Interview: Mr. George Walmsley: UNFPA Country Director for the Philippines.
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Asia↗
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Results for “Data Storage And Retrieval”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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Current developments in departmental PACS for ultrasound.
1. INTRODUCTION TO DEPARTMENTAL PACS. Full or partial Departmental PACS is generally taken to mean an image management system focused on serving the needs of a specific modality or modality application. It will provide a modality specific means of image acquisition, specialized redisplay of images, distribution, and local long term storage of images. A Departmental PACS can be considered in isolation or as a component in a distributed Radiology PACS which consists of one or more departmental work groups on a back bone, potentially with shared resources. 2. DEPARTMENTAL PACS Issues Implementation of a Departmental PACS requires an in-depth knowledge of departmental clinical practice and work flow in all affected areas in the department, including patient intake, image collection, data routing, retrieval of previous image data, reporting, and long term data management and storage. Optimization of modality specific image display systems requires significant involvement from representative physician users. System architectures and user interfaces must be flexible enough to support the span of variation in clinical practice encountered in the site. A departmental PACS should offer a variety of "open" communications interfaces, both local and wide area, recognizing that outreach efforts are often driven by specific imaging departments. Interfaces to other departmental PAC systems and other information systems must be considered in order to facilitate institutions developing "Best of Breed" PACS systems. As hospitals move toward the integrated electronic medical record, means need to exist for a client process launched from a physician desktop to acquire images and/or reports from a departmental system. At minimum, HIS/RIS interfaces need to be considered to minimize re-keying of data and reduce data entry errors. 3. DESIGN OBJECTIVES FOR ALI ULTRAPACS. The key objectives were to design a product which could function either as a free standing PACS or as a departmental subnet on a larger PACS backbone, one which could function in a local or mixed local and wide area environment and one which could provide a cost effective implementation based on currently available technologies. 4. IMPLEMENTATION STRATEGIES. In order to attain the product design objectives, ALI made the following critical implementation decisions: 1) to build the UltraPACS application as a suite of separable UNIX processes based on a message passing client server model; 2) to host the application and operating system on a Digital Equipment Corporation PC using an Intel microprocessor because of the competition and broad variety of suppliers in the PC arena; and 3) to use NEXTSTEP as the UNIX variant of choice because of NEXTSTEPUs strong object orientation, superb development tools, and the excellent integration between the Graphical User Interface level and the underlying operating system layers. 5. CONCLUSION. ALI is convinced that a departmental approach to PACS offers significant advantages over monolithic PACS in several key areas including: optimization for modality specific clinical practice and workflow, cost effectiveness, the potential for an institution to implement PACS in a stepwise fashion, starting with the department with the potential for the greatest savings, and the capability for an institution to build a "best of breed" solution for large scale PACS.
Radiology Department, Hospital↗
Swedish court rules against doctor at centre of row over destroyed research data.
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Humans↗
A database manager of biomedical images.
In order to allow an efficient archiving and retrieval of biomedical images, PACS would include an image DBMS. As biomedical images have complex structures we developed a specific DBMS over a relational one. The medical image database manager ensures a data description that takes into account data semantics so that consistency or existential constraints may be verified. It provides a unique language to retrieve images no matter what their storage format. It encompasses the queries of the user which constitute a filter over associated data. The manager can handle changes in the environment of the image. We implemented a manager prototype to show the validity of logical access possibilities. The user need no longer know the structure of the image database to access data. The logical access allows retrieval of images, whatever the architecture of the base. An automatic query construction consists of three functional levels including the interfaces towards the external environment which ensure a logical independence from the database, a query generator which creates the correspondence between the user's query and physical access queries, a dictionary which contains the structure of the image data and consistency constraints.
Computer Systems↗
The DExH/D protein family database.
DExH/D proteins are essential for all aspects of cellular RNA metabolism and processing, in the replication of many viruses and in DNA replication. DExH/D proteins are subject to current biological, biochemical and biophysical research which provides a continuous wealth of data. The DExH/D protein family database compiles this information and makes it available over the WWW (http://www.columbia.edu/ ej67/dbhome.htm ). The database can be fully searched by text based queries, facilitating fast access to specific information about this important class of enzymes.
Amino Acid Sequence↗
Structured physical examination data: a modeling challenge.
