Interactive, Automated Management of Icing Data

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.

2009-01-01

IceVal DatAssistant is software (see figure) that provides an automated, interactive solution for the management of data from research on aircraft icing. This software consists primarily of (1) a relational database component used to store ice shape and airfoil coordinates and associated data on operational and environmental test conditions and (2) a graphically oriented database access utility, used to upload, download, process, and/or display data selected by the user. The relational database component consists of a Microsoft Access 2003 database file with nine tables containing data of different types. Included in the database are the data for all publicly releasable ice tracings with complete and verifiable test conditions from experiments conducted to date in the Glenn Research Center Icing Research Tunnel. Ice shapes from computational simulations with the correspond ing conditions performed utilizing the latest version of the LEWICE ice shape prediction code are likewise included, and are linked to the equivalent experimental runs. The database access component includes ten Microsoft Visual Basic 6.0 (VB) form modules and three VB support modules. Together, these modules enable uploading, downloading, processing, and display of all data contained in the database. This component also affords the capability to perform various database maintenance functions for example, compacting the database or creating a new, fully initialized but empty database file.

HEDS - EPA DATABASE SYSTEM FOR PUBLIC ACCESS TO HUMAN EXPOSURE DATA

EPA Science Inventory

Human Exposure Database System (HEDS) is an Internet-based system developed to provide public access to human-exposure-related data from studies conducted by EPA's National Exposure Research Laboratory (NERL). HEDS was designed to work with the EPA Office of Research and Devel...

ZeBase: an open-source relational database for zebrafish laboratories.

PubMed

Hensley, Monica R; Hassenplug, Eric; McPhail, Rodney; Leung, Yuk Fai

2012-03-01

Abstract ZeBase is an open-source relational database for zebrafish inventory. It is designed for the recording of genetic, breeding, and survival information of fish lines maintained in a single- or multi-laboratory environment. Users can easily access ZeBase through standard web-browsers anywhere on a network. Convenient search and reporting functions are available to facilitate routine inventory work; such functions can also be automated by simple scripting. Optional barcode generation and scanning are also built-in for easy access to the information related to any fish. Further information of the database and an example implementation can be found at http://zebase.bio.purdue.edu.

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

DynAstVO : a Europlanet database of NEA orbits

NASA Astrophysics Data System (ADS)

Desmars, J.; Thuillot, W.; Hestroffer, D.; David, P.; Le Sidaner, P.

2017-09-01

DynAstVO is a new orbital database developed within the Europlanet 2020 RI and the Virtual European Solar and Planetary Access (VESPA) frameworks. The database is dedicated to Near-Earth asteroids and provide parameters related to orbits: osculating elements, observational information, ephemeris through SPICE kernel, and in particular, orbit uncertainty and associated covariance matrix. DynAstVO is daily updated on a automatic process of orbit determination on the basis of the Minor Planet Electronic Circulars that reports new observations or the discover of a new asteroid. This database conforms to EPN-TAP environment and is accessible through VO protocols and on the VESPA portal web access (http://vespa.obspm.fr/). A comparison with other classical databases such as Astorb, MPCORB, NEODyS and JPL is also presented.

Using linked administrative and disease-specific databases to study end-of-life care on a population level.

PubMed

Maetens, Arno; De Schreye, Robrecht; Faes, Kristof; Houttekier, Dirk; Deliens, Luc; Gielen, Birgit; De Gendt, Cindy; Lusyne, Patrick; Annemans, Lieven; Cohen, Joachim

2016-10-18

The use of full-population databases is under-explored to study the use, quality and costs of end-of-life care. Using the case of Belgium, we explored: (1) which full-population databases provide valid information about end-of-life care, (2) what procedures are there to use these databases, and (3) what is needed to integrate separate databases. Technical and privacy-related aspects of linking and accessing Belgian administrative databases and disease registries were assessed in cooperation with the database administrators and privacy commission bodies. For all relevant databases, we followed procedures in cooperation with database administrators to link the databases and to access the data. We identified several databases as fitting for end-of-life care research in Belgium: the InterMutualistic Agency's national registry of health care claims data, the Belgian Cancer Registry including data on incidence of cancer, and databases administrated by Statistics Belgium including data from the death certificate database, the socio-economic survey and fiscal data. To obtain access to the data, approval was required from all database administrators, supervisory bodies and two separate national privacy bodies. Two Trusted Third Parties linked the databases via a deterministic matching procedure using multiple encrypted social security numbers. In this article we describe how various routinely collected population-level databases and disease registries can be accessed and linked to study patterns in the use, quality and costs of end-of-life care in the full population and in specific diagnostic groups.

Accessing the public MIMIC-II intensive care relational database for clinical research.

PubMed

Scott, Daniel J; Lee, Joon; Silva, Ikaro; Park, Shinhyuk; Moody, George B; Celi, Leo A; Mark, Roger G

2013-01-10

The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge "Predicting mortality of ICU Patients". QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database.

The Politics of Information: Building a Relational Database To Support Decision-Making at a Public University.

ERIC Educational Resources Information Center

Friedman, Debra; Hoffman, Phillip

2001-01-01

Describes creation of a relational database at the University of Washington supporting ongoing academic planning at several levels and affecting the culture of decision making. Addresses getting started; sharing the database; questions, worries, and issues; improving access to high-demand courses; the advising function; management of instructional…

Component, Context and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2013-03-01

Penn State team were stored in a relational database for easy access, storage and maintainability. The relational database consisted of a PostGres ...file into a format that can be imported into the PostGres database. This same custom application was used to generate Microsoft Excel templates...Press Break Forming Equipment 4.14 Manufacturing Model Library Database Structure The data storage mechanism for the ARL PSU MML was a PostGres database

Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

PubMed

Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio

2015-03-01

In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.

libChEBI: an API for accessing the ChEBI database.

PubMed

Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

2016-01-01

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

Combining computational models, semantic annotations and simulation experiments in a graph database

PubMed Central

Henkel, Ron; Wolkenhauer, Olaf; Waltemath, Dagmar

2015-01-01

Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models’ structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried. Database URL: https://sems.uni-rostock.de/projects/masymos/ PMID:25754863

FIREMON Database

Treesearch

John F. Caratti

2006-01-01

The FIREMON database software allows users to enter data, store, analyze, and summarize plot data, photos, and related documents. The FIREMON database software consists of a Java application and a Microsoft® Access database. The Java application provides the user interface with FIREMON data through data entry forms, data summary reports, and other data management tools...

Health care access and poverty do not explain the higher esophageal cancer mortality in African Americans.

PubMed

Miller, Jordan A G; Rege, Robert V; Ko, Clifford Y; Livingston, Edward H

2004-07-01

Esophageal cancer mortality is increased in African Americans relative to white patients. The reasons for this are unknown but are thought to be related to inadequate access to health care secondary to a higher poverty rate in African American populations. The National Health Interview Survey database for years 1986 to 1994 were combined and linked to the National Death Index. Individuals who died from esophageal carcinoma were assessed in the combined database, thus enabling detailed analysis of their socioeconomic status, race, and health care access. Poverty was 4-fold more frequent in African Americans who died from esophageal carcinoma than whites. Despite poverty, African American patients' access to health care was good and was not statistically related to increased mortality. Although the esophageal carcinoma mortality rate is higher in African Americans than in whites, it is not clearly related to the presence of poverty or to limited health care access. The higher mortality may be related to lifestyle differences, environmental exposure, or difference in disease biology, but it is not related exclusively to socioeconomic factors.

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

2002-01-01

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easymore » access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.« less

Smart Location Mapping

EPA Pesticide Factsheets

The Smart Location Database, Access to Jobs and Workers via Transit, and National Walkability Index tools can help assess indicators related to the built environment, transit accessibility, and walkability.

Accessing the public MIMIC-II intensive care relational database for clinical research

PubMed Central

2013-01-01

Background The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. Results QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge “Predicting mortality of ICU Patients”. Conclusions QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database. PMID:23302652

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

2015-01-01

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

Exploration of the Chemical Space of Public Genomic Databases

EPA Science Inventory

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information.

A searching and reporting system for relational databases using a graph-based metadata representation.

PubMed

Hewitt, Robin; Gobbi, Alberto; Lee, Man-Ling

2005-01-01

Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

A Database as a Service for the Healthcare System to Store Physiological Signal Data.

PubMed

Chang, Hsien-Tsung; Lin, Tsai-Huei

2016-01-01

Wearable devices that measure physiological signals to help develop self-health management habits have become increasingly popular in recent years. These records are conducive for follow-up health and medical care. In this study, based on the characteristics of the observed physiological signal records- 1) a large number of users, 2) a large amount of data, 3) low information variability, 4) data privacy authorization, and 5) data access by designated users-we wish to resolve physiological signal record-relevant issues utilizing the advantages of the Database as a Service (DaaS) model. Storing a large amount of data using file patterns can reduce database load, allowing users to access data efficiently; the privacy control settings allow users to store data securely. The results of the experiment show that the proposed system has better database access performance than a traditional relational database, with a small difference in database volume, thus proving that the proposed system can improve data storage performance.

A Database as a Service for the Healthcare System to Store Physiological Signal Data

PubMed Central

Lin, Tsai-Huei

2016-01-01

Wearable devices that measure physiological signals to help develop self-health management habits have become increasingly popular in recent years. These records are conducive for follow-up health and medical care. In this study, based on the characteristics of the observed physiological signal records– 1) a large number of users, 2) a large amount of data, 3) low information variability, 4) data privacy authorization, and 5) data access by designated users—we wish to resolve physiological signal record-relevant issues utilizing the advantages of the Database as a Service (DaaS) model. Storing a large amount of data using file patterns can reduce database load, allowing users to access data efficiently; the privacy control settings allow users to store data securely. The results of the experiment show that the proposed system has better database access performance than a traditional relational database, with a small difference in database volume, thus proving that the proposed system can improve data storage performance. PMID:28033415

Database constraints applied to metabolic pathway reconstruction tools.

PubMed

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Understanding the patient perspective on research access to national health records databases for conduct of randomized registry trials.

PubMed

Avram, Robert; Marquis-Gravel, Guillaume; Simard, François; Pacheco, Christine; Couture, Étienne; Tremblay-Gravel, Maxime; Desplantie, Olivier; Malhamé, Isabelle; Bibas, Lior; Mansour, Samer; Parent, Marie-Claude; Farand, Paul; Harvey, Luc; Lessard, Marie-Gabrielle; Ly, Hung; Liu, Geoffrey; Hay, Annette E; Marc Jolicoeur, E

2018-07-01

Use of health administrative databases is proposed for screening and monitoring of participants in randomized registry trials. However, access to these databases raises privacy concerns. We assessed patient's preferences regarding use of personal information to link their research records with national health databases, as part of a hypothetical randomized registry trial. Cardiology patients were invited to complete an anonymous self-reported survey that ascertained preferences related to the concept of accessing government health databases for research, the type of personal identifiers to be shared and the type of follow-up preferred as participants in a hypothetical trial. A total of 590 responders completed the survey (90% response rate), the majority of which were Caucasians (90.4%), male (70.0%) with a median age of 65years (interquartile range, 8). The majority responders (80.3%) would grant researchers access to health administrative databases for screening and follow-up. To this end, responders endorsed the recording of their personal identifiers by researchers for future record linkage, including their name (90%), and health insurance number (83.9%), but fewer responders agreed with the recording of their social security number (61.4%, p<0.05 with date of birth as reference). Prior participation in a trial predicted agreement for granting researchers access to the administrative databases (OR: 1.69, 95% confidence interval: 1.03-2.90; p=0.04). The majority of Cardiology patients surveyed were supportive of use of their personal identifiers to access administrative health databases and conduct long-term monitoring in the context of a randomized registry trial. Copyright © 2018 Elsevier Ireland Ltd. All rights reserved.

An object-oriented approach to the management of meteorological and hydrological data

NASA Technical Reports Server (NTRS)

Graves, S. J.; Williams, S. F.; Criswell, E. A.

1990-01-01

An interface to several meteorological and hydrological databases have been developed that enables researchers efficiently to access and interrelate data through a customized menu system. By extending a relational database system with object-oriented concepts, each user or group of users may have different 'views' of the data to allow user access to data in customized ways without altering the organization of the database. An application to COHMEX and WetNet, two earth science projects within NASA Marshall Space Flight Center's Earth Science and Applications Division, are described.

ReprDB and panDB: minimalist databases with maximal microbial representation.

PubMed

Zhou, Wei; Gay, Nicole; Oh, Julia

2018-01-18

Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.

MIPS: a database for protein sequences, homology data and yeast genome information.

PubMed Central

Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

1997-01-01

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

Improved Information Retrieval Performance on SQL Database Using Data Adapter

NASA Astrophysics Data System (ADS)

Husni, M.; Djanali, S.; Ciptaningtyas, H. T.; Wicaksana, I. G. N. A.

2018-02-01

The NoSQL databases, short for Not Only SQL, are increasingly being used as the number of big data applications increases. Most systems still use relational databases (RDBs), but as the number of data increases each year, the system handles big data with NoSQL databases to analyze and access data more quickly. NoSQL emerged as a result of the exponential growth of the internet and the development of web applications. The query syntax in the NoSQL database differs from the SQL database, therefore requiring code changes in the application. Data adapter allow applications to not change their SQL query syntax. Data adapters provide methods that can synchronize SQL databases with NotSQL databases. In addition, the data adapter provides an interface which is application can access to run SQL queries. Hence, this research applied data adapter system to synchronize data between MySQL database and Apache HBase using direct access query approach, where system allows application to accept query while synchronization process in progress. From the test performed using data adapter, the results obtained that the data adapter can synchronize between SQL databases, MySQL, and NoSQL database, Apache HBase. This system spends the percentage of memory resources in the range of 40% to 60%, and the percentage of processor moving from 10% to 90%. In addition, from this system also obtained the performance of database NoSQL better than SQL database.

CottonGen: a genomics, genetics and breeding database for cotton research

USDA-ARS?s Scientific Manuscript database

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

ERIC Educational Resources Information Center

Angier, Jennifer J.; Epstein, Barbara A.

1980-01-01

Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

A VBA Desktop Database for Proposal Processing at National Optical Astronomy Observatories

NASA Astrophysics Data System (ADS)

Brown, Christa L.

National Optical Astronomy Observatories (NOAO) has developed a relational Microsoft Windows desktop database using Microsoft Access and the Microsoft Office programming language, Visual Basic for Applications (VBA). The database is used to track data relating to observing proposals from original receipt through the review process, scheduling, observing, and final statistical reporting. The database has automated proposal processing and distribution of information. It allows NOAO to collect and archive data so as to query and analyze information about our science programs in new ways.

Actinobase: Database on molecular diversity, phylogeny and biocatalytic potential of salt tolerant alkaliphilic actinomycetes.

PubMed

Sharma, Amit K; Gohel, Sangeeta; Singh, Satya P

2012-01-01

Actinobase is a relational database of molecular diversity, phylogeny and biocatalytic potential of haloalkaliphilic actinomycetes. The main objective of this data base is to provide easy access to range of information, data storage, comparison and analysis apart from reduced data redundancy, data entry, storage, retrieval costs and improve data security. Information related to habitat, cell morphology, Gram reaction, biochemical characterization and molecular features would allow researchers in understanding identification and stress adaptation of the existing and new candidates belonging to salt tolerant alkaliphilic actinomycetes. The PHP front end helps to add nucleotides and protein sequence of reported entries which directly help researchers to obtain the required details. Analysis of the genus wise status of the salt tolerant alkaliphilic actinomycetes indicated 6 different genera among the 40 classified entries of the salt tolerant alkaliphilic actinomycetes. The results represented wide spread occurrence of salt tolerant alkaliphilic actinomycetes belonging to diverse taxonomic positions. Entries and information related to actinomycetes in the database are publicly accessible at http://www.actinobase.in. On clustalW/X multiple sequence alignment of the alkaline protease gene sequences, different clusters emerged among the groups. The narrow search and limit options of the constructed database provided comparable information. The user friendly access to PHP front end facilitates would facilitate addition of sequences of reported entries. The database is available for free at http://www.actinobase.in.

Artificial intelligence techniques for modeling database user behavior

NASA Technical Reports Server (NTRS)

Tanner, Steve; Graves, Sara J.

1990-01-01

The design and development of the adaptive modeling system is described. This system models how a user accesses a relational database management system in order to improve its performance by discovering use access patterns. In the current system, these patterns are used to improve the user interface and may be used to speed data retrieval, support query optimization and support a more flexible data representation. The system models both syntactic and semantic information about the user's access and employs both procedural and rule-based logic to manipulate the model.

Relational Database for the Geology of the Northern Rocky Mountains - Idaho, Montana, and Washington

USGS Publications Warehouse

Causey, J. Douglas; Zientek, Michael L.; Bookstrom, Arthur A.; Frost, Thomas P.; Evans, Karl V.; Wilson, Anna B.; Van Gosen, Bradley S.; Boleneus, David E.; Pitts, Rebecca A.

2008-01-01

A relational database was created to prepare and organize geologic map-unit and lithologic descriptions for input into a spatial database for the geology of the northern Rocky Mountains, a compilation of forty-three geologic maps for parts of Idaho, Montana, and Washington in U.S. Geological Survey Open File Report 2005-1235. Not all of the information was transferred to and incorporated in the spatial database due to physical file limitations. This report releases that part of the relational database that was completed for that earlier product. In addition to descriptive geologic information for the northern Rocky Mountains region, the relational database contains a substantial bibliography of geologic literature for the area. The relational database nrgeo.mdb (linked below) is available in Microsoft Access version 2000, a proprietary database program. The relational database contains data tables and other tables used to define terms, relationships between the data tables, and hierarchical relationships in the data; forms used to enter data; and queries used to extract data.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov PMID:18073190

Clinician-Oriented Access to Data - C.O.A.D.: A Natural Language Interface to a VA DHCP Database

PubMed Central

Levy, Christine; Rogers, Elizabeth

1995-01-01

Hospitals collect enormous amounts of data related to the on-going care of patients. Unfortunately, a clinicians access to the data is limited by complexities of the database structure and/or programming skills required to access the database. The COAD project attempts to bridge the gap between the clinical user's need for specific information from the database, and the wealth of data residing in the hospital information system. The project design includes a natural language interface to data contained in a VA DHCP database. We have developed a prototype which links natural language software to certain DHCP data elements, including, patient demographics, prescriptions, diagnoses, laboratory data, and provider information. English queries can by typed onto the system, and answers to the questions are returned. Future work includes refinement of natural language/DHCP connections to enable more sophisticated queries, and optimization of the system to reduce response time to user questions.

Mashup of Geo and Space Science Data Provided via Relational Databases in the Semantic Web

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, J. S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2014-12-01

The use of RDBMS for the storage and management of geo and space science data and/or metadata is very common. Although the information stored in tables is based on a data model and therefore well organized and structured, a direct mashup with RDF based data stored in triple stores is not possible. One solution of the problem consists in the transformation of the whole content into RDF structures and storage in triple stores. Another interesting way is the use of a specific system/service, such as e.g. D2RQ, for the access to relational database content as virtual, read only RDF graphs. The Semantic Web based -proof of concept- GFZ ISDC uses the triple store Virtuoso for the storage of general context information/metadata to geo and space science satellite and ground station data. There is information about projects, platforms, instruments, persons, product types, etc. available but no detailed metadata about the data granuals itself. Such important information, as e.g. start or end time or the detailed spatial coverage of a single measurement is stored in RDBMS tables of the ISDC catalog system only. In order to provide a seamless access to all available information about the granuals/data products a mashup of the different data resources (triple store and RDBMS) is necessary. This paper describes the use of D2RQ for a Semantic Web/SPARQL based mashup of relational databases used for ISDC data server but also for the access to IUGONET and/or ESPAS and further geo and space science data resources. RDBMS Relational Database Management System RDF Resource Description Framework SPARQL SPARQL Protocol And RDF Query Language D2RQ Accessing Relational Databases as Virtual RDF Graphs GFZ ISDC German Research Centre for Geosciences Information System and Data Center IUGONET Inter-university Upper Atmosphere Global Observation Network (Japanese project) ESPAS Near earth space data infrastructure for e-science (European Union funded project)

Performance assessment of EMR systems based on post-relational database.

PubMed

Yu, Hai-Yan; Li, Jing-Song; Zhang, Xiao-Guang; Tian, Yu; Suzuki, Muneou; Araki, Kenji

2012-08-01

Post-relational databases provide high performance and are currently widely used in American hospitals. As few hospital information systems (HIS) in either China or Japan are based on post-relational databases, here we introduce a new-generation electronic medical records (EMR) system called Hygeia, which was developed with the post-relational database Caché and the latest platform Ensemble. Utilizing the benefits of a post-relational database, Hygeia is equipped with an "integration" feature that allows all the system users to access data-with a fast response time-anywhere and at anytime. Performance tests of databases in EMR systems were implemented in both China and Japan. First, a comparison test was conducted between a post-relational database, Caché, and a relational database, Oracle, embedded in the EMR systems of a medium-sized first-class hospital in China. Second, a user terminal test was done on the EMR system Izanami, which is based on the identical database Caché and operates efficiently at the Miyazaki University Hospital in Japan. The results proved that the post-relational database Caché works faster than the relational database Oracle and showed perfect performance in the real-time EMR system.

Breach Risk Magnitude: A Quantitative Measure of Database Security.

PubMed

Yasnoff, William A

2016-01-01

A quantitative methodology is described that provides objective evaluation of the potential for health record system breaches. It assumes that breach risk increases with the number of potential records that could be exposed, while it decreases when more authentication steps are required for access. The breach risk magnitude (BRM) is the maximum value for any system user of the common logarithm of the number of accessible database records divided by the number of authentication steps needed to achieve such access. For a one million record relational database, the BRM varies from 5.52 to 6 depending on authentication protocols. For an alternative data architecture designed specifically to increase security by separately storing and encrypting each patient record, the BRM ranges from 1.3 to 2.6. While the BRM only provides a limited quantitative assessment of breach risk, it may be useful to objectively evaluate the security implications of alternative database organization approaches.

Karst database development in Minnesota: Design and data assembly

USGS Publications Warehouse

Gao, Y.; Alexander, E.C.; Tipping, R.G.

2005-01-01

The Karst Feature Database (KFD) of Minnesota is a relational GIS-based Database Management System (DBMS). Previous karst feature datasets used inconsistent attributes to describe karst features in different areas of Minnesota. Existing metadata were modified and standardized to represent a comprehensive metadata for all the karst features in Minnesota. Microsoft Access 2000 and ArcView 3.2 were used to develop this working database. Existing county and sub-county karst feature datasets have been assembled into the KFD, which is capable of visualizing and analyzing the entire data set. By November 17 2002, 11,682 karst features were stored in the KFD of Minnesota. Data tables are stored in a Microsoft Access 2000 DBMS and linked to corresponding ArcView applications. The current KFD of Minnesota has been moved from a Windows NT server to a Windows 2000 Citrix server accessible to researchers and planners through networked interfaces. ?? Springer-Verlag 2005.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (). PMID:17202161

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

PubMed Central

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

A review of accessibility of administrative healthcare databases in the Asia-Pacific region.

PubMed

Milea, Dominique; Azmi, Soraya; Reginald, Praveen; Verpillat, Patrice; Francois, Clement

2015-01-01

We describe and compare the availability and accessibility of administrative healthcare databases (AHDB) in several Asia-Pacific countries: Australia, Japan, South Korea, Taiwan, Singapore, China, Thailand, and Malaysia. The study included hospital records, reimbursement databases, prescription databases, and data linkages. Databases were first identified through PubMed, Google Scholar, and the ISPOR database register. Database custodians were contacted. Six criteria were used to assess the databases and provided the basis for a tool to categorise databases into seven levels ranging from least accessible (Level 1) to most accessible (Level 7). We also categorised overall data accessibility for each country as high, medium, or low based on accessibility of databases as well as the number of academic articles published using the databases. Fifty-four administrative databases were identified. Only a limited number of databases allowed access to raw data and were at Level 7 [Medical Data Vision EBM Provider, Japan Medical Data Centre (JMDC) Claims database and Nihon-Chouzai Pharmacy Claims database in Japan, and Medicare, Pharmaceutical Benefits Scheme (PBS), Centre for Health Record Linkage (CHeReL), HealthLinQ, Victorian Data Linkages (VDL), SA-NT DataLink in Australia]. At Levels 3-6 were several databases from Japan [Hamamatsu Medical University Database, Medi-Trend, Nihon University School of Medicine Clinical Data Warehouse (NUSM)], Australia [Western Australia Data Linkage (WADL)], Taiwan [National Health Insurance Research Database (NHIRD)], South Korea [Health Insurance Review and Assessment Service (HIRA)], and Malaysia [United Nations University (UNU)-Casemix]. Countries were categorised as having a high level of data accessibility (Australia, Taiwan, and Japan), medium level of accessibility (South Korea), or a low level of accessibility (Thailand, China, Malaysia, and Singapore). In some countries, data may be available but accessibility was restricted based on requirements by data custodians. Compared with previous research, this study describes the landscape of databases in the selected countries with more granularity using an assessment tool developed for this purpose. A high number of databases were identified but most had restricted access, preventing their potential use to support research. We hope that this study helps to improve the understanding of the AHDB landscape, increase data sharing and database research in Asia-Pacific countries.

How Many People Search the ERIC Database Each Day?

ERIC Educational Resources Information Center

Rudner, Lawrence

This study estimated the number of people searching the ERIC database each day. The Educational Resources Information Center (ERIC) is a national information system designed to provide ready access to an extensive body of education-related literature. Federal funds traditionally have paid for the development of the database, but not the…

GrainGenes: Changing Times, Changing Databases, Digital Evolution.

USDA-ARS?s Scientific Manuscript database

The GrainGenes database is one of few agricultural databases that had an early start on the Internet and that has changed with the times. Initial goals were to collect a wide range of data relating to the developing maps and attributes of small grains crops, and to make them easily accessible. The ...

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.

PubMed

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L; Sherman, Westley A; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-06-15

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.

Mandatory and Location-Aware Access Control for Relational Databases

NASA Astrophysics Data System (ADS)

Decker, Michael

Access control is concerned with determining which operations a particular user is allowed to perform on a particular electronic resource. For example, an access control decision could say that user Alice is allowed to perform the operation read (but not write) on the resource research report. With conventional access control this decision is based on the user's identity whereas the basic idea of Location-Aware Access Control (LAAC) is to evaluate also a user's current location when making the decision if a particular request should be granted or denied. LAAC is an interesting approach for mobile information systems because these systems are exposed to specific security threads like the loss of a device. Some data models for LAAC can be found in literature, but almost all of them are based on RBAC and none of them is designed especially for Database Management Systems (DBMS). In this paper we therefore propose a LAAC-approach for DMBS and describe a prototypical implementation of that approach that is based on database triggers.

Reflective Database Access Control

ERIC Educational Resources Information Center

Olson, Lars E.

2009-01-01

"Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

The Computer Catalog: A Democratic or Authoritarian Technology?

ERIC Educational Resources Information Center

Adams, Judith A.

1988-01-01

Discussion of consequences of library automation argues that technology should be used to augment access to information. Online public access catalogs are considered in this context, along with several related issues such as system incompatibility, invasion of privacy, barriers to database access and manipulation, and user fees, which contribute…

The NASA ADS Abstract Service and the Distributed Astronomy Digital Library [and] Project Soup: Comparing Evaluations of Digital Collection Efforts [and] Cross-Organizational Access Management: A Digital Library Authentication and Authorization Architecture [and] BibRelEx: Exploring Bibliographic Databases by Visualization of Annotated Content-based Relations [and] Semantics-Sensitive Retrieval for Digital Picture Libraries [and] Encoded Archival Description: An Introduction and Overview.

ERIC Educational Resources Information Center

Kurtz, Michael J.; Eichorn, Guenther; Accomazzi, Alberto; Grant, Carolyn S.; Demleitner, Markus; Murray, Stephen S.; Jones, Michael L. W.; Gay, Geri K.; Rieger, Robert H.; Millman, David; Bruggemann-Klein, Anne; Klein, Rolf; Landgraf, Britta; Wang, James Ze; Li, Jia; Chan, Desmond; Wiederhold, Gio; Pitti, Daniel V.

1999-01-01

Includes six articles that discuss a digital library for astronomy; comparing evaluations of digital collection efforts; cross-organizational access management of Web-based resources; searching scientific bibliographic databases based on content-based relations between documents; semantics-sensitive retrieval for digital picture libraries; and…

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1992-01-01

One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

Sequential data access with Oracle and Hadoop: a performance comparison

NASA Astrophysics Data System (ADS)

Baranowski, Zbigniew; Canali, Luca; Grancher, Eric

2014-06-01

The Hadoop framework has proven to be an effective and popular approach for dealing with "Big Data" and, thanks to its scaling ability and optimised storage access, Hadoop Distributed File System-based projects such as MapReduce or HBase are seen as candidates to replace traditional relational database management systems whenever scalable speed of data processing is a priority. But do these projects deliver in practice? Does migrating to Hadoop's "shared nothing" architecture really improve data access throughput? And, if so, at what cost? Authors answer these questions-addressing cost/performance as well as raw performance- based on a performance comparison between an Oracle-based relational database and Hadoop's distributed solutions like MapReduce or HBase for sequential data access. A key feature of our approach is the use of an unbiased data model as certain data models can significantly favour one of the technologies tested.

CORAL Server and CORAL Server Proxy: Scalable Access to Relational Databases from CORAL Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valassi, A.; /CERN; Bartoldus, R.

The CORAL software is widely used at CERN by the LHC experiments to access the data they store on relational databases, such as Oracle. Two new components have recently been added to implement a model involving a middle tier 'CORAL server' deployed close to the database and a tree of 'CORAL server proxies', providing data caching and multiplexing, deployed close to the client. A first implementation of the two new components, released in the summer 2009, is now deployed in the ATLAS online system to read the data needed by the High Level Trigger, allowing the configuration of a farmmore » of several thousand processes. This paper reviews the architecture of the software, its development status and its usage in ATLAS.« less

A review of accessibility of administrative healthcare databases in the Asia-Pacific region

PubMed Central

Milea, Dominique; Azmi, Soraya; Reginald, Praveen; Verpillat, Patrice; Francois, Clement

2015-01-01

Objective We describe and compare the availability and accessibility of administrative healthcare databases (AHDB) in several Asia-Pacific countries: Australia, Japan, South Korea, Taiwan, Singapore, China, Thailand, and Malaysia. Methods The study included hospital records, reimbursement databases, prescription databases, and data linkages. Databases were first identified through PubMed, Google Scholar, and the ISPOR database register. Database custodians were contacted. Six criteria were used to assess the databases and provided the basis for a tool to categorise databases into seven levels ranging from least accessible (Level 1) to most accessible (Level 7). We also categorised overall data accessibility for each country as high, medium, or low based on accessibility of databases as well as the number of academic articles published using the databases. Results Fifty-four administrative databases were identified. Only a limited number of databases allowed access to raw data and were at Level 7 [Medical Data Vision EBM Provider, Japan Medical Data Centre (JMDC) Claims database and Nihon-Chouzai Pharmacy Claims database in Japan, and Medicare, Pharmaceutical Benefits Scheme (PBS), Centre for Health Record Linkage (CHeReL), HealthLinQ, Victorian Data Linkages (VDL), SA-NT DataLink in Australia]. At Levels 3–6 were several databases from Japan [Hamamatsu Medical University Database, Medi-Trend, Nihon University School of Medicine Clinical Data Warehouse (NUSM)], Australia [Western Australia Data Linkage (WADL)], Taiwan [National Health Insurance Research Database (NHIRD)], South Korea [Health Insurance Review and Assessment Service (HIRA)], and Malaysia [United Nations University (UNU)-Casemix]. Countries were categorised as having a high level of data accessibility (Australia, Taiwan, and Japan), medium level of accessibility (South Korea), or a low level of accessibility (Thailand, China, Malaysia, and Singapore). In some countries, data may be available but accessibility was restricted based on requirements by data custodians. Conclusions Compared with previous research, this study describes the landscape of databases in the selected countries with more granularity using an assessment tool developed for this purpose. A high number of databases were identified but most had restricted access, preventing their potential use to support research. We hope that this study helps to improve the understanding of the AHDB landscape, increase data sharing and database research in Asia-Pacific countries. PMID:27123180

An Efficient Method for the Retrieval of Objects by Topological Relations in Spatial Database Systems.

ERIC Educational Resources Information Center

Lin, P. L.; Tan, W. H.

2003-01-01

Presents a new method to improve the performance of query processing in a spatial database. Experiments demonstrated that performance of database systems can be improved because both the number of objects accessed and number of objects requiring detailed inspection are much less than those in the previous approach. (AEF)

MIPS: a database for protein sequences and complete genomes.

PubMed Central

Mewes, H W; Hani, J; Pfeiffer, F; Frishman, D

1998-01-01

The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled. PMID:9399795

Advanced Techniques for Deploying Reliable and Efficient Access Control: Application to E-healthcare.

PubMed

Jaïdi, Faouzi; Labbene-Ayachi, Faten; Bouhoula, Adel

2016-12-01

Nowadays, e-healthcare is a main advancement and upcoming technology in healthcare industry that contributes to setting up automated and efficient healthcare infrastructures. Unfortunately, several security aspects remain as main challenges towards secure and privacy-preserving e-healthcare systems. From the access control perspective, e-healthcare systems face several issues due to the necessity of defining (at the same time) rigorous and flexible access control solutions. This delicate and irregular balance between flexibility and robustness has an immediate impact on the compliance of the deployed access control policy. To address this issue, the paper defines a general framework to organize thinking about verifying, validating and monitoring the compliance of access control policies in the context of e-healthcare databases. We study the problem of the conformity of low level policies within relational databases and we particularly focus on the case of a medical-records management database defined in the context of a Medical Information System. We propose an advanced solution for deploying reliable and efficient access control policies. Our solution extends the traditional lifecycle of an access control policy and allows mainly managing the compliance of the policy. We refer to an example to illustrate the relevance of our proposal.

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1993-01-01

One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image datasets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate database search.

Using the Proteomics Identifications Database (PRIDE).

PubMed

Martens, Lennart; Jones, Phil; Côté, Richard

2008-03-01

The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer-reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE.

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

Starbase Data Tables: An ASCII Relational Database for Unix

NASA Astrophysics Data System (ADS)

Roll, John

2011-11-01

Database management is an increasingly important part of astronomical data analysis. Astronomers need easy and convenient ways of storing, editing, filtering, and retrieving data about data. Commercial databases do not provide good solutions for many of the everyday and informal types of database access astronomers need. The Starbase database system with simple data file formatting rules and command line data operators has been created to answer this need. The system includes a complete set of relational and set operators, fast search/index and sorting operators, and many formatting and I/O operators. Special features are included to enhance the usefulness of the database when manipulating astronomical data. The software runs under UNIX, MSDOS and IRAF.

The comparative effectiveness of conventional and digital image libraries.

PubMed

McColl, R I; Johnson, A

2001-03-01

Before introducing a hospital-wide image database to improve access, navigation and retrieval speed, a comparative study between a conventional slide library and a matching image database was undertaken to assess its relative benefits. Paired time trials and personal questionnaires revealed faster retrieval rates, higher image quality, and easier viewing for the pilot digital image database. Analysis of confidentiality, copyright and data protection exposed similar issues for both systems, thus concluding that the digital image database is a more effective library system. The authors suggest that in the future, medical images will be stored on large, professionally administered, centrally located file servers, allowing specialist image libraries to be tailored locally for individual users. The further integration of the database with web technology will enable cheap and efficient remote access for a wide range of users.

Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server.

PubMed

Vohradsky, Jiri; Janda, Ivan; Grünenfelder, Björn; Berndt, Peter; Röder, Daniel; Langen, Hanno; Weiser, Jaroslav; Jenal, Urs

2003-10-01

Here we present the Swiss-Czech Proteomics Server (SWICZ), which hosts the proteomic database summarizing information about the cell cycle of the aquatic bacterium Caulobacter crescentus. The database provides a searchable tool for easy access of global protein synthesis and protein stability data as examined during the C. crescentus cell cycle. Protein synthesis data collected from five different cell cycle stages were determined for each protein spot as a relative value of the total amount of [(35)S]methionine incorporation. Protein stability of pulse-labeled extracts were measured during a chase period equivalent to one cell cycle unit. Quantitative information for individual proteins together with descriptive data such as protein identities, apparent molecular masses and isoelectric points, were combined with information on protein function, genomic context, and the cell cycle stage, and were then assembled in a relational database with a world wide web interface (http://proteom.biomed.cas.cz), which allows the database records to be searched and displays the recovered information. A total of 1250 protein spots were reproducibly detected on two-dimensional gel electropherograms, 295 of which were identified by mass spectroscopy. The database is accessible either through clickable two-dimensional gel electrophoretic maps or by means of a set of dedicated search engines. Basic characterization of the experimental procedures, data processing, and a comprehensive description of the web site are presented. In its current state, the SWICZ proteome database provides a platform for the incorporation of new data emerging from extended functional studies on the C. crescentus proteome.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Epistemonikos: a free, relational, collaborative, multilingual database of health evidence.

PubMed

Rada, Gabriel; Pérez, Daniel; Capurro, Daniel

2013-01-01

Epistemonikos (www.epistemonikos.org) is a free, multilingual database of the best available health evidence. This paper describes the design, development and implementation of the Epistemonikos project. Using several web technologies to store systematic reviews, their included articles, overviews of reviews and structured summaries, Epistemonikos is able to provide a simple and powerful search tool to access health evidence for sound decision making. Currently, Epistemonikos stores more than 115,000 unique documents and more than 100,000 relationships between documents. In addition, since its database is translated into 9 different languages, Epistemonikos ensures that non-English speaking decision-makers can access the best available evidence without language barriers.

