, the samples used, and the fractions collected. The data structure of this database was designed to maintain the link between samples (including fractions) from chromatography separations and their analysis by gel electrophoresis. The database will allow laboratories to organize and maintain a large amount of separation and sample data in a uniform data environment. It will facilitate the retrieval of the separation history of important samples and the separation conditions used.

Chromatography↗

PubMed2004

KMD: an open-source port of the ArrayExpress microarray database.

UNLABELLED: The Keck Microarray Database (KMD) is a port of the ArrayExpress database from Oracle to the MySQL environment. The requirements for a locally available, open-source microarray database solution based on ArrayExpress are analysed in this article. The differences between the Oracle and MySQL environments are identified and the method to port to MySQL is described, providing a unified relational database management system (RDBMS) platform for both MIAMExpress and ArrayExpress. AVAILABILITY: The software and documentation are available from the Keck Graduate Institute of Applied Life Sciences website at http://public.kgi.edu/~jmainguy/applied-bioinformatics.htm.

Database Management Systems↗

PubMed1999

Multimedia explorer: image database, image proxy-server and search-engine.

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval.

Computer Graphics↗

PubMed1999

Medical student database development: a model for record management in a multi-departmental setting.

Student records flow through medical school offices at a rapid rate. Much of this data is often tracked on paper, spread across multiple departments. The Medical Student Informatics Group at the University of Utah School of Medicine identified offices and organizations documenting student information. We assessed departmental needs, identified records, and researched database software available within the private sector and academic community. Although a host of database applications exist, few publications discuss database models for storage and retrieval of student records. We developed and deployed an Internet based application to meet current requirements, and allow for future expandability. During a test period, users were polled regarding utility, security, stability, ease of use, data accuracy, and potential project expansion. Feedback demonstrated widespread approval, and considerable interest in additional feature development. This experience suggests that many medical schools would benefit from centralized database management of student records.

Consumer Behavior↗

PubMed1993

The ESA microgravity database.

To facilitate and optimise access to the results of previous microgravity experiments, ESA is establishing a Microgravity Database (MGDB). The database will give scientists access to descriptions of all experiments related to microgravity research carried out on ESA and NASA missions since the 1960s. MGDB incorporates both a local database available for PCs and Apple Macintoshes, and a remote database which can be accessed via the ESRIN Data Dissemination Network (DDN) and public X.25 networks.

Aerospace Medicine↗

PubMed2002

[IT systems for clinical databases--status and perspectives].

Generally, the use of clinical databases for quality development in the hospital sector has not been satisfactory. A substantial problem attaches to the IT systems used hitherto. This article describes a number of requirements which the National Indicator Project has specified for a forthcoming second generation of clinical database system. Besides, the second generation system Clinical Performance Measurements which is used in the Copenhagen Hospital Corporation for several disease areas and for The Danish Vascular Registry is described. This experience emphasizes the need for central management of development initiatives within clinical quality databases. The management must allow for coordination, rational management and experience-based further development of IT systems for the clinical databases and integration with present and forthcoming systems including electronic patient record systems. The management should also allow for the decisive interaction between clinical quality development and medical informatics.

Data Collection↗

PubMed2002

The Chronus II temporal database mediator.

Clinical databases typically contain a significant amount of temporal information. This information is often crucial in medical decision-support systems. Although temporal queries are common in clinical systems, the medical informatics field has no standard means for representing or querying temporal data. Over the past decade, the temporal database community has made a significant amount of progress in temporal systems. Much of this research can be applied to clinical database systems. This paper outlines a temporal database mediator called Chronus II. Chronus II extends the standard relational model and the SQL query language to support temporal queries. It provides an expressive general-purpose temporal query language that is tuned to the querying requirements of clinical decision support systems. This paper describes how we have used Chronus II to tackle a variety of clinical problems in decision support systems developed by our group.

Database Management Systems↗

PubMed2003

Gene expression databases and data mining.

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.

Breast Neoplasms↗

PubMed2003

Programmed database system at the Chang Gung Craniofacial Center: part II--digitizing photographs.

