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PubMed1991

[A survey of the best bibliographic searching system in occupational medicine and discussion of its implementation].

When occupational health personnel, especially occupational physicians search bibliographies, they usually have to search bibliographies by themselves. Also, if a library is not available because of the location of their work place, they might have to rely on online databases. Although there are many commercial databases in the world, people who seldom use them, will have problems with on-line searching, such as user-computer interface, keywords, and so on. The present study surveyed the best bibliographic searching system in the field of occupational medicine by questionnaire through the use of DIALOG OnDisc MEDLINE as a commercial database. In order to ascertain the problems involved in determining the best bibliographic searching system, a prototype bibliographic searching system was constructed and then evaluated. Finally, solutions for the problems were discussed. These led to the following conclusions: to construct the best bibliographic searching system at the present time, 1) a concept of micro-to-mainframe links (MML) is needed for the computer hardware network; 2) multi-lingual font standards and an excellent common user-computer interface are needed for the computer software; 3) a short course and education of database management systems, and support of personal information processing for retrieved data are necessary for the practical use of the system.

Computers↗
PubMed2001

Development, analysis, refinement, and utility of an interdisciplinary amyotrophic lateral sclerosis database.

The current status of evaluation and management provided by individual healthcare professionals (HCP) at amyotrophic lateral sclerosis (ALS) centers and clinics needs to be analyzed. This paper describes one ALS center's experiences with the development, analysis, refinement, and utility of an interdisciplinary, HCP-driven ALS database. The purpose and conceptual framework of the database, the general data that needed to be collected, and the types of reports that needed to be generated were determined, and, in collaboration with a computer programmer, data entry and database management systems were developed. Data were collected on 234 patients between September 1996 and August 1998, and were analyzed by a biostatistician. Based on review of the biostatistician's report and discussion of problems encountered with the systems, the database was then refined. Benefits of the database system included: systematization of data collection and reporting, reduction of redundant data collection by individuals, decreased variability of evaluation methods and management decisions from patient to patient, and increased availability of a variety of uniform patient information to assist team members in making care decisions. Ongoing refinement will ensure that this HCP-driven ALS database continues to be informative, practical and effective for decision-making and enhancing delivery of care.

Adult↗
PubMed1994

The technical conditions for an open architecture.

The development of Open Systems Architecture and the extensive networked interconnection of Health and Hospital Information Systems (HIS) offer great opportunities for improved care, but simultaneously these facilities pose a great danger to the overall security of the information held. The Geneva University Hospital which has built up it centralized informatics system over the last twenty years must now bring about the conditions for a migration towards open system, for although during the last ten years there have been declarations of intent, this architecture is still a long way from final implementation. Like others, the DIOGENE system (the Geneva HIS) has had to face difficult choices especially due to its own successful situation at the end of the eighties. This paper gives a brief explanation of the technical conditions needed in order to fully migrate towards an open system. The first choices towards obtaining optimum communication standards, operating systems and database management systems were the easiest. The real difficulties occurred when deciding on the choice for management tools in this open environment.

Computer Communication Networks↗
PubMed1997

Data note system for capturing laboratory data.

The complexity of genome data limits the usefulness of traditional database management systems. The highly interconnected structure of genome data can be captured in a data representation language based on the mathematical formalism of graphs. We have tailored graphs for describing genome data and have developed a database management system, called the Data Note System, for developing small databases to capture data from genome laboratories. To simplify the use of the Data Note System, a series of tools with graphical user interfaces has been developed. The system is designed to be easy to install and use by novice database developers with a minimal amount of computer expertise. We describe the tools and present examples of their use. The system consists of a storage facility, a schema editing tool to simplify the design of small databases, and three tools for data entry and querying.

Computers↗
PubMed1994

The development of a data security model for the Collaborative Social and Medical Services System.

This paper presents the development of the Collaborative Social and Medical Services System's (CSMSS) data security mechanism. This mechanism was synthesized from an analysis of the CSMSS problem domain, and from a study of the methods used by modern operating systems and database management systems. The resulting mechanism is more flexible and expressive than traditional access control methods and is generally applicable to the management of privacy and multi-provider access.

Ambulatory Care Information Systems↗
PubMed1991

A fact database for toxicological data at the National Institute of Hygienic Sciences, Japan.

The computerized fact database for the toxicity data of chemicals was constructed at the National Institute of Hygienic Sciences, Tokyo, Japan (biological database, BL-DB). The BL-DB stores data on mutagenicity, teratogenicity, carcinogenicity, and other toxicological tests of chemicals that appeared in the scientific literature. The BL-DB includes information about chemical identification, test system, results of the assays, and a bibliography. The system consists of five modules: data collection, data maintenance, data search, data downloading, and backup. ADABAS is used as a core database management system. Many kinds of test data are stored with the same formats; therefore, users can retrieve data of different toxicological data by the same manner. A user of the BL-DB can use about 50 kinds of commands to interact with the system, and the majority of fields are defined as search fields, thereby facilitating retrieval of target data through many ways. Currently, there are mainly data for the mutagenicity, especially on the Salmonella/microsome assay and the rodent micronucleus assay. These data can be retrieved and used for structure-activity relationship studies.

