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PubMed2002

Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems.

Exponential growth of data, largely from whole-genome analyses, has changed the way biologists think about and handle data. Optimal use of these data requires effective methods to analyze and manage these data sets. Computers, software and the World Wide Web are now integral components of biological discovery. Understanding how information is obtained, processed and annotated in public databases allows researchers to effectively organize, analyze and export their own data into these databases. In this review we focus largely on two areas related to management of genomic data. We cite examples of resources available in the public domain and describe some of the software for data management systems currently available for plant research. In addition, we discuss a few concepts of data management from the perspective of an individual or group that wishes to provide data to the public databases, to use the information in the public databases more efficiently, or to develop a database to manage large data sets internally or for public access. These concepts include data descriptions, exchange format, curation, attribution, and database implementation.

Databases, Nucleic Acid↗
PubMed1990

[Registration of detailed data in the medical record or how to translate "impressions" into measurable observations].

Every medical case record represents a mass of data (texts, pictures, figures, etc.) in an unstructured form. The physician needs to retrieve this data via several access routes: temporal (dependent on date or sequences of events), type of data (diagnostic, treatment, clinical signs, laboratory findings, image descriptors, all with their interrelationships), or depending on the severity of the disease, etc. Retrieval of this data fulfils several functions: circulation of a case record among specialists, assistance in summarizing a long and complex clinical course, comparison of patients, research, and teaching. Three projects are described which have the same aim: structuring of the case record in order to retrieve detailed data on patients as individuals and describe clinical courses on the basis of measurable observations. This structure must be understandable to a computer (directly or indirectly) so that searches and comparisons can be performed automatically. The first project, entitled "indexed paragraph prototype" reproduces the structure of the problem-oriented case record and is designed to input the Medical Outpatients Department's follow-up notes into the computer. The second, "automatic language analysis", aims to exploit two characteristics of medical language, its omnipresence in the case record and its reliability, in view of its status as the spontaneous vehicle of communication between physicians. The third, "collection of clinical signs during consultation", is based on a prospective collection of all elements of clinical observation, structured temporally consultation by consultation. The purpose of precise collection of detailed and measurable observations in individual patients is to identify those among the clinical signs which display the greatest power of discrimination, i.e. those which best serve to predict the case's evolution.

Abstracting and Indexing↗
PubMed1993

Exploratory data analysis in two-dimensional electrophoresis.

The use of computerized matching of proteins in the analysis of multiple two-dimensional electrophoresis (2DE) gels creates volumes of data that are readily accessible for exploratory analysis. When these data are used in health-effects studies or in studies to identify factors associated with particular diseases, hundreds or even thousands of hypotheses can be tested. Interpreting so many hypothesis tests requires some preliminary statistical evaluations of the data. In addition, prior to the preliminary statistical evaluations and subsequent hypothesis tests, accurate protein quantification and correct protein matching must be verified. In this report we present an approach used at the Centers for Disease Control to address these issues. This approach consists of a randomized experimental design incorporating replicate gels for each specimen, gel image analysis, protein matching, editing, Boolean unions of all gels to obtain correspondences and contradictions of match identification numbers, resolution of correspondences and contradictions, statistical tests to identify outliers, and finally an assessment of statistical and practical significance to focus attention on the proteins most likely to be associated with the effects under study. We illustrate our approach with data from an exploratory exposure-response study.

Blood Protein Electrophoresis↗
PubMed1995

Telepathology in Europe. Its practical use.

Progress in pathology is related to application of new biological techniques and impact of electronic devices affecting transfer of information and images. The increase of specification of all kinds of disease classification induces a specific need for data exchange and expert consultation. The momentary technical situation in communication lines connected with medical fields, especially pathology is characterized by parallel operation of two basically different communication systems, namely a) systems based upon computerized data exchange (E-mail, etc.), and b) systems working at public access, i.e. telephone lines and their successors (digitized network, satellite system). Practical use in telecommunication in pathology has been gathered nearly exclusively by use of the second (public) system, and includes intraoperative classification of histological images (frozen sections), expert consultations, panel discussions, quantitative measurements, and access to image data bank systems. The use of remote control microscopes has been reported to work without major errors from Norway and Switzerland. In Norway, images and diagnostic informations are transferred by use of broad band networks (satellite communication), whereas in Switzerland the digitized network ISDN is used. The experiences show clearly that remote control microscopes are practicable and reliable tools for daily diagnostic work of pathologists, and that the quality of the transferred images is sufficient to allow sophisticated diagnoses. Expert consultations are routinely performed by use of the common telephone network in lung pathology, and can not be underestimated in their impact on the daily work. Accuracy of diagnosis, quality of staining and tissue handling, and reliability of diagnosis are automatically improved besides the positive legal aspects.

Computer Communication Networks↗
PubMed1997

Access to health care. Part 1: Children.

