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Sample records for comprehensive database including

  1. The comprehensive peptaibiotics database.

    PubMed

    Stoppacher, Norbert; Neumann, Nora K N; Burgstaller, Lukas; Zeilinger, Susanne; Degenkolb, Thomas; Brückner, Hans; Schuhmacher, Rainer

    2013-05-01

    Peptaibiotics are nonribosomally biosynthesized peptides, which - according to definition - contain the marker amino acid α-aminoisobutyric acid (Aib) and possess antibiotic properties. Being known since 1958, a constantly increasing number of peptaibiotics have been described and investigated with a particular emphasis on hypocrealean fungi. Starting from the existing online 'Peptaibol Database', first published in 1997, an exhaustive literature survey of all known peptaibiotics was carried out and resulted in a list of 1043 peptaibiotics. The gathered information was compiled and used to create the new 'The Comprehensive Peptaibiotics Database', which is presented here. The database was devised as a software tool based on Microsoft (MS) Access. It is freely available from the internet at http://peptaibiotics-database.boku.ac.at and can easily be installed and operated on any computer offering a Windows XP/7 environment. It provides useful information on characteristic properties of the peptaibiotics included such as peptide category, group name of the microheterogeneous mixture to which the peptide belongs, amino acid sequence, sequence length, producing fungus, peptide subfamily, molecular formula, and monoisotopic mass. All these characteristics can be used and combined for automated search within the database, which makes The Comprehensive Peptaibiotics Database a versatile tool for the retrieval of valuable information about peptaibiotics. Sequence data have been considered as to December 14, 2012. PMID:23681723

  2. SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

    PubMed Central

    Preissner, Saskia; Kroll, Katharina; Dunkel, Mathias; Senger, Christian; Goldsobel, Gady; Kuzman, Daniel; Guenther, Stefan; Winnenburg, Rainer; Schroeder, Michael; Preissner, Robert

    2010-01-01

    Much of the information on the Cytochrome P450 enzymes (CYPs) is spread across literature and the internet. Aggregating knowledge about CYPs into one database makes the search more efficient. Text mining on 57 CYPs and drugs led to a mass of papers, which were screened manually for facts about metabolism, SNPs and their effects on drug degradation. Information was put into a database, which enables the user not only to look up a particular CYP and all metabolized drugs, but also to check tolerability of drug-cocktails and to find alternative combinations, to use metabolic pathways more efficiently. The SuperCYP database contains 1170 drugs with more than 3800 interactions including references. Approximately 2000 SNPs and mutations are listed and ordered according to their effect on expression and/or activity. SuperCYP (http://bioinformatics.charite.de/supercyp) is a comprehensive resource focused on CYPs and drug metabolism. Homology-modeled structures of the CYPs can be downloaded in PDB format and related drugs are available as MOL-files. Within the resource, CYPs can be aligned with each other, drug-cocktails can be ‘mixed’, SNPs, protein point mutations, and their effects can be viewed and corresponding PubMed IDs are given. SuperCYP is meant to be a platform and a starting point for scientists and health professionals for furthering their research. PMID:19934256

  3. Comprehensive T-Matrix Reference Database: A 2012 - 2013 Update

    NASA Technical Reports Server (NTRS)

    Mishchenko, Michael I.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

    2013-01-01

    The T-matrix method is one of the most versatile, efficient, and accurate theoretical techniques widely used for numerically exact computer calculations of electromagnetic scattering by single and composite particles, discrete random media, and particles imbedded in complex environments. This paper presents the fifth update to the comprehensive database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2012. It also lists several earlier publications not incorporated in the original database, including Peter Waterman's reports from the 1960s illustrating the history of the T-matrix approach and demonstrating that John Fikioris and Peter Waterman were the true pioneers of the multi-sphere method otherwise known as the generalized Lorenz - Mie theory.

  4. A comprehensive database of Martian landslides

    NASA Astrophysics Data System (ADS)

    Battista Crosta, Giovanni; Vittorio De Blasio, Fabio; Frattini, Paolo; Valbuzzi, Elena

    2016-04-01

    During a long-term project, we have identified and classified a large number (> 3000) of Martian landslides especially but not exclusively from Valles Marineris. This database provides a more complete basis for a statistical study of landslides on Mars and its relationship with geographical and environmental conditions. Landslides have been mapped according to standard geomorphological criteria, delineating both the landslide scar and accumulation limits, associating each scarp to a deposit, and using the program ArcGis for generation of a complete digital dataset. Multiple accumulations from the same source area or from different sources have been differentiated, where possible, to obtain a more complete dataset and to allow more refined analyses. Each landslide has been classified according to a set of criteria including: type, degree of confinement, possible trigger, elevation with respect to datum, geomorphological features, degree of multiplicity, and so on. The runout, fall height, and volume have been measured for each deposit. In fact, the database is revealing a series of trends that may assist at understanding landform processes on Mars and its past climatic conditions. One of the most interesting aspects of our dataset is the presence of a population of landslides whose particularly long mobility deviates from average behavior. While some landslides have travelled unimpeded on a usually flat area, others have travelled against obstacles or mounds. Therefore, landslides are also studied in relation to i) morphologies created by the landslide itself, ii) presence of mounds, barriers or elevations than have affected the movement of the landslide mass. In some extreme cases, the landslide was capable of travelling for several tens of km along the whole valley and upon reaching the opposite side it travelled upslope for several hundreds of meters, which is indication of high travelling speed. In other cases, the high speed is revealed by dynamic deformations

  5. Dynameomics: A comprehensive database of protein dynamics

    PubMed Central

    van der Kamp, Marc W.; Schaeffer, Richard D.; Jonsson, Amanda L.; Scouras, Alexander D.; Simms, Andrew; Toofanny, Rudesh D.; Benson, Noah C.; Anderson, Peter C.; Merkley, Eric D.; Rysavy, Steve; Bromley, Denny; Beck, David A. C.; Daggett, Valerie

    2010-01-01

    Summary The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 1000 proteins, representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through www.dynameomics.org. PMID:20399180

  6. Comprehensive Thematic T-matrix Reference Database: a 2013-2014 Update

    NASA Technical Reports Server (NTRS)

    Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

    2014-01-01

    This paper is the sixth update to the comprehensive thematic database of peer-reviewedT-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

  7. Development of a Comprehensive Database System for Safety Analyst.

    PubMed

    Paz, Alexander; Veeramisti, Naveen; Khanal, Indira; Baker, Justin; de la Fuente-Mella, Hanns

    2015-01-01

    This study addressed barriers associated with the use of Safety Analyst, a state-of-the-art tool that has been developed to assist during the entire Traffic Safety Management process but that is not widely used due to a number of challenges as described in this paper. As part of this study, a comprehensive database system and tools to provide data to multiple traffic safety applications, with a focus on Safety Analyst, were developed. A number of data management tools were developed to extract, collect, transform, integrate, and load the data. The system includes consistency-checking capabilities to ensure the adequate insertion and update of data into the database. This system focused on data from roadways, ramps, intersections, and traffic characteristics for Safety Analyst. To test the proposed system and tools, data from Clark County, which is the largest county in Nevada and includes the cities of Las Vegas, Henderson, Boulder City, and North Las Vegas, was used. The database and Safety Analyst together help identify the sites with the potential for safety improvements. Specifically, this study examined the results from two case studies. The first case study, which identified sites having a potential for safety improvements with respect to fatal and all injury crashes, included all roadway elements and used default and calibrated Safety Performance Functions (SPFs). The second case study identified sites having a potential for safety improvements with respect to fatal and all injury crashes, specifically regarding intersections; it used default and calibrated SPFs as well. Conclusions were developed for the calibration of safety performance functions and the classification of site subtypes. Guidelines were provided about the selection of a particular network screening type or performance measure for network screening. PMID:26167531

  8. Development of a Comprehensive Database System for Safety Analyst

    PubMed Central

    Paz, Alexander; Veeramisti, Naveen; Khanal, Indira; Baker, Justin; de la Fuente-Mella, Hanns

    2015-01-01

    This study addressed barriers associated with the use of Safety Analyst, a state-of-the-art tool that has been developed to assist during the entire Traffic Safety Management process but that is not widely used due to a number of challenges as described in this paper. As part of this study, a comprehensive database system and tools to provide data to multiple traffic safety applications, with a focus on Safety Analyst, were developed. A number of data management tools were developed to extract, collect, transform, integrate, and load the data. The system includes consistency-checking capabilities to ensure the adequate insertion and update of data into the database. This system focused on data from roadways, ramps, intersections, and traffic characteristics for Safety Analyst. To test the proposed system and tools, data from Clark County, which is the largest county in Nevada and includes the cities of Las Vegas, Henderson, Boulder City, and North Las Vegas, was used. The database and Safety Analyst together help identify the sites with the potential for safety improvements. Specifically, this study examined the results from two case studies. The first case study, which identified sites having a potential for safety improvements with respect to fatal and all injury crashes, included all roadway elements and used default and calibrated Safety Performance Functions (SPFs). The second case study identified sites having a potential for safety improvements with respect to fatal and all injury crashes, specifically regarding intersections; it used default and calibrated SPFs as well. Conclusions were developed for the calibration of safety performance functions and the classification of site subtypes. Guidelines were provided about the selection of a particular network screening type or performance measure for network screening. PMID:26167531

  9. A new comprehensive database of global volcanic gas analyses

    NASA Astrophysics Data System (ADS)

    Clor, L. E.; Fischer, T. P.; Lehnert, K. A.; McCormick, B.; Hauri, E. H.

    2013-12-01

    Volcanic volatiles are the driving force behind eruptions, powerful indicators of magma provenance, present localized hazards, and have implications for climate. Studies of volcanic emissions are necessary for understanding volatile cycling from the mantle to the atmosphere. Gas compositions vary with volcanic activity, making it important to track their chemical variability over time. As studies become increasingly interdisciplinary, it is critical to have a mechanism to integrate decades of gas studies across disciplines. Despite the value of this research to a variety of fields, there is currently no integrated network to house all volcanic and hydrothermal gas data, making spatial, temporal, and interdisciplinary comparison studies time-consuming. To remedy this, we are working to establish a comprehensive database of volcanic gas emissions and compositions worldwide, as part of the Deep Carbon Observatory's DECADE (Deep Carbon Degassing) initiative. Volcanic gas data have been divided into two broad categories: 1) chemical analyses from samples collected directly at the volcanic source, and 2) measurements of gas concentrations and fluxes, such as remotely by mini-DOAS or satellite, or in-plume such as by multiGAS. The gas flux database effort is realized by the Global Volcanism Program of the Smithsonian Institution (abstract by Brendan McCormick, this meeting). The direct-sampling data is the subject of this presentation. Data from direct techniques include samples of gases collected at the volcanic source from fumaroles and springs, tephras analyzed for gas contents, filter pack samples of gases collected in a plume, and any other data types that involve collection of a sample. Data are incorporated into the existing framework of the Petrological Database, PetDB. Association with PetDB is advantageous as it will allow volcanic gas data to be linked to chemical data from lava or tephra samples, forming more complete ties between the eruptive products and the

  10. Advanced type placement and geonames database: comprehensive coordination plan

    SciTech Connect

    Barnes, A.E.; Gough, E.C.; Brown, R.M.; Zied, A.

    1983-01-01

    This paper presents a preliminary comprehensive coordination plan for the technical development and integration of an automated names database capture and management of an overall automated cartographic system, for the Defense Mapping Agency. It broadly covers the technical issues associated with system and associated subsystems functional requirements, inter-subsystem interaction common technologies in hardware, software, database, and artificial intelligence. The 3-phase RandD cycles for each and all subsystems are also outlined.

  11. Database trial impact on graduate nursing comprehensive exams.

    PubMed

    Pionke, Katharine; Huckstadt, Alicia

    2015-10-01

    While the authors were doing a test period of databases, the question of whether or not databases affect outcomes of graduate nursing comprehensive examinations came up. This study explored that question through using citation analysis of exams that were taken during a database trial and exams that were not. The findings showed no difference in examination pass/fail rates. While the pass/fail rates did not change, a great deal was learned in terms of citation accuracy and types of materials that students used, leading to discussions about changing how citation and plagiarism awareness were taught. PMID:26512218

  12. Database trial impact on graduate nursing comprehensive exams

    PubMed Central

    Pionke, Katharine; Huckstadt, Alicia

    2015-01-01

    While the authors were doing a test period of databases, the question of whether or not databases affect outcomes of graduate nursing comprehensive examinations came up. This study explored that question through using citation analysis of exams that were taken during a database trial and exams that were not. The findings showed no difference in examination pass/fail rates. While the pass/fail rates did not change, a great deal was learned in terms of citation accuracy and types of materials that students used, leading to discussions about changing how citation and plagiarism awareness were taught. PMID:26512218

  13. 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 ...

  14. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

    PubMed

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed. PMID:19015126

  15. ClassLess: A Comprehensive Database of Young Stellar Objects

    NASA Astrophysics Data System (ADS)

    Hillenbrand, Lynne; Baliber, Nairn

    2015-01-01

    We have designed and constructed a database housing published measurements of Young Stellar Objects (YSOs) within ~1 kpc of the Sun. ClassLess, so called because it includes YSOs in all stages of evolution, is a relational database in which user interaction is conducted via HTML web browsers, queries are performed in scientific language, and all data are linked to the sources of publication. Each star is associated with a cluster (or clusters), and both spatially resolved and unresolved measurements are stored, allowing proper use of data from multiple star systems. With this fully searchable tool, myriad ground- and space-based instruments and surveys across wavelength regimes can be exploited. In addition to primary measurements, the database self consistently calculates and serves higher level data products such as extinction, luminosity, and mass. As a result, searches for young stars with specific physical characteristics can be completed with just a few mouse clicks.

  16. Wide-Field Plate Database: Included Ukrainian Plate Catalogues

    NASA Astrophysics Data System (ADS)

    Tsvetkova, Katya; Sergeeva, Tetyana

    2007-08-01

    We present the basic information for the archives of the Main Astronomical Observatory of the National Academy of Sciences of Ukraine, included into the Wide-Field Plate Database last two years with total number of plates - 11260. The plates were obtained with the 0.40m Double Wide-angle Astrograph (DWA); 10cm, 11cm and 15cm Three Cameras Astrograph (TCA) and 12 cm Double Short focus Astrograph (DSA) in the period 1949-1998 in the frames of the following observing programmes: Photographic Survey of the Northern Sky; Investigation of the kinematics and the structure in the main meridian section of the Galaxy; selection of reference stars, minor planets observations, comet investigations.

  17. Comprehensive T-matrix Reference Database: A 2009-2011 Update

    NASA Technical Reports Server (NTRS)

    Zakharova, Nadezhda T.; Videen, G.; Khlebtsov, Nikolai G.

    2012-01-01

    The T-matrix method is one of the most versatile and efficient theoretical techniques widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of peer-reviewed T-matrix publications compiled by us previously and includes the publications that appeared since 2009. It also lists several earlier publications not included in the original database.

  18. Comprehensive T-Matrix Reference Database: A 2007-2009 Update

    NASA Technical Reports Server (NTRS)

    Mishchenko, Michael I.; Zakharova, Nadia T.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

    2010-01-01

    The T-matrix method is among the most versatile, efficient, and widely used theoretical techniques for the numerically exact computation of electromagnetic scattering by homogeneous and composite particles, clusters of particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of T-matrix publications compiled by us previously and includes the publications that appeared since 2007. It also lists several earlier publications not included in the original database.

  19. ClassLess: A Comprehensive Database of Young Stellar Objects

    NASA Astrophysics Data System (ADS)

    Hillenbrand, Lynne A.; baliber, nairn

    2015-08-01

    We have designed and constructed a database intended to house catalog and literature-published measurements of Young Stellar Objects (YSOs) within ~1 kpc of the Sun. ClassLess, so called because it includes YSOs in all stages of evolution, is a relational database in which user interaction is conducted via HTML web browsers, queries are performed in scientific language, and all data are linked to the sources of publication. Each star is associated with a cluster (or clusters), and both spatially resolved and unresolved measurements are stored, allowing proper use of data from multiple star systems. With this fully searchable tool, myriad ground- and space-based instruments and surveys across wavelength regimes can be exploited. In addition to primary measurements, the database self consistently calculates and serves higher level data products such as extinction, luminosity, and mass. As a result, searches for young stars with specific physical characteristics can be completed with just a few mouse clicks. We are in the database population phase now, and are eager to engage with interested experts worldwide on local galactic star formation and young stellar populations.

  20. LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe.

    PubMed

    Srinivas, Vanishree; Gopal, Shubha

    2014-01-01

    There are a number of databases on the Listeria species and about their genome. However, these databases do not specifically address a set of network that is important in defence mechanism of the bacteria. Listeria monocytogenes EGDe is a well-established intracellular model organism to study host pathogenicity because of its versatility in the host environment. Here, we have focused on thiol disulphide redox metabolic network proteins, specifically in L. monocytogenes EGDe. The thiol redox metabolism is involved in oxidative stress mechanism and is found in all living cells. It functions to maintain the thiol disulphide balance required for protein folding by providing reducing power. Nevertheless, they are involved in the reversible oxidation of thiol groups in biomolecules by creating disulphide bonds; therefore, the term thiol disulphide redox metabolism (TDRM). TDRM network genes play an important role in oxidative stress mechanism and during host–pathogen interaction. Therefore, it is essential to have detailed information on these proteins with regard to other bacteria and its genome analysis to understand the presence of tRNA, transposons, and insertion elements for horizontal gene transfer. LmTDRM database is a new comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they were aggregated to produce a final representation. The web interface allows for various queries to understand the protein function and their annotation with respect to their relationship with other bacteria. LmTDRM is a major step towards the development of databases on thiol disulphide redox proteins; it would definitely help researchers to understand the mechanism of these proteins and their interaction. Database URL: www.lmtdrm.com. PMID:25228549

  1. Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...

  2. Comprehensive thematic T-matrix reference database: A 2014-2015 update

    NASA Astrophysics Data System (ADS)

    Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Videen, Gorden; Wriedt, Thomas

    2016-07-01

    The T-matrix method is one of the most versatile and efficient direct computer solvers of the macroscopic Maxwell equations and is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper is the seventh update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists a number of earlier publications overlooked previously.

  3. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.

    PubMed

    Fei, Zhangjun; Joung, Je-Gun; Tang, Xuemei; Zheng, Yi; Huang, Mingyun; Lee, Je Min; McQuinn, Ryan; Tieman, Denise M; Alba, Rob; Klee, Harry J; Giovannoni, James J

    2011-01-01

    Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. The database is functionally expanded from the previously described Tomato Expression Database by including metabolite profiles as well as large-scale tomato small RNA (sRNA) data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, respectively, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences. The suite of tools and interfaces in TFGD allow intelligent data mining of recently released and continually expanding large-scale tomato functional genomics data sets. TFGD is available at http://ted.bti.cornell.edu. PMID:20965973

  4. MIDAS (Material Implementation, Database, and Analysis Source): A comprehensive resource of material properties

    SciTech Connect

    Tang, M; Norquist, P; Barton, N; Durrenberger, K; Florando, J; Attia, A

    2010-12-13

    MIDAS is aimed to be an easy-to-use and comprehensive common source for material properties including both experimental data and models and their parameters. At LLNL, we will develop MIDAS to be the central repository for material strength related data and models with the long-term goal to encompass other material properties. MIDAS will allow the users to upload experimental data and updated models, to view and read materials data and references, to manipulate models and their parameters, and to serve as the central location for the application codes to access the continuously growing model source codes. MIDAS contains a suite of interoperable tools and utilizes components already existing at LLNL: MSD (material strength database), MatProp (database of materials properties files), and MSlib (library of material model source codes). MIDAS requires significant development of the computer science framework for the interfaces between different components. We present the current status of MIDAS and its future development in this paper.

  5. Comprehensive modeling of electrostatically actuated MEMS beams including uncertainty quantification

    NASA Astrophysics Data System (ADS)

    Snow, Michael G.

    MEMS switches have offered dramatic improvements in the performance of RF systems. However, difficulties with reliability has slowed the adoption of MEMS switches in RF systems. These reliability issues are partly due to the poor manufacturing tolerances endemic to MEMS manufacturing processes. These manufacturing tolerances may cause significant variations in performance characteristics. This work focuses on electrostatically actuated MEMS beam capacitive shunt switches. A non-linear dynamic model for these switches was developed. The model accounts for a variety of physical effects including; beam stretching, residual stress, non-rigid boundary conditions, initial curvature, electrostatic fringing field, finite electrodes, squeeze film damping, and distributed contact. The effects of uncertain parameters on the outputs of the model are discovered through response surface based uncertainty quantification techniques. The model accurately predicts the actuation voltages and switching times of these MEMS switches as well as the effects of uncertain parameters. The derived model is widely applicable and accuratly reproduces the results of other models in the literature. Future researchers will be able to rapidly iterate designs and accurately understand the behavior of these switches.

  6. IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.

    PubMed

    Giudicelli, Véronique; Duroux, Patrice; Ginestoux, Chantal; Folch, Géraldine; Jabado-Michaloud, Joumana; Chaume, Denys; Lefranc, Marie-Paule

    2006-01-01

    IMGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species. It was created in 1989 by LIGM, Montpellier, France and is the oldest and the largest database of IMGT. IMGT/LIGM-DB includes all germline (non-rearranged) and rearranged IG and TR genomic DNA (gDNA) and complementary DNA (cDNA) sequences published in generalist databases. IMGT/LIGM-DB allows searches from the Web interface according to biological and immunogenetic criteria through five distinct modules depending on the user interest. For a given entry, nine types of display are available including the IMGT flat file, the translation of the coding regions and the analysis by the IMGT/V-QUEST tool. IMGT/LIGM-DB distributes expertly annotated sequences. The annotations hugely enhance the quality and the accuracy of the distributed detailed information. They include the sequence identification, the gene and allele classification, the constitutive and specific motif description, the codon and amino acid numbering, and the sequence obtaining information, according to the main concepts of IMGT-ONTOLOGY. They represent the main source of IG and TR gene and allele knowledge stored in IMGT/GENE-DB and in the IMGT reference directory. IMGT/LIGM-DB is freely available at http://imgt.cines.fr. PMID:16381979

  7. MOAtox: A comprehensive mode of action and acute aquatic toxicity database for predictive model development.

    PubMed

    Barron, M G; Lilavois, C R; Martin, T M

    2015-04-01

    The mode of toxic action (MOA) has been recognized as a key determinant of chemical toxicity and as an alternative to chemical class-based predictive toxicity modeling. However, the development of quantitative structure activity relationship (QSAR) and other models has been limited by the availability of comprehensive high quality MOA and toxicity databases. The current study developed a dataset of MOA assignments for 1213 chemicals that included a diversity of metals, pesticides, and other organic compounds that encompassed six broad and 31 specific MOAs. MOA assignments were made using a combination of high confidence approaches that included international consensus classifications, QSAR predictions, and weight of evidence professional judgment based on an assessment of structure and literature information. A toxicity database of 674 acute values linked to chemical MOA was developed for fish and invertebrates. Additionally, species-specific measured or high confidence estimated acute values were developed for the four aquatic species with the most reported toxicity values: rainbow trout (Oncorhynchus mykiss), fathead minnow (Pimephales promelas), bluegill (Lepomis macrochirus), and the cladoceran (Daphnia magna). Measured acute toxicity values met strict standardization and quality assurance requirements. Toxicity values for chemicals with missing species-specific data were estimated using established interspecies correlation models and procedures (Web-ICE; http://epa.gov/ceampubl/fchain/webice/), with the highest confidence values selected. The resulting dataset of MOA assignments and paired toxicity values are provided in spreadsheet format as a comprehensive standardized dataset available for predictive aquatic toxicology model development. PMID:25700118

  8. MeioBase: a comprehensive database for meiosis.

    PubMed

    Li, Hao; Meng, Fanrui; Guo, Chunce; Wang, Yingxiang; Xie, Xiaojing; Zhu, Tiansheng; Zhou, Shuigeng; Ma, Hong; Shan, Hongyan; Kong, Hongzhi

    2014-01-01

    Meiosis is a special type of cell division process necessary for the sexual reproduction of all eukaryotes. The ever expanding meiosis research calls for an effective and specialized database that is not readily available yet. To fill this gap, we have developed a knowledge database MeioBase (http://meiosis.ibcas.ac.cn), which is comprised of two core parts, Resources and Tools. In the Resources part, a wealth of meiosis data collected by curation and manual review from published literatures and biological databases are integrated and organized into various sections, such as Cytology, Pathway, Species, Interaction, and Expression. In the Tools part, some useful tools have been integrated into MeioBase, such as Search, Download, Blast, Comparison, My Favorites, Submission, and Advice. With a simplified and efficient web interface, users are able to search against the database with gene model IDs or keywords, and batch download the data for local investigation. We believe that MeioBase can greatly facilitate the researches related to meiosis. PMID:25566299

  9. AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules th...

  10. Comprehensiveness of "Social Work Abstracts" as a Database for Researchers and Practitioners

    ERIC Educational Resources Information Center

    Shek, Daniel T. L.

    2008-01-01

    Objective: The comprehensiveness of "Social Work Abstracts (SWA)" as a database was examined. Method: The coverage of articles of "Research on Social Work Practice" and "Social Work Research" in "SWA" from 1995 to 2005 was examined. "SWA" was compared with other databases on several dimensions. A case study based on the author's publications was…

  11. Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders

    PubMed Central

    Chen, Chong; Jiang, Yi; Xu, Chenyang; Liu, Xinting; Hu, Lin; Xiang, Yanbao; Chen, Qingshuang; Chen, Denghui; Li, Huanzheng; Xu, Xueqin; Tang, Shaohua

    2016-01-01

    Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. In this study, combined with Nosology and Classification of genetic skeletal disorders, we developed the first comprehensive and annotated genetic skeletal disorders database, named ‘SkeletonGenetics’, which contains information about all GSD-related knowledge including 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases (2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiographic criteria from 1698 publications. Further annotations were performed to each entry including Gene Ontology, pathways analysis, protein–protein interaction, mutation annotations, disease–disease clustering and gene–disease networking. Furthermore, using concise search methods, intuitive graphical displays, convenient browsing functions and constantly updatable features, ‘SkeletonGenetics’ could serve as a central and integrative database for unveiling the genetic and pathways pre-dispositions of GSD. Database URL: http://101.200.211.232/skeletongenetics/ PMID:27580923

  12. Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders.

    PubMed

    Chen, Chong; Jiang, Yi; Xu, Chenyang; Liu, Xinting; Hu, Lin; Xiang, Yanbao; Chen, Qingshuang; Chen, Denghui; Li, Huanzheng; Xu, Xueqin; Tang, Shaohua

    2016-01-01

    Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. In this study, combined with Nosology and Classification of genetic skeletal disorders, we developed the first comprehensive and annotated genetic skeletal disorders database, named 'SkeletonGenetics', which contains information about all GSD-related knowledge including 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases (2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiographic criteria from 1698 publications. Further annotations were performed to each entry including Gene Ontology, pathways analysis, protein-protein interaction, mutation annotations, disease-disease clustering and gene-disease networking. Furthermore, using concise search methods, intuitive graphical displays, convenient browsing functions and constantly updatable features, 'SkeletonGenetics' could serve as a central and integrative database for unveiling the genetic and pathways pre-dispositions of GSD.Database URL: http://101.200.211.232/skeletongenetics/. PMID:27580923

  13. MGDB: a comprehensive database of genes involved in melanoma

    PubMed Central

    Zhang, Di; Zhu, Rongrong; Zhang, Hanqian; Zheng, Chun-Hou; Xia, Junfeng

    2015-01-01

    The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL: http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp PMID:26424083

  14. MGDB: a comprehensive database of genes involved in melanoma.

    PubMed

    Zhang, Di; Zhu, Rongrong; Zhang, Hanqian; Zheng, Chun-Hou; Xia, Junfeng

    2015-01-01

    The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL: http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp. PMID:26424083

  15. 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. PMID:25160362

  16. Improving pharmaceutical innovation by building a more comprehensive database on drug development and use.

    PubMed

    Daniel, Gregory W; Cazé, Alexis; Romine, Morgan H; Audibert, Céline; Leff, Jonathan S; McClellan, Mark B

    2015-02-01

    New drugs and biologics have had a tremendous impact on the treatment of many diseases. However, available measures suggest that pharmaceutical innovation has remained relatively flat, despite substantial growth in research and development spending. We review recent literature on pharmaceutical innovation to identify limitations in measuring and assessing innovation, and we describe the framework and collaborative approach we are using to develop more comprehensive, publicly available metrics for innovation. Our research teams at the Brookings Institution and Deerfield Institute are collaborating with experts from multiple areas of drug development and regulatory review to identify and collect comprehensive data elements related to key development and regulatory characteristics for each new molecular entity approved over the past several decades in the United States and the European Union. Subsequent phases of our effort will add data on downstream product use and patient outcomes and will also include drugs that have failed or been abandoned in development. Such a database will enable researchers to better analyze the drivers of drug innovation, trends in the output of new medicines, and the effect of policy efforts designed to improve innovation. PMID:25646113

  17. Historical seismometry database project: A comprehensive relational database for historical seismic records

    NASA Astrophysics Data System (ADS)

    Bono, Andrea

    2007-01-01

    The recovery and preservation of the patrimony made of the instrumental registrations regarding the historical earthquakes is with no doubt a subject of great interest. This attention, besides being purely historical, must necessarily be also scientific. In fact, the availability of a great amount of parametric information on the seismic activity in a given area is a doubtless help to the seismologic researcher's activities. In this article the project of the Sismos group of the National Institute of Geophysics and Volcanology of Rome new database is presented. In the structure of the new scheme the matured experience of five years of activity is summarized. We consider it useful for those who are approaching to "recovery and reprocess" computer based facilities. In the past years several attempts on Italian seismicity have followed each other. It has almost never been real databases. Some of them have had positive success because they were well considered and organized. In others it was limited in supplying lists of events with their relative hypocentral standards. What makes this project more interesting compared to the previous work is the completeness and the generality of the managed information. For example, it will be possible to view the hypocentral information regarding a given historical earthquake; it will be possible to research the seismograms in raster, digital or digitalized format, the information on times of arrival of the phases in the various stations, the instrumental standards and so on. The relational modern logic on which the archive is based, allows the carrying out of all these operations with little effort. The database described below will completely substitute Sismos' current data bank. Some of the organizational principles of this work are similar to those that inspire the database for the real-time monitoring of the seismicity in use in the principal offices of international research. A modern planning logic in a distinctly historical

  18. MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

    PubMed Central

    Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D’Elia, D.; Montalvo, A. de; Pinto, B. de; De Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H. V.; Sloof, P.; Saccone, C.

    2000-01-01

    MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl . The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme. PMID:10592207

  19. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... comprehensive plan (including five-year action plan). 968.320 Section 968.320 Housing and Urban Development... approval of comprehensive plan (including five-year action plan). (a) Submission of comprehensive plan. (1... Plan. After HUD approves the Comprehensive Plan (including the Five-Year Action Plan), or...

  20. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... comprehensive plan (including five-year action plan). 968.320 Section 968.320 Housing and Urban Development... approval of comprehensive plan (including five-year action plan). (a) Submission of comprehensive plan. (1... Plan. After HUD approves the Comprehensive Plan (including the Five-Year Action Plan), or...

  1. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... comprehensive plan (including five-year action plan). 968.320 Section 968.320 Housing and Urban Development... approval of comprehensive plan (including five-year action plan). (a) Submission of comprehensive plan. (1... Plan. After HUD approves the Comprehensive Plan (including the Five-Year Action Plan), or...

  2. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... comprehensive plan (including five-year action plan). 968.320 Section 968.320 Housing and Urban Development... approval of comprehensive plan (including five-year action plan). (a) Submission of comprehensive plan. (1... Plan. After HUD approves the Comprehensive Plan (including the Five-Year Action Plan), or...

  3. OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer

    PubMed Central

    2014-01-01

    Background Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer. However, although several oncomiRs have been identified and characterized, there is as yet no comprehensive compilation of this data which has rendered it underutilized by cancer biologists. There is therefore an unmet need in generating bioinformatic platforms to speed the identification of novel therapeutic targets. Description We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples. The database also lists their respective predicted targets, identified using miRanda, along with their IDs, sequences, chromosome location and detailed description. This database facilitates querying by search strings including microRNA name, sequence, accession number, target genes and organisms. The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm. Conclusion OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance. OncomiRdbB is freely available for download through the URL link http://tdb.ccmb.res.in/OncomiRdbB/index.htm. PMID:24428888

  4. 24 CFR 968.315 - Comprehensive Plan (including five-year action plan).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... comprehensive plan including, but not limited to, the physical and management needs assessments, viability... assessment under this paragraph (e)(2) and shall retain such source documents in its files; (3) Management..., and sanitary living conditions will be provided. The management needs assessment shall include...

  5. Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome

    PubMed Central

    Kim, Hyun-Jin; Baek, Kwang-Hyun; Lee, Seung-Won; Kim, JungEun; Lee, Bong-Woo; Cho, Hye-Sun; Kim, Woo Taek; Choi, Doil; Hur, Cheol-Goo

    2008-01-01

    Background There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (Capsicum annuum), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses. Results We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at . Conclusion The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome. PMID:18844979

  6. Comprehensive national database of tree effects on air quality and human health in the United States.

    PubMed

    Hirabayashi, Satoshi; Nowak, David J

    2016-08-01

    Trees remove air pollutants through dry deposition processes depending upon forest structure, meteorology, and air quality that vary across space and time. Employing nationally available forest, weather, air pollution and human population data for 2010, computer simulations were performed for deciduous and evergreen trees with varying leaf area index for rural and urban areas in every county in the conterminous United States. The results populated a national database of annual air pollutant removal, concentration changes, and reductions in adverse health incidences and costs for NO2, O3, PM2.5 and SO2. The developed database enabled a first order approximation of air quality and associated human health benefits provided by trees with any forest configurations anywhere in the conterminous United States over time. Comprehensive national database of tree effects on air quality and human health in the United States was developed. PMID:27176764

  7. 24 CFR 968.315 - Comprehensive Plan (including five-year action plan).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... under 24 CFR part 970); (5) Five-year action plan. (i) General. The comprehensive plan shall include a... entities are set up to plan and implement the consolidated plans (under 24 CFR part 91), the PHA shall...-year action plan). 968.315 Section 968.315 Housing and Urban Development REGULATIONS RELATING...

  8. 24 CFR 968.315 - Comprehensive Plan (including five-year action plan).

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... under 24 CFR part 970); (5) Five-year action plan. (i) General. The comprehensive plan shall include a... entities are set up to plan and implement the consolidated plans (under 24 CFR part 91), the PHA shall...-year action plan). 968.315 Section 968.315 Housing and Urban Development REGULATIONS RELATING...

  9. A comprehensive manually curated protein–protein interaction database for the Death Domain superfamily

    PubMed Central

    Kwon, Dongseop; Yoon, Jong Hwan; Shin, Soo-Yong; Jang, Tae-Ho; Kim, Hong-Gee; So, Insuk; Jeon, Ju-Hong; Park, Hyun Ho

    2012-01-01

    The Death Domain (DD) superfamily, which is one of the largest classes of protein interaction modules, plays a pivotal role in apoptosis, inflammation, necrosis and immune cell signaling pathways. Because aberrant or inappropriate DD superfamily-mediated signaling events are associated with various human diseases, such as cancers, neurodegenerative diseases and immunological disorders, the studies in these fields are of great biological and clinical importance. To facilitate the understanding of the molecular mechanisms by which the DD superfamily is associated with biological and disease processes, we have developed the DD database (http://www.deathdomain.org), a manually curated database that aims to offer comprehensive information on protein–protein interactions (PPIs) of the DD superfamily. The DD database was created by manually curating 295 peer-reviewed studies that were published in the literature; the current version documents 175 PPI pairs among the 99 DD superfamily proteins. The DD database provides a detailed summary of the DD superfamily proteins and their PPI data. Users can find in-depth information that is specified in the literature on relevant analytical methods, experimental resources and domain structures. Our database provides a definitive and valuable tool that assists researchers in understanding the signaling network that is mediated by the DD superfamily. PMID:22135292

  10. CracidMex1: a comprehensive database of global occurrences of cracids (Aves, Galliformes) with distribution in Mexico

    PubMed Central

    Pinilla-Buitrago, Gonzalo; Martínez-Morales, Miguel Angel; González-García, Fernando; Enríquez, Paula L.; Rangel-Salazar, José Luis; Romero, Carlos Alberto Guichard; Navarro-Sigüenza, Adolfo G.; Monterrubio-Rico, Tiberio César; Escalona-Segura, Griselda

    2014-01-01

    Abstract Cracids are among the most vulnerable groups of Neotropical birds. Almost half of the species of this family are included in a conservation risk category. Twelve taxa occur in Mexico, six of which are considered at risk at national level and two are globally endangered. Therefore, it is imperative that high quality, comprehensive, and high-resolution spatial data on the occurrence of these taxa are made available as a valuable tool in the process of defining appropriate management strategies for conservation at a local and global level. We constructed the CracidMex1 database by collating global records of all cracid taxa that occur in Mexico from available electronic databases, museum specimens, publications, “grey literature”, and unpublished records. We generated a database with 23,896 clean, validated, and standardized geographic records. Database quality control was an iterative process that commenced with the consolidation and elimination of duplicate records, followed by the geo-referencing of records when necessary, and their taxonomic and geographic validation using GIS tools and expert knowledge. We followed the geo-referencing protocol proposed by the Mexican National Commission for the Use and Conservation of Biodiversity. We could not estimate the geographic coordinates of 981 records due to inconsistencies or lack of sufficient information in the description of the locality. Given that current records for most of the taxa have some degree of distributional bias, with redundancies at different spatial scales, the CracidMex1 database has allowed us to detect areas where more sampling effort is required to have a better representation of the global spatial occurrence of these cracids. We also found that particular attention needs to be given to taxa identification in those areas where congeners or conspecifics co-occur in order to avoid taxonomic uncertainty. The construction of the CracidMex1 database represents the first comprehensive

  11. Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database.

    PubMed

    Lill, Christina M; Roehr, Johannes T; McQueen, Matthew B; Kavvoura, Fotini K; Bagade, Sachin; Schjeide, Brit-Maren M; Schjeide, Leif M; Meissner, Esther; Zauft, Ute; Allen, Nicole C; Liu, Tian; Schilling, Marcel; Anderson, Kari J; Beecham, Gary; Berg, Daniela; Biernacka, Joanna M; Brice, Alexis; DeStefano, Anita L; Do, Chuong B; Eriksson, Nicholas; Factor, Stewart A; Farrer, Matthew J; Foroud, Tatiana; Gasser, Thomas; Hamza, Taye; Hardy, John A; Heutink, Peter; Hill-Burns, Erin M; Klein, Christine; Latourelle, Jeanne C; Maraganore, Demetrius M; Martin, Eden R; Martinez, Maria; Myers, Richard H; Nalls, Michael A; Pankratz, Nathan; Payami, Haydeh; Satake, Wataru; Scott, William K; Sharma, Manu; Singleton, Andrew B; Stefansson, Kari; Toda, Tatsushi; Tung, Joyce Y; Vance, Jeffery; Wood, Nick W; Zabetian, Cyrus P; Young, Peter; Tanzi, Rudolph E; Khoury, Muin J; Zipp, Frauke; Lehrach, Hans; Ioannidis, John P A; Bertram, Lars

    2012-01-01

    More than 800 published genetic association studies have implicated dozens of potential risk loci in Parkinson's disease (PD). To facilitate the interpretation of these findings, we have created a dedicated online resource, PDGene, that comprehensively collects and meta-analyzes all published studies in the field. A systematic literature screen of -27,000 articles yielded 828 eligible articles from which relevant data were extracted. In addition, individual-level data from three publicly available genome-wide association studies (GWAS) were obtained and subjected to genotype imputation and analysis. Overall, we performed meta-analyses on more than seven million polymorphisms originating either from GWAS datasets and/or from smaller scale PD association studies. Meta-analyses on 147 SNPs were supplemented by unpublished GWAS data from up to 16,452 PD cases and 48,810 controls. Eleven loci showed genome-wide significant (P < 5 × 10(-8)) association with disease risk: BST1, CCDC62/HIP1R, DGKQ/GAK, GBA, LRRK2, MAPT, MCCC1/LAMP3, PARK16, SNCA, STK39, and SYT11/RAB25. In addition, we identified novel evidence for genome-wide significant association with a polymorphism in ITGA8 (rs7077361, OR 0.88, P  =  1.3 × 10(-8)). All meta-analysis results are freely available on a dedicated online database (www.pdgene.org), which is cross-linked with a customized track on the UCSC Genome Browser. Our study provides an exhaustive and up-to-date summary of the status of PD genetics research that can be readily scaled to include the results of future large-scale genetics projects, including next-generation sequencing studies. PMID:22438815

  12. PlantNATsDB: a comprehensive database of plant natural antisense transcripts

    PubMed Central

    Chen, Dijun; Yuan, Chunhui; Zhang, Jian; Zhang, Zhao; Bai, Lin; Meng, Yijun; Chen, Ling-Ling; Chen, Ming

    2012-01-01

    Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a ‘Gene Set Analysis’ module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/. PMID:22058132

  13. Including the Group Quarters Population in the US Synthesized Population Database

    PubMed Central

    Chasteen, Bernadette M.; Wheaton, William D.; Cooley, Philip C.; Ganapathi, Laxminarayana; Wagener, Diane K.

