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At least 451 records · Page 25Linked to original sources
PubMed2002

Biological data integration: wrapping data and tools.

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

Algorithms↗
PubMed2006

Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities.

BACKGROUND: Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. RESULTS: We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. CONCLUSION: Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at http://biozon.org.

Abstracting and Indexing↗
PubMed2003

Axiope tools for data management and data sharing.

Many areas of biological research generate large volumes of very diverse data. Managing this data can be a difficult and time-consuming process, particularly in an academic environment where there are very limited resources for IT support staff such as database administrators. The most economical and efficient solutions are those that enable scientists with minimal IT expertise to control and operate their own desktop systems. Axiope provides one such solution, Catalyzer, which acts as flexible cataloging system for creating structured records describing digital resources. The user is able specify both the content and structure of the information included in the catalog. Information and resources can be shared by a variety of means, including automatically generated sets of web pages. Federation and integration of this information, where needed, is handled by Axiope's Mercat server. Where there is a need for standardization or compatibility of the structures usedby different researchers this canbe achieved later by applying user-defined mappings in Mercat. In this way, large-scale data sharing can be achieved without imposing unnecessary constraints or interfering with the way in which individual scientists choose to record and catalog their work. We summarize the key technical issues involved in scientific data management and data sharing, describe the main features and functionality of Axiope Catalyzer and Axiope Mercat, and discuss future directions and requirements for an information infrastructure to support large-scale data sharing and scientific collaboration.

Animals↗
PubMed2003

[The medical profile of children for whom a medico-social institution is recommended by the Departmental Commission of Special Education in Var].

Since September 1999, the Commission of Special Education (CDES) in the French department of Var implemented a computer system to electronically handle medical records and information in conformance with the circular of November 5, 1998. The study presented here is based upon the first 247 orientation requests entered in the academic year 1998-1999. Six groups of children were categorised according to the main diagnostic clusters: psychosis, non-psychotic personality disorders and behavioural disorders, mental deficiency and chromosomal anomalies, instrumental malfunctioning and learning problems, central neurological problems, and motor and sensory difficulties. This study describes the medical diseases and handicaps of children for whom a medico-social assistance has been requested for the first time at the CDES based upon the recommended orientations. The revision of database management system foreseen by the implementation of the OPALES programme (Guide to Management and Administration of local Special Education) will integrate the medical, social and administrative parameters, and it will allow for the provision of a more streamlined analysis of and response to the problems and issues of handicapped children which are addressed to the CDES. The system will constitute a sustainable database on the handicaps of the children throughout the entire department.

Adolescent↗
PubMed1993

A multimedia relational database program for parasite identification.

Parasites are responsible for human and animal diseases causing suffering and economic loss all over the world. Parasite identification is an important step in treating and combating parasitic diseases. This task can be assisted by computer programs. Until now computer based systems for parasite identification were fixed tree-decision programs which had no updating or expansion capacity and no ability for optimal searching algorithms. A new program was developed by using a multimedia relational database management system with a graphical environment. This program can incorporate expert knowledge in its relational structure and identify the parasites by using its structured query language. Also, the program has the ability for partial identification by presenting the parasites that match the available incomplete information. In addition, the program can handle images and sound to present pictures and relevant information on the identified parasites. The advantages of the new program are its friendly graphical user interface and its unlimited capacity to incorporate new knowledge.

Algorithms↗
PubMed2002

The EBI SRS server--recent developments.

MOTIVATION: The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform interface--representing the domain knowledge. The SRS has become an integration system for both data retrieval and applications for data analysis. It provides capabilities to search multiple databases by shared attributes and to query across databases fast and efficiently. RESULTS: Here we present recent developments at the EBI SRS server (http://srs.ebi.ac.uk). The EBI SRS server contains today more than 130 biological databases and integrates more than 10 applications. It is a central resource for molecular biology data as well as a reference server for the latest developments in data integration. One of the latest additions to the EBI SRS server is the InterPro database-Integrated Resource of Protein Domains and Functional Sites. Distributed in XML format it became a turning point in low level XML-SRS integration. We present InterProScan as an example of data analysis applications, describe some advanced features of SRS6, and introduce the SRSQuickSearch JavaScript interfaces to SRS.

Computational Biology↗
PubMed2005

Benefits of automated crystallization plate tracking, imaging, and analysis.