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2010-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2009-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

A public HTLV-1 molecular epidemiology database for sequence management and data mining.

PubMed

Araujo, Thessika Hialla Almeida; Souza-Brito, Leandro Inacio; Libin, Pieter; Deforche, Koen; Edwards, Dustin; de Albuquerque-Junior, Antonio Eduardo; Vandamme, Anne-Mieke; Galvao-Castro, Bernardo; Alcantara, Luiz Carlos Junior

2012-01-01

It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/. All data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient. The HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.

DRUMS: a human disease related unique gene mutation search engine.

PubMed

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

Utilizing LIDAR data to analyze access management criteria in Utah.

DOT National Transportation Integrated Search

2017-05-01

The primary objective of this research was to increase understanding of the safety impacts across the state related to access management. This was accomplished by using the Light Detection and Ranging (LiDAR) database to evaluate driveway spacing and...

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

Distributed Access View Integrated Database (DAVID) system

NASA Technical Reports Server (NTRS)

Jacobs, Barry E.

1991-01-01

The Distributed Access View Integrated Database (DAVID) System, which was adopted by the Astrophysics Division for their Astrophysics Data System, is a solution to the system heterogeneity problem. The heterogeneous components of the Astrophysics problem is outlined. The Library and Library Consortium levels of the DAVID approach are described. The 'books' and 'kits' level is discussed. The Universal Object Typer Management System level is described. The relation of the DAVID project with the Small Business Innovative Research (SBIR) program is explained.

Simple re-instantiation of small databases using cloud computing.

PubMed

Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M

2013-01-01

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. PMID:24564380

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (www.ncbi.nlm.nih.gov).

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2005-01-01

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2006-01-01

GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

PubMed

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Fine-grained policy control in U.S. Army Research Laboratory (ARL) multimodal signatures database

NASA Astrophysics Data System (ADS)

Bennett, Kelly; Grueneberg, Keith; Wood, David; Calo, Seraphin

2014-06-01

The U.S. Army Research Laboratory (ARL) Multimodal Signatures Database (MMSDB) consists of a number of colocated relational databases representing a collection of data from various sensors. Role-based access to this data is granted to external organizations such as DoD contractors and other government agencies through a client Web portal. In the current MMSDB system, access control is only at the database and firewall level. In order to offer finer grained security, changes to existing user profile schemas and authentication mechanisms are usually needed. In this paper, we describe a software middleware architecture and implementation that allows fine-grained access control to the MMSDB at a dataset, table, and row level. Result sets from MMSDB queries issued in the client portal are filtered with the use of a policy enforcement proxy, with minimal changes to the existing client software and database. Before resulting data is returned to the client, policies are evaluated to determine if the user or role is authorized to access the data. Policies can be authored to filter data at the row, table or column level of a result set. The system uses various technologies developed in the International Technology Alliance in Network and Information Science (ITA) for policy-controlled information sharing and dissemination1. Use of the Policy Management Library provides a mechanism for the management and evaluation of policies to support finer grained access to the data in the MMSDB system. The GaianDB is a policy-enabled, federated database that acts as a proxy between the client application and the MMSDB system.

THE NATIONAL EXPOSURE RESEARCH LABORATORY'S CONSOLIDATED HUMAN ACTIVITY DATABASE

EPA Science Inventory

EPA's National Exposure Research Laboratory (NERL) has combined data from 12 U.S. studies related to human activities into one comprehensive data system that can be accessed via the Internet. The data system is called the Consolidated Human Activity Database (CHAD), and it is ...

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Transition Documentation on a Three-Element High-Lift Configuration at High Reynolds Numbers--Database. [conducted in the Langley Low Turbulence Pressure Tunnel

NASA Technical Reports Server (NTRS)

Bertelrud, Arild; Johnson, Sherylene; Anders, J. B. (Technical Monitor)

2002-01-01

A 2-D (two dimensional) high-lift system experiment was conducted in August of 1996 in the Low Turbulence Pressure Tunnel at NASA Langley Research Center, Hampton, VA. The purpose of the experiment was to obtain transition measurements on a three element high-lift system for CFD (computational fluid dynamics) code validation studies. A transition database has been created using the data from this experiment. The present report details how the hot-film data and the related pressure data are organized in the database. Data processing codes to access the data in an efficient and reliable manner are described and limited examples are given on how to access the database and store acquired information.

Information resources at the National Center for Biotechnology Information.

PubMed Central

Woodsmall, R M; Benson, D A

1993-01-01

The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, was established in 1988 to perform basic research in the field of computational molecular biology as well as build and distribute molecular biology databases. The basic research has led to new algorithms and analysis tools for interpreting genomic data and has been instrumental in the discovery of human disease genes for neurofibromatosis and Kallmann syndrome. The principal database responsibility is the National Institutes of Health (NIH) genetic sequence database, GenBank. NCBI, in collaboration with international partners, builds, distributes, and provides online and CD-ROM access to over 112,000 DNA sequences. Another major program is the integration of multiple sequences databases and related bibliographic information and the development of network-based retrieval systems for Internet access. PMID:8374583

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

PubMed

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

THE NATIONAL EXPOSURE RESEARCH LABORATORY'S COMPREHENSIVE HUMAN ACTIVITY DATABASE

EPA Science Inventory

EPA's National Exposure Research Laboratory (NERL) has combined data from nine U.S. studies related to human activities into one comprehensive data system that can be accessed via the world-wide web. The data system is called CHAD-Consolidated Human Activity Database-and it is ...

The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

PubMed

Waugh, M; Hraber, P; Weller, J; Wu, Y; Chen, G; Inman, J; Kiphart, D; Sobral, B

2000-01-01

The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

PubMed

Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

2017-01-01

Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Community Data Model for Hydrologic Observations

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Zaslavsky, I.; Maidment, D. R.; Valentine, D.; Jennings, B.

2006-12-01

The CUAHSI Hydrologic Information System project is developing information technology infrastructure to support hydrologic science. Hydrologic information science involves the description of hydrologic environments in a consistent way, using data models for information integration. This includes a hydrologic observations data model for the storage and retrieval of hydrologic observations in a relational database designed to facilitate data retrieval for integrated analysis of information collected by multiple investigators. It is intended to provide a standard format to facilitate the effective sharing of information between investigators and to facilitate analysis of information within a single study area or hydrologic observatory, or across hydrologic observatories and regions. The observations data model is designed to store hydrologic observations and sufficient ancillary information (metadata) about the observations to allow them to be unambiguously interpreted and used and provide traceable heritage from raw measurements to usable information. The design is based on the premise that a relational database at the single observation level is most effective for providing querying capability and cross dimension data retrieval and analysis. This premise is being tested through the implementation of a prototype hydrologic observations database, and the development of web services for the retrieval of data from and ingestion of data into the database. These web services hosted by the San Diego Supercomputer center make data in the database accessible both through a Hydrologic Data Access System portal and directly from applications software such as Excel, Matlab and ArcGIS that have Standard Object Access Protocol (SOAP) capability. This paper will (1) describe the data model; (2) demonstrate the capability for representing diverse data in the same database; (3) demonstrate the use of the database from applications software for the performance of hydrologic analysis across different observation types.

A COSTAR interface using WWW technology.

PubMed Central

Rabbani, U.; Morgan, M.; Barnett, O.

1998-01-01

The concentration of industry on modern relational databases has left many nonrelational and proprietary databases without support for integration with new technologies. Emerging interface tools and data-access methodologies can be applied with difficulty to medical record systems which have proprietary data representation. Users of such medical record systems usually must access the clinical content of such record systems with keyboard-intensive and time-consuming interfaces. COSTAR is a legacy ambulatory medical record system developed over 25 years ago that is still popular and extensively used at the Massachusetts General Hospital. We define a model for using middle layer services to extract and cache data from non-relational databases, and present an intuitive World-Wide Web interface to COSTAR. This model has been implemented and successfully piloted in the Internal Medicine Associates at Massachusetts General Hospital. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:9929310

Barriers related to prenatal care utilization among women

PubMed Central

Roozbeh, Nasibeh; Nahidi, Fatemeh; Hajiyan, Sepideh

2016-01-01

Objectives To investigate barriers related to prenatal care utilization among women. Methods Data was collected in both English and Persian databases. English databases included: the International Medical Sciences, Medline, Web of Science, Scopus, Google Scholar. The Persian databases included: the Iranmedex, the State Inpatient Databases (SID) with the use of related keywords, and on the basis of inclusion-exclusion criteria. The keywords included are barrier, prenatal care, women, access, and preventive factors. OR and AND were Boolean operators. After the study, articles were summarized, unrelated articles were rejected, and related articles were identified. Inclusion criteria were all published articles from 1990 to 2015, written in English and Persian languages. The titles and abstracts are related, and addressed all subjects about barriers related to prenatal care utilization. At the end, all duplicated articles were excluded. There were no restrictions for exclusion or inclusion of articles. Exclusion criteria were failure in reporting in studies, case studies, and lack of access to the full text. Results After searching various databases, 112 related articles were included. After reviewing articles’ titles, 67 unrelated articles and abstracts were rejected, 45 articles were evaluated, 20 of them were duplicated. Then, the qualities of 25 articles were analyzed. Therefore, 5 articles were excluded due to not mentioning the sample size, mismatches between method and data, or results. Total of 20 articles were selected for final analysis. Prenatal care utilization barrier can be divided into various domains such as individual barriers, financial barriers, organizational barriers, social, and cultural barriers. Conclusion To increase prenatal care coverage, it is necessary to pay attention to all domains, especially individual and financial barriers.

CEBS: a comprehensive annotated database of toxicological data

PubMed Central

Lea, Isabel A.; Gong, Hui; Paleja, Anand; Rashid, Asif; Fostel, Jennifer

2017-01-01

The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/databases/cebs/. PMID:27899660

Using the structure-function linkage database to characterize functional domains in enzymes.

PubMed

Brown, Shoshana; Babbitt, Patricia

2014-12-12

The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

Experience in running relational databases on clustered storage

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, Ruben; Potocky, Miroslav

2015-12-01

For past eight years, CERN IT Database group has based its backend storage on NAS (Network-Attached Storage) architecture, providing database access via NFS (Network File System) protocol. In last two and half years, our storage has evolved from a scale-up architecture to a scale-out one. This paper describes our setup and a set of functionalities providing key features to other services like Database on Demand [1] or CERN Oracle backup and recovery service. It also outlines possible trend of evolution that, storage for databases could follow.

Geothopica and the interactive analysis and visualization of the updated Italian National Geothermal Database

NASA Astrophysics Data System (ADS)

Trumpy, Eugenio; Manzella, Adele

2017-02-01

The Italian National Geothermal Database (BDNG), is the largest collection of Italian Geothermal data and was set up in the 1980s. It has since been updated both in terms of content and management tools: information on deep wells and thermal springs (with temperature > 30 °C) are currently organized and stored in a PostgreSQL relational database management system, which guarantees high performance, data security and easy access through different client applications. The BDNG is the core of the Geothopica web site, whose webGIS tool allows different types of user to access geothermal data, to visualize multiple types of datasets, and to perform integrated analyses. The webGIS tool has been recently improved by two specially designed, programmed and implemented visualization tools to display data on well lithology and underground temperatures. This paper describes the contents of the database and its software and data update, as well as the webGIS tool including the new tools for data lithology and temperature visualization. The geoinformation organized in the database and accessible through Geothopica is of use not only for geothermal purposes, but also for any kind of georesource and CO2 storage project requiring the organization of, and access to, deep underground data. Geothopica also supports project developers, researchers, and decision makers in the assessment, management and sustainable deployment of georesources.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Selective access and editing in a database

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Gawdiak, Yuri O. (Inventor)

2010-01-01

Method and system for providing selective access to different portions of a database by different subgroups of database users. Where N users are involved, up to 2.sup.N-1 distinguishable access subgroups in a group space can be formed, where no two access subgroups have the same members. Two or more members of a given access subgroup can edit, substantially simultaneously, a document accessible to each member.

Abstraction of the Relational Model from a Department of Veterans Affairs DHCP Database: Bridging Theory and Working Application

PubMed Central

Levy, C.; Beauchamp, C.

1996-01-01

This poster describes the methods used and working prototype that was developed from an abstraction of the relational model from the VA's hierarchical DHCP database. Overlaying the relational model on DHCP permits multiple user views of the physical data structure, enhances access to the database by providing a link to commercial (SQL based) software, and supports a conceptual managed care data model based on primary and longitudinal patient care. The goal of this work was to create a relational abstraction of the existing hierarchical database; to construct, using SQL data definition language, user views of the database which reflect the clinical conceptual view of DHCP, and to allow the user to work directly with the logical view of the data using GUI based commercial software of their choosing. The workstation is intended to serve as a platform from which a managed care information model could be implemented and evaluated.

WWW database of optical constants for astronomy

NASA Astrophysics Data System (ADS)

Henning, Th.; Il'In, V. B.; Krivova, N. A.; Michel, B.; Voshchinnikov, N. V.

1999-04-01

The database we announce contains references to the papers, data files and links to the Internet resources related to measurements and calculations of the optical constants of the materials of astronomical interest: different silicates, ices, oxides, sulfides, carbides, carbonaceous species from amorphous carbon to graphite and diamonds, etc. We describe the general structure and content of the database which has now free access via Internet: http://www.astro.spbu.ru/JPDOC/entry.html\\ or \\ http:// www. astro.uni-jena.de/Users/database/entry.html

Accessing the medical devices market in Egypt and Saudi Arabia: a systematic review of policies and regulations.

PubMed

Gad, Mohamed; Kriza, Christine; Fidler, Armin; Kolominsky-Rabas, Peter

2016-07-01

Despite the significant medical devices market size in Egypt and Saudi Arabia, information regarding policies and regulations for medical devices market access is highly deficient. The aim of this paper is to provide a systematic review on market access policies and regulations in both countries, to allow safe and timely access to medical technology. The following databases were searched: PubMed, Science Direct, Scopus, and Al Manhal Arabic database. Additionally, the web portals of regulatory authorities of both countries were searched. There are 34 records included in the qualitative synthesis of this review. Expert commentary: Main findings include; adopted regulatory framework from reference countries, and interim main regulatory documents, In conclusion, the market access schemes are relatively structured. However, some recommendations are put forward to navigate towards a more comprehensive policy framework in both countries.

Cry-Bt identifier: a biological database for PCR detection of Cry genes present in transgenic plants.

PubMed

Singh, Vinay Kumar; Ambwani, Sonu; Marla, Soma; Kumar, Anil

2009-10-23

We describe the development of a user friendly tool that would assist in the retrieval of information relating to Cry genes in transgenic crops. The tool also helps in detection of transformed Cry genes from Bacillus thuringiensis present in transgenic plants by providing suitable designed primers for PCR identification of these genes. The tool designed based on relational database model enables easy retrieval of information from the database with simple user queries. The tool also enables users to access related information about Cry genes present in various databases by interacting with different sources (nucleotide sequences, protein sequence, sequence comparison tools, published literature, conserved domains, evolutionary and structural data). http://insilicogenomics.in/Cry-btIdentifier/welcome.html.

Object-Oriented Approach to Integrating Database Semantics. Volume 4.

DTIC Science & Technology

1987-12-01

schemata for; 1. Object Classification Shema -- Entities 2. Object Structure and Relationship Schema -- Relations 3. Operation Classification and... relationships are represented in a database is non- intuitive for naive users. *It is difficult to access and combine information in multiple databases. In this...from the CURRENT-.CLASSES table. Choosing a selected item do-selects it. Choose 0 to exit. 1. STUDENTS 2. CUR~RENT-..CLASSES 3. MANAGMNT -.CLASS

Security Controls in the Stockpoint Logistics Integrated Communications Environment (SPLICE).

DTIC Science & Technology

1985-03-01

call programs as authorized after checks by the Terminal Management Subsystem on SAS databases . SAS overlays the TANDEM GUARDIAN operating system to...Security Access Profile database (SAP) and a query capability generating various security reports. SAS operates with the System Monitor (SMON) subsystem...system to DDN and other components. The first SAS component to be reviewed is the SAP database . SAP is organized into two types of files. Relational

SQLGEN: a framework for rapid client-server database application development.

PubMed

Nadkarni, P M; Cheung, K H

1995-12-01

SQLGEN is a framework for rapid client-server relational database application development. It relies on an active data dictionary on the client machine that stores metadata on one or more database servers to which the client may be connected. The dictionary generates dynamic Structured Query Language (SQL) to perform common database operations; it also stores information about the access rights of the user at log-in time, which is used to partially self-configure the behavior of the client to disable inappropriate user actions. SQLGEN uses a microcomputer database as the client to store metadata in relational form, to transiently capture server data in tables, and to allow rapid application prototyping followed by porting to client-server mode with modest effort. SQLGEN is currently used in several production biomedical databases.

Information technologies in public health management: a database on biocides to improve quality of life.

PubMed

Roman, C; Scripcariu, L; Diaconescu, Rm; Grigoriu, A

2012-01-01

Biocides for prolonging the shelf life of a large variety of materials have been extensively used over the last decades. It has estimated that the worldwide biocide consumption to be about 12.4 billion dollars in 2011, and is expected to increase in 2012. As biocides are substances we get in contact with in our everyday lives, access to this type of information is of paramount importance in order to ensure an appropriate living environment. Consequently, a database where information may be quickly processed, sorted, and easily accessed, according to different search criteria, is the most desirable solution. The main aim of this work was to design and implement a relational database with complete information about biocides used in public health management to improve the quality of life. Design and implementation of a relational database for biocides, by using the software "phpMyAdmin". A database, which allows for an efficient collection, storage, and management of information including chemical properties and applications of a large quantity of biocides, as well as its adequate dissemination into the public health environment. The information contained in the database herein presented promotes an adequate use of biocides, by means of information technologies, which in consequence may help achieve important improvement in our quality of life.

The OAuth 2.0 Web Authorization Protocol for the Internet Addiction Bioinformatics (IABio) Database.

PubMed

Choi, Jeongseok; Kim, Jaekwon; Lee, Dong Kyun; Jang, Kwang Soo; Kim, Dai-Jin; Choi, In Young

2016-03-01

Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2011-01-01

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

Challenges in Database Design with Microsoft Access

ERIC Educational Resources Information Center

Letkowski, Jerzy

2014-01-01

Design, development and explorations of databases are popular topics covered in introductory courses taught at business schools. Microsoft Access is the most popular software used in those courses. Despite quite high complexity of Access, it is considered to be one of the most friendly database programs for beginners. A typical Access textbook…

NIST Photoionization of CO2 (ARPES) Database

National Institute of Standards and Technology Data Gateway

SRD 119 NIST Photoionization of CO2 (ARPES) Database (Web, free access)   CO2 is studied using dispersed synchrotron radiation in the 650 Å to 850 Å spectral region. The vibrationally resolved photoelectron spectra are analyzed to generate relative vibrational transition amplitudes and the angular asymmetry parameters describing the various transitions observed.

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

PubMed

Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

2007-12-11

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

PubMed

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher; Carracedo, Angel

2008-10-10

In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.

S&MPO - An information system for ozone spectroscopy on the WEB

NASA Astrophysics Data System (ADS)

Babikov, Yurii L.; Mikhailenko, Semen N.; Barbe, Alain; Tyuterev, Vladimir G.

2014-09-01

Spectroscopy and Molecular Properties of Ozone ("S&MPO") is an Internet accessible information system devoted to high resolution spectroscopy of the ozone molecule, related properties and data sources. S&MPO contains information on original spectroscopic data (line positions, line intensities, energies, transition moments, spectroscopic parameters) recovered from comprehensive analyses and modeling of experimental spectra as well as associated software for data representation written in PHP Java Script, C++ and FORTRAN. The line-by-line list of vibration-rotation transitions and other information is organized as a relational database under control of MySQL database tools. The main S&MPO goal is to provide access to all available information on vibration-rotation molecular states and transitions under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for the S&MPO may include: education/training in molecular physics, radiative processes, laser physics; spectroscopic applications (analysis, Fourier transform spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The system is accessible via Internet on two sites: http://smpo.iao.ru and http://smpo.univ-reims.fr.

A Quality-Control-Oriented Database for a Mesoscale Meteorological Observation Network

NASA Astrophysics Data System (ADS)

Lussana, C.; Ranci, M.; Uboldi, F.

2012-04-01

In the operational context of a local weather service, data accessibility and quality related issues must be managed by taking into account a wide set of user needs. This work describes the structure and the operational choices made for the operational implementation of a database system storing data from highly automated observing stations, metadata and information on data quality. Lombardy's environmental protection agency, ARPA Lombardia, manages a highly automated mesoscale meteorological network. A Quality Assurance System (QAS) ensures that reliable observational information is collected and disseminated to the users. The weather unit in ARPA Lombardia, at the same time an important QAS component and an intensive data user, has developed a database specifically aimed to: 1) providing quick access to data for operational activities and 2) ensuring data quality for real-time applications, by means of an Automatic Data Quality Control (ADQC) procedure. Quantities stored in the archive include hourly aggregated observations of: precipitation amount, temperature, wind, relative humidity, pressure, global and net solar radiation. The ADQC performs several independent tests on raw data and compares their results in a decision-making procedure. An important ADQC component is the Spatial Consistency Test based on Optimal Interpolation. Interpolated and Cross-Validation analysis values are also stored in the database, providing further information to human operators and useful estimates in case of missing data. The technical solution adopted is based on a LAMP (Linux, Apache, MySQL and Php) system, constituting an open source environment suitable for both development and operational practice. The ADQC procedure itself is performed by R scripts directly interacting with the MySQL database. Users and network managers can access the database by using a set of web-based Php applications.

The plant phenological online database (PPODB): an online database for long-term phenological data.

PubMed

Dierenbach, Jonas; Badeck, Franz-W; Schaber, Jörg

2013-09-01

We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de .

Geothermal NEPA Database on OpenEI (Poster)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, K. R.; Levine, A.

2014-09-01

The National Renewable Energy Laboratory (NREL) developed the Geothermal National Environmental Policy Act (NEPA) Database as a platform for government agencies and industry to access and maintain information related to geothermal NEPA documents. The data were collected to inform analyses of NEPA timelines, and the collected data were made publically available via this tool in case others might find the data useful. NREL staff and contractors collected documents from agency websites, during visits to the two busiest Bureau of Land Management (BLM) field offices for geothermal development, and through email and phone call requests from other BLM field offices. Theymore » then entered the information into the database, hosted by Open Energy Information (http://en.openei.org/wiki/RAPID/NEPA). The long-term success of the project will depend on the willingness of federal agencies, industry, and others to populate the database with NEPA and related documents, and to use the data for their own analyses. As the information and capabilities of the database expand, developers and agencies can save time on new NEPA reports by accessing a single location to research related activities, their potential impacts, and previously proposed and imposed mitigation measures. NREL used a wiki platform to allow industry and agencies to maintain the content in the future so that it continues to provide relevant and accurate information to users.« less

Design and Implementation of a Three-Tiered Web-Based Inventory Ordering and Tracking System Prototype Using CORBA and Java

DTIC Science & Technology

2000-03-01

languages yet still be able to access the legacy relational databases that businesses have huge investments in. JDBC is a low-level API designed for...consider the return of investment . The system requirements, discussed in Chapter II, are the main source of input to developing the relational...1996. Inprise, Gatekeeper Guide, Inprise Corporation, 1999. Kroenke, D., Database Processing Fundementals , Design, and Implementation, Sixth Edition

SEER*Stat Software

Cancer.gov

If you have access to SEER Research Data, use SEER*Stat to analyze SEER and other cancer-related databases. View individual records and produce statistics including incidence, mortality, survival, prevalence, and multiple primary. Tutorials and related analytic software tools are available.

Fermilab Security Site Access Request Database

Science.gov Websites

Fermilab Security Site Access Request Database Use of the online version of the Fermilab Security Site Access Request Database requires that you login into the ESH&Q Web Site. Note: Only Fermilab generated from the ESH&Q Section's Oracle database on May 27, 2018 05:48 AM. If you have a question

The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire.

PubMed

Park, Hae-Min; Park, Ju-Hyeong; Kim, Yoon-Woo; Kim, Kyoung-Jin; Jeong, Hee-Jin; Jang, Kyoung-Soon; Kim, Byung-Gee; Kim, Yun-Gon

2013-11-15

In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells/organs in xenotransplantation and might eventually provide new targets in the α1,3-galactosyltransferase gene-knock out pigs era. The database can be accessed on the web at http://bioinformatics.snu.ac.kr/xdb.

The ATLAS TAGS database distribution and management - Operational challenges of a multi-terabyte distributed database

NASA Astrophysics Data System (ADS)

Viegas, F.; Malon, D.; Cranshaw, J.; Dimitrov, G.; Nowak, M.; Nairz, A.; Goossens, L.; Gallas, E.; Gamboa, C.; Wong, A.; Vinek, E.

2010-04-01

The TAG files store summary event quantities that allow a quick selection of interesting events. This data will be produced at a nominal rate of 200 Hz, and is uploaded into a relational database for access from websites and other tools. The estimated database volume is 6TB per year, making it the largest application running on the ATLAS relational databases, at CERN and at other voluntary sites. The sheer volume and high rate of production makes this application a challenge to data and resource management, in many aspects. This paper will focus on the operational challenges of this system. These include: uploading the data from files to the CERN's and remote sites' databases; distributing the TAG metadata that is essential to guide the user through event selection; controlling resource usage of the database, from the user query load to the strategy of cleaning and archiving of old TAG data.

Analysis and comparison of NoSQL databases with an introduction to consistent references in big data storage systems

NASA Astrophysics Data System (ADS)

Dziedzic, Adam; Mulawka, Jan

2014-11-01

NoSQL is a new approach to data storage and manipulation. The aim of this paper is to gain more insight into NoSQL databases, as we are still in the early stages of understanding when to use them and how to use them in an appropriate way. In this submission descriptions of selected NoSQL databases are presented. Each of the databases is analysed with primary focus on its data model, data access, architecture and practical usage in real applications. Furthemore, the NoSQL databases are compared in fields of data references. The relational databases offer foreign keys, whereas NoSQL databases provide us with limited references. An intermediate model between graph theory and relational algebra which can address the problem should be created. Finally, the proposal of a new approach to the problem of inconsistent references in Big Data storage systems is introduced.

IPD—the Immuno Polymorphism Database

PubMed Central

Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

2013-01-01

The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

47 CFR 54.410 - Subscriber eligibility determination and certification.

Code of Federal Regulations, 2012 CFR

2012-10-01

... eligibility by accessing one or more databases containing information regarding the subscriber's income (“income databases”), the eligible telecommunications carrier must access such income databases and... carrier cannot determine a prospective subscriber's income-based eligibility by accessing income databases...

47 CFR 54.410 - Subscriber eligibility determination and certification.

Code of Federal Regulations, 2013 CFR

2013-10-01

... eligibility by accessing one or more databases containing information regarding the subscriber's income (“income databases”), the eligible telecommunications carrier must access such income databases and... carrier cannot determine a prospective subscriber's income-based eligibility by accessing income databases...

47 CFR 54.410 - Subscriber eligibility determination and certification.

Code of Federal Regulations, 2014 CFR

2014-10-01

... eligibility by accessing one or more databases containing information regarding the subscriber's income (“income databases”), the eligible telecommunications carrier must access such income databases and... carrier cannot determine a prospective subscriber's income-based eligibility by accessing income databases...

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

PubMed Central

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L.; Sherman, Westley A.; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-01-01

Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP. Contact: sebastianms@bii.a-star.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online. PMID:22531216

21 CFR 1300.03 - Definitions relating to electronic orders for controlled substances and electronic prescriptions...

Code of Federal Regulations, 2010 CFR

2010-04-01

... records on its servers. Audit trail means a record showing who has accessed an information technology... identity of the user as a prerequisite to allowing access to the information application. Authentication... information in a database. (4) Comparing the biometric data with data contained in one or more reference...

May I Recruit through Your Agency? Considerations for Researchers of Spousal Caregivers

ERIC Educational Resources Information Center

Pote, Steven

2016-01-01

Few resources within social science literature provide helpful information related to participant recruitment for research on spousal caregivers of individuals with dementia. Independent researchers with limited resources may not have access to large databases or centers in which access to caregivers is readily available. As a result, these…

S/MARt DB: a database on scaffold/matrix attached regions.

PubMed

Liebich, Ines; Bode, Jürgen; Frisch, Matthias; Wingender, Edgar

2002-01-01

S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research.

PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.

PubMed

Damiano, F; Gallerani, R; Liuni, S; Licciulli, F; Ceci, L R

2001-01-01

The PLMItRNA database for mitochondrial tRNA molecules and genes in VIRIDIPLANTAE: (green plants) [Volpetti,V., Gallerani,R., DeBenedetto,C., Liuni,S., Licciulli,F. and Ceci,L.R. (2000) Nucleic Acids Res., 28, 159-162] has been enlarged to include algae. The database now contains 436 genes and 16 tRNA entries relative to 25 higher plants, eight green algae, four red algae (RHODOPHYTAE:) and two STRAMENOPILES: The PLMItRNA database is accessible via the WWW at http://bio-www.ba.cnr.it:8000/PLMItRNA.

Directory of On-Line Networks, Databases and Bulletin Boards on Assistive Technology. Second Edition. RESNA Technical Assistance Project.

ERIC Educational Resources Information Center

RESNA: Association for the Advancement of Rehabilitation Technology, Washington, DC.

This resource directory provides a selective listing of electronic networks, online databases, and bulletin boards that highlight technology-related services and products. For each resource, the following information is provided: name, address, and telephone number; description; target audience; hardware/software needs to access the system;…

The AAS Working Group on Accessibility and Disability (WGAD) Year 1 Highlights and Database Access

NASA Astrophysics Data System (ADS)

Knierman, Karen A.; Diaz Merced, Wanda; Aarnio, Alicia; Garcia, Beatriz; Monkiewicz, Jacqueline A.; Murphy, Nicholas Arnold

2017-06-01

The AAS Working Group on Accessibility and Disability (WGAD) was formed in January of 2016 with the express purpose of seeking equity of opportunity and building inclusive practices for disabled astronomers at all educational and career stages. In this presentation, we will provide a summary of current activities, focusing on developing best practices for accessibility with respect to astronomical databases, publications, and meetings. Due to the reliance of space sciences on databases, it is important to have user centered design systems for data retrieval. The cognitive overload that may be experienced by users of current databases may be mitigated by use of multi-modal interfaces such as xSonify. Such interfaces would be in parallel or outside the original database and would not require additional software efforts from the original database. WGAD is partnering with the IAU Commission C1 WG Astronomy for Equity and Inclusion to develop such accessibility tools for databases and methods for user testing. To collect data on astronomical conference and meeting accessibility considerations, WGAD solicited feedback from January AAS attendees via a web form. These data, together with upcoming input from the community and analysis of accessibility documents of similar conferences, will be used to create a meeting accessibility document. Additionally, we will update the progress of journal access guidelines and our social media presence via Twitter. We recommend that astronomical journals form committees to evaluate the accessibility of their publications by performing user-centered usability studies.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

Ground Support Software for Spaceborne Instrumentation

NASA Technical Reports Server (NTRS)

Anicich, Vincent; Thorpe, rob; Fletcher, Greg; Waite, Hunter; Xu, Hykua; Walter, Erin; Frick, Kristie; Farris, Greg; Gell, Dave; Furman, Jufy;

Alaska Geochemical Database - Mineral Exploration Tool for the 21st Century - PDF of presentation

USGS Publications Warehouse

Granitto, Matthew; Schmidt, Jeanine M.; Labay, Keith A.; Shew, Nora B.; Gamble, Bruce M.

2012-01-01

The U.S. Geological Survey has created a geochemical database of geologic material samples collected in Alaska. This database is readily accessible to anyone with access to the Internet. Designed as a tool for mineral or environmental assessment, land management, or mineral exploration, the initial version of the Alaska Geochemical Database - U.S. Geological Survey Data Series 637 - contains geochemical, geologic, and geospatial data for 264,158 samples collected from 1962-2009: 108,909 rock samples; 92,701 sediment samples; 48,209 heavy-mineral-concentrate samples; 6,869 soil samples; and 7,470 mineral samples. In addition, the Alaska Geochemical Database contains mineralogic data for 18,138 nonmagnetic-fraction heavy mineral concentrates, making it the first U.S. Geological Survey database of this scope that contains both geochemical and mineralogic data. Examples from the Alaska Range will illustrate potential uses of the Alaska Geochemical Database in mineral exploration. Data from the Alaska Geochemical Database have been extensively checked for accuracy of sample media description, sample site location, and analytical method using U.S. Geological Survey sample-submittal archives and U.S. Geological Survey publications (plus field notebooks and sample site compilation base maps from the Alaska Technical Data Unit in Anchorage, Alaska). The database is also the repository for nearly all previously released U.S. Geological Survey Alaska geochemical datasets. Although the Alaska Geochemical Database is a fully relational database in Microsoft® Access 2003 and 2010 formats, these same data are also provided as a series of spreadsheet files in Microsoft® Excel 2003 and 2010 formats, and as ASCII text files. A DVD version of the Alaska Geochemical Database was released in October 2011, as U.S. Geological Survey Data Series 637, and data downloads are available at http://pubs.usgs.gov/ds/637/. Also, all Alaska Geochemical Database data have been incorporated into the interactive U.S. Geological Survey Mineral Resource Data web portal, available at http://mrdata.usgs.gov/.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

Design and implementation of an audit trail in compliance with US regulations.

PubMed

Jiang, Keyuan; Cao, Xiang

2011-10-01

Audit trails have been used widely to ensure quality of study data and have been implemented in computerized clinical trials data systems. Increasingly, there is a need to audit access to study participant identifiable information to provide assurance that study participant privacy is protected and confidentiality is maintained. In the United States, several federal regulations specify how the audit trail function should be implemented. To describe the development and implementation of a comprehensive audit trail system that meets the regulatory requirements of assuring data quality and integrity and protecting participant privacy and that is also easy to implement and maintain. The audit trail system was designed and developed after we examined regulatory requirements, data access methods, prevailing application architecture, and good security practices. Our comprehensive audit trail system was developed and implemented at the database level using a commercially available database management software product. It captures both data access and data changes with the correct user identifier. Documentation of access is initiated automatically in response to either data retrieval or data change at the database level. Currently, our system has been implemented only on one commercial database management system. Although our audit trail algorithm does not allow for logging aggregate operations, aggregation does not reveal sensitive private participant information. Careful consideration must be given to data items selected for monitoring because selection of all data items using our system can dramatically increase the requirements for computer disk space. Evaluating the criticality and sensitivity of individual data items selected can control the storage requirements for clinical trial audit trail records. Our audit trail system is capable of logging data access and data change operations to satisfy regulatory requirements. Our approach is applicable to virtually any data that can be stored in a relational database.

LexisNexis

EPA Pesticide Factsheets

LexisNexis provides access to electronic legal and non-legal research databases to the Agency's attorneys, administrative law judges, law clerks, investigators, and certain non-legal staff (e.g. staff in the Office of Public Affairs). The agency requires access to the following types of electronic databases: Legal databases, Non-legal databases, Public Records databases, and Financial databases.

Palaeo sea-level and ice-sheet databases: problems, strategies and perspectives

NASA Astrophysics Data System (ADS)

Rovere, Alessio; Düsterhus, André; Carlson, Anders; Barlow, Natasha; Bradwell, Tom; Dutton, Andrea; Gehrels, Roland; Hibbert, Fiona; Hijma, Marc; Horton, Benjamin; Klemann, Volker; Kopp, Robert; Sivan, Dorit; Tarasov, Lev; Törnqvist, Torbjorn

2016-04-01

Databases of palaeoclimate data have driven many major developments in understanding the Earth system. The measurement and interpretation of palaeo sea-level and ice-sheet data that form such databases pose considerable challenges to the scientific communities that use them for further analyses. In this paper, we build on the experience of the PALSEA (PALeo constraints on SEA level rise) community, which is a working group inside the PAGES (Past Global Changes) project, to describe the challenges and best strategies that can be adopted to build a self-consistent and standardised database of geological and geochemical data related to palaeo sea levels and ice sheets. Our aim in this paper is to identify key points that need attention and subsequent funding when undertaking the task of database creation. We conclude that any sea-level or ice-sheet database must be divided into three instances: i) measurement; ii) interpretation; iii) database creation. Measurement should include postion, age, description of geological features, and quantification of uncertainties. All must be described as objectively as possible. Interpretation can be subjective, but it should always include uncertainties and include all the possible interpretations, without unjustified a priori exclusions. We propose that, in the creation of a database, an approach based on Accessibility, Transparency, Trust, Availability, Continued updating, Completeness and Communication of content (ATTAC3) must be adopted. Also, it is essential to consider the community structure that creates and benefits of a database. We conclude that funding sources should consider to address not only the creation of original data in specific research-question oriented projects, but also include the possibility to use part of the funding for IT-related and database creation tasks, which are essential to guarantee accessibility and maintenance of the collected data.

Selecting a database for literature searches in nursing: MEDLINE or CINAHL?