BACKGROUND: The archival tools used for digital images in advertising are not to fulfill the clinic requisition and are just beginning to develop. The storage of a large amount of conventional photographic slides needs a lot of space and special conditions. In spite of special precautions, degradation of the slides still occurs. The most common degradation is the appearance of fungus flecks. With the recent advances in digital technology, it is now possible to store voluminous numbers of photographs on a computer hard drive and keep them for a long time. METHODS: A self-programmed interface has been developed to integrate database and image browser system that can build and locate needed files archive in a matter of seconds with the click of a button. This system requires hardware and software were market provided. RESULTS: There are 25,200 patients recorded in the database that involve 24,331 procedures. In the image files, there are 6,384 patients with 88,366 digital pictures files. From 1999 through 2002, NT400,000 dollars have been saved using the new system. CONCLUSION: Photographs can be managed with the integrating Database and Browse software for database archiving. This allows labeling of the individual photographs with demographic information and browsing. Digitized images are not only more efficient and economical than the conventional slide images, but they also facilitate clinical studies.

Craniofacial Abnormalities↗

PubMed2004

Clustering of database sequences for fast homology search using upper bounds on alignment score.

Homology data are among the most important information used to predict the functions of unknown proteins and thus fast and accurate methods are needed. In this paper, we propose a new approach for fast and accurate homology search using pre-computed all-against-all similarity scores in a target database. We previously developed a method for derivation of an upper bound of the Smith-Waterman score (SW-score) between a query and a homolog candidate sequence using the SW-score between the candidate and a sequence similar to the query. In this paper, by using this upper bound, we first cluster the sequences in the target database so that upper bounds of SW-scores for all the members in the clusters are less than a given value and select representative sequences for respective clusters. Then, the query sequence is searched against the representative sequences and the upper bounds of SW-scores for respective clusters are estimated. Only if the upper bound is higher than a given threshold, SW-alignments are computed for all the sequences in the cluster. We performed computational experiments to test efficiency of the proposed method for the KEGG/GENES database using the KEGG/SSDB. The results suggest that our method is efficient for redundant databases that include multiple closely related species.

Algorithms↗

PubMed2006

[The development of database system of electrocardiographic information].

An ECG information database system was established with 1297 ECG information records and clinical informations. The data and the analysis software in this database can be shared with the international physiological signal databases such as MIT-BIH Arrhythmia. The establishment of this database will facilitate the clinical interpretation, diagnosis and prediction of cardiovascular diseases, especially the cardiac sudden death (SCD).

Artificial Intelligence↗

PubMed1991

Methanog: a specialized database on methanogenic bacteria.

A specialized, interdisciplinary database on various types of related information on methanogenic bacteria is described. Derived from other sequence databases etc., this database collects information from many sources, including unpublished work from research laboratories working in this field, and makes them accessible from a single source, to interested scientists, free of cost. It is presently held in eight 48 T.P.I. floppy disks and can be run on any IBM PC under DOS 3.0 or above, making this database of particular interest to researchers with limited resources and on-line search/access facilities.

Amino Acid Sequence↗

PubMed1994

VQLM: a Visual Query Language for Macromolecular structural databases.

Databases of macromolecular structures allow researchers to identify general principles of molecular behavior. They do this by providing a variety of data obtained under a number of different experimental conditions. Many new tools have been developed recently to aid in exploratory analysis of structural data. However, some queries of interest still require considerable manual filtering of data. In particular, studies attempting to make generalizations about complex arrangements of atoms or building blocks in macromolecular structures cannot be approached directly with existing tools. Such studies are frequently carried out on only a few structures or else require a labor-intensive process. To address this problem, we have developed a visual language, VQLM (Visual Query Language for Macromolecules). A query is formulated in this language by drawing an abstract picture of substructures to be searched for in the database and specifying constraints on the objects in them. To illustrate the usefulness of our language, we show how to encode a number of queries that were found scientifically interesting in the published literature in molecular biology. VQLM relies on VQL, a new database language, as its underlying engine for database retrieval and computation. We believe that VQLM will make macromolecular structural data more accessible to scientists, enabling faster and deeper data analysis.

Animals↗

PubMed1994

A clinical database as a component of a diagnostic hematology workstation.

A clinical database was designed as part of a comprehensive workstation for diagnostic laboratory hematology. The database stores coded findings pertinent to hematologic disorders including inherited abnormalities, previous surgery, malignancies, current therapy, and laboratory test results. The workstation includes knowledge-based systems for peripheral blood analysis, flow cytometry studies, and bone marrow morphology. The peripheral blood system renders an interpretive report based on data from a complete blood count with manual review of a blood smear by a technologist. The flow cytometry module interprets the immunophenotyping and DNA content results, and correlates them with the clinical findings and the peripheral blood data. The bone marrow system bases its report on all of the available information including the morphologic review of the bone marrow specimen by a physician, the peripheral blood data, immunophenotype, and clinical/laboratory findings. Before generating an interpretive report, each of the knowledge-based systems automatically searches the clinical database for specific information pertinent to the findings in the case. Since the workstation must function in situations where access to distributed databases is not feasible or not yet practical, a data entry module with a graphical user interface has been created.

