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PubMed1984

VAMPP: a veterinary automated management and production control programme for dairy farms (the application of MUMPS for data processing).

The application of MUMPS in a computerised recording system for herd health and production control on dairy farms is reviewed. MUMPS is an interactive multi-user database management system, which is both an operating system and a high level computer language. In this system, coding of veterinary and management events prior to data entry is not needed. Programmes and data structure can easily be adapted and extended due to the features of MUMPS. The system for dairy farms allows epidemiological analyses, due to the flexibility of the programme. The programme is used by farmers and veterinary surgeons by means of terminals linked to a central computer. The system provides action lists for farmers and veterinary surgeons; the information on these lists is presented in a multidisciplinary way. Several herd reports and analyses, including frequency distributions and graphs, are given. These reports enable the investigation of cross-relations between farm aspects, and aid in the detection of problem areas.

Animal Husbandry↗
PubMed2000

Informational aspects of telepathology in routine surgical pathology.

Application of computer and telecommunication technology calls serious challenges in routine diagnostic pathology. Complete data integration, fast access patients' data to usage of diagnosis thesaurus labeled with standardized codes and free text supplements, complex inquiry of the data contents, data exchange via teleconsultation and multilevel data protection are required functions of an integrated information system. Increasing requirement for teleconsultation transferring a large amount of multimedia data among different pathology information systems raises new questions in telepathology. Creation of complex telematic systems in pathology requires efficient methods of software engineering and implementation. Information technology of object-oriented modeling, usage of client server architecture and relational database management systems enables more compatible systems in field of telepathology. The aim of this paper is to present a practical example how to unify text based database, image archive and teleconsultation in a frame of an integrated telematic system and to discuss the main conceptual questions of information technology of telepathology.

Humans↗
PubMed1991

Dual purpose computer aided program for cardiac catheterization laboratory data management.

This communication describes the design criteria used in the early systems analysis activity of the cardiac laboratory. This analysis activity required an understanding of the cardiology laboratory environment, the establishment of needs to be answered by the program, and the goals of the entire system. The rationale for inclusion of various cardiologic, demographic, quality assurance, and personnel safety parameters is discussed. The input forms used, the database structure created, and the information provided by an applications system are described. Since the system is built around a general-purpose computer (the IBM PC or compatible) and widely available powerful general purpose software, the entire system may be used for many other cardiology laboratory data management tasks.

Cardiac Catheterization↗
PubMed2004

Constructing ontology-driven protein family databases.

MOTIVATION: Protein family databases provide a central focus for scientific communities as well as providing useful resources to aide research. However, such resources require constant curation and often become outdated and discontinued. We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability. RESULTS: Using protein phosphatases and ABC transporters as model protein families, we constructed two protein family database resources around a central DAML+OIL ontology. Each resource contains specialist information about each protein family, providing specialized domain-specific resources based on the same template structure. The formal structure, combined with the extraction of biological data using GO terms, allows for automated update strategies. Despite the functional differences between the two protein families, the ontology model was equally applicable to both, demonstrating the generic nature of the system. AVAILABILITY: The protein phosphatase resource, PhosphaBase, is freely available on the internet (http://www.bioinf.man.ac.uk/phosphabase). The DAML+OIL ontology for the protein phosphatases and the ABC transporters is available on request from the authors. CONTACT: kwolstencroft@cs.man.ac.uk.

ATP-Binding Cassette Transporters↗
PubMed1997

DNA Data Bank of Japan in the age of information biology.

DNA Data Bank of Japan (DDBJ) began its activities in 1986 in collaboration with EMBL in Europe and GenBank in the United States. DDBJ developed a data submission tool called Sakura, by which researchers can submit their newly sequenced data on WWW from every corner of the world. The data bank also built a database management system (Yamato II), incorporating the techniques and functions of the object-oriented database, in order to efficiently process the data it has collected. A number of research activities in information biology are also going on at DDBJ. Two such activities are also briefly introduced in this report.

Academies and Institutes↗
PubMed2005

mobilePDR: a mobile medical information system featuring update via Internet.

This paper presents an analysis of usability of mobile prescription reference systems in medical practice, and presents implementation of mobilePDR (Physician's Desk Reference). Various aspects of mobilePDR are discussed: main functions, information content, performance and design issues, independent evaluation with other similar tools, and lessons learned from the system development.

Computers, Handheld↗
PubMed2004

Pegasys: software for executing and integrating analyses of biological sequences.

BACKGROUND: We present Pegasys--a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. RESULTS: The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. CONCLUSIONS: The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

Computational Biology↗
PubMedDate not supplied

A flexible information management system. Better information management means increased productivity.

While the finite details and program listings have been purposely excluded, the system described in the preceding text provides the basis for a relatively inexpensive equipment management system. The Biomedical Engineering Department at Rochester General Hospital has utilized this system to increase productivity levels by nearly 15% since implementation in early 1990. With a seven-member technical staff this increase in productivity translated into the addition of approximately 2,100 man-hours in 1991, the equivalent of one extra person. The department was able to utilize these hours to expand into new areas of responsibility and reduce the average service cost per item by 58%. As previously indicated, the key to the system presented is flexibility. There is no hard and fast rule for this system, just a simple, common sense guideline: continuously review, revise, and develop the program. While adherence to this process provides a solid basis for any system whether computerized or manual, it is intended for use only as a "tool," not as a substitute for clinical engineering knowledge and instincts. The ease and speed with which studies are formulated facilitate the large-scale data dissection process so often associated with equipment management programs. Correspondingly, the ability to modify database structures and applications provides the means for expansion and refinement of the system on an ongoing basis.

Biomedical Engineering↗
PubMed2000

A simple client-server system using a personal computer as the server.