    2011-01-01

    In 2005, RTI International researchers developed methods to generate synthesized population data on US households for the US Synthesized Population Database. These data are used in agent-based modeling, which simulates large-scale social networks to test how changes in the behaviors of individuals affect the overall network. Group quarters are residences where individuals live in close proximity and interact frequently. Although the Synthesized Population Database represents the population living in households, data for the nation’s group quarters residents are not easily quantified because of US Census Bureau reporting methods designed to protect individuals’ privacy. Including group quarters population data can be an important factor in agent-based modeling because the number of residents and the frequency of their interactions are variables that directly affect modeling results. Particularly with infectious disease modeling, the increased frequency of agent interaction may increase the probability of infectious disease transmission between individuals and the probability of disease outbreaks. This report reviews our methods to synthesize data on group quarters residents to match US Census Bureau data. Our goal in developing the Group Quarters Population Database was to enable its use with RTI’s US Synthesized Population Database in the Modeling of Infectious Diseases Agent Study. PMID:21841972

  14. XML Storage for Magnetotelluric Transfer Functions: Towards a Comprehensive Online Reference Database

    NASA Astrophysics Data System (ADS)

    Kelbert, A.; Blum, C.

    2015-12-01

    Magnetotelluric Transfer Functions (MT TFs) represent most of the information about Earth electrical conductivity found in the raw electromagnetic data, providing inputs for further inversion and interpretation. To be useful for scientific interpretation, they must also contain carefully recorded metadata. Making these data available in a discoverable and citable fashion would provide the most benefit to the scientific community, but such a development requires that the metadata is not only present in the file but is also searchable. The most commonly used MT TF format to date, the historical Society of Exploration Geophysicists Electromagnetic Data Interchange Standard 1987 (EDI), no longer supports some of the needs of modern magnetotellurics, most notably accurate error bars recording. Moreover, the inherent heterogeneity of EDI's and other historic MT TF formats has mostly kept the community away from healthy data sharing practices. Recently, the MT team at Oregon State University in collaboration with IRIS Data Management Center developed a new, XML-based format for MT transfer functions, and an online system for long-term storage, discovery and sharing of MT TF data worldwide (IRIS SPUD; www.iris.edu/spud/emtf). The system provides a query page where all of the MT transfer functions collected within the USArray MT experiment and other field campaigns can be searched for and downloaded; an automatic on-the-fly conversion to the historic EDI format is also included. To facilitate conversion to the new, more comprehensive and sustainable, XML format for MT TFs, and to streamline inclusion of historic data into the online database, we developed a set of open source format conversion tools, which can be used for rotation of MT TFs as well as a general XML <-> EDI converter (https://seiscode.iris.washington.edu/projects/emtf-fcu). Here, we report on the newly established collaboration between the USGS Geomagnetism Program and the Oregon State University to gather

  15. RiceVarMap: a comprehensive database of rice genomic variations

    PubMed Central

    Zhao, Hu; Yao, Wen; Ouyang, Yidan; Yang, Wanneng; Wang, Gongwei; Lian, Xingming; Xing, Yongzhong; Chen, Lingling; Xie, Weibo

    2015-01-01

    Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species. PMID:25274737

  16. CoReCG: a comprehensive database of genes associated with colon-rectal cancer

    PubMed Central

    Agarwal, Rahul; Kumar, Binayak; Jayadev, Msk; Raghav, Dhwani; Singh, Ashutosh

    2016-01-01

    Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. Database URL: lms.snu.edu.in/corecg PMID:27114494

  17. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

    PubMed

    Yamasaki, Chisato; Murakami, Katsuhiko; Fujii, Yasuyuki; Sato, Yoshiharu; Harada, Erimi; Takeda, Jun-ichi; Taniya, Takayuki; Sakate, Ryuichi; Kikugawa, Shingo; Shimada, Makoto; Tanino, Motohiko; Koyanagi, Kanako O; Barrero, Roberto A; Gough, Craig; Chun, Hong-Woo; Habara, Takuya; Hanaoka, Hideki; Hayakawa, Yosuke; Hilton, Phillip B; Kaneko, Yayoi; Kanno, Masako; Kawahara, Yoshihiro; Kawamura, Toshiyuki; Matsuya, Akihiro; Nagata, Naoki; Nishikata, Kensaku; Noda, Akiko Ogura; Nurimoto, Shin; Saichi, Naomi; Sakai, Hiroaki; Sanbonmatsu, Ryoko; Shiba, Rie; Suzuki, Mami; Takabayashi, Kazuhiko; Takahashi, Aiko; Tamura, Takuro; Tanaka, Masayuki; Tanaka, Susumu; Todokoro, Fusano; Yamaguchi, Kaori; Yamamoto, Naoyuki; Okido, Toshihisa; Mashima, Jun; Hashizume, Aki; Jin, Lihua; Lee, Kyung-Bum; Lin, Yi-Chueh; Nozaki, Asami; Sakai, Katsunaga; Tada, Masahito; Miyazaki, Satoru; Makino, Takashi; Ohyanagi, Hajime; Osato, Naoki; Tanaka, Nobuhiko; Suzuki, Yoshiyuki; Ikeo, Kazuho; Saitou, Naruya; Sugawara, Hideaki; O'Donovan, Claire; Kulikova, Tamara; Whitfield, Eleanor; Halligan, Brian; Shimoyama, Mary; Twigger, Simon; Yura, Kei; Kimura, Kouichi; Yasuda, Tomohiro; Nishikawa, Tetsuo; Akiyama, Yutaka; Motono, Chie; Mukai, Yuri; Nagasaki, Hideki; Suwa, Makiko; Horton, Paul; Kikuno, Reiko; Ohara, Osamu; Lancet, Doron; Eveno, Eric; Graudens, Esther; Imbeaud, Sandrine; Debily, Marie Anne; Hayashizaki, Yoshihide; Amid, Clara; Han, Michael; Osanger, Andreas; Endo, Toshinori; Thomas, Michael A; Hirakawa, Mika; Makalowski, Wojciech; Nakao, Mitsuteru; Kim, Nam-Soon; Yoo, Hyang-Sook; De Souza, Sandro J; Bonaldo, Maria de Fatima; Niimura, Yoshihito; Kuryshev, Vladimir; Schupp, Ingo; Wiemann, Stefan; Bellgard, Matthew; Shionyu, Masafumi; Jia, Libin; Thierry-Mieg, Danielle; Thierry-Mieg, Jean; Wagner, Lukas; Zhang, Qinghua; Go, Mitiko; Minoshima, Shinsei; Ohtsubo, Masafumi; Hanada, Kousuke; Tonellato, Peter; Isogai, Takao; Zhang, Ji; Lenhard, Boris; Kim, Sangsoo; Chen, Zhu; Hinz, Ursula; Estreicher, Anne; Nakai, Kenta; Makalowska, Izabela; Hide, Winston; Tiffin, Nicola; Wilming, Laurens; Chakraborty, Ranajit; Soares, Marcelo Bento; Chiusano, Maria Luisa; Suzuki, Yutaka; Auffray, Charles; Yamaguchi-Kabata, Yumi; Itoh, Takeshi; Hishiki, Teruyoshi; Fukuchi, Satoshi; Nishikawa, Ken; Sugano, Sumio; Nomura, Nobuo; Tateno, Yoshio; Imanishi, Tadashi; Gojobori, Takashi

    2008-01-01

    Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group. PMID:18089548

  18. Tet-Transgenic Rodents: a comprehensive, up-to date database.

    PubMed

    Schönig, Kai; Freundlieb, Sabine; Gossen, Manfred

    2013-04-01

    Here we introduce the "Tet-Transgenic Rodents" database, documenting most of the published Tet-transgenic mouse lines generated in the past 2 decades. Aside from the >500 mouse lines listed, it also includes the first of the recently reported Tet-transgenic rat models. Since the Tet technology comprises two essential components, a cis-acting promoter (Ptet) and a trans-acting transactivator, the database has been organized accordingly. One section of the database summarizes the different transgenic mouse lines carrying mostly tissue specific promoters driving the Tet transactivator. Another section covers transgenic mouse lines carrying responder transgenes under Ptet control. The few existing rat transgenic lines are listed correspondingly. It is the purpose of this database to facilitate the repeated use of preexisting, validated transgenic lines as a shortcut for further research. PMID:23180363

  19. Phenol-Explorer: an online comprehensive database on polyphenol contents in foods

    PubMed Central

    Neveu, V.; Perez-Jiménez, J.; Vos, F.; Crespy, V.; du Chaffaut, L.; Mennen, L.; Knox, C.; Eisner, R.; Cruz, J.; Wishart, D.; Scalbert, A.

    2010-01-01

    A number of databases on the plant metabolome describe the chemistry and biosynthesis of plant chemicals. However, no such database is specifically focused on foods and more precisely on polyphenols, one of the major classes of phytochemicals. As antoxidants, polyphenols influence human health and may play a role in the prevention of a number of chronic diseases such as cardiovascular diseases, some cancers or type 2 diabetes. To determine polyphenol intake in populations and study their association with health, it is essential to have detailed information on their content in foods. However this information is not easily collected due to the variety of their chemical structures and the variability of their content in a given food. Phenol-Explorer is the first comprehensive web-based database on polyphenol content in foods. It contains more than 37 000 original data points collected from 638 scientific articles published in peer-reviewed journals. The quality of these data has been evaluated before they were aggregated to produce final representative mean content values for 502 polyphenols in 452 foods. The web interface allows making various queries on the aggregated data to identify foods containing a given polyphenol or polyphenols present in a given food. For each mean content value, it is possible to trace all original content values and their literature sources. Phenol-Explorer is a major step forward in the development of databases on food constituents and the food metabolome. It should help researchers to better understand the role of phytochemicals in the technical and nutritional quality of food, and food manufacturers to develop tailor-made healthy foods. Database URL: http://www.phenol-explorer.eu PMID:20428313

  20. An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

    NASA Technical Reports Server (NTRS)

    Wang, Ping; Cohen, David H.; MacFarlane, Joseph J.; Cassinelli, Joseph P.

    1997-01-01

    Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

  1. Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources

    PubMed Central

    2013-01-01

    Background Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities. Description Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436bacterial, fungal and archaea species from 52 collections in 25 countries and regions. A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM. Conclusion A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the

  2. ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

    PubMed Central

    Spivak, Aaron T.; Stormo, Gary D.

    2012-01-01

    Saccharomyces cerevisiae is a primary model for studies of transcriptional control, and the specificities of most yeast transcription factors (TFs) have been determined by multiple methods. However, it is unclear which position weight matrices (PWMs) are most useful; for the roughly 200 TFs in yeast, there are over 1200 PWMs in the literature. To address this issue, we created ScerTF, a comprehensive database of 1226 motifs from 11 different sources. We identified a single matrix for each TF that best predicts in vivo data by benchmarking matrices against chromatin immunoprecipitation and TF deletion experiments. We also used in vivo data to optimize thresholds for identifying regulatory sites with each matrix. To correct for biases from different methods, we developed a strategy to combine matrices. These aligned matrices outperform the best available matrix for several TFs. We used the matrices to predict co-occurring regulatory elements in the genome and identified many known TF combinations. In addition, we predict new combinations and provide evidence of combinatorial regulation from gene expression data. The database is available through a web interface at http://ural.wustl.edu/ScerTF. The site allows users to search the database with a regulatory site or matrix to identify the TFs most likely to bind the input sequence. PMID:22140105

  3. A European Flood Database: facilitating comprehensive flood research beyond administrative boundaries

    NASA Astrophysics Data System (ADS)

    Hall, J.; Arheimer, B.; Aronica, G. T.; Bilibashi, A.; Boháč, M.; Bonacci, O.; Borga, M.; Burlando, P.; Castellarin, A.; Chirico, G. B.; Claps, P.; Fiala, K.; Gaál, L.; Gorbachova, L.; Gül, A.; Hannaford, J.; Kiss, A.; Kjeldsen, T.; Kohnová, S.; Koskela, J. J.; Macdonald, N.; Mavrova-Guirguinova, M.; Ledvinka, O.; Mediero, L.; Merz, B.; Merz, R.; Molnar, P.; Montanari, A.; Osuch, M.; Parajka, J.; Perdigão, R. A. P.; Radevski, I.; Renard, B.; Rogger, M.; Salinas, J. L.; Sauquet, E.; Šraj, M.; Szolgay, J.; Viglione, A.; Volpi, E.; Wilson, D.; Zaimi, K.; Blöschl, G.

    2015-06-01

    The current work addresses one of the key building blocks towards an improved understanding of flood processes and associated changes in flood characteristics and regimes in Europe: the development of a comprehensive, extensive European flood database. The presented work results from ongoing cross-border research collaborations initiated with data collection and joint interpretation in mind. A detailed account of the current state, characteristics and spatial and temporal coverage of the European Flood Database, is presented. At this stage, the hydrological data collection is still growing and consists at this time of annual maximum and daily mean discharge series, from over 7000 hydrometric stations of various data series lengths. Moreover, the database currently comprises data from over 50 different data sources. The time series have been obtained from different national and regional data sources in a collaborative effort of a joint European flood research agreement based on the exchange of data, models and expertise, and from existing international data collections and open source websites. These ongoing efforts are contributing to advancing the understanding of regional flood processes beyond individual country boundaries and to a more coherent flood research in Europe.

  4. A comprehensive change detection method for updating the National Land Cover Database to circa 2011

    USGS Publications Warehouse

    Jin, Suming; Yang, Limin; Danielson, Patrick; Homer, Collin G.; Fry, Joyce; Xian, George

    2013-01-01

    The importance of characterizing, quantifying, and monitoring land cover, land use, and their changes has been widely recognized by global and environmental change studies. Since the early 1990s, three U.S. National Land Cover Database (NLCD) products (circa 1992, 2001, and 2006) have been released as free downloads for users. The NLCD 2006 also provides land cover change products between 2001 and 2006. To continue providing updated national land cover and change datasets, a new initiative in developing NLCD 2011 is currently underway. We present a new Comprehensive Change Detection Method (CCDM) designed as a key component for the development of NLCD 2011 and the research results from two exemplar studies. The CCDM integrates spectral-based change detection algorithms including a Multi-Index Integrated Change Analysis (MIICA) model and a novel change model called Zone, which extracts change information from two Landsat image pairs. The MIICA model is the core module of the change detection strategy and uses four spectral indices (CV, RCVMAX, dNBR, and dNDVI) to obtain the changes that occurred between two image dates. The CCDM also includes a knowledge-based system, which uses critical information on historical and current land cover conditions and trends and the likelihood of land cover change, to combine the changes from MIICA and Zone. For NLCD 2011, the improved and enhanced change products obtained from the CCDM provide critical information on location, magnitude, and direction of potential change areas and serve as a basis for further characterizing land cover changes for the nation. An accuracy assessment from the two study areas show 100% agreement between CCDM mapped no-change class with reference dataset, and 18% and 82% disagreement for the change class for WRS path/row p22r39 and p33r33, respectively. The strength of the CCDM is that the method is simple, easy to operate, widely applicable, and capable of capturing a variety of natural and

  5. Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods

    PubMed Central

    Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

    2016-01-01

    Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

  6. A Comprehensive Database for the Most Commonly Measured Paleoceanographic Proxies: Evaluating Global Carbon Burial Variations over the Last Deglaciation

    NASA Astrophysics Data System (ADS)

    Cartapanis, O. A.; Galbraith, E. D.; Bianchi, D.

    2014-12-01

    The paleoceanographic community has measured physical and chemical properties of thousands of sediment cores, in order to reconstruct past oceanic conditions across a wide range of timescales. Most of these datasets were archived in online data repositories in order to facilitate later analysis. However, the diversity of proxy types and heterogeneous reporting standards have hindered the analysis of globally distributed paleoceanographic time series, despite the tremendous potential utility of large datasets. In order for the existing archives of paleoceanographic data to contribute towards important unanswered issues, the datasets must be readily accessible in an organized structure, with an appropriate unified age model for each sediment site. Here we present a comprehensive database, built using MATLAB structure, for the most commonly measured proxies in marine sediment cores and surface sediment. These include the concentrations of carbonate, organic matter and opal, density of the sediment, the oxygen and carbon isotopic composition of benthic and planktonic foraminifera, sea surface temperature estimates, as well as chronological constrains. The records were downloaded from PANGAEA and NOAA databases and multiple records from the same sediment core were regrouped, allowing age models to be shared between records. The resulting database consists of more than 30,000 sites, facilitating rapid and accurate mapping of sediment composition for selected time periods, and retrieving and plotting time series. The greatest hurdle identified in building a unifi­ed dataproduct of this type is inconsistency in the reporting of depth measurements and chronological information. In our view, standardized reporting practices would greatly assist in developing global quantitative analysis, and requires community-wide action. We propose the development of a unified global sediment core registry, including metadata and chronological information for all marine sediment cores

  7. COMPREHENSIVE ADOLESCENT HEALTH PROGRAMS THAT INCLUDE SEXUAL AND REPRODUCTIVE HEALTH SERVICES: A SYSTEMATIC REVIEW

    PubMed Central

    Kågesten, Anna; Parekh, Jenita; Tunçalp, Özge; Turke, Shani; Blum, Robert Wm

    2015-01-01

    Objectives To describe the characteristics and evidence of comprehensive adolescent health (CAH) programs encompassing sexual and reproductive and other health services, educational and social support. Methods Systematic review of peer-reviewed and grey literature on CAH programs (1998-2013). Only programs with experimental, quasi-experimental or pre-post evaluations were included. Two independent reviewers screened 36,119 records and extracted articles using predefined criteria. Data was synthesised into descriptive characteristics; quality was assessed by evidence level (rigorous, strong, modest). Results Data was extracted on 46 programs (181 studies) of which 19 programs were defined as comprehensive; 9 were excluded due to insufficient evaluations. Ten CAH programs met all inclusion criteria. Most were US based; others were implemented in Egypt, Ethiopia and Mexico. Few programs (N=3) displayed rigorous evidence, 5 had strong and 2 had modest evidence. All programs with rigorous/strong evidence directly or indirectly influenced adolescent sexual and reproductive health. Common elements of these programs included: long-term commitment to adolescents, interpersonal connections, community mobilization, and skill-building elements. Conclusion The long term impact of many CAH programs cannot be proven due to insufficient evaluations. Evaluation approaches that take into account the complex operating conditions of many programs are needed to better understand mechanisms behind program effects. PMID:25320876

  8. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock

    PubMed Central

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

    2016-01-01

    Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf. PMID:26727469

  9. WATCHDOG: A Comprehensive All-sky Database of Galactic Black Hole X-ray Binaries

    NASA Astrophysics Data System (ADS)

    Tetarenko, B. E.; Sivakoff, G. R.; Heinke, C. O.; Gladstone, J. C.

    2016-02-01

    With the advent of more sensitive all-sky instruments, the transient universe is being probed in greater depth than ever before. Taking advantage of available resources, we have established a comprehensive database of black hole (and black hole candidate) X-ray binary (BHXB) activity between 1996 and 2015 as revealed by all-sky instruments, scanning surveys, and select narrow-field X-ray instruments on board the INTErnational Gamma-Ray Astrophysics Laboratory, Monitor of All-Sky X-ray Image, Rossi X-ray Timing Explorer, and Swift telescopes; the Whole-sky Alberta Time-resolved Comprehensive black-Hole Database Of the Galaxy or WATCHDOG. Over the past two decades, we have detected 132 transient outbursts, tracked and classified behavior occurring in 47 transient and 10 persistently accreting BHs, and performed a statistical study on a number of outburst properties across the Galactic population. We find that outbursts undergone by BHXBs that do not reach the thermally dominant accretion state make up a substantial fraction (∼40%) of the Galactic transient BHXB outburst sample over the past ∼20 years. Our findings suggest that this “hard-only” behavior, observed in transient and persistently accreting BHXBs, is neither a rare nor recent phenomenon and may be indicative of an underlying physical process, relatively common among binary BHs, involving the mass-transfer rate onto the BH remaining at a low level rather than increasing as the outburst evolves. We discuss how the larger number of these “hard-only” outbursts and detected outbursts in general have significant implications for both the luminosity function and mass-transfer history of the Galactic BHXB population.

  10. 24 CFR 968.315 - Comprehensive Plan (including five-year action plan).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...) Contents of comprehensive plan. The comprehensive plan shall identify all of the physical and management...): (1) The management, financial, and accounting control systems of the PHA; (2) The adequacy and... comprehensive plan. In addition, the PHA shall consult with resident management corporations (RMCs) to...

  11. dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes

    PubMed Central

    Uzun, Alper; Triche, Elizabeth W.; Schuster, Jessica; Dewan, Andrew T.; Padbury, James F.

    2016-01-01

    Preeclampsia is one of the most common causes of fetal and maternal morbidity and mortality in the world. We built a Database for Preeclampsia (dbPEC) consisting of the clinical features, concurrent conditions, published literature and genes associated with Preeclampsia. We included gene sets associated with severity, concurrent conditions, tissue sources and networks. The published scientific literature is the primary repository for all information documenting human disease. We used semantic data mining to retrieve and extract the articles pertaining to preeclampsia-associated genes and performed manual curation. We deposited the articles, genes, preeclampsia phenotypes and other supporting information into the dbPEC. It is publicly available and freely accessible. Previously, we developed a database for preterm birth (dbPTB) using a similar approach. Using the gene sets in dbPTB, we were able to successfully analyze a genome-wide study of preterm birth including 4000 women and children. We identified important genes and pathways associated with preterm birth that were not otherwise demonstrable using genome-wide approaches. dbPEC serves not only as a resources for genes and articles associated with preeclampsia, it is a robust source of gene sets to analyze a wide range of high-throughput data for gene set enrichment analysis. Database URL: http://ptbdb.cs.brown.edu/dbpec/ PMID:26946289

  12. Feasibility of including green tea products for an analytically verified dietary supplement database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Dietary Supplement Ingredient Database (DSID) is a federally-funded, publically-accessible dietary supplement database that currently contains analytically derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in di...

  13. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

    PubMed Central

    Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

  14. A Comprehensive Opacities/Atomic Database for the Analysis of Astrophysical Spectra and Modeling

    NASA Technical Reports Server (NTRS)

    Pradhan, Anil K. (Principal Investigator)

    1997-01-01

    The main goals of this ADP award have been accomplished. The electronic database TOPBASE, consisting of the large volume of atomic data from the Opacity Project, has been installed and is operative at a NASA site at the Laboratory for High Energy Astrophysics Science Research Center (HEASRC) at the Goddard Space Flight Center. The database will be continually maintained and updated by the PI and collaborators. TOPBASE is publicly accessible from IP: topbase.gsfc.nasa.gov. During the last six months (since the previous progress report), considerable work has been carried out to: (1) put in the new data for low ionization stages of iron: Fe I - V, beginning with Fe II, (2) high-energy photoionization cross sections computed by Dr. Hong Lin Zhang (consultant on the Project) were 'merged' with the current Opacity Project data and input into TOPbase; (3) plans laid out for a further extension of TOPbase to include TIPbase, the database for collisional data to complement the radiative data in TOPbase.

  15. Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

    PubMed

    Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

    2016-08-01

    Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality. PMID:27287925

  16. An automated DICOM database capable of arbitrary data mining (including radiation dose indicators) for quality monitoring.

    PubMed

    Wang, Shanshan; Pavlicek, William; Roberts, Catherine C; Langer, Steve G; Zhang, Muhong; Hu, Mengqi; Morin, Richard L; Schueler, Beth A; Wellnitz, Clinton V; Wu, Teresa

    2011-04-01

    The U.S. National Press has brought to full public discussion concerns regarding the use of medical radiation, specifically x-ray computed tomography (CT), in diagnosis. A need exists for developing methods whereby assurance is given that all diagnostic medical radiation use is properly prescribed, and all patients' radiation exposure is monitored. The "DICOM Index Tracker©" (DIT) transparently captures desired digital imaging and communications in medicine (DICOM) tags from CT, nuclear imaging equipment, and other DICOM devices across an enterprise. Its initial use is recording, monitoring, and providing automatic alerts to medical professionals of excursions beyond internally determined trigger action levels of radiation. A flexible knowledge base, aware of equipment in use, enables automatic alerts to system administrators of newly identified equipment models or software versions so that DIT can be adapted to the new equipment or software. A dosimetry module accepts mammography breast organ dose, skin air kerma values from XA modalities, exposure indices from computed radiography, etc. upon receipt. The American Association of Physicists in Medicine recommended a methodology for effective dose calculations which are performed with CT units having DICOM structured dose reports. Web interface reporting is provided for accessing the database in real-time. DIT is DICOM-compliant and, thus, is standardized for international comparisons. Automatic alerts currently in use include: email, cell phone text message, and internal pager text messaging. This system extends the utility of DICOM for standardizing the capturing and computing of radiation dose as well as other quality measures. PMID:20824303

  17. A User’s Guide to the Comprehensive Water Quality Database for Groundwater in the Vicinity of the Nevada Test Site, Rev. No.: 1

    SciTech Connect

    Farnham, Irene

    2006-09-01

    This water quality database (viz.GeochemXX.mdb) has been developed as part of the Underground Test Area (UGTA) Program with the cooperation of several agencies actively participating in ongoing evaluation and characterization activities under contract to the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO). The database has been constructed to provide up-to-date, comprehensive, and quality controlled data in a uniform format for the support of current and future projects. This database provides a valuable tool for geochemical and hydrogeologic evaluations of the Nevada Test Site (NTS) and surrounding region. Chemistry data have been compiled for groundwater within the NTS and the surrounding region. These data include major ions, organic compounds, trace elements, radionuclides, various field parameters, and environmental isotopes. Colloid data are also included in the database. The GeochemXX.mdb database is distributed on an annual basis. The extension ''XX'' within the database title is replaced by the last two digits of the release year (e.g., Geochem06 for the version released during the 2006 fiscal year). The database is distributed via compact disc (CD) and is also uploaded to the Common Data Repository (CDR) in order to make it available to all agencies with DOE intranet access. This report provides an explanation of the database configuration and summarizes the general content and utility of the individual data tables. In addition to describing the data, subsequent sections of this report provide the data user with an explanation of the quality assurance/quality control (QA/QC) protocols for this database.

  18. SMPD1 Mutation Update: Database and Comprehensive Analysis of Published and Novel Variants.

    PubMed

    Zampieri, Stefania; Filocamo, Mirella; Pianta, Annalisa; Lualdi, Susanna; Gort, Laura; Coll, Maria Jose; Sinnott, Richard; Geberhiwot, Tarekegn; Bembi, Bruno; Dardis, Andrea

    2016-02-01

    Niemann-Pick Types A and B (NPA/B) diseases are autosomal recessive lysosomal storage disorders caused by the deficient activity of acid sphingomyelinase (ASM) because of the mutations in the SMPD1 gene. Here, we provide a comprehensive updated review of already reported and newly identified SMPD1 variants. Among them, 185 have been found in NPA/B patients. Disease-causing variants are equally distributed along the SMPD1 gene; most of them are missense (65.4%) or frameshift (19%) mutations. The most frequently reported mutation worldwide is the p.R610del, clearly associated with an attenuated NP disease type B phenotype. The available information about the impact of 52 SMPD1 variants on ASM mRNA and/or enzymatic activity has been collected and whenever possible, phenotype/genotype correlations were established. In addition, we created a locus-specific database easily accessible at http://www.inpdr.org/genes that catalogs the 417 SMPD1 variants reported to date and provides data on their in silico predicted effects on ASM protein function or mRNA splicing. The information reviewed in this article, providing new insights into the genotype/phenotype correlation, is extremely valuable to facilitate diagnosis and genetic counseling of families affected by NPA/B. PMID:26499107

  19. Chemical composition of ferromanganese crusts in the world ocean: a review and comprehensive database

    USGS Publications Warehouse

    Manheim, Frank T.; Lane-Bostwick, Candice M.

    1989-01-01

    A comprehensive database of chemical and mineralogical properties for ferromanganese crusts collected throughout the Atlantic, Pacific, and Indian Oceans, and has been assembled from published and unpublished sources which provide collection and analytical information for these samples. These crusts, their chemical compositions and natural distribution, have been a topic of interest to scientific research, as well as to industrial and military applications. Unlike abyssal ferromanganese nodules, which form in areas of low disturbance and high sediment accumulation, crusts have been found to contain three to five times more cobalt than these nodules, and can be found on harder, steeper substrates which can be too steep for permanent sediment accumulation. They have also been documented on seamounts and plateaus within the U.S. exclusive economic zone in both Pacific and Atlantic Oceans, and these are therefore of strategic importance to the United States Government, as well as to civilian mining and metallurgical industries. The data tables provided in this report have been digitized and previously uploaded to the National Oceanic and Atmospheric Administration National Geophysical Data Center in 1991 for online distribution, and were provided in plain text format. The 2014 update to the original U.S. Geological Survey open-file report published in 1989 provides these data tables in a slightly reformatted version to make them easier to ingest into geographic information system software, converted to shapefiles, and have completed metadata written and associated with them.

  20. EpiFactors: a comprehensive database of human epigenetic factors and complexes

    PubMed Central

    Medvedeva, Yulia A.; Lennartsson, Andreas; Ehsani, Rezvan; Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Panahandeh, Pouda; Khimulya, Grigory; Kasukawa, Takeya; Drabløs, Finn

    2015-01-01

    Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones affect gene expression and genome stability via proteins that recognize and act upon such modifications. Many enzymes that catalyse epigenetic modifications or are critical for enzymatic complexes have been discovered, and this is encouraging investigators to study the role of these proteins in diverse normal and pathological processes. Rapidly growing knowledge in the area has resulted in the need for a resource that compiles, organizes and presents curated information to the researchers in an easily accessible and user-friendly form. Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. For 789 of these genes, we include expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians. Database URL: http://epifactors.autosome.ru PMID:26153137

  1. AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

    PubMed Central

    Fallmann, Jörg; Sedlyarov, Vitaly; Tanzer, Andrea; Kovarik, Pavel; Hofacker, Ivo L.

    2016-01-01

    AREsite2 represents an update for AREsite, an on-line resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3′UTR sequences. The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs. Improvements include annotation of motifs not only in 3′UTRs but in the whole gene body including introns, additional genomes, and locally stable secondary structures from genome wide scans. Furthermore, we include data from CLIP-Seq experiments in order to highlight motifs with validated protein interaction. Additionally, we provide a REST interface for experienced users to interact with the database in a semi-automated manner. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite PMID:26602692

  2. Outcome of the cementless Taperloc stem: a comprehensive literature review including arthroplasty register data

    PubMed Central

    2011-01-01

    Background and purpose The validity of various data sources for the assessment of the outcome quality of medical devices was investigated by comparative analysis of the published data sources available for a sample of implants. It was the aim of the study to determine the performance of this implant and to identify potential bias factors inherent to the various datasets. Methods A comprehensive literature search was carried out from English-language, peer-reviewed journals and worldwide reports from national arthroplasty registers. Publications from Medline-listed journals were included. The main parameter was revision rate, calculated as “revisions per 100 observed component years” to allow adjusted direct comparison of different datasets. Results Of 16 clinical studies that met the inclusion criteria, 9 originated from the implant developer's hospital. In the clinical studies category, publications from the developer's hospital suggested considerably lower revision rates than the other datasets. In fact, the values quoted were 5.5 times below the average of all other studies, and 9.51 times lower than in the Australian arthroplasty register. These differences are statistically significant. Interpretation The cementless Taperloc stem is an implant that shows good performance regarding revision rates in registry data and in clinical studies. However, the excellent results published by the developer's clinic are generally not reproducible by other surgeons. In terms of reference data, registry data are able to make an important contribution to the assessment of clinical sample-based studies, particularly regarding evaluation of the extent to which published results are reproducible in daily routine. PMID:21463220

  3. A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates

    PubMed Central

    Rodríguez-Rey, Marta; Herrando-Pérez, Salvador; Brook, Barry W.; Saltré, Frédérik; Alroy, John; Beeton, Nicholas; Bird, Michael I.; Cooper, Alan; Gillespie, Richard; Jacobs, Zenobia; Johnson, Christopher N.; Miller, Gifford H.; Prideaux, Gavin J.; Roberts, Richard G.; Turney, Chris S.M.; Bradshaw, Corey J.A.

    2016-01-01

    The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery. PMID:27434208

  4. A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.

    PubMed

    Rodríguez-Rey, Marta; Herrando-Pérez, Salvador; Brook, Barry W; Saltré, Frédérik; Alroy, John; Beeton, Nicholas; Bird, Michael I; Cooper, Alan; Gillespie, Richard; Jacobs, Zenobia; Johnson, Christopher N; Miller, Gifford H; Prideaux, Gavin J; Roberts, Richard G; Turney, Chris S M; Bradshaw, Corey J A

    2016-01-01

    The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery. PMID:27434208

  5. The MiST2 database: a comprehensive genomics resource on microbial signal transduction

    PubMed Central

    Ulrich, Luke E.; Zhulin, Igor B.

    2010-01-01

    The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%). PMID:19900966

  6. InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes

    PubMed Central

    Tota, Kumudini; Rayabarapu, Nihar; Moosa, Sowmya; Talla, Venu; Bhyravbhatla, Balaji; Rao, Srinivasa

    2013-01-01

    According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian medicinal plants that captures their role in anti-diabetic activity. InDiaMed's features include chemical, pharmacological, biochemical and geographical information of the medicinal plant, scientifically relevant information of the plant, and the coherent research done on it in the field of diabetes. The database also includes the list of poly-herbal formulations which are used for treatment of diabetes in India. Availability http://www.indiamed.info PMID:23750084

  7. The development of a comprehensive regional digital geospatial database for geothermal exploration in the West-Central Great Basin, U.S.A.

    SciTech Connect

    Nash, G.D.; Hernandez, M.W.

    1996-08-01

    The Earth Sciences and Resources Institute, Geomatics Laboratory, (EGL), Department of Civil and Environmental Engineering, University of Utah, has compiled and initiated the use of a comprehensive digital geospatial database for geothermal exploration in the west-central Great Basin, U.S.A. The database consists of hydrothermal alteration, lineament, recent earthquake, aeromagnetic, gravity, hot spring, mining district, heat flow, geochemical, and geologic unit digital maps in a GIS format. Several problems were encountered during the development of this geospatial database. These primarily included (1) data availability and coverage of the study area, (2) data accuracy (both spatial and thematic), (3) inconsistent data formats, and (4) a lack of metadata. These problems were all overcome satisfactorily. The data are currently being used to create a regional geothermal potential model for the study area.

  8. Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation.

    PubMed

    Medvar, Barbara; Raghuram, Viswanathan; Pisitkun, Trairak; Sarkar, Abhijit; Knepper, Mark A

    2016-07-01

    Aquaporin-2 (AQP2) is regulated in part via vasopressin-mediated changes in protein half-life that are in turn dependent on AQP2 ubiquitination. Here we addressed the question, "What E3 ubiquitin ligase is most likely to be responsible for AQP2 ubiquitination?" using large-scale data integration based on Bayes' rule. The first step was to bioinformatically identify all E3 ligase genes coded by the human genome. The 377 E3 ubiquitin ligases identified in the human genome, consisting predominant of HECT, RING, and U-box proteins, have been used to create a publically accessible and downloadable online database (https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/). We also curated a second database of E3 ligase accessory proteins that included BTB domain proteins, cullins, SOCS-box proteins, and F-box proteins. Using Bayes' theorem to integrate information from multiple large-scale proteomic and transcriptomic datasets, we ranked these 377 E3 ligases with respect to their probability of interaction with AQP2. Application of Bayes' rule identified the E3 ligases most likely to interact with AQP2 as (in order of probability): NEDD4 and NEDD4L (tied for first), AMFR, STUB1, ITCH, ZFPL1. Significantly, the two E3 ligases tied for top rank have also been studied extensively in the reductionist literature as regulatory proteins in renal tubule epithelia. The concordance of conclusions from reductionist and systems-level data provides strong motivation for further studies of the roles of NEDD4 and NEDD4L in the regulation of AQP2 protein turnover. PMID:27199454

  9. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits.

    PubMed

    Ghosal, Suman; Das, Shaoli; Sen, Rituparno; Basak, Piyali; Chakrabarti, Jayprokas

    2013-01-01

    Circular RNAs are new players in regulation of post transcriptional gene expression. Animal genomes express many circular RNAs from diverse genomic locations. A recent study has validated a fairly large number of circular RNAs in human, mouse, and nematode. Circular RNAs play a crucial role in fine tuning the level of miRNA mediated regulation of gene expression by sequestering the miRNAs. Their interaction with disease associated miRNAs indicates that circular RNAs are important for disease regulation. In this paper we studied the potential association of circular RNAs (circRNA) with human diseases in two different ways. Firstly, the interactions of circRNAs with disease associated miRNAs were identified, following which the likelihood of a circRNA being associated with a disease was calculated. For the miRNAs associated with individual diseases, we constructed a network of predicted interactions between the miRNAs and protein coding, long non-coding and circular RNA genes. We carried out gene ontology (GO) enrichment analysis on the set of protein coding genes in the miRNA- circRNA interactome of individual diseases to check the enrichment of genes associated with particular biological processes. Secondly, disease associated SNPs were mapped on circRNA loci, and Argonaute (Ago) interaction sites on circular RNAs were identified. We compiled a database of disease-circRNA association in Circ2Traits (http://gyanxet-beta.com/circdb/), the first comprehensive knowledgebase of potential association of circular RNAs with diseases in human. PMID:24339831

  10. Feasibility of Including Green Tea Products for an Analytically Verified Dietary Supplement Database

    PubMed Central

    Saldanha, Leila; Dwyer, Johanna; Andrews, Karen; Betz, Joseph; Harnely, James; Pehrsson, Pamela; Rimmer, Catherine; Savarala, Sushma

    2015-01-01

    The Dietary Supplement Ingredient Database (DSID) is a federally funded, publicly accessible dietary supplement database that currently contains analytically-derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in dietary supplement products such as botanicals are also of interest and thus are being considered for inclusion in the DSID. Thirty-eight constituents, mainly botanicals were identified and prioritized by a federal interagency committee. Green tea was selected from this list as the botanical for expansion of the DSID. This paper describes the process for prioritizing dietary ingredients in the DSID. It also discusses the criteria for inclusion of these ingredients, and the approach for selecting and testing products for the green tea pilot study. PMID:25817236

  11. The National Deep-Sea Coral and Sponge Database: A Comprehensive Resource for United States Deep-Sea Coral and Sponge Records

    NASA Astrophysics Data System (ADS)

    Dornback, M.; Hourigan, T.; Etnoyer, P.; McGuinn, R.; Cross, S. L.

    2014-12-01

    Research on deep-sea corals has expanded rapidly over the last two decades, as scientists began to realize their value as long-lived structural components of high biodiversity habitats and archives of environmental information. The NOAA Deep Sea Coral Research and Technology Program's National Database for Deep-Sea Corals and Sponges is a comprehensive resource for georeferenced data on these organisms in U.S. waters. The National Database currently includes more than 220,000 deep-sea coral records representing approximately 880 unique species. Database records from museum archives, commercial and scientific bycatch, and from journal publications provide baseline information with relatively coarse spatial resolution dating back as far as 1842. These data are complemented by modern, in-situ submersible observations with high spatial resolution, from surveys conducted by NOAA and NOAA partners. Management of high volumes of modern high-resolution observational data can be challenging. NOAA is working with our data partners to incorporate this occurrence data into the National Database, along with images and associated information related to geoposition, time, biology, taxonomy, environment, provenance, and accuracy. NOAA is also working to link associated datasets collected by our program's research, to properly archive them to the NOAA National Data Centers, to build a robust metadata record, and to establish a standard protocol to simplify the process. Access to the National Database is provided through an online mapping portal. The map displays point based records from the database. Records can be refined by taxon, region, time, and depth. The queries and extent used to view the map can also be used to download subsets of the database. The database, map, and website is already in use by NOAA, regional fishery management councils, and regional ocean planning bodies, but we envision it as a model that can expand to accommodate data on a global scale.

  12. DOG-SPOT database for comprehensive management of dog genetic research data.

    PubMed

    Powell, Julie As; Allen, Jeremy; Sutter, Nathan B

    2010-01-01

    Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides. PMID:21159202

  13. ECO: A Generic Eutrophication Model Including Comprehensive Sediment-Water Interaction

    PubMed Central

    Smits, Johannes G. C.; van Beek, Jan K. L.

    2013-01-01

    The content and calibration of the comprehensive generic 3D eutrophication model ECO for water and sediment quality is presented. Based on a computational grid for water and sediment, ECO is used as a tool for water quality management to simulate concentrations and mass fluxes of nutrients (N, P, Si), phytoplankton species, detrital organic matter, electron acceptors and related substances. ECO combines integral simulation of water and sediment quality with sediment diagenesis and closed mass balances. Its advanced process formulations for substances in the water column and the bed sediment were developed to allow for a much more dynamic calculation of the sediment-water exchange fluxes of nutrients as resulting from steep concentration gradients across the sediment-water interface than is possible with other eutrophication models. ECO is to more accurately calculate the accumulation of organic matter and nutrients in the sediment, and to allow for more accurate prediction of phytoplankton biomass and water quality in response to mitigative measures such as nutrient load reduction. ECO was calibrated for shallow Lake Veluwe (The Netherlands). Due to restoration measures this lake underwent a transition from hypertrophic conditions to moderately eutrophic conditions, leading to the extensive colonization by submerged macrophytes. ECO reproduces observed water quality well for the transition period of ten years. The values of its process coefficients are in line with ranges derived from literature. ECO’s calculation results underline the importance of redox processes and phosphate speciation for the nutrient return fluxes. Among other things, the results suggest that authigenic formation of a stable apatite-like mineral in the sediment can contribute significantly to oligotrophication of a lake after a phosphorus load reduction. PMID:23844160

  14. Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics.