We describe the design of a database and software for managing and organizing protein crystallization data. We also outline the considerations behind the design of a fast web interface linking protein production data, crystallization images, and automated image analysis. The database and associated interfaces underpin the Oxford Protein Production Facility (OPPF) crystallization laboratory, collecting, in a routine and automatic manner, up to 100,000 images per day. Over 17 million separate images are currently held in this database. We discuss the substantial scientific benefits automated tracking, imaging, and analysis of crystallizations offers to the structural biologist: analysis of the time course of the trial and easy analysis of trials with related crystallization conditions. Features of this system address requirements common to many crystallographic laboratories that are currently setting up (semi-)automated crystallization imaging systems.

Crystallization↗
PubMed1986

The Physician Data Query (PDQ) cancer information system.

PDQ is an online database that provides information about the prognosis and treatment of all major types of cancer. It represents a major effort by the NCI to communicate advances in cancer treatment using computer technology, and serves as a major component of the Institute's program to reduce cancer mortality nationwide. PDQ utilizes a modern large-scale computer to provide processing speed, a general purpose database management system to provide retrieval and display functions, and commercial telecommunication networks to provide online access to up-to-date information on cancer treatment. A series of user-friendly menus allow searching, browsing, and displaying without having to learn a specialized search language. PDQ is accessible through the National Library of Medicine's computer system via a computer terminal or personal computer and is available to the medical community at over 2000 medical libraries and centers and through individual access codes. PDQ is also available as an online database under a special license agreement with NCI through two medical information systems produced by commercial database vendors: BRS/Saunders' COLLEAGUE and Mead Data Central's MEDIS.

Drugs, Investigational↗
PubMed1987

The physician data query (PDQ) cancer information system.

PDQ is an online database that provides information about the prognosis and treatment of all major types of cancer. It represents a major effort by the NCI to communicate advances in cancer treatment using computer technology, and serves as a major component of the Institute's program to reduce cancer mortality nationwide. PDQ utilizes a modern large-scale computer to provide processing speed, a general purpose database management system to provide retrieval and display functions, and commercial telecommunication networks to provide online access to up-to-date information on cancer treatment. A series of user-friendly menus allow searching, browsing, and displaying without having to learn a specialized search language. PDQ is accessible through the National Library of Medicine's computer system via a computer terminal or personal computer and is available to the medical community at over 6,000 medical libraries and centers and through individual access codes. PDQ is also available as an online database under a special license agreement with NCI through two medical information systems produced by commercial database vendors: BRS/Saunders' COLLEAGUE Mead Data Central's MEDIS, and Telmed, a Swiss database.

Clinical Trials as Topic↗
PubMedDate not supplied

Models-of-data and models-of-processes in the post-genomic era.

As we are entering the post-genomic era, models-of-data, such as mining and filtering methods for gene sequences and microarrays and the clustering of co-expressed genes, must be complemented with models-of-processes that explain relationships between genomic information and phenomena at biochemical and physiological levels. Many of these models will have the structure of compartment models, whose conceptualization, identification and analysis will fundamentally benefit from the seminal work of John Jacquez. The article indicates with three vignettes that non-linear compartment models in the formulation of biochemical systems theory are viable candidates for post-genomic models-of-processes.

Animals↗
PubMed2001

GeneLynx: a gene-centric portal to the human genome.

GeneLynx is a meta-database providing an extensive collection of hyperlinks to human gene-specific information in diverse databases available on the Internet. The GeneLynx project is based on the simple notion that given any gene-specific identifier (accession number, gene name, text, or sequence), scientists should be able to access a single location that provides a set of links to all the publicly available information pertinent to the specified human gene. GeneLynx was implemented as an extensible relational database with an intuitive and user-friendly Web interface. The data are automatically extracted from more than 40 external resources, using appropriate approaches to maximize coverage of the available data. Construction and curation of the system is mediated by a custom set of software tools. An indexing utility is provided to facilitate the establishment of hyperlinks in external databases. A unique feature of the GeneLynx system is a communal curation system for user-aided annotation. GeneLynx can be accessed freely at http://www.genelynx.org.

Database Management Systems↗
PubMed1985

Database management in family medicine.

A computerized database will serve a practice well if physicians and staff make their expectations and needs explicit, establish clear database specifications, and use those specifications as the basis for selecting appropriate data management software and computer hardware. Any computerized database management system introduced into a practice should be thoroughly documented, and the process of implementing the system should be planned in advance. Finally, because a practice's information-related needs, expectations, and capabilities change over time, database usage should be reviewed and refined regularly.