Hospital information systems have recently grown into huge, complex systems. As a result, the cost of development and maintenance of application programs has increased and become a serious problem. We have constructed an order entry system using server-client architecture as part of a hospital intranet information system in which a personal computer is used as a server. Using a commercial database management system and software development tools, an easily maintained order entry system was developed within only three months by one programmer. Since slow response when the number of clients increased was possible, we measured turn-around times when one or ten clients accessed simultaneously. Turn-around times were 8 and 10 sec, respectively. Because we expect much better performance from personal computers in the near future, application systems using personal computers as Intranet servers will be cost and time effective and easy to develop and maintain.

Computer Communication Networks↗
PubMed1984

GENAS: a database system for nucleic acid sequence analysis.

A database system, named GENAS (GENe Analyzing System), for computer analysis of sequence was constructed using Adbis which is a relational database management system (1). GENAS enables us to retrieve any sequence data from EMBL nucleotide sequence data library (2) and readily to analyze them (if necessary, together with private data) by various application programs in a interactive manner. Analysis of structure of replication origin of replicons was demonstrated using this system.

Base Sequence↗
PubMed2003

Open, flexible and portable secure web-based health applications.

This paper presents a totally generic client-server model for accessing legacy and new databases according to the three tier architecture principles. It is based on an integrated environment that eases the dynamic creation and instantiation of secure web applications that access multiple database management systems. Emphasis is placed on the ability to query almost any type of relational database and queries can simultaneously address a multitude of data sources. The information is collected, assembled and presented to users depending on a possible set of user profiles. These profiles originate from work on securing the conduct of clinical studies. This has been achieved in the context of the EU funded project HARP (Harmonisation for the Security of Web Technologies and Applications). The generic character of the model is exploited through an accompanying set of development tools. This permits efficient and effective creation and maintenance of applications in several domains of health telematics and beyond. Main merit is the lightweight character of the resulting platform, whereby all necessary instantiations are accomplished through a set of related XML documents.

Computer Security↗
PubMed2004

[A system for capturing and showing micrographs of genetics experiments].

A system for capturing and showing micrographs of genetics was designed with Microsoft Visual Basic 6.0. The system includes many functions such as capturing and editing images, typing and editing text, teaching experiments, showing images, image retrieval, database management, system maintenance and help, all of them were developed with the form of Windows. The system could collect images not only from image-grabber card in real-time but also from scanner, digital camera, clipboard and files. After utilizing the image compression technology, the images will be saved in database along with experiment instruction. With all the features referred above, the system can be used as a wonderful assistant both for the teaching of genetics experiments and for the students' learning by themselves.

Computer-Assisted Instruction↗
PubMed2006

Genomic pathways database and biological data management.

In this paper, we discuss the properties of biological data and challenges it poses for data management, and argue that, in order to meet the data management requirements for 'digital biology', careful integration of the existing technologies and the development of new data management techniques for biological data are needed. Based on this premise, we present PathCase: Case Pathways Database System. PathCase is an integrated set of software tools for modelling, storing, analysing, visualizing and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (i) genomic information integrated with other biological data and presented starting from pathways; (ii) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (iii) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels and to pose exploratory queries; (iv) a wide range of different types of queries including, 'path' and 'neighbourhood queries' and graphical visualization of query outputs; and (v) an implementation that allows for web (XML)-based dissemination of query outputs (i.e. pathways data in BIOPAX format) to researchers in the community, giving them control on the use of pathways data.

Computational Biology↗
PubMed1980

GENFILES: a computerized medical genetics information network. I. An overview.

GENFILES is a comprehensive computer information network to serve research, service, and administrative needs in medical genetics. Four major databases contain detailed information generated by the cytogenetics laboratory, the prenatal diagnosis program, the diagnostic and genetic counseling clinics, and the human cell culture facility. Unique aspects are the use of RAMIS, a commercial database management system, and of microprocessor computers as "intelligent" terminals with significant data-handling capabilities. All databases are no-line in a directly accessed large timesharing computer. The system, which has been designed, controlled and maintained by regular genetics staff, is an easy to use, moderate-cost tool well suited for use as a regional clinical genetics information system.

Computers↗
PubMed2001

[Current developments in the German Perinatal Survey. Modular analysis tools operating on a database platform].

The introduction of the modified data set for quality assurance in obstetrics (formerly perinatal survey) in Lower Saxony and Bavaria as early as 1999 saw the urgent requirement for a corresponding new statistical analysis of the revised data. The general outline of a new data reporting concept was originally presented by the Bavarian Commission for Perinatology and Neonatology at the Munich Perinatal Conference in November 1997. These ideas are germinal to content and layout of the new quality report for obstetrics currently in its nationwide harmonisation phase coordinated by the federal office for quality assurance in hospital care. A flexible and modular database oriented analysis tool developed in Bavaria is now in its second year of successful operation. The functionalities of this system are described in detail.

Data Collection↗
PubMed2001

Database-driven multi locus sequence typing (MLST) of bacterial pathogens.

MOTIVATION: Multi Locus Sequence Typing (MLST) is a newly developed typing method for bacteria based on the sequence determination of internal fragments of seven house-keeping genes. It has proved useful in characterizing and monitoring disease-causing and antibiotic resistant lineages of bacteria. The strength of this approach is that unlike data obtained using most other typing methods, sequence data are unambiguous, can be held on a central database and be queried through a web server. RESULTS: A database-driven software system (mlstdb) has been developed, which is used by public health laboratories and researchers globally to query their nucleotide sequence data against centrally held databases over the internet. The mlstdb system consists of a set of perl scripts for defining the database tables and generating the database management interface and dynamic web pages for querying the databases. AVAILABILITY: http://www.mlst.net.

Bacteria↗