PubMed

Brazier, H; Begley, C M

1996-10-01

This study compares the usefulness of the MEDLINE and CINAHL databases for students on post-registration nursing courses. We searched for nine topics, using title words only. Identical searches of the two databases retrieved 1162 references, of which 88% were in MEDLINE, 33% in CINAHL and 20% in both sources. The relevance of the references was assessed by student reviewers. The positive predictive value of CINAHL (70%) was higher than that of MEDLINE (54%), but MEDLINE produced more than twice as many relevant references as CINAHL. The sensitivity of MEDLINE was 85% (95% CI 82-88%), and that of CINAHL was 41% (95% CI 37-45%). To assess the ease of obtaining the references, we developed an index of accessibility, based on the holdings of a number of Irish and British libraries. Overall, 47% of relevant references were available in the students' own library, and 64% could be obtained within 48 hours. There was no difference between the two databases overall, but when two topics relating specifically to the organization of nursing were excluded, references found in MEDLINE were significantly more accessible. We recommend that MEDLINE should be regarded as the first choice of bibliographic database for any subject other than one related strictly to the organization of nursing.

MIPS: curated databases and comprehensive secondary data resources in 2010.

PubMed

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

MIPS: curated databases and comprehensive secondary data resources in 2010

PubMed Central

Mewes, H. Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F.X.; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de). PMID:21109531

JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms

PubMed Central

Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

2015-01-01

The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/ PMID:26424080

JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

PubMed

Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

2015-01-01

The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. © The Author(s) 2015. Published by Oxford University Press.

Open access intrapartum CTG database.

PubMed

Chudáček, Václav; Spilka, Jiří; Burša, Miroslav; Janků, Petr; Hruban, Lukáš; Huptych, Michal; Lhotská, Lenka

2014-01-13

Cardiotocography (CTG) is a monitoring of fetal heart rate and uterine contractions. Since 1960 it is routinely used by obstetricians to assess fetal well-being. Many attempts to introduce methods of automatic signal processing and evaluation have appeared during the last 20 years, however still no significant progress similar to that in the domain of adult heart rate variability, where open access databases are available (e.g. MIT-BIH), is visible. Based on a thorough review of the relevant publications, presented in this paper, the shortcomings of the current state are obvious. A lack of common ground for clinicians and technicians in the field hinders clinically usable progress. Our open access database of digital intrapartum cardiotocographic recordings aims to change that. The intrapartum CTG database consists in total of 552 intrapartum recordings, which were acquired between April 2010 and August 2012 at the obstetrics ward of the University Hospital in Brno, Czech Republic. All recordings were stored in electronic form in the OB TraceVue®;system. The recordings were selected from 9164 intrapartum recordings with clinical as well as technical considerations in mind. All recordings are at most 90 minutes long and start a maximum of 90 minutes before delivery. The time relation of CTG to delivery is known as well as the length of the second stage of labor which does not exceed 30 minutes. The majority of recordings (all but 46 cesarean sections) is - on purpose - from vaginal deliveries. All recordings have available biochemical markers as well as some more general clinical features. Full description of the database and reasoning behind selection of the parameters is presented in the paper. A new open-access CTG database is introduced which should give the research community common ground for comparison of results on reasonably large database. We anticipate that after reading the paper, the reader will understand the context of the field from clinical and technical perspectives which will enable him/her to use the database and also understand its limitations.

DamaGIS: a multisource geodatabase for collection of flood-related damage data

NASA Astrophysics Data System (ADS)

Saint-Martin, Clotilde; Javelle, Pierre; Vinet, Freddy

2018-06-01

Every year in France, recurring flood events result in several million euros of damage, and reducing the heavy consequences of floods has become a high priority. However, actions to reduce the impact of floods are often hindered by the lack of damage data on past flood events. The present paper introduces a new database for collection and assessment of flood-related damage. The DamaGIS database offers an innovative bottom-up approach to gather and identify damage data from multiple sources, including new media. The study area has been defined as the south of France considering the high frequency of floods over the past years. This paper presents the structure and contents of the database. It also presents operating instructions in order to keep collecting damage data within the database. This paper also describes an easily reproducible method to assess the severity of flood damage regardless of the location or date of occurrence. A first analysis of the damage contents is also provided in order to assess data quality and the relevance of the database. According to this analysis, despite its lack of comprehensiveness, the DamaGIS database presents many advantages. Indeed, DamaGIS provides a high accuracy of data as well as simplicity of use. It also has the additional benefit of being accessible in multiple formats and is open access. The DamaGIS database is available at https://doi.org/10.5281/zenodo.1241089.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

interPopula: a Python API to access the HapMap Project dataset

PubMed Central

2010-01-01

Background The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. Results interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. Conclusions interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset. PMID:21210977

The plant phenological online database (PPODB): an online database for long-term phenological data

NASA Astrophysics Data System (ADS)

Dierenbach, Jonas; Badeck, Franz-W.; Schaber, Jörg

2013-09-01

We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de .

47 CFR 15.711 - Interference avoidance methods.

Code of Federal Regulations, 2011 CFR

2011-10-01

... channel availability for a TVBD is determined based on the geo-location and database access method described in paragraphs (a) and (b) of this section. (a) Geo-location and database access. A TVBD shall rely on the geo-location and database access mechanism to identify available television channels...

47 CFR 15.711 - Interference avoidance methods.

Code of Federal Regulations, 2013 CFR

2013-10-01

... channel availability for a TVBD is determined based on the geo-location and database access method described in paragraphs (a) and (b) of this section. (a) Geo-location and database access. A TVBD shall rely on the geo-location and database access mechanism to identify available television channels...

47 CFR 15.711 - Interference avoidance methods.

Code of Federal Regulations, 2014 CFR

2014-10-01

... channel availability for a TVBD is determined based on the geo-location and database access method described in paragraphs (a) and (b) of this section. (a) Geo-location and database access. A TVBD shall rely on the geo-location and database access mechanism to identify available television channels...

47 CFR 15.711 - Interference avoidance methods.

Code of Federal Regulations, 2012 CFR

2012-10-01

... channel availability for a TVBD is determined based on the geo-location and database access method described in paragraphs (a) and (b) of this section. (a) Geo-location and database access. A TVBD shall rely on the geo-location and database access mechanism to identify available television channels...

Use of a Relational Database to Support Clinical Research: Application in a Diabetes Program

PubMed Central

Lomatch, Diane; Truax, Terry; Savage, Peter

1981-01-01

A database has been established to support conduct of clinical research and monitor delivery of medical care for 1200 diabetic patients as part of the Michigan Diabetes Research and Training Center (MDRTC). Use of an intelligent microcomputer to enter and retrieve the data and use of a relational database management system (DBMS) to store and manage data have provided a flexible, efficient method of achieving both support of small projects and monitoring overall activity of the Diabetes Center Unit (DCU). Simplicity of access to data, efficiency in providing data for unanticipated requests, ease of manipulations of relations, security and “logical data independence” were important factors in choosing a relational DBMS. The ability to interface with an interactive statistical program and a graphics program is a major advantage of this system. Out database currently provides support for the operation and analysis of several ongoing research projects.

Heuristic query optimization for query multiple table and multiple clausa on mobile finance application

NASA Astrophysics Data System (ADS)

Indrayana, I. N. E.; P, N. M. Wirasyanti D.; Sudiartha, I. KG

2018-01-01

Mobile application allow many users to access data from the application without being limited to space, space and time. Over time the data population of this application will increase. Data access time will cause problems if the data record has reached tens of thousands to millions of records.The objective of this research is to maintain the performance of data execution for large data records. One effort to maintain data access time performance is to apply query optimization method. The optimization used in this research is query heuristic optimization method. The built application is a mobile-based financial application using MySQL database with stored procedure therein. This application is used by more than one business entity in one database, thus enabling rapid data growth. In this stored procedure there is an optimized query using heuristic method. Query optimization is performed on a “Select” query that involves more than one table with multiple clausa. Evaluation is done by calculating the average access time using optimized and unoptimized queries. Access time calculation is also performed on the increase of population data in the database. The evaluation results shown the time of data execution with query heuristic optimization relatively faster than data execution time without using query optimization.

Unified Access Architecture for Large-Scale Scientific Datasets

NASA Astrophysics Data System (ADS)

Karna, Risav

2014-05-01

Data-intensive sciences have to deploy diverse large scale database technologies for data analytics as scientists have now been dealing with much larger volume than ever before. While array databases have bridged many gaps between the needs of data-intensive research fields and DBMS technologies (Zhang 2011), invocation of other big data tools accompanying these databases is still manual and separate the database management's interface. We identify this as an architectural challenge that will increasingly complicate the user's work flow owing to the growing number of useful but isolated and niche database tools. Such use of data analysis tools in effect leaves the burden on the user's end to synchronize the results from other data manipulation analysis tools with the database management system. To this end, we propose a unified access interface for using big data tools within large scale scientific array database using the database queries themselves to embed foreign routines belonging to the big data tools. Such an invocation of foreign data manipulation routines inside a query into a database can be made possible through a user-defined function (UDF). UDFs that allow such levels of freedom as to call modules from another language and interface back and forth between the query body and the side-loaded functions would be needed for this purpose. For the purpose of this research we attempt coupling of four widely used tools Hadoop (hadoop1), Matlab (matlab1), R (r1) and ScaLAPACK (scalapack1) with UDF feature of rasdaman (Baumann 98), an array-based data manager, for investigating this concept. The native array data model used by an array-based data manager provides compact data storage and high performance operations on ordered data such as spatial data, temporal data, and matrix-based data for linear algebra operations (scidbusr1). Performances issues arising due to coupling of tools with different paradigms, niche functionalities, separate processes and output data formats have been anticipated and considered during the design of the unified architecture. The research focuses on the feasibility of the designed coupling mechanism and the evaluation of the efficiency and benefits of our proposed unified access architecture. Zhang 2011: Zhang, Ying and Kersten, Martin and Ivanova, Milena and Nes, Niels, SciQL: Bridging the Gap Between Science and Relational DBMS, Proceedings of the 15th Symposium on International Database Engineering Applications, 2011. Baumann 98: Baumann, P., Dehmel, A., Furtado, P., Ritsch, R., Widmann, N., "The Multidimensional Database System RasDaMan", SIGMOD 1998, Proceedings ACM SIGMOD International Conference on Management of Data, June 2-4, 1998, Seattle, Washington, 1998. hadoop1: hadoop.apache.org, "Hadoop", http://hadoop.apache.org/, [Online; accessed 12-Jan-2014]. scalapack1: netlib.org/scalapack, "ScaLAPACK", http://www.netlib.org/scalapack,[Online; accessed 12-Jan-2014]. r1: r-project.org, "R", http://www.r-project.org/,[Online; accessed 12-Jan-2014]. matlab1: mathworks.com, "Matlab Documentation", http://www.mathworks.de/de/help/matlab/,[Online; accessed 12-Jan-2014]. scidbusr1: scidb.org, "SciDB User's Guide", http://scidb.org/HTMLmanual/13.6/scidb_ug,[Online; accessed 01-Dec-2013].

The National Institute on Disability, Independent Living, and Rehabilitation Research Burn Model System: Twenty Years of Contributions to Clinical Service and Research.

PubMed

Goverman, Jeremy; Mathews, Katie; Holavanahalli, Radha K; Vardanian, Andrew; Herndon, David N; Meyer, Walter J; Kowalske, Karen; Fauerbach, Jim; Gibran, Nicole S; Carrougher, Gretchen J; Amtmann, Dagmar; Schneider, Jeffrey C; Ryan, Colleen M

The National Institute on Disability, Independent Living, and Rehabilitation Research (NIDILRR) established the Burn Model System (BMS) in 1993 to improve the lives of burn survivors. The BMS program includes 1) a multicenter longitudinal database describing the functional and psychosocial recovery of burn survivors; 2) site-specific burn-related research; and 3) a knowledge dissemination component directed toward patients and providers. Output from each BMS component was analyzed. Database structure, content, and access procedures are described. Publications using the database were identified and categorized to illustrate the content area of the work. Unused areas of the database were identified for future study. Publications related to site-specific projects were cataloged. The most frequently cited articles are summarized to illustrate the scope of these projects. The effectiveness of dissemination activities was measured by quantifying website hits and information downloads. There were 25 NIDILRR-supported publications that utilized the database. These articles covered topics related to psychological outcomes, functional outcomes, community reintegration, and burn demographics. There were 172 site-specific publications; highly cited articles demonstrate a wide scope of study. For information dissemination, visits to the BMS website quadrupled between 2013 and 2014, with 124,063 downloads of educational material in 2014. The NIDILRR BMS program has played a major role in defining the course of burn recovery, and making that information accessible to the general public. The accumulating information in the database serves as a rich resource to the burn community for future study. The BMS is a model for collaborative research that is multidisciplinary and outcome focused.

Chesapeake Bay Program Water Quality Database

EPA Pesticide Factsheets

The Chesapeake Information Management System (CIMS), designed in 1996, is an integrated, accessible information management system for the Chesapeake Bay Region. CIMS is an organized, distributed library of information and software tools designed to increase basin-wide public access to Chesapeake Bay information. The information delivered by CIMS includes technical and public information, educational material, environmental indicators, policy documents, and scientific data. Through the use of relational databases, web-based programming, and web-based GIS a large number of Internet resources have been established. These resources include multiple distributed on-line databases, on-demand graphing and mapping of environmental data, and geographic searching tools for environmental information. Baseline monitoring data, summarized data and environmental indicators that document ecosystem status and trends, confirm linkages between water quality, habitat quality and abundance, and the distribution and integrity of biological populations are also available. One of the major features of the CIMS network is the Chesapeake Bay Program's Data Hub, providing users access to a suite of long- term water quality and living resources databases. Chesapeake Bay mainstem and tidal tributary water quality, benthic macroinvertebrates, toxics, plankton, and fluorescence data can be obtained for a network of over 800 monitoring stations.

Microcomputers: Means to Achievement. Using Information More Efficiently for Special Needs Learners.

ERIC Educational Resources Information Center

Brown, James M.

1984-01-01

Discusses database management systems for special needs student information management. Considers data access policies, implementation, software selection criteria, and special needs related uses. (SK)

Quality, language, subdiscipline and promotion were associated with article accesses on Physiotherapy Evidence Database (PEDro).

PubMed

Yamato, Tiê P; Arora, Mohit; Stevens, Matthew L; Elkins, Mark R; Moseley, Anne M

2018-03-01

To quantify the relationship between the number of times articles are accessed on the Physiotherapy Evidence Database (PEDro) and the article characteristics. A secondary aim was to examine the relationship between accesses and the number of citations of articles. The study was conducted to derive prediction models for the number of accesses of articles indexed on PEDro from factors that may influence an article's accesses. All articles available on PEDro from August 2014 to January 2015 were included. We extracted variables relating to the algorithm used to present PEDro search results (research design, year of publication, PEDro score, source of systematic review (Cochrane or non-Cochrane)) plus language, subdiscipline of physiotherapy, and whether articles were promoted to PEDro users. Three predictive models were examined using multiple regression analysis. Citation and journal impact factor were downloaded. There were 29,313 articles indexed in this period. We identified seven factors that predicted the number of accesses. More accesses were noted for factors related to the algorithm used to present PEDro search results (synthesis research (i.e., guidelines and reviews), recent articles, Cochrane reviews, and higher PEDro score) plus publication in English and being promoted to PEDro users. The musculoskeletal, neurology, orthopaedics, sports, and paediatrics subdisciplines were associated with more accesses. We also found that there was no association between number of accesses and citations. The number of times an article is accessed on PEDro is partly predicted by how condensed and high quality the evidence it contains is. Copyright © 2017 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.

Freely Accessible Chemical Database Resources of Compounds for in Silico Drug Discovery.

PubMed

Yang, JingFang; Wang, Di; Jia, Chenyang; Wang, Mengyao; Hao, GeFei; Yang, GuangFu

2018-05-07

In silico drug discovery has been proved to be a solidly established key component in early drug discovery. However, this task is hampered by the limitation of quantity and quality of compound databases for screening. In order to overcome these obstacles, freely accessible database resources of compounds have bloomed in recent years. Nevertheless, how to choose appropriate tools to treat these freely accessible databases are crucial. To the best of our knowledge, this is the first systematic review on this issue. The existed advantages and drawbacks of chemical databases were analyzed and summarized based on the collected six categories of freely accessible chemical databases from literature in this review. Suggestions on how and in which conditions the usage of these databases could be reasonable were provided. Tools and procedures for building 3D structure chemical libraries were also introduced. In this review, we described the freely accessible chemical database resources for in silico drug discovery. In particular, the chemical information for building chemical database appears as attractive resources for drug design to alleviate experimental pressure. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

47 CFR 51.217 - Nondiscriminatory access: Telephone numbers, operator services, directory assistance services...

Code of Federal Regulations, 2011 CFR

2011-10-01

... to have access to its directory assistance services, including directory assistance databases, so... provider, including transfer of the LECs' directory assistance databases in readily accessible magnetic.... Updates to the directory assistance database shall be made in the same format as the initial transfer...

A Web-Based Database for Nurse Led Outreach Teams (NLOT) in Toronto.

PubMed

Li, Shirley; Kuo, Mu-Hsing; Ryan, David

2016-01-01

A web-based system can provide access to real-time data and information. Healthcare is moving towards digitizing patients' medical information and securely exchanging it through web-based systems. In one of Ontario's health regions, Nurse Led Outreach Teams (NLOT) provide emergency mobile nursing services to help reduce unnecessary transfers from long-term care homes to emergency departments. Currently the NLOT team uses a Microsoft Access database to keep track of the health information on the residents that they serve. The Access database lacks scalability, portability, and interoperability. The objective of this study is the development of a web-based database using Oracle Application Express that is easily accessible from mobile devices. The web-based database will allow NLOT nurses to enter and access resident information anytime and from anywhere.

Digital Library Services: Perceptions and Expectations of User Communities and Librarians in a New Zealand Academic Library.

ERIC Educational Resources Information Center

Xia, Wei

2003-01-01

Provides an overview of research conducted at Victoria University of Wellington regarding differing perceptions and expectations of user communities and librarians related to the usability of digital services. Considers access to services, currency of information on the Web site, the online public access catalog, databases, electronic journals,…

The YeastGenome app: the Saccharomyces Genome Database at your fingertips.

PubMed

Wong, Edith D; Karra, Kalpana; Hitz, Benjamin C; Hong, Eurie L; Cherry, J Michael

2013-01-01

The Saccharomyces Genome Database (SGD) is a scientific database that provides researchers with high-quality curated data about the genes and gene products of Saccharomyces cerevisiae. To provide instant and easy access to this information on mobile devices, we have developed YeastGenome, a native application for the Apple iPhone and iPad. YeastGenome can be used to quickly find basic information about S. cerevisiae genes and chromosomal features regardless of internet connectivity. With or without network access, you can view basic information and Gene Ontology annotations about a gene of interest by searching gene names and gene descriptions or by browsing the database within the app to find the gene of interest. With internet access, the app provides more detailed information about the gene, including mutant phenotypes, references and protein and genetic interactions, as well as provides hyperlinks to retrieve detailed information by showing SGD pages and views of the genome browser. SGD provides online help describing basic ways to navigate the mobile version of SGD, highlights key features and answers frequently asked questions related to the app. The app is available from iTunes (http://itunes.com/apps/yeastgenome). The YeastGenome app is provided freely as a service to our community, as part of SGD's mission to provide free and open access to all its data and annotations.

A new relational database structure and online interface for the HITRAN database

NASA Astrophysics Data System (ADS)

Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

2013-11-01

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Palaeo-sea-level and palaeo-ice-sheet databases: problems, strategies, and perspectives

NASA Astrophysics Data System (ADS)

Düsterhus, André; Rovere, Alessio; Carlson, Anders E.; Horton, Benjamin P.; Klemann, Volker; Tarasov, Lev; Barlow, Natasha L. M.; Bradwell, Tom; Clark, Jorie; Dutton, Andrea; Gehrels, W. Roland; Hibbert, Fiona D.; Hijma, Marc P.; Khan, Nicole; Kopp, Robert E.; Sivan, Dorit; Törnqvist, Torbjörn E.

2016-04-01

Sea-level and ice-sheet databases have driven numerous advances in understanding the Earth system. We describe the challenges and offer best strategies that can be adopted to build self-consistent and standardised databases of geological and geochemical information used to archive palaeo-sea-levels and palaeo-ice-sheets. There are three phases in the development of a database: (i) measurement, (ii) interpretation, and (iii) database creation. Measurement should include the objective description of the position and age of a sample, description of associated geological features, and quantification of uncertainties. Interpretation of the sample may have a subjective component, but it should always include uncertainties and alternative or contrasting interpretations, with any exclusion of existing interpretations requiring a full justification. During the creation of a database, an approach based on accessibility, transparency, trust, availability, continuity, completeness, and communication of content (ATTAC3) must be adopted. It is essential to consider the community that creates and benefits from a database. We conclude that funding agencies should not only consider the creation of original data in specific research-question-oriented projects, but also include the possibility of using part of the funding for IT-related and database creation tasks, which are essential to guarantee accessibility and maintenance of the collected data.

Designing a data portal for synthesis modeling

NASA Astrophysics Data System (ADS)

Holmes, M. A.

2006-12-01

Processing of field and model data in multi-disciplinary integrated science studies is a vital part of synthesis modeling. Collection and storage techniques for field data vary greatly between the participating scientific disciplines due to the nature of the data being collected, whether it be in situ, remotely sensed, or recorded by automated data logging equipment. Spreadsheets, personal databases, text files and binary files are used in the initial storage and processing of the raw data. In order to be useful to scientists, engineers and modelers the data need to be stored in a format that is easily identifiable, accessible and transparent to a variety of computing environments. The Model Operations and Synthesis (MOAS) database and associated web portal were created to provide such capabilities. The industry standard relational database is comprised of spatial and temporal data tables, shape files and supporting metadata accessible over the network, through a menu driven web-based portal or spatially accessible through ArcSDE connections from the user's local GIS desktop software. A separate server provides public access to spatial data and model output in the form of attributed shape files through an ArcIMS web-based graphical user interface.

New tools and methods for direct programmatic access to the dbSNP relational database.

PubMed

Saccone, Scott F; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A; Rice, John P

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

The Spanish National Reference Database for Ionizing Radiations (BANDRRI)

PubMed

Los Arcos JM; Bailador; Gonzalez; Gonzalez; Gorostiza; Ortiz; Sanchez; Shaw; Williart

2000-03-01

The Spanish National Reference Database for Ionizing Radiations (BANDRRI) is being implemented by a reasearch team in the frame of a joint project between CIEMAT (Unidad de Metrologia de Radiaciones Ionizantes and Direccion de Informatica) and the Universidad Nacional de Educacion a Distancia (UNED, Departamento de Mecanica y Departamento de Fisica de Materiales). This paper presents the main objectives of BANDRRI, its dynamic and relational data base structure, interactive Web accessibility and its main radionuclide-related contents at this moment.

External access to ALICE controls conditions data

NASA Astrophysics Data System (ADS)

Jadlovský, J.; Jadlovská, A.; Sarnovský, J.; Jajčišin, Š.; Čopík, M.; Jadlovská, S.; Papcun, P.; Bielek, R.; Čerkala, J.; Kopčík, M.; Chochula, P.; Augustinus, A.

2014-06-01

ALICE Controls data produced by commercial SCADA system WINCCOA is stored in ORACLE database on the private experiment network. The SCADA system allows for basic access and processing of the historical data. More advanced analysis requires tools like ROOT and needs therefore a separate access method to the archives. The present scenario expects that detector experts create simple WINCCOA scripts, which retrieves and stores data in a form usable for further studies. This relatively simple procedure generates a lot of administrative overhead - users have to request the data, experts needed to run the script, the results have to be exported outside of the experiment network. The new mechanism profits from database replica, which is running on the CERN campus network. Access to this database is not restricted and there is no risk of generating a heavy load affecting the operation of the experiment. The developed tools presented in this paper allow for access to this data. The users can use web-based tools to generate the requests, consisting of the data identifiers and period of time of interest. The administrators maintain full control over the data - an authorization and authentication mechanism helps to assign privileges to selected users and restrict access to certain groups of data. Advanced caching mechanism allows the user to profit from the presence of already processed data sets. This feature significantly reduces the time required for debugging as the retrieval of raw data can last tens of minutes. A highly configurable client allows for information retrieval bypassing the interactive interface. This method is for example used by ALICE Offline to extract operational conditions after a run is completed. Last but not least, the software can be easily adopted to any underlying database structure and is therefore not limited to WINCCOA.

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.

Montreal Archive of Sleep Studies: an open-access resource for instrument benchmarking and exploratory research.

PubMed

O'Reilly, Christian; Gosselin, Nadia; Carrier, Julie; Nielsen, Tore

2014-12-01

Manual processing of sleep recordings is extremely time-consuming. Efforts to automate this process have shown promising results, but automatic systems are generally evaluated on private databases, not allowing accurate cross-validation with other systems. In lacking a common benchmark, the relative performances of different systems are not compared easily and advances are compromised. To address this fundamental methodological impediment to sleep study, we propose an open-access database of polysomnographic biosignals. To build this database, whole-night recordings from 200 participants [97 males (aged 42.9 ± 19.8 years) and 103 females (aged 38.3 ± 18.9 years); age range: 18-76 years] were pooled from eight different research protocols performed in three different hospital-based sleep laboratories. All recordings feature a sampling frequency of 256 Hz and an electroencephalography (EEG) montage of 4-20 channels plus standard electro-oculography (EOG), electromyography (EMG), electrocardiography (ECG) and respiratory signals. Access to the database can be obtained through the Montreal Archive of Sleep Studies (MASS) website (http://www.ceams-carsm.ca/en/MASS), and requires only affiliation with a research institution and prior approval by the applicant's local ethical review board. Providing the research community with access to this free and open sleep database is expected to facilitate the development and cross-validation of sleep analysis automation systems. It is also expected that such a shared resource will be a catalyst for cross-centre collaborations on difficult topics such as improving inter-rater agreement on sleep stage scoring. © 2014 European Sleep Research Society.

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

PubMed

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

A comprehensive clinical research database based on CDISC ODM and i2b2.

PubMed

Meineke, Frank A; Stäubert, Sebastian; Löbe, Matthias; Winter, Alfred

2014-01-01

We present a working approach for a clinical research database as part of an archival information system. The CDISC ODM standard is target for clinical study and research relevant routine data, thus decoupling the data ingest process from the access layer. The presented research database is comprehensive as it covers annotating, mapping and curation of poorly annotated source data. Besides a conventional relational database the medical data warehouse i2b2 serves as main frontend for end-users. The system we developed is suitable to support patient recruitment, cohort identification and quality assurance in daily routine.

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

PubMed Central

Liolios, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Kyrpides, Nikos C.

2006-01-01

The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public databases. GOLD v.2 has been expanded to provide information related to organism properties such as phenotype, ecotype and disease. Furthermore, project relevance and availability information is now included. GOLD is available at . It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece at PMID:16381880

An Integrated Intranet and Dynamic Database Application for the Security Manager at Naval Postgraduate School

DTIC Science & Technology

2002-09-01

Basic for Applications ( VBA ) 6.0 as macros may not be supported in 8 future versions of Access. Access 2000 offers Internet- related features for...security features from Microsoft’s SQL Server. [1] 3. System Requirements Access 2000 is a resource-intensive application as are all Office 2000...1] • Modules – Functions and procedures written in the Visual Basic for Applications ( VBA ) programming language. The capabilities of modules

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

PubMed

Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

2016-07-04

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

Scale out databases for CERN use cases

NASA Astrophysics Data System (ADS)

Baranowski, Zbigniew; Grzybek, Maciej; Canali, Luca; Lanza Garcia, Daniel; Surdy, Kacper

2015-12-01

Data generation rates are expected to grow very fast for some database workloads going into LHC run 2 and beyond. In particular this is expected for data coming from controls, logging and monitoring systems. Storing, administering and accessing big data sets in a relational database system can quickly become a very hard technical challenge, as the size of the active data set and the number of concurrent users increase. Scale-out database technologies are a rapidly developing set of solutions for deploying and managing very large data warehouses on commodity hardware and with open source software. In this paper we will describe the architecture and tests on database systems based on Hadoop and the Cloudera Impala engine. We will discuss the results of our tests, including tests of data loading and integration with existing data sources and in particular with relational databases. We will report on query performance tests done with various data sets of interest at CERN, notably data from the accelerator log database.

Sequencing of cDNA Clones from the Genetic Map of Tomato (Lycopersicon esculentum)

PubMed Central

Ganal, Martin W.; Czihal, Rosemarie; Hannappel, Ulrich; Kloos, Dorothee-U.; Polley, Andreas; Ling, Hong-Qing

1998-01-01

The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes was found. The information will permit the conversion of those markers to STS markers and allow their use in PCR-based mapping experiments. Furthermore, it will facilitate the comparative mapping of genes across distantly related plant species by direct comparison of DNA sequences and map positions. [cDNA sequence data reported in this paper have been submitted to the EMBL database under accession nos. AA824695–AA825005 and the dbEST_Id database under accession nos. 1546519–1546862.] PMID:9724330

AgeFactDB--the JenAge Ageing Factor Database--towards data integration in ageing research.

PubMed

Hühne, Rolf; Thalheim, Torsten; Sühnel, Jürgen

2014-01-01

AgeFactDB (http://agefactdb.jenage.de) is a database aimed at the collection and integration of ageing phenotype data including lifespan information. Ageing factors are considered to be genes, chemical compounds or other factors such as dietary restriction, whose action results in a changed lifespan or another ageing phenotype. Any information related to the effects of ageing factors is called an observation and is presented on observation pages. To provide concise access to the complete information for a particular ageing factor, corresponding observations are also summarized on ageing factor pages. In a first step, ageing-related data were primarily taken from existing databases such as the Ageing Gene Database--GenAge, the Lifespan Observations Database and the Dietary Restriction Gene Database--GenDR. In addition, we have started to include new ageing-related information. Based on homology data taken from the HomoloGene Database, AgeFactDB also provides observation and ageing factor pages of genes that are homologous to known ageing-related genes. These homologues are considered as candidate or putative ageing-related genes. AgeFactDB offers a variety of search and browse options, and also allows the download of ageing factor or observation lists in TSV, CSV and XML formats.

DoD Identity Matching Engine for Security and Analysis (IMESA) Access to Criminal Justice Information (CJI) and Terrorist Screening Databases (TSDB)

DTIC Science & Technology

2016-05-04

IMESA) Access to Criminal Justice Information (CJI) and Terrorist Screening Databases (TSDB) References: See Enclosure 1 1. PURPOSE. In...CJI database mirror image files. (3) Memorandums of understanding with the FBI CJIS as the data broker for DoD organizations that need access ...not for access determinations. (3) Legal restrictions established by the Sex Offender Registration and Notification Act (SORNA) jurisdictions on

The Neotoma Paleoecology Database

NASA Astrophysics Data System (ADS)

Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

2015-12-01

The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community. Research is supported by NSF EAR-0622349.

GALT protein database: querying structural and functional features of GALT enzyme.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2014-09-01

Knowledge of the impact of variations on protein structure can enhance the comprehension of the mechanisms of genetic diseases related to that protein. Here, we present a new version of GALT Protein Database, a Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to classic Galactosemia, a rare genetic disease. This new version of this database now contains the models of 201 missense variants of GALT enzyme, including heterozygous variants, and it allows users not only to retrieve information about the missense variations affecting this protein, but also to investigate their impact on substrate binding, intersubunit interactions, stability, and other structural features. In addition, it allows the interactive visualization of the models of variants collected into the database. We have developed additional tools to improve the use of the database by nonspecialized users. This Web-accessible database (http://bioinformatica.isa.cnr.it/GALT/GALT2.0) represents a model of tools potentially suitable for application to other proteins that are involved in human pathologies and that are subjected to genetic variations. © 2014 WILEY PERIODICALS, INC.

Materials engineering data base

NASA Technical Reports Server (NTRS)

1995-01-01

The various types of materials related data that exist at the NASA Marshall Space Flight Center and compiled into databases which could be accessed by all the NASA centers and by other contractors, are presented.

The USA-NPN Information Management System: A tool in support of phenological assessments

NASA Astrophysics Data System (ADS)

Rosemartin, A.; Vazquez, R.; Wilson, B. E.; Denny, E. G.

2009-12-01

The USA National Phenology Network (USA-NPN) serves science and society by promoting a broad understanding of plant and animal phenology and the relationships among phenological patterns and all aspects of environmental change. Data management and information sharing are central to the USA-NPN mission. The USA-NPN develops, implements, and maintains a comprehensive Information Management System (IMS) to serve the needs of the network, including the collection, storage and dissemination of phenology data, access to phenology-related information, tools for data interpretation, and communication among partners of the USA-NPN. The IMS includes components for data storage, such as the National Phenology Database (NPD), and several online user interfaces to accommodate data entry, data download, data visualization and catalog searches for phenology-related information. The IMS is governed by a set of standards to ensure security, privacy, data access, and data quality. The National Phenology Database is designed to efficiently accommodate large quantities of phenology data, to be flexible to the changing needs of the network, and to provide for quality control. The database stores phenology data from multiple sources (e.g., partner organizations, researchers and citizen observers), and provides for integration with legacy datasets. Several services will be created to provide access to the data, including reports, visualization interfaces, and web services. These services will provide integrated access to phenology and related information for scientists, decision-makers and general audiences. Phenological assessments at any scale will rely on secure and flexible information management systems for the organization and analysis of phenology data. The USA-NPN’s IMS can serve phenology assessments directly, through data management and indirectly as a model for large-scale integrated data management.

NCBI GEO: mining millions of expression profiles--database and tools.

PubMed

Barrett, Tanya; Suzek, Tugba O; Troup, Dennis B; Wilhite, Stephen E; Ngau, Wing-Chi; Ledoux, Pierre; Rudnev, Dmitry; Lash, Alex E; Fujibuchi, Wataru; Edgar, Ron

2005-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30,000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

Effective spatial database support for acquiring spatial information from remote sensing images

NASA Astrophysics Data System (ADS)

Jin, Peiquan; Wan, Shouhong; Yue, Lihua

2009-12-01

In this paper, a new approach to maintain spatial information acquiring from remote-sensing images is presented, which is based on Object-Relational DBMS. According to this approach, the detected and recognized results of targets are stored and able to be further accessed in an ORDBMS-based spatial database system, and users can access the spatial information using the standard SQL interface. This approach is different from the traditional ArcSDE-based method, because the spatial information management module is totally integrated into the DBMS and becomes one of the core modules in the DBMS. We focus on three issues, namely the general framework for the ORDBMS-based spatial database system, the definitions of the add-in spatial data types and operators, and the process to develop a spatial Datablade on Informix. The results show that the ORDBMS-based spatial database support for image-based target detecting and recognition is easy and practical to be implemented.

PseudoBase: a database with RNA pseudoknots.

PubMed

van Batenburg, F H; Gultyaev, A P; Pleij, C W; Ng, J; Oliehoek, J

2000-01-01

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio. Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.

The burden of rheumatoid arthritis and access to treatment: determinants of access.

PubMed

Lundqvist, J; Kastäng, F; Kobelt, G; Jönsson, B

2008-01-01

As part of the study "The Burden of Rheumatoid Arthritis (RA) and Patient Access to Treatment", this paper reviews the impact on access to RA drugs of the approval processes, pricing and funding decisions and times to market (access) in different countries. In addition, an overview of health technology assessments (HTA) and the economic literature related to RA treatments is provided. The time from approval to market access ranged from immediate to over 500 days in the countries included in the study. A total of 55 HTA reports were identified, 40 of them in the period between 2002 and 2006; 29 were performed by European HTA agencies, 14 in Canada and 7 in the United States. A total of 239 economic evaluations related to RA were identified in a specialized health economic database (HEED).

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool. Part 4 - GLOS/GLCFS Database

DTIC Science & Technology

2014-06-01

and Coastal Data Information Program ( CDIP ). This User’s Guide includes step-by-step instructions for accessing the GLOS/GLCFS database via WaveNet...access, processing and analysis tool; part 3 – CDIP database. ERDC/CHL CHETN-xx-14. Vicksburg, MS: U.S. Army Engineer Research and Development Center

Evaluation of an Online Instructional Database Accessed by QR Codes to Support Biochemistry Practical Laboratory Classes

ERIC Educational Resources Information Center

Yip, Tor; Melling, Louise; Shaw, Kirsty J.

2016-01-01

An online instructional database containing information on commonly used pieces of laboratory equipment was created. In order to make the database highly accessible and to promote its use, QR codes were utilized. The instructional materials were available anytime and accessed using QR codes located on the equipment itself and within undergraduate…

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2013 CFR

2013-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2011 CFR

2011-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2014 CFR

2014-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2012 CFR

2012-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

Follicle Online: an integrated database of follicle assembly, development and ovulation.

PubMed

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Cooke, Howard J; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43,000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php © The Author(s) 2015. Published by Oxford University Press.

Follicle Online: an integrated database of follicle assembly, development and ovulation

PubMed Central

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database ‘Follicle Online’ that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43 000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php PMID:25931457

IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data.

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.Graphical abstractFDA approved drug data integration for predictive modeling.

VaProS: a database-integration approach for protein/genome information retrieval.

PubMed

Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

2016-12-01

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts' knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/ .

Flight Deck Interval Management Display. [Elements, Information and Annunciations Database User Guide

NASA Technical Reports Server (NTRS)

Lancaster, Jeff; Dillard, Michael; Alves, Erin; Olofinboba, Olu

2014-01-01

The User Guide details the Access Database provided with the Flight Deck Interval Management (FIM) Display Elements, Information, & Annunciations program. The goal of this User Guide is to support ease of use and the ability to quickly retrieve and select items of interest from the Database. The Database includes FIM Concepts identified in a literature review preceding the publication of this document. Only items that are directly related to FIM (e.g., spacing indicators), which change or enable FIM (e.g., menu with control buttons), or which are affected by FIM (e.g., altitude reading) are included in the database. The guide has been expanded from previous versions to cover database structure, content, and search features with voiced explanations.

