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Results for “Database Management Systems”

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At least 667 records · Page 37Linked to original sources

PubMed2004

Human-Mouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databases.

UNLABELLED: An open-access World Wide Web application has been developed which enables the cross-linking of anatomical data on the phenotypic manifestations of human and mouse malformation syndromes to data on gene function and/or expression patterns in the mouse GXD database. Ultimately, the system has been designed to assist biologists in the process of discovering hitherto unidentified malformation genes. More specifically, it facilitates search from the phenotypic level. AVAILABILITY: The application and further information is available at http://genetics.ich.ucl.ac.uk/linksearchtool.

Animals↗

PubMed2005

MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites.

The three-dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database. For each bound molecule the biological assembly of the quaternary structure has been used to determine all contact residues and a fast interactive search and retrieval system has been developed. Prosite pattern and short sequence search options are available together with a novel graphical query generator for inter-residue contacts. The database and its query interface are accessible from the Internet through a web server located at: http://www.ebi.ac.uk/msd-srv/msdsite.

Amino Acid Sequence↗

PubMed1991

GenBank.

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service.

Base Sequence↗

PubMed2003

Soap-HT-BLAST: high throughput BLAST based on Web services.

SUMMARY: A high throughput Basic Local Alignment Search Tool (BLAST) system based on Web services is implemented. It provides an alternative BLAST service and allows users to perform multiple BLAST queries at one run in a distributed, parallel environment through the Internet. AVAILABILITY: It is available at http://mammoth.bii.a-star.edu.sg/webservices/htblast/index.html and at http://www.bii.a-star.edu.sg/jiren/download.html

Amino Acid Sequence↗

PubMed1997

Clinical applications of an ATM/Ethernet network in departments of neuroradiology and radiotherapy.

An integrated system for the multimedia management of images and clinical information has been developed at the Isituto Nazionale Neurologico C. Besta in Milan. The Institute physicians have the daily need of consulting images coming from various modalities. The high volume of archived material and the need of retrieving and displaying new and past images and clinical information has motivated the development of a Picture Archiving and Communication System (PACS) for the automatic management of images and clinical data, related not only to the Radiology Department, but also to the Radiotherapy Department for 3D virtual simulation, to remote teleconsulting, and in the following to all the wards, ambulatories and labs.

Computer Communication Networks↗

PubMed1998

Modifiable templates facilitate customization of physician order entry.

Physician order entry is a key factor in improving the quality of healthcare, while simultaneously reducing its cost. This paper describes an editor, a database, and a run-time system for creating and executing highly customized, user modifiable, order entry templates. The system allows non-programmers to create new order entry templates rapidly. Over the past 18 months, the templates have been used on over 2500 patients to enter over 40,000 separate orders.

Database Management Systems↗

PubMed2006

[The development of database system of electrocardiographic information].

An ECG information database system was established with 1297 ECG information records and clinical informations. The data and the analysis software in this database can be shared with the international physiological signal databases such as MIT-BIH Arrhythmia. The establishment of this database will facilitate the clinical interpretation, diagnosis and prediction of cardiovascular diseases, especially the cardiac sudden death (SCD).

Artificial Intelligence↗

PubMed2000

Integration of a hematopoietic progenitor cell program using the ACT/DB database system.

Infusion of hematopoietic progenitor cells following high-dose chemotherapy is frequently used to treat patients with hematological malignancies and solid tumors. We have developed a comprehensive software system to monitor these patients once they are entered into an experimental protocol. The captured data encompasses all phases of progenitor cell therapy including progenitor cell mobilization and collection, stem cell processing, as well as cell infusion and engraftment kinetics. Particular attention was paid to the quality assurance and quality control functionality of the software during development of data entry forms and reports. The system was developed using the ACT/DB client-server database, which utilizes Microsoft Access as a front-end and accesses either an Oracle or SQL Server database. ACT/DB has been modified for deployment on the Internet in order to take advantage of Web-based technology. Information technology can help to integrate the diverse data requirements of complex therapeutic trials.

Database Management Systems↗

PubMed2005

Deriving an ontology for human gene expression sources from the CYTOMER database on human organs and cell types.

CYTOMER is a relational database of organs/tissues, cell types, physiological systems and developmental stages that currently focuses on the human system. From this database, we have derived an ontology for anatomical and morphological structures for the human organism which includes all embryonal stages and the cell types constituting these structures. The ontology has been transferred to the OWL format and is freely available for download at http://cytomer/bioinf.med.uni-goettingen.de.

Animals↗

PubMedDate not supplied

An image retrieval system based on fractal dimension.