Abnormalities, Drug-Induced↗
PubMedDate not supplied

Development of an electronic radiologist's office in a private institute.

A computer system that improves the quality, user-friendliness, accessibility, and management of radiology data (images, reports, databases, knowledge) was implemented at a private institute. A picture archiving and communication system (PACS) was integrated with the radiology information system (RIS). Two servers and 12 personal computers form the integrated system. The first server is dedicated to management and archiving of Digital Imaging and Communications in Medicine (DICOM) images. The second server is dedicated to management of the RIS and archiving of patient data (Structured Query Language database), reports (hypertext markup language [HTML]), and images in the Joint Photographic Experts Group (JPEG) format (mini-PACS). There are three main client-server networks: a common network of imaging modalities (magnetic resonance imaging, computed tomography, ultrasonography, digital radiography) and two fast Ethernet networks (the PACS network and the RIS network). The RIS-PACS is linked remotely with other workstations and servers via Integrated Services Digital Network (ISDN). Images and reports can be distributed to referring physicians in the form of multimedia HTML and JPEG documents, which can also be used for quick and easy archiving, distribution, and reviewing within the institute. However, referring physicians have been reluctant to use electronic reports and images.

Attitude of Health Personnel↗
PubMed1993

Development of a statewide trauma registry using multiple linked sources of data.

In order to develop a cost-effective method of injury surveillance and trauma system evaluation in a rural state, computer programs were written linking records from two major hospital trauma registries, a statewide trauma tracking study, hospital discharge abstracts, death certificates, and ambulance run reports. A general-purpose database management system, programming language, and operating system were used. Data from 1991 appeared to be successfully linked using only indirect identifying information. Familiarity with local geography and the idiosyncracies of each data source were helpful in programming for effective matching of records. For each individual case identified in this way, data from all available sources were then merged and imported into a standard database format. This inexpensive, population-based approach, maintaining flexibility for end-users with some database training, may be adaptable for other regions. There is a need for further improvement and simplification of the record-linkage process for this and similar purposes.

Computer Communication Networks↗
PubMed2004

Cardio: a web-based knowledge resource of genes and proteins related to cardiovascular disease.

BACKGROUND: Cardiovascular disease (CVD) is the leading killer for human. In order to understand the linkage between cardiovascular diseases and genes or proteins, it is essential to construct a database to organize the body of knowledge. While the existing molecular biological databases focus on the sequence and structural aspects of biological macromolecules, i.e. DNAs, RNAs and proteins, Cardio is the web-based system we built to provide a knowledge environment with visual interface to integrate information about major cardiovascular diseases in relation to genes and proteins. METHODS: We collected the information from the web by using a group of software we developed and used a relational database management system to manage the information of these data. RESULTS: Cardio consists of six sections: GENE, PROTEIN, DISEASE, DRUG, LINKS, and REFERENCE. Each section contains relevant information about the topic. Using a phenotype-driven approach, we can identify genetic mechanisms underlying the physiology and pathophysiology of specific cardiovascular disease, such as atherosclerosis, hypertension, heart failure, and stroke. CONCLUSION: The website titled "Database of Genes and Proteins Related to Cardiovascular Disease (Cardio)" is available at along with additional information on cardiovascular disease, supplementary materials and related figures.

Cardiovascular Diseases↗
PubMedDate not supplied

[Creation and management of a data bank in oncologic radiotherapy].

Clinical, scientific and technological development has greatly widened the scope and range of oncological radiotherapy. As for database management, favorable conditions come from new available hardware and software facilities and from well-consolidated and universally accepted classifications. The authors' aim was to create and to verify an original database management system for oncological radiotherapy, proved with internationally accepted classifications and directly interfaced to a new package for clinical and epidemiological statistics. An ordinary personal computer was used and a 802-subject statistics was analyzed relative to 1987-1988 series from the Istituto del Radio "O. Alberti", General Hospital and University - Radiotherapy Department, Brescia, Italy. The system seems to be suitable for routine use as well as for research, with good potentials for multicentric use.

Database Management Systems↗
PubMedDate not supplied

Design and realization of an on-line database for multidimensional microscopic images of biological specimens.

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.

Animals↗
PubMed2004

AmpliBASE MT: a Mycobacterium tuberculosis diversity knowledgebase.