Hierarchical data security in a Query-By-Example interface for a shared database.

PubMed

Taylor, Merwyn

2002-06-01

Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security module that limits access to the data. The security module ensures that researchers working in one clinic do not get access to data from another clinic. The security can be based on a flexible taxonomy structure that allows ordinary users to access data from individual clinics and super users to access data from all clinics. All researchers submit queries through the same interface and the security module processes the taxonomy and user identifiers to limit access. Using this system, two different users with different access rights can submit the same query and get different results thus reducing the need to create different interfaces for different clinics and access rights.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

The Design of Lexical Database for Indonesian Language

NASA Astrophysics Data System (ADS)

Gunawan, D.; Amalia, A.

2017-03-01

Kamus Besar Bahasa Indonesia (KBBI), an official dictionary for Indonesian language, provides lists of words with their meaning. The online version can be accessed via Internet network. Another online dictionary is Kateglo. KBBI online and Kateglo only provides an interface for human. A machine cannot retrieve data from the dictionary easily without using advanced techniques. Whereas, lexical of words is required in research or application development which related to natural language processing, text mining, information retrieval or sentiment analysis. To address this requirement, we need to build a lexical database which provides well-defined structured information about words. A well-known lexical database is WordNet, which provides the relation among words in English. This paper proposes the design of a lexical database for Indonesian language based on the combination of KBBI 4th edition, Kateglo and WordNet structure. Knowledge representation by utilizing semantic networks depict the relation among words and provide the new structure of lexical database for Indonesian language. The result of this design can be used as the foundation to build the lexical database for Indonesian language.

Overcoming barriers to a research-ready national commercial claims database.

PubMed

Newman, David; Herrera, Carolina-Nicole; Parente, Stephen T

2014-11-01

Billions of dollars have been spent on the goal of making healthcare data available to clinicians and researchers in the hopes of improving healthcare and lowering costs. However, the problems of data governance, distribution, and accessibility remain challenges for the healthcare system to overcome. In this study, we discuss some of the issues around holding, reporting, and distributing data, including the newest "big data" challenge: making the data accessible to researchers and policy makers. This article presents a case study in "big healthcare data" involving the Health Care Cost Institute (HCCI). HCCI is a nonprofit, nonpartisan, independent research institute that serves as a voluntary repository of national commercial healthcare claims data. Governance of large healthcare databases is complicated by the data-holding model and further complicated by issues related to distribution to research teams. For multi-payer healthcare claims databases, the 2 most common models of data holding (mandatory and voluntary) have different data security requirements. Furthermore, data transport and accessibility may require technological investment. HCCI's efforts offer insights from which other data managers and healthcare leaders may benefit when contemplating a data collaborative.

Integration of an Evidence Base into a Probabilistic Risk Assessment Model. The Integrated Medical Model Database: An Organized Evidence Base for Assessing In-Flight Crew Health Risk and System Design

NASA Technical Reports Server (NTRS)

Saile, Lynn; Lopez, Vilma; Bickham, Grandin; FreiredeCarvalho, Mary; Kerstman, Eric; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

This slide presentation reviews the Integrated Medical Model (IMM) database, which is an organized evidence base for assessing in-flight crew health risk. The database is a relational database accessible to many people. The database quantifies the model inputs by a ranking based on the highest value of the data as Level of Evidence (LOE) and the quality of evidence (QOE) score that provides an assessment of the evidence base for each medical condition. The IMM evidence base has already been able to provide invaluable information for designers, and for other uses.

The Steward Observatory asteroid relational database

NASA Technical Reports Server (NTRS)

Sykes, Mark V.; Alvarezdelcastillo, Elizabeth M.

1991-01-01

The Steward Observatory Asteroid Relational Database (SOARD) was created as a flexible tool for undertaking studies of asteroid populations and sub-populations, to probe the biases intrinsic to asteroid databases, to ascertain the completeness of data pertaining to specific problems, to aid in the development of observational programs, and to develop pedagogical materials. To date, SOARD has compiled an extensive list of data available on asteroids and made it accessible through a single menu-driven database program. Users may obtain tailored lists of asteroid properties for any subset of asteroids or output files which are suitable for plotting spectral data on individual asteroids. The program has online help as well as user and programmer documentation manuals. The SOARD already has provided data to fulfill requests by members of the astronomical community. The SOARD continues to grow as data is added to the database and new features are added to the program.

Insect barcode information system.

PubMed

Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

2014-01-01

Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. http://www.nabg-nbaii.res.in/barcode.

An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave.

PubMed

Silva, Ikaro; Moody, George B

The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

Designing a Relational Database to Facilitate Military Family Housing Utilization Decisions

DTIC Science & Technology

2001-06-01

TOOLS 73 A. INTRODUCTION Z"*73 B. MICROSOFT ACCESS TOOLS 74 C. GEOGRAPHIC INFORMATION SYSTEM 77 D. SUMMARY 90 VIII. CONCLUSIONS AND...FAMILYMEMBER Objects 36 Figure 5-1. The Design View for the "Find duplicates" Query 46 Figure 5-2. MS Access Design View of the Housing Inventory...55 Figure 5-6. Access Query to Weed Out Null Appliance Rows 58 Figure 6-1. HATS Main Menu (Switchboard Form) 62 Figure 6-2. Using Drop-down Menus on

Database of Geoscientific References Through 2007 for Afghanistan, Version 2

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2007-01-01

This report describes an accompanying database of geoscientific references for the country of Afghanistan. Included is an accompanying Microsoft? Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan's energy, mineral, and water resources, and geologic hazards, currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,462) and unpublished (n = 174) references compiled through September, 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable, interface and only minimum knowledge of the use of Microsoft? Access is required.

Food Composition Database Format and Structure: A User Focused Approach

PubMed Central

Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

2015-01-01

This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User’s also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user’s understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered. PMID:26554836

Building an Integrated Environment for Multimedia

NASA Technical Reports Server (NTRS)

1997-01-01

Multimedia courseware on the solar system and earth science suitable for use in elementary, middle, and high schools was developed under this grant. The courseware runs on Silicon Graphics, Incorporated (SGI) workstations and personal computers (PCs). There is also a version of the courseware accessible via the World Wide Web. Accompanying multimedia database systems were also developed to enhance the multimedia courseware. The database systems accompanying the PC software are based on the relational model, while the database systems accompanying the SGI software are based on the object-oriented model.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

X-ray Photoelectron Spectroscopy Database (Version 4.1)

National Institute of Standards and Technology Data Gateway

SRD 20 X-ray Photoelectron Spectroscopy Database (Version 4.1) (Web, free access)   The NIST XPS Database gives access to energies of many photoelectron and Auger-electron spectral lines. The database contains over 22,000 line positions, chemical shifts, doublet splittings, and energy separations of photoelectron and Auger-electron lines.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

Population groups: indexing, coverage, and retrieval effectiveness of ethnically related health care issues in health sciences databases.

PubMed Central

Efthimiadis, E N; Afifi, M

1996-01-01

OBJECTIVES: This study examined methods of accessing (for indexing and retrieval purposes) medical research on population groups in the major abstracting and indexing services of the health sciences literature. DESIGN: The study of diseases in specific population groups is facilitated by the indexing of both diseases and populations in a database. The MEDLINE, PsycINFO, and Embase databases were selected for the study. The published thesauri for these databases were examined to establish the vocabulary in use. Indexing terms were identified and examined as to their representation in the current literature. Terms were clustered further into groups thought to reflect an end user's perspective and to facilitate subsequent analysis. The medical literature contained in the three online databases was searched with both controlled vocabulary and natural language terms. RESULTS: The three thesauri revealed shallow pre-coordinated hierarchical structures, rather difficult-to-use terms for post-coordination, and a blurring of cultural, genetic, and racial facets of populations. Post-coordination is difficult because of the system-oriented terminology, which is intended mostly for information professionals. The terminology unintentionally restricts access by the end users who lack the knowledge needed to use the thesauri effectively for information retrieval. CONCLUSIONS: Population groups are not represented adequately in the index languages of health sciences databases. Users of these databases need to be alerted to the difficulties that may be encountered in searching for information on population groups. Information and health professionals may not be able to access the literature if they are not familiar with the indexing policies on population groups. Consequently, the study points to a problem that needs to be addressed, through either the redesign of existing systems or the design of new ones to meet the goals of Healthy People 2000 and beyond. PMID:8883987

New tools and methods for direct programmatic access to the dbSNP relational database

PubMed Central

Saccone, Scott F.; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A.; Rice, John P.

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale. PMID:21037260

MIPS: analysis and annotation of proteins from whole genomes in 2005

PubMed Central

Mewes, H. W.; Frishman, D.; Mayer, K. F. X.; Münsterkötter, M.; Noubibou, O.; Pagel, P.; Rattei, T.; Oesterheld, M.; Ruepp, A.; Stümpflen, V.

2006-01-01

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (). PMID:16381839

MIPS: analysis and annotation of proteins from whole genomes in 2005.

PubMed

Mewes, H W; Frishman, D; Mayer, K F X; Münsterkötter, M; Noubibou, O; Pagel, P; Rattei, T; Oesterheld, M; Ruepp, A; Stümpflen, V

2006-01-01

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein-protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.gsf.de).

The INFN-CNAF Tier-1 GEMSS Mass Storage System and database facility activity

NASA Astrophysics Data System (ADS)

Ricci, Pier Paolo; Cavalli, Alessandro; Dell'Agnello, Luca; Favaro, Matteo; Gregori, Daniele; Prosperini, Andrea; Pezzi, Michele; Sapunenko, Vladimir; Zizzi, Giovanni; Vagnoni, Vincenzo

2015-05-01

The consolidation of Mass Storage services at the INFN-CNAF Tier1 Storage department that has occurred during the last 5 years, resulted in a reliable, high performance and moderately easy-to-manage facility that provides data access, archive, backup and database services to several different use cases. At present, the GEMSS Mass Storage System, developed and installed at CNAF and based upon an integration between the IBM GPFS parallel filesystem and the Tivoli Storage Manager (TSM) tape management software, is one of the largest hierarchical storage sites in Europe. It provides storage resources for about 12% of LHC data, as well as for data of other non-LHC experiments. Files are accessed using standard SRM Grid services provided by the Storage Resource Manager (StoRM), also developed at CNAF. Data access is also provided by XRootD and HTTP/WebDaV endpoints. Besides these services, an Oracle database facility is in production characterized by an effective level of parallelism, redundancy and availability. This facility is running databases for storing and accessing relational data objects and for providing database services to the currently active use cases. It takes advantage of several Oracle technologies, like Real Application Cluster (RAC), Automatic Storage Manager (ASM) and Enterprise Manager centralized management tools, together with other technologies for performance optimization, ease of management and downtime reduction. The aim of the present paper is to illustrate the state-of-the-art of the INFN-CNAF Tier1 Storage department infrastructures and software services, and to give a brief outlook to forthcoming projects. A description of the administrative, monitoring and problem-tracking tools that play a primary role in managing the whole storage framework is also given.

Design and Implementation of an Environmental Mercury Database for Northeastern North America

NASA Astrophysics Data System (ADS)

Clair, T. A.; Evers, D.; Smith, T.; Goodale, W.; Bernier, M.

2002-12-01

An important issue faced when attempting to interpret geochemical variability studies across large regions, is the accumulation, access and consistent display of data from a large number of sources. We were given the opportunity to provide a regional assessment of mercury distribution in surface waters, sediments, invertebrates, fish, and birds in a region extending from New York State to the Island of Newfoundland. We received over 20 individual databases from State, Provincial, and Federal governments, as well as university researchers from both Canada and the United States. These databases came in a variety of formats and sizes. Our challenge was to find a way of accumulating and presenting the large amounts of acquired data, in a consistent, easily accessible fashion, which could then be more easily interpreted. Moreover, the database had to be portable and easily distributable to the large number of study participants. We developed a static database structure using a web-based approach which we were then able to mount on a server which was accessible to all project participants. The site also contained all the necessary documentation related to the data, its acquisition, as well as the methods used in its analysis and interpretation. We then copied the complete web site on CDROM's which we then distributed to all project participants, funding agencies, and other interested parties. The CDROM formed a permanent record of the project and was issued ISSN and ISBN numbers so that the information remained accessible to researchers in perpetuity. Here we present an overview of the CDROM and data structures, of the information accumulated over the first year of the study, and initial interpretation of the results.

DASTCOM5: A Portable and Current Database of Asteroid and Comet Orbit Solutions

NASA Astrophysics Data System (ADS)

Giorgini, Jon D.; Chamberlin, Alan B.

2014-11-01

A portable direct-access database containing all NASA/JPL asteroid and comet orbit solutions, with the software to access it, is available for download (ftp://ssd.jpl.nasa.gov/pub/xfr/dastcom5.zip; unzip -ao dastcom5.zip). DASTCOM5 contains the latest heliocentric IAU76/J2000 ecliptic osculating orbital elements for all known asteroids and comets as determined by a least-squares best-fit to ground-based optical, spacecraft, and radar astrometric measurements. Other physical, dynamical, and covariance parameters are included when known. A total of 142 parameters per object are supported within DASTCOM5. This information is suitable for initializing high-precision numerical integrations, assessing orbit geometry, computing trajectory uncertainties, visual magnitude, and summarizing physical characteristics of the body. The DASTCOM5 distribution is updated as often as hourly to include newly discovered objects or orbit solution updates. It includes an ASCII index of objects that supports look-ups based on name, current or past designation, SPK ID, MPC packed-designations, or record number. DASTCOM5 is the database used by the NASA/JPL Horizons ephemeris system. It is a subset exported from a larger MySQL-based relational Small-Body Database ("SBDB") maintained at JPL. The DASTCOM5 distribution is intended for programmers comfortable with UNIX/LINUX/MacOSX command-line usage who need to develop stand-alone applications. The goal of the implementation is to provide small, fast, portable, and flexibly programmatic access to JPL comet and asteroid orbit solutions. The supplied software library, examples, and application programs have been verified under gfortran, Lahey, Intel, and Sun 32/64-bit Linux/UNIX FORTRAN compilers. A command-line tool ("dxlook") is provided to enable database access from shell or script environments.

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

Mewes, H. W.; Amid, C.; Arnold, R.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Münsterkötter, M.; Pagel, P.; Strack, N.; Stümpflen, V.; Warfsmann, J.; Ruepp, A.

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein–protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

The Hong Kong/AAO/Strasbourg Hα (HASH) Planetary Nebula Database

NASA Astrophysics Data System (ADS)

Bojičić, Ivan S.; Parker, Quentin A.; Frew, David J.

2017-10-01

The Hong Kong/AAO/Strasbourg Hα (HASH) planetary nebula database is an online research platform providing free and easy access to the largest and most comprehensive catalogue of known Galactic PNe and a repository of observational data (imaging and spectroscopy) for these and related astronomical objects. The main motivation for creating this system is resolving some of long standing problems in the field e.g. problems with mimics and dubious and/or misidentifications, errors in observational data and consolidation of the widely scattered data-sets. This facility allows researchers quick and easy access to the archived and new observational data and creating and sharing of non-redundant PN samples and catalogues.

The Génolevures database.

PubMed

Martin, Tiphaine; Sherman, David J; Durrens, Pascal

2011-01-01

The Génolevures online database (URL: http://www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several campaigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedicated to large-scale comparison of these genomes, storing not only the different chromosomal elements detected in the sequences, but also the logical relations between them. The database is divided into a public part, accessible to anyone through Internet, and a private part where the Consortium members make genome annotations with our Magus annotation system; this system is used to annotate several related genomes in parallel. The public database is widely consulted and offers structured data, organized using a REST web site architecture that allows for automated requests. The implementation of the database, as well as its associated tools and methods, is evolving to cope with the influx of genome sequences produced by Next Generation Sequencing (NGS). Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

A user-defined data type for the storage of time series data allowing efficient similarity screening.

PubMed

Sorokin, Anatoly; Selkov, Gene; Goryanin, Igor

2012-07-16

The volume of the experimentally measured time series data is rapidly growing, while storage solutions offering better data types than simple arrays of numbers or opaque blobs for keeping series data are sorely lacking. A number of indexing methods have been proposed to provide efficient access to time series data, but none has so far been integrated into a tried-and-proven database system. To explore the possibility of such integration, we have developed a data type for time series storage in PostgreSQL, an object-relational database system, and equipped it with an access method based on SAX (Symbolic Aggregate approXimation). This new data type has been successfully tested in a database supporting a large-scale plant gene expression experiment, and it was additionally tested on a very large set of simulated time series data. Copyright © 2011 Elsevier B.V. All rights reserved.

Prevalence and Citation Advantage of Gold Open Access in the Subject Areas of the Scopus Database

ERIC Educational Resources Information Center

Dorta-González, Pablo; Santana-Jiménez, Yolanda

2018-01-01

The potential benefit of open access (OA) in relation to citation impact has been discussed in the literature in depth. The methodology used to test the OA citation advantage includes comparing OA vs. non-OA journal impact factors and citations of OA vs. non-OA articles published in the same non-OA journals. However, one problem with many studies…

LSE-Sign: A lexical database for Spanish Sign Language.

PubMed

Gutierrez-Sigut, Eva; Costello, Brendan; Baus, Cristina; Carreiras, Manuel

2016-03-01

The LSE-Sign database is a free online tool for selecting Spanish Sign Language stimulus materials to be used in experiments. It contains 2,400 individual signs taken from a recent standardized LSE dictionary, and a further 2,700 related nonsigns. Each entry is coded for a wide range of grammatical, phonological, and articulatory information, including handshape, location, movement, and non-manual elements. The database is accessible via a graphically based search facility which is highly flexible both in terms of the search options available and the way the results are displayed. LSE-Sign is available at the following website: http://www.bcbl.eu/databases/lse/.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reisman, D.J.

A variety of issues must be addressed in development of software for information resources. One is accessibility and use of information. Another is that to properly design, abstract, index, and do quality control on a database requires the effort of well-trained and knowledgeable personnel as well as substantial financial resources. Transferring data to other locations has inherent difficulties, including those related to incompatibility. The main issue in developing health risk assessment databases is the needs of the user.

Military Personnel: DOD Has Processes for Operating and Managing Its Sexual Assault Incident Database

DTIC Science & Technology

2017-01-01

each change and its implementation status as well as supporting the audit of products to verify conformance to requirements. Through these change...management process for modifying DSAID aligns with information technology and project management industry standards. GAO reviewed DOD documents, and...Acknowledgments 32 Related GAO Products 33 Tables Table 1: Roles and Access Rights for Users of the Defense Sexual Assault Incident Database (DSAID

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

PubMed

Schomburg, Ida; Chang, Antje; Placzek, Sandra; Söhngen, Carola; Rother, Michael; Lang, Maren; Munaretto, Cornelia; Ulas, Susanne; Stelzer, Michael; Grote, Andreas; Scheer, Maurice; Schomburg, Dietmar

2013-01-01

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalysed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models.

Scrubchem: Building Bioactivity Datasets from Pubchem ...

EPA Pesticide Factsheets

The PubChem Bioassay database is a non-curated public repository with data from 64 sources, including: ChEMBL, BindingDb, DrugBank, EPA Tox21, NIH Molecular Libraries Screening Program, and various other academic, government, and industrial contributors. Methods for extracting this public data into quality datasets, useable for analytical research, presents several big-data challenges for which we have designed manageable solutions. According to our preliminary work, there are approximately 549 million bioactivity values and related meta-data within PubChem that can be mapped to over 10,000 biological targets. However, this data is not ready for use in data-driven research, mainly due to lack of structured annotations.We used a pragmatic approach that provides increasing access to bioactivity values in the PubChem Bioassay database. This included restructuring of individual PubChem Bioassay files into a relational database (ScrubChem). ScrubChem contains all primary PubChem Bioassay data that was: reparsed; error-corrected (when applicable); enriched with additional data links from other NCBI databases; and improved by adding key biological and assay annotations derived from logic-based language processing rules. The utility of ScrubChem and the curation process were illustrated using an example bioactivity dataset for the androgen receptor protein. This initial work serves as a trial ground for establishing the technical framework for accessing, integrating, cu

Compilation of Physicochemical and Toxicological Information About Hydraulic Fracturing-Related Chemicals (Draft Database)

EPA Science Inventory

The purpose of this product is to make accessible the information about the 1,173 hydraulic fracturing-related chemicals that were listed in the external review draft of the Hydraulic Fracturing Drinking Water Assessment that was released recently. The product consists of a serie...

Development of Human Face Literature Database Using Text Mining Approach: Phase I.

PubMed

Kaur, Paramjit; Krishan, Kewal; Sharma, Suresh K

2018-06-01

The face is an important part of the human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. The amount of experiments being performed and the number of research papers being published under the domain of human face have surged in the past few decades. Several scientific disciplines, which are conducting research on human face include: Medical Science, Anthropology, Information Technology (Biometrics, Robotics, and Artificial Intelligence, etc.), Psychology, Forensic Science, Neuroscience, etc. This alarms the need of collecting and managing the data concerning human face so that the public and free access of it can be provided to the scientific community. This can be attained by developing databases and tools on human face using bioinformatics approach. The current research emphasizes on creating a database concerning literature data of human face. The database can be accessed on the basis of specific keywords, journal name, date of publication, author's name, etc. The collected research papers will be stored in the form of a database. Hence, the database will be beneficial to the research community as the comprehensive information dedicated to the human face could be found at one place. The information related to facial morphologic features, facial disorders, facial asymmetry, facial abnormalities, and many other parameters can be extracted from this database. The front end has been developed using Hyper Text Mark-up Language and Cascading Style Sheets. The back end has been developed using hypertext preprocessor (PHP). The JAVA Script has used as scripting language. MySQL (Structured Query Language) is used for database development as it is most widely used Relational Database Management System. XAMPP (X (cross platform), Apache, MySQL, PHP, Perl) open source web application software has been used as the server.The database is still under the developmental phase and discusses the initial steps of its creation. The current paper throws light on the work done till date.

Update on NASA Space Shuttle Earth Observations Photography on the laser videodisc for rapid image access

NASA Technical Reports Server (NTRS)

Lulla, Kamlesh

1994-01-01

There have been many significant improvements in the public access to the Space Shuttle Earth Observations Photography Database. New information is provided for the user community on the recently released videodisc of this database. Topics covered included the following: earlier attempts; our first laser videodisc in 1992; the new laser videodisc in 1994; and electronic database access.

Context indexing of digital cardiac ultrasound records in PACS

NASA Astrophysics Data System (ADS)

Lobodzinski, S. Suave; Meszaros, Georg N.

1998-07-01

Recent wide adoption of the DICOM 3.0 standard by ultrasound equipment vendors created a need for practical clinical implementations of cardiac imaging study visualization, management and archiving, DICOM 3.0 defines only a logical and physical format for exchanging image data (still images, video, patient and study demographics). All DICOM compliant imaging studies must presently be archived on a 650 Mb recordable compact disk. This is a severe limitation for ultrasound applications where studies of 3 to 10 minutes long are a common practice. In addition, DICOM digital echocardiography objects require physiological signal indexing, content segmentation and characterization. Since DICOM 3.0 is an interchange standard only, it does not define how to database composite video objects. The goal of this research was therefore to address the issues of efficient storage, retrieval and management of DICOM compliant cardiac video studies in a distributed PACS environment. Our Web based implementation has the advantage of accommodating both DICOM defined entity-relation modules (equipment data, patient data, video format, etc.) in standard relational database tables and digital indexed video with its attributes in an object relational database. Object relational data model facilitates content indexing of full motion cardiac imaging studies through bi-directional hyperlink generation that tie searchable video attributes and related objects to individual video frames in the temporal domain. Benefits realized from use of bi-directionally hyperlinked data models in an object relational database include: (1) real time video indexing during image acquisition, (2) random access and frame accurate instant playback of previously recorded full motion imaging data, and (3) time savings from faster and more accurate access to data through multiple navigation mechanisms such as multidimensional queries on an index, queries on a hyperlink attribute, free search and browsing.

Legal assessment tool (LAT): an interactive tool to address privacy and data protection issues for data sharing.

PubMed

Kuchinke, Wolfgang; Krauth, Christian; Bergmann, René; Karakoyun, Töresin; Woollard, Astrid; Schluender, Irene; Braasch, Benjamin; Eckert, Martin; Ohmann, Christian

2016-07-07

In an unprecedented rate data in the life sciences is generated and stored in many different databases. An ever increasing part of this data is human health data and therefore falls under data protected by legal regulations. As part of the BioMedBridges project, which created infrastructures that connect more than 10 ESFRI research infrastructures (RI), the legal and ethical prerequisites of data sharing were examined employing a novel and pragmatic approach. We employed concepts from computer science to create legal requirement clusters that enable legal interoperability between databases for the areas of data protection, data security, Intellectual Property (IP) and security of biosample data. We analysed and extracted access rules and constraints from all data providers (databases) involved in the building of data bridges covering many of Europe's most important databases. These requirement clusters were applied to five usage scenarios representing the data flow in different data bridges: Image bridge, Phenotype data bridge, Personalised medicine data bridge, Structural data bridge, and Biosample data bridge. A matrix was built to relate the important concepts from data protection regulations (e.g. pseudonymisation, identifyability, access control, consent management) with the results of the requirement clusters. An interactive user interface for querying the matrix for requirements necessary for compliant data sharing was created. To guide researchers without the need for legal expert knowledge through legal requirements, an interactive tool, the Legal Assessment Tool (LAT), was developed. LAT provides researchers interactively with a selection process to characterise the involved types of data and databases and provides suitable requirements and recommendations for concrete data access and sharing situations. The results provided by LAT are based on an analysis of the data access and sharing conditions for different kinds of data of major databases in Europe. Data sharing for research purposes must be opened for human health data and LAT is one of the means to achieve this aim. In summary, LAT provides requirements in an interactive way for compliant data access and sharing with appropriate safeguards, restrictions and responsibilities by introducing a culture of responsibility and data governance when dealing with human data.

Social media based NPL system to find and retrieve ARM data: Concept paper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

Database documentation of marine mammal stranding and mortality: current status review and future prospects.

PubMed

Chan, Derek K P; Tsui, Henry C L; Kot, Brian C W

2017-11-21

Databases are systematic tools to archive and manage information related to marine mammal stranding and mortality events. Stranding response networks, governmental authorities and non-governmental organizations have established regional or national stranding networks and have developed unique standard stranding response and necropsy protocols to document and track stranded marine mammal demographics, signalment and health data. The objectives of this study were to (1) describe and review the current status of marine mammal stranding and mortality databases worldwide, including the year established, types of database and their goals; and (2) summarize the geographic range included in the database, the number of cases recorded, accessibility, filter and display methods. Peer-reviewed literature was searched, focussing on published databases of live and dead marine mammal strandings and mortality and information released from stranding response organizations (i.e. online updates, journal articles and annual stranding reports). Databases that were not published in the primary literature or recognized by government agencies were excluded. Based on these criteria, 10 marine mammal stranding and mortality databases were identified, and strandings and necropsy data found in these databases were evaluated. We discuss the results, limitations and future prospects of database development. Future prospects include the development and application of virtopsy, a new necropsy investigation tool. A centralized web-accessed database of all available postmortem multimedia from stranded marine mammals may eventually support marine conservation and policy decisions, which will allow the use of marine animals as sentinels of ecosystem health, working towards a 'One Ocean-One Health' ideal.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Heterogeneous distributed query processing: The DAVID system

NASA Technical Reports Server (NTRS)

Jacobs, Barry E.

1985-01-01

The objective of the Distributed Access View Integrated Database (DAVID) project is the development of an easy to use computer system with which NASA scientists, engineers and administrators can uniformly access distributed heterogeneous databases. Basically, DAVID will be a database management system that sits alongside already existing database and file management systems. Its function is to enable users to access the data in other languages and file systems without having to learn the data manipulation languages. Given here is an outline of a talk on the DAVID project and several charts.

The NOAO Data Lab PHAT Photometry Database

NASA Astrophysics Data System (ADS)

Olsen, Knut; Williams, Ben; Fitzpatrick, Michael; PHAT Team

2018-01-01

We present a database containing both the combined photometric object catalog and the single epoch measurements from the Panchromatic Hubble Andromeda Treasury (PHAT). This database is hosted by the NOAO Data Lab (http://datalab.noao.edu), and as such exposes a number of data services to the PHAT photometry, including access through a Table Access Protocol (TAP) service, direct PostgreSQL queries, web-based and programmatic query interfaces, remote storage space for personal database tables and files, and a JupyterHub-based Notebook analysis environment, as well as image access through a Simple Image Access (SIA) service. We show how the Data Lab database and Jupyter Notebook environment allow for straightforward and efficient analyses of PHAT catalog data, including maps of object density, depth, and color, extraction of light curves of variable objects, and proper motion exploration.

Establishment of an international database for genetic variants in esophageal cancer.

PubMed

Vihinen, Mauno

2016-10-01

The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer-related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels--DNA, RNA, and protein-whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage. © 2016 New York Academy of Sciences.

Thailand mutation and variation database (ThaiMUT).

PubMed

Ruangrit, Uttapong; Srikummool, Metawee; Assawamakin, Anunchai; Ngamphiw, Chumpol; Chuechote, Suparat; Thaiprasarnsup, Vilasinee; Agavatpanitch, Gallissara; Pasomsab, Ekawat; Yenchitsomanus, Pa-Thai; Mahasirimongkol, Surakameth; Chantratita, Wasun; Palittapongarnpim, Prasit; Uyyanonvara, Bunyarit; Limwongse, Chanin; Tongsima, Sissades

2008-08-01

With the completion of the human genome project, novel sequencing and genotyping technologies had been utilized to detect mutations. Such mutations have continually been produced at exponential rate by researchers in various communities. Based on the population's mutation spectra, occurrences of Mendelian diseases are different across ethnic groups. A proportion of Mendelian diseases can be observed in some countries at higher rates than others. Recognizing the importance of mutation effects in Thailand, we established a National and Ethnic Mutation Database (NEMDB) for Thai people. This database, named Thailand Mutation and Variation database (ThaiMUT), offers a web-based access to genetic mutation and variation information in Thai population. This NEMDB initiative is an important informatics tool for both research and clinical purposes to retrieve and deposit human variation data. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches. ThaiMUT can be publicly accessed from http://gi.biotec.or.th/thaimut.

Improving retrospective characterization of the food environment for a large region in the United States during a historic time period.

PubMed

Auchincloss, Amy H; Moore, Kari A B; Moore, Latetia V; Diez Roux, Ana V

2012-11-01

Access to healthy foods has received increasing attention due to growing prevalence of obesity and diet-related health conditions yet there are major obstacles in characterizing the local food environment. This study developed a method to retrospectively characterize supermarkets for a single historic year, 2005, in 19 counties in 6 states in the USA using a supermarket chain-name list and two business databases. Data preparation, merging, overlaps, added-value amongst various approaches and differences by census tract area-level socio-demographic characteristics are described. Agreement between two food store databases was modest: 63%. Only 55% of the final list of supermarkets were identified by a single business database and selection criteria that included industry classification codes and sales revenue ≥$2 million. The added-value of using a supermarket chain-name list and second business database was identification of an additional 14% and 30% of supermarkets, respectively. These methods are particularly useful to retrospectively characterize access to supermarkets during a historic period and when field observations are not feasible and business databases are used. Copyright © 2012 Elsevier Ltd. All rights reserved.

PMAG: Relational Database Definition

NASA Astrophysics Data System (ADS)

Keizer, P.; Koppers, A.; Tauxe, L.; Constable, C.; Genevey, A.; Staudigel, H.; Helly, J.

2002-12-01

The Scripps center for Physical and Chemical Earth References (PACER) was established to help create databases for reference data and make them available to the Earth science community. As part of these efforts PACER supports GERM, REM and PMAG and maintains multiple online databases under the http://earthref.org umbrella website. This website has been built on top of a relational database that allows for the archiving and electronic access to a great variety of data types and formats, permitting data queries using a wide range of metadata. These online databases are designed in Oracle 8.1.5 and they are maintained at the San Diego Supercomputer Center. They are directly available via http://earthref.org/databases/. A prototype of the PMAG relational database is now operational within the existing EarthRef.org framework under http://earthref.org/databases/PMAG/. As will be shown in our presentation, the PMAG design focuses around the general workflow that results in the determination of typical paleo-magnetic analyses. This ensures that individual data points can be traced between the actual analysis and the specimen, sample, site, locality and expedition it belongs to. These relations guarantee traceability of the data by distinguishing between original and derived data, where the actual (raw) measurements are performed on the specimen level, and data on the sample level and higher are then derived products in the database. These relations may also serve to recalculate site means when new data becomes available for that locality. The PMAG data records are extensively described in terms of metadata. These metadata are used when scientists search through this online database in order to view and download their needed data. They minimally include method descriptions for field sampling, laboratory techniques and statistical analyses. They also include selection criteria used during the interpretation of the data and, most importantly, critical information about the site location (latitude, longitude, elevation), geography (continent, country, region), geological setting (lithospheric plate or block, tectonic setting), geological age (age range, timescale name, stratigraphic position) and materials (rock type, classification, alteration state). Each data point and method description is also related to its peer-reviewed reference [citation ID] as archived in the EarthRef Reference Database (ERR). This guarantees direct traceability all the way to its original source, where the user can find the bibliography of each PMAG reference along with every abstract, data table, technical note and/or appendix that are available in digital form and that can be downloaded as PDF/JPEG images and Microsoft Excel/Word data files. This may help scientists and teachers in performing their research since they have easy access to all the scientific data. It also allows for checking potential errors during the digitization process. Please visit the PMAG website at http://earthref.org/PMAG/ for more information.

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

PubMed Central

Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

2015-01-01

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

A Model Based Mars Climate Database for the Mission Design

NASA Technical Reports Server (NTRS)

2005-01-01

A viewgraph presentation on a model based climate database is shown. The topics include: 1) Why a model based climate database?; 2) Mars Climate Database v3.1 Who uses it ? (approx. 60 users!); 3) The new Mars Climate database MCD v4.0; 4) MCD v4.0: what's new ? 5) Simulation of Water ice clouds; 6) Simulation of Water ice cycle; 7) A new tool for surface pressure prediction; 8) Acces to the database MCD 4.0; 9) How to access the database; and 10) New web access

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS

EPA Science Inventory

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models
Ann M. Richard
US Environmental Protection Agency, Research Triangle Park, NC, USA

Distributed: Decentralized set of standardized, field-delimited databases,...

Software Engineering Laboratory (SEL) database organization and user's guide, revision 2

NASA Technical Reports Server (NTRS)

Morusiewicz, Linda; Bristow, John

1992-01-01

The organization of the Software Engineering Laboratory (SEL) database is presented. Included are definitions and detailed descriptions of the database tables and views, the SEL data, and system support data. The mapping from the SEL and system support data to the base table is described. In addition, techniques for accessing the database through the Database Access Manager for the SEL (DAMSEL) system and via the ORACLE structured query language (SQL) are discussed.

Software Engineering Laboratory (SEL) database organization and user's guide

NASA Technical Reports Server (NTRS)

So, Maria; Heller, Gerard; Steinberg, Sandra; Spiegel, Douglas

1989-01-01

The organization of the Software Engineering Laboratory (SEL) database is presented. Included are definitions and detailed descriptions of the database tables and views, the SEL data, and system support data. The mapping from the SEL and system support data to the base tables is described. In addition, techniques for accessing the database, through the Database Access Manager for the SEL (DAMSEL) system and via the ORACLE structured query language (SQL), are discussed.

EPA GHG Certification of Medium- and Heavy-Duty Vehicles: Development of Road Grade Profiles Representative of US Controlled Access Highways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Eric; Duran, Adam; Burton, Evan

This report includes a detailed comparison of the TomTom national road grade database relative to a local road grade dataset generated by Southwest Research Institute and a national elevation dataset publically available from the U.S. Geological Survey. This analysis concluded that the TomTom national road grade database was a suitable source of road grade data for purposes of this study.

Cloud-Based Distributed Control of Unmanned Systems

DTIC Science & Technology

2015-04-01

during mission execution. At best, the data is saved onto hard-drives and is accessible only by the local team. Data history in a form available and...following open source technologies: GeoServer, OpenLayers, PostgreSQL , and PostGIS are chosen to implement the back-end database and server. A brief...geospatial map data. 3. PostgreSQL : An SQL-compliant object-relational database that easily scales to accommodate large amounts of data - upwards to

The geographical accessibility of hospitals to the aged: a geographic information systems analysis within Illinois.

PubMed Central

Love, D; Lindquist, P

1995-01-01

OBJECTIVE. This article uses geographic information systems and their related tools to empirically measure and display the geographic accessibility of the aged population to hospital facilities within Illinois. DATA SOURCES AND STUDY SETTING. Geographic accessibility of Illinois' aged population is measured from each of the state's 10,796 census block groups to the state's 214 hospital facilities. Block group demographic compositions and centroids are obtained from 1990 census files. Hospital coordinates are obtained by the authors. STUDY DESIGN. Of five alternative measures of accessibility considered, empirical estimates are obtained for two: choice set and minimum distance. Access to both general hospitals and the subset having specialized geriatric facilities is measured with special attention to differences in accessibility between the aged within metropolitan statistical areas (MSAs) and those outside MSAs. Cumulative accessibility distributions and their summary statistics provide a basis of comparison among subgroups. DATA COLLECTION AND EXTRACTION. Geographic information systems (GIS) and their related tools are used as a means of efficiently capturing, organizing, storing, and retrieving the required data. Hospitals and census block groups are geocoded to specific locations in the database, and aspatial attributes are assigned to the hospitals and block groups. The GIS database is queried to produce shaded isarithm and point distribution maps that show the location of hospitals relative to surrounding aged populations. CONCLUSION. The vast majority of Illinois' aged population is within close proximity to hospital facilities. Eighty percent (1,147,504 persons) of the aged in Illinois are within 4.8 miles (7.7 km) of a hospital and 11.6 miles (18.7 km) of two hospitals. However, geographic accessibility differences between the aged living in MSAs and those living outside MSAs to hospitals offering geriatric services are substantial; but there is no evidence that the aged's geographical accessibility to hospitals is less favorable than that of the general population. Detailed accessibility measures permitted by geographic information system technology call into question the continued use of crude empirical accessibility measures. Images Figure 2 PMID:7860317

Authomatization of Digital Collection Access Using Mobile and Wireless Data Terminals

NASA Astrophysics Data System (ADS)

Leontiev, I. V.