Artificial Intelligence↗

PubMed1993

Computerized relational database for monitoring clozapine therapy.

The use of a computerized relational database to satisfy the patient-monitoring requirements of clozapine's manufacturer at an Oregon state psychiatric facility is described. The pharmacy department designed a computerized system to efficiently manage the patient-monitoring requirements of clozapine's manufacturer. A relational database program allows information in database files to be readily retrieved and organized into standardized or customized reports. These reports provide white blood cell (WBC) counts to the drug's manufacturer, patient discharge information to other clozapine providers, psychiatric test results to treating physicians, financial data to hospital administration, and other key data related to the facility's clozapine treatment system. The computerized system minimized the additional workload required to dispense clozapine, decreased the cost of clozapine by $234,441 compared with the cost under the closed distribution system, and provided for comprehensive clinical monitoring. Between May 1991 and October 1992, 168 clozapine recipients were monitored; pharmacists notified physicians about 86 patients not meeting WBC-count criteria. The use of a computerized relational database enabled a state psychiatric hospital to efficiently manage the burden of monitoring clozapine recipients.

Clinical Pharmacy Information Systems↗

PubMed1997

Development of an enterprise-wide clinical data repository: merging multiple legacy databases.

We describe the development of a clinical data repository whose core consists of four years of inpatient administrative and billing data from the mainframe legacy systems of the University of Virginia Health System (UVAHS). To these data we have linked a cardiac surgery clinical database and our physician billing data (inpatient and outpatient). Other databases will be merged in the future. A relational database management system (Sybase) running on a dedicated IBM RS/6000 minicomputer was employed to assemble 2.5 Gigabytes of core data describing approximately 100,000 hospital admissions over the four year period. To enable convenient data queries, the system has been equipped with a custom-built WWW user interface, which generates Structured Query Language (SQL) automatically. We illustrate the rapid reporting capabilities of the resulting system with reference to patients undergoing coronary artery bypass graft surgery (CABG). We conclude that this information system: a) constitutes a convenient and low-cost method to increase data availability across the UVAHS; b) provides clinicians with a tool for surveillance of patient care and outcomes; c) forms the core of a comprehensive database from which clinical research may proceed; d) provides a flexible interface empowering a wide variety of clinical departments to share and enrich their own clinical data.

Computer Communication Networks↗

PubMedDate not supplied

Questions & answers about database searching.

Bibliographic databases such as RNdex, CINAHL, and MEDLINE help you find current clinical practice information beyond what is available in textbooks and reference manuals. There are many options for accessing these information resources, including some that are convenient and affordable for students. By learning basic search principles and techniques for searching these databases, you can save yourself time and be more successful in locating the information you need. Important search skills include being able to identify the component parts of your search topic, locate relevant subject headings in a database thesaurus, and use logical connectors to combine topic components. The better your skills at searching for information, the easier your study and research assignments will be. The information seeking skills you learn now will be applicable in the future too, as information resources evolve and as your learning needs change. Developing competence in database searching will help prepare you for a rich life of learning as you pursue your career as a nursing professional.

Computer User Training↗

PubMed1998

IMGT/LIGM-DB: a systematized approach for ImMunoGeneTics database coherence and data distribution improvement.

IMGT, the international ImMunoGeneTics database (http:(/)/imgt.cnusc.fr:8104), created by Marie-Paule Lefranc, Montpellier, France, is an integrated database specializing in antigen receptors and MHC of all vertebrate species. IMGT includes LIGM-DB, developed for Immunoglobulins and T-cell-receptors. LIGM-DB distributes high quality data with an important increment value added by the LIGM expert annotations. LIGM-DB accurate immunogenetics data is based on the standardization of biological knowledge related to keywords, annotation labels and gene identification. The management of such data resulting from biological research requires an high flexible implementation to quickly reflect up-to-date results, and to integrate new knowledge. We developed a systematized approach and defined LIGM-DB systems which manage and realize the major tasks for the database survey. In this paper, we will focus on the coherence system, which became absolutely crucial to maintain data quality as the database is growing up and as the biological knowledge continues to improve, and on the distribution system which makes LIGM-DB data easy to access, download and reuse. Efforts have been done to improve the data distribution procedures and adapt them to the current bioinformatics needs. Recently, we have developed an API which allows Java programmers to remotely access and integrate LIGM-DB data in other computer environments.

Animals↗