AmpliBASE MT is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT is based on a relational database management system that is hyperlinked to visualize genotyping results in the form of DNA fingerprint images for individual strains. A flexible search system based on systematic comparisons of fragment sizes in base pairs allows inter-laboratory comparison of FAFLP profiles. Besides this, the database also displays previously published data on IS6110 profiles, spoligotypes, MIRU-VNTRs and large sequence polymorphisms along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT is expected to be a very helpful tool in strengthening the concept of 'geographic genomics' and will be very helpful to molecular epidemiologists and those interested in diagnostic development for tuberculosis.

DNA Fingerprinting↗
PubMedDate not supplied

Integrating query of relational and textual data in clinical databases: a case study.

OBJECTIVES: The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). DESIGN: Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. MEASUREMENTS: Results are relevance-ranked using either "total documents per patient" or "report type weighting." RESULTS: Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. CONCLUSION: A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers.

Abstracting and Indexing↗
PubMed1991

Exploring a hospital-wide database: integrating statistical functions with ClinQuery.

Routinely collected clinical data are a valuable source of information for clinical epidemiology, health services research, and outcomes research. To explore, graph, and analyze such a large amount of material easily, one needs three kind of tools: a database management system, graphic displays, and statistical software. Although commercial software packages with these three functions do exist, it may be difficult to find one that fulfills the multiple requirements of a large hospital, allowing researchers to use the hospital information system to study various hypotheses. To address this issue we have integrated new exploratory modules with ClinQuery, a user-friendly computer program for online searching of clinical data. In this paper we describe some of the newly implemented graphics and statistical functions, along with practical examples of the way they may be used.

Boston↗
PubMed1994

A Turbo Pascal program to convert ICD-9CM coded injury diagnoses into injury severity scores: ICDTOAIS.

Diagnoses of injuries as a result of trauma are commonly coded by means of the International Classification of Diseases (9th rev.) Clinical Modification (ICD-9CM). The Abbreviated Injury Scale (AIS) is frequently employed to assess the severity of injury per body region. The Injury Severity Score (ISS) is an over-all index or summary of the severity of injury. To compute one of these two types of scores the entire medical record of each patient must be examined. The program ICDTOAIS replaces the manual coding or translation between the two scores. The program converts the ICD-9CM coded diagnoses into AIS and ISS scores. The program also computes the maximum AIS (MAXAIS) per body region, enabling the researcher to assess the relative impact of the severity of trauma of different body regions in both morbidity and mortality studies. The program locates invalid ICD-9CM rubrics in the data file. ICDTOAIS may be employed as a program alone or as a procedure in database management systems (e.g., DBase III plus, DBase IV, or the different versions of FOXPRO). The program is written in Turbo Pascal, Version 6.

Abbreviated Injury Scale↗
PubMed2004

Tools for loading MEDLINE into a local relational database.

BACKGROUND: Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. RESULTS: We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated. CONCLUSIONS: Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu.

Database Management Systems↗
PubMed1998

WWW-based access to object-oriented clinical databases: the KHOSPAD project.

KHOSPAD is a project aiming at improving the quality of the process of patient care concerning general practitioner-patient-hospital relationships, using current information and networking technologies. The studied application field is a cardiology division, with hemodynamic laboratory and the population of PTCA patients. Data related to PTCA patients are managed by ARCADIA, an object-oriented database management system developed for the considered clinical setting. We defined a remotely accessible view of ARCADIA medical record, suitable for general practitioners (GPs) caring patients after PTCA, during the follow-up period. Using a PC, a modem and Internet, an authorized GP can consult remotely the medical records of his PTCA patients. Main features of the application are related to the management and display of complex data, specifically characterized by multimedia and temporal features, based on an object-oriented temporal data model.

Angioplasty, Balloon, Coronary↗
PubMed2006

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.

BACKGROUND: The application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory networks. This data along with literature-derived knowledge on regulation of gene expression has opened the way for genome-wide reconstruction of transcriptional regulatory networks. These large-scale reconstructions can be converted into in silico models of bacterial cells that allow a systematic analysis of network behavior in response to changing environmental conditions. DESCRIPTION: CoryneRegNet was designed to facilitate the genome-wide reconstruction of transcriptional regulatory networks of corynebacteria relevant in biotechnology and human medicine. During the import and integration process of data derived from experimental studies or literature knowledge CoryneRegNet generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure. Reconstructed regulatory networks can be visualized by using the yFiles JAVA graph library. As an application example of CoryneRegNet, we have reconstructed the global transcriptional regulation of a cellular module involved in SOS and stress response of corynebacteria. CONCLUSION: CoryneRegNet is an ontology-based data warehouse that allows a pertinent data management of regulatory interactions along with the genome-scale reconstruction of transcriptional regulatory networks. These models can further be combined with metabolic networks to build integrated models of cellular function including both metabolism and its transcriptional regulation.

Computer Graphics↗