Information technologies become vital due to information processing needs, database access, data analysis and decision support. Currently, a lot of scientific projects are oriented on database integration of heterogeneous systems. The problem of on-line and rapid access to large integrated systems of digital collections is also very important. Usually users move between different locations, either at work or at home. In most cases users need an efficient and remote access to information, stored in integrated data collections. Desktop computers are unable to fulfill the needs, so mobile and wireless devices become helpful. Handhelds and data terminals are nessessary in medical assistance (they store detailed information about each patient, and helpful for nurses), immediate access to data collections is used in a Highway patrol services (databanks of cars, owners, driver licences). Using mobile access, warehouse operations can be validated. Library and museum items cyclecounting will speed up using online barcode-scanning and central database access. That's why mobile devices - cell phones, PDA, handheld computers with wireless access, WindowsCE and PalmOS terminals become popular. Generally, mobile devices have a relatively slow processor, and limited display capabilities, but they are effective for storing and displaying textual data, recognize user hand-writing with stylus, support GUI. Users can perform operations on handheld terminal, and exchange data with the main system (using immediate radio access, or offline access during syncronization process) for update. In our report, we give an approach for mobile access to data collections, which raises an efficiency of data processing in a book library, helps to control available books, books in stock, validate service charges, eliminate staff mistakes, generate requests for book delivery. Our system uses mobile devices Symbol RF (with radio-channel access), and data terminals Symbol Palm Terminal for batch-processing and synchronization with remote library databases. We discuss the use of PalmOS-compatible devices, and WindowsCE terminals. Our software system is based on modular, scalable three-tier architecture. Additional functionality can be easily customized. Scalability is also supplied by Internet / Intranet technologies, and radio-access points. The base module of the system supports generic warehouse operations: cyclecounting with handheld barcode-scanners, efficient items delivery and issue, item movement, reserving, report generating on finished and in-process operations. Movements are optimized using worker's current location, operations are sorted in a priority order and transmitted to mobile and wireless worker's terminals. Mobile terminals improve of tasks processing control, eliminate staff mistakes, display actual information about main processes, provide data for online-reports, and significantly raise the efficiency of data exchange.

New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

PubMed

Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

2013-07-01

Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

'The surface management system' (SuMS) database: a surface-based database to aid cortical surface reconstruction, visualization and analysis

NASA Technical Reports Server (NTRS)

Dickson, J.; Drury, H.; Van Essen, D. C.

2001-01-01

Surface reconstructions of the cerebral cortex are increasingly widely used in the analysis and visualization of cortical structure, function and connectivity. From a neuroinformatics perspective, dealing with surface-related data poses a number of challenges. These include the multiplicity of configurations in which surfaces are routinely viewed (e.g. inflated maps, spheres and flat maps), plus the diversity of experimental data that can be represented on any given surface. To address these challenges, we have developed a surface management system (SuMS) that allows automated storage and retrieval of complex surface-related datasets. SuMS provides a systematic framework for the classification, storage and retrieval of many types of surface-related data and associated volume data. Within this classification framework, it serves as a version-control system capable of handling large numbers of surface and volume datasets. With built-in database management system support, SuMS provides rapid search and retrieval capabilities across all the datasets, while also incorporating multiple security levels to regulate access. SuMS is implemented in Java and can be accessed via a Web interface (WebSuMS) or using downloaded client software. Thus, SuMS is well positioned to act as a multiplatform, multi-user 'surface request broker' for the neuroscience community.

Full-Text Linking: Affiliated versus Nonaffiliated Access in a Free Database.

ERIC Educational Resources Information Center

Grogg, Jill E.; Andreadis, Debra K.; Kirk, Rachel A.

2002-01-01

Presents a comparison of access to full-text articles from a free bibliographic database (PubSCIENCE) for affiliated and unaffiliated users. Found that affiliated users had access to more full-text articles than unaffiliated users had, and that both types of users could increase their level of access through additional searching and greater…

TMDB: a literature-curated database for small molecular compounds found from tea.

PubMed

Yue, Yi; Chu, Gang-Xiu; Liu, Xue-Shi; Tang, Xing; Wang, Wei; Liu, Guang-Jin; Yang, Tao; Ling, Tie-Jun; Wang, Xiao-Gang; Zhang, Zheng-Zhu; Xia, Tao; Wan, Xiao-Chun; Bao, Guan-Hu

2014-09-16

Tea is one of the most consumed beverages worldwide. The healthy effects of tea are attributed to a wealthy of different chemical components from tea. Thousands of studies on the chemical constituents of tea had been reported. However, data from these individual reports have not been collected into a single database. The lack of a curated database of related information limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application. The Tea Metabolome database (TMDB), a manually curated and web-accessible database, was developed to provide detailed, searchable descriptions of small molecular compounds found in Camellia spp. esp. in the plant Camellia sinensis and compounds in its manufactured products (different kinds of tea infusion). TMDB is currently the most complete and comprehensive curated collection of tea compounds data in the world. It contains records for more than 1393 constituents found in tea with information gathered from 364 published books, journal articles, and electronic databases. It also contains experimental 1H NMR and 13C NMR data collected from the purified reference compounds or collected from other database resources such as HMDB. TMDB interface allows users to retrieve tea compounds entries by keyword search using compound name, formula, occurrence, and CAS register number. Each entry in the TMDB contains an average of 24 separate data fields including its original plant species, compound structure, formula, molecular weight, name, CAS registry number, compound types, compound uses including healthy benefits, reference literatures, NMR, MS data, and the corresponding ID from databases such as HMDB and Pubmed. Users can also contribute novel regulatory entries by using a web-based submission page. The TMDB database is freely accessible from the URL of http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp. The TMDB is designed to address the broad needs of tea biochemists, natural products chemists, nutritionists, and members of tea related research community. The TMDB database provides a solid platform for collection, standardization, and searching of compounds information found in tea. As such this database will be a comprehensive repository for tea biochemistry and tea health research community.

Mediterranean Founder Mutation Database (MFMD): Taking Advantage from Founder Mutations in Genetics Diagnosis, Genetic Diversity and Migration History of the Mediterranean Population.

PubMed

Charoute, Hicham; Bakhchane, Amina; Benrahma, Houda; Romdhane, Lilia; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Abdelhak, Sonia; Lenaers, Guy; Barakat, Abdelhamid

2015-11-01

The Mediterranean basin has been the theater of migration crossroads followed by settlement of several societies and cultures in prehistoric and historical times, with important consequences on genetic and genomic determinisms. Here, we present the Mediterranean Founder Mutation Database (MFMD), established to offer web-based access to founder mutation information in the Mediterranean population. Mutation data were collected from the literature and other online resources and systematically reviewed and assembled into this database. The information provided for each founder mutation includes DNA change, amino-acid change, mutation type and mutation effect, as well as mutation frequency and coalescence time when available. Currently, the database contains 383 founder mutations found in 210 genes related to 219 diseases. We believe that MFMD will help scientists and physicians to design more rapid and less expensive genetic diagnostic tests. Moreover, the coalescence time of founder mutations gives an overview about the migration history of the Mediterranean population. MFMD can be publicly accessed from http://mfmd.pasteur.ma. © 2015 WILEY PERIODICALS, INC.

Using GenBank.

PubMed

Wheeler, David

2007-01-01

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

A User-Friendly, Keyword-Searchable Database of Geoscientific References Through 2007 for Afghanistan

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2008-01-01

This report includes a document and accompanying Microsoft Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan?s energy, mineral, and water resources, and geologic hazards currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,489) and unpublished (n = 176) references compiled through calendar year 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable interface and only minimum knowledge of the use of Microsoft Access is required.

Data Model and Relational Database Design for Highway Runoff Water-Quality Metadata

USGS Publications Warehouse

Granato, Gregory E.; Tessler, Steven

2001-01-01

A National highway and urban runoff waterquality metadatabase was developed by the U.S. Geological Survey in cooperation with the Federal Highway Administration as part of the National Highway Runoff Water-Quality Data and Methodology Synthesis (NDAMS). The database was designed to catalog available literature and to document results of the synthesis in a format that would facilitate current and future research on highway and urban runoff. This report documents the design and implementation of the NDAMS relational database, which was designed to provide a catalog of available information and the results of an assessment of the available data. All the citations and the metadata collected during the review process are presented in a stratified metadatabase that contains citations for relevant publications, abstracts (or previa), and reportreview metadata for a sample of selected reports that document results of runoff quality investigations. The database is referred to as a metadatabase because it contains information about available data sets rather than a record of the original data. The database contains the metadata needed to evaluate and characterize how valid, current, complete, comparable, and technically defensible published and available information may be when evaluated for application to the different dataquality objectives as defined by decision makers. This database is a relational database, in that all information is ultimately linked to a given citation in the catalog of available reports. The main database file contains 86 tables consisting of 29 data tables, 11 association tables, and 46 domain tables. The data tables all link to a particular citation, and each data table is focused on one aspect of the information collected in the literature search and the evaluation of available information. This database is implemented in the Microsoft (MS) Access database software because it is widely used within and outside of government and is familiar to many existing and potential customers. The stratified metadatabase design for the NDAMS program is presented in the MS Access file DBDESIGN.mdb and documented with a data dictionary in the NDAMS_DD.mdb file recorded on the CD-ROM. The data dictionary file includes complete documentation of the table names, table descriptions, and information about each of the 419 fields in the database.

Second-Tier Database for Ecosystem Focus, 2002-2003 Annual Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Holmes, Chris; Muongchanh, Christine; Anderson, James J.

2003-11-01

The Second-Tier Database for Ecosystem Focus (Contract 00004124) provides direct and timely public access to Columbia Basin environmental, operational, fishery and riverine data resources for federal, state, public and private entities. The Second-Tier Database known as Data Access in Realtime (DART) integrates public data for effective access, consideration and application. DART also provides analysis tools and performance measures helpful in evaluating the condition of Columbia Basin salmonid stocks.

MoonDB — A Data System for Analytical Data of Lunar Samples

NASA Astrophysics Data System (ADS)

Lehnert, K.; Ji, P.; Cai, M.; Evans, C.; Zeigler, R.

2018-04-01

MoonDB is a data system that makes analytical data from the Apollo lunar sample collection and lunar meteorites accessible by synthesizing published and unpublished datasets in a relational database with an online search interface.

49 CFR 239.303 - Electronic recordkeeping.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Electronic recordkeeping. 239.303 Section 239.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... limits and controls accessibility to such information retained in its database system and identifies...

49 CFR 234.315 - Electronic recordkeeping.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Electronic recordkeeping. 234.315 Section 234.315 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... railroad adequately limits and controls accessibility to the records retained in its electronic database...

49 CFR 234.315 - Electronic recordkeeping.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Electronic recordkeeping. 234.315 Section 234.315 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... railroad adequately limits and controls accessibility to the records retained in its electronic database...

49 CFR 234.315 - Electronic recordkeeping.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Electronic recordkeeping. 234.315 Section 234.315 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... railroad adequately limits and controls accessibility to the records retained in its electronic database...

A hydrophysical database to develop pedotransfer functions for Brazilian soils: challenges and perspectives

USDA-ARS?s Scientific Manuscript database

Access to soil hydrological data is vital for hydrology projects and for supporting decision-making in issues related to the availability of food and water and the forecasting of phenomena related to soil surface stability. Brazil is a country of continental dimensions and has accumulated a signific...

A service-oriented data access control model

NASA Astrophysics Data System (ADS)

Meng, Wei; Li, Fengmin; Pan, Juchen; Song, Song; Bian, Jiali

2017-01-01

The development of mobile computing, cloud computing and distributed computing meets the growing individual service needs. Facing with complex application system, it's an urgent problem to ensure real-time, dynamic, and fine-grained data access control. By analyzing common data access control models, on the basis of mandatory access control model, the paper proposes a service-oriented access control model. By regarding system services as subject and data of databases as object, the model defines access levels and access identification of subject and object, and ensures system services securely to access databases.

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide.

PubMed

van Baal, Sjozef; Kaimakis, Polynikis; Phommarinh, Manyphong; Koumbi, Daphne; Cuppens, Harry; Riccardino, Francesca; Macek, Milan; Scriver, Charles R; Patrinos, George P

2007-01-01

Frequency of INherited Disorders database (FINDbase) (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with its frequency in that population. The initial information is derived from the published literature, locus-specific databases and genetic disease consortia. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations. Query outputs can be either in a table or graphical format, accompanied by reference(s) on the data source. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected interface. Databaseaccess is free of charge and there are no registration requirements for data querying. FINDbase provides a simple, web-based system for population-based mutation data collection and retrieval and can serve not only as a valuable online tool for molecular genetic testing of inherited disorders but also as a non-profit model for sustainable database funding, in the form of a 'database-journal'.

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

The article describes the developed database designed as comprehensive data storage of the fixed target experiment BM@N [1] at Joint Institute for Nuclear Research (JINR) in Dubna. The structure and purposes of the BM@N facility will be briefly presented. The scheme of the unified database and its parameters will be described in detail. The use of the BM@N database implemented on the PostgreSQL database management system (DBMS) allows one to provide user access to the actual information of the experiment. Also the interfaces developed for the access to the database will be presented. One was implemented as the set of C++ classes to access the data without SQL statements, the other-Web-interface being available on the Web page of the BM@N experiment.

Access to digital library databases in higher education: design problems and infrastructural gaps.

PubMed

Oswal, Sushil K

2014-01-01

After defining accessibility and usability, the author offers a broad survey of the research studies on digital content databases which have thus far primarily depended on data drawn from studies conducted by sighted researchers with non-disabled users employing screen readers and low vision devices. This article aims at producing a detailed description of the difficulties confronted by blind screen reader users with online library databases which now hold most of the academic, peer-reviewed journal and periodical content essential for research and teaching in higher education. The approach taken here is borrowed from descriptive ethnography which allows the author to create a complete picture of the accessibility and usability problems faced by an experienced academic user of digital library databases and screen readers. The author provides a detailed analysis of the different aspects of accessibility issues in digital databases under several headers with a special focus on full-text PDF files. The author emphasizes that long-term studies with actual, blind screen reader users employing both qualitative and computerized research tools can yield meaningful data for the designers and developers to improve these databases to a level that they begin to provide an equal access to the blind.

REDIdb: the RNA editing database.

PubMed

Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

2007-01-01

The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

Evolution of the use of relational and NoSQL databases in the ATLAS experiment

NASA Astrophysics Data System (ADS)

Barberis, D.

2016-09-01

The ATLAS experiment used for many years a large database infrastructure based on Oracle to store several different types of non-event data: time-dependent detector configuration and conditions data, calibrations and alignments, configurations of Grid sites, catalogues for data management tools, job records for distributed workload management tools, run and event metadata. The rapid development of "NoSQL" databases (structured storage services) in the last five years allowed an extended and complementary usage of traditional relational databases and new structured storage tools in order to improve the performance of existing applications and to extend their functionalities using the possibilities offered by the modern storage systems. The trend is towards using the best tool for each kind of data, separating for example the intrinsically relational metadata from payload storage, and records that are frequently updated and benefit from transactions from archived information. Access to all components has to be orchestrated by specialised services that run on front-end machines and shield the user from the complexity of data storage infrastructure. This paper describes this technology evolution in the ATLAS database infrastructure and presents a few examples of large database applications that benefit from it.

Atomic Spectra Database (ASD)

National Institute of Standards and Technology Data Gateway

SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

Gene annotation from scientific literature using mappings between keyword systems.

PubMed

Pérez, Antonio J; Perez-Iratxeta, Carolina; Bork, Peer; Thode, Guillermo; Andrade, Miguel A

2004-09-01

The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene. To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%). The algorithm can be publicly accessed and used for the annotation of sequences through a web server at http://www.bork.embl.de/kat

Databases for LDEF results

NASA Technical Reports Server (NTRS)

Bohnhoff-Hlavacek, Gail

1992-01-01

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

The ChArMEx database

NASA Astrophysics Data System (ADS)

Ferré, Hélène; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Cloché, Sophie; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mière, Arnaud; Ramage, Karim; Vermeulen, Anne; Boulanger, Damien

2015-04-01

The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters , intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services, such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between ICARE, IPSL and OMP data centers and has been set up in the framework of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. ChArMEx data, either produced or used by the project, are documented and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. The website offers the usual but user-friendly functionalities: data catalog, user registration procedure, search tool to select and access data... The metadata (data description) are standardized, and comply with international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). A Digital Object Identifier (DOI) assignement procedure allows to automatically register the datasets, in order to make them easier to access, cite, reuse and verify. At present, the ChArMEx database contains about 120 datasets, including more than 80 in situ datasets (2012, 2013 and 2014 summer campaigns, background monitoring station of Ersa...), 25 model output sets (dust model intercomparison, MEDCORDEX scenarios...), a high resolution emission inventory over the Mediterranean... Many in situ datasets have been inserted in a relational database, in order to enable more accurate selection and download of different datasets in a shared format. Many dedicated satellite products (SEVIRI, TRIMM, PARASOL...) are processed and will soon be accessible through the database website. In order to meet the operational needs of the airborne and ground based observational teams during the ChArMEx campaigns, a day-to-day chart display website has been developed and operated: http://choc.sedoo.org. It offers a convenient way to browse weather conditions and chemical composition during the campaign periods. Every scientist is invited to visit the ChArMEx websites, to register and to request data. Feel free to contact charmex-database@sedoo.fr for any question.

The AMMA database

NASA Astrophysics Data System (ADS)

Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

2010-05-01

The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can concern local, satellite and model data. - Documentation: catalogue of all the available data and their metadata. These tools have been developed using standard and free languages and softwares: - Linux system with an Apache web server and a Tomcat application server; - J2EE tools : JSF and Struts frameworks, hibernate; - relational database management systems: PostgreSQL and MySQL; - OpenLDAP directory. In order to facilitate the access to the data by African scientists, the complete system has been mirrored at AGHRYMET Regional Centre in Niamey and is operational there since January 2009. Users can now access metadata and request data through one or the other of two equivalent portals: http://database.amma-international.org or http://amma.agrhymet.ne/amma-data.

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

PubMed Central

Blenda, Anna; Scheffler, Jodi; Scheffler, Brian; Palmer, Michael; Lacape, Jean-Marc; Yu, John Z; Jesudurai, Christopher; Jung, Sook; Muthukumar, Sriram; Yellambalase, Preetham; Ficklin, Stephen; Staton, Margaret; Eshelman, Robert; Ulloa, Mauricio; Saha, Sukumar; Burr, Ben; Liu, Shaolin; Zhang, Tianzhen; Fang, Deqiu; Pepper, Alan; Kumpatla, Siva; Jacobs, John; Tomkins, Jeff; Cantrell, Roy; Main, Dorrie

2006-01-01

Background The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. Description At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. Conclusion The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp. PMID:16737546

Electronic Reference Library: Silverplatter's Database Networking Solution.

ERIC Educational Resources Information Center

Millea, Megan

Silverplatter's Electronic Reference Library (ERL) provides wide area network access to its databases using TCP/IP communications and client-server architecture. ERL has two main components: The ERL clients (retrieval interface) and the ERL server (search engines). ERL clients provide patrons with seamless access to multiple databases on multiple…

Development and applications of the EntomopathogenID MLSA database for use in agricultural systems

USDA-ARS?s Scientific Manuscript database

The current study reports the development and application of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal was to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identi...

48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Procurement Data System—Public access to data. (a) The FPDS database. The General Services Administration awarded a contract for creation and operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments and agencies as required by Federal Acquisition...

48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Procurement Data System—Public access to data. (a) The FPDS database. The General Services Administration awarded a contract for creation and operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments and agencies as required by Federal Acquisition...

Web client and ODBC access to legacy database information: a low cost approach.

PubMed Central

Sanders, N. W.; Mann, N. H.; Spengler, D. M.

1997-01-01

A new method has been developed for the Department of Orthopaedics of Vanderbilt University Medical Center to access departmental clinical data. Previously this data was stored only in the medical center's mainframe DB2 database, it is now additionally stored in a departmental SQL database. Access to this data is available via any ODBC compliant front-end or a web client. With a small budget and no full time staff, we were able to give our department on-line access to many years worth of patient data that was previously inaccessible. PMID:9357735

Conceptual Model Formalization in a Semantic Interoperability Service Framework: Transforming Relational Database Schemas to OWL.

PubMed

Bravo, Carlos; Suarez, Carlos; González, Carolina; López, Diego; Blobel, Bernd

2014-01-01

Healthcare information is distributed through multiple heterogeneous and autonomous systems. Access to, and sharing of, distributed information sources are a challenging task. To contribute to meeting this challenge, this paper presents a formal, complete and semi-automatic transformation service from Relational Databases to Web Ontology Language. The proposed service makes use of an algorithm that allows to transform several data models of different domains by deploying mainly inheritance rules. The paper emphasizes the relevance of integrating the proposed approach into an ontology-based interoperability service to achieve semantic interoperability.

A structural informatics approach to mine kinase knowledge bases.

PubMed

Brooijmans, Natasja; Mobilio, Dominick; Walker, Gary; Nilakantan, Ramaswamy; Denny, Rajiah A; Feyfant, Eric; Diller, David; Bikker, Jack; Humblet, Christine

2010-03-01

In this paper, we describe a combination of structural informatics approaches developed to mine data extracted from existing structure knowledge bases (Protein Data Bank and the GVK database) with a focus on kinase ATP-binding site data. In contrast to existing systems that retrieve and analyze protein structures, our techniques are centered on a database of ligand-bound geometries in relation to residues lining the binding site and transparent access to ligand-based SAR data. We illustrate the systems in the context of the Abelson kinase and related inhibitor structures. 2009 Elsevier Ltd. All rights reserved.

Clinical Databases for Chest Physicians.

PubMed

Courtwright, Andrew M; Gabriel, Peter E

2018-04-01

A clinical database is a repository of patient medical and sociodemographic information focused on one or more specific health condition or exposure. Although clinical databases may be used for research purposes, their primary goal is to collect and track patient data for quality improvement, quality assurance, and/or actual clinical management. This article aims to provide an introduction and practical advice on the development of small-scale clinical databases for chest physicians and practice groups. Through example projects, we discuss the pros and cons of available technical platforms, including Microsoft Excel and Access, relational database management systems such as Oracle and PostgreSQL, and Research Electronic Data Capture. We consider approaches to deciding the base unit of data collection, creating consensus around variable definitions, and structuring routine clinical care to complement database aims. We conclude with an overview of regulatory and security considerations for clinical databases. Copyright © 2018 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Heterogeneous distributed databases: A case study

NASA Technical Reports Server (NTRS)

Stewart, Tracy R.; Mukkamala, Ravi

1991-01-01

Alternatives are reviewed for accessing distributed heterogeneous databases and a recommended solution is proposed. The current study is limited to the Automated Information Systems Center at the Naval Sea Combat Systems Engineering Station at Norfolk, VA. This center maintains two databases located on Digital Equipment Corporation's VAX computers running under the VMS operating system. The first data base, ICMS, resides on a VAX11/780 and has been implemented using VAX DBMS, a CODASYL based system. The second database, CSA, resides on a VAX 6460 and has been implemented using the ORACLE relational database management system (RDBMS). Both databases are used for configuration management within the U.S. Navy. Different customer bases are supported by each database. ICMS tracks U.S. Navy ships and major systems (anti-sub, sonar, etc.). Even though the major systems on ships and submarines have totally different functions, some of the equipment within the major systems are common to both ships and submarines.

Design and implementation of relational databases relevant to the diverse needs of a tuberculosis case contact study in the Gambia.

PubMed

Jeffries, D J; Donkor, S; Brookes, R H; Fox, A; Hill, P C

2004-09-01

The data requirements of a large multidisciplinary tuberculosis case contact study are complex. We describe an ACCESS-based relational database system that meets our rigorous requirements for data entry and validation, while being user-friendly, flexible, exportable, and easy to install on a network or stand alone system. This includes the development of a double data entry package for epidemiology and laboratory data, semi-automated entry of ELISPOT data directly from the plate reader, and a suite of new programmes for the manipulation and integration of flow cytometry data. The double entered epidemiology and immunology databases are combined into a separate database, providing a near-real-time analysis of immuno-epidemiological data, allowing important trends to be identified early and major decisions about the study to be made and acted on. This dynamic data management model is portable and can easily be applied to other studies.

Integrating Scientific Array Processing into Standard SQL

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Bachhuber, Johannes; Baumann, Peter

2014-05-01

We live in a time that is dominated by data. Data storage is cheap and more applications than ever accrue vast amounts of data. Storing the emerging multidimensional data sets efficiently, however, and allowing them to be queried by their inherent structure, is a challenge many databases have to face today. Despite the fact that multidimensional array data is almost always linked to additional, non-array information, array databases have mostly developed separately from relational systems, resulting in a disparity between the two database categories. The current SQL standard and SQL DBMS supports arrays - and in an extension also multidimensional arrays - but does so in a very rudimentary and inefficient way. This poster demonstrates the practicality of an SQL extension for array processing, implemented in a proof-of-concept multi-faceted system that manages a federation of array and relational database systems, providing transparent, efficient and scalable access to the heterogeneous data in them.

The Steward Observatory asteroid relational database

NASA Technical Reports Server (NTRS)

Sykes, Mark V.; Alvarezdelcastillo, Elizabeth M.

1992-01-01

The Steward Observatory Asteroid Relational Database (SOARD) was created as a flexible tool for undertaking studies of asteroid populations and sub-populations, to probe the biases intrinsic to asteroid databases, to ascertain the completeness of data pertaining to specific problems, to aid in the development of observational programs, and to develop pedagogical materials. To date SOARD has compiled an extensive list of data available on asteroids and made it accessible through a single menu-driven database program. Users may obtain tailored lists of asteroid properties for any subset of asteroids or output files which are suitable for plotting spectral data on individual asteroids. A browse capability allows the user to explore the contents of any data file. SOARD offers, also, an asteroid bibliography containing about 13,000 references. The program has online help as well as user and programmer documentation manuals. SOARD continues to provide data to fulfill requests by members of the astronomical community and will continue to grow as data is added to the database and new features are added to the program.

Financing a future for public biological data.

PubMed

Ellis, L B; Kalumbi, D

1999-09-01

The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available; database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions. This study examines the finances and use statistics of a few of these organizations in more depth, and reviews several economic models that may help sustain them. Six organizations were studied. Their administrative overhead is fairly low; non-administrative personnel and computer-related costs account for 77% of expenses. One smaller, more specialized US database, in 1997, had 60% of total access from US domains; a majority (56%) of its US accesses came from commercial domains, although only 2% of the 153 databases originally studied received any industrial support. The most popular model used to gain industrial support is asymmetric pricing: preferentially charging the commercial users of a database. At least five biological databases have recently begun using this model. Advertising is another model which may be useful for the more general, more heavily used sites. Microcommerce has promise, especially for databases that do not attract advertisers, but needs further testing. The least income reported for any of the databases studied was $50,000/year; applying this rate to 400 biological databases (a lower limit of the number of such databases, many of which require far larger resources) would mean annual support need of at least $20 million. To obtain this level of support is challenging, yet failure to accept the challenge could be catastrophic. lynda@tc.umn. edu

Evolution of grid-wide access to database resident information in ATLAS using Frontier

NASA Astrophysics Data System (ADS)

Barberis, D.; Bujor, F.; de Stefano, J.; Dewhurst, A. L.; Dykstra, D.; Front, D.; Gallas, E.; Gamboa, C. F.; Luehring, F.; Walker, R.

2012-12-01

The ATLAS experiment deployed Frontier technology worldwide during the initial year of LHC collision data taking to enable user analysis jobs running on the Worldwide LHC Computing Grid to access database resident data. Since that time, the deployment model has evolved to optimize resources, improve performance, and streamline maintenance of Frontier and related infrastructure. In this presentation we focus on the specific changes in the deployment and improvements undertaken, such as the optimization of cache and launchpad location, the use of RPMs for more uniform deployment of underlying Frontier related components, improvements in monitoring, optimization of fail-over, and an increasing use of a centrally managed database containing site specific information (for configuration of services and monitoring). In addition, analysis of Frontier logs has allowed us a deeper understanding of problematic queries and understanding of use cases. Use of the system has grown beyond user analysis and subsystem specific tasks such as calibration and alignment, extending into production processing areas, such as initial reconstruction and trigger reprocessing. With a more robust and tuned system, we are better equipped to satisfy the still growing number of diverse clients and the demands of increasingly sophisticated processing and analysis.

49 CFR 239.303 - Electronic recordkeeping.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Electronic recordkeeping. 239.303 Section 239.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... accessibility to such information retained in its database system and identifies those individuals who have such...

49 CFR 239.303 - Electronic recordkeeping.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Electronic recordkeeping. 239.303 Section 239.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... accessibility to such information retained in its database system and identifies those individuals who have such...

49 CFR 239.303 - Electronic recordkeeping.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Electronic recordkeeping. 239.303 Section 239.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... accessibility to such information retained in its database system and identifies those individuals who have such...

49 CFR 239.303 - Electronic recordkeeping.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Electronic recordkeeping. 239.303 Section 239.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... accessibility to such information retained in its database system and identifies those individuals who have such...

Geographic Disparities in Access to Agencies Providing Income-Related Social Services.

PubMed

Bauer, Scott R; Monuteaux, Michael C; Fleegler, Eric W

2015-10-01

Geographic location is an important factor in understanding disparities in access to health-care and social services. The objective of this cross-sectional study is to evaluate disparities in the geographic distribution of income-related social service agencies relative to populations in need within Boston. Agency locations were obtained from a comprehensive database of social services in Boston. Geographic information systems mapped the spatial relationship of the agencies to the population using point density estimation and was compared to census population data. A multivariate logistic regression was conducted to evaluate factors associated with categories of income-related agency density. Median agency density within census block groups ranged from 0 to 8 agencies per square mile per 100 population below the federal poverty level (FPL). Thirty percent (n = 31,810) of persons living below the FPL have no access to income-related social services within 0.5 miles, and 77 % of persons living below FPL (n = 83,022) have access to 2 or fewer agencies. 27.0 % of Blacks, 30.1 % of Hispanics, and 41.0 % of non-Hispanic Whites with incomes below FPL have zero access. In conclusion, some neighborhoods in Boston with a high concentration of low-income populations have limited access to income-related social service agencies.

Genomics Portals: integrative web-platform for mining genomics data.

PubMed

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

TOXNET and Beyond: Using the National Library of Medicine's Environmental Health and Toxicology Portal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Templin-Branner, W.

2010-10-20

The National Library of Medicine's Environmental Health and Toxicology Portal provides access to numerous databases that can help you explore environmental chemicals and risks. TOXNET and Beyond: Using NLM's Environmental Health and Toxicology Portal conveys the fundamentals of searching the NLM's TOXNET system of databases in chemistry, toxicology, environmental health, and related fields. In addition to TOXNET, the course will highlight various resources available through the Environmental Health and Toxicology Portal.

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

[The database server for the medical bibliography database at Charles University].

PubMed

Vejvalka, J; Rojíková, V; Ulrych, O; Vorísek, M

1998-01-01

In the medical community, bibliographic databases are widely accepted as a most important source of information both for theoretical and clinical disciplines. To improve access to medical bibliographic databases at Charles University, a database server (ERL by Silver Platter) was set up at the 2nd Faculty of Medicine in Prague. The server, accessible by Internet 24 hours/7 days, hosts now 14 years' MEDLINE and 10 years' EMBASE Paediatrics. Two different strategies are available for connecting to the server: a specialized client program that communicates over the Internet (suitable for professional searching) and a web-based access that requires no specialized software (except the WWW browser) on the client side. The server is now offered to academic community to host further databases, possibly subscribed by consortia whose individual members would not subscribe them by themselves.

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... places that information into a common database that the covered affiliate may access. (3) Service... maintains or accesses a common database that the covered affiliate may access) receives eligibility... the notice and opt-out provisions under other privacy rules under the FCRA, the GLB Act or the CEA. ...

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... places that information into a common database that the covered affiliate may access. (3) Service... maintains or accesses a common database that the covered affiliate may access) receives eligibility... the notice and opt-out provisions under other privacy rules under the FCRA, the GLB Act or the CEA. ...

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... places that information into a common database that the covered affiliate may access. (3) Service... maintains or accesses a common database that the covered affiliate may access) receives eligibility... the notice and opt-out provisions under other privacy rules under the FCRA, the GLB Act or the CEA. ...

EROS Main Image File: A Picture Perfect Database for Landsat Imagery and Aerial Photography.

ERIC Educational Resources Information Center

Jack, Robert F.

1984-01-01

Describes Earth Resources Observation System online database, which provides access to computerized images of Earth obtained via satellite. Highlights include retrieval system and commands, types of images, search strategies, other online functions, and interpretation of accessions. Satellite information, sources and samples of accessions, and…

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

RESIS-II: An Updated Version of the Original Reservoir Sedimentation Survey Information System (RESIS) Database

USGS Publications Warehouse

Ackerman, Katherine V.; Mixon, David M.; Sundquist, Eric T.; Stallard, Robert F.; Schwarz, Gregory E.; Stewart, David W.

2009-01-01

The Reservoir Sedimentation Survey Information System (RESIS) database, originally compiled by the Soil Conservation Service (now the Natural Resources Conservation Service) in collaboration with the Texas Agricultural Experiment Station, is the most comprehensive compilation of data from reservoir sedimentation surveys throughout the conterminous United States (U.S.). The database is a cumulative historical archive that includes data from as early as 1755 and as late as 1993. The 1,823 reservoirs included in the database range in size from farm ponds to the largest U.S. reservoirs (such as Lake Mead). Results from 6,617 bathymetric surveys are available in the database. This Data Series provides an improved version of the original RESIS database, termed RESIS-II, and a report describing RESIS-II. The RESIS-II relational database is stored in Microsoft Access and includes more precise location coordinates for most of the reservoirs than the original database but excludes information on reservoir ownership. RESIS-II is anticipated to be a template for further improvements in the database.

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean.

PubMed

Pagliosa, Paulo R; Doria, João G; Misturini, Dairana; Otegui, Mariana B P; Oortman, Mariana S; Weis, Wilson A; Faroni-Perez, Larisse; Alves, Alexandre P; Camargo, Maurício G; Amaral, A Cecília Z; Marques, Antonio C; Lana, Paulo C

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/.

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

PubMed Central

Pagliosa, Paulo R.; Doria, João G.; Misturini, Dairana; Otegui, Mariana B. P.; Oortman, Mariana S.; Weis, Wilson A.; Faroni-Perez, Larisse; Alves, Alexandre P.; Camargo, Maurício G.; Amaral, A. Cecília Z.; Marques, Antonio C.; Lana, Paulo C.

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/ PMID:24573879

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

48 CFR 504.605-70 - Federal Procurement Data System-Public access to data.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Procurement Data System—Public access to data. (a) The FPDS database. The General Services Administration awarded a contract for creation and operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments and agencies as required by FAR subpart 4.6. One of...

48 CFR 504.605-70 - Federal Procurement Data System-Public access to data.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Procurement Data System—Public access to data. (a) The FPDS database. The General Services Administration awarded a contract for creation and operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments and agencies as required by FAR subpart 4.6. One of...

48 CFR 504.605-70 - Federal Procurement Data System-Public access to data.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Procurement Data System—Public access to data. (a) The FPDS database. The General Services Administration awarded a contract for creation and operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments and agencies as required by FAR subpart 4.6. One of...

Tao of Gateway: Providing Internet Access to Licensed Databases.

ERIC Educational Resources Information Center

McClellan, Gregory A.; Garrison, William V.

1997-01-01

Illustrates an approach for providing networked access to licensed databases over the Internet by positioning the library between patron and vendor. Describes how the gateway systems and database connection servers work and discusses how treatment of security has evolved with the introduction of the World Wide Web. Outlines plans to reimplement…

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main See statistics for JOIDES members. See statistics for Janus database. 1997 October November December accessible only on www-odp.tamu.edu. ** End of ODP, start of IODP. Privacy Policy ODP | Search | Database

Windows on the brain: the emerging role of atlases and databases in neuroscience

NASA Technical Reports Server (NTRS)

Van Essen, David C.; VanEssen, D. C. (Principal Investigator)

2002-01-01

Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data. Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities and internet access.

A national look at carbon capture and storage-National carbon sequestration database and geographical information system (NatCarb)

USGS Publications Warehouse

Carr, T.R.; Iqbal, A.; Callaghan, N.; ,; Look, K.; Saving, S.; Nelson, K.