    PubMed

    Nelson, P S; Han, D; Rochon, Y; Corthals, G L; Lin, B; Monson, A; Nguyen, V; Franza, B R; Plymate, S R; Aebersold, R; Hood, L

    2000-05-01

    Several methods have been developed for the comprehensive analysis of gene expression in complex biological systems. Generally these procedures assess either a portion of the cellular transcriptome or a portion of the cellular proteome. Each approach has distinct conceptual and methodological advantages and disadvantages. We have investigated the application of both methods to characterize the gene expression pathway mediated by androgens and the androgen receptor in prostate cancer cells. This pathway is of critical importance for the development and progression of prostate cancer. Of clinical importance, modulation of androgens remains the mainstay of treatment for patients with advanced disease. To facilitate global gene expression studies we have first sought to define the prostate transcriptome by assembling and annotating prostate-derived expressed sequence tags (ESTs). A total of 55000 prostate ESTs were assembled into a set of 15953 clusters putatively representing 15953 distinct transcripts. These clusters were used to construct cDNA microarrays suitable for examining the androgen-response pathway at the level of transcription. The expression of 20 genes was found to be induced by androgens. This cohort included known androgen-regulated genes such as prostate-specific antigen (PSA) and several novel complementary DNAs (cDNAs). Protein expression profiles of androgen-stimulated prostate cancer cells were generated by two-dimensional electrophoresis (2-DE). Mass spectrometric analysis of androgen-regulated proteins in these cells identified the metastasis-suppressor gene NDKA/nm23, a finding that may explain a marked reduction in metastatic potential when these cells express a functional androgen receptor pathway. PMID:10870968

  15. PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.

    PubMed

    Das, Arindam Atanu; Sharma, Om Prakash; Kumar, Muthuvel Suresh; Krishna, Ramadas; Mathur, Premendu P

    2013-08-01

    Protein-peptide interactions, where one partner is a globular protein (domain) and the other is a flexible linear peptide, are key components of cellular processes predominantly in signaling and regulatory networks, hence are prime targets for drug design. To derive the details of the protein-peptide interaction mechanism is often a cumbersome task, though it can be made easier with the availability of specific databases and tools. The Peptide Binding Protein Database (PepBind) is a curated and searchable repository of the structures, sequences and experimental observations of 3100 protein-peptide complexes. The web interface contains a computational tool, protein inter-chain interaction (PICI), for computing several types of weak or strong interactions at the protein-peptide interaction interface and visualizing the identified interactions between residues in Jmol viewer. This initial database release focuses on providing protein-peptide interface information along with structure and sequence information for protein-peptide complexes deposited in the Protein Data Bank (PDB). Structures in PepBind are classified based on their cellular activity. More than 40% of the structures in the database are found to be involved in different regulatory pathways and nearly 20% in the immune system. These data indicate the importance of protein-peptide complexes in the regulation of cellular processes. PMID:23896518

  16. Comprehension.

    ERIC Educational Resources Information Center

    Bollenbach, Carolyn

    1986-01-01

    Teaching comprehension skills requires teaching to intuition with activities such as presenting puzzling situations to introduce a topic, using art to elicit latent feelings, using imagery and improvisations to enhance visualization, and using music and dance to encourage nonverbal expressions. (DB)

  17. SU-E-T-153: Establish a Comprehensive Patient-Specific Plan QA Database for Instituitional Quality Control Program

    SciTech Connect

    Ding, X; Olszanski, A; Scheuermann, R; Bellerive, M; Solberg, T

    2014-06-01

    Purpose: Since the publication of TG-119, several new treatment techniques requiring new QA devices have been implemented in the clinic. To monitor and analyze our institutional QA performance, we have created a comprehensive QA database using Research Electronic Data Capture (REDCap). The database will also assist us in creating IMRT QA Analysis practice guidelines. Methods: Since Oct. 2013, 336 patient plan QA results were entered into the database. Plan parameters such as plan ID, treatment site, technique, energy, optimization constraints, modulation factor, leaf speed, leaf opening.etc were automatically extracted from the Varian Eclipse database to allow us to refine our evaluation and analysis method. Specific QA device, LINAC-related information, and measurement and analysis results were manually entered by the QA team. IMRT plans were measured using MapCHECK2 while RapidArc plans were measured using ArcCHECK. Distance-To-Agreement 3%/3mm without global maximum normalization was used. Results: The data indicates that different treatment techniques might benefit from a different site-specific action level(AL) depending on the complexity of the plan and optimization parameter used (e.g., breast IMRT QA= 97.8% and pelvis IMRT QA=93.1%). Different QA devices may also benefit from a different AL (MapCHECK2 = 94.1% while ArcCHECK = 83.0%). The relationship between the parameters and passing rate suggests that the complexity of each plan, characterized by leaf travel, leaf opening and modulation factor, affect the passing rate significantly. The database is reviewed regularly, and any abnormal point of the QA result or a trend of lower QA passing rate on a specific LINAC is further investigated. Conclusion: Establishing a comprehensive QA database provides an overview of the quality assurance program. It not only helps in answering the question “what is a reasonable and achievable standard for each institution”, but also saves time in monitoring and

  18. Comprehensive functional characterization of murine infantile Batten disease including Parkinson-like behavior and dopaminergic markers.

    PubMed

    Dearborn, Joshua T; Harmon, Steven K; Fowler, Stephen C; O'Malley, Karen L; Taylor, George T; Sands, Mark S; Wozniak, David F

    2015-01-01

    Infantile neuronal ceroid lipofuscinosis (INCL, Infantile Batten disease) is a neurodegenerative lysosomal storage disease caused by a deficiency in palmitoyl protein thioesterase-1 (PPT1). The PPT1-deficient mouse (Cln1(-/-)) is a useful phenocopy of human INCL. Cln1(-/-) mice display retinal dysfunction, seizures, motor deficits, and die at ~8 months of age. However, little is known about the cognitive and behavioral functions of Cln1(-/-) mice during disease progression. In the present study, younger (~1-2 months of age) Cln1(-/-) mice showed minor deficits in motor/sensorimotor functions while older (~5-6 months of age) Cln1(-/-) mice exhibited more severe impairments, including decreased locomotor activity, inferior cued water maze performance, decreased running wheel ability, and altered auditory cue conditioning. Unexpectedly, certain cognitive functions such as some learning and memory capabilities seemed intact in older Cln1(-/-) mice. Younger and older Cln1(-/-) mice presented with walking initiation defects, gait abnormalities, and slowed movements, which are analogous to some symptoms reported in INCL and parkinsonism. However, there was no evidence of alterations in dopaminergic markers in Cln1(-/-) mice. Results from this study demonstrate quantifiable changes in behavioral functions during progression of murine INCL and suggest that Parkinson-like motor/sensorimotor deficits in Cln1(-/-) mice are not mediated by dopamine deficiency. PMID:26238334

  19. Comprehensive functional characterization of murine infantile Batten disease including Parkinson-like behavior and dopaminergic markers

    PubMed Central

    Dearborn, Joshua T.; Harmon, Steven K.; Fowler, Stephen C.; O’Malley, Karen L.; Taylor, George T.; Sands, Mark S.; Wozniak, David F.

    2015-01-01

    Infantile neuronal ceroid lipofuscinosis (INCL, Infantile Batten disease) is a neurodegenerative lysosomal storage disease caused by a deficiency in palmitoyl protein thioesterase-1 (PPT1). The PPT1-deficient mouse (Cln1−/−) is a useful phenocopy of human INCL. Cln1−/− mice display retinal dysfunction, seizures, motor deficits, and die at ~8 months of age. However, little is known about the cognitive and behavioral functions of Cln1−/− mice during disease progression. In the present study, younger (~1–2 months of age) Cln1−/− mice showed minor deficits in motor/sensorimotor functions while older (~5–6 months of age) Cln1−/− mice exhibited more severe impairments, including decreased locomotor activity, inferior cued water maze performance, decreased running wheel ability, and altered auditory cue conditioning. Unexpectedly, certain cognitive functions such as some learning and memory capabilities seemed intact in older Cln1−/− mice. Younger and older Cln1−/− mice presented with walking initiation defects, gait abnormalities, and slowed movements, which are analogous to some symptoms reported in INCL and parkinsonism. However, there was no evidence of alterations in dopaminergic markers in Cln1−/− mice. Results from this study demonstrate quantifiable changes in behavioral functions during progression of murine INCL and suggest that Parkinson-like motor/sensorimotor deficits in Cln1−/− mice are not mediated by dopamine deficiency. PMID:26238334

  20. The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms.

    PubMed

    McGuffin, Liam J; Street, Stefano A; Bryson, Kevin; Sørensen, Søren-Aksel; Jones, David T

    2004-01-01

    Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures. PMID:14681393

  1. Dental health services research utilizing comprehensive clinical databases and information technology.

    PubMed

    Hayden, W J

    1997-01-01

    Marketplace pressures for accountability in dentistry have made clear dental delivery systems' weaknesses in information generation, management, and analysis methods. Without this type of information, dentistry is unable to quantify and document the outcomes of the dental care services it provides. The Pew Health Professions Commission and the Institute of Medicine both suggest that dental schools should be among the leaders in the development and teaching of dental information capabilities, as well as the source of fundamental dental health services research. This paper argues that dental schools are the logical location for the development of valid, reliable, and acceptable health services research methods and databases. It describes the development of an insurance claims database to demonstrate the types of investigations possible, as well as the weaknesses and shortcomings of pure administrative data. PMID:9024342

  2. A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

    PubMed Central

    Gaby, John Christian; Buckley, Daniel H.

    2014-01-01

    We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm PMID:24501396

  3. Volcanic hazard in Mexico: a comprehensive on-line database for risk mitigation

    NASA Astrophysics Data System (ADS)

    Manea, Marina; Constantin Manea, Vlad; Capra, Lucia; Bonasia, Rosanna

    2013-04-01

    Researchers are currently working on several key aspects of the Mexican volcanoes, such as remote sensing, field data of old and recent volcaniclastic deposits, structural framework, monitoring (rainfall data and visual observation of lahars), and laboratory experiment (analogue models and numerical simulations - fall3D, titan2D). Each investigation is focused on specific processes, but it is fundamental to visualize the global status of the volcano in order to understand its behavior and to mitigate future hazards. The Mexican Volcanoes @nline represents a novel initiative aimed to collect, on a systematic basis, the complete set of data obtained so far on the volcanoes, and to continuously update the database with new data. All the information is compiled from published works and updated frequently. Maps, such as the geological map of the Mexican volcanos and the associated hazard zonation, as well as point data, such as stratigraphic sections, sedimentology and diagrams of rainfall intensities, are presented in Google Earth format in order to be easily accessed by the scientific community and the general public. An important section of this online database is the presentation of numerical simulations results for ash dispersion associated with the principal Mexican active volcanoes. Daily prediction of ash flow dispersion (based on real-time data from CENAPRED and the Mexican Meteorological Service), as well as large-scale high-resolution subduction simulations performed on HORUS (the Computational Geodynamics Laboratory's supercomputer) represent a central part of the Mexican Volcanos @nline database. The Mexican Volcanoes @nline database is maintained by the Computational Geodynamics Laboratory and it is based entirely on Open Source software. The website can be visited at: http://www.geociencias.unam.mx/mexican_volcanoes.

  4. HNOCDB: a comprehensive database of genes and miRNAs relevant to head and neck and oral cancer.

    PubMed

    Mitra, Sanga; Das, Smarajit; Das, Shaoli; Ghosal, Suman; Chakrabarti, Jayprokas

    2012-02-01

    In spite of the wide prevalence of head, neck and oral cancer, HNOC, there is no integrated database on genes and miRNAs associated with all the carcinoma subtypes of HNOC. The objective is to compile a multilayered and comprehensive database of HNOC as a user-friendly resource for researchers devising novel therapeutic strategies. We present HNOCDB, the head, neck and oral cancer database, with the following key features: (i) it tabulates all the different categories of HNOC separately under appropriate subtype-names, and then puts them together in a table headlined All; (ii) the oncogenes/oncomiRs that cause HNOC are listed; their mutations, methylations and polymorphisms loci are marked, and the variations in their expression profiles relative to the normal are recorded; (iii) HNOCDB contains a chromosomal map of HNOC genes and miRNA; (iv) contains references that experimentally validate the reason for the inclusion of the genes and the miRNAs in HNOCDB. HNOCDB is freely accessible for academic and non-profit users via http://gyanxet.com/hno.html. PMID:22024348

  5. GSE: A COMPREHENSIVE DATABASE SYSTEM FOR THE REPRESENTATION, RETRIEVAL, AND ANALYSIS OF MICROARRAY DATA

    PubMed Central

    Danford, Timothy; Rolfe, Alex; Gifford, David

    2009-01-01

    We present GSE, the Genomic Spatial Event database, a system to store, retrieve, and analyze all types of high-throughput microarray data. GSE handles expression datasets, ChIP-chip data, genomic annotations, functional annotations, the results of our previously published Joint Binding Deconvolution algorithm for ChIP-chip, and precomputed scans for binding events. GSE can manage data associated with multiple species; it can also simultaneously handle data associated with multiple ‘builds’ of the genome from a single species. The GSE system is built upon a middle software layer for representing streams of biological data; we outline this layer, called GSEBricks, and show how it is used to build an interactive visualization application for ChIP-chip data. The visualizer software is written in Java and communicates with the GSE database system over the network. We also present a system to formulate and record binding hypotheses- simple descriptions of the relationships that may hold between different ChIP-chip experiments. We provide a reference software implementation for the GSE system. PMID:18229714

  6. DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.

    PubMed

    Karyala, Prashanthi; Metri, Rahul; Bathula, Christopher; Yelamanchi, Syam K; Sahoo, Lipika; Arjunan, Selvam; Sastri, Narayan P; Chandra, Nagasuma

    2016-09-01

    Dengue virus (DENV) is a human pathogen and its etiology has been widely established. There are many interactions between DENV and human proteins that have been reported in literature. However, no publicly accessible resource for efficiently retrieving the information is yet available. In this study, we mined all publicly available dengue-human interactions that have been reported in the literature into a database called DenHunt. We retrieved 682 direct interactions of human proteins with dengue viral components, 382 indirect interactions and 4120 differentially expressed human genes in dengue infected cell lines and patients. We have illustrated the importance of DenHunt by mapping the dengue-human interactions on to the host interactome and observed that the virus targets multiple host functional complexes of important cellular processes such as metabolism, immune system and signaling pathways suggesting a potential role of these interactions in viral pathogenesis. We also observed that 7 percent of the dengue virus interacting human proteins are also associated with other infectious and non-infectious diseases. Finally, the understanding that comes from such analyses could be used to design better strategies to counteract the diseases caused by dengue virus. The whole dataset has been catalogued in a searchable database, called DenHunt (http://proline.biochem.iisc.ernet.in/DenHunt/). PMID:27618709

  7. GenoBase: comprehensive resource database of Escherichia coli K-12.

    PubMed

    Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G; Bochner, Barry R; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E; Tohsato, Yukako; Wanner, Barry L; Mori, Hirotada

    2015-01-01

    Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. PMID:25399415

  8. LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces.

    PubMed Central

    Dölz, R; Mossé, M O; Slonimski, P P; Bairoch, A; Linder, P

    1996-01-01

    We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. As in previous editions the genetic names are consistently associated to each sequence with a known and confirmed ORF. If necessary, synonyms are given in the case of allelic duplicated sequences. Although the first publication of a sequence gives-according to our rules-the genetic name of a gene, in some instances more commonly used names are given to avoid nomenclature problems and the use of ancient designations which are no longer used. In these cases the old designation is given as synonym. Thus sequences can be found either by the name or by synonyms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, SWISSPROT and EMBL accession numbers. New entries will also contain the name from the systematic sequencing efforts. Since the release of LISTA4.1 we update the database continuously. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. This release includes reports from full Smith and Watermann peptide-level searches against a non-redundant protein sequence database. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). The database is available by FTP and on World Wide Web. PMID:8594599

  9. MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data.

    PubMed

    Montague, Elizabeth; Stanberry, Larissa; Higdon, Roger; Janko, Imre; Lee, Elaine; Anderson, Nathaniel; Choiniere, John; Stewart, Elizabeth; Yandl, Gregory; Broomall, William; Kolker, Natali; Kolker, Eugene

    2014-06-01

    Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org ) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org ) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding. PMID:24910945

  10. Human Transporter Database: Comprehensive Knowledge and Discovery Tools in the Human Transporter Genes

    PubMed Central

    Ye, Adam Y.; Liu, Qing-Rong; Li, Chuan-Yun; Zhao, Min; Qu, Hong

    2014-01-01

    Transporters are essential in homeostatic exchange of endogenous and exogenous substances at the systematic, organic, cellular, and subcellular levels. Gene mutations of transporters are often related to pharmacogenetics traits. Recent developments in high throughput technologies on genomics, transcriptomics and proteomics allow in depth studies of transporter genes in normal cellular processes and diverse disease conditions. The flood of high throughput data have resulted in urgent need for an updated knowledgebase with curated, organized, and annotated human transporters in an easily accessible way. Using a pipeline with the combination of automated keywords query, sequence similarity search and manual curation on transporters, we collected 1,555 human non-redundant transporter genes to develop the Human Transporter Database (HTD) (http://htd.cbi.pku.edu.cn). Based on the extensive annotations, global properties of the transporter genes were illustrated, such as expression patterns and polymorphisms in relationships with their ligands. We noted that the human transporters were enriched in many fundamental biological processes such as oxidative phosphorylation and cardiac muscle contraction, and significantly associated with Mendelian and complex diseases such as epilepsy and sudden infant death syndrome. Overall, HTD provides a well-organized interface to facilitate research communities to search detailed molecular and genetic information of transporters for development of personalized medicine. PMID:24558441

  11. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    PubMed

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/. PMID:24489955

  12. TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice.

    PubMed

    Kawahara, Yoshihiro; Oono, Youko; Wakimoto, Hironobu; Ogata, Jun; Kanamori, Hiroyuki; Sasaki, Harumi; Mori, Satomi; Matsumoto, Takashi; Itoh, Takeshi

    2016-01-01

    Here we present TENOR (Transcriptome ENcyclopedia Of Rice, http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNA sequencing (mRNA-Seq) data obtained from rice under a wide variety of conditions. Since the elucidation of the ability of plants to adapt to various growing conditions is a key issue in plant sciences, it is of great interest to understand the regulatory networks of genes responsible for environmental changes. We used mRNA-Seq and performed a time-course transcriptome analysis of rice, Oryza sativa L. (cv. Nipponbare), under 10 abiotic stress conditions (high salinity; high and low phosphate; high, low and extremely low cadmium; drought; osmotic; cold; and flood) and two plant hormone treatment conditions (ABA and jasmonic acid). A large number of genes that were responsive to abiotic stresses and plant hormones were detected by differential expression analysis. Furthermore, several responsive genes were found to encode transcription factors that could control the transcriptional network of stress responses, but the timing of the induction of these genes was not uniform across conditions. A significant number of cis-regulatory elements were enriched in the promoter regions of the responsive genes and were shared among conditions. These data suggest that some key components of gene regulation networks are shared between different stress signaling pathways. All the resources (novel genes identified from mRNA-Seq data, expression profiles, co-expressed genes and cis-regulatory elements) can be searched for and are available in TENOR. PMID:26578693

  13. Deadlock detection and resolution in data-base management systems: A comprehensive approach

    SciTech Connect

    Park, Y.C.

    1989-01-01

    In this dissertation, several algorithms for deadlock detection and resolution in database management systems are presented, where two-phase locking -is assumed for ensuring serializability, the lock requests obey the granularity locking protocol and each granule may be locked in one of the following lock modes: IS, IX, S, SIX and X. For each object, lock requests are honored according to a first-come-first-served basis except for lock upgradations. The author presents algorithms for deadlock detection and resolution in sequential transaction processing to achieve the goal of early deadlock detection with the appropriate victim selection. He also presents a deadlock detection and resolution algorithm for parallel transaction processing which achieves the same objectives and an algorithm for distribute transaction processing which minimizes the amount of inter-site message communications. He proposes a new efficient algorithm for deadlock detection in sequential transaction processing, where the basic idea is the construction of a directed graph called a Holder/Walter-Transaction Waited-By Graph. He establishes guidelines for the identification of a victim in a deadlock cycle and show how deadlocks can be resolved with minimal victim cost. In addition, his algorithm allows us to resolve some deadlocks without aborting any transaction. In the case of parallel transaction processing, a transaction can have multiple outstanding lock requests. He introduces two types of deadlocks: explicit deadlocks and implicit deadlocks. To detect deadlocks in this environment, he introduces a new type of directed graph called a transaction waited-by graph. He presents deadlock detection mechanisms, identify deadlock detection time, and show how victims can be selected with minimal cost.

  14. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

    PubMed Central

    Monzon, Alexander Miguel; Rohr, Cristian Oscar; Fornasari, María Silvina; Parisi, Gustavo

    2016-01-01

    CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL: http://ufq.unq.edu.ar/codnas PMID:27022160

  15. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.

    PubMed

    Monzon, Alexander Miguel; Rohr, Cristian Oscar; Fornasari, María Silvina; Parisi, Gustavo

    2016-01-01

    CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL:http://ufq.unq.edu.ar/codnas. PMID:27022160

  16. Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.

    PubMed

    McIntyre, K M; Setzkorn, C; Wardeh, M; Hepworth, P J; Radford, A D; Baylis, M

    2014-10-01

    What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus

  17. MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases.

    PubMed

    Rappaport, Noa; Twik, Michal; Nativ, Noam; Stelzer, Gil; Bahir, Iris; Stein, Tsippi Iny; Safran, Marilyn; Lancet, Doron

    2014-01-01

    Systems medicine provides insights into mechanisms of human diseases, and expedites the development of better diagnostics and drugs. To facilitate such strategies, we initiated MalaCards, a compendium of human diseases and their annotations, integrating and often remodeling information from 64 data sources. MalaCards employs, among others, the proven automatic data-mining strategies established in the construction of GeneCards, our widely used compendium of human genes. The development of MalaCards poses many algorithmic challenges, such as disease name unification, integrated classification, gene-disease association, and disease-targeted expression analysis. MalaCards displays a Web card for each of >19,000 human diseases, with 17 sections, including textual summaries, related diseases, related genes, genetic variations and tests, and relevant publications. Also included are a powerful search engine and a variety of categorized disease lists. This unit describes two basic protocols to search and browse MalaCards effectively. PMID:25199789

  18. LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces.

    PubMed Central

    Dölz, R; Mossé, M O; Slonimski, P P; Bairoch, A; Linder, P

    1994-01-01

    We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. In this database each sequence has been attributed a single genetic name. In the case of duplicated sequences a simple method has been applied to distinguish between sequences of one and the same gene from non-allelic sequences of duplicated genes. If necessary, synonyms are given in the case of allelic duplicated sequences. Thus sequences can be found either by the name or by synonyms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, Swissprot and EMBL accession numbers. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). PMID:7937046

  19. Increasing resource allocation and research into tobacco control activities: a comprehensive approach including primary prevention, treatment and brief intervention.

    PubMed

    Richmond, R

    1993-01-01

    The range of tobacco control activities should be viewed as essential parts of a complex multi-component puzzle. Intervention strategies designed to address tobacco control should be comprehensive and include both primary and secondary prevention activities and be multi-faceted and capable of bringing about change at both the individual and broader social and cultural levels. In this paper I argue for a mutually inclusive framework in which the various components contribute in important and different ways. I examine the prevalence of smoking and identify the high risk groups, then I examine the range of available strategies and present the evidence for their success. I discuss the primary prevention approaches such as warning labels, taxes, price increases, workplace bans, education in schools, mass media and self-help materials, as well as brief interventions and treatment strategies which are conducted at the worksite, general practice and specialized cessation clinics. The areas for future research are delineated for increased resource allocation and include: the best ways to disseminate brief interventions to smokers, methods to motivate smokers; training of health professionals to deliver brief interventions; enhancing quitting and access to existing treatment resources among specific disadvantaged minority groups, e.g. migrants, unemployed youth, the effect on smoking prevalence of warning labels on cigarette packets and price rises on cigarettes. PMID:16818330

  20. The Antimicrobial Index: a comprehensive literature-based antimicrobial database and reference work

    PubMed Central

    Amirkia, Vafa David; Qiubao, Pan

    2011-01-01

    Although the ever-growing usage of antimicrobials in the fields of medicine, pharmacology, and microbiology have undoubtedly allowed for unprecedented advances in the scientific world, these advances are nevertheless accompanied by unprecedented challenges. Sharp increases in antibiotic usages have led to inefficient and wasteful usage practices. Bacterial resistances have dramatically increased and therefore hindered the effectiveness of traditional antibiotics, thus forcing many life-science professionals to turn to plant extracts and synthetic chemicals [1]. The Antimicrobial Index (TAMI) seeks to alleviate some of these mounting difficulties through the collection and centralization of relevant antimicrobial susceptibility data from journals. Data compiled for antimicrobials include: method of action, physical properties, resistance genes, side effects, and minimal inhibitory concentrations (MIC50, MIC90 and/or ranges). TAMI currently contains data on 960 antimicrobials and over 24,000 microorganisms (3,500 unique strains) which were collected from over 400 pieces of published literature. Volume and scope of the index have been and will continue to increase and it is hoped that such an index will further foster international cooperation and communication of antimicrobial-related knowledge. TAMI can be accessed at: http://antibiotics.toku-e.com/. PMID:21383924

  1. Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB▿

    PubMed Central

    Woo, Patrick C. Y.; Teng, Jade L. L.; Yeung, Juilian M. Y.; Tse, Herman; Lau, Susanna K. P.; Yuen, Kwok-Yung

    2011-01-01

    Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (http://147.8.74.24/16SpathDB) based on the 16S rRNA gene sequences of all medically important bacteria listed in the Manual of Clinical Microbiology and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the “best match in 16SpathDB.” For the isolate (Gordonibacter pamelaeae) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the Manual of Clinical Microbiology. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories. PMID:21389154

  2. Fatal toxicity index of medicinal drugs based on a comprehensive toxicology database.

    PubMed

    Ojanperä, Ilkka; Kriikku, Pirkko; Vuori, Erkki

    2016-09-01

    The fatal toxicity index (FTI) is the absolute number of fatal poisonings caused by a particular drug divided by its consumption figure. Consequently, it is a useful measure in evaluating toxicity of the drug and its relevance in fatal poisonings. In this study, we assessed the FTI of medicinal drugs in 3 years (2005, 2009, and 2013) in Finland. As the measure of drug consumption, we used the number of defined daily doses (DDD) per population in each year. There were 70 medicinal drugs in Finland for which the mean FTI expressed as the number of deaths per million DDD over the three study years was higher or equal to 0.1. The Anatomical Therapeutic Chemical (ATC) classification system was used for the classification of the active ingredients of medicinal drugs according to the organ or system which they act on. Of these 70 drugs, 55 drugs (78.6 %) acted on the nervous system (denoted by ATC code N), 11 (15.7 %) on the cardiovascular system (C), three (4.3 %) on the alimentary tract and metabolism (A), and one (1.4 %) on the musculoskeletal system (M). The nervous system drugs consisted of 20 psycholeptics, (ATC code N05), 20 psychoanaleptics (N06), eight analgesics (N02), six antiepileptics (N03), and one other nervous system drug (N07). The highest individual FTIs were associated with the opioids methadone, dextropropoxyphene, oxycodone, tramadol, and morphine; the antipsychotics levomepromazine and chlorprothixene; and the antidepressants doxepin, amitriptyline, trimipramine, and bupropion. Buprenorphine was not included in the study, because most of the fatal buprenorphine poisonings were due to smuggled tablets. A clearly increasing trend in FTI was observed with pregabalin and possibly with bupropion, both drugs emerging as abused substances. PMID:26987318

  3. Comprehensive mollusk acute toxicity database improves the use of Interspecies Correlation Estimation (ICE) models to predict toxicity of untested freshwater and endangered mussel species

    EPA Science Inventory

    Interspecies correlation estimation (ICE) models extrapolate acute toxicity data from surrogate test species to untested taxa. A suite of ICE models developed from a comprehensive database is available on the US Environmental Protection Agency’s web-based application, Web-I...

  4. SUPERSITES INTEGRATED RELATIONAL DATABASE (SIRD)

    EPA Science Inventory

    As part of EPA's Particulate Matter (PM) Supersites Program (Program), the University of Maryland designed and developed the Supersites Integrated Relational Database (SIRD). Measurement data in SIRD include comprehensive air quality data from the 7 Supersite program locations f...

  5. Potash: a global overview of evaporate-related potash resources, including spatial databases of deposits, occurrences, and permissive tracts: Chapter S in Global mineral resource assessment

    USGS Publications Warehouse

    Orris, Greta J.; Cocker, Mark D.; Dunlap, Pamela; Wynn, Jeff C.; Spanski, Gregory T.; Briggs, Deborah A.; Gass, Leila; Bliss, James D.; Bolm, Karen S.; Yang, Chao; Lipin, Bruce R.; Ludington, Stephen; Miller, Robert J.; Slowakiewicz, Miroslaw

    2014-01-01

    This report describes a global, evaporite-related potash deposits and occurrences database and a potash tracts database. Chapter 1 summarizes potash resource history and use. Chapter 2 describes a global potash deposits and occurrences database, which contains more than 900 site records. Chapter 3 describes a potash tracts database, which contains 84 tracts with geology permissive for the presence of evaporite-hosted potash resources, including areas with active evaporite-related potash production, areas with known mineralization that has not been quantified or exploited, and areas with potential for undiscovered potash resources. Chapter 4 describes geographic information system (GIS) data files that include (1) potash deposits and occurrences data, (2) potash tract data, (3) reference databases for potash deposit and tract data, and (4) representative graphics of geologic features related to potash tracts and deposits. Summary descriptive models for stratabound potash-bearing salt and halokinetic potash-bearing salt are included in appendixes A and B, respectively. A glossary of salt- and potash-related terms is contained in appendix C and a list of database abbreviations is given in appendix D. Appendix E describes GIS data files, and appendix F is a guide to using the geodatabase.

  6. Including Emotional and Behavioural Difficulties Pupils in a Mainstream Comprehensive: A Study of the Behaviour of Pupils and Classes

    ERIC Educational Resources Information Center

    Swinson, Jeremy; Woof, Catherine; Melling, Richard

    2003-01-01

    A group of twelve pupils from an emotional and behavioural difficulties (EBD) school were transferred to a mainstream comprehensive school. They were supported by a specialist teacher and two Educational Support Assistants. The behaviour of the pupils was monitored. The behaviour of the EBD pupils was found to be very similar to that of the other…

  7. Spanish public awareness regarding DNA profile databases in forensic genetics: what type of DNA profiles should be included?

    PubMed Central

    Gamero, Joaquín J; Romero, Jose‐Luis; Peralta, Juan‐Luis; Carvalho, Mónica; Corte‐Real, Francisco

    2007-01-01

    The importance of non‐codifying DNA polymorphism for the administration of justice is now well known. In Spain, however, this type of test has given rise to questions in recent years: (a) Should consent be obtained before biological samples are taken from an individual for DNA analysis? (b) Does society perceive these techniques and methods of analysis as being reliable? (c) There appears to be lack of knowledge concerning the basic norms that regulate databases containing private or personal information and the protection that information of this type must be given. This opinion survey and the subsequent analysis of the results in ethical terms may serve to reveal the criteria and the degree of information that society has with regard to DNA databases. In the study, 73.20% (SE 1.12%) of the population surveyed was in favour of specific legislation for computer files in which DNA analysis results for forensic purposes are stored. PMID:17906059

  8. Alaska Geochemical Database, Version 2.0 (AGDB2)--including “best value” data compilations for rock, sediment, soil, mineral, and concentrate sample media

    USGS Publications Warehouse

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

    2013-01-01

    The Alaska Geochemical Database Version 2.0 (AGDB2) contains new geochemical data compilations in which each geologic material sample has one “best value” determination for each analyzed species, greatly improving speed and efficiency of use. Like the Alaska Geochemical Database (AGDB, http://pubs.usgs.gov/ds/637/) before it, the AGDB2 was created and designed to compile and integrate geochemical data from Alaska in order to facilitate geologic mapping, petrologic studies, mineral resource assessments, definition of geochemical baseline values and statistics, environmental impact assessments, and studies in medical geology. This relational database, created from the Alaska Geochemical Database (AGDB) that was released in 2011, serves as a data archive in support of present and future Alaskan geologic and geochemical projects, and contains data tables in several different formats describing historical and new quantitative and qualitative geochemical analyses. The analytical results were determined by 85 laboratory and field analytical methods on 264,095 rock, sediment, soil, mineral and heavy-mineral concentrate samples. Most samples were collected by U.S. Geological Survey personnel and analyzed in U.S. Geological Survey laboratories or, under contracts, in commercial analytical laboratories. These data represent analyses of samples collected as part of various U.S. Geological Survey programs and projects from 1962 through 2009. In addition, mineralogical data from 18,138 nonmagnetic heavy-mineral concentrate samples are included in this database. The AGDB2 includes historical geochemical data originally archived in the U.S. Geological Survey Rock Analysis Storage System (RASS) database, used from the mid-1960s through the late 1980s and the U.S. Geological Survey PLUTO database used from the mid-1970s through the mid-1990s. All of these data are currently maintained in the National Geochemical Database (NGDB). Retrievals from the NGDB were used to generate

  9. Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

    PubMed

    Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

    2016-08-01

    Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. PMID:27318307

  10. Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease.

    PubMed

    Holtman, Inge R; Noback, Michiel; Bijlsma, Marieke; Duong, Kim N; van der Geest, Marije A; Ketelaars, Peer T; Brouwer, Nieske; Vainchtein, Ilia D; Eggen, Bart J L; Boddeke, Hendrikus W G M

    2015-09-01

    Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via www.goad.education. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology. PMID:25808223

  11. New Comprehensive Cytogenetic Scoring System for Primary Myelodysplastic Syndromes (MDS) and Oligoblastic Acute Myeloid Leukemia After MDS Derived From an International Database Merge

    PubMed Central

    Schanz, Julie; Tüchler, Heinz; Solé, Francesc; Mallo, Mar; Luño, Elisa; Cervera, José; Granada, Isabel; Hildebrandt, Barbara; Slovak, Marilyn L.; Ohyashiki, Kazuma; Steidl, Christian; Fonatsch, Christa; Pfeilstöcker, Michael; Nösslinger, Thomas; Valent, Peter; Giagounidis, Aristoteles; Aul, Carlo; Lübbert, Michael; Stauder, Reinhard; Krieger, Otto; Garcia-Manero, Guillermo; Faderl, Stefan; Pierce, Sherry; Le Beau, Michelle M.; Bennett, John M.; Greenberg, Peter; Germing, Ulrich; Haase, Detlef

    2012-01-01

    Purpose The karyotype is a strong independent prognostic factor in myelodysplastic syndromes (MDS). Since the implementation of the International Prognostic Scoring System (IPSS) in 1997, knowledge concerning the prognostic impact of abnormalities has increased substantially. The present study proposes a new and comprehensive cytogenetic scoring system based on an international data collection of 2,902 patients. Patients and Methods Patients were included from the German-Austrian MDS Study Group (n = 1,193), the International MDS Risk Analysis Workshop (n = 816), the Spanish Hematological Cytogenetics Working Group (n = 849), and the International Working Group on MDS Cytogenetics (n = 44) databases. Patients with primary MDS and oligoblastic acute myeloid leukemia (AML) after MDS treated with supportive care only were evaluated for overall survival (OS) and AML evolution. Internal validation by bootstrap analysis and external validation in an independent patient cohort were performed to confirm the results. Results In total, 19 cytogenetic categories were defined, providing clear prognostic classification in 91% of all patients. The abnormalities were classified into five prognostic subgroups (P < .001): very good (median OS, 61 months; hazard ratio [HR], 0.5; n = 81); good (49 months; HR, 1.0 [reference category]; n = 1,809); intermediate (26 months; HR, 1.6; n = 529); poor (16 months; HR, 2.6; n = 148); and very poor (6 months; HR, 4.2; n = 187). The internal and external validations confirmed the results of the score. Conclusion In conclusion, these data should contribute to the ongoing efforts to update the IPSS by refining the cytogenetic risk categories. PMID:22331955

  12. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency

    PubMed Central

    Rubinstein, Wendy S.; Maglott, Donna R.; Lee, Jennifer M.; Kattman, Brandi L.; Malheiro, Adriana J.; Ovetsky, Michael; Hem, Vichet; Gorelenkov, Viatcheslav; Song, Guangfeng; Wallin, Craig; Husain, Nora; Chitipiralla, Shanmuga; Katz, Kenneth S.; Hoffman, Douglas; Jang, Wonhee; Johnson, Mark; Karmanov, Fedor; Ukrainchik, Alexander; Denisenko, Mikhail; Fomous, Cathy; Hudson, Kathy; Ostell, James M.

    2013-01-01

    The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information’s databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html). PMID:23193275

  13. Project Jukebox: "We Are Digitizing Our Oral History Collection...and We're Including a Database."

    ERIC Educational Resources Information Center

    Smith, Steve

    Project Jukebox is an enterprise of the Rasmuson Library at the University of Alaska. The project aims to digitize 6,000 hours of oral history. The special oral collection of the history of Alaska includes audiotapes of major and minor politicians in the state, average citizens, and Native leaders. The audiotapes created problems for guaranteeing…

  14. Isotopic reconstruction of ancient human migrations: A comprehensive Sr isotope reference database for France and the first case study at Tumulus de Sables, south-western France

    NASA Astrophysics Data System (ADS)

    Willmes, M.; Boel, C.; Grün, R.; Armstrong, R.; Chancerel, A.; Maureille, B.; Courtaud, P.

    2012-04-01

    Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further

  15. MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

    PubMed Central

    Montague, Elizabeth; Stanberry, Larissa; Higdon, Roger; Janko, Imre; Lee, Elaine; Anderson, Nathaniel; Choiniere, John; Stewart, Elizabeth; Yandl, Gregory; Broomall, William; Kolker, Natali

    2014-01-01

    Abstract Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding. PMID:24910945

  16. A Comprehensive Software and Database Management System for Glomerular Filtration Rate Estimation by Radionuclide Plasma Sampling and Serum Creatinine Methods

    PubMed Central

    Jha, Ashish Kumar

    2015-01-01

    Glomerular filtration rate (GFR) estimation by plasma sampling method is considered as the gold standard. However, this method is not widely used because the complex technique and cumbersome calculations coupled with the lack of availability of user-friendly software. The routinely used Serum Creatinine method (SrCrM) of GFR estimation also requires the use of online calculators which cannot be used without internet access. We have developed user-friendly software “GFR estimation software” which gives the options to estimate GFR by plasma sampling method as well as SrCrM. We have used Microsoft Windows® as operating system and Visual Basic 6.0 as the front end and Microsoft Access® as database tool to develop this software. We have used Russell's formula for GFR calculation by plasma sampling method. GFR calculations using serum creatinine have been done using MIRD, Cockcroft-Gault method, Schwartz method, and Counahan-Barratt methods. The developed software is performing mathematical calculations correctly and is user-friendly. This software also enables storage and easy retrieval of the raw data, patient's information and calculated GFR for further processing and comparison. This is user-friendly software to calculate the GFR by various plasma sampling method and blood parameter. This software is also a good system for storing the raw and processed data for future analysis. PMID:26097422

  17. CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae

    PubMed Central

    Koh, Judice L. Y.; Chong, Yolanda T.; Friesen, Helena; Moses, Alan; Boone, Charles; Andrews, Brenda J.; Moffat, Jason

    2015-01-01

    Changes in protein subcellular localization and abundance are central to biological regulation in eukaryotic cells. Quantitative measures of protein dynamics in vivo are therefore highly useful for elucidating specific regulatory pathways. Using a combinatorial approach of yeast synthetic genetic array technology, high-content screening, and machine learning classifiers, we developed an automated platform to characterize protein localization and abundance patterns from images of log phase cells from the open-reading frame−green fluorescent protein collection in the budding yeast, Saccharomyces cerevisiae. For each protein, we produced quantitative profiles of localization scores for 16 subcellular compartments at single-cell resolution to trace proteome-wide relocalization in conditions over time. We generated a collection of ∼300,000 micrographs, comprising more than 20 million cells and ∼9 billion quantitative measurements. The images depict the localization and abundance dynamics of more than 4000 proteins under two chemical treatments and in a selected mutant background. Here, we describe CYCLoPs (Collection of Yeast Cells Localization Patterns), a web database resource that provides a central platform for housing and analyzing our yeast proteome dynamics datasets at the single cell level. CYCLoPs version 1.0 is available at http://cyclops.ccbr.utoronto.ca. CYCLoPs will provide a valuable resource for the yeast and eukaryotic cell biology communities and will be updated as new experiments become available. PMID:26048563

  18. The CEBAF Element Database and Related Operational Software

    SciTech Connect

    Larrieu, Theodore; Slominski, Christopher; Keesee, Marie; Turner, Dennison; Joyce, Michele

    2015-09-01

    The newly commissioned 12GeV CEBAF accelerator relies on a flexible, scalable and comprehensive database to define the accelerator. This database delivers the configuration for CEBAF operational tools, including hardware checkout, the downloadable optics model, control screens, and much more. The presentation will describe the flexible design of the CEBAF Element Database (CED), its features and assorted use case examples.

  19. Nuclear Science References Database

    SciTech Connect

    Pritychenko, B.; Běták, E.; Singh, B.; Totans, J.