OBJECTIVES: This report presents national estimates of access to medical care and unmet health care needs for children through 17 years of age by selected sociodemographic variables including sex, age, race and/or ethnicity, family income, family structure, place of residence, and health status. In addition, the impact of children's health insurance status on access to care is described. METHODS: Data from the 1993 Access to Care and Health Insurance questionnaires of the National Health Interview Survey (NHIS) are analyzed to examine access indicators. The NHIS is a continuing household survey of the civilian noninstitutionalized population of the United States. The sample included 16,907 children from infants through 17 years of age from 24,071 households. RESULTS: In 1993, over 7.3 million U.S. children had at least one unmet health care need or had medical care delayed because of worry about the cost of care. These health care needs included medical care, dental care, prescription medicine, glasses, and mental health care. In addition, almost 4.2 million children lacked a regular source of health care. Factors related to access indicators included health insurance, family income, race and/or ethnicity, family structure, and place of residence. The lack of health insurance or inability to afford care was the main reason given by respondents for children lacking a regular source of medical care. CONCLUSIONS: In the United States, millions of children do not receive needed health care services. Uninsured children and those in families with low income are at the greatest risk of having unmet health needs.

Adolescent↗
PubMed2003

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org).

Animals↗
PubMed2004

Basic Surveillance Network, a European database for surveillance data on infectious diseases.

The Basic Surveillance Network was started in 2000 and is one of the networks on infectious diseases funded by the European Commission. The network collects and makes readily available basic surveillance data on infectious diseases from all the 'old' (pre-2004) European Union member states. The aim is to provide easy access to descriptive data that already exist in national databases, so that it is possible to monitor and compare incidence trends for infectious diseases in the EU member states. The list of diseases covered by the network has recently been expanded from 10 initial 'pilot' diseases to over 40 diseases listed by the EU to be under surveillance. In the near future, the new member states will be invited to participate in the network. Data are case-based and comprise date of onset of disease, age and sex. Only a very short list of disease specific additional variables, such as country of infection or immunisation status, is collected. Classification of cases (possible, probable, confirmed) is specified according to EU case definitions. The participants of the network have access to an internal web site were all the data is presented in tables and graphs. An open website is available for the public at https://www.eubsn.org./BSN/

Communicable Diseases↗
PubMed2001

Perceived barriers to receiving HIV services in groups of traditionally underserved individuals: empirical models.

Persons living with HIV/AIDS face many issues that make them highly vulnerable to a number of health and social problems. As the demographics of the epidemic have shifted in recent years, many members of traditionally underserved groups have encountered barriers to entering the services system. This article uses data from seven national demonstration projects funded to enroll persons with HIV/AIDS who tend to "fall through the cracks" and help them access needed services. Data on the initial perceptions of the participants about barriers to accessing services were related to 17 indicators of traditionally underserved status including demographic characteristics and behavioral variables using the data modeling method of Exhaustive CHAID (Chi-squared Automatic Interaction Detector). Through the modeling methods, the groups most likely to experience a large number of barriers to service participation are identified. Having children needing care is particularly predictive of the level of barriers to care.

Adult↗
PubMed2003

MADGE: scalable distributed data management software for cDNA microarrays.

MOTIVATION: The human genome project and the development of new high-throughput technologies have created unparalleled opportunities to study the mechanism of diseases, monitor the disease progression and evaluate effective therapies. Gene expression profiling is a critical tool to accomplish these goals. The use of nucleic acid microarrays to assess the gene expression of thousands of genes simultaneously has seen phenomenal growth over the past five years. Although commercial sources of microarrays exist, investigators wanting more flexibility in the genes represented on the array will turn to in-house production. The creation and use of cDNA microarrays is a complicated process that generates an enormous amount of information. Effective data management of this information is essential to efficiently access, analyze, troubleshoot and evaluate the microarray experiments. RESULTS: We have developed a distributable software package designed to track and store the various pieces of data generated by a cDNA microarray facility. This includes the clone collection storage data, annotation data, workflow queues, microarray data, data repositories, sample submission information, and project/investigator information. This application was designed using a 3-tier client server model. The data access layer (1st tier) contains the relational database system tuned to support a large number of transactions. The data services layer (2nd tier) is a distributed COM server with full database transaction support. The application layer (3rd tier) is an internet based user interface that contains both client and server side code for dynamic interactions with the user. AVAILABILITY: This software is freely available to academic institutions and non-profit organizations at http://www.genomics.mcg.edu/niddkbtc.

Database Management Systems↗
PubMed1985

Access to care: where are the holes in the net? The plight of the uninsured.