2009-01-01

The US Department of Energy's Regional Carbon Sequestration Partnerships (RCSPs) are responsible for generating geospatial data for the maps displayed in the Carbon Sequestration Atlas of the United States and Canada. Key geospatial data (carbon sources, potential storage sites, transportation, land use, etc.) are required for the Atlas, and for efficient implementation of carbon sequestration on a national and regional scale. The National Carbon Sequestration Database and Geographical Information System (NatCarb) is a relational database and geographic information system (GIS) that integrates carbon storage data generated and maintained by the RCSPs and various other sources. The purpose of NatCarb is to provide a national view of the carbon capture and storage potential in the U.S. and Canada. The digital spatial database allows users to estimate the amount of CO2 emitted by sources (such as power plants, refineries and other fossil-fuel-consuming industries) in relation to geologic formations that can provide safe, secure storage sites over long periods of time. The NatCarb project is working to provide all stakeholders with improved online tools for the display and analysis of CO2 carbon capture and storage data. NatCarb is organizing and enhancing the critical information about CO2 sources and developing the technology needed to access, query, model, analyze, display, and distribute natural resource data related to carbon management. Data are generated, maintained and enhanced locally at the RCSP level, or at specialized data warehouses, and assembled, accessed, and analyzed in real-time through a single geoportal. NatCarb is a functional demonstration of distributed data-management systems that cross the boundaries between institutions and geographic areas. It forms the first step toward a functioning National Carbon Cyberinfrastructure (NCCI). NatCarb provides access to first-order information to evaluate the costs, economic potential and societal issues of CO2 capture and storage, including public perception and regulatory aspects. NatCarb online access has been modified to address the broad needs of a spectrum of users. NatCarb includes not only GIS and database query tools for high-end user, but simplified display for the general public using readily available web tools such as Google Earth???and Google Maps???. Not only is NatCarb connected to all the RCSPs, but data are also pulled from public servers including the U.S. Geological Survey-EROS Data Center and from the Geography Network. Data for major CO2 sources have been obtained from U.S. Environmental Protection Agency (EPA) databases, and data on major coal basins and coalbed methane wells were obtained from the Energy Information Administration (EIA). ?? 2009 Elsevier Ltd. All rights reserved.

Pan European Phenological database (PEP725): a single point of access for European data.

PubMed

Templ, Barbara; Koch, Elisabeth; Bolmgren, Kjell; Ungersböck, Markus; Paul, Anita; Scheifinger, Helfried; Rutishauser, This; Busto, Montserrat; Chmielewski, Frank-M; Hájková, Lenka; Hodzić, Sabina; Kaspar, Frank; Pietragalla, Barbara; Romero-Fresneda, Ramiro; Tolvanen, Anne; Vučetič, Višnja; Zimmermann, Kirsten; Zust, Ana

2018-06-01

The Pan European Phenology (PEP) project is a European infrastructure to promote and facilitate phenological research, education, and environmental monitoring. The main objective is to maintain and develop a Pan European Phenological database (PEP725) with an open, unrestricted data access for science and education. PEP725 is the successor of the database developed through the COST action 725 "Establishing a European phenological data platform for climatological applications" working as a single access point for European-wide plant phenological data. So far, 32 European meteorological services and project partners from across Europe have joined and supplied data collected by volunteers from 1868 to the present for the PEP725 database. Most of the partners actively provide data on a regular basis. The database presently holds almost 12 million records, about 46 growing stages and 265 plant species (including cultivars), and can be accessed via http://www.pep725.eu/ . Users of the PEP725 database have studied a diversity of topics ranging from climate change impact, plant physiological question, phenological modeling, and remote sensing of vegetation to ecosystem productivity.

Pan European Phenological database (PEP725): a single point of access for European data

NASA Astrophysics Data System (ADS)

Templ, Barbara; Koch, Elisabeth; Bolmgren, Kjell; Ungersböck, Markus; Paul, Anita; Scheifinger, Helfried; Rutishauser, This; Busto, Montserrat; Chmielewski, Frank-M.; Hájková, Lenka; Hodzić, Sabina; Kaspar, Frank; Pietragalla, Barbara; Romero-Fresneda, Ramiro; Tolvanen, Anne; Vučetič, Višnja; Zimmermann, Kirsten; Zust, Ana

2018-02-01

The Pan European Phenology (PEP) project is a European infrastructure to promote and facilitate phenological research, education, and environmental monitoring. The main objective is to maintain and develop a Pan European Phenological database (PEP725) with an open, unrestricted data access for science and education. PEP725 is the successor of the database developed through the COST action 725 "Establishing a European phenological data platform for climatological applications" working as a single access point for European-wide plant phenological data. So far, 32 European meteorological services and project partners from across Europe have joined and supplied data collected by volunteers from 1868 to the present for the PEP725 database. Most of the partners actively provide data on a regular basis. The database presently holds almost 12 million records, about 46 growing stages and 265 plant species (including cultivars), and can be accessed via http://www.pep725.eu/. Users of the PEP725 database have studied a diversity of topics ranging from climate change impact, plant physiological question, phenological modeling, and remote sensing of vegetation to ecosystem productivity.

The CoFactor database: organic cofactors in enzyme catalysis.

PubMed

Fischer, Julia D; Holliday, Gemma L; Thornton, Janet M

2010-10-01

Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes. The database is publicly available and can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/CoFactor.

Foot and Ankle Fellowship Websites: An Assessment of Accessibility and Quality.

PubMed

Hinds, Richard M; Danna, Natalie R; Capo, John T; Mroczek, Kenneth J

2017-08-01

The Internet has been reported to be the first informational resource for many fellowship applicants. The objective of this study was to assess the accessibility of orthopaedic foot and ankle fellowship websites and to evaluate the quality of information provided via program websites. The American Orthopaedic Foot and Ankle Society (AOFAS) and the Fellowship and Residency Electronic Interactive Database (FREIDA) fellowship databases were accessed to generate a comprehensive list of orthopaedic foot and ankle fellowship programs. The databases were reviewed for links to fellowship program websites and compared with program websites accessed from a Google search. Accessible fellowship websites were then analyzed for the quality of recruitment and educational content pertinent to fellowship applicants. Forty-seven orthopaedic foot and ankle fellowship programs were identified. The AOFAS database featured direct links to 7 (15%) fellowship websites with the independent Google search yielding direct links to 29 (62%) websites. No direct website links were provided in the FREIDA database. Thirty-six accessible websites were analyzed for content. Program websites featured a mean 44% (range = 5% to 75%) of the total assessed content. The most commonly presented recruitment and educational content was a program description (94%) and description of fellow operative experience (83%), respectively. There is substantial variability in the accessibility and quality of orthopaedic foot and ankle fellowship websites. Recognition of deficits in accessibility and content quality may assist foot and ankle fellowships in improving program information online. Level IV.

Information access in a dual-task context: testing a model of optimal strategy selection.

PubMed

Wickens, C D; Seidler, K S

1997-09-01

Pilots were required to access information from a hierarchical aviation database by navigating under single-task conditions (Experiment 1) and when this task was time-shared with an altitude-monitoring task of varying bandwidth and priority (Experiment 2). In dual-task conditions, pilots had 2 viewports available, 1 always used for the information task and the other to be allocated to either task. Dual-task strategy, inferred from the decision of which task to allocate to the 2nd viewport, revealed that allocation was generally biased in favor of the monitoring task and was only partly sensitive to the difficulty of the 2 tasks and their relative priorities. Some dominant sources of navigational difficulties failed to adaptively influence selection strategy. The implications of the results are to provide tools for jumping to the top of the database, to provide 2 viewports into the common database, and to provide training as to the optimum viewport management strategy in a multitask environment.

Compression technique for large statistical data bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eggers, S.J.; Olken, F.; Shoshani, A.

1981-03-01

The compression of large statistical databases is explored and are proposed for organizing the compressed data, such that the time required to access the data is logarithmic. The techniques exploit special characteristics of statistical databases, namely, variation in the space required for the natural encoding of integer attributes, a prevalence of a few repeating values or constants, and the clustering of both data of the same length and constants in long, separate series. The techniques are variations of run-length encoding, in which modified run-lengths for the series are extracted from the data stream and stored in a header, which ismore » used to form the base level of a B-tree index into the database. The run-lengths are cumulative, and therefore the access time of the data is logarithmic in the size of the header. The details of the compression scheme and its implementation are discussed, several special cases are presented, and an analysis is given of the relative performance of the various versions.« less

Coastal Prairie Restoration Information System: Version 1 (Louisiana)

USGS Publications Warehouse

Allain, Larry

2007-01-01

The Coastal Prairie Restoration Information System (CPR) is a Microsoft Access database that allows users to query and view data about Louisiana coastal prairie species. Less than 0.1% of Louisiana's coastal prairie vegetation remains in a relatively undisturbed condition. Encompassing as much as 1 million hectares of land, coastal prairie is a hybrid of coastal wetlands and tall grass prairie. Over 550 plant species have been identified in Louisiana's coastal prairies to date. Efforts to conserve and restore this endangered ecosystem are limited by the ability of workers to identify and access knowledge about this diverse group of plants. In this database, a variety of data are provided for each of 650 coastal prairie species in Louisiana. The database was developed at the U.S. Geological Survey National Wetlands Research Center by Larry Allain, with software development by Myra Silva. Additional funding was provided by the biology department of the University of Louisiana at Lafayette (ULL), the ULL Center for Environmental and Ecological Technology, and the National Science Foundation.

Scientific Use Cases for the Virtual Atomic and Molecular Data Center

NASA Astrophysics Data System (ADS)

Dubernet, M. L.; Aboudarham, J.; Ba, Y. A.; Boiziot, M.; Bottinelli, S.; Caux, E.; Endres, C.; Glorian, J. M.; Henry, F.; Lamy, L.; Le Sidaner, P.; Møller, T.; Moreau, N.; Rénié, C.; Roueff, E.; Schilke, P.; Vastel, C.; Zwoelf, C. M.

2014-12-01

VAMDC Consortium is a worldwide consortium which federates interoperable Atomic and Molecular databases through an e-science infrastructure. The contained data are of the highest scientific quality and are crucial for many applications: astrophysics, atmospheric physics, fusion, plasma and lighting technologies, health, etc. In this paper we present astrophysical scientific use cases in relation to the use of the VAMDC e-infrastructure. Those will cover very different applications such as: (i) modeling the spectra of interstellar objects using the myXCLASS software tool implemented in the Common Astronomy Software Applications package (CASA) or using the CASSIS software tool, in its stand-alone version or implemented in the Herschel Interactive Processing Environment (HIPE); (ii) the use of Virtual Observatory tools accessing VAMDC databases; (iii) the access of VAMDC from the Paris solar BASS2000 portal; (iv) the combination of tools and database from the APIS service (Auroral Planetary Imaging and Spectroscopy); (v) combination of heterogeneous data for the application to the interstellar medium from the SPECTCOL tool.

Information access in a dual-task context: testing a model of optimal strategy selection

NASA Technical Reports Server (NTRS)

Wickens, C. D.; Seidler, K. S.

1997-01-01

Pilots were required to access information from a hierarchical aviation database by navigating under single-task conditions (Experiment 1) and when this task was time-shared with an altitude-monitoring task of varying bandwidth and priority (Experiment 2). In dual-task conditions, pilots had 2 viewports available, 1 always used for the information task and the other to be allocated to either task. Dual-task strategy, inferred from the decision of which task to allocate to the 2nd viewport, revealed that allocation was generally biased in favor of the monitoring task and was only partly sensitive to the difficulty of the 2 tasks and their relative priorities. Some dominant sources of navigational difficulties failed to adaptively influence selection strategy. The implications of the results are to provide tools for jumping to the top of the database, to provide 2 viewports into the common database, and to provide training as to the optimum viewport management strategy in a multitask environment.

The Molecule Pages database

PubMed Central

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community. PMID:17965093

The Molecule Pages database.

PubMed

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar; Vadivelu, Ilango

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

Methodologies and Methods for User Behavioral Research.

ERIC Educational Resources Information Center

Wang, Peiling

1999-01-01

Discusses methodological issues in empirical studies of information-related behavior in six specific research areas: information needs and uses; information seeking; relevance judgment; online searching (including online public access catalog, online database, and the Web); human-system interactions; and reference transactions. (Contains 191…

DEFINING THE CHEMICAL SPACE OF PUBLIC GENOMIC DATA (S)

EPA Science Inventory

The current project aims to chemically index the genomics content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. By defining the chemical space of public genomic data, it is possibl...

Erectile Dysfunction Herbs: A Natural Treatment for ED?

MedlinePlus

... Analysis. 2015;102:476. DHEA. Natural Medicines Comprehensive Database. http://www.naturaldatabase.com. Accessed Nov. 1, 2015. L-arginine. Natural Medicines Comprehensive Database. http://www.naturaldatabase.com. Accessed Nov. 1, 2015. ...

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

Interacting with the National Database for Autism Research (NDAR) via the LONI Pipeline workflow environment.

PubMed

Torgerson, Carinna M; Quinn, Catherine; Dinov, Ivo; Liu, Zhizhong; Petrosyan, Petros; Pelphrey, Kevin; Haselgrove, Christian; Kennedy, David N; Toga, Arthur W; Van Horn, John Darrell

2015-03-01

Under the umbrella of the National Database for Clinical Trials (NDCT) related to mental illnesses, the National Database for Autism Research (NDAR) seeks to gather, curate, and make openly available neuroimaging data from NIH-funded studies of autism spectrum disorder (ASD). NDAR has recently made its database accessible through the LONI Pipeline workflow design and execution environment to enable large-scale analyses of cortical architecture and function via local, cluster, or "cloud"-based computing resources. This presents a unique opportunity to overcome many of the customary limitations to fostering biomedical neuroimaging as a science of discovery. Providing open access to primary neuroimaging data, workflow methods, and high-performance computing will increase uniformity in data collection protocols, encourage greater reliability of published data, results replication, and broaden the range of researchers now able to perform larger studies than ever before. To illustrate the use of NDAR and LONI Pipeline for performing several commonly performed neuroimaging processing steps and analyses, this paper presents example workflows useful for ASD neuroimaging researchers seeking to begin using this valuable combination of online data and computational resources. We discuss the utility of such database and workflow processing interactivity as a motivation for the sharing of additional primary data in ASD research and elsewhere.

Development of a database system for near-future climate change projections under the Japanese National Project SI-CAT

NASA Astrophysics Data System (ADS)

Nakagawa, Y.; Kawahara, S.; Araki, F.; Matsuoka, D.; Ishikawa, Y.; Fujita, M.; Sugimoto, S.; Okada, Y.; Kawazoe, S.; Watanabe, S.; Ishii, M.; Mizuta, R.; Murata, A.; Kawase, H.

2017-12-01

Analyses of large ensemble data are quite useful in order to produce probabilistic effect projection of climate change. Ensemble data of "+2K future climate simulations" are currently produced by Japanese national project "Social Implementation Program on Climate Change Adaptation Technology (SI-CAT)" as a part of a database for Policy Decision making for Future climate change (d4PDF; Mizuta et al. 2016) produced by Program for Risk Information on Climate Change. Those data consist of global warming simulations and regional downscaling simulations. Considering that those data volumes are too large (a few petabyte) to download to a local computer of users, a user-friendly system is required to search and download data which satisfy requests of the users. We develop "a database system for near-future climate change projections" for providing functions to find necessary data for the users under SI-CAT. The database system for near-future climate change projections mainly consists of a relational database, a data download function and user interface. The relational database using PostgreSQL is a key function among them. Temporally and spatially compressed data are registered on the relational database. As a first step, we develop the relational database for precipitation, temperature and track data of typhoon according to requests by SI-CAT members. The data download function using Open-source Project for a Network Data Access Protocol (OPeNDAP) provides a function to download temporally and spatially extracted data based on search results obtained by the relational database. We also develop the web-based user interface for using the relational database and the data download function. A prototype of the database system for near-future climate change projections are currently in operational test on our local server. The database system for near-future climate change projections will be released on Data Integration and Analysis System Program (DIAS) in fiscal year 2017. Techniques of the database system for near-future climate change projections might be quite useful for simulation and observational data in other research fields. We report current status of development and some case studies of the database system for near-future climate change projections.

Databases and Electronic Resources - Betty Petersen Memorial Library

Science.gov Websites

of NOAA-Wide and Open Access Databases on the NOAA Central Library website. American Meteorological to a nonfederal website. Open Science Directory Open Science Directory contains collections of Open Access Journals (e.g. Directory of Open Access Journals) and journals in the special programs (Hinari

Looking for Cancer Clues in Publicly Accessible Databases

PubMed Central

Lemkin, Peter F.; Smythers, Gary W.; Munroe, David J.

2004-01-01

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways. PMID:18629065

Looking for cancer clues in publicly accessible databases.

PubMed

Medjahed, Djamel; Lemkin, Peter F; Smythers, Gary W; Munroe, David J

2004-01-01

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways.

Crystallography Open Database – an open-access collection of crystal structures

PubMed Central

Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T.; Yokochi, A. F. T.; Quirós, Miguel; Lutterotti, Luca; Manakova, Elena; Butkus, Justas; Moeck, Peter; Le Bail, Armel

2009-01-01

The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. PMID:22477773

TOXINZ, the New Zealand Internet poisons information database: The first decade.

PubMed

Fountain, John S; Slaughter, Robin J

2016-06-01

The New Zealand National Poisons Centre has, over a number of years, developed an electronic poisons information database. In 2002, this was released as toxinz™ (University of Otago, Dunedin, New Zealand), an Internet accessible version. The objective of this study is to describe New Zealand subscriber utilisation of TOXINZ with an emphasis on pharmaceutical monographs viewed. A retrospective review was conducted of records of New Zealand subscriber access to TOXINZ monographs during the period 1 January 2003 to 31 December 2012. Telephone enquiry data to the New Zealand National Poisons Centre was also obtained for the same time period. Over the decade, 201 255 TOXINZ monographs were accessed, with annual numbers of documents viewed doubling from 13 718 in 2003 to 28 782 in 2012. Pharmaceuticals were the largest group viewed with 132 316 documents accessed (65.7% of all documents), followed by monographs relating to chemicals 46 061 (22.9%), substances of abuse 6698 (3.3%), plants 6563 (3.3%), supportive care 4668 (2.3%), animals 2553 (1.3%), and other 2396 (1.2%). In regard to the pharmaceuticals, high or rapidly increasing levels of enquiries were identified for venlafaxine, quetiapine, paracetamol, zopiclone and tramadol. Investigation of telephone enquiries to the New Zealand National Poisons Centre showed total poisoning calls increased slightly over the 10 year period, whereas telephone enquiries from hospitals halved. The TOXINZ Internet accessible poisons information database has proved to be a well-utilised addition to the New Zealand National Poisons Centre's service. © 2016 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

A Unified Satellite-Observation Polar Stratospheric Cloud (PSC) Database for Long-Term Climate-Change Studies

NASA Technical Reports Server (NTRS)

Fromm, Michael; Pitts, Michael; Alfred, Jerome

2000-01-01

This report summarizes the project team's activity and accomplishments during the period 12 February, 1999 - 12 February, 2000. The primary objective of this project was to create and test a generic algorithm for detecting polar stratospheric clouds (PSC), an algorithm that would permit creation of a unified, long term PSC database from a variety of solar occultation instruments that measure aerosol extinction near 1000 nm The second objective was to make a database of PSC observations and certain relevant related datasets. In this report we describe the algorithm, the data we are making available, and user access options. The remainder of this document provides the details of the algorithm and the database offering.

DITOP: drug-induced toxicity related protein database.

PubMed

Zhang, Jing-Xian; Huang, Wei-Juan; Zeng, Jing-Hua; Huang, Wen-Hui; Wang, Yi; Zhao, Rui; Han, Bu-Cong; Liu, Qing-Feng; Chen, Yu-Zong; Ji, Zhi-Liang

2007-07-01

Drug-induced toxicity related proteins (DITRPs) are proteins that mediate adverse drug reactions (ADRs) or toxicities through their binding to drugs or reactive metabolites. Collection of these proteins facilitates better understanding of the molecular mechanisms of drug-induced toxicity and the rational drug discovery. Drug-induced toxicity related protein database (DITOP) is such a database that is intending to provide comprehensive information of DITRPs. Currently, DITOP contains 1501 records, covering 618 distinct literature-reported DITRPs, 529 drugs/ligands and 418 distinct toxicity terms. These proteins were confirmed experimentally to interact with drugs or their reactive metabolites, thus directly or indirectly cause adverse effects or toxicities. Five major types of drug-induced toxicities or ADRs are included in DITOP, which are the idiosyncratic adverse drug reactions, the dose-dependent toxicities, the drug-drug interactions, the immune-mediated adverse drug effects (IMADEs) and the toxicities caused by genetic susceptibility. Molecular mechanisms underlying the toxicity and cross-links to related resources are also provided while available. Moreover, a series of user-friendly interfaces were designed for flexible retrieval of DITRPs-related information. The DITOP can be accessed freely at http://bioinf.xmu.edu.cn/databases/ADR/index.html. Supplementary data are available at Bioinformatics online.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prather, J. C.; Smith, S. K.; Watson, C. R.

The National Radiobiology Archives is a comprehensive effort to gather, organize, and catalog original data, representative specimens, and supporting materials related to significant radiobiology studies. This provides researchers with information for analyses which compare or combine results of these and other studies and with materials for analysis by advanced molecular biology techniques. This Programmer's Guide document describes the database access software, NRADEMO, and the subset loading script NRADEMO/MAINT/MAINTAIN, which comprise the National Laboratory Archives Distributed Access Package. The guide is intended for use by an experienced database management specialist. It contains information about the physical and logical organization of themore » software and data files. It also contains printouts of all the scripts and associated batch processing files. It is part of a suite of documents published by the National Radiobiology Archives.« less

PomBase: a comprehensive online resource for fission yeast

PubMed Central

Wood, Valerie; Harris, Midori A.; McDowall, Mark D.; Rutherford, Kim; Vaughan, Brendan W.; Staines, Daniel M.; Aslett, Martin; Lock, Antonia; Bähler, Jürg; Kersey, Paul J.; Oliver, Stephen G.

2012-01-01

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance. PMID:22039153

HotRegion: a database of predicted hot spot clusters.

PubMed

Cukuroglu, Engin; Gursoy, Attila; Keskin, Ozlem

2012-01-01

Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. HotRegion is accessible at http://prism.ccbb.ku.edu.tr/hotregion.

Network Configuration of Oracle and Database Programming Using SQL

NASA Technical Reports Server (NTRS)

Davis, Melton; Abdurrashid, Jibril; Diaz, Philip; Harris, W. C.

2000-01-01

A database can be defined as a collection of information organized in such a way that it can be retrieved and used. A database management system (DBMS) can further be defined as the tool that enables us to manage and interact with the database. The Oracle 8 Server is a state-of-the-art information management environment. It is a repository for very large amounts of data, and gives users rapid access to that data. The Oracle 8 Server allows for sharing of data between applications; the information is stored in one place and used by many systems. My research will focus primarily on SQL (Structured Query Language) programming. SQL is the way you define and manipulate data in Oracle's relational database. SQL is the industry standard adopted by all database vendors. When programming with SQL, you work on sets of data (i.e., information is not processed one record at a time).

A digital library for medical imaging activities

NASA Astrophysics Data System (ADS)

dos Santos, Marcelo; Furuie, Sérgio S.

2007-03-01

This work presents the development of an electronic infrastructure to make available a free, online, multipurpose and multimodality medical image database. The proposed infrastructure implements a distributed architecture for medical image database, authoring tools, and a repository for multimedia documents. Also it includes a peer-reviewed model that assures quality of dataset. This public repository provides a single point of access for medical images and related information to facilitate retrieval tasks. The proposed approach has been used as an electronic teaching system in Radiology as well.

Slushie World: An In-Class Access Database Tutorial

ERIC Educational Resources Information Center

Wynn, Donald E., Jr.; Pratt, Renée M. E.

2015-01-01

The Slushie World case study is designed to teach the basics of Microsoft Access and database management over a series of three 75-minute class sessions. Students are asked to build a basic database to track sales and inventory for a small business. Skills to be learned include table creation, data entry and importing, form and report design,…

NATIONAL URBAN DATABASE AND ACCESS PORTAL TOOL (NUDAPT): FACILITATING ADVANCEMENTS IN URBAN METEOROLOGY AND CLIMATE MODELING WITH COMMUNITY-BASED URBAN DATABASES

EPA Science Inventory

We discuss the initial design and application of the National Urban Database and Access Portal Tool (NUDAPT). This new project is sponsored by the USEPA and involves collaborations and contributions from many groups from federal and state agencies, and from private and academic i...

Data Aggregation System: A system for information retrieval on demand over relational and non-relational distributed data sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ball, G.; Kuznetsov, V.; Evans, D.

We present the Data Aggregation System, a system for information retrieval and aggregation from heterogenous sources of relational and non-relational data for the Compact Muon Solenoid experiment on the CERN Large Hadron Collider. The experiment currently has a number of organically-developed data sources, including front-ends to a number of different relational databases and non-database data services which do not share common data structures or APIs (Application Programming Interfaces), and cannot at this stage be readily converged. DAS provides a single interface for querying all these services, a caching layer to speed up access to expensive underlying calls and the abilitymore » to merge records from different data services pertaining to a single primary key.« less

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

PubMed

Mishima, Hiroyuki; Aerts, Jan; Katayama, Toshiaki; Bonnal, Raoul J P; Yoshiura, Koh-ichiro

2012-09-21

The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

The Ruby UCSC API: accessing the UCSC genome database using Ruby

PubMed Central

2012-01-01

Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/. PMID:22994508

Data Architecture in an Open Systems Environment.

ERIC Educational Resources Information Center

Bernbom, Gerald; Cromwell, Dennis

1993-01-01

The conceptual basis for structured data architecture, and its integration with open systems technology at Indiana University, are described. Key strategic goals guiding these efforts are discussed: commitment to improved data access; migration to relational database technology, and deployment of a high-speed, multiprotocol network; and…

Astronomical Software Directory Service

NASA Technical Reports Server (NTRS)

Hanisch, R. J.; Payne, H.; Hayes, J.

1998-01-01

This is the final report on the development of the Astronomical Software Directory Service (ASDS), a distributable, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URL's indexed for full-text searching.

Linking Data Access to Data Models to Applications: The Estuary Data Mapper

EPA Science Inventory

The U.S. Environmental Protection Agency (US EPA) is developing e-Estuary, a decision-support system for coastal management. E-Estuary has three elements: an estuarine geo-referenced relational database, watershed GIS coverages, and tools to support decision-making. To facilita...

Scalable global grid catalogue for Run3 and beyond

NASA Astrophysics Data System (ADS)

Martinez Pedreira, M.; Grigoras, C.; ALICE Collaboration

2017-10-01

The AliEn (ALICE Environment) file catalogue is a global unique namespace providing mapping between a UNIX-like logical name structure and the corresponding physical files distributed over 80 storage elements worldwide. Powerful search tools and hierarchical metadata information are integral parts of the system and are used by the Grid jobs as well as local users to store and access all files on the Grid storage elements. The catalogue has been in production since 2005 and over the past 11 years has grown to more than 2 billion logical file names. The backend is a set of distributed relational databases, ensuring smooth growth and fast access. Due to the anticipated fast future growth, we are looking for ways to enhance the performance and scalability by simplifying the catalogue schema while keeping the functionality intact. We investigated different backend solutions, such as distributed key value stores, as replacement for the relational database. This contribution covers the architectural changes in the system, together with the technology evaluation, benchmark results and conclusions.

CERES Search and Subset Tool

Atmospheric Science Data Center

2016-06-24

... data granules using a high resolution spatial metadata database and directly accessing the archived data granules. Subset results are ... data granules using a high resolution spatial metadata database and directly accessing the archived data granules. Subset results are ...

Wireless access to a pharmaceutical database: a demonstrator for data driven Wireless Application Protocol (WAP) applications in medical information processing.

PubMed

Schacht Hansen, M; Dørup, J

2001-01-01

The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control.

Wireless access to a pharmaceutical database: A demonstrator for data driven Wireless Application Protocol applications in medical information processing

PubMed Central

Hansen, Michael Schacht

2001-01-01

Background The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. Objectives To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. Methods We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. Results A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. Conclusions We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control. PMID:11720946

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

PubMed Central

Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang

2018-01-01

Abstract SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements. PMID:29092055

Towards pathogenomics: a web-based resource for pathogenicity islands

PubMed Central

Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.

2007-01-01

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at . PMID:17090594

MouseNet database: digital management of a large-scale mutagenesis project.

PubMed

Pargent, W; Heffner, S; Schäble, K F; Soewarto, D; Fuchs, H; Hrabé de Angelis, M

2000-07-01

The Munich ENU Mouse Mutagenesis Screen is a large-scale mutant production, phenotyping, and mapping project. It encompasses two animal breeding facilities and a number of screening groups located in the general area of Munich. A central database is required to manage and process the immense amount of data generated by the mutagenesis project. This database, which we named MouseNet(c), runs on a Sybase platform and will finally store and process all data from the entire project. In addition, the system comprises a portfolio of functions needed to support the workflow management of the core facility and the screening groups. MouseNet(c) will make all of the data available to the participating screening groups, and later to the international scientific community. MouseNet(c) will consist of three major software components:* Animal Management System (AMS)* Sample Tracking System (STS)* Result Documentation System (RDS)MouseNet(c) provides the following major advantages:* being accessible from different client platforms via the Internet* being a full-featured multi-user system (including access restriction and data locking mechanisms)* relying on a professional RDBMS (relational database management system) which runs on a UNIX server platform* supplying workflow functions and a variety of plausibility checks.

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS ...

EPA Pesticide Factsheets

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction ModelsAnn M. RichardUS Environmental Protection Agency, Research Triangle Park, NC, USADistributed: Decentralized set of standardized, field-delimited databases, each separatelyauthored and maintained, that are able to accommodate diverse toxicity data content;Structure-Searchable: Standard format (SDF) structure-data files that can be readily imported into available chemical relational databases and structure-searched;Tox: Toxicity data as it exists in widely disparate forms in current public databases, spanning diverse toxicity endpoints, test systems, levels of biological content, degrees of summarization, and information content.INTRODUCTIONThe economic and social pressures to reduce the need for animal testing and to better anticipate the potential for human and eco-toxicity of environmental, industrial, or pharmaceutical chemicals are as pressing today as at any time prior. However, the goal of predicting chemical toxicity in its many manifestations, the `T' in 'ADMET' (adsorption, distribution, metabolism, elimination, toxicity), remains one of the most difficult and largely unmet challenges in a chemical screening paradigm [1]. It is widely acknowledged that the single greatest hurdle to improving structure-activity relationship (SAR) toxicity prediction capabilities, in both the pharmaceutical and environmental regulation arenas, is the lack of suffici

WaveNet: A Web-Based Metocean Data Access, Processing, and Analysis Tool. Part 3 - CDIP Database

DTIC Science & Technology

2014-06-01

and Analysis Tool; Part 3 – CDIP Database by Zeki Demirbilek, Lihwa Lin, and Derek Wilson PURPOSE: This Coastal and Hydraulics Engineering...Technical Note (CHETN) describes coupling of the Coastal Data Information Program ( CDIP ) database to WaveNet, the first module of MetOcnDat (Meteorological...provides a step-by-step procedure to access, process, and analyze wave and wind data from the CDIP database. BACKGROUND: WaveNet addresses a basic

NNDC Data Services

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuli, J.K.; Sonzogni,A.

The National Nuclear Data Center has provided remote access to some of its resources since 1986. The major databases and other resources available currently through NNDC Web site are summarized. The National Nuclear Data Center (NNDC) has provided remote access to the nuclear physics databases it maintains and to other resources since 1986. With considerable innovation access is now mostly through the Web. The NNDC Web pages have been modernized to provide a consistent state-of-the-art style. The improved database services and other resources available from the NNOC site at www.nndc.bnl.govwill be described.

Globe Teachers Guide and Photographic Data on the Web

NASA Technical Reports Server (NTRS)

Kowal, Dan

2004-01-01

The task of managing the GLOBE Online Teacher s Guide during this time period focused on transforming the technology behind the delivery system of this document. The web application transformed from a flat file retrieval system to a dynamic database access approach. The new methodology utilizes Java Server Pages (JSP) on the front-end and an Oracle relational database on the backend. This new approach allows users of the web site, mainly teachers, to access content efficiently by grade level and/or by investigation or educational concept area. Moreover, teachers can gain easier access to data sheets and lab and field guides. The new online guide also included updated content for all GLOBE protocols. The GLOBE web management team was given documentation for maintaining the new application. Instructions for modifying the JSP templates and managing database content were included in this document. It was delivered to the team by the end of October, 2003. The National Geophysical Data Center (NGDC) continued to manage the school study site photos on the GLOBE website. 333 study site photo images were added to the GLOBE database and posted on the web during this same time period for 64 schools. Documentation for processing study site photos was also delivered to the new GLOBE web management team. Lastly, assistance was provided in transferring reference applications such as the Cloud and LandSat quizzes and Earth Systems Online Poster from NGDC servers to GLOBE servers along with documentation for maintaining these applications.

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems.

PubMed

Memišević, Vesna; Kumar, Kamal; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

2016-09-20

Burkholderia mallei and B. pseudomallei are the causative agents of glanders and melioidosis, respectively, diseases with high morbidity and mortality rates. B. mallei and B. pseudomallei are closely related genetically; B. mallei evolved from an ancestral strain of B. pseudomallei by genome reduction and adaptation to an obligate intracellular lifestyle. Although these two bacteria cause different diseases, they share multiple virulence factors, including bacterial secretion systems, which represent key components of bacterial pathogenicity. Despite recent progress, the secretion system proteins for B. mallei and B. pseudomallei, their pathogenic mechanisms of action, and host factors are not well characterized. We previously developed a manually curated database, DBSecSys, of bacterial secretion system proteins for B. mallei. Here, we report an expansion of the database with corresponding information about B. pseudomallei. DBSecSys 2.0 contains comprehensive literature-based and computationally derived information about B. mallei ATCC 23344 and literature-based and computationally derived information about B. pseudomallei K96243. The database contains updated information for 163 B. mallei proteins from the previous database and 61 additional B. mallei proteins, and new information for 281 B. pseudomallei proteins associated with 5 secretion systems, their 1,633 human- and murine-interacting targets, and 2,400 host-B. mallei interactions and 2,286 host-B. pseudomallei interactions. The database also includes information about 13 pathogenic mechanisms of action for B. mallei and B. pseudomallei secretion system proteins inferred from the available literature or computationally. Additionally, DBSecSys 2.0 provides details about 82 virulence attenuation experiments for 52 B. mallei secretion system proteins and 98 virulence attenuation experiments for 61 B. pseudomallei secretion system proteins. We updated the Web interface and data access layer to speed-up users' search of detailed information for orthologous proteins related to secretion systems of the two pathogens. The updates of DBSecSys 2.0 provide unique capabilities to access comprehensive information about secretion systems of B. mallei and B. pseudomallei. They enable studies and comparisons of corresponding proteins of these two closely related pathogens and their host-interacting partners. The database is available at http://dbsecsys.bhsai.org .

Secure, web-accessible call rosters for academic radiology departments.

PubMed

Nguyen, A V; Tellis, W M; Avrin, D E

2000-05-01

Traditionally, radiology department call rosters have been posted via paper and bulletin boards. Frequently, changes to these lists are made by multiple people independently, but often not synchronized, resulting in confusion among the house staff and technical staff as to who is on call and when. In addition, multiple and disparate copies exist in different sections of the department, and changes made would not be propagated to all the schedules. To eliminate such difficulties, a paperless call scheduling application was developed. Our call scheduling program allowed Java-enabled web access to a database by designated personnel from each radiology section who have privileges to make the necessary changes. Once a person made a change, everyone accessing the database would see the modification. This eliminates the chaos resulting from people swapping shifts at the last minute and not having the time to record or broadcast the change. Furthermore, all changes to the database were logged. Users are given a log-in name and password and can only edit their section; however, all personnel have access to all sections' schedules. Our applet was written in Java 2 using the latest technology in database access. We access our Interbase database through the DataExpress and DB Swing (Borland, Scotts Valley, CA) components. The result is secure access to the call rosters via the web. There are many advantages to the web-enabled access, mainly the ability for people to make changes and have the changes recorded and propagated in a single virtual location and available to all who need to know.

Visibility of medical informatics regarding bibliometric indices and databases

PubMed Central

2011-01-01

Background The quantitative study of the publication output (bibliometrics) deeply influences how scientific work is perceived (bibliometric visibility). Recently, new bibliometric indices and databases have been established, which may change the visibility of disciplines, institutions and individuals. This study examines the effects of the new indices on the visibility of Medical Informatics. Methods By objective criteria, three sets of journals are chosen, two representing Medical Informatics and a third addressing Internal Medicine as a benchmark. The availability of index data (index coverage) and the aggregate scores of these corpora are compared for journal-related (Journal impact factor, Eigenfactor metrics, SCImago journal rank) and author-related indices (Hirsch-index, Egghes G-index). Correlation analysis compares the dependence of author-related indices. Results The bibliometric visibility depended on the research focus and the citation database: Scopus covers more journals relevant for Medical Informatics than ISI/Thomson Reuters. Journals focused on Medical Informatics' methodology were negatively affected by the Eigenfactor metrics, while the visibility profited from an interdisciplinary research focus. The correlation between Hirsch-indices computed on citation databases and the Internet was strong. Conclusions The visibility of smaller technology-oriented disciplines like Medical Informatics is changed by the new bibliometric indices and databases possibly leading to suitably changed publication strategies. Freely accessible author-related indices enable an easy and adequate individual assessment. PMID:21496230

Graph Databases for Large-Scale Healthcare Systems: A Framework for Efficient Data Management and Data Services

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Yubin; Shankar, Mallikarjun; Park, Byung H.