    2014-06-15

    The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energy Agency (http://www-nds.iaea.org/nsr)

  20. Color Comprehension and Color Categories among Blind Students: A Multi-Sensory Approach in Implementing Concrete Language to Include All Students in Advanced Writing Classes

    ERIC Educational Resources Information Center

    Antarasena, Salinee

    2009-01-01

    This study investigates teaching methods regarding color comprehension and color categorization among blind students, as compared to their non-blind peers and whether they understand and represent the same color comprehension and color categories. Then after digit codes for color comprehension teaching and assistive technology for the blind had…

  1. The formation and design of the 'Acute Admission Database'- a database including a prospective, observational cohort of 6279 patients triaged in the emergency department in a larger Danish hospital

    PubMed Central

    2012-01-01

    Background Management and care of the acutely ill patient has improved over the last years due to introduction of systematic assessment and accelerated treatment protocols. We have, however, sparse knowledge of the association between patient status at admission to hospital and patient outcome. A likely explanation is the difficulty in retrieving all relevant information from one database. The objective of this article was 1) to describe the formation and design of the 'Acute Admission Database', and 2) to characterize the cohort included. Methods All adult patients triaged at the Emergency Department at Hillerød Hospital and admitted either to the observationary unit or to a general ward in-hospital were prospectively included during a period of 22 weeks. The triage system used was a Danish adaptation of the Swedish triage system, ADAPT. Data from 3 different data sources was merged using a unique identifier, the Central Personal Registry number; 1) Data from patient admission; time and date, vital signs, presenting complaint and triage category, 2) Blood sample results taken at admission, including a venous acid-base status, and 3) Outcome measures, e.g. length of stay, admission to Intensive Care Unit, and mortality within 7 and 28 days after admission. Results In primary triage, patients were categorized as red (4.4%), orange (25.2%), yellow (38.7%) and green (31.7%). Abnormal vital signs were present at admission in 25% of the patients, most often temperature (10.5%), saturation of peripheral oxygen (9.2%), Glasgow Coma Score (6.6%) and respiratory rate (4.8%). A venous acid-base status was obtained in 43% of all patients. The majority (78%) had a pH within the normal range (7.35-7.45), 15% had acidosis (pH < 7.35) and 7% had alkalosis (pH > 7.45). Median length of stay was 2 days (range 1-123). The proportion of patients admitted to Intensive Care Unit was 1.6% (95% CI 1.2-2.0), 1.8% (95% CI 1.5-2.2) died within 7 days, and 4.2% (95% CI 3.7-4.7) died within

  2. Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration

    PubMed Central

    Duda, Stephany N; Farr, Amanda M; Lindegren, Mary Lou; Blevins, Meridith; Wester, C William; Wools-Kaloustian, Kara; Ekouevi, Didier K; Egger, Matthias; Hemingway-Foday, Jennifer; Cooper, David A; Moore, Richard D; McGowan, Catherine C; Nash, Denis

    2014-01-01

    Introduction HIV care and treatment programmes worldwide are transforming as they push to deliver universal access to essential prevention, care and treatment services to persons living with HIV and their communities. The characteristics and capacity of these HIV programmes affect patient outcomes and quality of care. Despite the importance of ensuring optimal outcomes, few studies have addressed the capacity of HIV programmes to deliver comprehensive care. We sought to describe such capacity in HIV programmes in seven regions worldwide. Methods Staff from 128 sites in 41 countries participating in the International epidemiologic Databases to Evaluate AIDS completed a site survey from 2009 to 2010, including sites in the Asia-Pacific region (n=20), Latin America and the Caribbean (n=7), North America (n=7), Central Africa (n=12), East Africa (n=51), Southern Africa (n=16) and West Africa (n=15). We computed a measure of the comprehensiveness of care based on seven World Health Organization-recommended essential HIV services. Results Most sites reported serving urban (61%; region range (rr): 33–100%) and both adult and paediatric populations (77%; rr: 29–96%). Only 45% of HIV clinics that reported treating children had paediatricians on staff. As for the seven essential services, survey respondents reported that CD4+ cell count testing was available to all but one site, while tuberculosis (TB) screening and community outreach services were available in 80 and 72%, respectively. The remaining four essential services – nutritional support (82%), combination antiretroviral therapy adherence support (88%), prevention of mother-to-child transmission (PMTCT) (94%) and other prevention and clinical management services (97%) – were uniformly available. Approximately half (46%) of sites reported offering all seven services. Newer sites and sites in settings with low rankings on the UN Human Development Index (HDI), especially those in the President's Emergency Plan

  3. Electronic Databases.

    ERIC Educational Resources Information Center

    Williams, Martha E.

    1985-01-01

    Presents examples of bibliographic, full-text, and numeric databases. Also discusses how to access these databases online, aids to online retrieval, and several issues and trends (including copyright and downloading, transborder data flow, use of optical disc/videodisc technology, and changing roles in database generation and processing). (JN)

  4. THE ECOTOX DATABASE

    EPA Science Inventory

    The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

  5. The Gaia Parameter Database

    NASA Astrophysics Data System (ADS)

    de Bruijne, J. H. J.; Lammers, U.; Perryman, M. A. C.

    2005-01-01

    The parallel development of many aspects of a complex mission like Gaia, which includes numerous participants in ESA, industrial companies, and a large and active scientific collaboration throughout Europe, makes keeping track of the many design changes, instrument and operational complexities, and numerical values for the data analysis a very challenging problem. A comprehensive, easily-accessible, up-to-date, and definitive compilation of a large range of numerical quantities is required, and the Gaia parameter database has been established to satisfy these needs. The database is a centralised repository containing, besides mathematical, physical, and astronomical constants, many satellite and subsystem design parameters. At the end of 2004, more than 1600 parameters had been included. Version control has been implemented, providing, next to a `live' version with the most recent parameters, well-defined reference versions of the full database contents. The database can be queried or browsed using a regular Web browser (http://www.rssd.esa.int/Gaia/paramdb). Query results are formated by default in HTML. Data can also be retrieved as Fortran-77, Fortran-90, Java, ANSIC, C++, or XML structures for direct inclusion into software codes in these languages. The idea is that all collaborating scientists can use the database parameters and values, once retrieved, directly linked to computational routines. An off-line access mode is also available, enabling users to automatically download the contents of the database. The database will be maintained actively, and significant extensions of the contents are planned. Consistent use in the future of the database by the Gaia community at large, including all industrial teams, will ensure correct numerical values throughout the complex software systems being built up as details of the Gaia design develop. The database is already being used for the telemetry simulation chain in ESTEC, and in the data simulations for GDAAS2.

  6. The Comprehensive, Powerful, Academic Database (CPAD): An Evaluative Study of a Predictive Tool Designed for Elementary School Personnel in Identifying At-Risk Students through Progress, Curriculum, and Performance Monitoring

    ERIC Educational Resources Information Center

    Chavez-Gibson, Sarah

    2013-01-01

    The purpose of this study is to exam in-depth, the Comprehensive, Powerful, Academic Database (CPAD), a data decision-making tool that determines and identifies students at-risk of dropping out of school, and how the CPAD assists administrators and teachers at an elementary campus to monitor progress, curriculum, and performance to improve student…

  7. Comprehensive analysis of ß-lactam antibiotics including penicillins, cephalosporins, and carbapenems in poultry muscle using liquid chromatography coupled to tandem mass spectrometry.

    PubMed

    Berendsen, Bjorn J A; Gerritsen, Henk W; Wegh, Robin S; Lameris, Steven; van Sebille, Ralph; Stolker, Alida A M; Nielen, Michel W F

    2013-09-01

    A comprehensive method for the quantitative residue analysis of trace levels of 22 ß-lactam antibiotics, including penicillins, cephalosporins, and carbapenems, in poultry muscle by liquid chromatography in combination with tandem mass spectrometric detection is reported. The samples analyzed for ß-lactam residues are hydrolyzed using piperidine in order to improve compound stability and to include the total residue content of the cephalosporin ceftifour. The reaction procedure was optimized using a full experimental design. Following detailed isotope labeling, tandem mass spectrometry studies and exact mass measurements using high-resolution mass spectrometry reaction schemes could be proposed for all ß-lactams studied. The main reaction occurring is the hydrolysis of the ß-lactam ring under formation of the piperidine substituted amide. For some ß-lactams, multiple isobaric hydrolysis reaction products are obtained, in accordance with expectations, but this did not hamper quantitative analysis. The final method was fully validated as a quantitative confirmatory residue analysis method according to Commission Decision 2002/657/EC and showed satisfactory quantitative performance for all compounds with trueness between 80 and 110% and within-laboratory reproducibility below 22% at target level, except for biapenem. For biapenem, the method proved to be suitable for qualitative analysis only. PMID:23430185

  8. Caenorhabditis elegans par2.1/mtssb-1 is essential for mitochondrial DNA replication and its defect causes comprehensive transcriptional alterations including a hypoxia response

    SciTech Connect

    Sugimoto, Tomoko; Mori, Chihiro; Takanami, Takako; Sasagawa, Yohei; Saito, Rumiko; Ichiishi, Eiichiro; Higashitani, Atsushi

    2008-01-01

    DNA polymerase {gamma} and mtSSB are key components of the mtDNA replication machinery. To study the biological influences of defects in mtDNA replication, we used RNAi to deplete the gene for a putative mtSSB, par2.1, in Caenorhabditis elegans. In previous systematic RNAi screens, downregulation of this gene has not caused any clearly defective phenotypes. Here, we continuously fed a dsRNA targeting par2.1 to C. elegans over generations. Seventy-nine percent of F1 progeny produced 60-72 h after feeding grew to adulthood but were completely sterile, with an arrest of germline cell proliferation. Analyses of mtDNA copy number and cell cytology indicated that the sterile hermaphrodites had fewer mitochondria. These results indicated that par2.1 essentially functions for germline cell proliferation through mtDNA replication; we therefore termed it mtssb-1. Comprehensive transcriptional alterations including hypoxia response induction dependent on and independent of hif-1 function, occurred by RNAi depletion of mtssb-1. Treatment with ethidium bromide, which impairs mtDNA replication and transcription, caused similar transcriptional alterations. In addition, the frequency of apoptosis in the germline cells was reduced in fertile progeny with a partial RNAi effect. These suggest that RNAi depletion of C. elegans mtssb-1 is useful as a model system of mitochondrial dysfunction.

  9. Marine and Hydrokinetic Technology Database

    DOE Data Explorer

    DOE’s Marine and Hydrokinetic Technology Database provides up-to-date information on marine and hydrokinetic renewable energy, both in the U.S. and around the world. The database includes wave, tidal, current, and ocean thermal energy, and contains information on the various energy conversion technologies, companies active in the field, and development of projects in the water. Depending on the needs of the user, the database can present a snapshot of projects in a given region, assess the progress of a certain technology type, or provide a comprehensive view of the entire marine and hydrokinetic energy industry. Results are displayed as a list of technologies, companies, or projects. Data can be filtered by a number of criteria, including country/region, technology type, generation capacity, and technology or project stage. The database was updated in 2009 to include ocean thermal energy technologies, companies, and projects.

  10. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  11. Leading-edge forensic DNA analyses and the necessity of including crime scene investigators, police officers and technicians in a DNA elimination database.

    PubMed

    Lapointe, Martine; Rogic, Anita; Bourgoin, Sarah; Jolicoeur, Christine; Séguin, Diane

    2015-11-01

    In recent years, sophisticated technology has significantly increased the sensitivity and analytical power of genetic analyses so that very little starting material may now produce viable genetic profiles. This sensitivity however, has also increased the risk of detecting unknown genetic profiles assumed to be that of the perpetrator, yet originate from extraneous sources such as from crime scene workers. These contaminants may mislead investigations, keeping criminal cases active and unresolved for long spans of time. Voluntary submission of DNA samples from crime scene workers is fairly low, therefore we have created a promotional method for our staff elimination database that has resulted in a significant increase in voluntary samples since 2011. Our database enforces privacy safeguards and allows for optional anonymity to all staff members. We also offer information sessions at various police precincts to advise crime scene workers of the importance and success of our staff elimination database. This study, a pioneer in its field, has obtained 327 voluntary submissions from crime scene workers to date, of which 46 individual profiles (14%) have been matched to 58 criminal cases. By implementing our methods and respect for individual privacy, forensic laboratories everywhere may see similar growth and success in explaining unidentified genetic profiles in stagnate criminal cases. PMID:26117338

  12. Aviation Safety Issues Database

    NASA Technical Reports Server (NTRS)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

  13. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  14. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

    PubMed

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. PMID:27242033

  15. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

    PubMed Central

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species. Database URL: http://geve.med.u-tokai.ac.jp PMID:27242033

  16. Development of a Clinically Comprehensive Database and a Simple Procedure for Identification of Molds from Solid Media by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

    PubMed Central

    Drake, Steven K.; Calhoun, Leslie B.; Henderson, Christina M.; Zelazny, Adrian M.

    2013-01-01

    Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the rapid and highly accurate identification of clinical pathogens but has not been utilized extensively in clinical mycology due to challenges in developing an effective protein extraction method and the limited databases available. Here, we developed an alternate extraction procedure and constructed a highly stringent database comprising 294 individual isolates representing 76 genera and 152 species. To our knowledge, this is the most comprehensive clinically relevant mold database developed to date. When challenged with 421 blinded clinical isolates from our institution, by use of the BioTyper software, accurate species-level (score of ≥2.0) and genus-level (score of ≥1.7) identifications were obtained for 370 (88.9%) and 18 (4.3%) isolates, respectively. No isolates were misidentified. Of the 33 isolates (7.8%) for which there was no identification (score of <1.7), 25 were basidiomycetes not associated with clinical disease and 8 were Penicillium species that were not represented in the database. Our library clearly outperformed the manufacturer's database that was obtained with the instrument, which identified only 3 (0.7%) and 26 (6.2%) isolates at species and genus levels, respectively. Identification was not affected by different culture conditions. Implementation into our routine workflow has revolutionized our mycology laboratory efficiency, with improved accuracy and decreased time for mold identification, eliminating reliance on traditional phenotypic features. PMID:23269728

  17. Overlap in Bibliographic Databases.

    ERIC Educational Resources Information Center

    Hood, William W.; Wilson, Concepcion S.

    2003-01-01

    Examines the topic of Fuzzy Set Theory to determine the overlap of coverage in bibliographic databases. Highlights include examples of comparisons of database coverage; frequency distribution of the degree of overlap; records with maximum overlap; records unique to one database; intra-database duplicates; and overlap in the top ten databases.…

  18. SEISMIC-REFLECTOR DATABASE SOFTWARE.

    USGS Publications Warehouse

    Wright, Evelyn L.; Hosom, John-Paul

    1986-01-01

    The seismic data analysis (SDA) software system facilitates generation of marine seismic reflector databases composed of reflector depths, travel times, root-mean-square and interval velocities, geographic coordinates, and identifying information. System processes include digitizing of seismic profiles and velocity semblance curves, merging of velocity and navigation data with profile travel-time data, calculation of reflector depths in meters, profile and map graphic displays, data editing and smoothing, and entry of finalized data into a comprehensive database. An overview of concepts, file structures, and programs is presented.

  19. Database Marketplace 2002: The Database Universe.

    ERIC Educational Resources Information Center

    Tenopir, Carol; Baker, Gayle; Robinson, William

    2002-01-01

    Reviews the database industry over the past year, including new companies and services, company closures, popular database formats, popular access methods, and changes in existing products and services. Lists 33 firms and their database services; 33 firms and their database products; and 61 company profiles. (LRW)

  20. CottonDB: Cotton Genome Database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CottonDB (www.cottondb.org) is the first and most comprehensive source of cotton genome information. CottonDB is maintained at the Southern Plains Agricultural Research Center in College Station, TX. The project includes a website and database creating a repository of information for over 355,000 ...

  1. Managing Rock and Paleomagnetic Data Flow with the MagIC Database: from Measurement and Analysis to Comprehensive Archive and Visualization

    NASA Astrophysics Data System (ADS)

    Koppers, A. A.; Minnett, R. C.; Tauxe, L.; Constable, C.; Donadini, F.

    2008-12-01

    The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by rock and paleomagnetic data. The goal of MagIC is to archive all measurements and derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Organizing data for presentation in peer-reviewed publications or for ingestion into databases is a time-consuming task, and to facilitate these activities, three tightly integrated tools have been developed: MagIC-PY, the MagIC Console Software, and the MagIC Online Database. A suite of Python scripts is available to help users port their data into the MagIC data format. They allow the user to add important metadata, perform basic interpretations, and average results at the specimen, sample and site levels. These scripts have been validated for use as Open Source software under the UNIX, Linux, PC and Macintosh© operating systems. We have also developed the MagIC Console Software program to assist in collating rock and paleomagnetic data for upload to the MagIC database. The program runs in Microsoft Excel© on both Macintosh© computers and PCs. It performs routine consistency checks on data entries, and assists users in preparing data for uploading into the online MagIC database. The MagIC website is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual FlashMap interface to browse and select locations. Users can also browse the database by data type (inclination, intensity, VGP, hysteresis, susceptibility) or by data compilation to view all contributions associated with previous databases, such as PINT, GMPDB or TAFI or other user

  2. Tautomerism in large databases

    PubMed Central

    Sitzmann, Markus; Ihlenfeldt, Wolf-Dietrich

    2010-01-01

    We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis was carried out using calculable chemical structure identifiers developed by the NCI CADD Group, based on hash codes available in the chemoinformatics toolkit CACTVS and a newly developed scoring scheme to define a canonical tautomer for any encountered structure. CACTVS’s tautomerism definition, a set of 21 transform rules expressed in SMIRKS line notation, was used, which takes a comprehensive stance as to the possible types of tautomeric interconversion included. Tautomerism was found to be possible for more than 2/3 of the unique structures in the CSDB. A total of 680 million tautomers were calculated from, and including, the original structure records. Tautomerism overlap within the same individual database (i.e. at least one other entry was present that was really only a different tautomeric representation of the same compound) was found at an average rate of 0.3% of the original structure records, with values as high as nearly 2% for some of the databases in CSDB. Projected onto the set of unique structures (by FICuS identifier), this still occurred in about 1.5% of the cases. Tautomeric overlap across all constituent databases in CSDB was found for nearly 10% of the records in the collection. PMID:20512400

  3. Geminivirus database (GVDB): first database of family Geminiviridae and its genera Begomovirus.

    PubMed

    Prajapat, Rajneesh; Marwal, Avinash; Shaikh, Zuber; Gaur, Rajarshi Kumar

    2012-07-15

    Geminivirus Database (GVDB) is an online interactive database of Geminiviridae family. GVDB comprises of partial and complete nucleotide sequences along with duly annotated expressed genes of isolated Begomovirus species. The in silico homology modeling, docking and recombination results obtained for different begomoviral sequences are also mentioned. This database is endowed with comprehensive information about Geminivirus members which grounds infection in various plants species in India assorting from crops, ornamentals plants and common weeds. The home page of this database offers various links associated with current research projects and also the publications related to molecular and in silico study of Begomovirus infection. The main feature of GVDB includes flexible database designs based on platform of PHP allows easy retrieval of the information. The database is made available at www.wikigeminivirus.org. PMID:24171254

  4. National Vulnerability Database (NVD)

    National Institute of Standards and Technology Data Gateway

    National Vulnerability Database (NVD) (Web, free access)   NVD is a comprehensive cyber security vulnerability database that integrates all publicly available U.S. Government vulnerability resources and provides references to industry resources. It is based on and synchronized with the CVE vulnerability naming standard.

  5. Solubility Database

    National Institute of Standards and Technology Data Gateway

    SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

  6. DMTB: the magnetotactic bacteria database

    NASA Astrophysics Data System (ADS)

    Pan, Y.; Lin, W.

    2012-12-01

    Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

  7. Databases: Beyond the Basics.

    ERIC Educational Resources Information Center

    Whittaker, Robert

    This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

  8. YMDB: the Yeast Metabolome Database.

    PubMed

    Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S

    2012-01-01

    The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

  9. ECMDB: the E. coli Metabolome Database.

    PubMed

    Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S

    2013-01-01

    The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry. PMID:23109553

  10. HMDB: the Human Metabolome Database

    PubMed Central

    Wishart, David S.; Tzur, Dan; Knox, Craig; Eisner, Roman; Guo, An Chi; Young, Nelson; Cheng, Dean; Jewell, Kevin; Arndt, David; Sawhney, Summit; Fung, Chris; Nikolai, Lisa; Lewis, Mike; Coutouly, Marie-Aude; Forsythe, Ian; Tang, Peter; Shrivastava, Savita; Jeroncic, Kevin; Stothard, Paul; Amegbey, Godwin; Block, David; Hau, David. D.; Wagner, James; Miniaci, Jessica; Clements, Melisa; Gebremedhin, Mulu; Guo, Natalie; Zhang, Ying; Duggan, Gavin E.; MacInnis, Glen D.; Weljie, Alim M.; Dowlatabadi, Reza; Bamforth, Fiona; Clive, Derrick; Greiner, Russ; Li, Liang; Marrie, Tom; Sykes, Brian D.; Vogel, Hans J.; Querengesser, Lori

    2007-01-01

    The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: PMID:17202168

  11. HMDB: the Human Metabolome Database.

    PubMed

    Wishart, David S; Tzur, Dan; Knox, Craig; Eisner, Roman; Guo, An Chi; Young, Nelson; Cheng, Dean; Jewell, Kevin; Arndt, David; Sawhney, Summit; Fung, Chris; Nikolai, Lisa; Lewis, Mike; Coutouly, Marie-Aude; Forsythe, Ian; Tang, Peter; Shrivastava, Savita; Jeroncic, Kevin; Stothard, Paul; Amegbey, Godwin; Block, David; Hau, David D; Wagner, James; Miniaci, Jessica; Clements, Melisa; Gebremedhin, Mulu; Guo, Natalie; Zhang, Ying; Duggan, Gavin E; Macinnis, Glen D; Weljie, Alim M; Dowlatabadi, Reza; Bamforth, Fiona; Clive, Derrick; Greiner, Russ; Li, Liang; Marrie, Tom; Sykes, Brian D; Vogel, Hans J; Querengesser, Lori

    2007-01-01

    The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca. PMID:17202168

  12. A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel ITIM protein

    PubMed Central

    Senis, Yotis A.; Tomlinson, Michael G.; García, Ángel; Dumon, Stephanie; Heath, Victoria L.; Herbert, John; Cobbold, Stephen P.; Spalton, Jennifer C.; Ayman, Sinem; Antrobus, Robin; Zitzmann, Nicole; Bicknell, Roy; Frampton, Jon; Authi, Kalwant; Martin, Ashley; Wakelam, Michael J.O.; Watson, Stephen P.

    2007-01-01

    Summary The platelet surface is poorly characterized due to the low abundance of many membrane proteins and the lack of specialist tools for their investigation. In this study we have identified novel human platelet and mouse megakaryocyte membrane proteins using specialist proteomic and genomic approaches. Three separate methods were used to enrich platelet surface proteins prior to identification by liquid chromatography and tandem mass spectrometry: lectin affinity chromatography; biotin/NeutrAvidin affinity chromatography; and free flow electrophoresis. Many known, abundant platelet surface transmembrane proteins and several novel proteins were identified using each receptor enrichment strategy. In total, two or more unique peptides were identified for 46, 68 and 22 surface membrane, intracellular membrane and membrane proteins of unknown sub-cellular localization, respectively. The majority of these were single transmembrane proteins. To complement the proteomic studies, we analysed the transcriptome of a highly purified preparation of mature primary mouse megakaryocytes using serial analysis of gene expression in view of the increasing importance of mutant mouse models in establishing protein function in platelets. This approach identified all of the major classes of platelet transmembrane receptors, including multi-transmembrane proteins. Strikingly, 17 of the 25 most megakaryocyte-specific genes (relative to 30 other SAGE libraries) were transmembrane proteins, illustrating the unique nature of the megakaryocyte/platelet surface. The list of novel plasma membrane proteins identified using proteomics includes the immunoglobulin superfamily member G6b, which undergoes extensive alternate splicing. Specific antibodies were used to demonstrate expression of the G6b-B isoform, which contains an immunoreceptor tyrosine-based inhibition motif. G6b-B undergoes tyrosine phosphorylation and association with the SH2-containing phosphatase, SHP-1, in stimulated

  13. The EXOSAT database system. Available databases.

    NASA Astrophysics Data System (ADS)

    Barron, C.

    1991-02-01

    This User's Guide describes the databases that are currently available by remote login to the EXOSAT/ESTEC site of the EXOSAT database system. This includes where ever possible the following: brief descriptions of each observatory, telescope and instrument references to more complete observatory descriptions a list of the contents of each database and how it was generated, parameter descriptions.

  14. Trace elements in sediments, blue spotted tilapia Oreochromis leucostictus (Trewavas, 1933) and its parasite Contracaecum multipapillatum from Lake Naivasha, Kenya, including a comprehensive health risk analysis.

    PubMed

    Otachi, Elick O; Körner, Wilfried; Avenant-Oldewage, Annemariè; Fellner-Frank, Christine; Jirsa, Franz

    2014-06-01

    This study presents the distribution of 15 major and trace elements in sediments and fish and their pericardial parasites from Lake Naivasha, Kenya. The lake is one of the few freshwater lakes in the Great Rift Valley and is under strong anthropogenic pressure mainly due to agricultural activities. Its fish provide a valuable protein source for approximately 100,000 people in the area. Fish and their parasites have been acknowledged as indicators of environmental quality due to their accumulation potential for both essential and nonessential trace elements. A total of 34 specimens of the blue spotted tilapia Oreochromis leucostictus and pooled samples of their pericardial parasite, the anisakid nematode Contracaecum multipapillatum (larvae 3), were examined. Element concentrations were determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and graphite furnace atomic absorption spectrometry (GF-AAS). The concentrations of elements in the sediments reflected the geology of the area and did not point to pollution: none of the investigated trace elements, including Pb, Cd, Cu, and Zn, showed elevated values. In contrast, concentrations in the fish muscle were elevated for Li, Sr, Cd, and Zn, with high target hazard quotients (THQ > 0.1) indicating a potential health risk to the consumers of this fish. Fish liver showed significantly higher concentrations of the trace elements Fe, Mn, Cd, and Cu compared to the muscle and C. multipapillatum. In the parasite, Zn had the highest concentration, but the worms only minimally accumulated trace elements in relation to their fish host. PMID:24573461

  15. Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

    PubMed Central

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

  16. Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis.

    PubMed

    Sharma, Om Prakash; Kumar, Muthuvel Suresh

    2016-01-01

    Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in. PMID:26806463

  17. Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase-a comprehensive drug target database for Lymphatic filariasis

    PubMed Central

    Sharma, Om Prakash; Kumar, Muthuvel Suresh

    2016-01-01

    Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in. PMID:26806463

  18. A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD.

    PubMed

    Hendrich, Lars; Morinière, Jérôme; Haszprunar, Gerhard; Hebert, Paul D N; Hausmann, Axel; Köhler, Frank; Balke, Michael

    2015-07-01

    Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters. PMID:25469559

  19. Building a Comprehensive Mill-Level Database for the Industrial Sectors Integrated Solutions (ISIS) Model of the U.S. Pulp and Paper Sector

    PubMed Central

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector. PMID:25806516

  20. Building a comprehensive mill-level database for the Industrial Sectors Integrated Solutions (ISIS) model of the U.S. pulp and paper sector.

    PubMed

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector. PMID:25806516

  1. The Transporter Classification Database (TCDB): recent advances

    PubMed Central

    Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V.; Ahmed, Muhammad Saad; Li, Chun; Moreno-Hagelsieb, Gabriel

    2016-01-01

    The Transporter Classification Database (TCDB; http://www.tcdb.org) is a freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness. Here we present a comprehensive update of the database contents and features and summarize recent discoveries recorded in TCDB. PMID:26546518

  2. The PIR-International Protein Sequence Database.

    PubMed

    George, D G; Barker, W C; Mewes, H W; Pfeiffer, F; Tsugita, A

    1996-01-01

    From its origin the Protein Sequence Database has been designed to support research and has focused on comprehensive coverage, quality control and organization of the data in accordance with biological principles. Since 1988 the database has been maintained collaboratively within the framework of PIR-International, an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. The database is widely distributed and is available on the World Wide Web, via ftp, email server, on CD-ROM and magnetic media. It is widely redistributed and incorporated into many other protein sequence data compilations, including SWISS-PROT and the Entrez system of the NCBI. PMID:8594572

  3. Comprehension of Connected Discourse.

    ERIC Educational Resources Information Center

    Mosberg, Ludwig; Shima, Fred

    A rationale was developed for researching reading comprehension based on information gain. Previous definitions of comprehension which were reviewed included operational vs. nonoperational and skills vs. processes. Comprehension was viewed as an informational processing event which includes a constellation of cognitive and learning processes. Two…

  4. Plant and Crop Databases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Databases have become an integral part of all aspects of biological research, including basic and applied plant biology. The importance of databases continues to increase as the volume of data from direct and indirect genomics approaches expands. What is not always obvious to users of databases is t...

  5. Aero/fluids database system

    NASA Technical Reports Server (NTRS)

    Reardon, John E.; Violett, Duane L., Jr.

    1991-01-01

    The AFAS Database System was developed to provide the basic structure of a comprehensive database system for the Marshall Space Flight Center (MSFC) Structures and Dynamics Laboratory Aerophysics Division. The system is intended to handle all of the Aerophysics Division Test Facilities as well as data from other sources. The system was written for the DEC VAX family of computers in FORTRAN-77 and utilizes the VMS indexed file system and screen management routines. Various aspects of the system are covered, including a description of the user interface, lists of all code structure elements, descriptions of the file structures, a description of the security system operation, a detailed description of the data retrieval tasks, a description of the session log, and a description of the archival system.

  6. BIAdb: A curated database of benzylisoquinoline alkaloids

    PubMed Central

    2010-01-01

    Background Benzylisoquinoline is the structural backbone of many alkaloids with a wide variety of structures including papaverine, noscapine, codeine, morphine, apomorphine, berberine, protopine and tubocurarine. Many benzylisoquinoline alkaloids have been reported to show therapeutic properties and to act as novel medicines. Thus it is important to collect and compile benzylisoquinoline alkaloids in order to explore their usage in medicine. Description We extract information about benzylisoquinoline alkaloids from various sources like PubChem, KEGG, KNApSAcK and manual curation from literature. This information was processed and compiled in order to create a comprehensive database of benzylisoquinoline alkaloids, called BIAdb. The current version of BIAdb contains information about 846 unique benzylisoquinoline alkaloids, with multiple entries in term of source, function leads to total number of 2504 records. One of the major features of this database is that it provides data about 627 different plant species as a source of benzylisoquinoline and 114 different types of function performed by these compounds. A large number of online tools have been integrated, which facilitate user in exploring full potential of BIAdb. In order to provide additional information, we give external links to other resources/databases. One of the important features of this database is that it is tightly integrated with Drugpedia, which allows managing data in fixed/flexible format. Conclusions A database of benzylisoquinoline compounds has been created, which provides comprehensive information about benzylisoquinoline alkaloids. This database will be very useful for those who are working in the field of drug discovery based on natural products. This database will also serve researchers working in the field of synthetic biology, as developing medicinally important alkaloids using synthetic process are one of important challenges. This database is available from http

  7. Protein sequence databases.

    PubMed

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium. PMID:15036160

  8. A snapshot in time - the new TRUplanner database

    SciTech Connect

    Estill, Wesley Gordon; Crawford, Beverly; Van Soest, Greg

    2010-01-01

    A new database was developed to augment transuranic (TRU) waste inventory information already captured within the Comprehensive Inventory Database (CID). This new database, known as the TRUplanner, includes information focused on site capability for TRU waste certification and availability to ship to either the Waste Isolation Pilot Plant (WIPP) or Idaho National Laboratory for final characterization and certification before coming to WIPP. Waste stream specific data is imported from the CID to the TRUplanner, and additional data is collected and entered as a result of interviews and site visits. This data is continuously updated as sites are visited.

  9. Inorganic Materials Database for Exploring the Nature of Material

    NASA Astrophysics Data System (ADS)

    Xu, Yibin; Yamazaki, Masayoshi; Villars, Pierre

    2011-11-01

    An inorganic materials database system, AtomWork, has been developed and released on the Internet. It includes the phase diagram, crystal structure, X-ray powder diffraction, and property data of more than 80,000 inorganic materials extracted from scientific literature. The feature of this database is that the information of the synthesis, identification, and property of materials is organically linked, which enables the data reported in different papers to be grouped and compared at four different levels: chemical system, compound, substance, and material. The database can provide users with a comprehensive overview of substances and necessary information to understand the relationships among chemical component, structure, and property.

  10. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

    SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

  11. Central Asia Active Fault Database

    NASA Astrophysics Data System (ADS)

    Mohadjer, Solmaz; Ehlers, Todd A.; Kakar, Najibullah

    2014-05-01

    The ongoing collision of the Indian subcontinent with Asia controls active tectonics and seismicity in Central Asia. This motion is accommodated by faults that have historically caused devastating earthquakes and continue to pose serious threats to the population at risk. Despite international and regional efforts to assess seismic hazards in Central Asia, little attention has been given to development of a comprehensive database for active faults in the region. To address this issue and to better understand the distribution and level of seismic hazard in Central Asia, we are developing a publically available database for active faults of Central Asia (including but not limited to Afghanistan, Tajikistan, Kyrgyzstan, northern Pakistan and western China) using ArcGIS. The database is designed to allow users to store, map and query important fault parameters such as fault location, displacement history, rate of movement, and other data relevant to seismic hazard studies including fault trench locations, geochronology constraints, and seismic studies. Data sources integrated into the database include previously published maps and scientific investigations as well as strain rate measurements and historic and recent seismicity. In addition, high resolution Quickbird, Spot, and Aster imagery are used for selected features to locate and measure offset of landforms associated with Quaternary faulting. These features are individually digitized and linked to attribute tables that provide a description for each feature. Preliminary observations include inconsistent and sometimes inaccurate information for faults documented in different studies. For example, the Darvaz-Karakul fault which roughly defines the western margin of the Pamir, has been mapped with differences in location of up to 12 kilometers. The sense of motion for this fault ranges from unknown to thrust and strike-slip in three different studies despite documented left-lateral displacements of Holocene and late

  12. Common hyperspectral image database design

    NASA Astrophysics Data System (ADS)

    Tian, Lixun; Liao, Ningfang; Chai, Ali

    2009-11-01

    This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

  13. Human protein reference database--2006 update.

    PubMed

    Mishra, Gopa R; Suresh, M; Kumaran, K; Kannabiran, N; Suresh, Shubha; Bala, P; Shivakumar, K; Anuradha, N; Reddy, Raghunath; Raghavan, T Madhan; Menon, Shalini; Hanumanthu, G; Gupta, Malvika; Upendran, Sapna; Gupta, Shweta; Mahesh, M; Jacob, Bincy; Mathew, Pinky; Chatterjee, Pritam; Arun, K S; Sharma, Salil; Chandrika, K N; Deshpande, Nandan; Palvankar, Kshitish; Raghavnath, R; Krishnakanth, R; Karathia, Hiren; Rekha, B; Nayak, Rashmi; Vishnupriya, G; Kumar, H G Mohan; Nagini, M; Kumar, G S Sameer; Jose, Rojan; Deepthi, P; Mohan, S Sujatha; Gandhi, T K B; Harsha, H C; Deshpande, Krishna S; Sarker, Malabika; Prasad, T S Keshava; Pandey, Akhilesh

    2006-01-01

    Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein-protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (http://www.genprot.org), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data. PMID:16381900

  14. Navigating Public Microarray Databases

    PubMed Central

    Bähler, Jürg

    2004-01-01

    With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources. PMID:18629145

  15. Navigating public microarray databases.

    PubMed

    Penkett, Christopher J; Bähler, Jürg

    2004-01-01

    With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources. PMID:18629145

  16. Geologic map and map database of northeastern San Francisco Bay region, California, [including] most of Solano County and parts of Napa, Marin, Contra Costa, San Joaquin, Sacramento, Yolo, and Sonoma Counties

    USGS Publications Warehouse

    Graymer, Russell Walter; Jones, David Lawrence; Brabb, Earl E.

    2002-01-01

    This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (nesfmf.ps, nesfmf.pdf, nesfmf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller.

  17. RNAcentral: A vision for an international database of RNA sequences.

    PubMed

    Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A; Bujnicki, Janusz M; Cochrane, Guy; Cole, James R; Dinger, Marcel E; Enright, Anton J; Gardner, Paul P; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H; Huang, Hsien-Da; Kelly, Krystyna A; Kersey, Paul; Kozomara, Ana; Lowe, Todd M; Marz, Manja; Moxon, Simon; Pruitt, Kim D; Samuelsson, Tore; Stadler, Peter F; Vilella, Albert J; Vogel, Jan-Hinnerk; Williams, Kelly P; Wright, Mathew W; Zwieb, Christian

    2011-11-01

    During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

  18. RNAcentral: A vision for an international database of RNA sequences

    PubMed Central

    Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian

    2011-01-01

    During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

  19. TRIP Database: a manually curated database of protein–protein interactions for mammalian TRP channels

    PubMed Central

    Shin, Young-Cheul; Shin, Soo-Yong; So, Insuk; Kwon, Dongseop; Jeon, Ju-Hong

    2011-01-01

    Transient receptor potential (TRP) channels are a superfamily of Ca2+-permeable cation channels that translate cellular stimuli into electrochemical signals. Aberrant activity of TRP channels has been implicated in a variety of human diseases, such as neurological disorders, cardiovascular disease and cancer. To facilitate the understanding of the molecular network by which TRP channels are associated with biological and disease processes, we have developed the TRIP (TRansient receptor potential channel-Interacting Protein) Database (http://www.trpchannel.org), a manually curated database that aims to offer comprehensive information on protein–protein interactions (PPIs) of mammalian TRP channels. The TRIP Database was created by systematically curating 277 peer-reviewed literature; the current version documents 490 PPI pairs, 28 TRP channels and 297 cellular proteins. The TRIP Database provides a detailed summary of PPI data that fit into four categories: screening, validation, characterization and functional consequence. Users can find in-depth information specified in the literature on relevant analytical methods and experimental resources, such as gene constructs and cell/tissue types. The TRIP Database has user-friendly web interfaces with helpful features, including a search engine, an interaction map and a function for cross-referencing useful external databases. Our TRIP Database will provide a valuable tool to assist in understanding the molecular regulatory network of TRP channels. PMID:20851834

  20. Biofuel Database

    National Institute of Standards and Technology Data Gateway

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  1. DPTEdb, an integrative database of transposable elements in dioecious plants

    PubMed Central

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants. Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php PMID:27173524

  2. DPTEdb, an integrative database of transposable elements in dioecious plants.

    PubMed

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php. PMID:27173524

  3. Database Administrator

    ERIC Educational Resources Information Center

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  4. 2010 Worldwide Gasification Database

    DOE Data Explorer

    The 2010 Worldwide Gasification Database describes the current world gasification industry and identifies near-term planned capacity additions. The database lists gasification projects and includes information (e.g., plant location, number and type of gasifiers, syngas capacity, feedstock, and products). The database reveals that the worldwide gasification capacity has continued to grow for the past several decades and is now at 70,817 megawatts thermal (MWth) of syngas output at 144 operating plants with a total of 412 gasifiers.

  5. Advanced transportation system studies. Alternate propulsion subsystem concepts: Propulsion database

    NASA Technical Reports Server (NTRS)

    Levack, Daniel

    1993-01-01

    The Advanced Transportation System Studies alternate propulsion subsystem concepts propulsion database interim report is presented. The objective of the database development task is to produce a propulsion database which is easy to use and modify while also being comprehensive in the level of detail available. The database is to be available on the Macintosh computer system. The task is to extend across all three years of the contract. Consequently, a significant fraction of the effort in this first year of the task was devoted to the development of the database structure to ensure a robust base for the following years' efforts. Nonetheless, significant point design propulsion system descriptions and parametric models were also produced. Each of the two propulsion databases, parametric propulsion database and propulsion system database, are described. The descriptions include a user's guide to each code, write-ups for models used, and sample output. The parametric database has models for LOX/H2 and LOX/RP liquid engines, solid rocket boosters using three different propellants, a hybrid rocket booster, and a NERVA derived nuclear thermal rocket engine.

  6. Advanced transportation system studies. Alternate propulsion subsystem concepts: Propulsion database

    NASA Astrophysics Data System (ADS)

    Levack, Daniel

    1993-04-01

    The Advanced Transportation System Studies alternate propulsion subsystem concepts propulsion database interim report is presented. The objective of the database development task is to produce a propulsion database which is easy to use and modify while also being comprehensive in the level of detail available. The database is to be available on the Macintosh computer system. The task is to extend across all three years of the contract. Consequently, a significant fraction of the effort in this first year of the task was devoted to the development of the database structure to ensure a robust base for the following years' efforts. Nonetheless, significant point design propulsion system descriptions and parametric models were also produced. Each of the two propulsion databases, parametric propulsion database and propulsion system database, are described. The descriptions include a user's guide to each code, write-ups for models used, and sample output. The parametric database has models for LOX/H2 and LOX/RP liquid engines, solid rocket boosters using three different propellants, a hybrid rocket booster, and a NERVA derived nuclear thermal rocket engine.

  7. Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses.