The success of systems facilitating collection of structured data by clinicians is largely dependent on the flexibility of the interface. The Open Record for CAre (ORCA) makes use of a generic model to support knowledge-based structured data entry for a variety of medical domains. An endeavor undertaken recently aimed to cover the broader area of Physical Examination by expanding the contents of the knowledge base. The model was found to be adequately expressive for supporting this task. Maintaining the balance between flexibility of the interface and constraints dictated by reliable retrieval, however, proved to be a considerable challenge. In this paper we illustrate through specific examples the effect of this trade off on the modeling process, together with the rationale for the chosen solutions and suggestions for future research focus.
Artificial Intelligence↗
An evaluation of unmediated versus mediated retrieval services.
To understand if unmediated services could serve the data retrieval needs for the Mayo research investigator, a study was conducted to determine researcher interest, ability, and outcome of using a clinical data retrieval system. The results indicate about 25% of the research investigators would use a self-service retrieval tool. However, there is clear evidence a majority of the research investigators are satisfied with and prefer the mediated service because of convenience, retrieval specialist knowledge, and lack of time to perform the search themselves. Approximately 61% of the non-participants indicated they would be willing to pay a fee for continued use of the mediated service. This study confirms the interest in self-service retrieval tools, but the actual interest is lower than anticipated. The recommendation is to continue the use of mediated services and to offer self-service methods as needed, allowing the most options to the research investigator.
Biomedical Research↗
A microcomputer approach to storage of qualitative patient data using key words.
A microcomputer program is presented which stores and retrieves qualitative patient information, such as diagnosis and physical findings. Users can design and enter a key word list and modify it as needed. Using those key words, up to 5000 patient entries can be made on a single floppy disk. Application of the program to CT scan study results is discussed.
Computers↗
Standardized one- and two-dimensional thin-layer chromatographic methods for the identification of secondary metabolites in Penicillium and other fungi.
Standardized thin-layer chromatographic (TLC) data in two solvent systems are presented for secondary metabolites of Penicillium and other fungi to assist in the identification of products of Penicillium species, based on a study of 304 strains. Rapid identification aids are needed to check for activity during preservation for mycotoxin production, and for screening systematic and biotechnological purposes. The data are stored on a microcomputer which permits flexible storage, retrieval, and updating of information. Of 107 metabolites detected with TLC system 1 [solvent: toluene-ethyl acetate-90% formic acid (5:4:1, v/v/v)], 80 (75%) are named and 27 (25%) as yet unidentified compounds are alloted reference numbers; in the case of the 97 metabolites detected by system 2 [solvent: chloroform-acetone-propan-2-ol (85:15:20, v/v/v)] the equivalent figures are 79 (81%) and 18 (19%) respectively.
Chromatography, Thin Layer↗
Representation of chemical information in OASIS centralized 3D database for existing chemicals.
The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of data items. Database statistics are maintained on the number and quality of structures, conformers, and descriptors. Reports can be generated presenting any chosen subset of structures and descriptors into different formats suitable for inclusion into documents. In addition to fixed report formats, there is a powerful report template designer module with a visual report template editor to produce a customized page layout. The database is compatible at the import/export level with SDF, MOL, SMILES, and other known formats. The precalculated centralized 3D database could be useful for quantitative structure-activity relationship developers avoiding the time-consuming and cumbersome 3D calculation phase of model development.
Algorithms↗
Applications of microcomputer technology to cytophotometry.
Lack of appropriate software support for microprocessor program development has previously limited the applications of such technology in the field of microspectrophotometry. This paper describes our use of a Vickers M86 integrating microdensitometer coupled through a custom-designed interface circuit to a Processor Technology SOL III microcomputer. W e have developed a series of interactive, user-oriented programs for DNA-Feulgen cytophotometry with this instrument to allow automatic storage of data in files on floppy disks and instant retrieval of sets of measurements for statistical processing. The same data files can also be used to generate graphic displays in the form of bar histograms or plots of linear regressions on a video monitor and to produce hardcopy output of data files and graphic displays through the use of a high speed DIABLO printer.
Animals↗
Computer processing of audiological and vestibular data. II. A further note.
This paper provides an addendum to an earlier paper describing the development of a computer record system for patient data. The specific problems addressed pertain to the storage and retrieval of historical information, physical signs and diagnosis. Some preliminary comparisons of audiological and vestibular test results are given for groups of patients with diagnoses of acoustic neuroma, Ménière's disease, temporal bone fracture and vestibular neuronitis.