Designing a database system for both efficient data management and data services has been one of the enduring challenges in the healthcare domain. In many healthcare systems, data services and data management are often viewed as two orthogonal tasks; data services refer to retrieval and analytic queries such as search, joins, statistical data extraction, and simple data mining algorithms, while data management refers to building error-tolerant and non-redundant database systems. The gap between service and management has resulted in rigid database systems and schemas that do not support effective analytics. We compose a rich graph structure from an abstracted healthcaremore » RDBMS to illustrate how we can fill this gap in practice. We show how a healthcare graph can be automatically constructed from a normalized relational database using the proposed 3NF Equivalent Graph (3EG) transformation.We discuss a set of real world graph queries such as finding self-referrals, shared providers, and collaborative filtering, and evaluate their performance over a relational database and its 3EG-transformed graph. Experimental results show that the graph representation serves as multiple de-normalized tables, thus reducing complexity in a database and enhancing data accessibility of users. Based on this finding, we propose an ensemble framework of databases for healthcare applications.« less

Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.

PubMed

Krystkowiak, Izabella; Lenart, Jakub; Debski, Konrad; Kuterba, Piotr; Petas, Michal; Kaminska, Bozena; Dabrowski, Michal

2013-01-01

We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql -h database.nencki-genomics.org -u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface.

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs

PubMed Central

Krystkowiak, Izabella; Lenart, Jakub; Debski, Konrad; Kuterba, Piotr; Petas, Michal; Kaminska, Bozena; Dabrowski, Michal

2013-01-01

We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql –h database.nencki-genomics.org –u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface. Database URL: http://www.nencki-genomics.org. PMID:24089456

SchizConnect: Mediating Neuroimaging Databases on Schizophrenia and Related Disorders for Large-Scale Integration

PubMed Central

Wang, Lei; Alpert, Kathryn I.; Calhoun, Vince D.; Cobia, Derin J.; Keator, David B.; King, Margaret D.; Kogan, Alexandr; Landis, Drew; Tallis, Marcelo; Turner, Matthew D.; Potkin, Steven G.; Turner, Jessica A.; Ambite, Jose Luis

2015-01-01

SchizConnect (www.schizconnect.org) is built to address the issues of multiple data repositories in schizophrenia neuroimaging studies. It includes a level of mediation—translating across data sources—so that the user can place one query, e.g. for diffusion images from male individuals with schizophrenia, and find out from across participating data sources how many datasets there are, as well as downloading the imaging and related data. The current version handles the Data Usage Agreements across different studies, as well as interpreting database-specific terminologies into a common framework. New data repositories can also be mediated to bring immediate access to existing datasets. Compared with centralized, upload data sharing models, SchizConnect is a unique, virtual database with a focus on schizophrenia and related disorders that can mediate live data as information are being updated at each data source. It is our hope that SchizConnect can facilitate testing new hypotheses through aggregated datasets, promoting discovery related to the mechanisms underlying schizophrenic dysfunction. PMID:26142271

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

A Content Analysis of Turkish Newspapers: Prevalence of Articles Containing Health Information Related to Physical Activity

ERIC Educational Resources Information Center

Koksal, Leyla; Subasi, Feryal; Luleci, Emel; Hey, William

2012-01-01

This study was retrospective in design and the purpose was to review health information related to PA (physical activity) in articles of Turkish newspapers. The search covered newspaper articles printed between January 1, 2002 and December 31, 2004 in all Turkish newspapers that are accessible via the electronic newspaper database. Four daily…

High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorders

PubMed Central

Butler, Merlin G.; Rafi, Syed K.; Manzardo, Ann M.

2015-01-01

Recently, autism-related research has focused on the identification of various genes and disturbed pathways causing the genetically heterogeneous group of autism spectrum disorders (ASD). The list of autism-related genes has significantly increased due to better awareness with advances in genetic technology and expanding searchable genomic databases. We compiled a master list of known and clinically relevant autism spectrum disorder genes identified with supporting evidence from peer-reviewed medical literature sources by searching key words related to autism and genetics and from authoritative autism-related public access websites, such as the Simons Foundation Autism Research Institute autism genomic database dedicated to gene discovery and characterization. Our list consists of 792 genes arranged in alphabetical order in tabular form with gene symbols placed on high-resolution human chromosome ideograms, thereby enabling clinical and laboratory geneticists and genetic counsellors to access convenient visual images of the location and distribution of ASD genes. Meaningful correlations of the observed phenotype in patients with suspected/confirmed ASD gene(s) at the chromosome region or breakpoint band site can be made to inform diagnosis and gene-based personalized care and provide genetic counselling for families. PMID:25803107

Advanced technologies for scalable ATLAS conditions database access on the grid

NASA Astrophysics Data System (ADS)

Basset, R.; Canali, L.; Dimitrov, G.; Girone, M.; Hawkings, R.; Nevski, P.; Valassi, A.; Vaniachine, A.; Viegas, F.; Walker, R.; Wong, A.

2010-04-01

During massive data reprocessing operations an ATLAS Conditions Database application must support concurrent access from numerous ATLAS data processing jobs running on the Grid. By simulating realistic work-flow, ATLAS database scalability tests provided feedback for Conditions Db software optimization and allowed precise determination of required distributed database resources. In distributed data processing one must take into account the chaotic nature of Grid computing characterized by peak loads, which can be much higher than average access rates. To validate database performance at peak loads, we tested database scalability at very high concurrent jobs rates. This has been achieved through coordinated database stress tests performed in series of ATLAS reprocessing exercises at the Tier-1 sites. The goal of database stress tests is to detect scalability limits of the hardware deployed at the Tier-1 sites, so that the server overload conditions can be safely avoided in a production environment. Our analysis of server performance under stress tests indicates that Conditions Db data access is limited by the disk I/O throughput. An unacceptable side-effect of the disk I/O saturation is a degradation of the WLCG 3D Services that update Conditions Db data at all ten ATLAS Tier-1 sites using the technology of Oracle Streams. To avoid such bottlenecks we prototyped and tested a novel approach for database peak load avoidance in Grid computing. Our approach is based upon the proven idea of pilot job submission on the Grid: instead of the actual query, an ATLAS utility library sends to the database server a pilot query first.

The SMile Card: a computerised data card for multiple sclerosis patients. SMile Card Scientific Board.

PubMed

Mancardi, G L; Uccelli, M M; Sonnati, M; Comi, G; Milanese, C; De Vincentiis, A; Battaglia, M A

2000-04-01

The SMile Card was developed as a means for computerising clinical information for the purpose of transferability, accessibility, standardisation and compilation of a national database of demographic and clinical information about multiple sclerosis (MS) patients. In many European countries, centres for MS are organised independently from one another making collaboration, consultation and patient referral complicated. Only the more highly advanced clinical centres, generally located in large urban areas, have had the possibility to utilise technical possibilities for improving the organisation of patient clinical and research information, although independently from other centres. The information system, developed utilising the Visual Basic language for Microsoft Windows 95, stores information via a 'smart card' in a database which is initiated and updated utilising a microprocessor, located at each neurological clinic. The SMile Card, currently being tested in Italy, permits patients to carry with them all relevant medical information without limitations. Neurologists are able to access and update, via the microprocessor, the patient's entire medical history and MS-related information, including the complete neurological examination and laboratory test results. The SMile Card provides MS patients and neurologists with a complete computerised archive of clinical information which is accessible throughout the country. In addition, data from the SMile Card system can be exported to other database programs.

Are There Any Natural Remedies That Reduce Chronic Fatigue Associated with Chronic Fatigue Syndrome?

MedlinePlus

... management of chronic fatigue syndrome. Natural Medicines Comprehensive Database. http://www.naturaldatabase.com. Accessed Feb. 23, 2015. Magnesium. Natural Medicines Comprehensive Database. http://www.naturaldatabase.com. Accessed Feb. 24, 2015. ...

Pan European Phenological database (PEP725): a single point of access for European data

NASA Astrophysics Data System (ADS)

Templ, Barbara; Koch, Elisabeth; Bolmgren, Kjell; Ungersböck, Markus; Paul, Anita; Scheifinger, Helfried; Rutishauser, This; Busto, Montserrat; Chmielewski, Frank-M.; Hájková, Lenka; Hodzić, Sabina; Kaspar, Frank; Pietragalla, Barbara; Romero-Fresneda, Ramiro; Tolvanen, Anne; Vučetič, Višnja; Zimmermann, Kirsten; Zust, Ana

2018-06-01

The Pan European Phenology (PEP) project is a European infrastructure to promote and facilitate phenological research, education, and environmental monitoring. The main objective is to maintain and develop a Pan European Phenological database (PEP725) with an open, unrestricted data access for science and education. PEP725 is the successor of the database developed through the COST action 725 "Establishing a European phenological data platform for climatological applications" working as a single access point for European-wide plant phenological data. So far, 32 European meteorological services and project partners from across Europe have joined and supplied data collected by volunteers from 1868 to the present for the PEP725 database. Most of the partners actively provide data on a regular basis. The database presently holds almost 12 million records, about 46 growing stages and 265 plant species (including cultivars), and can be accessed via http://www.pep725.eu/ . Users of the PEP725 database have studied a diversity of topics ranging from climate change impact, plant physiological question, phenological modeling, and remote sensing of vegetation to ecosystem productivity.

Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

PubMed

Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

2014-01-01

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

Correspondence: World Wide Web access to the British Universities Human Embryo Database

PubMed Central

AITON, JAMES F.; MCDONOUGH, ARIANA; MCLACHLAN, JOHN C.; SMART, STEVEN D.; WHITEN, SUSAN C.

1997-01-01

The British Universities Human Embryo Database has been created by merging information from the Walmsley Collection of Human Embryos at the School of Biological and Medical Sciences, University of St Andrews and from the Boyd Collection of Human Embryos at the Department of Anatomy, University of Cambridge. The database has been made available electronically on the Internet and World Wide Web browsers can be used to implement interactive access to the information stored in the British Universities Human Embryo Database. The database can, therefore, be accessed and searched from remote sites and specific embryos can be identified in terms of their location, age, developmental stage, plane of section, staining technique, and other parameters. It is intended to add information from other similar collections in the UK as it becomes available. PMID:9034891

Using a centralised database system and server in the European Union Framework Programme 7 project SEPServer

NASA Astrophysics Data System (ADS)

Heynderickx, Daniel

2012-07-01

The main objective of the SEPServer project (EU FP7 project 262773) is to produce a new tool, which greatly facilitates the investigation of solar energetic particles (SEPs) and their origin: a server providing SEP data, related electromagnetic (EM) observations and analysis methods, a comprehensive catalogue of the observed SEP events, and educational/outreach material on solar eruptions. The project is coordinated by the University of Helsinki. The project will combine data and knowledge from 11 European partners and several collaborating parties from Europe and US. The datasets provided by the consortium partners are collected in a MySQL database (using the ESA Open Data Interface under licence) on a server operated by DH Consultancy, which also hosts a web interface providing browsing, plotting and post-processing and analysis tools developed by the consortium, as well as a Solar Energetic Particle event catalogue. At this stage of the project, a prototype server has been established, which is presently undergoing testing by users inside the consortium. Using a centralized database has numerous advantages, including: homogeneous storage of the data, which eliminates the need for dataset specific file access routines once the data are ingested in the database; a homogeneous set of metadata describing the datasets on both a global and detailed level, allowing for automated access to and presentation of the various data products; standardised access to the data in different programming environments (e.g. php, IDL); elimination of the need to download data for individual data requests. SEPServer will, thus, add value to several space missions and Earth-based observations by facilitating the coordinated exploitation of and open access to SEP data and related EM observations, and promoting correct use of these data for the entire space research community. This will lead to new knowledge on the production and transport of SEPs during solar eruptions and facilitate the development of models for predicting solar radiation storms and calculation of expected fluxes/fluences of SEPs encountered by spacecraft in the interplanetary medium.

PS1-41: Just Add Data: Implementing an Event-Based Data Model for Clinical Trial Tracking

PubMed Central

Fuller, Sharon; Carrell, David; Pardee, Roy

2012-01-01

Background/Aims Clinical research trials often have similar fundamental tracking needs, despite being quite variable in their specific logic and activities. A model tracking database that can be quickly adapted by a variety of studies has the potential to achieve significant efficiencies in database development and maintenance. Methods Over the course of several different clinical trials, we have developed a database model that is highly adaptable to a variety of projects. Rather than hard-coding each specific event that might occur in a trial, along with its logical consequences, this model considers each event and its parameters to be a data record in its own right. Each event may have related variables (metadata) describing its prerequisites, subsequent events due, associated mailings, or events that it overrides. The metadata for each event is stored in the same record with the event name. When changes are made to the study protocol, no structural changes to the database are needed. One has only to add or edit events and their metadata. Changes in the event metadata automatically determine any related logic changes. In addition to streamlining application code, this model simplifies communication between the programmer and other team members. Database requirements can be phrased as changes to the underlying data, rather than to the application code. The project team can review a single report of events and metadata and easily see where changes might be needed. In addition to benefitting from streamlined code, the front end database application can also implement useful standard features such as automated mail merges and to do lists. Results The event-based data model has proven itself to be robust, adaptable and user-friendly in a variety of study contexts. We have chosen to implement it as a SQL Server back end and distributed Access front end. Interested readers may request a copy of the Access front end and scripts for creating the back end database. Discussion An event-based database with a consistent, robust set of features has the potential to significantly reduce development time and maintenance expense for clinical trial tracking databases.

An Examination of Multi-Tier Designs for Legacy Data Access

DTIC Science & Technology

1997-12-01

heterogeneous relational database management systems. The first test system incorporates a two-tier architecture design using Java, and the second system...employs a three-tier architecture design using Java and CORBA. Data on replication times for the two-tier and three-tier designs are presented

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

TRENDS: A flight test relational database user's guide and reference manual

NASA Technical Reports Server (NTRS)

Bondi, M. J.; Bjorkman, W. S.; Cross, J. L.

1994-01-01

This report is designed to be a user's guide and reference manual for users intending to access rotocraft test data via TRENDS, the relational database system which was developed as a tool for the aeronautical engineer with no programming background. This report has been written to assist novice and experienced TRENDS users. TRENDS is a complete system for retrieving, searching, and analyzing both numerical and narrative data, and for displaying time history and statistical data in graphical and numerical formats. This manual provides a 'guided tour' and a 'user's guide' for the new and intermediate-skilled users. Examples for the use of each menu item within TRENDS is provided in the Menu Reference section of the manual, including full coverage for TIMEHIST, one of the key tools. This manual is written around the XV-15 Tilt Rotor database, but does include an appendix on the UH-60 Blackhawk database. This user's guide and reference manual establishes a referrable source for the research community and augments NASA TM-101025, TRENDS: The Aeronautical Post-Test, Database Management System, Jan. 1990, written by the same authors.

What is access to radiation therapy? A conceptual framework and review of influencing factors.

PubMed

Sundaresan, Puma; Stockler, Martin R; Milross, Christopher G

2016-02-01

Optimal radiation therapy (RT) utilisation rates (RURs) have been defined for various cancer indications through extensive work in Australia and overseas. These benchmarks remain unrealised. The gap between optimal RUR and actual RUR has been attributed to inadequacies in 'RT access'. We aimed to develop a conceptual framework for the consideration of 'RT access' by examining the literature for existing constructs and translating it to the context of RT services. We further aimed to use this framework to identify and examine factors influencing 'RT access'. Existing models of health care access were reviewed and used to develop a multi-dimensional conceptual framework for 'RT access'. A review of the literature was then conducted to identify factors reported to affect RT access and utilisation. The electronic databases searched, the host platform and date range of the databases searched were Ovid MEDLINE, 1946 to October 2014 and PsycINFO via OvidSP,1806 to October 2014. The framework developed demonstrates that 'RT access' encompasses opportunity for RT as well as the translation of this opportunity to RT utilisation. Opportunity for RT includes availability, affordability, adequacy (quality) and acceptability of RT services. Several factors at the consumer, referrer and RT service levels affect the translation of this opportunity for RT to actual RT utilisation. 'Access' is a term that is widely used in the context of health service related research, planning and political discussions. It is a multi-faceted concept with many descriptions. We propose a conceptual framework for the consideration of 'RT access' so that factors affecting RT access and utilisation may be identified and examined. Understanding these factors, and quantifying them where possible, will allow objective evaluation of their impact on RT utilisation and guide implementation of strategies to modify their effects.

Public Access to Digital Material; A Call to Researchers: Digital Libraries Need Collaboration across Disciplines; Greenstone: Open-Source Digital Library Software; Retrieval Issues for the Colorado Digitization Project's Heritage Database; Report on the 5th European Conference on Digital Libraries, ECDL 2001; Report on the First Joint Conference on Digital Libraries.

ERIC Educational Resources Information Center

Kahle, Brewster; Prelinger, Rick; Jackson, Mary E.; Boyack, Kevin W.; Wylie, Brian N.; Davidson, George S.; Witten, Ian H.; Bainbridge, David; Boddie, Stefan J.; Garrison, William A.; Cunningham, Sally Jo; Borgman, Christine L.; Hessel, Heather

2001-01-01

These six articles discuss various issues relating to digital libraries. Highlights include public access to digital materials; intellectual property concerns; the need for collaboration across disciplines; Greenstone software for construction and presentation of digital information collections; the Colorado Digitization Project; and conferences…

78 FR 48177 - Submission for OMB Review; 30-day Comment Request: National Institute of Mental Health Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-07

... Access Request and Use Certification (previously National Database for Autism Research Data Access... approval for use of the National Database for Autism Research (NDAR) Data Use Certification (DUC) Form...

The "GeneTrustee": a universal identification system that ensures privacy and confidentiality for human genetic databases.

PubMed

Burnett, Leslie; Barlow-Stewart, Kris; Proos, Anné L; Aizenberg, Harry

2003-05-01

This article describes a generic model for access to samples and information in human genetic databases. The model utilises a "GeneTrustee", a third-party intermediary independent of the subjects and of the investigators or database custodians. The GeneTrustee model has been implemented successfully in various community genetics screening programs and has facilitated research access to genetic databases while protecting the privacy and confidentiality of research subjects. The GeneTrustee model could also be applied to various types of non-conventional genetic databases, including neonatal screening Guthrie card collections, and to forensic DNA samples.

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.

PubMed

Hardison, Ross C; Chui, David H K; Giardine, Belinda; Riemer, Cathy; Patrinos, George P; Anagnou, Nicholas; Miller, Webb; Wajcman, Henri

2002-03-01

We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci. Copyright 2002 Wiley-Liss, Inc.

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

Bikakis, Nikos; Gioldasis, Nektarios; Tsinaraki, Chrisa; Christodoulakis, Stavros

SPARQL is today the standard access language for Semantic Web data. In the recent years XML databases have also acquired industrial importance due to the widespread applicability of XML in the Web. In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases. Our approach assumes that fairly generic mappings between ontology constructs and XML Schema constructs have been automatically derived or manually specified. The mappings are used to automatically translate SPARQL queries to semantically equivalent XQuery queries which are used to access the XML databases. We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.

Second-Tier Database for Ecosystem Focus, 2003-2004 Annual Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

University of Washington, Columbia Basin Research, DART Project Staff,

2004-12-01

The Second-Tier Database for Ecosystem Focus (Contract 00004124) provides direct and timely public access to Columbia Basin environmental, operational, fishery and riverine data resources for federal, state, public and private entities essential to sound operational and resource management. The database also assists with juvenile and adult mainstem passage modeling supporting federal decisions affecting the operation of the FCRPS. The Second-Tier Database known as Data Access in Real Time (DART) integrates public data for effective access, consideration and application. DART also provides analysis tools and performance measures for evaluating the condition of Columbia Basin salmonid stocks. These services are critical tomore » BPA's implementation of its fish and wildlife responsibilities under the Endangered Species Act (ESA).« less

[The opening of the French national health database: Opportunities and difficulties. The experience of the Gazel and Constances cohorts].

PubMed

Goldberg, M; Carton, M; Gourmelen, J; Genreau, M; Montourcy, M; Le Got, S; Zins, M

2016-09-01

In France, the national health database (SNIIRAM) is an administrative health database that collects data on hospitalizations and healthcare consumption for more than 60 million people. Although it does not record behavioral and environmental data, these data have a major interest for epidemiology, surveillance and public health. One of the most interesting uses of SNIIRAM is its linkage with surveys collecting data directly from persons. Access to the SNIIRAM data is currently relatively limited, but in the near future changes in regulations will largely facilitate open access. However, it is a huge and complex database and there are some important methodological and technical difficulties for using it due to its volume and architecture. We are developing tools for facilitating the linkage of the Gazel and Constances cohorts to the SNIIRAM: interactive documentation on the SNIIRAM database, software for the verification of the completeness and validity of the data received from the SNIIRAM, methods for constructing indicators from the raw data in order to flag the presence of certain events (specific diagnosis, procedure, drug…), standard queries for producing a set of variables on a specific area (drugs, diagnoses during a hospital stay…). Moreover, the REDSIAM network recently set up aims to develop, evaluate and make available algorithms to identify pathologies in SNIIRAM. In order to fully benefit from the exceptional potential of the SNIIRAM database, it is essential to develop tools to facilitate its use. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

McMaster Optimal Aging Portal: an evidence-based database for geriatrics-focused health professionals.

PubMed

Barbara, Angela M; Dobbins, Maureen; Brian Haynes, R; Iorio, Alfonso; Lavis, John N; Raina, Parminder; Levinson, Anthony J

2017-07-11

The objective of this work was to provide easy access to reliable health information based on good quality research that will help health care professionals to learn what works best for seniors to stay as healthy as possible, manage health conditions and build supportive health systems. This will help meet the demands of our aging population that clinicians provide high quality care for older adults, that public health professionals deliver disease prevention and health promotion strategies across the life span, and that policymakers address the economic and social need to create a robust health system and a healthy society for all ages. The McMaster Optimal Aging Portal's (Portal) professional bibliographic database contains high quality scientific evidence about optimal aging specifically targeted to clinicians, public health professionals and policymakers. The database content comes from three information services: McMaster Premium LiteratUre Service (MacPLUS™), Health Evidence™ and Health Systems Evidence. The Portal is continually updated, freely accessible online, easily searchable, and provides email-based alerts when new records are added. The database is being continually assessed for value, usability and use. A number of improvements are planned, including French language translation of content, increased linkages between related records within the Portal database, and inclusion of additional types of content. While this article focuses on the professional database, the Portal also houses resources for patients, caregivers and the general public, which may also be of interest to geriatric practitioners and researchers.

Oceanography Information System of Spanish Institute of Oceanography (IEO)

NASA Astrophysics Data System (ADS)

Tello, Olvido; Gómez, María; González, Sonsoles

2016-04-01

Since 1914, the Spanish Institute of Oceanography (IEO) performs multidisciplinary studies of the marine environment. In same case are systematic studies and in others are specific studies for special requirements (El Hierro submarine volcanic episode, spill Prestige, others.). Different methodologies and data acquisition techniques are used depending on studies aims. The acquired data are stored and presented in different formats. The information is organized into different databases according to the subject and the variables represented (geology, fisheries, aquaculture, pollution, habitats, etc.). Related to physical and chemical oceanography data, in 1964 was created the DATA CENTER of IEO (CEDO), in order to organize the data about physical and chemical variables, to standardize this information and to serve the international data network SeaDataNet. www.seadatanet.org. This database integrates data about temperature, salinity, nutrients, and tidal data. CEDO allows consult and download the data. http://indamar.ieo.es On the other hand, related to data about marine species in 1999 was developed SIRENO DATABASE. All data about species collected in oceanographic surveys carried out by researches of IEO, and data from observers on fishing vessels are incorporated in SIRENO database. In this database is stored catch data, biomass, abundance, etc. This system is based on architecture ORACLE. Due to the large amount of information collected over the 100 years of IEO history, there is a clear need to organize, standardize, integrate and relate the different databases and information, and to provide interoperability and access to the information. Consequently, in 2000 it emerged the first initiative to organize the IEO spatial information in an Oceanography Information System, based on a Geographical Information System (GIS). The GIS was consolidated as IEO institutional GIS and was created the Spatial Data Infrastructure of IEO (IDEO) following trend of INSPIRE. All data included in the GIS have their corresponding metadata about ISO19115 and INSPIRE. IDEO is based on Web services, Quality of Services, Open standards, ISO (OGC) and INSPIRE standards, and both provide access to the geographical marine information of IEO. The GIS allows the information to be organized, visualized, consulted and analyzed. The data from different IEO databases are integrated into a GIS corporate Geodatabase (Esri format). This tool is essential in the decision making of aspects like: - Protection of marine environment - Sustainable management of resources - Natural Hazards. - Marine spatial planning. Examples of the use of GIS as a spatial analysis tool are: - Mud volcanoes explored in LIFE-INDEMARES project. - Cartographic series about Spanish continental shelf, developed from data integrated in IEO marine GIS, acquired from oceanographic surveys in ESPACE project. - Cartography developed from the information gathered in Initial Assessment of Marine Strategy Framework Directive. - Studies of natural hazards related to submarine canyons in southeast region marine Spanish. Currently the IEO is participating in many European initiatives, especially in several lots of EMODNET. The IEO besides is working in consonance with INSPIRE, Growth Blue, Horizon 2020, etc., to contribute to, the knowledge of marine environment, its protection and its spatial planning are extremely relevant issues. In order to facilitate the access to the Spatial Data Infrastructure of IEO, the IEO Geoportal was developed in 2012. It mainly involves a metadata catalog, access to the data viewers and Web Services of IDEO. http://www.geo-ideo.ieo.es/geoportalideo/catalog/main/home.page

First use of LHC Run 3 Conditions Database infrastructure for auxiliary data files in ATLAS

NASA Astrophysics Data System (ADS)

Aperio Bella, L.; Barberis, D.; Buttinger, W.; Formica, A.; Gallas, E. J.; Rinaldi, L.; Rybkin, G.; ATLAS Collaboration

2017-10-01

Processing of the large amount of data produced by the ATLAS experiment requires fast and reliable access to what we call Auxiliary Data Files (ADF). These files, produced by Combined Performance, Trigger and Physics groups, contain conditions, calibrations, and other derived data used by the ATLAS software. In ATLAS this data has, thus far for historical reasons, been collected and accessed outside the ATLAS Conditions Database infrastructure and related software. For this reason, along with the fact that ADF are effectively read by the software as binary objects, this class of data appears ideal for testing the proposed Run 3 conditions data infrastructure now in development. This paper describes this implementation as well as the lessons learned in exploring and refining the new infrastructure with the potential for deployment during Run 2.

Prototype Packaged Databases and Software in Health

PubMed Central

Gardenier, Turkan K.

1980-01-01

This paper describes the recent demand for packaged databases and software for health applications in light of developments in mini-and micro-computer technology. Specific features for defining prospective user groups are discussed; criticisms generated for large-scale epidemiological data use as a means of replacing clinical trials and associated controls are posed to the reader. The available collaborative efforts for access and analysis of jointly structured health data are stressed, with recommendations for new analytical techniques specifically geared to monitoring data such as the CTSS (Cumulative Transitional State Score) generated for tacking ongoing patient status over time in clinical trials. Examples of graphic display are given from the Domestic Information Display System (DIDS) which is a collaborative multi-agency effort to computerize and make accessible user-specified U.S. and local maps relating to health, environment, socio-economic and energy data.

Comparison of Online Agricultural Information Services.

ERIC Educational Resources Information Center

Reneau, Fred; Patterson, Richard

1984-01-01

Outlines major online agricultural information services--agricultural databases, databases with agricultural services, educational databases in agriculture--noting services provided, access to the database, and costs. Benefits of online agricultural database sources (availability of agricultural marketing, weather, commodity prices, management…

NATIONAL URBAN DATABASE AND ACCESS PROTAL TOOL

EPA Science Inventory

Current mesoscale weather prediction and microscale dispersion models are limited in their ability to perform accurate assessments in urban areas. A project called the National Urban Database with Access Portal Tool (NUDAPT) is beginning to provide urban data and improve the para...

VO Access to BASECOL Database

NASA Astrophysics Data System (ADS)

Moreau, N.; Dubernet, M. L.

2006-07-01

Basecol is a combination of a website (using PHP and HTML) and a MySQL database concerning molecular ro-vibrational transitions induced by collisions with atoms or molecules. This database has been created in view of the scientific preparation of the Heterodyne Instrument for the Far-Infrared on board the Herschel Space Observatory (HSO). Basecol offers an access to numerical and bibliographic data through various output methods such as ASCII, HTML or VOTable (which is a first step towards a VO compliant system). A web service using Apache Axis has been developed in order to provide a direct access to data for external applications.

Designing a Multi-Petabyte Database for LSST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becla, Jacek; Hanushevsky, Andrew; Nikolaev, Sergei

2007-01-10

The 3.2 giga-pixel LSST camera will produce approximately half a petabyte of archive images every month. These data need to be reduced in under a minute to produce real-time transient alerts, and then added to the cumulative catalog for further analysis. The catalog is expected to grow about three hundred terabytes per year. The data volume, the real-time transient alerting requirements of the LSST, and its spatio-temporal aspects require innovative techniques to build an efficient data access system at reasonable cost. As currently envisioned, the system will rely on a database for catalogs and metadata. Several database systems are beingmore » evaluated to understand how they perform at these data rates, data volumes, and access patterns. This paper describes the LSST requirements, the challenges they impose, the data access philosophy, results to date from evaluating available database technologies against LSST requirements, and the proposed database architecture to meet the data challenges.« less

EMU Lessons Learned Database

NASA Technical Reports Server (NTRS)

Matthews, Kevin M., Jr.; Crocker, Lori; Cupples, J. Scott

2011-01-01

As manned space exploration takes on the task of traveling beyond low Earth orbit, many problems arise that must be solved in order to make the journey possible. One major task is protecting humans from the harsh space environment. The current method of protecting astronauts during Extravehicular Activity (EVA) is through use of the specially designed Extravehicular Mobility Unit (EMU). As more rigorous EVA conditions need to be endured at new destinations, the suit will need to be tailored and improved in order to accommodate the astronaut. The Objective behind the EMU Lessons Learned Database(LLD) is to be able to create a tool which will assist in the development of next-generation EMUs, along with maintenance and improvement of the current EMU, by compiling data from Failure Investigation and Analysis Reports (FIARs) which have information on past suit failures. FIARs use a system of codes that give more information on the aspects of the failure, but if one is unfamiliar with the EMU they will be unable to decipher the information. A goal of the EMU LLD is to not only compile the information, but to present it in a user-friendly, organized, searchable database accessible to all familiarity levels with the EMU; both newcomers and veterans alike. The EMU LLD originally started as an Excel database, which allowed easy navigation and analysis of the data through pivot charts. Creating an entry requires access to the Problem Reporting And Corrective Action database (PRACA), which contains the original FIAR data for all hardware. FIAR data are then transferred to, defined, and formatted in the LLD. Work is being done to create a web-based version of the LLD in order to increase accessibility to all of Johnson Space Center (JSC), which includes converting entries from Excel to the HTML format. FIARs related to the EMU have been completed in the Excel version, and now focus has shifted to expanding FIAR data in the LLD to include EVA tools and support hardware such as the Pistol Grip Tool (PGT) and the Battery Charger Module (BCM), while adding any recently closed EMU-related FIARs.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

PubMed

Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general.

Alternative treatment technology information center computer database system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sullivan, D.

1995-10-01

The Alternative Treatment Technology Information Center (ATTIC) computer database system was developed pursuant to the 1986 Superfund law amendments. It provides up-to-date information on innovative treatment technologies to clean up hazardous waste sites. ATTIC v2.0 provides access to several independent databases as well as a mechanism for retrieving full-text documents of key literature. It can be accessed with a personal computer and modem 24 hours a day, and there are no user fees. ATTIC provides {open_quotes}one-stop shopping{close_quotes} for information on alternative treatment options by accessing several databases: (1) treatment technology database; this contains abstracts from the literature on all typesmore » of treatment technologies, including biological, chemical, physical, and thermal methods. The best literature as viewed by experts is highlighted. (2) treatability study database; this provides performance information on technologies to remove contaminants from wastewaters and soils. It is derived from treatability studies. This database is available through ATTIC or separately as a disk that can be mailed to you. (3) underground storage tank database; this presents information on underground storage tank corrective actions, surface spills, emergency response, and remedial actions. (4) oil/chemical spill database; this provides abstracts on treatment and disposal of spilled oil and chemicals. In addition to these separate databases, ATTIC allows immediate access to other disk-based systems such as the Vendor Information System for Innovative Treatment Technologies (VISITT) and the Bioremediation in the Field Search System (BFSS). The user may download these programs to their own PC via a high-speed modem. Also via modem, users are able to download entire documents through the ATTIC system. Currently, about fifty publications are available, including Superfund Innovative Technology Evaluation (SITE) program documents.« less

Exploration of the Chemical Space of Public Genomic ...

EPA Pesticide Factsheets

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. By evaluating the chemical space of public genomic data in relation to public toxicological data, it is possible to identify classes of chemicals on which to develop methodologies for the integration of chemogenomic data into predictive toxicology.

GIS and RDBMS Used with Offline FAA Airspace Databases

NASA Technical Reports Server (NTRS)

Clark, J.; Simmons, J.; Scofield, E.; Talbott, B.

1994-01-01

A geographic information system (GIS) and relational database management system (RDBMS) were used in a Macintosh environment to access, manipulate, and display off-line FAA databases of airport and navigational aid locations, airways, and airspace boundaries. This proof-of-concept effort used data available from the Adaptation Controlled Environment System (ACES) and Digital Aeronautical Chart Supplement (DACS) databases to allow FAA cartographers and others to create computer-assisted charts and overlays as reference material for air traffic controllers. These products were created on an engineering model of the future GRASP (GRaphics Adaptation Support Position) workstation that will be used to make graphics and text products for the Advanced Automation System (AAS), which will upgrade and replace the current air traffic control system. Techniques developed during the prototyping effort have shown the viability of using databases to create graphical products without the need for an intervening data entry step.

BIRS - Bioterrorism Information Retrieval System.

PubMed

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. The database is freely available at http://www.bioterrorism.biowaves.org.

The Unified Database for BM@N experiment data handling

NASA Astrophysics Data System (ADS)

Gertsenberger, Konstantin; Rogachevsky, Oleg

2018-04-01

The article describes the developed Unified Database designed as a comprehensive relational data storage for the BM@N experiment at the Joint Institute for Nuclear Research in Dubna. The BM@N experiment, which is one of the main elements of the first stage of the NICA project, is a fixed target experiment at extracted Nuclotron beams of the Laboratory of High Energy Physics (LHEP JINR). The structure and purposes of the BM@N setup are briefly presented. The article considers the scheme of the Unified Database, its attributes and implemented features in detail. The use of the developed BM@N database provides correct multi-user access to actual information of the experiment for data processing. It stores information on the experiment runs, detectors and their geometries, different configuration, calibration and algorithm parameters used in offline data processing. An important part of any database - user interfaces are presented.

The development of digital library system for drug research information.

PubMed

Kim, H J; Kim, S R; Yoo, D S; Lee, S H; Suh, O K; Cho, J H; Shin, H T; Yoon, J P

1998-01-01

The sophistication of computer technology and information transmission on internet has made various cyber information repository available to information consumers. In the era of information super-highway, the digital library which can be accessed from remote sites at any time is considered the prototype of information repository. Using object-oriented DBMS, the very first model of digital library for pharmaceutical researchers and related professionals in Korea has been developed. The published research papers and researchers' personal information was included in the database. For database with research papers, 13 domestic journals were abstracted and scanned for full-text image files which can be viewed by Internet web browsers. The database with researchers' personal information was also developed and interlinked to the database with research papers. These database will be continuously updated and will be combined with world-wide information as the unique digital library in the field of pharmacy.

Multiple imputation as one tool to provide longitudinal databases for modelling human height and weight development.

PubMed

Aßmann, C

2016-06-01

Besides large efforts regarding field work, provision of valid databases requires statistical and informational infrastructure to enable long-term access to longitudinal data sets on height, weight and related issues. To foster use of longitudinal data sets within the scientific community, provision of valid databases has to address data-protection regulations. It is, therefore, of major importance to hinder identifiability of individuals from publicly available databases. To reach this goal, one possible strategy is to provide a synthetic database to the public allowing for pretesting strategies for data analysis. The synthetic databases can be established using multiple imputation tools. Given the approval of the strategy, verification is based on the original data. Multiple imputation by chained equations is illustrated to facilitate provision of synthetic databases as it allows for capturing a wide range of statistical interdependencies. Also missing values, typically occurring within longitudinal databases for reasons of item non-response, can be addressed via multiple imputation when providing databases. The provision of synthetic databases using multiple imputation techniques is one possible strategy to ensure data protection, increase visibility of longitudinal databases and enhance the analytical potential.

NASA Thesaurus. Volume 1: Hierarchical listing. Volume 2: Access vocabulary. Volume 3: Definitions

NASA Technical Reports Server (NTRS)

1994-01-01

There are over 17,500 postable terms and some 4,000 nonpostable terms approved for use in the NASA Scientific and Technical Information Database in the Hierarchical Listing of the NASA Thesaurus. The generic structure is presented for many terms. The broader term and narrower term relationships are shown in an indented fashion that illustrates the generic structure better than the more widely used BT and NT listings. Related terms are generously applied, thus enhancing the usefulness of the Hierarchical Listing. Greater access to the Hierarchical Listing may be achieved with the collateral use of Volume 2 - Access Vocabulary and Volume 3 - Definitions.