    PubMed

    Park, Heejin; Bae, Junwoo; Kim, Hyunwoo; Kim, Sangok; Kim, Hokeun; Mun, Dong-Gi; Joh, Yoonsung; Lee, Wonyeop; Chae, Sehyun; Lee, Sanghyuk; Kim, Hark Kyun; Hwang, Daehee; Lee, Sang-Won; Paek, Eunok

    2014-12-01

    In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variants--single nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target-decoy setting. Our method searches the unified database once, but performs target-decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide-spectrum matches. PMID:25316439

  8. Backing up DMF Databases

    NASA Technical Reports Server (NTRS)

    Cardo, Nicholas P.; Woodrow, Thomas (Technical Monitor)

    1994-01-01

    A complete backup of the Cray Data Migration Facility (DMF) databases should include the data migration databases, all media specific process' (MSP's) databases, and the journal file. The backup should be able to accomplished without impacting users or stopping DMF. The High Speed Processors group at the Numerical Aerodynamics Simulation (NAS) Facility at NASA Ames Research Center undertook the task of finding an effective and efficient way to backup all DMF databases. This has been accomplished by taking advantage of new features introduced in DMF 2.0 and adding a minor modification to the dmdaemon. This paper discusses the investigation and the changes necessary to implement these enhancements.

  9. Dictionary as Database.

    ERIC Educational Resources Information Center

    Painter, Derrick

    1996-01-01

    Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

  10. A Quality System Database

    NASA Technical Reports Server (NTRS)

    Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

    2010-01-01

    A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

  11. Specialist Bibliographic Databases.

    PubMed

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

    2016-05-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  12. Specialist Bibliographic Databases

    PubMed Central

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  13. Immunome database for marsupials and monotremes

    PubMed Central

    2011-01-01

    Background To understand the evolutionary origins of our own immune system, we need to characterise the immune system of our distant relatives, the marsupials and monotremes. The recent sequencing of the genomes of two marsupials (opossum and tammar wallaby) and a monotreme (platypus) provides an opportunity to characterise the immune gene repertoires of these model organisms. This was required as many genes involved in immunity evolve rapidly and fail to be detected by automated gene annotation pipelines. Description We have developed a database of immune genes from the tammar wallaby, red-necked wallaby, northern brown bandicoot, brush-tail possum, opossum, echidna and platypus. The resource contains 2,235 newly identified sequences and 3,197 sequences which had been described previously. This comprehensive dataset was built from a variety of sources, including EST projects and expert-curated gene predictions generated through a variety of methods including chained-BLAST and sensitive HMMER searches. To facilitate systems-based research we have grouped sequences based on broad Gene Ontology categories as well as by specific functional immune groups. Sequences can be extracted by keyword, gene name, protein domain and organism name. Users can also search the database using BLAST. Conclusion The Immunome Database for Marsupials and Monotremes (IDMM) is a comprehensive database of all known marsupial and monotreme immune genes. It provides a single point of reference for genomic and transcriptomic datasets. Data from other marsupial and monotreme species will be added to the database as it become available. This resource will be utilized by marsupial and monotreme immunologists as well as researchers interested in the evolution of mammalian immunity. PMID:21854560

  14. Statistical databases

    SciTech Connect

    Kogalovskii, M.R.

    1995-03-01

    This paper presents a review of problems related to statistical database systems, which are wide-spread in various fields of activity. Statistical databases (SDB) are referred to as databases that consist of data and are used for statistical analysis. Topics under consideration are: SDB peculiarities, properties of data models adequate for SDB requirements, metadata functions, null-value problems, SDB compromise protection problems, stored data compression techniques, and statistical data representation means. Also examined is whether the present Database Management Systems (DBMS) satisfy the SDB requirements. Some actual research directions in SDB systems are considered.

  15. NEUSE RIVER WATER QUALITY DATABASE

    EPA Science Inventory

    The Neuse River water quality database is a Microsoft Access application that includes multiple data tables and some associated queries. The database was developed by Prof. Jim Bowen's research group.

  16. HCSD: the human cancer secretome database

    PubMed Central

    Feizi, Amir; Banaei-Esfahani, Amir; Nielsen, Jens

    2015-01-01

    The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology. The secreted proteins from cancer cells are believed to play a deterministic role in cancer progression and therefore may be the key to find novel therapeutic targets and biomarkers for many cancers. Consequently, huge data on cancer secretome have been generated in recent years and the lack of a coherent database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer types. It has a simple and user friendly query system for basic and advanced search based on gene name, cancer type and data type as the three main query options. The results are visualized in an explicit and interactive manner. An example of a result page includes annotations, cross references, cancer secretome data and secretory features for each identified protein. Database URL: www.cancersecretome.org. PMID:26078477

  17. GMDD: a database of GMO detection methods

    PubMed Central

    Dong, Wei; Yang, Litao; Shen, Kailin; Kim, Banghyun; Kleter, Gijs A; Marvin, Hans JP; Guo, Rong; Liang, Wanqi; Zhang, Dabing

    2008-01-01

    Background Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of GMO labelling regulations. Protein and nucleic acid-based detection techniques have been developed and utilized for GMOs identification and quantification. However, the information for harmonization and standardization of GMO analysis methods at global level is needed. Results GMO Detection method Database (GMDD) has collected almost all the previous developed and reported GMOs detection methods, which have been grouped by different strategies (screen-, gene-, construct-, and event-specific), and also provide a user-friendly search service of the detection methods by GMO event name, exogenous gene, or protein information, etc. In this database, users can obtain the sequences of exogenous integration, which will facilitate PCR primers and probes design. Also the information on endogenous genes, certified reference materials, reference molecules, and the validation status of developed methods is included in this database. Furthermore, registered users can also submit new detection methods and sequences to this database, and the newly submitted information will be released soon after being checked. Conclusion GMDD contains comprehensive information of GMO detection methods. The database will make the GMOs analysis much easier. PMID:18522755

  18. The Autoimmune Disease Database: a dynamically compiled literature-derived database

    PubMed Central

    Karopka, Thomas; Fluck, Juliane; Mevissen, Heinz-Theodor; Glass, Änne

    2006-01-01

    Background Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, are classified as autoimmune diseases. Although their etiology is unclear these diseases share certain similarities at the molecular level i.e. susceptibility regions on the chromosomes or the involvement of common genes. To gain an overview of these related diseases it is not feasible to do a literary review but it requires methods of automated analyses of the more than 500,000 Medline documents related to autoimmune disorders. Results In this paper we present the first version of the Autoimmune Disease Database which to our knowledge is the first comprehensive literature-based database covering all known or suspected autoimmune diseases. This dynamically compiled database allows researchers to link autoimmune diseases to the candidate genes or proteins through the use of named entity recognition which identifies genes/proteins in the corresponding Medline abstracts. The Autoimmune Disease Database covers 103 autoimmune disease concepts. This list was expanded to include synonyms and spelling variants yielding a list of over 1,200 disease names. The current version of the database provides links to 541,690 abstracts and over 5,000 unique genes/proteins. Conclusion The Autoimmune Disease Database provides the researcher with a tool to navigate potential gene-disease relationships in Medline abstracts in the context of autoimmune diseases. PMID:16803617

  19. Cascadia Tsunami Deposit Database

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

    2003-01-01

    The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

  20. DRAG: a database for recognition and analasys of gait

    NASA Astrophysics Data System (ADS)

    Kuchi, Prem; Hiremagalur, Raghu Ram V.; Huang, Helen; Carhart, Michael; He, Jiping; Panchanathan, Sethuraman

    2003-11-01

    A novel approach is proposed for creating a standardized and comprehensive database for gait analysis. The field of gait analysis is gaining increasing attention for applications such as visual surveillance, human-computer interfaces, and gait recognition and rehabilitation. Numerous algorithms have been developed for analyzing and processing gait data; however, a standard database for their systematic evaluation does not exist. Instead, existing gait databases consist of subsets of kinematic, kinetic, and electromyographic activity recordings by different investigators, at separate laboratories, and under varying conditions. Thus, the existing databases are neither homogenous nor sufficiently populated to statistically validate the algorithms. In this paper, a methodology for creating a database is presented, which can be used as a common ground to test the performance of algorithms that rely upon external marker data, ground reaction loading data, and/or video images. The database consists of: (1) synchronized motion-capture data (3D marker data) obtained using external markers, (2) computed joint angles, and (3) ground reaction loading acquired with plantar pressure insoles. This database could be easily expanded to include synchronized video, which will facilitate further development of video-based algorithms for motion tracking. This eventually could lead to the realization of markerless gait tracking. Such a system would have extensive applications in gait recognition, as well as gait rehabilitation. The entire database (marker, angle, and force data) will be placed in the public domain, and made available for downloads over the World Wide Web.

  1. Database Manager

    ERIC Educational Resources Information Center

    Martin, Andrew

    2010-01-01

    It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

  2. Maize databases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

  3. Comprehensive Planning.

    ERIC Educational Resources Information Center

    Pavlenko, Victor V.

    Comprehensive planning, defined as the work of those who engage in efforts, within a delimited geographic area, to identify and order the physical, social, and economic relationships of that area, is discussed in the four sections of this paper. Section I, Introduction, describes what "planning" and "comprehensive planning" are. In Section II, Why…

  4. NCCDPHP PUBLICATION DATABASE

    EPA Science Inventory

    This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

  5. Who's Gonna Pay the Piper for Free Online Databases?

    ERIC Educational Resources Information Center

    Jacso, Peter

    1996-01-01

    Discusses new pricing models for some online services and considers the possibilities for the traditional online database market. Topics include multimedia music databases, including copyright implications; other retail-oriented databases; and paying for free databases with advertising. (LRW)

  6. Integration of test methodology, material database, and material selection/deselection strategies for a chemical-material compatibility database system

    SciTech Connect

    Shuely, W.J.

    1995-12-31

    The effect of chemical exposure on the degradation of material properties is important to material evaluation and selection for both commercial and military products. Described here are a set of enhancements to a traditional chemical-material compatibility database that were required to support the early selection of chemically resistant materials in a concurrent engineering environment. This initial phase in the development of an integrated chemical-material compatibility system included: organization of tests into a comprehensive scheme, test selection for the initial screening tests in the scheme, the increased standardization of test procedures and reports required to support database queries, and the control of data set flow from the test laboratory directly to the database. Emphasized here is the design of modular database files based on material, chemical, and test specification descriptors that are indexed to the resulting test properties database module. ASTM Committee E49 formats were employed where available. The polymeric material documentation has been implemented by development of a menu-driven laboratory database version of ASTM Guide for the Identification of Polymers (Excludes Thermoset Elastomers) in Computerized Material Property Databases (E 1308-92). Examples are provided from the screening test found in the initial section of the test method scheme. One is able to execute a rapid paperless transfer of predictive and experimental screening results to the chemical-material compatibility database, query the results to eliminate a substantial fraction of materials and rank a more limited set of candidate materials to provide a useful ``deselection`` capability.

  7. Phase Equilibria Diagrams Database

    National Institute of Standards and Technology Data Gateway

    SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase)   The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.

  8. Version 3 of the GEOMAGIA50 Paleomagnetic Database

    NASA Astrophysics Data System (ADS)

    Brown, M. C.; Donadini, F.; Nilsson, A.; Korte, M. C.; Panovska, S.; Frank, U.; Korhonen, K.; Lodge, A.; Lengyel, S. N.; Schuberth, M.; Constable, C.

    2015-12-01

    Version 3 of GEOMAGIA50 is the product of an international collaboration to develop a comprehensive online database that allows easy access to published paleomagnetic and chronological data from the past 50 ka. The overarching scientific goal is to improve our understanding of changes in the geomagnetic field, with applications ranging from the deep Earth, to past environments and climate, to the interaction of the geomagnetic field with the space environment. We present the large range of modifications made to the database since its initial release in 2006. The most significant is the addition of paleomagnetic, rock magnetic and chronological data obtained from lake and marine sediments. An emphasis has been placed on geochronological data from sediments and the database includes comprehensive radiocarbon age data, oxygen isotope data, varve ages and tephra ages. In the archeomagnetic and volcanic database, the amount of declination, inclination and paleointensity data has been increased greatly and now exceeds 15,000. In addition, a number of new metadata fields have been added, e.g., more specific information about the archaeological or volcanic sites the data were obtained from. Finally, the web interface has been updated. This includes a new query form for the sediment database and improved functionality of the archeomagnetic and volcanic query form. The webpage can be found at found at http://geomagia.gfz-potsdam.de.

  9. RNAcentral: an international database of ncRNA sequences

    PubMed Central

    2015-01-01

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species. PMID:25352543

  10. RNAcentral: an international database of ncRNA sequences.

    PubMed

    2015-01-01

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species. PMID:25352543

  11. RNAcentral: an international database of ncRNA sequences

    DOE PAGESBeta

    Williams, Kelly Porter

    2014-10-28

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

  12. Expert systems identify fossils and manage large paleontological databases

    SciTech Connect

    Beightol, D.S. ); Conrad, M.A.

    1988-02-01

    EXPAL is a computer program permitting creation and maintenance of comprehensive databases in marine paleontology. It is designed to assist specialists and non-specialists. EXPAL includes a powerful expert system based on the morphological descriptors specific to a given group of fossils. The expert system may be used, for example, to describe and automatically identify an unknown specimen. EXPAL was first applied to Dasycladales (Calcareous green algae). Projects are under way for corresponding expert systems and databases on planktonic foraminifers and calpionellids. EXPAL runs on an IBM XT or compatible microcomputer.

  13. PADB : Published Association Database

    PubMed Central

    Rhee, Hwanseok; Lee, Jin-Sung

    2007-01-01

    Background Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing or insufficient in current genetic association databases. In addition, only a few of the environmental risk factors are included as gene-environment interactions, and the risk measures of associations are not indexed in any association databases. Description We have developed a published association database (PADB; ) that includes both the genetic associations and the environmental risk factors available in PubMed database. Each genetic risk factor is linked to a molecular pathway database and the HapMap database through human gene symbols identified in the abstracts. And the risk measures such as odds ratios or hazard ratios are extracted automatically from the abstracts when available. Thus, users can review the association data sorted by the risk measures, and genetic associations can be grouped by human genes or molecular pathways. The search results can also be saved to tab-delimited text files for further sorting or analysis. Currently, PADB indexes more than 1,500,000 PubMed abstracts that include 3442 human genes, 461 molecular pathways and about 190,000 risk measures ranging from 0.00001 to 4878.9. Conclusion PADB is a unique online database of published associations that will serve as a novel and powerful resource for reviewing and interpreting huge association data of complex human diseases. PMID:17877839

  14. BIOMARKERS DATABASE

    EPA Science Inventory

    This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

  15. Comprehensive Care

    MedlinePlus

    ... Text Larger Text Print In this article A complex disease requires a comprehensive approach Today multiple sclerosis ( ... Your Whole Health, Your Whole Team: Managing Your Complex MS Symptoms Webinar/telelearning presented by Roz Kalb, ...

  16. Online interactive U.S. Reservoir Sedimentation Survey Database

    USGS Publications Warehouse

    Gray, J.B.; Bernard, J.M.; Schwarz, G.E.; Stewart, D.W.; Ray, K.T.

    2009-01-01

    In April 2009, the U.S. Geological Survey and the Natural Resources Conservation Service (prior to 1994, the Soil Conservation Service) created the Reservoir Sedimentation Survey Database (RESSED) and Web site, the most comprehensive compilation of data from reservoir bathymetric and dry basin surveys in the United States. RESSED data can be useful for a number of purposes, including calculating changes in reservoir storage characteristics, quantifying rates of sediment delivery to reservoirs, and estimating erosion rates in a reservoir's watershed.

  17. 75 FR 65611 - Native American Tribal Insignia Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-26

    ... Patent and Trademark Office Native American Tribal Insignia Database ACTION: Proposed collection; comment... recommendations made in the report was that the USPTO create and maintain an accurate and comprehensive database... database. The USPTO database of official tribal insignias assists trademark attorneys in their...

  18. 78 FR 60861 - Native American Tribal Insignia Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-02

    ... United States Patent and Trademark Office Native American Tribal Insignia Database ACTION: Proposed... maintain an accurate and comprehensive database containing the official insignia of all federally and state... Appropriations directed the USPTO to create this database. The USPTO database of official tribal...

  19. Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

    PubMed

    Ito, Yuichi; Arikawa, Kohji; Antonio, Baltazar A; Ohta, Isamu; Naito, Shinji; Mukai, Yoshiyuki; Shimano, Atsuko; Masukawa, Masatoshi; Shibata, Michie; Yamamoto, Mayu; Ito, Yukiyo; Yokoyama, Junri; Sakai, Yasumichi; Sakata, Katsumi; Nagamura, Yoshiaki; Namiki, Nobukazu; Matsumoto, Takashi; Higo, Kenichi; Sasaki, Takuji

    2005-01-01

    A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/. PMID:15608281

  20. Comprehensive Epidemiologic Data Resource (CEDR) (Poster)

    SciTech Connect

    Oak Ridge Institute for Science and Education

    2012-12-12

    This poster introduces the Comprehensive Epidemiologic Data Resource (CEDR), an electronic database with demographic, health outcome, and exposure information for over a million DOE nuclear plant and laboratory workers.

  1. The ribosomal database project.

    PubMed Central

    Larsen, N; Olsen, G J; Maidak, B L; McCaughey, M J; Overbeek, R; Macke, T J; Marsh, T L; Woese, C R

    1993-01-01

    The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server. PMID:8332524

  2. Experiment Databases

    NASA Astrophysics Data System (ADS)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  3. ECOTOX database; new additions and future direction

    EPA Science Inventory

    The ECOTOXicology database (ECOTOX) is a comprehensive, publicly available knowledgebase developed and maintained by ORD/NHEERL. It is used for environmental toxicity data on aquatic life, terrestrial plants and wildlife. Publications are identified for potential applicability af...

  4. The Lava Morphology Database (LAMDA)

    NASA Astrophysics Data System (ADS)

    Peckyno, R. S.; de Silva, S. L.; Lopes, R. M.; Pieri, D. C.

    2009-12-01

    Many previous investigations of lava morphology have explored the relationship between flow properties (e.g., length, area, thickness) or flow features (e.g. lobation, flow ridging, aspect ratio), and process variables such as lava viscosity, yield strength, temperature, effusion rate, and local slope. Previous studies, however, have focused on individual attributes and features across a limited dataset of lava flows and have often noted the lack of a larger baseline dataset for comparison. Today, ready availability of high spatial and spectral resolution data for Earth’s volcanoes, coupled with computing advances, enable substantially enhanced network interaction between satellite analysis and field investigators around the world. We therefore propose a community effort, the Lava Morphology Database (LAMDA), to develop a comprehensive database for the morphology of terrestrial lava flows of varying composition, using GIS to integrate, georeference, and compare multiple datasets as well as automating many of the basic calculations. In a preliminary effort, we have measured and compiled lava flow features and attributes at 38 volcanoes including flow distance, surface area, aspect ratio, margin lobation, radii of curvature, height, and arc-length, corresponding cleft angle, flow surface ridging wavelength, lobe and landscape level slope, etc. As an example of the utility of this prototype database we present the initial results of an analysis of these data in light of existing viscosity and effusion rate based morphological models. Data resolution, computing power, and the number of field samples that can be practically analyzed have often necessitated that researchers assume that local slopes, viscosities, chemistries, and temperatures are constant across a flow. In contrast, LAMBDA will enable the exploration of factors that impact the emplacement of terrestrial lava flows at a much higher resolution than previous studies, as well as provide an extensive

  5. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    DOE Data Explorer

    Loots, Gabriela G. [LLNL; Ovcharenko, I. [LLNL

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

  6. ResPlan Database

    NASA Technical Reports Server (NTRS)

    Zellers, Michael L.

    2003-01-01

    The main project I was involved in was new application development for the existing CIS0 Database (ResPlan). This database application was developed in Microsoft Access. Initial meetings with Greg Follen, Linda McMillen, Griselle LaFontaine and others identified a few key weaknesses with the existing database. The weaknesses centered around that while the database correctly modeled the structure of Programs, Projects and Tasks, once the data was entered, the database did not capture any dynamic status information, and as such was of limited usefulness. After the initial meetings my goals were identified as follows: Enhance the ResPlan Database to include qualitative and quantitative status information about the Programs, Projects and Tasks Train staff members about the ResPlan database from both the user perspective and the developer perspective Give consideration to a Web Interface for reporting. Initially, the thought was that there would not be adequate time to actually develop the Web Interface, Greg wanted it understood that this was an eventual goal and as such should be a consideration throughout the development process.

  7. Biomedical term mapping databases.

    PubMed

    Wren, Jonathan D; Chang, Jeffrey T; Pustejovsky, James; Adar, Eytan; Garner, Harold R; Altman, Russ B

    2005-01-01

    Longer words and phrases are frequently mapped onto a shorter form such as abbreviations or acronyms for efficiency of communication. These abbreviations are pervasive in all aspects of biology and medicine and as the amount of biomedical literature grows, so does the number of abbreviations and the average number of definitions per abbreviation. Even more confusing, different authors will often abbreviate the same word/phrase differently. This ambiguity impedes our ability to retrieve information, integrate databases and mine textual databases for content. Efforts to standardize nomenclature, especially those doing so retrospectively, need to be aware of different abbreviatory mappings and spelling variations. To address this problem, there have been several efforts to develop computer algorithms to identify the mapping of terms between short and long form within a large body of literature. To date, four such algorithms have been applied to create online databases that comprehensively map biomedical terms and abbreviations within MEDLINE: ARGH (http://lethargy.swmed.edu/ARGH/argh.asp), the Stanford Biomedical Abbreviation Server (http://bionlp.stanford.edu/abbreviation/), AcroMed (http://medstract.med.tufts.edu/acro1.1/index.htm) and SaRAD (http://www.hpl.hp.com/research/idl/projects/abbrev.html). In addition to serving as useful computational tools, these databases serve as valuable references that help biologists keep up with an ever-expanding vocabulary of terms. PMID:15608198

  8. The Validity of Reading Comprehension Rate: Reading Speed, Comprehension, and Comprehension Rates

    ERIC Educational Resources Information Center

    Skinner, Christopher H.; Williams, Jacqueline L.; Morrow, Jennifer Ann; Hale, Andre D.; Neddenriep, Christine E.; Hawkins, Renee O.

    2009-01-01

    This article describes a secondary analysis of a brief reading comprehension rate measure, percent comprehension questions correct per minute spent reading (%C/M). This measure includes reading speed (seconds to read) in the denominator and percentage of comprehension questions answered correctly in the numerator. Participants were 22 4th-, 29…

  9. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

    PubMed

    Pruitt, Kim D; Tatusova, Tatiana; Maglott, Donna R

    2005-01-01

    The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

  10. Chemical Kinetics Database

    National Institute of Standards and Technology Data Gateway

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  11. The Transporter Classification Database

    PubMed Central

    Saier, Milton H.; Reddy, Vamsee S.; Tamang, Dorjee G.; Västermark, Åke

    2014-01-01

    The Transporter Classification Database (TCDB; http://www.tcdb.org) serves as a common reference point for transport protein research. The database contains more than 10 000 non-redundant proteins that represent all currently recognized families of transmembrane molecular transport systems. Proteins in TCDB are organized in a five level hierarchical system, where the first two levels are the class and subclass, the second two are the family and subfamily, and the last one is the transport system. Superfamilies that contain multiple families are included as hyperlinks to the five tier TC hierarchy. TCDB includes proteins from all types of living organisms and is the only transporter classification system that is both universal and recognized by the International Union of Biochemistry and Molecular Biology. It has been expanded by manual curation, contains extensive text descriptions providing structural, functional, mechanistic and evolutionary information, is supported by unique software and is interconnected to many other relevant databases. TCDB is of increasing usefulness to the international scientific community and can serve as a model for the expansion of database technologies. This manuscript describes an update of the database descriptions previously featured in NAR database issues. PMID:24225317

  12. USGS releases comprehensive land surface data

    NASA Astrophysics Data System (ADS)

    Wendel, JoAnna

    2014-04-01

    The U.S. Geological Survey (USGS) has released the latest edition of its National Land Cover Database (NLCD 2011), the nation's most comprehensive look at land surface conditions. The database divides the lower 48 states into 9 billion geographic cells, providing consistent information about land conditions on regional and nationwide scales.

  13. The Institute for Rock Magnetism Facility Database

    NASA Astrophysics Data System (ADS)

    Jackson, M. J.; Sølheid, P.; Bowles, J. A.; Moskowitz, B. M.; Feinberg, J. M.

    2012-12-01

    The Institute for Rock Magnetism (IRM) is one of 19 National Multi-User Facilities supported by the Instruments and Facilities program of NSF for geoscience research that requires complex, expensive and advanced instrumentation. Visiting and in-house researchers at the IRM have access to sensitive laboratory instruments for magnetometry, magnetic microscopy and Mössbauer spectroscopy, for carrying out a wide variety of experiments under a range of applied field and temperature conditions. Results are used to gain insight into a very diverse assortment of natural materials and phenomena including biomagnetism, environmental magnetism, petrofabrics, nanophase materials, shocked materials, and paleomagnetism of terrestrial and extraterrestrial materials. A comprehensive laboratory database has been in operation since 2004, storing detailed experimental data and metadata for more than 250 facility users, with measurements on over 50,000 specimens, including over one million remanence measurements and 45,000 hysteresis loops. Custom software tools provide consistent and reliable handling of basic data processing (e.g., mass normalization and unit conversion), as well as more advanced interactive analysis (e.g., deconvolution of u-channel paleomagnetic data; filtering and statistical tests for high-field nonlinearity in calculating hysteresis loop parameters; thermal fluctuation tomography using T-dependent switching-field distributions from backfield remanence measurements or hysteresis loops). Users are also able to access their data and the custom software tools remotely once they leave the IRM for their home institutions. A key advantage of an integrated database/software system for a facility like the IRM is that it provides a rapid and automatic means of combining different kinds of data measured on different instruments. An important design consideration in the development of the facility database has been structural compatibility with the community-wide Mag

  14. Enabling heterogenous multi-scale database for emergency service functions through geoinformation technologies

    NASA Astrophysics Data System (ADS)

    Bhanumurthy, V.; Venugopala Rao, K.; Srinivasa Rao, S.; Ram Mohan Rao, K.; Chandra, P. Satya; Vidhyasagar, J.; Diwakar, P. G.; Dadhwal, V. K.

    2014-11-01

    Geographical Information Science (GIS) is now graduated from traditional desktop system to Internet system. Internet GIS is emerging as one of the most promising technologies for addressing Emergency Management. Web services with different privileges are playing an important role in dissemination of the emergency services to the decision makers. Spatial database is one of the most important components in the successful implementation of Emergency Management. It contains spatial data in the form of raster, vector, linked with non-spatial information. Comprehensive data is required to handle emergency situation in different phases. These database elements comprise core data, hazard specific data, corresponding attribute data, and live data coming from the remote locations. Core data sets are minimum required data including base, thematic, infrastructure layers to handle disasters. Disaster specific information is required to handle a particular disaster situation like flood, cyclone, forest fire, earth quake, land slide, drought. In addition to this Emergency Management require many types of data with spatial and temporal attributes that should be made available to the key players in the right format at right time. The vector database needs to be complemented with required resolution satellite imagery for visualisation and analysis in disaster management. Therefore, the database is interconnected and comprehensive to meet the requirement of an Emergency Management. This kind of integrated, comprehensive and structured database with appropriate information is required to obtain right information at right time for the right people. However, building spatial database for Emergency Management is a challenging task because of the key issues such as availability of data, sharing policies, compatible geospatial standards, data interoperability etc. Therefore, to facilitate using, sharing, and integrating the spatial data, there is a need to define standards to build

  15. Comprehensive rotorcraft analysis methods

    NASA Technical Reports Server (NTRS)

    Stephens, Wendell B.; Austin, Edward E.

    1988-01-01

    The development and application of comprehensive rotorcraft analysis methods in the field of rotorcraft technology are described. These large scale analyses and the resulting computer programs are intended to treat the complex aeromechanical phenomena that describe the behavior of rotorcraft. They may be used to predict rotor aerodynamics, acoustic, performance, stability and control, handling qualities, loads and vibrations, structures, dynamics, and aeroelastic stability characteristics for a variety of applications including research, preliminary and detail design, and evaluation and treatment of field problems. The principal comprehensive methods developed or under development in recent years and generally available to the rotorcraft community because of US Army Aviation Research and Technology Activity (ARTA) sponsorship of all or part of the software systems are the Rotorcraft Flight Simulation (C81), Dynamic System Coupler (DYSCO), Coupled Rotor/Airframe Vibration Analysis Program (SIMVIB), Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics (CAMRAD), General Rotorcraft Aeromechanical Stability Program (GRASP), and Second Generation Comprehensive Helicopter Analysis System (2GCHAS).

  16. Drinking Water Treatability Database (Database)

    EPA Science Inventory

    The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

  17. AmphibiaChina: an online database of Chinese Amphibians.

    PubMed

    Che, Jing; Wang, Kai

    2016-01-18

    AmphibiaChina, an open-access, web-based database, is designed to provide comprehensive and up-to-date information on Chinese amphibians. It offers an integrated module with six major sections. Compared to other known databases including AmphibiaWeb and Amphibian Species of the World, AmphibiaChina has the following new functions: (1) online species identification based on DNA barcode sequences; (2) comparisons and discussions of different major taxonomic systems; and (3) phylogenetic progress on Chinese amphibians. This database offers a window for the world to access available information of Chinese amphibians. AmphibiaChina with its Chinese version can be accessed at http://www.amphibiachina.org. PMID:26828034

  18. AmphibiaChina: an online database of Chinese Amphibians

    PubMed Central

    CHE, Jing; WANG, Kai

    2016-01-01

    AmphibiaChina, an open-access, web-based database, is designed to provide comprehensive and up-to-date information on Chinese amphibians. It offers an integrated module with six major sections. Compared to other known databases including AmphibiaWeb and Amphibian Species of the World, AmphibiaChina has the following new functions: (1) online species identification based on DNA barcode sequences; (2) comparisons and discussions of different major taxonomic systems; and (3) phylogenetic progress on Chinese amphibians. This database offers a window for the world to access available information of Chinese amphibians. AmphibiaChina with its Chinese version can be accessed at http://www.amphibiachina.org. PMID:26828034

  19. Integration of NASA/GSFC and USGS Rock Magnetic Databases.

    NASA Astrophysics Data System (ADS)

    Nazarova, K. A.; Glen, J. M.

    2004-05-01

    A global Magnetic Petrology Database (MPDB) was developed and continues to be updated at NASA/Goddard Space Flight Center. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via the Internet for a more realistic interpretation of satellite (as well as aeromagnetic and ground) lithospheric magnetic anomalies. The MPDB contains data on rocks from localities around the world (about 19,000 samples) including the Ukranian and Baltic Shields, Kamchatka, Iceland, Urals Mountains, etc. The MPDB is designed, managed and presented on the web as a research oriented database. Several database applications have been specifically developed for data manipulation and analysis of the MPDB. The geophysics unit at the USGS in Menlo Park has over 17,000 rock-property data, largely from sites within the western U.S. This database contains rock-density and rock-magnetic parameters collected for use in gravity and magnetic field modeling, and paleomagnetic studies. Most of these data were taken from surface outcrops and together they span a broad range of rock types. Measurements were made either in-situ at the outcrop, or in the laboratory on hand samples and paleomagnetic cores acquired in the field. The USGS and NASA/GSFC data will be integrated as part of an effort to provide public access to a single, uniformly maintained database. Due to the large number of data and the very large area sampled, the database can yield rock-property statistics on a broad range of rock types; it is thus applicable to study areas beyond the geographic scope of the database. The intent of this effort is to provide incentive for others to further contribute to the database, and a tool with which the geophysical community can entertain studies formerly precluded.

  20. FishTraits Database

    USGS Publications Warehouse

    Angermeier, Paul L.; Frimpong, Emmanuel A.

    2009-01-01

    The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. FishTraits is a database of >100 traits for 809 (731 native and 78 exotic) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database contains information on four major categories of traits: (1) trophic ecology, (2) body size and reproductive ecology (life history), (3) habitat associations, and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status is also included. Together, we refer to the traits, distribution, and conservation status information as attributes. Descriptions of attributes are available here. Many sources were consulted to compile attributes, including state and regional species accounts and other databases.

  1. Drinking Water Database

    NASA Technical Reports Server (NTRS)

    Murray, ShaTerea R.

    2004-01-01

    This summer I had the opportunity to work in the Environmental Management Office (EMO) under the Chemical Sampling and Analysis Team or CS&AT. This team s mission is to support Glenn Research Center (GRC) and EM0 by providing chemical sampling and analysis services and expert consulting. Services include sampling and chemical analysis of water, soil, fbels, oils, paint, insulation materials, etc. One of this team s major projects is the Drinking Water Project. This is a project that is done on Glenn s water coolers and ten percent of its sink every two years. For the past two summers an intern had been putting together a database for this team to record the test they had perform. She had successfully created a database but hadn't worked out all the quirks. So this summer William Wilder (an intern from Cleveland State University) and I worked together to perfect her database. We began be finding out exactly what every member of the team thought about the database and what they would change if any. After collecting this data we both had to take some courses in Microsoft Access in order to fix the problems. Next we began looking at what exactly how the database worked from the outside inward. Then we began trying to change the database but we quickly found out that this would be virtually impossible.

  2. Benefits of an International Database for UF6 Cylinders

    SciTech Connect

    Babcock, R A; Whitaker, J M; Murphy, J; Oakberg, J

    2008-06-30

    A reasonable expectation regarding the nuclear energy renaissance is that the location of fuel cycle nuclear materials throughout the world will be known. We ask--would an international system for uranium hexafluoride (UF{sub 6}) cylinders provide the effective assurances expected for international fuel supply and of the international fuel centers? This paper introduces the question and discusses the potential benefits of tracking UF{sub 6} cylinders through the development of an international database. The nonproliferation benefits of an international database for UF{sub 6} cylinders being used in the fuel cycle include an enhanced capability to reconcile nuclear material imports and exports. Currently, import and export declarations only require the reporting of total 'rolled up' quantities of nuclear materials contained in all items--not the quantities of materials in individual items like individual UF{sub 6} cylinders. The database could provide supplier countries with more assurance on the location of the UF{sub 6} cylinders they export. Additionally, a comprehensive database on all declared cylinders would be a valuable resource in detecting and recognizing undeclared cylinders. The database could potentially be administered by the IAEA and be accessible to authorized countries around the world. During the nuclear renaissance, the general public, as well as the participants will expect transparency and quality information about movement of nuclear fuel cycle nuclear materials. We will discuss the potential benefits of such a database for the suppliers, inspectorates, and general public.

  3. GLOBAL ECOSYSTEMS DATABASE: DATABASE DOCUMENTATION AND CD-ROM

    EPA Science Inventory

    The primary objective of this cooperative research and development is to produce an integrated, quality controlled, global database (including time sequences) for spatially distributed modeling. he project concentrates on modern observational data, including remotely sensed data ...

  4. 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.

  5. Chemical Explosion Database

    NASA Astrophysics Data System (ADS)

    Johansson, Peder; Brachet, Nicolas

    2010-05-01

    A database containing information on chemical explosions, recorded and located by the International Data Center (IDC) of the CTBTO, should be established in the IDC prior to entry into force of the CTBT. Nearly all of the large chemical explosions occur in connection with mining activity. As a first step towards the establishment of this database, a survey of presumed mining areas where sufficiently large explosions are conducted has been done. This is dominated by the large coal mining areas like the Powder River (U.S.), Kuznetsk (Russia), Bowen (Australia) and Ekibastuz (Kazakhstan) basins. There are also several other smaller mining areas, in e.g. Scandinavia, Poland, Kazakhstan and Australia, with large enough explosions for detection. Events in the Reviewed Event Bulletin (REB) of the IDC that are located in or close to these mining areas, and which therefore are candidates for inclusion in the database, have been investigated. Comparison with a database of infrasound events has been done as many mining blasts generate strong infrasound signals and therefore also are included in the infrasound database. Currently there are 66 such REB events in 18 mining areas in the infrasound database. On a yearly basis several hundreds of events in mining areas have been recorded and included in the REB. Establishment of the database of chemical explosions requires confirmation and ground truth information from the States Parties regarding these events. For an explosion reported in the REB, the appropriate authority in whose country the explosion occurred is encouraged, on a voluntary basis, to seek out information on the explosion and communicate this information to the IDC.

  6. Database Technology in Digital Libraries.

    ERIC Educational Resources Information Center

    Preston, Carole; Lin, Binshan

    2002-01-01

    Reviews issues relating to database technology and digital libraries. Highlights include resource sharing; ongoing digital library projects; metadata; user interfaces; query processing; interoperability; data quality; copyright infringement; and managerial implications, including electronic versus printed materials, accessibility,…

  7. Analysis of Landslide Hazard Impact Using the Landslide Database for Germany

    NASA Astrophysics Data System (ADS)

    Klose, M.; Damm, B.

    2014-12-01

    The Federal Republic of Germany has long been among the few European countries that lack a national landslide database. Systematic collection and inventory of landslide data still shows a comprehensive research history in Germany, but only one focused on development of databases with local or regional coverage. This has changed in recent years with the launch of a database initiative aimed at closing the data gap existing at national level. The present contribution reports on this project that is based on a landslide database which evolved over the last 15 years to a database covering large parts of Germany. A strategy of systematic retrieval, extraction, and fusion of landslide data is at the heart of the methodology, providing the basis for a database with a broad potential of application. The database offers a data pool of more than 4,200 landslide data sets with over 13,000 single data files and dates back to 12th century. All types of landslides are covered by the database, which stores not only core attributes, but also various complementary data, including data on landslide causes, impacts, and mitigation. The current database migration to PostgreSQL/PostGIS is focused on unlocking the full scientific potential of the database, while enabling data sharing and knowledge transfer via a web GIS platform. In this contribution, the goals and the research strategy of the database project are highlighted at first, with a summary of best practices in database development providing perspective. Next, the focus is on key aspects of the methodology, which is followed by the results of different case studies in the German Central Uplands. The case study results exemplify database application in analysis of vulnerability to landslides, impact statistics, and hazard or cost modeling.

  8. Database machines for large statistical databases. Final report, January 16, 1983-January 15, 1986

    SciTech Connect

    DeWitt, D.J.

    1986-01-01

    Research activities have been directed towards the design and implementation of a high performance database machine for accessing, manipulating, and analyzing very large statistical data sets. Topics of discussion include statistical databases, parallel algorithms and secondary storage methods, methodology for database system performance evaluation, implementation techniques for main memory database systems, intelligent buffer management systems, Gamma-a high performance dataflow database machine, and extensible database management systems. 1 fig. (DWL)

  9. [DICOM data conversion technology research for database].

    PubMed

    Wang, Shiyu; Lin, Hao

    2010-12-01

    A comprehensive medical image platform built for medical images network access, measurements and virtual surgery navigation needs the support of medical image databases. The medical image database we built contains two-dimensional images and three-dimensional models. The common databases based on DICOM storing do not meet the requirements. We use the technology of DICOM conversion to convert DICOM into BMP images and indispensable data elements, and then we use the BMP images and indispensable data elements to reconstruct the three-dimensional model. The reliability of DICOM data conversion is verified, and on this basis, a human hip joint medical image database is built. Experimental results show that this method used in building the medical image database can not only meet the requirements of database application, but also greatly reduce the amount of database storage. PMID:21374999

  10. Patent Family Databases.

    ERIC Educational Resources Information Center

    Simmons, Edlyn S.

    1985-01-01

    Reports on retrieval of patent information online and includes definition of patent family, basic and equivalent patents, "parents and children" applications, designated states, patent family databases--International Patent Documentation Center, World Patents Index, APIPAT (American Petroleum Institute), CLAIMS (IFI/Plenum). A table noting country…

  11. PlantCAZyme: a database for plant carbohydrate-active enzymes

    PubMed Central

    Ekstrom, Alexander; Taujale, Rahil; McGinn, Nathan; Yin, Yanbin

    2014-01-01

    PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data. Database URL: http://cys.bios.niu.edu/plantcazyme/ PMID:25125445

  12. The Ribosomal Database Project.

    PubMed Central

    Maidak, B L; Larsen, N; McCaughey, M J; Overbeek, R; Olsen, G J; Fogel, K; Blandy, J; Woese, C R

    1994-01-01

    The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server/rdp.life.uiuc.edu) and gopher (rdpgopher.life.uiuc.edu). The electronic mail server also provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for chimeric nature of newly sequenced rRNAs, and automated alignment. PMID:7524021

  13. Development of a national, dynamic reservoir-sedimentation database

    USGS Publications Warehouse

    Gray, J.R.; Bernard, J.M.; Stewart, D.W.; McFaul, E.J.; Laurent, K.W.; Schwarz, G.E.; Stinson, J.T.; Jonas, M.M.; Randle, T.J.; Webb, J.W.

    2010-01-01

    The importance of dependable, long-term water supplies, coupled with the need to quantify rates of capacity loss of the Nation’s re servoirs due to sediment deposition, were the most compelling reasons for developing the REServoir- SEDimentation survey information (RESSED) database and website. Created under the auspices of the Advisory Committee on Water Information’s Subcommittee on Sedimenta ion by the U.S. Geological Survey and the Natural Resources Conservation Service, the RESSED database is the most comprehensive compilation of data from reservoir bathymetric and dry-basin surveys in the United States. As of March 2010, the database, which contains data compiled on the 1950s vintage Soil Conservation Service’s Form SCS-34 data sheets, contained results from 6,616 surveys on 1,823 reservoirs in the United States and two surveys on one reservoir in Puerto Rico. The data span the period 1755–1997, with 95 percent of the surveys performed from 1930–1990. The reservoir surface areas range from sub-hectare-scale farm ponds to 658 km2 Lake Powell. The data in the RESSED database can be useful for a number of purposes, including calculating changes in reservoir-storage characteristics, quantifying sediment budgets, and estimating erosion rates in a reservoir’s watershed. The March 2010 version of the RESSED database has a number of deficiencies, including a cryptic and out-of-date database architecture; some geospatial inaccuracies (although most have been corrected); other data errors; an inability to store all data in a readily retrievable manner; and an inability to store all data types that currently exist. Perhaps most importantly, the March 2010 version of RESSED database provides no publically available means to submit new data and corrections to existing data. To address these and other deficiencies, the Subcommittee on Sedimentation, through the U.S. Geological Survey and the U.S. Army Corps of Engineers, began a collaborative project in

  14. Designing a Comprehensive Curriculum

    ERIC Educational Resources Information Center

    Faulkner, T. L.