This paper presents a new kind of image retrieval system which obtains the feature vectors of images by estimating their fractal dimension; and at the same time establishes a tree-structure image database. After preprocessing and feature extracting, a given image is matched with the standard images in the image database using a hierarchical method of image indexing.

Abstracting and Indexing↗

PubMed2002

Architectural decisions with respect to the introduction of PACS.

In this paper we report on a study on the possible scenarios for the introduction of PACS that was conducted at the LUMC in 2002 by a workgroup. The results of this study should facilitate the decision on PACS to be taken by the management of the LUMC at a later stage. In this paper our main research question is to what extent the decisions to be made at the introduction of PACS can be derived from an information system architecture in place, and vice versa: how can these decisions help to refine an information system architecture that is still immature.

Computer Systems↗

PubMed2005

The next generation of literature analysis: integration of genomic analysis into text mining.

Text-mining systems are indispensable tools to reduce the increasing flux of information in scientific literature to topics pertinent to a particular interest in focus. Most of the scientific literature is published as unstructured free text, complicating the development of data processing tools, which rely on structured information. To overcome the problems of free text analysis, structured, hand-curated information derived from literature is integrated in text-mining systems to improve precision and recall. In this paper several text-mining approaches are reviewed and the next step in development of text-mining systems, which is based on a concept of multiple lines of evidence, is described: results from literature analysis are combined with evidence from experiments and genome analysis to improve the accuracy of results and to generate additional knowledge beyond what is known solely from literature.

Abstracting and Indexing↗

PubMed1998

Toward a general model for the description of multimedia clinical data.

The patient folder integrates information originating from heterogeneous sources. For this reason computerized tools for patient data management should exploit the advantages of multimediality and offer an integrated environment for data presentation, and image and biosignal visualization. Object-oriented modeling is the best approach for designing systems for multimedia patient folder management. We propose an object-oriented model, able to define the entities constituting the patient folder and their logical organization. This model has sufficient flexibility to adapt to the most varied clinical environments. It allows the physician to structure the information needed for his/her patient folder without employing a programming language.

Computer Simulation↗

PubMed2002

A relational database for cryoEM: experience at one year and 50 000 images.

For the past year we have been using a relational database as part of an automated data collection system for cryoEM. The database is vital for keeping track of the very large number of images collected and analyzed by the automated system and essential for quantitatively evaluating the utility of methods and algorithms used in the data collection. The database can be accessed using a variety of tools including specially developed Web-based interfaces that enable a user to annotate and categorize images using a Web-based form.

Algorithms↗

PubMed2005

Browsing isolated population data.

BACKGROUND: In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80-85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships. To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies. RESULTS: The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects. AVAILABILITY: PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site http://www.shardna.com.

Algorithms↗

PubMed1999

'LABNOTE', a laboratory notebook system designed for academic genomics groups.

We have developed a relational laboratory database system, adapted to the daily book-keeping needs of laboratories that must keep track of information acquired on hundreds or thousands of clones in an effective and user-friendly fashion. Data, whether final or related to experiments in progress, can be accessed in many different ways, e.g. by clone name, by gene, by experiment or through DNA sequence. Updating, import and export of results is made easier by specially developed tools. This system, in network version, serves several groups in our Institute and (over the Internet) elsewhere, and is instrumental in collaborative studies based on expression profiling. It can be used in many similar situations involving progressiveaccumulation of information on sets of clones or related objects.

Database Management Systems↗

PubMed2006

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.

BACKGROUND: The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations. Local array data management solutions are instrumental for efficient processing of the results and for subsequent uploading of data and annotations to a global certified data repository at the EBI (ArrayExpress) or the NCBI (GeneOmnibus). DESCRIPTION: To facilitate and accelerate annotation of high-throughput expression profiling experiments, the Microarray Information Management and Annotation System (MIMAS) was developed. The system is fully compliant with the Minimal Information About a Microarray Experiment (MIAME) convention. MIMAS provides life scientists with a highly flexible and focused GeneChip data storage and annotation platform essential for subsequent analysis and interpretation of experimental results with clustering and mining tools. The system software can be downloaded for academic use upon request. CONCLUSION: MIMAS implements a novel concept for nation-wide GeneChip data management whereby a network of facilities is centered on one data node directly connected to the European certified public microarray data repository located at the EBI. The solution proposed may serve as a prototype approach to array data management between research institutes organized in a consortium.

Database Management Systems↗

PubMed2006

Purdue ionomics information management system. An integrated functional genomics platform.

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.

Arabidopsis↗