A geodata warehouse: Using denormalisation techniques as a tool for delivering spatially enabled integrated geological information to geologists

NASA Astrophysics Data System (ADS)

Kingdon, Andrew; Nayembil, Martin L.; Richardson, Anne E.; Smith, A. Graham

2016-11-01

New requirements to understand geological properties in three dimensions have led to the development of PropBase, a data structure and delivery tools to deliver this. At the BGS, relational database management systems (RDBMS) has facilitated effective data management using normalised subject-based database designs with business rules in a centralised, vocabulary controlled, architecture. These have delivered effective data storage in a secure environment. However, isolated subject-oriented designs prevented efficient cross-domain querying of datasets. Additionally, the tools provided often did not enable effective data discovery as they struggled to resolve the complex underlying normalised structures providing poor data access speeds. Users developed bespoke access tools to structures they did not fully understand sometimes delivering them incorrect results. Therefore, BGS has developed PropBase, a generic denormalised data structure within an RDBMS to store property data, to facilitate rapid and standardised data discovery and access, incorporating 2D and 3D physical and chemical property data, with associated metadata. This includes scripts to populate and synchronise the layer with its data sources through structured input and transcription standards. A core component of the architecture includes, an optimised query object, to deliver geoscience information from a structure equivalent to a data warehouse. This enables optimised query performance to deliver data in multiple standardised formats using a web discovery tool. Semantic interoperability is enforced through vocabularies combined from all data sources facilitating searching of related terms. PropBase holds 28.1 million spatially enabled property data points from 10 source databases incorporating over 50 property data types with a vocabulary set that includes 557 property terms. By enabling property data searches across multiple databases PropBase has facilitated new scientific research, previously considered impractical. PropBase is easily extended to incorporate 4D data (time series) and is providing a baseline for new "big data" monitoring projects.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman, Andre M.; Johnson, Gary E.; Borde, Amy B.

Pacific Northwest National Laboratory (PNNL) conducted this project for the U.S. Army Corps of Engineers, Portland District (Corps). The purpose of the project is to develop a geospatial, web-accessible database (called “Oncor”) for action effectiveness and related data from monitoring and research efforts for the Columbia Estuary Ecosystem Restoration Program (CEERP). The intent is for the Oncor database to enable synthesis and evaluation, the results of which can then be applied in subsequent CEERP decision-making. This is the first annual report in what is expected to be a 3- to 4-year project, which commenced on February 14, 2012.

AgeFactDB—the JenAge Ageing Factor Database—towards data integration in ageing research

PubMed Central

Hühne, Rolf; Thalheim, Torsten; Sühnel, Jürgen

2014-01-01

AgeFactDB (http://agefactdb.jenage.de) is a database aimed at the collection and integration of ageing phenotype data including lifespan information. Ageing factors are considered to be genes, chemical compounds or other factors such as dietary restriction, whose action results in a changed lifespan or another ageing phenotype. Any information related to the effects of ageing factors is called an observation and is presented on observation pages. To provide concise access to the complete information for a particular ageing factor, corresponding observations are also summarized on ageing factor pages. In a first step, ageing-related data were primarily taken from existing databases such as the Ageing Gene Database—GenAge, the Lifespan Observations Database and the Dietary Restriction Gene Database—GenDR. In addition, we have started to include new ageing-related information. Based on homology data taken from the HomoloGene Database, AgeFactDB also provides observation and ageing factor pages of genes that are homologous to known ageing-related genes. These homologues are considered as candidate or putative ageing-related genes. AgeFactDB offers a variety of search and browse options, and also allows the download of ageing factor or observation lists in TSV, CSV and XML formats. PMID:24217911

Web Based Data Access to the World Data Center for Climate

NASA Astrophysics Data System (ADS)

Toussaint, F.; Lautenschlager, M.

2006-12-01

The World Data Center for Climate (WDC-Climate, www.wdc-climate.de) is hosted by the Model &Data Group (M&D) of the Max Planck Institute for Meteorology. The M&D department is financed by the German government and uses the computers and mass storage facilities of the German Climate Computing Centre (Deutsches Klimarechenzentrum, DKRZ). The WDC-Climate provides web access to 200 Terabytes of climate data; the total mass storage archive contains nearly 4 Petabytes. Although the majority of the datasets concern model output data, some satellite and observational data are accessible as well. The underlying relational database is distributed on five servers. The CERA relational data model is used to integrate catalogue data and mass data. The flexibility of the model allows to store and access very different types of data and metadata. The CERA metadata catalogue provides easy access to the content of the CERA database as well as to other data in the web. Visit ceramodel.wdc-climate.de for additional information on the CERA data model. The majority of the users access data via the CERA metadata catalogue, which is open without registration. However, prior to retrieving data user are required to check in and apply for a userid and password. The CERA metadata catalogue is servlet based. So it is accessible worldwide through any web browser at cera.wdc-climate.de. In addition to data and metadata access by the web catalogue, WDC-Climate offers a number of other forms of web based data access. All metadata are available via http request as xml files in various metadata formats (ISO, DC, etc., see wini.wdc-climate.de) which allows for easy data interchange with other catalogues. Model data can be retrieved in GRIB, ASCII, NetCDF, and binary (IEEE) format. WDC-Climate serves as data centre for various projects. Since xml files are accessible by http, the integration of data into applications of different projects is very easy. Projects supported by WDC-Climate are e.g. CEOP, IPCC, and CARIBIC. A script tool for data download (jblob) is offered on the web page, to make retrieval of huge data quantities more comfortable.

Creating a sampling frame for population-based veteran research: representativeness and overlap of VA and Department of Defense databases.

PubMed

Washington, Donna L; Sun, Su; Canning, Mark

2010-01-01

Most veteran research is conducted in Department of Veterans Affairs (VA) healthcare settings, although most veterans obtain healthcare outside the VA. Our objective was to determine the adequacy and relative contributions of Veterans Health Administration (VHA), Veterans Benefits Administration (VBA), and Department of Defense (DOD) administrative databases for representing the U.S. veteran population, using as an example the creation of a sampling frame for the National Survey of Women Veterans. In 2008, we merged the VHA, VBA, and DOD databases. We identified the number of unique records both overall and from each database. The combined databases yielded 925,946 unique records, representing 51% of the 1,802,000 U.S. women veteran population. The DOD database included 30% of the population (with 8% overlap with other databases). The VHA enrollment database contributed an additional 20% unique women veterans (with 6% overlap with VBA databases). VBA databases contributed an additional 2% unique women veterans (beyond 10% overlap with other databases). Use of VBA and DOD databases substantially expands access to the population of veterans beyond those in VHA databases, regardless of VA use. Adoption of these additional databases would enhance the value and generalizability of a wide range of studies of both male and female veterans.

The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

PubMed Central

Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

2005-01-01

Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

PubMed Central

Meereis, Florian; Kaufmann, Michael

2008-01-01

Background The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries. Results Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at . Conclusion NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document. PMID:19014535

HypoxiaDB: a database of hypoxia-regulated proteins

PubMed Central

Khurana, Pankaj; Sugadev, Ragumani; Jain, Jaspreet; Singh, Shashi Bala

2013-01-01

There has been intense interest in the cellular response to hypoxia, and a large number of differentially expressed proteins have been identified through various high-throughput experiments. These valuable data are scattered, and there have been no systematic attempts to document the various proteins regulated by hypoxia. Compilation, curation and annotation of these data are important in deciphering their role in hypoxia and hypoxia-related disorders. Therefore, we have compiled HypoxiaDB, a database of hypoxia-regulated proteins. It is a comprehensive, manually-curated, non-redundant catalog of proteins whose expressions are shown experimentally to be altered at different levels and durations of hypoxia. The database currently contains 72 000 manually curated entries taken on 3500 proteins extracted from 73 peer-reviewed publications selected from PubMed. HypoxiaDB is distinctive from other generalized databases: (i) it compiles tissue-specific protein expression changes under different levels and duration of hypoxia. Also, it provides manually curated literature references to support the inclusion of the protein in the database and establish its association with hypoxia. (ii) For each protein, HypoxiaDB integrates data on gene ontology, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, protein–protein interactions, protein family (Pfam), OMIM (Online Mendelian Inheritance in Man), PDB (Protein Data Bank) structures and homology to other sequenced genomes. (iii) It also provides pre-compiled information on hypoxia-proteins, which otherwise requires tedious computational analysis. This includes information like chromosomal location, identifiers like Entrez, HGNC, Unigene, Uniprot, Ensembl, Vega, GI numbers and Genbank accession numbers associated with the protein. These are further cross-linked to respective public databases augmenting HypoxiaDB to the external repositories. (iv) In addition, HypoxiaDB provides an online sequence-similarity search tool for users to compare their protein sequences with HypoxiaDB protein database. We hope that HypoxiaDB will enrich our knowledge about hypoxia-related biology and eventually will lead to the development of novel hypothesis and advancements in diagnostic and therapeutic activities. HypoxiaDB is freely accessible for academic and non-profit users via http://www.hypoxiadb.com. Database URL: http://www.hypoxiadb.com PMID:24178989

An effective model for store and retrieve big health data in cloud computing.

PubMed

Goli-Malekabadi, Zohreh; Sargolzaei-Javan, Morteza; Akbari, Mohammad Kazem

2016-08-01

The volume of healthcare data including different and variable text types, sounds, and images is increasing day to day. Therefore, the storage and processing of these data is a necessary and challenging issue. Generally, relational databases are used for storing health data which are not able to handle the massive and diverse nature of them. This study aimed at presenting the model based on NoSQL databases for the storage of healthcare data. Despite different types of NoSQL databases, document-based DBs were selected by a survey on the nature of health data. The presented model was implemented in the Cloud environment for accessing to the distribution properties. Then, the data were distributed on the database by applying the Shard property. The efficiency of the model was evaluated in comparison with the previous data model, Relational Database, considering query time, data preparation, flexibility, and extensibility parameters. The results showed that the presented model approximately performed the same as SQL Server for "read" query while it acted more efficiently than SQL Server for "write" query. Also, the performance of the presented model was better than SQL Server in the case of flexibility, data preparation and extensibility. Based on these observations, the proposed model was more effective than Relational Databases for handling health data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease.

PubMed

Moskalev, Alexey; Chernyagina, Elizaveta; de Magalhães, João Pedro; Barardo, Diogo; Thoppil, Harikrishnan; Shaposhnikov, Mikhail; Budovsky, Arie; Fraifeld, Vadim E; Garazha, Andrew; Tsvetkov, Vasily; Bronovitsky, Evgeny; Bogomolov, Vladislav; Scerbacov, Alexei; Kuryan, Oleg; Gurinovich, Roman; Jellen, Leslie C; Kennedy, Brian; Mamoshina, Polina; Dobrovolskaya, Evgeniya; Aliper, Alex; Kaminsky, Dmitry; Zhavoronkov, Alex

2015-09-01

As the level of interest in aging research increases, there is a growing number of geroprotectors, or therapeutic interventions that aim to extend the healthy lifespan and repair or reduce aging-related damage in model organisms and, eventually, in humans. There is a clear need for a manually-curated database of geroprotectors to compile and index their effects on aging and age-related diseases and link these effects to relevant studies and multiple biochemical and drug databases. Here, we introduce the first such resource, Geroprotectors (http://geroprotectors.org). Geroprotectors is a public, rapidly explorable database that catalogs over 250 experiments involving over 200 known or candidate geroprotectors that extend lifespan in model organisms. Each compound has a comprehensive profile complete with biochemistry, mechanisms, and lifespan effects in various model organisms, along with information ranging from chemical structure, side effects, and toxicity to FDA drug status. These are presented in a visually intuitive, efficient framework fit for casual browsing or in-depth research alike. Data are linked to the source studies or databases, providing quick and convenient access to original data. The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching. Geroprotectors is a one-stop, knowledge-sharing, time-saving resource for researchers seeking healthy aging solutions.

Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease

PubMed Central

Moskalev, Alexey; Chernyagina, Elizaveta; de Magalhães, João Pedro; Barardo, Diogo; Thoppil, Harikrishnan; Shaposhnikov, Mikhail; Budovsky, Arie; Fraifeld, Vadim E.; Garazha, Andrew; Tsvetkov, Vasily; Bronovitsky, Evgeny; Bogomolov, Vladislav; Scerbacov, Alexei; Kuryan, Oleg; Gurinovich, Roman; Jellen, Leslie C.; Kennedy, Brian; Mamoshina, Polina; Dobrovolskaya, Evgeniya; Aliper, Alex; Kaminsky, Dmitry; Zhavoronkov, Alex

2015-01-01

As the level of interest in aging research increases, there is a growing number of geroprotectors, or therapeutic interventions that aim to extend the healthy lifespan and repair or reduce aging-related damage in model organisms and, eventually, in humans. There is a clear need for a manually-curated database of geroprotectors to compile and index their effects on aging and age-related diseases and link these effects to relevant studies and multiple biochemical and drug databases. Here, we introduce the first such resource, Geroprotectors (http://geroprotectors.org). Geroprotectors is a public, rapidly explorable database that catalogs over 250 experiments involving over 200 known or candidate geroprotectors that extend lifespan in model organisms. Each compound has a comprehensive profile complete with biochemistry, mechanisms, and lifespan effects in various model organisms, along with information ranging from chemical structure, side effects, and toxicity to FDA drug status. These are presented in a visually intuitive, efficient framework fit for casual browsing or in-depth research alike. Data are linked to the source studies or databases, providing quick and convenient access to original data. The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching. Geroprotectors is a one-stop, knowledge-sharing, time-saving resource for researchers seeking healthy aging solutions. PMID:26342919

Open-access databases as unprecedented resources and drivers of cultural change in fisheries science

DOE Office of Scientific and Technical Information (OSTI.GOV)

McManamay, Ryan A; Utz, Ryan

2014-01-01

Open-access databases with utility in fisheries science have grown exponentially in quantity and scope over the past decade, with profound impacts to our discipline. The management, distillation, and sharing of an exponentially growing stream of open-access data represents several fundamental challenges in fisheries science. Many of the currently available open-access resources may not be universally known among fisheries scientists. We therefore introduce many national- and global-scale open-access databases with applications in fisheries science and provide an example of how they can be harnessed to perform valuable analyses without additional field efforts. We also discuss how the development, maintenance, and utilizationmore » of open-access data are likely to pose technical, financial, and educational challenges to fisheries scientists. Such cultural implications that will coincide with the rapidly increasing availability of free data should compel the American Fisheries Society to actively address these problems now to help ease the forthcoming cultural transition.« less

[Status of libraries and databases for natural products at abroad].

PubMed

Zhao, Li-Mei; Tan, Ning-Hua

2015-01-01

For natural products are one of the important sources for drug discovery, libraries and databases of natural products are significant for the development and research of natural products. At present, most of compound libraries at abroad are synthetic or combinatorial synthetic molecules, resulting to access natural products difficult; for information of natural products are scattered with different standards, it is difficult to construct convenient, comprehensive and large-scale databases for natural products. This paper reviewed the status of current accessing libraries and databases for natural products at abroad and provided some important information for the development of libraries and database for natural products.

FRED, a Front End for Databases.

ERIC Educational Resources Information Center

Crystal, Maurice I.; Jakobson, Gabriel E.

1982-01-01

FRED (a Front End for Databases) was conceived to alleviate data access difficulties posed by the heterogeneous nature of online databases. A hardware/software layer interposed between users and databases, it consists of three subsystems: user-interface, database-interface, and knowledge base. Architectural alternatives for this database machine…

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

NASA Technical Reports Server (NTRS)

Moore, Reagan; Marciano, Richard; Wan, Michael; Sherwin, Tom; Frost, Richard

1996-01-01

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

Genomics and Public Health Research: Can the State Allow Access to Genomic Databases?

PubMed Central

Cousineau, J; Girard, N; Monardes, C; Leroux, T; Jean, M Stanton

2012-01-01

Because many diseases are multifactorial disorders, the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State’s role and authority on matters related to public health, in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec). Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec, as examples of key tools framing public health decision-making process. We observed that State powers in public health, are not, in Quebec, well adapted to the expansion of genomics research. We propose that the scope of the concept of research in public health should be clear and include the following characteristics: a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up, consent, etc.). We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters. PMID:23113174

The HISTMAG database: combining historical, archaeomagnetic and volcanic data

NASA Astrophysics Data System (ADS)

Arneitz, Patrick; Leonhardt, Roman; Schnepp, Elisabeth; Heilig, Balázs; Mayrhofer, Franziska; Kovacs, Peter; Hejda, Pavel; Valach, Fridrich; Vadasz, Gergely; Hammerl, Christa; Egli, Ramon; Fabian, Karl; Kompein, Niko

2017-09-01

Records of the past geomagnetic field can be divided into two main categories. These are instrumental historical observations on the one hand, and field estimates based on the magnetization acquired by rocks, sediments and archaeological artefacts on the other hand. In this paper, a new database combining historical, archaeomagnetic and volcanic records is presented. HISTMAG is a relational database, implemented in MySQL, and can be accessed via a web-based interface (http://www.conrad-observatory.at/zamg/index.php/data-en/histmag-database). It combines available global historical data compilations covering the last ∼500 yr as well as archaeomagnetic and volcanic data collections from the last 50 000 yr. Furthermore, new historical and archaeomagnetic records, mainly from central Europe, have been acquired. In total, 190 427 records are currently available in the HISTMAG database, whereby the majority is related to historical declination measurements (155 525). The original database structure was complemented by new fields, which allow for a detailed description of the different data types. A user-comment function provides the possibility for a scientific discussion about individual records. Therefore, HISTMAG database supports thorough reliability and uncertainty assessments of the widely different data sets, which are an essential basis for geomagnetic field reconstructions. A database analysis revealed systematic offset for declination records derived from compass roses on historical geographical maps through comparison with other historical records, while maps created for mining activities represent a reliable source.

The International Experimental Thermal Hydraulic Systems database – TIETHYS: A new NEA validation tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rohatgi, Upendra S.

Nuclear reactor codes require validation with appropriate data representing the plant for specific scenarios. The thermal-hydraulic data is scattered in different locations and in different formats. Some of the data is in danger of being lost. A relational database is being developed to organize the international thermal hydraulic test data for various reactor concepts and different scenarios. At the reactor system level, that data is organized to include separate effect tests and integral effect tests for specific scenarios and corresponding phenomena. The database relies on the phenomena identification sections of expert developed PIRTs. The database will provide a summary ofmore » appropriate data, review of facility information, test description, instrumentation, references for the experimental data and some examples of application of the data for validation. The current database platform includes scenarios for PWR, BWR, VVER, and specific benchmarks for CFD modelling data and is to be expanded to include references for molten salt reactors. There are place holders for high temperature gas cooled reactors, CANDU and liquid metal reactors. This relational database is called The International Experimental Thermal Hydraulic Systems (TIETHYS) database and currently resides at Nuclear Energy Agency (NEA) of the OECD and is freely open to public access. Going forward the database will be extended to include additional links and data as they become available. https://www.oecd-nea.org/tiethysweb/« less

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

Universal Index System

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

1993-01-01

The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

Village Green Project: Web-accessible Database

EPA Science Inventory

The purpose of this web-accessible database is for the public to be able to view instantaneous readings from a solar-powered air monitoring station located in a public location (prototype pilot test is outside of a library in Durham County, NC). The data are wirelessly transmitte...

Designing a multi-petabyte database for LSST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becla, J; Hanushevsky, A

2005-12-21

The 3.2 giga-pixel LSST camera will produce over half a petabyte of raw images every month. This data needs to be reduced in under a minute to produce real-time transient alerts, and then cataloged and indexed to allow efficient access and simplify further analysis. The indexed catalogs alone are expected to grow at a speed of about 600 terabytes per year. The sheer volume of data, the real-time transient alerting requirements of the LSST, and its spatio-temporal aspects require cutting-edge techniques to build an efficient data access system at reasonable cost. As currently envisioned, the system will rely on amore » database for catalogs and metadata. Several database systems are being evaluated to understand how they will scale and perform at these data volumes in anticipated LSST access patterns. This paper describes the LSST requirements, the challenges they impose, the data access philosophy, and the database architecture that is expected to be adopted in order to meet the data challenges.« less

A veterinary anatomy tutoring system.

PubMed

Theodoropoulos, G; Loumos, V; Antonopoulos, J

1994-02-14

A veterinary anatomy tutoring system was developed by using Knowledge Pro, an object-oriented software development tool with hypermedia capabilities, and MS Access, a relational database. Communication between them is facilitated by using the Structured Query Language (SQL). The architecture of the system is based on knowledge sets, each of which covers four different descriptions of an organ, namely gross anatomy (general description), gross anatomy (comparative features), histology, and embryology, which constitute the knowledge units. These knowledge units are linked with three global variables that define the animals, the topographies, and the system to which this organ belongs, creating three data-bases. These three data-bases are interrelated through the organ field in order to establish a relational model. This system allows versatility in the student's navigation through the information space by offering different modes for information location and presentation. These include course mode, review mode, reference mode, dissection mode, and comparison mode. In addition, the system provides a self-evaluation mode.

Space Station Freedom environmental database system (FEDS) for MSFC testing

NASA Technical Reports Server (NTRS)

Story, Gail S.; Williams, Wendy; Chiu, Charles

1991-01-01

The Water Recovery Test (WRT) at Marshall Space Flight Center (MSFC) is the first demonstration of integrated water recovery systems for potable and hygiene water reuse as envisioned for Space Station Freedom (SSF). In order to satisfy the safety and health requirements placed on the SSF program and facilitate test data assessment, an extensive laboratory analysis database was established to provide a central archive and data retrieval function. The database is required to store analysis results for physical, chemical, and microbial parameters measured from water, air and surface samples collected at various locations throughout the test facility. The Oracle Relational Database Management System (RDBMS) was utilized to implement a secured on-line information system with the ECLSS WRT program as the foundation for this system. The database is supported on a VAX/VMS 8810 series mainframe and is accessible from the Marshall Information Network System (MINS). This paper summarizes the database requirements, system design, interfaces, and future enhancements.

EMEN2: An Object Oriented Database and Electronic Lab Notebook

PubMed Central

Rees, Ian; Langley, Ed; Chiu, Wah; Ludtke, Steven J.

2013-01-01

Transmission electron microscopy and associated methods such as single particle analysis, 2-D crystallography, helical reconstruction and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments, and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source. PMID:23360752

Distributed query plan generation using multiobjective genetic algorithm.

PubMed

Panicker, Shina; Kumar, T V Vijay

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability.

Distributed Query Plan Generation Using Multiobjective Genetic Algorithm

PubMed Central

Panicker, Shina; Vijay Kumar, T. V.

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability. PMID:24963513

Navigating through the Jungle of Allergens: Features and Applications of Allergen Databases.

PubMed

Radauer, Christian

2017-01-01

The increasing number of available data on allergenic proteins demanded the establishment of structured, freely accessible allergen databases. In this review article, features and applications of 6 of the most widely used allergen databases are discussed. The WHO/IUIS Allergen Nomenclature Database is the official resource of allergen designations. Allergome is the most comprehensive collection of data on allergens and allergen sources. AllergenOnline is aimed at providing a peer-reviewed database of allergen sequences for prediction of allergenicity of proteins, such as those planned to be inserted into genetically modified crops. The Structural Database of Allergenic Proteins (SDAP) provides a database of allergen sequences, structures, and epitopes linked to bioinformatics tools for sequence analysis and comparison. The Immune Epitope Database (IEDB) is the largest repository of T-cell, B-cell, and major histocompatibility complex protein epitopes including epitopes of allergens. AllFam classifies allergens into families of evolutionarily related proteins using definitions from the Pfam protein family database. These databases contain mostly overlapping data, but also show differences in terms of their targeted users, the criteria for including allergens, data shown for each allergen, and the availability of bioinformatics tools. © 2017 S. Karger AG, Basel.

Assesment of access to bibliographic databases and telemetry databases in Astronomy: A groundswell for development.

NASA Astrophysics Data System (ADS)

Diaz-Merced, Wanda Liz; Casado, Johanna; Garcia, Beatriz; Aarnio, Alicia; Knierman, Karen; Monkiewicz, Jacqueline; Alicia Aarnio.

2018-01-01

Big Data" is a subject that has taken special relevance today, particularly in Astrophysics, where continuous advances in technology are leading to ever larger data sets. A multimodal approach in perception of astronomical data data (achieved through sonification used for the processing of data) increases the detection of signals in very low signal-to-noise ratio limits and is of special importance to achieve greater inclusion in the field of Astronomy. In the last ten years, different software tools have been developed that perform the sonification of astronomical data from tables or databases, among them the best known and in multiplatform development are Sonification Sandbox, MathTrack, and xSonify.In order to determine the accessibility of software we propose to start carrying out a conformity analysis of ISO (International Standard Organization) 9241-171171: 2008. This standard establishes the general guidelines that must be taken into account for accessibility in software design, and it is applied to software used in work, public places, and at home. To analyze the accessibility of web databases, we take into account the "Web Content Content Accessibility Guidelines (WCAG) 2.0", accepted and published by ISO in the ISO / IEC 40500: 2012 standard.In this poster, we present a User Centered Design (UCD), Human Computer Interaction (HCI), and User Experience (UX) framework to address a non-segregational provision of access to bibliographic databases and telemetry databases in Astronomy. Our framework is based on an ISO evaluation on a selection of data bases such as ADS, Simbad and SDSS. The WCAG 2.0 and ISO 9241-171171: 2008 should not be taken as absolute accessibility standards: these guidelines are very general, are not absolute, and do not address particularities. They are not to be taken as a substitute for UCD, HCI, UX design and evaluation. Based on our results, this research presents the framework for a focus group and qualitative data analysis aimed to lay the foundations for the employment of UCD functionalities on astronomical databases.

Recent improvements in the NASA technical report server

NASA Technical Reports Server (NTRS)

Maa, Ming-Hokng; Nelson, Michael L.

1995-01-01

The NASA Technical Report Server (NTRS), a World Wide Web (WWW) report distribution service, has been modified to allow parallel database queries, significantly decreasing user access time by an average factor of 2.3, access from clients behind firewalls and/or proxies which truncate excessively long Uniform Resource Locators (URL's), access to non-Wide Area Information Server (WAIS) databases, and compatibility with the Z39-50.3 protocol.

A mapping review of the literature on UK-focused health and social care databases.

PubMed

Cooper, Chris; Rogers, Morwenna; Bethel, Alison; Briscoe, Simon; Lowe, Jenny

2015-03-01

Bibliographic databases are a day-to-day tool of the researcher: they offer the researcher easy and organised access to knowledge, but how much is actually known about the databases on offer? The focus of this paper is UK health and social care databases. These databases are often small, specialised by topic, and provide a complementary literature to the large, international databases. There is, however, good evidence that these databases are overlooked in systematic reviews, perhaps because little is known about what they can offer. To systematically locate and map, published and unpublished literature on the key UK health and social care bibliographic databases. Systematic searching and mapping. Two hundred and forty-two items were identified which specifically related to the 24 of the 34 databases under review. There is little published or unpublished literature specifically analysing the key UK health and social care databases. Since several UK databases have closed, others are at risk, and some are overlooked in reviews, better information is required to enhance our knowledge. Further research on UK health and social care databases is required. This paper suggests the need to develop the evidence base through a series of case studies on each of the databases. © 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Journal.

The ChArMEx database

NASA Astrophysics Data System (ADS)

Ferré, Helene; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mastrorillo, Laurence; Mière, Arnaud; Vermeulen, Anne

2014-05-01

The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters, intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services, such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between OMP and ICARE data centres and has been set up in the framework of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. All the data produced by or of interest for the ChArMEx community will be documented in the data catalogue and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. At present, the ChArMEx database contains about 75 datasets, including 50 in situ datasets (2012 and 2013 campaigns, Ersa background monitoring station), 25 model outputs (dust model intercomparison, MEDCORDEX scenarios), and a high resolution emission inventory over the Mediterranean. Many in situ datasets have been inserted in a relational database, in order to enable more accurate data selection and download of different datasets in a shared format. The database website offers different tools: - A registration procedure which enables any scientist to accept the data policy and apply for a user database account. - A data catalogue that complies with metadata international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). - Metadata forms to document observations or products that will be provided to the database. - A search tool to browse the catalogue using thematic, geographic and/or temporal criteria. - A shopping-cart web interface to order in situ data files. - A web interface to select and access to homogenized datasets. Interoperability between the two data centres is being set up using the OPEnDAP protocol. The data portal will soon propose a user-friendly access to satellite products managed by the ICARE data centre (SEVIRI, TRIMM, PARASOL...). In order to meet the operational needs of the airborne and ground based observational teams during the ChArMEx 2012 and 2013 campaigns, a day-to-day chart and report display website has been developed too: http://choc.sedoo.org. It offers a convenient way to browse weather conditions and chemical composition during the campaign periods.

Taiwan Biobank: making cross-database convergence possible in the Big Data era

PubMed Central

Lin, Jui-Chu; Fan, Chien-Te; Liao, Chia-Cheng; Chen, Yao-Sheng

2018-01-01

Abstract The Taiwan Biobank (TWB) is a biomedical research database of biopsy data from 200 000 participants. Access to this database has been granted to research communities taking part in the development of precision medicines; however, this has raised issues surrounding TWB’s access to electronic medical records (EMRs). The Personal Data Protection Act of Taiwan restricts access to EMRs for purposes not covered by patients’ original consent. This commentary explores possible legal solutions to help ensure that the access TWB has to EMR abides with legal obligations, and with governance frameworks associated with ethical, legal, and social implications. We suggest utilizing “hash function” algorithms to create nonretrospective, anonymized data for the purpose of cross-transmission and/or linkage with EMR. PMID:29149267

The Binding Database: data management and interface design.

PubMed

Chen, Xi; Lin, Yuhmei; Liu, Ming; Gilson, Michael K

2002-01-01

The large and growing body of experimental data on biomolecular binding is of enormous value in developing a deeper understanding of molecular biology, in developing new therapeutics, and in various molecular design applications. However, most of these data are found only in the published literature and are therefore difficult to access and use. No existing public database has focused on measured binding affinities and has provided query capabilities that include chemical structure and sequence homology searches. We have created Binding DataBase (BindingDB), a public, web-accessible database of measured binding affinities. BindingDB is based upon a relational data specification for describing binding measurements via Isothermal Titration Calorimetry (ITC) and enzyme inhibition. A corresponding XML Document Type Definition (DTD) is used to create and parse intermediate files during the on-line deposition process and will also be used for data interchange, including collection of data from other sources. The on-line query interface, which is constructed with Java Servlet technology, supports standard SQL queries as well as searches for molecules by chemical structure and sequence homology. The on-line deposition interface uses Java Server Pages and JavaBean objects to generate dynamic HTML and to store intermediate results. The resulting data resource provides a range of functionality with brisk response-times, and lends itself well to continued development and enhancement.

Surveillance of obesity-related policies in multiple environments: the Missouri Obesity, Nutrition, and Activity Policy Database, 2007-2009.

PubMed

Haire-Joshu, Debra; Elliott, Michael; Schermbeck, Rebecca; Taricone, Elsa; Green, Scoie; Brownson, Ross C

2010-07-01

The objective of this study was to develop the Missouri Obesity, Nutrition, and Activity Policy Database, a geographically representative baseline of Missouri's existing obesity-related local policies on healthy eating and physical activity. The database is organized to reflect 7 local environments (government, community, health care, worksite, school, after school, and child care) and to describe the prevalence of obesity-related policies in these environments. We employed a stratified nested cluster design using key informant interviews and review of public records to sample 2,356 sites across the 7 target environments for the presence or absence of obesity-related policies. The school environment had the most policies (88%), followed by after school (47%) and health care (32%). Community, government, and child care environments reported smaller proportions of obesity-related policies but higher rates of funding for these policies. Worksite environments had low numbers of obesity-related policies and low funding levels (17% and 6%, respectively). Sixteen of the sampled counties had high obesity-related policy occurrence; 65 had moderate and 8 had low occurrences. Except in Missouri schools, the presence of obesity-related policies is limited. More obesity-related policies are needed so that people have access to environments that support the model behaviors necessary to halt the obesity epidemic. The Missouri Obesity, Nutrition, and Activity Policy Database provides a benchmark for evaluating progress toward the development of obesity-related policies across multiple environments in Missouri.

eMelanoBase: an online locus-specific variant database for familial melanoma.

PubMed

Fung, David C Y; Holland, Elizabeth A; Becker, Therese M; Hayward, Nicholas K; Bressac-de Paillerets, Brigitte; Mann, Graham J

2003-01-01

A proportion of melanoma-prone individuals in both familial and non-familial contexts has been shown to carry inactivating mutations in either CDKN2A or, rarely, CDK4. CDKN2A is a complex locus that encodes two unrelated proteins from alternately spliced transcripts that are read in different frames. The alpha transcript (exons 1alpha, 2, and 3) produces the p16INK4A cyclin-dependent kinase inhibitor, while the beta transcript (exons 1beta and 2) is translated as p14ARF, a stabilizing factor of p53 levels through binding to MDM2. Mutations in exon 2 can impair both polypeptides and insertions and deletions in exons 1alpha, 1beta, and 2, which can theoretically generate p16INK4A-p14ARF fusion proteins. No online database currently takes into account all the consequences of these genotypes, a situation compounded by some problematic previous annotations of CDKN2A-related sequences and descriptions of their mutations. As an initiative of the international Melanoma Genetics Consortium, we have therefore established a database of germline variants observed in all loci implicated in familial melanoma susceptibility. Such a comprehensive, publicly accessible database is an essential foundation for research on melanoma susceptibility and its clinical application. Our database serves two types of data as defined by HUGO. The core dataset includes the nucleotide variants on the genomic and transcript levels, amino acid variants, and citation. The ancillary dataset includes keyword description of events at the transcription and translation levels and epidemiological data. The application that handles users' queries was designed in the model-view-controller architecture and was implemented in Java. The object-relational database schema was deduced using functional dependency analysis. We hereby present our first functional prototype of eMelanoBase. The service is accessible via the URL www.wmi.usyd.edu.au:8080/melanoma.html. Copyright 2002 Wiley-Liss, Inc.

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases

PubMed Central

Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general. PMID:26038727

Gender-Related Barriers and Delays in Accessing Tuberculosis Diagnostic and Treatment Services: A Systematic Review of Qualitative Studies

PubMed Central

Akande, Tokunbo; Shankar, Anita V.; McIntire, Katherine N.; Gounder, Celine R.; Gupta, Amita; Yang, Wei-Teng

2014-01-01

Background. Tuberculosis (TB) remains a significant global public health problem with known gender-related (male versus female) disparities. We reviewed the qualitative evidence (written/spoken narrative) for gender-related differences limiting TB service access from symptom onset to treatment initiation. Methods. Following a systematic process, we searched 12 electronic databases, included qualitative studies that assessed gender differences in accessing TB diagnostic and treatment services, abstracted data, and assessed study validity. Using a modified “inductive coding” system, we synthesized emergent themes within defined barriers and delays limiting access at the individual and provider/system levels and examined gender-related differences. Results. Among 13,448 studies, 28 studies were included. All were conducted in developing countries and assessed individual-level barriers; 11 (39%) assessed provider/system-level barriers, 18 (64%) surveyed persons with suspected or diagnosed TB, and 7 (25%) exclusively surveyed randomly sampled community members or health care workers. Each barrier affected both genders but had gender-variable nature and impact reflecting sociodemographic themes. Women experienced financial and physical dependence, lower general literacy, and household stigma, whereas men faced work-related financial and physical barriers and community-based stigma. Conclusions. In developing countries, barriers limiting access to TB care have context-specific gender-related differences that can inform integrated interventions to optimize TB services. PMID:24900921

Java Web Simulation (JWS); a web based database of kinetic models.

PubMed

Snoep, J L; Olivier, B G

2002-01-01

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

Innovations in health service organization and delivery in northern rural and remote regions: a review of the literature.

PubMed

Mitton, Craig; Dionne, Francois; Masucci, Lisa; Wong, Sabrina; Law, Susan

2011-01-01

To identify and review innovations relevant to improving access, quality, efficiency and/or effectiveness in the organization and delivery of health care services in rural and remote areas. Literature review. Key bibliographic databases that index health research were searched: MEDLINE, EMBASE and CINAHL. Other databases relevant to Arctic health were also accessed. Abstracts were assessed for relevancy and full articles were reviewed and categorized according to emergent themes. Many innovations in delivering services to rural and remote areas were identified, particularly in the public health realm. These innovations were grouped into 4 key themes: organizational structure of health services; utilization of telehealth and ehealth; medical transportation; and public health challenges. Despite the challenges facing rural and remote regions, there is a distinctly positive message from this broad literature review. Evidence-based initiatives exist across a range of areas - which include operational efficiency and integration, access to care, organizational structure, public health, continuing education and workforce composition - that have the potential to positively impact health care quality and health-related outcomes.

Toward an open-access global database for mapping, control, and surveillance of neglected tropical diseases.

PubMed

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F L; Utzinger, Jürg; Kristensen, Thomas K; Vounatsou, Penelope

2011-12-01

After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and 'grey literature'), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay.

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

Secure Cooperative Data Access in Multi-Cloud Environment

ERIC Educational Resources Information Center

Le, Meixing

2013-01-01

In this dissertation, we discuss the problem of enabling cooperative query execution in a multi-cloud environment where the data is owned and managed by multiple enterprises. Each enterprise maintains its own relational database using a private cloud. In order to implement desired business services, parties need to share selected portion of their…

Clinical Views: Object-Oriented Views for Clinical Databases

PubMed Central

Portoni, Luisa; Combi, Carlo; Pinciroli, Francesco

1998-01-01

We present here a prototype of a clinical information system for the archiving and the management of multimedia and temporally-oriented clinical data related to PTCA patients. The system is based on an object-oriented DBMS and supports multiple views and view schemas on patients' data. Remote data access is supported too.

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2013 CFR

2013-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...