The issue of access to health care has re-emerged on the national health care scene. Is health care accessible to those who need it, and why has this issue again risen to receive national attention? The three current indices of access to health care, the number of uninsured individuals, utilization of health care services, and health status, have revealed conflicting and insufficient data on the access to health care. However, they have revealed no major increase in the size of the problem. The renewed interest in the access problem stems from the emphasis on prudent buyer concepts by all of the major purchasers of health care and the resulting switch from implicit to explicit financing of health care--especially the health care of the uninsured.

Adolescent↗
PubMed2006

Spectral imaging microscopy web sites and data.

The Internet is enabling greater access to spectral imaging publications, spectral graphs, and data than that was available a generation ago. The spectral imaging systems discussed in this issue of Cytometry work because reagent and hardware spectra are reproducible, reusable, and provide input to spectral unmixing and spectral components recognition algorithms. These spectra need to be readily available in order to determine what to purchase, how to use it, and what the output means. We refer to several commercially sponsored and academic spectral web sites and discuss our spectral graphing and data sites. Sites include fluorescent dye graph servers from Invitrogen/Molecular Probes, BD Biosciences, Zeiss/Bio-Rad Cell Sciences, and filter set servers from Chroma Technology and Omega Optical. Several of these sites include data download capabilities. Recently, two microscope manufacturers have published on their web sites transmission curves for select objective lenses-crucial data for anyone doing multiphoton excitation microscopy. Notable among the academic sites, PhotoChemCAD 2.0 has over 200 dyes and a downloadable database/graphing program, and the USC-A Chemistry UV-vis Database displays absorption spectra of many dyes and indicators used in clinical histology and pathology. Our Fluorescent Spectra graphing/calculator site presents dyes, filters, and illumination data from many of these and additional sources. PubSpectra is our free download site which uses Microsoft Excel files as standardized human/machine readable format with over 2,000 biomedical spectra. The principle that data is not subject to copyright provides a framework in which all scientific data should be made freely accessible.

Algorithms↗
PubMed2003

Reliability of a modified medication appropriateness index in community pharmacies.

BACKGROUND: The medication appropriateness index (MAI) has demonstrated reliability in selected outpatient clinics where medical data were easily accessible from medical charts. However, its use in the community setting where patient data may be limited has not been examined. OBJECTIVE: To evaluate the usefulness of a modified MAI for use in the community pharmacy setting by testing interrater reliability using 3 different rating schemes. METHODS: Two raters evaluated 160 medications for 32 elderly ambulatory patients. Patient information was acquired using community pharmacist-collected medication histories. A summated MAI score, percent agreement, kappa, positive agreement, negative agreement, and intraclass correlation coefficient were calculated for each criterion using 3 scoring schemes. A paired samples t-test (95% CI) was used to test interrater reliability. RESULTS: The kappa statistics were >0.75 for indication and effectiveness, but good (0.41-0.66) for the remaining criteria using the Hanlon scoring scheme. The intraclass coefficients (0.82, 0.86, 0.87) and overall kappa (0.65, 0.66, 0.61) were similar for the 3 schemes. CONCLUSIONS: This study suggests that the modified MAI has the potential to detect medication appropriateness and inappropriateness in the community pharmacy setting; however, it is not without limitations. Because the MAI has the most clinimetric and psychometric data available, the instrument should be studied further to increase its reliability and generalizability.

Data Collection↗
PubMed1992

A computerized system to store and retrieve data on biological and biotechnological veterinary products of the American continent.

The Veterinary Biologics Information System is a project the main goal of which is to collect, analyze and manage data concerning registered veterinary biologics and biotechnological products employed to control animal diseases by the countries of the Americas. Data from each country was gathered by cataloguing each biological product on a questionnaire form. The collected data was then fed into an electronic data base system. A retrieval program was subsequently developed, allowing the user quick access to all data stored in the system. The system operates in English and Spanish and includes such information as the product name, registration number, ingredients, species for which the product is approved for use, the disease against which the product is used, names of manufacturers and distributors and other distinguishing characteristics of the product including expiry dates and withdrawal times. This computerized system, with on-line data bases which can be quickly updated, provides a dynamic answer to the question of timely information concerning veterinary biological products.

Animal Diseases↗
PubMed1979

[Radiological reporting systems. The viewpoint of the central radiodiagnostic department in an university hospital (author's transl)].

The use of automatic Roentgen diagnostic reporting systems is limited. Therefore, the capabilities of these systems should be expanded, and should include an integral patient identification as well as relevant data regarding the clinical patient information. By this way, appropriate data considering payments and statistics can be collected. In addition, there is selective access to the data from previous investigations. Thus, the evaluation of the entire information about a patient, including a verification of previous diagnosis is possible. Based on the radiology reporting system of Wheeler (Sirep, Siemens Ltd.) and of Vadraux-Vernier (Sacre, CGR, Ltd.), an additional set of input and output parameter is described as well as their use in a system comprising a small central processor and large external storage unit.

Computers↗