    1970-01-01

    A comprehensive rural "agribusiness industry" curriculum might include: (1) The World of Work (Grade 7 or 8), (2) Vocational Orientation (Grade 9), (3) Basic Agriculture and Industry (Grade 10), (4) Specialized Agribusiness Industry (Grade 11), and (5) Advanced Agribusiness Industry (Grade 12). (DM)

  15. Comprehensive Environmental Management Process

    SciTech Connect

    Hjeresen, D.L.; Roybal, S.L.

    1994-08-01

    This report contains information about Los Alamos National Laboratory`s Comprehensive Environmental Management Plan. The topics covered include: waste minimization, waste generation, environmental concerns, public relations of the laboratory, and how this plan will help to answer to the demands of the laboratory as their mission changes.

  16. Comprehensive stormwater management study

    SciTech Connect

    Morrison, T. ); Alter, M. ); Wassum, R.H. )

    1994-02-01

    This article examines Tucson, Arizona's approach to stormwater management. The topics of the article include the quantity and quality of stormwater, developing the stormwater master plan, meeting environmental and regulatory constraints. Tucson's comprehensive, watershed by watershed approach to public works planning and stormwater program development is described.

  17. Mouse genome database 2016

    PubMed Central

    Bult, Carol J.; Eppig, Janan T.; Blake, Judith A.; Kadin, James A.; Richardson, Joel E.

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  18. National Ambient Radiation Database

    SciTech Connect

    Dziuban, J.; Sears, R.

    2003-02-25

    The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

  19. Mouse genome database 2016.

    PubMed

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  20. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1992-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

  1. DBGC: A Database of Human Gastric Cancer.

    PubMed

    Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

    2015-01-01

    The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do. PMID:26566288

  2. ADANS database specification

    SciTech Connect

    1997-01-16

    The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

  3. The Chandra Bibliography Database

    NASA Astrophysics Data System (ADS)

    Rots, A. H.; Winkelman, S. L.; Paltani, S.; Blecksmith, S. E.; Bright, J. D.

    2004-07-01

    Early in the mission, the Chandra Data Archive started the development of a bibliography database, tracking publications in refereed journals and on-line conference proceedings that are based on Chandra observations, allowing our users to link directly to articles in the ADS from our archive, and to link to the relevant data in the archive from the ADS entries. Subsequently, we have been working closely with the ADS and other data centers, in the context of the ADEC-ITWG, on standardizing the literature-data linking. We have also extended our bibliography database to include all Chandra-related articles and we are also keeping track of the number of citations of each paper. Obviously, in addition to providing valuable services to our users, this database allows us to extract a wide variety of statistical information. The project comprises five components: the bibliography database-proper, a maintenance database, an interactive maintenance tool, a user browsing interface, and a web services component for exchanging information with the ADS. All of these elements are nearly mission-independent and we intend make the package as a whole available for use by other data centers. The capabilities thus provided represent support for an essential component of the Virtual Observatory.

  4. Shuttle Hypervelocity Impact Database

    NASA Technical Reports Server (NTRS)

    Hyde, James L.; Christiansen, Eric L.; Lear, Dana M.

    2011-01-01

    With three missions outstanding, the Shuttle Hypervelocity Impact Database has nearly 3000 entries. The data is divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. Details and insights on the contents of the database including examples of descriptive statistics will be provided. Post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will also be discussed. Potential enhancements to the database structure and availability of the data for other researchers will be addressed in the Future Work section. A related database of returned surfaces from the International Space Station will also be introduced.

  5. Shuttle Hypervelocity Impact Database

    NASA Technical Reports Server (NTRS)

    Hyde, James I.; Christiansen, Eric I.; Lear, Dana M.

    2011-01-01

    With three flights remaining on the manifest, the shuttle impact hypervelocity database has over 2800 entries. The data is currently divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. The paper will provide details and insights on the contents of the database including examples of descriptive statistics using the impact data. A discussion of post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will be presented. Future work to be discussed will be possible enhancements to the database structure and availability of the data for other researchers. A related database of ISS returned surfaces that are under development will also be introduced.

  6. Integrating Paleoecological Databases

    NASA Astrophysics Data System (ADS)

    Blois, Jessica; Goring, Simon; Smith, Alison

    2011-02-01

    Neotoma Consortium Workshop; Madison, Wisconsin, 23-26 September 2010 ; Paleoecology can contribute much to global change science, as paleontological records provide rich information about species range shifts, changes in vegetation composition and productivity, aquatic and terrestrial ecosystem responses to abrupt climate change, and paleoclimate reconstruction, for example. However, while paleoecology is increasingly a multidisciplinary, multiproxy field focused on biotic responses to global change, most paleo databases focus on single-proxy groups. The Neotoma Paleoecology Database (http://www.neotomadb.org) aims to remedy this limitation by integrating discipline-specific databases to facilitate cross-community queries and analyses. In September, Neotoma consortium members and representatives from other databases and data communities met at the University of Wisconsin-Madison to launch the second development phase of Neotoma. The workshop brought together 54 international specialists, including Neotoma data stewards, users, and developers. Goals for the meeting were fourfold: (1) develop working plans for existing data communities; (2) identify new data types and sources; (3) enhance data access, visualization, and analysis on the Neotoma Web site; and (4) coordinate with other databases and cooperate in tool development and sharing.

  7. Comprehensive analysis of transport aircraft flight performance

    NASA Astrophysics Data System (ADS)

    Filippone, Antonio

    2008-04-01

    This paper reviews the state-of-the art in comprehensive performance codes for fixed-wing aircraft. The importance of system analysis in flight performance is discussed. The paper highlights the role of aerodynamics, propulsion, flight mechanics, aeroacoustics, flight operation, numerical optimisation, stochastic methods and numerical analysis. The latter discipline is used to investigate the sensitivities of the sub-systems to uncertainties in critical state parameters or functional parameters. The paper discusses critically the data used for performance analysis, and the areas where progress is required. Comprehensive analysis codes can be used for mission fuel planning, envelope exploration, competition analysis, a wide variety of environmental studies, marketing analysis, aircraft certification and conceptual aircraft design. A comprehensive program that uses the multi-disciplinary approach for transport aircraft is presented. The model includes a geometry deck, a separate engine input deck with the main parameters, a database of engine performance from an independent simulation, and an operational deck. The comprehensive code has modules for deriving the geometry from bitmap files, an aerodynamics model for all flight conditions, a flight mechanics model for flight envelopes and mission analysis, an aircraft noise model and engine emissions. The model is validated at different levels. Validation of the aerodynamic model is done against the scale models DLR-F4 and F6. A general model analysis and flight envelope exploration are shown for the Boeing B-777-300 with GE-90 turbofan engines with intermediate passenger capacity (394 passengers in 2 classes). Validation of the flight model is done by sensitivity analysis on the wetted area (or profile drag), on the specific air range, the brake-release gross weight and the aircraft noise. A variety of results is shown, including specific air range charts, take-off weight-altitude charts, payload-range performance

  8. 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

  9. Stackfile Database

    NASA Technical Reports Server (NTRS)

    deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

    2013-01-01

    This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

  10. Databases for K-8 Students

    ERIC Educational Resources Information Center

    Young, Terrence E., Jr.

    2004-01-01

    Today's elementary school students have been exposed to computers since birth, so it is not surprising that they are so proficient at using them. As a result, they are ready to search databases that include topics and information appropriate for their age level. Subscription databases are digital copies of magazines, newspapers, journals,…

  11. Wind turbine reliability database update.

    SciTech Connect

    Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.; Veers, Paul S.

    2009-03-01

    This report documents the status of the Sandia National Laboratories' Wind Plant Reliability Database. Included in this report are updates on the form and contents of the Database, which stems from a fivestep process of data partnerships, data definition and transfer, data formatting and normalization, analysis, and reporting. Selected observations are also reported.

  12. ePlantLIBRA: A composition and biological activity database for bioactive compounds in plant food supplements.

    PubMed

    Plumb, J; Lyons, J; Nørby, K; Thomas, M; Nørby, E; Poms, R; Bucchini, L; Restani, P; Kiely, M; Finglas, P

    2016-02-15

    The newly developed ePlantLIBRA database is a comprehensive and searchable database, with up-to-date coherent and validated scientific information on plant food supplement (PFS) bioactive compounds, with putative health benefits as well as adverse effects, and contaminants and residues. It is the only web-based database available compiling peer reviewed publications and case studies on PFS. A user-friendly, efficient and flexible interface has been developed for searching, extracting, and exporting the data, including links to the original references. Data from over 570 publications have been quality evaluated and entered covering 70 PFS or their botanical ingredients. PMID:26433297

  13. Database of recent tsunami deposits

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce E.

    2010-01-01

    This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

  14. Information Literacy Skills: Comparing and Evaluating Databases

    ERIC Educational Resources Information Center

    Grismore, Brian A.

    2012-01-01

    The purpose of this database comparison is to express the importance of teaching information literacy skills and to apply those skills to commonly used Internet-based research tools. This paper includes a comparison and evaluation of three databases (ProQuest, ERIC, and Google Scholar). It includes strengths and weaknesses of each database based…

  15. CANCER PREVENTION AND CONTROL (CP) DATABASE

    EPA Science Inventory

    This database focuses on breast, cervical, skin, and colorectal cancer emphasizing the application of early detection and control program activities and risk reduction efforts. The database provides bibliographic citations and abstracts of various types of materials including jou...

  16. DIDA: A curated and annotated digenic diseases database.

    PubMed

    Gazzo, Andrea M; Daneels, Dorien; Cilia, Elisa; Bonduelle, Maryse; Abramowicz, Marc; Van Dooren, Sonia; Smits, Guillaume; Lenaerts, Tom

    2016-01-01

    DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest. PMID:26481352

  17. Environmental Sustainability - Including Land and Water Use

    EPA Science Inventory

    Assessments of environmental sustainability can be conducted in many ways with one of the most quantitative methods including Life Cycle Impact Assessment (LCIA). While historically LCIA has included a comprehensive list of impact categories including: ozone depletion, global c...

  18. An Index to PGE-Ni-Cr Deposits and Occurrences in Selected Mineral-Occurrence Databases

    USGS Publications Warehouse

    Causey, J. Douglas; Galloway, John P.; Zientek, Michael L.

    2009-01-01

    Databases of mineral deposits and occurrences are essential to conducting assessments of undiscovered mineral resources. In the USGS's (U.S. Geological Survey) global assessment of undiscovered resources of copper, potash, and the platinum-group elements (PGE), only a few mineral deposit types will be evaluated. For example, only porphyry-copper and sediment-hosted copper deposits will be considered for the copper assessment. To support the global assessment, the USGS prepared comprehensive compilations of the occurrences of these two deposit types in order to develop grade and tonnage models and delineate permissive areas for undiscovered deposits of those types. This publication identifies previously published databases and database records that describe PGE, nickel, and chromium deposits and occurrences. Nickel and chromium were included in this overview because of the close association of PGE with nickel and chromium mineralization. Users of this database will need to refer to the original databases for detailed information about the deposits and occurrences. This information will be used to develop a current and comprehensive global database of PGE deposits and occurrences.

  19. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    PubMed

    Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

    2013-02-01

    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics. PMID:23299411

  20. MAGIC database and interfaces: an integrated package for gene discovery and expression.

    PubMed

    Cordonnier-Pratt, Marie-Michèle; Liang, Chun; Wang, Haiming; Kolychev, Dmitri S; Sun, Feng; Freeman, Robert; Sullivan, Robert; Pratt, Lee H

    2004-01-01

    The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance. PMID:18629159

  1. The International Nucleotide Sequence Database Collaboration.

    PubMed

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Takagi, Toshihisa

    2016-01-01

    The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain nucleotide sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences. PMID:26657633

  2. ARTI refrigerant database

    SciTech Connect

    Calm, J.M.

    1998-08-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  3. InterAction Database (IADB)

    Cancer.gov

    The InterAction Database includes demographic and prescription information for more than 500,000 patients in the northern and middle Netherlands and has been integrated with other systems to enhance data collection and analysis.

  4. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1992-11-09

    The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

  5. The Exoplanet Orbit Database

    NASA Astrophysics Data System (ADS)

    Wright, J. T.; Fakhouri, O.; Marcy, G. W.; Han, E.; Feng, Y.; Johnson, John Asher; Howard, A. W.; Fischer, D. A.; Valenti, J. A.; Anderson, J.; Piskunov, N.

    2011-04-01

    We present a database of well-determined orbital parameters of exoplanets, and their host stars' properties. This database comprises spectroscopic orbital elements measured for 427 planets orbiting 363 stars from radial velocity and transit measurements as reported in the literature. We have also compiled fundamental transit parameters, stellar parameters, and the method used for the planets discovery. This Exoplanet Orbit Database includes all planets with robust, well measured orbital parameters reported in peer-reviewed articles. The database is available in a searchable, filterable, and sortable form online through the Exoplanets Data Explorer table, and the data can be plotted and explored through the Exoplanet Data Explorer plotter. We use the Data Explorer to generate publication-ready plots, giving three examples of the signatures of exoplanet migration and dynamical evolution: We illustrate the character of the apparent correlation between mass and period in exoplanet orbits, the different selection biases between radial velocity and transit surveys, and that the multiplanet systems show a distinct semimajor-axis distribution from apparently singleton systems.

  6. High Performance Buildings Database

    DOE Data Explorer

    The High Performance Buildings Database is a shared resource for the building industry, a unique central repository of in-depth information and data on high-performance, green building projects across the United States and abroad. The database includes information on the energy use, environmental performance, design process, finances, and other aspects of each project. Members of the design and construction teams are listed, as are sources for additional information. In total, up to twelve screens of detailed information are provided for each project profile. Projects range in size from small single-family homes or tenant fit-outs within buildings to large commercial and institutional buildings and even entire campuses. The database is a data repository as well. A series of Web-based data-entry templates allows anyone to enter information about a building project into the database. Once a project has been submitted, each of the partner organizations can review the entry and choose whether or not to publish that particular project on its own Web site.

  7. LQTS gene LOVD database.

    PubMed

    Zhang, Tao; Moss, Arthur; Cong, Peikuan; Pan, Min; Chang, Bingxi; Zheng, Liangrong; Fang, Quan; Zareba, Wojciech; Robinson, Jennifer; Lin, Changsong; Li, Zhongxiang; Wei, Junfang; Zeng, Qiang; Qi, Ming

    2010-11-01

    The Long QT Syndrome (LQTS) is a group of genetically heterogeneous disorders that predisposes young individuals to ventricular arrhythmias and sudden death. LQTS is mainly caused by mutations in genes encoding subunits of cardiac ion channels (KCNQ1, KCNH2,SCN5A, KCNE1, and KCNE2). Many other genes involved in LQTS have been described recently(KCNJ2, AKAP9, ANK2, CACNA1C, SCNA4B, SNTA1, and CAV3). We created an online database(http://www.genomed.org/LOVD/introduction.html) that provides information on variants in LQTS-associated genes. As of February 2010, the database contains 1738 unique variants in 12 genes. A total of 950 variants are considered pathogenic, 265 are possible pathogenic, 131 are unknown/unclassified, and 292 have no known pathogenicity. In addition to these mutations collected from published literature, we also submitted information on gene variants, including one possible novel pathogenic mutation in the KCNH2 splice site found in ten Chinese families with documented arrhythmias. The remote user is able to search the data and is encouraged to submit new mutations into the database. The LQTS database will become a powerful tool for both researchers and clinicians. PMID:20809527

  8. World electric power plants database

    SciTech Connect

    2006-06-15

    This global database provides records for 104,000 generating units in over 220 countries. These units include installed and projected facilities, central stations and distributed plants operated by utilities, independent power companies and commercial and self-generators. Each record includes information on: geographic location and operating company; technology, fuel and boiler; generator manufacturers; steam conditions; unit capacity and age; turbine/engine; architect/engineer and constructor; and pollution control equipment. The database is issued quarterly.

  9. MEROPS: the peptidase database

    PubMed Central

    Rawlings, Neil D.; Barrett, Alan J.

    2000-01-01

    Important additions have been made to the MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/Merops.htm ). These include sequence alignments and cladograms for many of the families of peptidases, and these have proved very helpful in the difficult task of distinguishing the sequences of peptidases that are simply species variants of already known enzymes from those that represent novel enzymes. PMID:10592261

  10. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA

    PubMed Central

    Thakur, Nishant; Qureshi, Abid; Kumar, Manoj

    2012-01-01

    RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb. PMID:22139916

  11. Producing an Index with Your Microcomputer Database Manager.

    ERIC Educational Resources Information Center

    Jonassen, David

    1985-01-01

    Describes a procedure for using commonly available database management systems to produce indexes on microcomputers. Production steps discussed include creation of the database, data entry, database sort, formatting, and editing. (Author/MBR)

  12. ARTI refrigerant database

    SciTech Connect

    Calm, J.M.

    1997-02-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  13. Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

    PubMed

    Sakurai, Nozomu; Ara, Takeshi; Enomoto, Mitsuo; Motegi, Takeshi; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

    2014-01-01

    A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data. PMID:24949426

  14. Laminin-database v.2.0: an update on laminins in health and neuromuscular disorders

    PubMed Central

    Golbert, Daiane C. F.; Santana-van-Vliet, Eliane; Mundstein, Alex S.; Calfo, Vicente; Savino, Wilson; de Vasconcelos, Ana Tereza R.

    2014-01-01

    The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of information concerning LMs related to health and disease, with particular emphasis on the haemopoietic system. Users can easily access several tabs for LMs and LM-related molecules, as well as LM nomenclatures and direct links to PubMed. The LM-database version 2.0 integrates data from several publications to achieve a more comprehensive knowledge of LMs in health and disease. The novel features include the addition of two new tabs, ‘Neuromuscular Disorders’ and ‘miRNA-–LM Relationship’. More specifically, in this updated version, an expanding set of data has been displayed concerning the role of LMs in neuromuscular and neurodegenerative diseases, as well as the putative involvement of microRNAs. Given the importance of LMs in several biological processes, such as cell adhesion, proliferation, differentiation, migration and cell death, this upgraded version expands for users a panoply of information, regarding complex molecular circuitries that involve LMs in health and disease, including neuromuscular and neurodegenerative disorders. PMID:24106090

  15. Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

    PubMed Central

    Enomoto, Mitsuo; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

    2014-01-01

    A metabolome—the collection of comprehensive quantitative data on metabolites in an organism—has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data. PMID:24949426

  16. Laminin-database v.2.0: an update on laminins in health and neuromuscular disorders.

    PubMed

    Golbert, Daiane C F; Santana-van-Vliet, Eliane; Mundstein, Alex S; Calfo, Vicente; Savino, Wilson; de Vasconcelos, Ana Tereza R

    2014-01-01

    The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of information concerning LMs related to health and disease, with particular emphasis on the haemopoietic system. Users can easily access several tabs for LMs and LM-related molecules, as well as LM nomenclatures and direct links to PubMed. The LM-database version 2.0 integrates data from several publications to achieve a more comprehensive knowledge of LMs in health and disease. The novel features include the addition of two new tabs, 'Neuromuscular Disorders' and 'miRNA--LM Relationship'. More specifically, in this updated version, an expanding set of data has been displayed concerning the role of LMs in neuromuscular and neurodegenerative diseases, as well as the putative involvement of microRNAs. Given the importance of LMs in several biological processes, such as cell adhesion, proliferation, differentiation, migration and cell death, this upgraded version expands for users a panoply of information, regarding complex molecular circuitries that involve LMs in health and disease, including neuromuscular and neurodegenerative disorders. PMID:24106090

  17. CastorDB: a comprehensive knowledge base for Ricinus communis

    PubMed Central

    2011-01-01

    Background Ricinus communis is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, R. communis genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of R. communis is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant. Findings CastorDB is a specialized and comprehensive database for the oil seed plant R. communis, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein. Conclusion CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners. PMID:21914200

  18. Windshear database for forward-looking systems certification

    NASA Technical Reports Server (NTRS)

    Switzer, G. F.; Proctor, F. H.; Hinton, D. A.; Aanstoos, J. V.

    1993-01-01

    This document contains a description of a comprehensive database that is to be used for certification testing of airborne forward-look windshear detection systems. The database was developed by NASA Langley Research Center, at the request of the Federal Aviation Administration (FAA), to support the industry initiative to certify and produce forward-look windshear detection equipment. The database contains high resolution, three dimensional fields for meteorological variables that may be sensed by forward-looking systems. The database is made up of seven case studies which have been generated by the Terminal Area Simulation System, a state-of-the-art numerical system for the realistic modeling of windshear phenomena. The selected cases represent a wide spectrum of windshear events. General descriptions and figures from each of the case studies are included, as well as equations for F-factor, radar-reflectivity factor, and rainfall rate. The document also describes scenarios and paths through the data sets, jointly developed by NASA and the FAA, to meet FAA certification testing objectives. Instructions for reading and verifying the data from tape are included.

  19. Establishing a database of radionuclide transfer parameters for freshwater wildlife.

    PubMed

    Yankovich, T; Beresford, N A; Fesenko, S; Fesenko, J; Phaneuf, M; Dagher, E; Outola, I; Andersson, P; Thiessen, K; Ryan, J; Wood, M D; Bollhöfer, A; Barnett, C L; Copplestone, D

    2013-12-01

    Environmental assessments to evaluate potentials risks to humans and wildlife often involve modelling to predict contaminant exposure through key pathways. Such models require input of parameter values, including concentration ratios, to estimate contaminant concentrations in biota based on measurements or estimates of concentrations in environmental media, such as water. Due to the diversity of species and the range in physicochemical conditions in natural ecosystems, concentration ratios can vary by orders of magnitude, even within similar species. Therefore, to improve model input parameter values for application in aquatic systems, freshwater concentration ratios were collated or calculated from national grey literature, Russian language publications, and refereed papers. Collated data were then input into an international database that is being established by the International Atomic Energy Agency. The freshwater database enables entry of information for all radionuclides listed in ICRP (1983), in addition to the corresponding stable elements, and comprises a total of more than 16,500 concentration ratio (CRwo-water) values. Although data were available for all broad wildlife groups (with the exception of birds), data were sparse for many organism types. For example, zooplankton, crustaceans, insects and insect larvae, amphibians, and mammals, for which there were CRwo-water values for less than eight elements. Coverage was most comprehensive for fish, vascular plants, and molluscs. To our knowledge, the freshwater database that has now been established represents the most comprehensive set of CRwo-water values for freshwater species currently available for use in radiological environmental assessments. PMID:23103210

  20. Comprehensive care in hemophilia.

    PubMed

    Ruiz-Sáez, Arlette

    2012-04-01

    Hemophilia is a chronic and inherited X-linked bleeding disorder that requires life-long medical care. Hemophilia treatment is costly and complex partly because of the cost of the factor concentrates used in replacement therapy. However, the management of hemophilia is not based solely on achieving access to better treatment with safe factor concentrates; it also includes accurately diagnosing the disorder and providing specialized comprehensive care by a multidisciplinary team of specialists trained in hemophilia management. Comprehensive care for the person with hemophilia is defined as the continuous supervision of all medical and psychological aspects affecting the patient and his family and it demands the establishment of specialized centers, called Hemophilia Treatment Centers. The services that should be offered by a comprehensive hemophilia healthcare center are diverse and the multidisciplinary team should be coordinated preferably by a hematologist with the participation of other health professionals. It has been demonstrated that the benefits of establishing hemophilia centers are observed even in developing countries and that changes can be achieved when resources are re-organized, especially when education and training are provided at all levels. To reach these objectives, it is essential to have the participation of the patient and family members, and to strive to obtain the financial and legislative support from the State or Government in order to achieve a national comprehensive care program contemplating all the aspects needed for improving the quality of life for the community of patients with hemophilia and other bleeding disorders. PMID:22507803

  1. YCRD: Yeast Combinatorial Regulation Database

    PubMed Central

    Wu, Wei-Sheng; Hsieh, Yen-Chen; Lai, Fu-Jou

    2016-01-01

    In eukaryotes, the precise transcriptional control of gene expression is typically achieved through combinatorial regulation using cooperative transcription factors (TFs). Therefore, a database which provides regulatory associations between cooperative TFs and their target genes is helpful for biologists to study the molecular mechanisms of transcriptional regulation of gene expression. Because there is no such kind of databases in the public domain, this prompts us to construct a database, called Yeast Combinatorial Regulation Database (YCRD), which deposits 434,197 regulatory associations between 2535 cooperative TF pairs and 6243 genes. The comprehensive collection of more than 2500 cooperative TF pairs was retrieved from 17 existing algorithms in the literature. The target genes of a cooperative TF pair (e.g. TF1-TF2) are defined as the common target genes of TF1 and TF2, where a TF’s experimentally validated target genes were downloaded from YEASTRACT database. In YCRD, users can (i) search the target genes of a cooperative TF pair of interest, (ii) search the cooperative TF pairs which regulate a gene of interest and (iii) identify important cooperative TF pairs which regulate a given set of genes. We believe that YCRD will be a valuable resource for yeast biologists to study combinatorial regulation of gene expression. YCRD is available at http://cosbi.ee.ncku.edu.tw/YCRD/ or http://cosbi2.ee.ncku.edu.tw/YCRD/. PMID:27392072

  2. 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

  3. An Online Database Producer's Memoirs and Memories of an Online Pioneer and The Database Industry: Looking into the Future.

    ERIC Educational Resources Information Center

    Kollegger, James G.; And Others

    1988-01-01

    In the first of three articles, the producer of Energyline, Energynet, and Tele/Scope recalls the development of the databases and database business strategies. The second describes the development of biomedical online databases, and the third discusses future developments, including full text databases, database producers as online host, and…

  4. 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

  5. Database History: From Dinosaurs to Compact Discs.

    ERIC Educational Resources Information Center

    Neufeld, M. Lynne; Cornog, Martha

    1986-01-01

    Summarizes the growth of databases, including major milestones, issues, and trends of the past 20 years, during which time the database/online industry had become a large and thriving segment of the information industry. A time line overview of database developments from 1951 to 1985 is appended. (42 references) (EJS)

  6. Annual Review of Database Developments 1991.

    ERIC Educational Resources Information Center

    Basch, Reva

    1991-01-01

    Review of developments in databases highlights a new emphasis on accessibility. Topics discussed include the internationalization of databases; databases that deal with finance, drugs, and toxic waste; access to public records, both personal and corporate; media online; reducing large files of data to smaller, more manageable files; and…

  7. Selecting Software for a Development Information Database.

    ERIC Educational Resources Information Center

    Geethananda, Hemamalee

    1991-01-01

    Describes software selection criteria considered for use with the bibliographic database of the Development Information Network for South Asia (DEVINSA), which is located in Sri Lanka. Highlights include ease of database creation, database size, input, editing, data validation, inverted files, searching, storing searches, vocabulary control, user…

  8. Climate Change Database Development and Learning Networks Establishment

    NASA Astrophysics Data System (ADS)

    Zganjar, C.; Deblieu, J.; Bachelet, D.; Stanley, B.

    2007-12-01

    The Nature Conservancy is developing a comprehensive database that includes the most relevant climate change data for its conservation practitioners. The database is developed in close collaboration with the field. Data mining tools and web base interface are refined to simplify the acquisition and analysis of the relevant information such as future climate change scenarios. Significant challenges arise when local strategies to address climate change issues require land managers to develop new strategies to manage preserves or purchase properties. The resolution of future climate projections are usually too coarse and too uncertain to be considered as useful by practical land stewards. The Conservancy Climate Change Science Team is working in collaboration with government agencies, academia and other NGOs to quantify the uncertainty and package climate change information to help on the ground actions around the world. The team is also developing a climate change learning network to bridge the gap between scientific knowledge and on the ground expertise.

  9. Database machines

    NASA Technical Reports Server (NTRS)

    Stiefel, M. L.

    1983-01-01

    The functions and performance characteristics of data base machines (DBM), including machines currently being studied in research laboratories and those currently offered on a commerical basis are discussed. The cost/benefit considerations that must be recognized in selecting a DBM are discussed, as well as the future outlook for such machines.

  10. CIRRIE DATABASE

    EPA Science Inventory

    International rehabilitation research published between 1990 and the present. Over 18,000 citations. In addition to indexing from mainstream journals and Internet sites, CIRRIE also includes citations to resources not readily available to U.S. researchers. There are over 18,000 c...

  11. ARTI Refrigerant Database

    SciTech Connect

    Cain, J.M.

    1993-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

  12. Protein Model Database

    SciTech Connect

    Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

    2005-02-23

    The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

  13. MGFD: the maize gene families database

    PubMed Central

    Sheng, Lei; Jiang, Haiyang; Yan, Hanwei; Li, Xiaoyu; Lin, Yongxiang; Ye, Hui; Cheng, Beijiu

    2016-01-01

    Most gene families are transcription factor (TF) families, which have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and have been employed to manipulate various types of metabolic, developmental and stress response pathways in plants. Maize (Zea mays) is one of the most important cereal crops in the world due its importance to human nutrition and health. Thus, identifying and annotating all the gene families in maize is an important primary step in defining their functions and understanding their roles in the regulation of diverse biological processes. In this study, we identified 96 predicted maize gene families and systematically characterized all 5826 of the genes in those families. We have also developed a comprehensive database of maize gene families (the MGFD). To further explore the functions of these gene families, we extensively annotated the genes, including such basic information as protein sequence features, gene structure, Gene Ontology classifications, phylogenetic relationships and expression profiles. The MGFD has a user-friendly web interface with multiple browse and search functions, as well as data downloading. The MGFD is freely available to users at http://mgfd.ahau.edu.cn/. Database URL: http://mgfd.ahau.edu.cn/ PMID:26896848

  14. The Dfam database of repetitive DNA families.

    PubMed

    Hubley, Robert; Finn, Robert D; Clements, Jody; Eddy, Sean R; Jones, Thomas A; Bao, Weidong; Smit, Arian F A; Wheeler, Travis J

    2016-01-01

    Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download. PMID:26612867

  15. Database of small molecule thermochemistry for combustion.

    PubMed

    Goldsmith, C Franklin; Magoon, Gregory R; Green, William H

    2012-09-13

    High-accuracy ab initio thermochemistry is presented for 219 small molecules relevant in combustion chemistry, including many radical, biradical, and triplet species. These values are critical for accurate kinetic modeling. The RQCISD(T)/cc-PV∞QZ//B3LYP/6-311++G(d,p) method was used to compute the electronic energies. A bond additivity correction for this method has been developed to remove systematic errors in the enthalpy calculations, using the Active Thermochemical Tables as reference values. On the basis of comparison with the benchmark data, the 3σ uncertainty in the standard-state heat of formation is 0.9 kcal/mol, or within chemical accuracy. An uncertainty analysis is presented for the entropy and heat capacity. In many cases, the present values are the most accurate and comprehensive numbers available. The present work is compared to several published databases. In some cases, there are large discrepancies and errors in published databases; the present work helps to resolve these problems. PMID:22873426

  16. MGFD: the maize gene families database.

    PubMed

    Sheng, Lei; Jiang, Haiyang; Yan, Hanwei; Li, Xiaoyu; Lin, Yongxiang; Ye, Hui; Cheng, Beijiu

    2016-01-01

    Most gene families are transcription factor (TF) families, which have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and have been employed to manipulate various types of metabolic, developmental and stress response pathways in plants. Maize (Zea mays) is one of the most important cereal crops in the world due its importance to human nutrition and health. Thus, identifying and annotating all the gene families in maize is an important primary step in defining their functions and understanding their roles in the regulation of diverse biological processes. In this study, we identified 96 predicted maize gene families and systematically characterized all 5826 of the genes in those families. We have also developed a comprehensive database of maize gene families (the MGFD). To further explore the functions of these gene families, we extensively annotated the genes, including such basic information as protein sequence features, gene structure, Gene Ontology classifications, phylogenetic relationships and expression profiles. The MGFD has a user-friendly web interface with multiple browse and search functions, as well as data downloading. The MGFD is freely available to users at http://mgfd.ahau.edu.cn/. Database URL: http://mgfd.ahau.edu.cn/. PMID:26896848

  17. The Dfam database of repetitive DNA families

    PubMed Central

    Hubley, Robert; Finn, Robert D.; Clements, Jody; Eddy, Sean R.; Jones, Thomas A.; Bao, Weidong; Smit, Arian F.A.; Wheeler, Travis J.

    2016-01-01

    Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download. PMID:26612867

  18. Lessons Learned From Developing Reactor Pressure Vessel Steel Embrittlement Database

    SciTech Connect

    Wang, Jy-An John

    2010-08-01

    Materials behaviors caused by neutron irradiation under fission and/or fusion environments can be little understood without practical examination. Easily accessible material information system with large material database using effective computers is necessary for design of nuclear materials and analyses or simulations of the phenomena. The developed Embrittlement Data Base (EDB) at ORNL is this comprehensive collection of data. EDB database contains power reactor pressure vessel surveillance data, the material test reactor data, foreign reactor data (through bilateral agreements authorized by NRC), and the fracture toughness data. The lessons learned from building EDB program and the associated database management activity regarding Material Database Design Methodology, Architecture and the Embedded QA Protocol are described in this report. The development of IAEA International Database on Reactor Pressure Vessel Materials (IDRPVM) and the comparison of EDB database and IAEA IDRPVM database are provided in the report. The recommended database QA protocol and database infrastructure are also stated in the report.

  19. New geothermal database for Utah

    USGS Publications Warehouse

    Blackett, Robert E.

    1993-01-01

    The Utah Geological Survey complied a preliminary database consisting of over 800 records on thermal wells and springs in Utah with temperatures of 20??C or greater. Each record consists of 35 fields, including location of the well or spring, temperature, depth, flow-rate, and chemical analyses of water samples. Developed for applications on personal computers, the database will be useful for geochemical, statistical, and other geothermal related studies. A preliminary map of thermal wells and springs in Utah, which accompanies the database, could eventually incorporate heat-flow information, bottom-hole temperatures from oil and gas wells, traces of Quaternary faults, and locations of young volcanic centers.

  20. The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

    PubMed Central

    Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2013-01-01

    The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:23203983

  1. SynProt: A Database for Proteins of Detergent-Resistant Synaptic Protein Preparations

    PubMed Central

    Pielot, Rainer; Smalla, Karl-Heinz; Müller, Anke; Landgraf, Peter; Lehmann, Anne-Christin; Eisenschmidt, Elke; Haus, Utz-Uwe; Weismantel, Robert; Gundelfinger, Eckart D.; Dieterich, Daniela C.

    2012-01-01

    Chemical synapses are highly specialized cell–cell contacts for communication between neurons in the CNS characterized by complex and dynamic protein networks at both synaptic membranes. The cytomatrix at the active zone (CAZ) organizes the apparatus for the regulated release of transmitters from the presynapse. At the postsynaptic side, the postsynaptic density constitutes the machinery for detection, integration, and transduction of the transmitter signal. Both pre- and postsynaptic protein networks represent the molecular substrates for synaptic plasticity. Their function can be altered both by regulating their composition and by post-translational modification of their components. For a comprehensive understanding of synaptic networks the entire ensemble of synaptic proteins has to be considered. To support this, we established a comprehensive database for synaptic junction proteins (SynProt database) primarily based on proteomics data obtained from biochemical preparations of detergent-resistant synaptic junctions. The database currently contains 2,788 non-redundant entries of rat, mouse, and some human proteins, which mainly have been manually extracted from 12 proteomic studies and annotated for synaptic subcellular localization. Each dataset is completed with manually added information including protein classifiers as well as automatically retrieved and updated information from public databases (UniProt and PubMed). We intend that the database will be used to support modeling of synaptic protein networks and rational experimental design. PMID:22737123

  2. Data Conversion and Indexing: How To Get the Most out of Your Machine-Readable Database. DataResearch Automation Guide Series, Number Two.

    ERIC Educational Resources Information Center

    Data Research Associates, Inc., St. Louis, MO.

    In today's library environment, the library's most important asset is its machine-readable database. In order to maintain this investment, Data Research Associates provides several comprehensive data conversion services, including retrospective conversion and authority control. For bibliographic records not yet in MARC (machine readable…

  3. The GLIMS Glacier Database

    NASA Astrophysics Data System (ADS)

    Raup, B. H.; Khalsa, S. S.; Armstrong, R.

    2007-12-01

    Info, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

  4. The TOAR Database of Global Surface Ozone Observations

    NASA Astrophysics Data System (ADS)

    Schultz, M. G.

    2015-12-01

    We constructed a comprehensive database of long-term global surface ozone observations for use in the Tropospheric Ozone Assessment Report (TOAR) analyses. Currently, the database contains more than 7000 data records primarily from open access archives, but we are increasingly receiving additional data from various national or state networks or individual researchers which have never before been included in global compilations. Time resolution of ozone data in the archive is hourly. The data are accompanied by detailed metadata with harmonized content. A modern web interface allows easy access and visualisation of the data. Standardized quality control plots are available for each dataset and we are combining fragmented data to allow for longer-term analyses where this is applicable. We are in close contact with the data providers in order to ensure correctness and robustness of th edata and metadata and to keep the database up-to-date. An extensive set of metrics for analysis of health or vegetation impacts and for evaluation of regional and global atmospheric chemistry models will be made available soon. The TOAR database and web interface at Juelich form an essential part of the TOAR initiative and prompts further investigation of the statistical robustness of ozone metrics.

  5. TreeGenes: A Forest Tree Genome Database

    PubMed Central

    Wegrzyn, Jill L.; Lee, Jennifer M.; Tearse, Brandon R.; Neale, David B.

    2008-01-01

    The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange. PMID:18725987

  6. A traceable quantitative infrared spectral database of chemical agents

    NASA Astrophysics Data System (ADS)

    Samuels, Alan C.; Williams, Barry R.; Ben-David, Avishai; Hulet, Melissa; Roelant, Geoffrey J.; Miles, Ronald W., Jr.; Green, Norman; Zhu, Changjiang

    2004-12-01

    Recent experimental field trials have demonstrated the ability of both Fourier transform infrared (FTIR) and active light detection and ranging (LIDAR) sensors to detect particulate matter, including simulants for biological materials. Both systems require a reliable, validated, quantitative database of the mid infrared spectra of the targeted threat agents. While several databases are available, none are validated and traceable to primary standards for reference quality reliability. Most of the existing chemical agent databases have been developed using a bubbler or syringe-fed vapor generator, and all are fraught with errors and uncertainties as a result. In addition, no quantitative condensed phase data on the low volatility chemicals and biological agents have been reported. We are filling this data gap through the systematic measurement of gas phase chemical agent materials generated using a unique vapor-liquid equilibrium approach that allows the quantitation of the cross-sections using a mass measurement calibrated to primary, National Institutes of Standards and Technology (NIST) standards. In addition, we have developed quantitative methods for the measurement of condensed phase materials in both transmission and diffuse reflectance modes. The latter data are valuable for the development of complex index of refraction data, which is required for both system modeling and algorithm development of both FTIR and LIDAR based sensor systems. We will describe our measurement approach and progress toward compiling the first known comprehensive and validated database of both vapor and condensed phase chemical warfare agents.

  7. The European Narcolepsy Network (EU-NN) database.

    PubMed

    Khatami, Ramin; Luca, Gianina; Baumann, Christian R; Bassetti, Claudio L; Bruni, Oliviero; Canellas, Francesca; Dauvilliers, Yves; Del Rio-Villegas, Rafael; Feketeova, Eva; Ferri, Raffaele; Geisler, Peter; Högl, Birgit; Jennum, Poul; Kornum, Birgitte R; Lecendreux, Michel; Martins-da-Silva, Antonio; Mathis, Johannes; Mayer, Geert; Paiva, Teresa; Partinen, Markku; Peraita-Adrados, Rosa; Plazzi, Guiseppe; Santamaria, Joan; Sonka, Karel; Riha, Renata; Tafti, Mehdi; Wierzbicka, Aleksandra; Young, Peter; Lammers, Gert Jan; Overeem, Sebastiaan

    2016-06-01

    Narcolepsy with cataplexy is a rare disease with an estimated prevalence of 0.02% in European populations. Narcolepsy shares many features of rare disorders, in particular the lack of awareness of the disease with serious consequences for healthcare supply. Similar to other rare diseases, only a few European countries have registered narcolepsy cases in databases of the International Classification of Diseases or in registries of the European health authorities. A promising approach to identify disease-specific adverse health effects and needs in healthcare delivery in the field of rare diseases is to establish a distributed expert network. A first and important step is to create a database that allows collection, storage and dissemination of data on narcolepsy in a comprehensive and systematic way. Here, the first prospective web-based European narcolepsy database hosted by the European Narcolepsy Network is introduced. The database structure, standardization of data acquisition and quality control procedures are described, and an overview provided of the first 1079 patients from 18 European specialized centres. Due to its standardization this continuously increasing data pool is most promising to provide a better insight into many unsolved aspects of narcolepsy and related disorders, including clear phenotype characterization of subtypes of narcolepsy, more precise epidemiological data and knowledge on the natural history of narcolepsy, expectations about treatment effects, identification of post-marketing medication side-effects, and will contribute to improve clinical trial designs and provide facilities to further develop phase III trials. PMID:26809504

  8. A database for The Geysers geothermal field

    SciTech Connect

    Bodvarsson, G.S.; Cox, B.L.; Fuller, P.; Ripperda, M.; Tulinius, H.; Witherspoon, P.A.; Goldstein, N.; Flexser, S.; Pruess, K. ); Truesdell, A. )

    1989-09-01

    In Fiscal Year 1985-1986 the Earth Sciences Division of Lawrence Berkeley Laboratory (LBL) began a multi-year project for SLC to organize and analyze the field data from The Geysers. In the first year, most of the work concentrated on the development of a comprehensive database for The Geysers, and conventional reservoir engineering analysis of the data. Essentially, all non-proprietary data for wells at The Geysers have been incorporated into the database, as well as proprietary data from wells located on State leases. In following years, a more detailed analysis of The Geysers data has been carried out. This report is a summary of the non- proprietary work performed in FY 1985--1986. It describes various aspects of the database and also includes: review sections on Field Development, Geology, Geophysics, Geochemistry and Reservoir Engineering. It should be emphasized that these background chapters were written in 1986, and therefore only summarize the information available at that time. The appendices contain individual plots of wellhead pressures, degree of superheat, steam flow rates, cumulative mass flows, injection rates and cumulative injection through 1988 for approximately 250 wells. All of the data contained in this report are non-proprietary, from State and non-State leases. The production/injection and heat flow data from the wells were obtained from the California State Division of Oil and gas (DOG) (courtesy of Dick Thomas). Most of the other data were obtained from SLC files in Sacramento (courtesy of Charles Priddy), or DOG files in Santa Rosa (courtesy of Ken Stelling). 159 refs., 23 figs., 3 tabs.