Diagnosis, Computer-Assisted↗
Ordinal discrimination of ECG orthogonal features.
A rigorous mathematical analysis of Electrocardiogram (ECG) data is presented in this paper, as a decision support system for ECG interpretation. The mathematical analysis: provides a new insight to the ECG data, provides flexibility for future understanding of the heart system or the ECG, and avoids the need of measurements of parameters and the disagreement concerning the standard criteria of those parameters. The system enables compressed storage of the ECG data and an easy and accurate retrieval ability. An "ordinal straight line" method is presented for simple description of the ECG features as a combination of straight lines. A new developed discrimination method--the bisector method--is used for discrimination and classification between the normal and pathological groups. The physician's decision is based on both the physician's heuristic approach and the system's classification.
Data Collection↗
[Foreign international bibliographic databases. Index Medicus: presentation and use (CD-ROM edition)].
This paper provides technical assistance for bibliographic retrieval using the Medline CDRom, Medfive, with Ovid Search Software. Using a particular search as an example, we show, step by step and screen by screen, how to work using all the available features of this valuable bibliographic search tool.
CD-ROM↗
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs.
The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogs evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, the molecular targets of anti-HIV therapy (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences, including submissions from International Collaboration databases and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the antiretroviral drug treatment history of the individual from whom the isolate was obtained. During the past year 3500 sequences have been added and the data model has been expanded to include drug susceptibility data on sequenced isolates. Database content has also been integrated with didactic text and the output of two sequence analysis programs.
Amino Acid Sequence↗
FCP: functional coverage of the proteome by structures.
MOTIVATION: Tools and resources for translating the remarkable growth witnessed in recent years in the number of protein structures determined experimentally into actual gain in the functional coverage of the proteome are becoming increasingly necessary. We introduce FCP, a publicly accessible web tool dedicated to analyzing the current state and trends of the population of structures within protein families. FCP offers both graphical and quantitative data on the degree of functional coverage of enzymes and nuclear receptors by existing structures, as well as on the bias observed in the distribution of structures along their respective functional classification schemes. AVAILABILITY: http://cgl.imim.es/fcp CONTACT: jmestres@imim.es.
Algorithms↗
tGRAP, the G-protein coupled receptors mutant database.
The searchable mutant database tGRAP (previously called tinyGRAP) at the University of Tromsø contains data on mutated G-protein coupled receptors (GPCRs). All data have been extracted from scientific papers and entered manually into the database. The current version of the tGRAP mutant database (tGRAP.uit.no, release 10, April 2001) contains around 10 500 mutants extracted from almost 1400 research papers containing mutant data on five families of GPCRs, i.e. Family A, rhodopsin-like; Family B, secretin-like; Family C, metabotropic glutamate-like; Family D, pheromone; Family E, cAMP receptors. A query form provides rapid and simple access to relevant mutant information. In addition to this query form, a tool that enables the user to access mutation data via sequence alignments has been introduced. The ability to access mutant data from such alignments increases the usefulness of the mutant database and facilitates comparison of mutagenesis data between receptors. Moreover, this tool allows the construction of tailor-made sequence alignment views from any combination of receptors belonging to the same class. The database is available at http://tGRAP.uit.no/.
Amino Acid Sequence↗
Advances in the Exon-Intron Database (EID).
Investigation of exon-intron gene structures is a non-trivial task due to enormous expansions of the eukaryotic genomes, great variety of gene forms, and the imperfectness in sequence data. A number of available informational systems on various gene characteristics complement each other and are indispensable for many genomic studies. Among them, the Exon-Intron Database (EID) is a good choice for large-scale computational examination of exon/intron structure and splicing. It has many internal filters that control for sequence quality, consistency of gene descriptions, accordance to standards, and possible errors. New innovations in EID are described. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. Examples of statistical analyses of gene sequences using EID are provided. We present the latest data on our comparison of intron positions in 11,025 orthologous genes of human, mouse and rat, and find no convincing cases of intron gain. We discuss relevant data-quality issues of genomic databases. In particular, 5% of genes in genomic databases contain internal stop codons. This fact is due to a combination of biological reasons and also to errors in sequence annotations. The EID is freely available at www.meduohio.edu/bioinfo/eid/.
Base Sequence↗