Family Practice↗
PubMed1999

Perinatal information systems for quality improvement: visions for today.

Today clinical information is used for a multitude of purposes beyond patient care documentation including quality review and improvement processes, allocation of resources, budgetary and long-term planning, productivity measurement, and justification to payers for services provided. Providers in perinatal medicine are faced with the challenge of finding methods to meet these information needs. Case examples of the different approaches to collecting and using obstetric and neonatal information are described. The role of computer-based patient records is outlined and solutions available to perinatal medicine are reviewed.

Data Collection↗
PubMed2000

Application of neurobehavioral toxicology methods to the military deployment toxicology assessment program.

The military Tri-Service (Army, Navy & Marines, Air Force) Deployment Toxicology Assessment Program (DTAP) represents a 30-year (1996-2026) planning effort to implement comprehensive systems for the protection of internationally deployed troops against toxicant exposures. A major objective of DTAP is the implementation of a global surveillance system to identify chemicals with the potential to reduce human performance capacity. Implementation requires prior development of complex human risk assessment models, known collectively as the Neurobehavioral Toxicity Evaluation Instrument (NTEI), based on mathematical interpolation of results from tissue-based and in vivo animal studies validated by human performance assessment research. The Neurobehavioral Toxicity Assessment Group (NTAG) at the Naval Health Research Center Detachment-Toxicology (NHRC-TD), Dayton, OH, and associated academic institutions are developing and cross-validating cellular-level (NTAS), laboratory small animal (NTAB), nonhuman primate (GASP), and human-based (GASH) toxicity assessment batteries. These batteries will be utilized to develop and evaluate mathematical predictors of human neurobehavioral toxicity, as a function of laboratory performance deficits predicted by quantitative structural analysis relationship (QSAR-like) properties of potential toxicants identified by international surveillance systems. Finally, physiologically-based pharmacokinetic (PBPK) and pharmacodynamic (PBPD) modeling of NTAS, NTAB, GASP, GASH data will support multi-organizational development and validation of the NTEI. The validated NTEI tool will represent a complex database management system, integrating global satellite surveillance input to provide real-time decision-making support for deployed military personnel.

Animals↗
PubMed1993

A medical illustration information management system for the Apple Macintosh computer.

Collection and collation of statistical information is an ever-increasing requirement in the modern medical illustration department. Business planning and general management decisions are all based on such criteria. As the NHS 'market place' philosophy evolves, traditional manual systems of record-keeping are no longer adequate. This paper describes the 'in-house' development of a customized database using the Apple Macintosh computer, and outlines the reasons for this choice of system.

Computer Systems↗
PubMed2005

A Distributed Database and a New Application for the DRG System.

The article presents a new solution for the implementation of the DRG classifying system used in Romania to finance hospitals. The new solution implies two proposals. The first one refers to the use of a fragmented and distributed database at level of each hospital, and the second refers to the management and the viewing of this database by means of an on-line application implemented in Java. The solution proposes that the distributed database should be managed by two powerful tools, meaning Oracle8 Server and Net8. Different types of users are proposed, each type with his own rights for managing and viewing the database. Excepting local users who use only their local database, there are also global users from National DRG Bureau who can see data from all local databases, at any time. This solution is more efficient, secure and modern, than the one used now.

Computer Communication Networks↗
PubMed2005

Systems for the management of pharmacogenomic information.

Recent breakthroughs in biological research have been made possible by remarkable advances in high-performance computing and the establishment of a highly sophisticated information technology infrastructure. This chapter gives an overview of the main and most important technologies needed for the management of pharmacogenomic information, namely database management systems and software and hardware architectures. Because pharmacogenomics deals with a great many of public and/or proprietary data, the most prominent ways for easy storage, retrieval, analysis, and exchange are presented. Processing these data requires the use of sophisticated software architectures. Several most recent practices useful for a pharmacogenomic environment are explained. Multitiered application design and web services are discussed and described independent of the major enterprise development platforms. Because life sciences are becoming increasingly quantitative and because state-of-the-art software architectures use many system resources, this chapter presents the most recent and powerful systems for parallel data processing and data storage. Finally, shared and distributed memory systems and combinations of them as well as different storage architectures such as directly attached storage, network-attached storage, and storage-area network are explained in detail.

Animals↗