  9. The Cambridge Structural Database

    PubMed Central

    Groom, Colin R.; Bruno, Ian J.; Lightfoot, Matthew P.; Ward, Suzanna C.

    2016-01-01

    The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface. PMID:27048719

  10. The Cambridge Structural Database.

    PubMed

    Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

    2016-04-01

    The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface. PMID:27048719

  11. State Analysis Database Tool

    NASA Technical Reports Server (NTRS)

    Rasmussen, Robert; Bennett, Matthew

    2006-01-01

    The State Analysis Database Tool software establishes a productive environment for collaboration among software and system engineers engaged in the development of complex interacting systems. The tool embodies State Analysis, a model-based system engineering methodology founded on a state-based control architecture (see figure). A state represents a momentary condition of an evolving system, and a model may describe how a state evolves and is affected by other states. The State Analysis methodology is a process for capturing system and software requirements in the form of explicit models and states, and defining goal-based operational plans consistent with the models. Requirements, models, and operational concerns have traditionally been documented in a variety of system engineering artifacts that address different aspects of a mission s lifecycle. In State Analysis, requirements, models, and operations information are State Analysis artifacts that are consistent and stored in a State Analysis Database. The tool includes a back-end database, a multi-platform front-end client, and Web-based administrative functions. The tool is structured to prompt an engineer to follow the State Analysis methodology, to encourage state discovery and model description, and to make software requirements and operations plans consistent with model descriptions.

  12. Multi-Database Searching in Forensic Psychology.

    ERIC Educational Resources Information Center

    Piotrowski, Chris; Perdue, Robert W.

    Traditional library skills have been augmented since the introduction of online computerized database services. Because of the complexity of the field, forensic psychology can benefit enormously from the application of comprehensive bibliographic search strategies. The study reported here demonstrated the bibliographic results obtained when a…

  13. Teach with Databases: Toxics Release Inventory. [Multimedia].

    ERIC Educational Resources Information Center

    Barracato, Jay; Spooner, Barbara

    This curriculum unit provides students with real world applications of science as it pertains to toxic releases into the environment. This boxed package contains the Toxics Release Inventory (TRI) Teacher's Guide, TRI Database Basics guide, comprehensive TRI compact disk with user's guide, "Getting Started: A Guide to Bringing Environmental…

  14. Database of Properties of Meteors

    NASA Technical Reports Server (NTRS)

    Suggs, Rob; Anthea, Coster

    2006-01-01

    A database of properties of meteors, and software that provides access to the database, are being developed as a contribution to continuing efforts to model the characteristics of meteors with increasing accuracy. Such modeling is necessary for evaluation of the risk of penetration of spacecraft by meteors. For each meteor in the database, the record will include an identification, date and time, radiant properties, ballistic coefficient, radar cross section, size, density, and orbital elements. The property of primary interest in the present case is density, and one of the primary goals in this case is to derive densities of meteors from their atmospheric decelerations. The database and software are expected to be valid anywhere in the solar system. The database will incorporate new data plus results of meteoroid analyses that, heretofore, have not been readily available to the aerospace community. Taken together, the database and software constitute a model that is expected to provide improved estimates of densities and to result in improved risk analyses for interplanetary spacecraft. It is planned to distribute the database and software on a compact disk.

  15. Database tomography for commercial application

    NASA Technical Reports Server (NTRS)

    Kostoff, Ronald N.; Eberhart, Henry J.

    1994-01-01

    Database tomography is a method for extracting themes and their relationships from text. The algorithms, employed begin with word frequency and word proximity analysis and build upon these results. When the word 'database' is used, think of medical or police records, patents, journals, or papers, etc. (any text information that can be computer stored). Database tomography features a full text, user interactive technique enabling the user to identify areas of interest, establish relationships, and map trends for a deeper understanding of an area of interest. Database tomography concepts and applications have been reported in journals and presented at conferences. One important feature of the database tomography algorithm is that it can be used on a database of any size, and will facilitate the users ability to understand the volume of content therein. While employing the process to identify research opportunities it became obvious that this promising technology has potential applications for business, science, engineering, law, and academe. Examples include evaluating marketing trends, strategies, relationships and associations. Also, the database tomography process would be a powerful component in the area of competitive intelligence, national security intelligence and patent analysis. User interests and involvement cannot be overemphasized.

  16. 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…

  17. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

    PubMed

    Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

    2008-01-01

    The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org. PMID:17932055

  18. Comprehensive Repertoire of Foldable Regions within Whole Genomes

    PubMed Central

    Faure, Guilhem; Callebaut, Isabelle

    2013-01-01

    In order to get a comprehensive repertoire of foldable domains within whole proteomes, including orphan domains, we developed a novel procedure, called SEG-HCA. From only the information of a single amino acid sequence, SEG-HCA automatically delineates segments possessing high densities in hydrophobic clusters, as defined by Hydrophobic Cluster Analysis (HCA). These hydrophobic clusters mainly correspond to regular secondary structures, which together form structured or foldable regions. Genome-wide analyses revealed that SEG-HCA is opposite of disorder predictors, both addressing distinct structural states. Interestingly, there is however an overlap between the two predictions, including small segments of disordered sequences, which undergo coupled folding and binding. SEG-HCA thus gives access to these specific domains, which are generally poorly represented in domain databases. Comparison of the whole set of SEG-HCA predictions with the Conserved Domain Database (CDD) also highlighted a wide proportion of predicted large (length >50 amino acids) segments, which are CDD orphan. These orphan sequences may either correspond to highly divergent members of already known families or belong to new families of domains. Their comprehensive description thus opens new avenues to investigate new functional and/or structural features, which remained so far uncovered. Altogether, the data described here provide new insights into the protein architecture and organization throughout the three kingdoms of life. PMID:24204229

  19. NOAA Data Rescue of Key Solar Databases and Digitization of Historical Solar Images

    NASA Astrophysics Data System (ADS)

    Coffey, H. E.

    2006-08-01

    Over a number of years, the staff at NOAA National Geophysical Data Center (NGDC) has worked to rescue key solar databases by converting them to digital format and making them available via the World Wide Web. NOAA has had several data rescue programs where staff compete for funds to rescue important and critical historical data that are languishing in archives and at risk of being lost due to deteriorating condition, loss of any metadata or descriptive text that describe the databases, lack of interest or funding in maintaining databases, etc. The Solar-Terrestrial Physics Division at NGDC was able to obtain funds to key in some critical historical tabular databases. Recently the NOAA Climate Database Modernization Program (CDMP) funded a project to digitize historical solar images, producing a large online database of historical daily full disk solar images. The images include the wavelengths Calcium K, Hydrogen Alpha, and white light photos, as well as sunspot drawings and the comprehensive drawings of a multitude of solar phenomena on one daily map (Fraunhofer maps and Wendelstein drawings). Included in the digitization are high resolution solar H-alpha images taken at the Boulder Solar Observatory 1967-1984. The scanned daily images document many phases of solar activity, from decadal variation to rotational variation to daily changes. Smaller versions are available online. Larger versions are available by request. See http://www.ngdc.noaa.gov/stp/SOLAR/ftpsolarimages.html. The tabular listings and solar imagery will be discussed.

  20. Overview of selected molecular biological databases

    SciTech Connect

    Rayl, K.D.; Gaasterland, T.

    1994-11-01

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  1. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  2. Creating databases for biological information: an introduction.

    PubMed

    Stein, Lincoln

    2013-06-01

    The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, relational databases, and NoSQL databases. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system. PMID:23749755

  3. The Hidden Dimensions of Databases.

    ERIC Educational Resources Information Center

    Jacso, Peter

    1994-01-01

    Discusses methods of evaluating commercial online databases and provides examples that illustrate their hidden dimensions. Topics addressed include size, including the number of records or the number of titles; the number of years covered; and the frequency of updates. Comparisons of Readers' Guide Abstracts and Magazine Article Summaries are…

  4. The CIS Database: Occupational Health and Safety Information Online.

    ERIC Educational Resources Information Center

    Siegel, Herbert; Scurr, Erica

    1985-01-01

    Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

  5. The role of databases in areawide pest management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A database is a comprehensive collection of related data organized for convenient access, generally in a computer. The evolution of computer software and the need to distinguish the specialized computer systems for storing and manipulating data, stimulated development of database management systems...

  6. Accessing the BIOSIS Previews Database in Clinical Psychology.

    ERIC Educational Resources Information Center

    Piotrowski, Chris; Perdue, Bob

    The efficacy of using the BIOSIS Previews database as an online information retrieval tool in clinical psychology was investigated in a study conducted at the University of West Florida. Recognizing the importance of multi-database searching strategies when seeking comprehensive results, this study compared the citation output of this…

  7. A Comprehensive Urban Atmosphere Database: The Urgent Archive At Badc

    NASA Astrophysics Data System (ADS)

    de Rudder, A.

    Launched by the British Natural Environment Research Council (NERC) in 1996, the Urban Regeneration and the Environment (URGENT) thematic programme funds 41 research projects related to urban pollution of water, soil, air and ecology and to the assessment of its influence on human health. The studies focus on urban and suburban areas in Great Britain. Fourteen of them pertain to atmospheric research and address issues as diverse as urban meteorology, dispersion of pollutants, homogeneous and heterogeneous chemistry, aerosol particle size distribution and composition, urban tree planting in relation to air composition, and particle toxicity. Adopted methodologies range from the analysis of data from field experiments to model simulations, often combining both. A few projects are interconnected; some conduct studies in collabo- ration with municipal authorities or industry. In addition to their scientific nature, some of the deliverables target an audience of urban planners and city council officials. Data collected or generated by the air projects are currently being submitted to the British Atmospheric Data Centre (BADC), which is the body designated by NERC to archive, maintain and distribute atmospheric data sets issued by NERC funded re- search and to provide support to researchers in issues related to data. The access to the data, which is kept restricted to the programme participants during the year following each project end, will be made public afterwards: by the end of 2002, two thirds of the archived data will have been released to the public domain. The present contribution will give a synthetic overview of the URGENT air project topics and deliverables and will outline the data distribution system of the BADC.

  8. Content Evaluation of Textual CD-ROM and Web Databases. Database Searching Series.

    ERIC Educational Resources Information Center

    Jacso, Peter

    This book provides guidelines for evaluating a variety of database types, including abstracting and indexing, directory, full-text, and page-image databases available in online and/or CD-ROM formats. The book discusses the purpose and techniques of comparing and evaluating the most important characteristics of textual databases, such as their…

  9. PanSNPdb: The Pan-Asian SNP Genotyping Database

    PubMed Central

    Ngamphiw, Chumpol; Assawamakin, Anunchai; Xu, Shuhua; Shaw, Philip J.; Yang, Jin Ok; Ghang, Ho; Bhak, Jong; Liu, Edison; Tongsima, Sissades

    2011-01-01

    The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP. PMID:21731755

  10. EMAGE mouse embryo spatial gene expression database: 2014 update.

    PubMed

    Richardson, Lorna; Venkataraman, Shanmugasundaram; Stevenson, Peter; Yang, Yiya; Moss, Julie; Graham, Liz; Burton, Nicholas; Hill, Bill; Rao, Jianguo; Baldock, Richard A; Armit, Chris

    2014-01-01

    EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities. PMID:24265223

  11. The mouse genome informatics and the mouse genome database

    SciTech Connect

    Maltais, L.J.; Blackburn, R.E.; Bradt, D.W.

    1994-09-01

    The Mouse Genome Database (MGD) is a centralized, comprehensive database of the mouse genome that includes genetic mapping data, comparative mapping data, gene descriptions, mutant phenotype descriptions, strains and allelic polymorphism data, inbred strain characteristics, physical mapping data, and molecular probes and clones data. Data in MGD are obtained from the published literature and by electronic transfer from laboratories working on large backcross panels of mice. MGD provides tools that enable the user to search the database, retrieve data, generate reports, analyze data, annotate records, and build genetic maps. The Encyclopedia of the Mouse Genome provides a graphic user interface to mouse genome data. It consists of software tools including: LinkMap, a graphic display of genetic linkage maps with the ability to magnify regions of high locus density: CytoMap, a graphic display of cytogenetic maps showing banded chromosomes with cytogenetic locations of genes and chromosomal aberrations; CATS, a catalog searching tool for text retrieval of mouse locus descriptions. These software tools provide access to the following data sets: Chromosome Committee Reports, MIT Genome Center data, GBASE reports, Mouse Locus Catalog (MLC), and Mouse Cytogenetic Mapping Data. The MGD is available to the scientific community through the World Wide Web (WWW) and Gopher. In addition GBASE can be accessed via the Internet.

  12. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

    PubMed

    Galperin, Michael Y; Fernández-Suárez, Xosé M

    2012-01-01

    The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). PMID:22144685

  13. SmallSat Database

    NASA Technical Reports Server (NTRS)

    Petropulos, Dolores; Bittner, David; Murawski, Robert; Golden, Bert

    2015-01-01

    The SmallSat has an unrealized potential in both the private industry and in the federal government. Currently over 70 companies, 50 universities and 17 governmental agencies are involved in SmallSat research and development. In 1994, the U.S. Army Missile and Defense mapped the moon using smallSat imagery. Since then Smart Phones have introduced this imagery to the people of the world as diverse industries watched this trend. The deployment cost of smallSats is also greatly reduced compared to traditional satellites due to the fact that multiple units can be deployed in a single mission. Imaging payloads have become more sophisticated, smaller and lighter. In addition, the growth of small technology obtained from private industries has led to the more widespread use of smallSats. This includes greater revisit rates in imagery, significantly lower costs, the ability to update technology more frequently and the ability to decrease vulnerability of enemy attacks. The popularity of smallSats show a changing mentality in this fast paced world of tomorrow. What impact has this created on the NASA communication networks now and in future years? In this project, we are developing the SmallSat Relational Database which can support a simulation of smallSats within the NASA SCaN Compatability Environment for Networks and Integrated Communications (SCENIC) Modeling and Simulation Lab. The NASA Space Communications and Networks (SCaN) Program can use this modeling to project required network support needs in the next 10 to 15 years. The SmallSat Rational Database could model smallSats just as the other SCaN databases model the more traditional larger satellites, with a few exceptions. One being that the smallSat Database is designed to be built-to-order. The SmallSat database holds various hardware configurations that can be used to model a smallSat. It will require significant effort to develop as the research material can only be populated by hand to obtain the unique data

  14. Comprehension of Discourse Markers and Reading Comprehension

    ERIC Educational Resources Information Center

    Khatib, Mohamad

    2011-01-01

    According to many research findings, the presence of discourse markers (DMs) enhances readers' comprehension of the texts they read. However, there is a paucity of research on the relationship between knowledge of DMs and reading comprehension (RC) and the present study explores the relationship between them. Knowledge of DMs is measured through…

  15. Idaho Chemical Processing Plant failure rate database

    SciTech Connect

    Alber, T.G.; Hunt, C.R.; Fogarty, S.P.; Wilson, J.R.

    1995-08-01

    This report represents the first major upgrade to the Idaho Chemical Processing Plant (ICPP) Failure Rate Database. This upgrade incorporates additional site-specific and generic data while improving on the previous data reduction techniques. In addition, due to a change in mission at the ICPP, the status of certain equipment items has changed from operating to standby or off-line. A discussion of how this mission change influenced the relevance of failure data also has been included. This report contains two data sources: the ICPP Failure Rate Database and a generic failure rate database. A discussion is presented on the approaches and assumptions used to develop the data in the ICPP Failure Rate Database. The generic database is included along with a short discussion of its application. A brief discussion of future projects recommended to strengthen and lend credibility to the ICPP Failure Rate Database also is included.

  16. Marine casualty and pollution database (raw data only) (on CD-ROM). Data file

    SciTech Connect

    1998-06-01

    The Marine Casualty and Pollution Database provides details about marine casualty and pollution incidents investigated by the US Coast Guard Marine Safety Officer. The database is an invaluable source of information to understand particulars and circumstances of marine accidents and pollution incidents. The CD-ROM contains forty data tables derived from marine casualty and pollution investigations conducted by investigators at US Coast Guard Marine Safety Offices throughout the United States. The data collection period began in 1973 and is ongoing. Also included on the CD-ROM are vessel and facility tables with specific information on vessel and facility constitution and operating details. The Coast Guard maintains a comprehensive database on approximately 460,000 US and foreign vessels and 32,000 facilities. Entity and attribute descriptions and suggested solutions to general marine pollution, vessel casualty, and personnel injury and death questions are outlined in the documentation.

  17. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

    PubMed Central

    Fernández-Suárez, Xosé M.; Rigden, Daniel J.; Galperin, Michael Y.

    2014-01-01

    The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI’s MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:24316579

  18. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

    PubMed

    Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

    2014-01-01

    The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:24316579

  19. 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

  20. Mars Global Digital Dune Database: MC2-MC29

    USGS Publications Warehouse

    Hayward, Rosalyn K.; Mullins, Kevin F.; Fenton, L.K.; Hare, T.M.; Titus, T.N.; Bourke, M.C.; Colaprete, Anthony; Christensen, P.R.

    2007-01-01

    Introduction The Mars Global Digital Dune Database presents data and describes the methodology used in creating the database. The database provides a comprehensive and quantitative view of the geographic distribution of moderate- to large-size dune fields from 65? N to 65? S latitude and encompasses ~ 550 dune fields. The database will be expanded to cover the entire planet in later versions. Although we have attempted to include all dune fields between 65? N and 65? S, some have likely been excluded for two reasons: 1) incomplete THEMIS IR (daytime) coverage may have caused us to exclude some moderate- to large-size dune fields or 2) resolution of THEMIS IR coverage (100m/pixel) certainly caused us to exclude smaller dune fields. The smallest dune fields in the database are ~ 1 km2 in area. While the moderate to large dune fields are likely to constitute the largest compilation of sediment on the planet, smaller stores of sediment of dunes are likely to be found elsewhere via higher resolution data. Thus, it should be noted that our database excludes all small dune fields and some moderate to large dune fields as well. Therefore the absence of mapped dune fields does not mean that such dune fields do not exist and is not intended to imply a lack of saltating sand in other areas. Where availability and quality of THEMIS visible (VIS) or Mars Orbiter Camera narrow angle (MOC NA) images allowed, we classifed dunes and included dune slipface measurements, which were derived from gross dune morphology and represent the prevailing wind direction at the last time of significant dune modification. For dunes located within craters, the azimuth from crater centroid to dune field centroid was calculated. Output from a general circulation model (GCM) is also included. In addition to polygons locating dune fields, the database includes over 1800 selected Thermal Emission Imaging System (THEMIS) infrared (IR), THEMIS visible (VIS) and Mars Orbiter Camera Narrow Angle (MOC NA

  1. Annual Review of Database Development: 1992.

    ERIC Educational Resources Information Center

    Basch, Reva

    1992-01-01

    Reviews recent trends in databases and online systems. Topics discussed include new access points for established databases; acquisitions, consolidations, and competition between vendors; European coverage; international services; online reference materials, including telephone directories; political and legal materials and public records;…

  2. Electronic Databases for Linguistic and Language Research.

    ERIC Educational Resources Information Center

    Oshika, Beatrice T.; Krausse, Sylvia C.

    1992-01-01

    Reviews electronic language data oriented specifically toward linguistic and language research, including machine-readable versions of established dictionaries; text databases, including newspapers and books; speech databases with phonetic/orthographic transcriptions; and bulletin boards and news groups available over computer networks. (17…

  3. The Molecular Biology Database Collection: 2004 update

    PubMed Central

    Galperin, Michael Y.

    2004-01-01

    The Molecular Biology Database Collection is a public resource listing key databases of value to the biologist, including those featured in this issue of Nucleic Acids Research, and other high-quality databases. All databases included in this Collection are freely available to the public. This listing aims to serve as a convenient starting point for searching the web for reliable information on various aspects of molecular biology, biochemistry and genetics. This year’s update includes 548 databases, 162 more than the previous one. The databases are organized in a hierarchical classification that should simplify finding the right database for each given task. Each database in the list comes with a recently updated brief description. The database list and the database descriptions can be accessed online at the Nucleic Acids Research web site http://nar.oupjournals.org/. The great challenge in biological research today is how to turn data into knowledge. I have met people who think data is knowledge but these people are then striving for a means of turning knowledge into understanding.Sydney Brenner. The Scientist 16[6]:12, March 18, 2002 PMID:14681349

  4. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

    PubMed Central

    Caspi, Ron; Billington, Richard; Ferrer, Luciana; Foerster, Hartmut; Fulcher, Carol A.; Keseler, Ingrid M.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Ong, Quang; Paley, Suzanne; Subhraveti, Pallavi; Weaver, Daniel S.; Karp, Peter D.

    2016-01-01

    The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service. PMID:26527732

  5. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002

    PubMed Central

    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present CyanOmics, a database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for systematic and comprehensive analysis of all those data. Powerful browsing and searching tools are integrated to help users directly access information of interest with enhanced visualization of the analytical results. Furthermore, Blast is included for sequence-based similarity searching and Cluster 3.0, as well as the R hclust function is provided for cluster analyses, to increase CyanOmics’s usefulness. To the best of our knowledge, it is the first integrated omics analysis database for cyanobacteria. This database should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp. PCC 7002 and other cyanobacteria. Additionally, the entire database framework is applicable to any sequenced prokaryotic genome and could be applied to other integrated omics analysis projects. Database URL: http://lag.ihb.ac.cn/cyanomics PMID:25632108

  6. Sharing the Load: A Planning Checklist for Consortial Database Use.

    ERIC Educational Resources Information Center

    Klingler, Tom

    1999-01-01

    Provides a checklist of concerns for libraries planning to implement shared research databases in a consortium environment, based on experiences at OhioLINK. Highlights include database selection criteria, licensing, pricing, funding, vendor considerations, database profiling, custom data processing, hardware selection, database access,…

  7. Mouse Phenome Database

    PubMed Central

    Grubb, Stephen C.; Bult, Carol J.; Bogue, Molly A.

    2014-01-01

    The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements. PMID:24243846

  8. Ribosomal Database Project II

    DOE Data Explorer

    The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial small-subunit 16S rRNA sequences. As of March 2008, RDP Release 10 is available and currently (August 2009) contains 1,074,075 aligned 16S rRNA sequences. Data that can be downloaded include zipped GenBank and FASTA alignment files, a histogram (in Excel) of the number of RDP sequences spanning each base position, data in the Functional Gene Pipeline Repository, and various user submitted data. The RDP-II website also provides numerous analysis tools.[From the RDP-II home page at http://rdp.cme.msu.edu/index.jsp

  9. Mouse phenome database.

    PubMed

    Grubb, Stephen C; Bult, Carol J; Bogue, Molly A

    2014-01-01

    The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements. PMID:24243846

  10. View generated database

    NASA Technical Reports Server (NTRS)

    Downward, James G.

    1992-01-01

    This document represents the final report for the View Generated Database (VGD) project, NAS7-1066. It documents the work done on the project up to the point at which all project work was terminated due to lack of project funds. The VGD was to provide the capability to accurately represent any real-world object or scene as a computer model. Such models include both an accurate spatial/geometric representation of surfaces of the object or scene, as well as any surface detail present on the object. Applications of such models are numerous, including acquisition and maintenance of work models for tele-autonomous systems, generation of accurate 3-D geometric/photometric models for various 3-D vision systems, and graphical models for realistic rendering of 3-D scenes via computer graphics.

  11. NeuroPep: a comprehensive resource of neuropeptides

    PubMed Central

    Wang, Yan; Wang, Mingxia; Yin, Sanwen; Jang, Richard; Wang, Jian; Xue, Zhidong; Xu, Tao

    2015-01-01

    Neuropeptides play a variety of roles in many physiological processes and serve as potential therapeutic targets for the treatment of some nervous-system disorders. In recent years, there has been a tremendous increase in the number of identified neuropeptides. Therefore, we have developed NeuroPep, a comprehensive resource of neuropeptides, which holds 5949 non-redundant neuropeptide entries originating from 493 organisms belonging to 65 neuropeptide families. In NeuroPep, the number of neuropeptides in invertebrates and vertebrates is 3455 and 2406, respectively. It is currently the most complete neuropeptide database. We extracted entries deposited in UniProt, the database (www.neuropeptides.nl) and NeuroPedia, and used text mining methods to retrieve entries from the MEDLINE abstracts and full text articles. All the entries in NeuroPep have been manually checked. 2069 of the 5949 (35%) neuropeptide sequences were collected from the scientific literature. Moreover, NeuroPep contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures (if available) and literature references. Information derived from these peptide sequences such as amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. A quick search feature allows users to search the database with keywords such as sequence, name, family, etc., and an advanced search page helps users to combine queries with logical operators like AND/OR. In addition, user-friendly web tools like browsing, sequence alignment and mapping are also integrated into the NeuroPep database. Database URL: http://isyslab.info/NeuroPep PMID:25931458

  12. NeuroPep: a comprehensive resource of neuropeptides.

    PubMed

    Wang, Yan; Wang, Mingxia; Yin, Sanwen; Jang, Richard; Wang, Jian; Xue, Zhidong; Xu, Tao

    2015-01-01

    Neuropeptides play a variety of roles in many physiological processes and serve as potential therapeutic targets for the treatment of some nervous-system disorders. In recent years, there has been a tremendous increase in the number of identified neuropeptides. Therefore, we have developed NeuroPep, a comprehensive resource of neuropeptides, which holds 5949 non-redundant neuropeptide entries originating from 493 organisms belonging to 65 neuropeptide families. In NeuroPep, the number of neuropeptides in invertebrates and vertebrates is 3455 and 2406, respectively. It is currently the most complete neuropeptide database. We extracted entries deposited in UniProt, the database (www.neuropeptides.nl) and NeuroPedia, and used text mining methods to retrieve entries from the MEDLINE abstracts and full text articles. All the entries in NeuroPep have been manually checked. 2069 of the 5949 (35%) neuropeptide sequences were collected from the scientific literature. Moreover, NeuroPep contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures (if available) and literature references. Information derived from these peptide sequences such as amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. A quick search feature allows users to search the database with keywords such as sequence, name, family, etc., and an advanced search page helps users to combine queries with logical operators like AND/OR. In addition, user-friendly web tools like browsing, sequence alignment and mapping are also integrated into the NeuroPep database. Database URL: http://isyslab.info/NeuroPep PMID:25931458

  13. A Magnetic Petrology Database for Satellite Magnetic Anomaly Interpretations

    NASA Astrophysics Data System (ADS)

    Nazarova, K.; Wasilewski, P.; Didenko, A.; Genshaft, Y.; Pashkevich, I.

    2002-05-01

    A Magnetic Petrology Database (MPDB) is now being compiled at NASA/Goddard Space Flight Center in cooperation with Russian and Ukrainian Institutions. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via Internet for more realistic interpretation of satellite magnetic anomalies. Magnetic Petrology Data had been accumulated in NASA/Goddard Space Flight Center, United Institute of Physics of the Earth (Russia) and Institute of Geophysics (Ukraine) over several decades and now consists of many thousands of records of data in our archives. The MPDB was, and continues to be in big demand especially since recent launching in near Earth orbit of the mini-constellation of three satellites - Oersted (in 1999), Champ (in 2000), and SAC-C (in 2000) which will provide lithospheric magnetic maps with better spatial and amplitude resolution (about 1 nT). The MPDB is focused on lower crustal and upper mantle rocks and will include data on mantle xenoliths, serpentinized ultramafic rocks, granulites, iron quartzites and rocks from Archean-Proterozoic metamorphic sequences from all around the world. A substantial amount of data is coming from the area of unique Kursk Magnetic Anomaly and Kola Deep Borehole (which recovered 12 km of continental crust). A prototype MPDB can be found on the Geodynamics Branch web server of Goddard Space Flight Center at http://core2.gsfc.nasa.gov/terr_mag/magnpetr.html. The MPDB employs a searchable relational design and consists of 7 interrelated tables. The schema of database is shown at http://core2.gsfc.nasa.gov/terr_mag/doc.html. MySQL database server was utilized to implement MPDB. The SQL (Structured Query Language) is used to query the database. To present the results of queries on WEB and for WEB programming we utilized PHP scripting language and CGI scripts. The prototype MPDB is designed to search database by major satellite magnetic

  14. Physiological Information Database (PID)

    EPA Science Inventory

    EPA has developed a physiological information database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence as well as similar data for laboratory animal spec...

  15. Network II Database

    Energy Science and Technology Software Center (ESTSC)

    1994-11-07

    The Oak Ridge National Laboratory (ORNL) Rail and Barge Network II Database is a representation of the rail and barge system of the United States. The network is derived from the Federal Rail Administration (FRA) rail database.

  16. Household Products Database: Pesticides

    MedlinePlus

    ... Names Types of Products Manufacturers Ingredients About the Database FAQ Product Recalls Help Glossary Contact Us More ... holders. Information is extracted from Consumer Product Information Database ©2001-2015 by DeLima Associates. All rights reserved. ...

  17. TeloPIN: a database of telomeric proteins interaction network in mammalian cells

    PubMed Central

    Luo, Zhenhua; Dai, Zhiming; Xie, Xiaowei; Feng, Xuyang; Liu, Dan; Songyang, Zhou; Xiong, Yuanyan

    2015-01-01

    Interaction network surrounding telomeres has been intensively studied during the past two decades. However, no specific resource by integrating telomere interaction information data is currently available. To facilitate the understanding of the molecular interaction network by which telomeres are associated with biological process and diseases, we have developed TeloPIN (Telomeric Proteins Interaction Network) database (http://songyanglab.sysu.edu.cn/telopin/), a novel database that points to provide comprehensive information on protein–protein, protein–DNA and protein–RNA interaction of telomeres. TeloPIN database contains four types of interaction data, including (i) protein–protein interaction (PPI) data, (ii) telomeric proteins ChIP-seq data, (iii) telomere-associated proteins data and (iv) telomeric repeat-containing RNAs (TERRA)-interacting proteins data. By analyzing these four types of interaction data, we found that 358 and 199 proteins have more than one type of interaction information in human and mouse cells, respectively. We also developed table browser and TeloChIP genome browser to help researchers with better integrated visualization of interaction data from different studies. The current release of TeloPIN database includes 1111 PPI, eight telomeric protein ChIP-seq data sets, 1391 telomere-associated proteins and 183 TERRA-interacting proteins from 92 independent studies in mammalian cells. The interaction information provided by TeloPIN database will greatly expand our knowledge of telomeric proteins interaction network. Database URL: TeloPIN database address is http://songyanglab.sysu.edu.cn/telopin. TeloPIN database is freely available to non-commercial use. PMID:25792605

  18. MPlus Database system

    SciTech Connect

    Not Available

    1989-01-20

    The MPlus Database program was developed to keep track of mail received. This system was developed by TRESP for the Department of Energy/Oak Ridge Operations. The MPlus Database program is a PC application, written in dBase III+'' and compiled with Clipper'' into an executable file. The files you need to run the MPLus Database program can be installed on a Bernoulli, or a hard drive. This paper discusses the use of this database.

  19. Mission and Assets Database

    NASA Technical Reports Server (NTRS)

    Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

    2009-01-01

    Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

  20. Asbestos Exposure Assessment Database

    NASA Technical Reports Server (NTRS)

    Arcot, Divya K.

    2010-01-01

    Exposure to particular hazardous materials in a work environment is dangerous to the employees who work directly with or around the materials as well as those who come in contact with them indirectly. In order to maintain a national standard for safe working environments and protect worker health, the Occupational Safety and Health Administration (OSHA) has set forth numerous precautionary regulations. NASA has been proactive in adhering to these regulations by implementing standards which are often stricter than regulation limits and administering frequent health risk assessments. The primary objective of this project is to create the infrastructure for an Asbestos Exposure Assessment Database specific to NASA Johnson Space Center (JSC) which will compile all of the exposure assessment data into a well-organized, navigable format. The data includes Sample Types, Samples Durations, Crafts of those from whom samples were collected, Job Performance Requirements (JPR) numbers, Phased Contrast Microscopy (PCM) and Transmission Electron Microscopy (TEM) results and qualifiers, Personal Protective Equipment (PPE), and names of industrial hygienists who performed the monitoring. This database will allow NASA to provide OSHA with specific information demonstrating that JSC s work procedures are protective enough to minimize the risk of future disease from the exposures. The data has been collected by the NASA contractors Computer Sciences Corporation (CSC) and Wyle Laboratories. The personal exposure samples were collected from devices worn by laborers working at JSC and by building occupants located in asbestos-containing buildings.

  1. International Nuclear Safety Center (INSC) database

    SciTech Connect

    Sofu, T.; Ley, H.; Turski, R.B.

    1997-08-01

    As an integral part of DOE`s International Nuclear Safety Center (INSC) at Argonne National Laboratory, the INSC Database has been established to provide an interactively accessible information resource for the world`s nuclear facilities and to promote free and open exchange of nuclear safety information among nations. The INSC Database is a comprehensive resource database aimed at a scope and level of detail suitable for safety analysis and risk evaluation for the world`s nuclear power plants and facilities. It also provides an electronic forum for international collaborative safety research for the Department of Energy and its international partners. The database is intended to provide plant design information, material properties, computational tools, and results of safety analysis. Initial emphasis in data gathering is given to Soviet-designed reactors in Russia, the former Soviet Union, and Eastern Europe. The implementation is performed under the Oracle database management system, and the World Wide Web is used to serve as the access path for remote users. An interface between the Oracle database and the Web server is established through a custom designed Web-Oracle gateway which is used mainly to perform queries on the stored data in the database tables.

  2. PeptiSite: a structural database of peptide binding sites in 4D.

    PubMed

    Acharya, Chayan; Kufareva, Irina; Ilatovskiy, Andrey V; Abagyan, Ruben

    2014-03-21

    We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include: (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions and (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://peptisite.ucsd.edu/ link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark. PMID:24406170

  3. 34 CFR 303.15 - Include; including.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Include; including. 303.15 Section 303.15 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION EARLY INTERVENTION PROGRAM FOR INFANTS AND TODDLERS...

  4. NIST Databases on Atomic Spectra

    NASA Astrophysics Data System (ADS)

    Reader, J.; Wiese, W. L.; Martin, W. C.; Musgrove, A.; Fuhr, J. R.

    2002-11-01

    The NIST atomic and molecular spectroscopic databases now available on the World Wide Web through the NIST Physics Laboratory homepage include Atomic Spectra Database, Ground Levels and Ionization Energies for the Neutral Atoms, Spectrum of Platinum Lamp for Ultraviolet Spectrograph Calibration, Bibliographic Database on Atomic Transition Probabilities, Bibliographic Database on Atomic Spectral Line Broadening, and Electron-Impact Ionization Cross Section Database. The Atomic Spectra Database (ASD) [1] offers evaluated data on energy levels, wavelengths, and transition probabilities for atoms and atomic ions. Data are given for some 950 spectra and 70,000 energy levels. About 91,000 spectral lines are included, with transition probabilities for about half of these. Additional data resulting from our ongoing critical compilations will be included in successive new versions of ASD. We plan to include, for example, our recently published data for some 16,000 transitions covering most ions of the iron-group elements, as well as Cu, Kr, and Mo [2]. Our compilations benefit greatly from experimental and theoretical atomic-data research being carried out in the NIST Atomic Physics Division. A new compilation covering spectra of the rare gases in all stages of ionization, for example, revealed a need for improved data in the infrared. We have thus measured these needed data with our high-resolution Fourier transform spectrometer [3]. An upcoming new database will give wavelengths and intensities for the stronger lines of all neutral and singly-ionized atoms, along with energy levels and transition probabilities for the persistent lines [4]. A critical compilation of the transition probabilities of Ba I and Ba II [5] has been completed and several other compilations of atomic transition probabilities are nearing completion. These include data for all spectra of Na, Mg, Al, and Si [6]. Newly compiled data for selected ions of Ne, Mg, Si and S, will form the basis for a new

  5. Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information

    PubMed Central

    Tong, Joo Chuan; Lim, Shen Jean; Muh, Hon Cheng; Chew, Fook Tim; Tammi, Martti T.

    2009-01-01

    Summary: A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains. Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/. Contact: martti@nus.edu.sg. PMID:19213741

  6. Teaching Comprehension Skills.

    ERIC Educational Resources Information Center

    Georgia Association of School Superintendents.

    Materials used in a one-day conference on teaching reading comprehension skills are summarized in this publication. Contents consist of three articles on teaching the comprehension skills, informal reading inventories in science and in geography, Lincoln's Gettysburg Address with comprehension questions, a checklist for the evaluation of teaching…

  7. Rystrom Reading Comprehension Test.

    ERIC Educational Resources Information Center

    Rystrom, Richard

    Designed to measure specific dimensions of reading comprehension, the items for this test are based on a comprehension model which suggests that comprehension can be defined as six different skill areas: vocabulary, syntax, item recall, item sequence, interpretation, and evaluation. The test is divided into sections to correspond to each of the…

  8. An automated system for terrain database construction

    NASA Technical Reports Server (NTRS)

    Johnson, L. F.; Fretz, R. K.; Logan, T. L.; Bryant, N. A.

    1987-01-01

    An automated Terrain Database Preparation System (TDPS) for the construction and editing of terrain databases used in computerized wargaming simulation exercises has been developed. The TDPS system operates under the TAE executive, and it integrates VICAR/IBIS image processing and Geographic Information System software with CAD/CAM data capture and editing capabilities. The terrain database includes such features as roads, rivers, vegetation, and terrain roughness.

  9. When Is the Same Database Not the Same? Database Differences among Systems.

    ERIC Educational Resources Information Center

    Tenopir, Carol; Hover, Katie

    1993-01-01

    Examines how online versions of databases vary on different systems. Differences are grouped into three categories: obvious differences, including easily available information such as updating, dates covered, and price; database choice, including subfile structure, field structure, and content; and system choice, including support and system…

  10. Selective Comprehensives: The Social Composition of Top Comprehensive Schools

    ERIC Educational Resources Information Center

    Sutton Trust, 2013

    2013-01-01

    This study looks at publicly available data on the proportion of pupils eligible and claiming for free school meals (FSM) in the top 500 comprehensive state schools and at how representative they are of their localities and of their school type. We have looked at the top 500 when measured by five good GCSEs including English and Maths and at the…

  11. Safeguarding Databases Basic Concepts Revisited.

    ERIC Educational Resources Information Center

    Cardinali, Richard

    1995-01-01

    Discusses issues of database security and integrity, including computer crime and vandalism, human error, computer viruses, employee and user access, and personnel policies. Suggests some precautions to minimize system vulnerability such as careful personnel screening, audit systems, passwords, and building and software security systems. (JKP)

  12. TeloPIN: a database of telomeric proteins interaction network in mammalian cells.

    PubMed

    Luo, Zhenhua; Dai, Zhiming; Xie, Xiaowei; Feng, Xuyang; Liu, Dan; Songyang, Zhou; Xiong, Yuanyan

    2015-01-01

    Interaction network surrounding telomeres has been intensively studied during the past two decades. However, no specific resource by integrating telomere interaction information data is currently available. To facilitate the understanding of the molecular interaction network by which telomeres are associated with biological process and diseases, we have developed TeloPIN (Telomeric Proteins Interaction Network) database (http://songyanglab.sysu.edu.cn/telopin/), a novel database that points to provide comprehensive information on protein-protein, protein-DNA and protein-RNA interaction of telomeres. TeloPIN database contains four types of interaction data, including (i) protein--protein interaction (PPI) data, (ii) telomeric proteins ChIP-seq data, (iii) telomere-associated proteins data and (iv) telomeric repeat-containing RNAs (TERRA)-interacting proteins data. By analyzing these four types of interaction data, we found that 358 and 199 proteins have more than one type of interaction information in human and mouse cells, respectively. We also developed table browser and TeloChIP genome browser to help researchers with better integrated visualization of interaction data from different studies. The current release of TeloPIN database includes 1111 PPI, eight telomeric protein ChIP-seq data sets, 1391 telomere-associated proteins and 183 TERRA-interacting proteins from 92 independent studies in mammalian cells. The interaction information provided by TeloPIN database will greatly expand our knowledge of telomeric proteins interaction network. PMID:25792605

  13. Seismic databases of The Caucasus

    NASA Astrophysics Data System (ADS)

    Gunia, I.; Sokhadze, G.; Mikava, D.; Tvaradze, N.; Godoladze, T.

    2012-12-01

    The Caucasus is one of the active segments of the Alpine-Himalayan collision belt. The region needs continues seismic monitoring systems for better understanding of tectonic processes going in the region. Seismic Monitoring Center of Georgia (Ilia State University) is operating the digital seismic network of the country and is also collecting and exchanging data with neighboring countries. The main focus of our study was to create seismic database which is well organized, easily reachable and is convenient for scientists to use. The seismological database includes the information about more than 100 000 earthquakes from the whole Caucasus. We have to mention that it includes data from analog and digital seismic networks. The first analog seismic station in Georgia was installed in 1899 in the Caucasus in Tbilisi city. The number of analog seismic stations was increasing during next decades and in 1980s about 100 analog stations were operated all over the region. From 1992 due to political and economical situation the number of stations has been decreased and in 2002 just two analog equipments was operated. New digital seismic network was developed in Georgia since 2003. The number of digital seismic stations was increasing and in current days there are more than 25 digital stations operating in the country. The database includes the detailed information about all equipments installed on seismic stations. Database is available online. That will make convenient interface for seismic data exchange data between Caucasus neighboring countries. It also makes easier both the seismic data processing and transferring them to the database and decreases the operator's mistakes during the routine work. The database was created using the followings: php, MySql, Javascript, Ajax, GMT, Gmap, Hypoinverse.

  14. Digital map databases in support of avionic display systems

    NASA Astrophysics Data System (ADS)

    Trenchard, Michael E.; Lohrenz, Maura C.; Rosche, Henry, III; Wischow, Perry B.

    1991-08-01

    The emergence of computerized mission planning systems (MPS) and airborne digital moving map systems (DMS) has necessitated the development of a global database of raster aeronautical chart data specifically designed for input to these systems. The Naval Oceanographic and Atmospheric Research Laboratory''s (NOARL) Map Data Formatting Facility (MDFF) is presently dedicated to supporting these avionic display systems with the development of the Compressed Aeronautical Chart (CAC) database on Compact Disk Read Only Memory (CDROM) optical discs. The MDFF is also developing a series of aircraft-specific Write-Once Read Many (WORM) optical discs. NOARL has initiated a comprehensive research program aimed at improving the pilots'' moving map displays current research efforts include the development of an alternate image compression technique and generation of a standard set of color palettes. The CAC database will provide digital aeronautical chart data in six different scales. CAC is derived from the Defense Mapping Agency''s (DMA) Equal Arc-second (ARC) Digitized Raster Graphics (ADRG) a series of scanned aeronautical charts. NOARL processes ADRG to tailor the chart image resolution to that of the DMS display while reducing storage requirements through image compression techniques. CAC is being distributed by DMA as a library of CDROMs.

  15. Visualization of multidimensional database

    NASA Astrophysics Data System (ADS)

    Lee, Chung

    2008-01-01

    The concept of multidimensional databases has been extensively researched and wildly used in actual database application. It plays an important role in contemporary information technology, but due to the complexity of its inner structure, the database design is a complicated process and users are having a hard time fully understanding and using the database. An effective visualization tool for higher dimensional information system helps database designers and users alike. Most visualization techniques focus on displaying dimensional data using spreadsheets and charts. This may be sufficient for the databases having three or fewer dimensions but for higher dimensions, various combinations of projection operations are needed and a full grasp of total database architecture is very difficult. This study reviews existing visualization techniques for multidimensional database and then proposes an alternate approach to visualize a database of any dimension by adopting the tool proposed by Kiviat for software engineering processes. In this diagramming method, each dimension is represented by one branch of concentric spikes. This paper documents a C++ based visualization tool with extensive use of OpenGL graphics library and GUI functions. Detailed examples of actual databases demonstrate the feasibility and effectiveness in visualizing multidimensional databases.

  16. PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes

    PubMed Central

    Bhawna; Bonthala, V.S.; Gajula, MNV Prasad

    2016-01-01

    The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely. Database URL: http://www.multiomics.in/PvTFDB/ PMID:27465131

  17. The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource

    PubMed Central

    2012-01-01

    Background Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species. Description The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers (“Isolate Accession”), the first five of which correspond to the collection site (“Environmental Accession”). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages. Conclusions HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and

  18. PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.

    PubMed

    Bhawna; Bonthala, V S; Gajula, Mnv Prasad

    2016-01-01

    The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely.Database URL: http://www.multiomics.in/PvTFDB/. PMID:27465131

  19. ZFIN: enhancements and updates to the zebrafish model organism database

    PubMed Central

    Bradford, Yvonne; Conlin, Tom; Dunn, Nathan; Fashena, David; Frazer, Ken; Howe, Douglas G.; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra A. T.; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruef, Barbara J.; Ruzicka, Leyla; Bauer Schaper, Holle; Schaper, Kevin; Shao, Xiang; Singer, Amy; Sprague, Judy; Sprunger, Brock; Van Slyke, Ceri; Westerfield, Monte

    2011-01-01

    ZFIN, the Zebrafish Model Organism Database, http://zfin.org, serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data represented in ZFIN are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations. ZFIN is a dynamic resource with data added daily as part of our ongoing curation process. Software updates are frequent. Here, we describe recent additions to ZFIN including (i) enhanced access to images, (ii) genomic features, (iii) genome browser, (iv) transcripts, (v) antibodies and (vi) a community wiki for protocols and antibodies. PMID:21036866

  20. Quality control of EUVE databases

    NASA Technical Reports Server (NTRS)

    John, L. M.; Drake, J.

    1992-01-01

    The publicly accessible databases for the Extreme Ultraviolet Explorer include: the EUVE Archive mailserver; the CEA ftp site; the EUVE Guest Observer Mailserver; and the Astronomical Data System node. The EUVE Performance Assurance team is responsible for verifying that these public EUVE databases are working properly, and that the public availability of EUVE data contained therein does not infringe any data rights which may have been assigned. In this poster, we describe the Quality Assurance (QA) procedures we have developed from the approach of QA as a service organization, thus reflecting the overall EUVE philosophy of Quality Assurance integrated into normal operating procedures, rather than imposed as an external, post facto, control mechanism.

  1. DDD: Dynamic Database for Diatomics

    NASA Technical Reports Server (NTRS)

    Schwenke, David

    2004-01-01

    We have developed as web-based database containing spectra of diatomic moiecuies. All data is computed from first principles, and if a user requests data for a molecule/ion that is not in the database, new calculations are automatically carried out on that species. Rotational, vibrational, and electronic transitions are included. Different levels of accuracy can be selected from qualitatively correct to the best calculations that can be carried out. The user can view and modify spectroscopic constants, view potential energy curves, download detailed high temperature linelists, or view synthetic spectra.

  2. An Introduction to Database Structure and Database Machines.

    ERIC Educational Resources Information Center

    Detweiler, Karen

    1984-01-01

    Enumerates principal management objectives of database management systems (data independence, quality, security, multiuser access, central control) and criteria for comparison (response time, size, flexibility, other features). Conventional database management systems, relational databases, and database machines used for backend processing are…

  3. [COMPREHENSIVE GERIATRIC ASSESSMENT SCALES].

    PubMed

    Casado Verdejo, Inés; Postigo Mota, Salvador; Muñoz Bermejo, Laura; Vallejo Villalobos, José Ramón; Arrabal Léon, Nazaret; Pinto Montealegre, Jose Eduardo

    2016-01-01

    The process of comprehensive geriatric assessment is one of the key elements of geriatric care management aimed at the population. it includes evaluating the clinical, functional, mental and social aspects of aging result and/or pathological processes that appear at this stage of the life cycle. For their achievement, as well as other tools, professionals have a large number of validated rating scales specifically designed in the assessment of the different areas or fields. Its use can be very useful, especially for the objectification of evaluation results. The future of research in this area goes through deepening the adequacy of the scales to the characteristics and needs of older people in each care level or place of care. PMID:26996044

  4. DOE Global Energy Storage Database

    DOE Data Explorer

    The DOE International Energy Storage Database has more than 400 documented energy storage projects from 34 countries around the world. The database provides free, up-to-date information on grid-connected energy storage projects and relevant state and federal policies. More than 50 energy storage technologies are represented worldwide, including multiple battery technologies, compressed air energy storage, flywheels, gravel energy storage, hydrogen energy storage, pumped hydroelectric, superconducting magnetic energy storage, and thermal energy storage. The policy section of the database shows 18 federal and state policies addressing grid-connected energy storage, from rules and regulations to tariffs and other financial incentives. It is funded through DOE’s Sandia National Laboratories, and has been operating since January 2012.

  5. The Life Support Database system

    NASA Technical Reports Server (NTRS)

    Likens, William C.

    1991-01-01

    The design and implementation of the database system are described with specific reference to data available from the Build-1 version and techniques for its utilization. The review of the initial documents for the Life Support Database is described in terms of title format and sequencing, and the users are defined as participants in NASA-sponsored life-support research. The software and hardware selections are based respectively on referential integrity and compatibility, and the implementation of the user interface is achieved by means of an applications-programming tool. The current Beta-Test implementation of the system includes several thousand acronyms and bibliographic references as well as chemical properties and exposure limits, equipment, construction materials, and mission data. In spite of modifications in the database the system is found to be effective and a potentially significant resource for the aerospace community.

  6. Blocks database and its applications.

    PubMed

    Henikoff, J G; Henikoff, S

    1996-01-01

    Protein blocks consist of multiply aligned sequence segments without gaps that represent the most highly conserved regions of protein families. A database of blocks has been constructed by successive application of the fully automated PROTOMAT system to lists of protein family members obtained from Prosite documentation. Currently, Blocks 8.0 based on protein families documented in Prosite 12 consists of 2884 blocks representing 770 families. Searches of the Blocks Database are carried out using protein or DNA sequence queries, and results are returned with measures of significance for both single and multiple block hits. The databse has also proved useful for derivation of amino acid substitution matrices (the Blosum series) and other sets of parameters. WWW and E-mail servers provide access to the database and associated functions, including a block maker for sequences provided by the user. PMID:8743679

  7. Reference ballistic imaging database performance.

    PubMed

    De Kinder, Jan; Tulleners, Frederic; Thiebaut, Hugues

    2004-03-10

    Ballistic imaging databases allow law enforcement to link recovered cartridge cases to other crime scenes and to firearms. The success of these databases has led many to propose that all firearms in circulation be entered into a reference ballistic image database (RBID). To assess the performance of an RBID, we fired 4200 cartridge cases from 600 9mm Para Sig Sauer model P226 series pistols. Each pistol fired two Remington cartridges, one of which was imaged in the RBID, and five additional cartridges, consisting of Federal, Speer, Winchester, Wolf, and CCI brands. Randomly selected samples from the second series of Remington cartridge cases and from the five additional brands were then correlated against the RBID. Of the 32 cartridges of the same make correlated against the RBID, 72% ranked in the top 10 positions. Likewise, of the 160 cartridges of the five different brands correlated against the database, 21% ranked in the top 10 positions. Generally, the ranking position increased as the size of the RBID increased. We obtained similar results when we expanded the RBID to include firearms with the same class characteristics for breech face marks, firing pin impressions, and extractor marks. The results of our six queries against the RBID indicate that a reference ballistics image database of new guns is currently fraught with too many difficulties to be an effective and efficient law enforcement tool. PMID:15036442

  8. Developing a DNA variant database.

    PubMed

    Fung, David C Y

    2008-01-01

    Disease- and locus-specific variant databases have been a valuable resource to clinical and research geneticists. With the recent rapid developments in technologies, the number of DNA variants detected in a typical molecular genetics laboratory easily exceeds 1,000. To keep track of the growing inventory of DNA variants, many laboratories employ information technology to store the data as well as distributing the data and its associated information to clinicians and researchers via the Web. While it is a valuable resource, the hosting of a web-accessible database requires collaboration between bioinformaticians and biologists and careful planning to ensure its usability and availability. In this chapter, a series of tutorials on building a local DNA variant database out of a sample dataset will be provided. However, this tutorial will not include programming details on building a web interface and on constructing the web application necessary for web hosting. Instead, an introduction to the two commonly used methods for hosting web-accessible variant databases will be described. Apart from the tutorials, this chapter will also consider the resources and planning required for making a variant database project successful. PMID:18453092

  9. The Plant Organelles Database 3 (PODB3) update 2014: integrating electron micrographs and new options for plant organelle research.

    PubMed

    Mano, Shoji; Nakamura, Takanori; Kondo, Maki; Miwa, Tomoki; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nagatani, Akira; Nishimura, Mikio

    2014-01-01

    The Plant Organelles Database 2 (PODB2), which was first launched in 2006 as PODB, provides static image and movie data of plant organelles, protocols for plant organelle research and external links to relevant websites. PODB2 has facilitated plant organellar research and the understanding of plant organelle dynamics. To provide comprehensive information on plant organelles in more detail, PODB2 was updated to PODB3 (http://podb.nibb.ac.jp/Organellome/). PODB3 contains two additional components: the electron micrograph database and the perceptive organelles database. Through the electron micrograph database, users can examine the subcellular and/or suborganellar structures in various organs of wild-type and mutant plants. The perceptive organelles database provides information on organelle dynamics in response to external stimuli. In addition to the extra components, the user interface for access has been enhanced in PODB3. The data in PODB3 are directly submitted by plant researchers and can be freely downloaded for use in further analysis. PODB3 contains all the information included in PODB2, and the volume of data and protocols deposited in PODB3 continue to grow steadily. We welcome contributions of data from all plant researchers to enhance the utility and comprehensiveness of PODB3. PMID:24092884

  10. ONRLDB—manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery

    PubMed Central

    Nanduri, Ravikanth; Bhutani, Isha; Somavarapu, Arun Kumar; Mahajan, Sahil; Parkesh, Raman; Gupta, Pawan

    2015-01-01

    Orphan nuclear receptors are potential therapeutic targets. The Orphan Nuclear Receptor Ligand Binding Database (ONRLDB) is an interactive, comprehensive and manually curated database of small molecule ligands targeting orphan nuclear receptors. Currently, ONRLDB consists of ∼11 000 ligands, of which ∼6500 are unique. All entries include information for the ligand, such as EC50 and IC50, number of aromatic rings and rotatable bonds, XlogP, hydrogen donor and acceptor count, molecular weight (MW) and structure. ONRLDB is a cross-platform database, where either the cognate small molecule modulators of a receptor or the cognate receptors to a ligand can be searched. The database can be searched using three methods: text search, advanced search or similarity search. Substructure search, cataloguing tools, and clustering tools can be used to perform advanced analysis of the ligand based on chemical similarity fingerprints, hierarchical clustering, binning partition and multidimensional scaling. These tools, together with the Tree function provided, deliver an interactive platform and a comprehensive resource for identification of common and unique scaffolds. As demonstrated, ONRLDB is designed to allow selection of ligands based on various properties and for designing novel ligands or to improve the existing ones. Database URL: http://www.onrldb.org/ PMID:26637529

  11. The Comprehensive Assessment of Symptoms and History (CASH). An instrument for assessing diagnosis and psychopathology.

    PubMed

    Andreasen, N C; Flaum, M; Arndt, S

    1992-08-01

    The Comprehensive Assessment of Symptoms and History was developed for research studies of schizophrenia spectrum conditions and affective spectrum conditions. It is designed to provide a comprehensive information base concerning current and past signs and symptoms, premorbid functioning, cognitive functioning, sociodemographic status, treatment, and course of illness. Because the information base is broad, it is not wedded to a specific diagnostic system but rather permits clinicians and investigators to make diagnoses using a wide range of systems, including Research Diagnostic Criteria, DSM-III, DSM-III-R, and the International Classification of Diseases. Given the fact that disorders in psychiatry are not defined at the etiological or pathophysiological level, diagnostic criteria are prone to ongoing revision as our knowledge base changes. Research strategies suggest that investigators should maintain a flexible database to permit them to adapt to changes in diagnostic systems, to do comparative nosological studies, and, ultimately, to develop new diagnostic systems based on knowledge concerning the underlying neurobiological nature of disorders. Because it provides a comprehensive information base, the Comprehensive Assessment of Symptoms and History facilitates research of this type. Extensive developmental work has been done with the Comprehensive Assessment of Symptoms and History, including interrater and test-retest reliability studies, validity studies, training programs, and data entry programs. PMID:1637251

  12. Petrophysical database of Uganda

    NASA Astrophysics Data System (ADS)

    Ruotoistenmäki, Tapio; Birungi, Nelson R.

    2015-06-01

    The petrophysical database of Uganda contains data on ca. 5800 rock samples collected and analyzed during 2009-2012 in international geological and geophysical projects covering the main part of the land area of Uganda. The parameters included are the susceptibilities and densities of all available field samples. Susceptibilities were measured from the samples from three directions. Using these parameters, we also calculated the ratios of susceptibility maxima/minima reflecting direction homogeneity of magnetic minerals, and estimated the iron content of paramagnetic samples and the magnetite content of ferrimagnetic samples. Statistical and visual analysis of the petrophysical data of Uganda demonstrated their wide variation, thus emphasizing their importance in analyzing the bedrock variations in three dimensions. Using the density-susceptibility diagram, the data can be classified into six main groups: 1. A low density and susceptibility group, consisting of sedimentary and altered rocks. 2. Low-susceptibility, felsic rocks (e.g. quartzites and metasandstones). 3. Paramagnetic, felsic rocks (e.g. granites). 4. Ferrimagnetic, magnetite-containing felsic rocks (e.g. granites). 5. Paramagnetic mafic rocks (e.g. amphibolites and dolerites). 6. Ferrimagnetic, mafic rocks containing magnetite and high-density mafic minerals (mainly dolerites). Moreover, analysis revealed that the parameter distributions of even a single rock type (e.g. granites) can be very variable, forming separate clusters. This demonstrates that the simple calculation of density or susceptibility averages of rock types can be highly erratic. For example, the average can lie between two groups, where only few, if any, samples exist. Therefore, estimation of the representative density and susceptibility must be visually verified from these diagrams. The areal distribution of parameters and their calculated derivatives generally correlate well with the regional distribution of lithological and

  13. A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools.

    PubMed

    Athanasiadis, Emmanouil I; Antonopoulou, Kyriaki; Chatzinasiou, Foteini; Lill, Christina M; Bourdakou, Marilena M; Sakellariou, Argiris; Kypreou, Katerina; Stefanaki, Irene; Evangelou, Evangelos; Ioannidis, John P A; Bertram, Lars; Stratigos, Alexander J; Spyrou, George M

    2014-01-01

    The publicly available online database MelGene provides a comprehensive, regularly updated, collection of data from genetic association studies in cutaneous melanoma (CM), including random-effects meta-analysis results of all eligible polymorphisms. The updated database version includes data from 192 publications with information on 1114 significantly associated polymorphisms across 280 genes, along with new front-end and back-end capabilities. Various types of relationships between data are calculated and visualized as networks. We constructed 13 different networks containing the polymorphisms and the genes included in MelGene. We explored the derived network representations under the following questions: (i) are there nodes that deserve consideration regarding their network connectivity characteristics? (ii) What is the relation of either the genome-wide or nominally significant CM polymorphisms/genes with the ones highlighted by the network representation? We show that our network approach using the MelGene data reveals connections between statistically significant genes/ polymorphisms and other genes/polymorphisms acting as 'hubs' in the reconstructed networks. To the best of our knowledge, this is the first database containing data from a comprehensive field synopsis and systematic meta-analyses of genetic polymorphisms in CM that provides user-friendly tools for in-depth molecular network visualization and exploration. The proposed network connections highlight potentially new loci requiring further investigation of their relation to melanoma risk. Database URL: http://www.melgene.org. PMID:25380778

  14. A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools

    PubMed Central

    Athanasiadis, Emmanouil I.; Antonopoulou, Kyriaki; Chatzinasiou, Foteini; Lill, Christina M.; Bourdakou, Marilena M.; Sakellariou, Argiris; Kypreou, Katerina; Stefanaki, Irene; Evangelou, Evangelos; Ioannidis, John P.A.; Bertram, Lars; Stratigos, Alexander J.; Spyrou, George M.

    2014-01-01

    The publicly available online database MelGene provides a comprehensive, regularly updated, collection of data from genetic association studies in cutaneous melanoma (CM), including random-effects meta-analysis results of all eligible polymorphisms. The updated database version includes data from 192 publications with information on 1114 significantly associated polymorphisms across 280 genes, along with new front-end and back-end capabilities. Various types of relationships between data are calculated and visualized as networks. We constructed 13 different networks containing the polymorphisms and the genes included in MelGene. We explored the derived network representations under the following questions: (i) are there nodes that deserve consideration regarding their network connectivity characteristics? (ii) What is the relation of either the genome-wide or nominally significant CM polymorphisms/genes with the ones highlighted by the network representation? We show that our network approach using the MelGene data reveals connections between statistically significant genes/ polymorphisms and other genes/polymorphisms acting as ‘hubs’ in the reconstructed networks. To the best of our knowledge, this is the first database containing data from a comprehensive field synopsis and systematic meta-analyses of genetic polymorphisms in CM that provides user-friendly tools for in-depth molecular network visualization and exploration. The proposed network connections highlight potentially new loci requiring further investigation of their relation to melanoma risk. Database URL: http://www.melgene.org. PMID:25380778

  15. Applicability of large databases in outcomes research.

    PubMed

    Malay, Sunitha; Shauver, Melissa J; Chung, Kevin C

    2012-07-01

    Outcomes research serves as a mechanism to assess the quality of care, cost effectiveness of treatment, and other aspects of health care. The use of administrative databases in outcomes research is increasing in all medical specialties, including hand surgery. However, the real value of databases can be maximized with a thorough understanding of their contents, advantages, and limitations. We performed a literature review pertaining to databases in medical, surgical, and epidemiologic research, with special emphasis on orthopedic and hand surgery. This article provides an overview of the available database resources for outcomes research, their potential value to hand surgeons, and suggestions to improve their effective use. PMID:22522104

  16. Construction of Database for Pulsating Variable Stars

    NASA Astrophysics Data System (ADS)

    Chen, B. Q.; Yang, M.; Jiang, B. W.

    2011-07-01

    A database for the pulsating variable stars is constructed for Chinese astronomers to study the variable stars conveniently. The database includes about 230000 variable stars in the Galactic bulge, LMC and SMC observed by the MACHO (MAssive Compact Halo Objects) and OGLE (Optical Gravitational Lensing Experiment) projects at present. The software used for the construction is LAMP, i.e., Linux+Apache+MySQL+PHP. A web page is provided to search the photometric data and the light curve in the database through the right ascension and declination of the object. More data will be incorporated into the database.

  17. SymbioGenomesDB: a database for the integration and access to knowledge on host–symbiont relationships

    PubMed Central

    Reyes-Prieto, Mariana; Vargas-Chávez, Carlos; Latorre, Amparo; Moya, Andrés

    2015-01-01

    Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic–host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major

  18. SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships.

    PubMed

    Reyes-Prieto, Mariana; Vargas-Chávez, Carlos; Latorre, Amparo; Moya, Andrés

    2015-01-01

    Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic-host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major

  19. Developing Database Files for Student Use.

    ERIC Educational Resources Information Center

    Warner, Michael

    1988-01-01

    Presents guidelines for creating student database files that supplement classroom teaching. Highlights include determining educational objectives, planning the database with computer specialists and subject area specialists, data entry, and creating student worksheets. Specific examples concerning elements of the periodic table and…

  20. Database Handling Software and Scientific Applications.

    ERIC Educational Resources Information Center

    Gabaldon, Diana J.

    1984-01-01

    Discusses the general characteristics of database management systems and file systems. Also gives a basic framework for evaluating such software and suggests characteristics that should be considered when buying software for specific scientific applications. A list of vendor addresses for popular database management systems is included. (JN)

  1. Library Instruction and Online Database Searching.

    ERIC Educational Resources Information Center

    Mercado, Heidi

    1999-01-01

    Reviews changes in online database searching in academic libraries. Topics include librarians conducting all searches; the advent of end-user searching and the need for user instruction; compact disk technology; online public catalogs; the Internet; full text databases; electronic information literacy; user education and the remote library user;…

  2. Diet History Questionnaire: Database Utility Program

    Cancer.gov

    If you need to modify the standard nutrient database, a single nutrient value must be provided by gender and portion size. If you have modified the database to have fewer or greater demographic groups, nutrient values must be included for each group.

  3. Diet History Questionnaire II: Database Utility Program

    Cancer.gov

    If you need to modify the standard nutrient database, a single nutrient value must be provided by gender and portion size. If you have modified the database to have fewer or greater demographic groups, nutrient values must be included for each group.

  4. The Status of Statewide Subscription Databases

    ERIC Educational Resources Information Center

    Krueger, Karla S.

    2012-01-01

    This qualitative content analysis presents subscription databases available to school libraries through statewide purchases. The results may help school librarians evaluate grade and subject-area coverage, make comparisons to recommended databases, and note potential suggestions for their states to include in future contracts or for local…

  5. Designing Corporate Databases to Support Technology Innovation

    ERIC Educational Resources Information Center

    Gultz, Michael Jarett

    2012-01-01

    Based on a review of the existing literature on database design, this study proposed a unified database model to support corporate technology innovation. This study assessed potential support for the model based on the opinions of 200 technology industry executives, including Chief Information Officers, Chief Knowledge Officers and Chief Learning…

  6. Development of a Water Infrastructure Knowledge Database

    EPA Science Inventory

    This paper presents a methodology for developing a national database, as applied to water infrastructure systems, which includes both drinking water and wastewater. The database is branded as "WATERiD" and can be accessed at www.waterid.org. Water infrastructure in the U.S. is ag...

  7. Online Databases as Sources of Linguistic Information.

    ERIC Educational Resources Information Center

    Sano, Hikomaro

    1988-01-01

    This description of the types of linguistic information obtainable from online databases generally used to acquire technical information includes examples of equivalent words, English usage, and statistical linguistic data. The implications of online databases as substitutes for dictionaries and as corpora for linguistic survey are considered.…

  8. US-LHC MAGNET DATABASE AND CONVENTIONS.

    SciTech Connect

    WEI,J.; MCCHESNEY,D.; JAIN,A.; PEGGS,S.; PILAT,F.; BOTTURA,L.; SABBI,G.

    1999-03-29

    The US-LHC Magnet Database is designed for production-magnet quality assurance, field and alignment error impact analysis, cryostat assembly assistance, and ring installation assistance. The database consists of tables designed to store magnet field and alignment measurements data and quench data. This information will also be essential for future machine operations including local IR corrections.

  9. DRAMP: a comprehensive data repository of antimicrobial peptides.

    PubMed

    Fan, Linlin; Sun, Jian; Zhou, Meifeng; Zhou, Jie; Lao, Xingzhen; Zheng, Heng; Xu, Hanmei

    2016-01-01

    The growing problem of antibiotic-resistant microorganisms results in an urgent need for substitutes to conventional antibiotics with novel modes of action and effective activities. Antimicrobial peptides (AMPs), produced by a wide variety of living organisms acting as a defense mechanism against invading pathogenic microbes, are considered to be such promising alternatives. AMPs display a broad spectrum of antimicrobial activity and a low propensity for developing resistance. Therefore, a thorough understanding of AMPs is essential to exploit them as antimicrobial drugs. Considering this, we developed a comprehensive user-friendly data repository of antimicrobial peptides (DRAMP), which holds 17349 antimicrobial sequences, including 4571 general AMPs, 12704 patented sequences and 74 peptides in drug development. Entries in the database have detailed annotations, especially detailed antimicrobial activity data (shown as target organism with MIC value) and structure information. Annotations also include accession numbers crosslinking to Pubmed, Swiss-prot and Protein Data Bank (PDB). The website of the database comes with easy-to-operate browsing as well as searching with sorting and filtering functionalities. Several useful sequence analysis tools are provided, including similarity search, sequence alignment and conserved domain search (CD-Search). DRAMP should be a useful resource for the development of novel antimicrobial peptide drugs. PMID:27075512

  10. DRAMP: a comprehensive data repository of antimicrobial peptides

    PubMed Central

    Fan, Linlin; Sun, Jian; Zhou, Meifeng; Zhou, Jie; Lao, Xingzhen; Zheng, Heng; Xu, Hanmei

    2016-01-01

    The growing problem of antibiotic-resistant microorganisms results in an urgent need for substitutes to conventional antibiotics with novel modes of action and effective activities. Antimicrobial peptides (AMPs), produced by a wide variety of living organisms acting as a defense mechanism against invading pathogenic microbes, are considered to be such promising alternatives. AMPs display a broad spectrum of antimicrobial activity and a low propensity for developing resistance. Therefore, a thorough understanding of AMPs is essential to exploit them as antimicrobial drugs. Considering this, we developed a comprehensive user-friendly data repository of antimicrobial peptides (DRAMP), which holds 17349 antimicrobial sequences, including 4571 general AMPs, 12704 patented sequences and 74 peptides in drug development. Entries in the database have detailed annotations, especially detailed antimicrobial activity data (shown as target organism with MIC value) and structure information. Annotations also include accession numbers crosslinking to Pubmed, Swiss-prot and Protein Data Bank (PDB). The website of the database comes with easy-to-operate browsing as well as searching with sorting and filtering functionalities. Several useful sequence analysis tools are provided, including similarity search, sequence alignment and conserved domain search (CD-Search). DRAMP should be a useful resource for the development of novel antimicrobial peptide drugs. PMID:27075512

  11. PAGES-Powell North America 2k database

    NASA Astrophysics Data System (ADS)

    McKay, N.

    2014-12-01

    Syntheses of paleoclimate data in North America are essential for understanding long-term spatiotemporal variability in climate and for properly assessing risk on decadal and longer timescales. Existing reconstructions of the past 2,000 years rely almost exclusively on tree-ring records, which can underestimate low-frequency variability and rarely extend beyond the last millennium. Meanwhile, many records from the full spectrum of paleoclimate archives are available and hold the potential of enhancing our understanding of past climate across North America over the past 2000 years. The second phase of the Past Global Changes (PAGES) North America 2k project began in 2014, with a primary goal of assembling these disparate paleoclimate records into a unified database. This effort is currently supported by the USGS Powell Center together with PAGES. Its success requires grassroots support from the community of researchers developing and interpreting paleoclimatic evidence relevant to the past 2000 years. Most likely, fewer than half of the published records appropriate for this database are publicly archived, and far fewer include the data needed to quantify geochronologic uncertainty, or to concisely describe how best to interpret the data in context of a large-scale paleoclimatic synthesis. The current version of the database includes records that (1) have been published in a peer-reviewed journal (including evidence of the record's relationship to climate), (2) cover a substantial portion of the past 2000 yr (>300 yr for annual records, >500 yr for lower frequency records) at relatively high resolution (<50 yr/observation), and (3) have reasonably small and quantifiable age uncertainty. Presently, the database includes records from boreholes, ice cores, lake and marine sediments, speleothems, and tree rings. This poster presentation will display the site locations and basic metadata of the records currently in the database. We invite anyone with interest in

  12. Integrating Variances into an Analytical Database

    NASA Technical Reports Server (NTRS)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  13. A Scalable Database Infrastructure

    NASA Astrophysics Data System (ADS)

    Arko, R. A.; Chayes, D. N.

    2001-12-01

    The rapidly increasing volume and complexity of MG&G data, and the growing demand from funding agencies and the user community that it be easily accessible, demand that we improve our approach to data management in order to reach a broader user-base and operate more efficient and effectively. We have chosen an approach based on industry-standard relational database management systems (RDBMS) that use community-wide data specifications, where there is a clear and well-documented external interface that allows use of general purpose as well as customized clients. Rapid prototypes assembled with this approach show significant advantages over the traditional, custom-built data management systems that often use "in-house" legacy file formats, data specifications, and access tools. We have developed an effective database prototype based a public domain RDBMS (PostgreSQL) and metadata standard (FGDC), and used it as a template for several ongoing MG&G database management projects - including ADGRAV (Antarctic Digital Gravity Synthesis), MARGINS, the Community Review system of the Digital Library for Earth Science Education, multibeam swath bathymetry metadata, and the R/V Maurice Ewing onboard acquisition system. By using standard formats and specifications, and working from a common prototype, we are able to reuse code and deploy rapidly. Rather than spend time on low-level details such as storage and indexing (which are built into the RDBMS), we can focus on high-level details such as documentation and quality control. In addition, because many commercial off-the-shelf (COTS) and public domain data browsers and visualization tools have built-in RDBMS support, we can focus on backend development and leave the choice of a frontend client(s) up to the end user. While our prototype is running under an open source RDBMS on a single processor host, the choice of standard components allows this implementation to scale to commercial RDBMS products and multiprocessor servers as

  14. National Geochronological Database

    USGS Publications Warehouse

    Revised by Sloan, Jan; Henry, Christopher D.; Hopkins, Melanie; Ludington, Steve; Original database by Zartman, Robert E.; Bush, Charles A.; Abston, Carl

    2003-01-01

    The National Geochronological Data Base (NGDB) was established by the United States Geological Survey (USGS) to collect and organize published isotopic (also known as radiometric) ages of rocks in the United States. The NGDB (originally known as the Radioactive Age Data Base, RADB) was started in 1974. A committee appointed by the Director of the USGS was given the mission to investigate the feasibility of compiling the published radiometric ages for the United States into a computerized data bank for ready access by the user community. A successful pilot program, which was conducted in 1975 and 1976 for the State of Wyoming, led to a decision to proceed with the compilation of the entire United States. For each dated rock sample reported in published literature, a record containing information on sample location, rock description, analytical data, age, interpretation, and literature citation was constructed and included in the NGDB. The NGDB was originally constructed and maintained on a mainframe computer, and later converted to a Helix Express relational database maintained on an Apple Macintosh desktop computer. The NGDB and a program to search the data files were published and distributed on Compact Disc-Read Only Memory (CD-ROM) in standard ISO 9660 format as USGS Digital Data Series DDS-14 (Zartman and others, 1995). As of May 1994, the NGDB consisted of more than 18,000 records containing over 30,000 individual ages, which is believed to represent approximately one-half the number of ages published for the United States through 1991. Because the organizational unit responsible for maintaining the database was abolished in 1996, and because we wanted to provide the data in more usable formats, we have reformatted the data, checked and edited the information in some records, and provided this online version of the NGDB. This report describes the changes made to the data and formats, and provides instructions for the use of the database in geographic

  15. The worldwide collapse caldera database (CCDB): A tool for studying and understanding caldera processes

    NASA Astrophysics Data System (ADS)

    Geyer, Adelina; Marti, Joan

    2015-04-01

    Collapse calderas are one of the most important volcanic structures not only because of their hazard implications, but also because of their high geothermal energy potential and their association with mineral deposits of economic interest. In 2008 we presented a new general worldwide Collapse Caldera DataBase (CCDB), in order to provide a useful and accessible tool for studying and understanding caldera collapse processes. The principal aim of the CCDB is to update the current field based knowledge on calderas, merging together the existing databases and complementing them with new examples found in the bibliography, and leaving it open for the incorporation of new data from future studies. Currently, the database includes over 450 documented calderas around the world, trying to be representative enough to promote further studies and analyses. We have performed a comprehensive compilation of published field studies of collapse calderas including more than 500 references, and their information has been summarized in a database linked to a Geographical Information System (GIS) application. Thus, it is possible to visualize the selected calderas on a world map and to filter them according to different features recorded in the database (e.g. age, structure). The information recorded in the CCDB can be grouped in seven main information classes: caldera features, properties of the caldera-forming deposits, magmatic system, geodynamic setting, pre-caldera volcanism,caldera-forming eruption sequence and post-caldera activity. Additionally, we have added two extra classes. The first records the references consulted for each caldera. The second allows users to introduce comments on the caldera sample such as possible controversies concerning the caldera origin. During the last seven years, the database has been available on-line at http://www.gvb-csic.es/CCDB.htm previous registration. This year, the CCDB webpage will be updated and improved so the database content can be

  16. The asteroid lightcurve database

    NASA Astrophysics Data System (ADS)

    Warner, Brian D.; Harris, Alan W.; Pravec, Petr

    2009-07-01

    The compilation of a central database for asteroid lightcurve data, i.e., rotation rate and amplitude along with ancillary information such as diameter and albedo (known or estimated), taxonomic class, etc., has been important to statistical studies for several decades. Having such a compilation saves the researcher hours of effort combing through any number of journals, some obvious and some not, to check on prior research. Harris has been compiling such data in the Asteroid Lightcurve Database (LCDB) for more than 25 years with Warner and Pravec assisting the past several years. The main data included in the LCDB are lightcurve rotation periods and amplitudes, color indices, H-G parameters, diameters (actual or derived), basic binary asteroid parameters, and spin axis and shape models. As time permits we are reviewing existing entries to enter data not previously recorded ( e.g., phase angle data). As of 2008 December, data for 3741 asteroids based on more than 10650 separate detail records derived from entries in various journals were included in the LCDB. Of those 3741 asteroids, approximately 3100 have data of sufficient quality for statistical analysis, including 7 that have "dual citizenship" - meaning that they have (or had) asteroid designations as well comet designations. Here we present a discussion of the nature of LCDB data, i.e., which values are actually measured and which are derived. For derived data, we give our justification for specific values. We also present some analysis based on the LCDB data, including new default albedo ( p) and phase slope parameter ( G) values for the primary taxonomic classes and a review of the frequency-diameter distribution of all asteroids as well as some selected subsets. The most recent version of data used in this analysis is available for download from the Collaborative Asteroid Lightcurve Link (CALL) site at http://www.MinorPlanetObserver.com/astlc/default.htm. Other data sets, some only subsets of the full

  17. ITS-90 Thermocouple Database

    National Institute of Standards and Technology Data Gateway

    SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

  18. Reference Fluid Thermodynamic and Transport Properties Database (REFPROP)

    National Institute of Standards and Technology Data Gateway

    SRD 23 NIST Reference Fluid Thermodynamic and Transport Properties Database (REFPROP) (PC database for purchase)   NIST 23 contains revised data in a Windows version of the database, including 105 pure fluids and allowing mixtures of up to 20 components. The fluids include the environmentally acceptable HFCs, traditional HFCs and CFCs and 'natural' refrigerants like ammonia

  19. The UCSC Genome Browser database: 2015 update.

    PubMed

    Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T; Li, Chin H; Miga, Karen H; Nguyen, Ngan; Paten, Benedict; Raney, Brian J; Smit, Arian F A; Speir, Matthew L; Zweig, Ann S; Haussler, David; Kuhn, Robert M; Kent, W James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

  20. The UCSC Genome Browser database: 2015 update

    PubMed Central

    Rosenbloom, Kate R.; Armstrong, Joel; Barber, Galt P.; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R.; Fujita, Pauline A.; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A.; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S.; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T.; Li, Chin H.; Miga, Karen H.; Nguyen, Ngan; Paten, Benedict; Raney, Brian J.; Smit, Arian F. A.; Speir, Matthew L.; Zweig, Ann S.; Haussler, David; Kuhn, Robert M.; Kent, W. James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), ‘mined the web’ for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

  1. Opening CEM vendor databases

    SciTech Connect

    Long, A.; Patel, D.

    1995-12-31

    CEM database performance requirements (i.e., voluminous data storage, rapid response times) often conflict with the concept of an open, accessible database. Utilities would like to use their CEM data for more purposes than simply submitting environmental reports. But in most cases, other uses are inhibited because today`s sophisticated CEM systems incorporate databases that have forsaken openness and accessibility in favor of performance. Several options are available for CEM vendors wishing to move in the direction of open, accessible CEM databases.

  2. Databases for Microbiologists

    PubMed Central

    2015-01-01

    Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists. PMID:26013493

  3. Veterans Administration Databases

    Cancer.gov

    The Veterans Administration Information Resource Center provides database and informatics experts, customer service, expert advice, information products, and web technology to VA researchers and others.

  4. Interactive bibliographical database on color

    NASA Astrophysics Data System (ADS)

    Caivano, Jose L.

    2002-06-01

    The paper describes the methodology and results of a project under development, aimed at the elaboration of an interactive bibliographical database on color in all fields of application: philosophy, psychology, semiotics, education, anthropology, physical and natural sciences, biology, medicine, technology, industry, architecture and design, arts, linguistics, geography, history. The project is initially based upon an already developed bibliography, published in different journals, updated in various opportunities, and now available at the Internet, with more than 2,000 entries. The interactive database will amplify that bibliography, incorporating hyperlinks and contents (indexes, abstracts, keywords, introductions, or eventually the complete document), and devising mechanisms for information retrieval. The sources to be included are: books, doctoral dissertations, multimedia publications, reference works. The main arrangement will be chronological, but the design of the database will allow rearrangements or selections by different fields: subject, Decimal Classification System, author, language, country, publisher, etc. A further project is to develop another database, including color-specialized journals or newsletters, and articles on color published in international journals, arranged in this case by journal name and date of publication, but allowing also rearrangements or selections by author, subject and keywords.

  5. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

    PubMed Central

    Rigden, Daniel J.; Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  6. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

    PubMed

    Rigden, Daniel J; Fernández-Suárez, Xosé M; Galperin, Michael Y

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  7. Nuclear data made easily accessible through the Notre Dame Nuclear Database

    NASA Astrophysics Data System (ADS)

    Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

    2014-09-01

    In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

  8. The InterPro Database, 2003 brings increased coverage and new features.

    PubMed

    Mulder, Nicola J; Apweiler, Rolf; Attwood, Teresa K; Bairoch, Amos; Barrell, Daniel; Bateman, Alex; Binns, David; Biswas, Margaret; Bradley, Paul; Bork, Peer; Bucher, Phillip; Copley, Richard R; Courcelle, Emmanuel; Das, Ujjwal; Durbin, Richard; Falquet, Laurent; Fleischmann, Wolfgang; Griffiths-Jones, Sam; Haft, Daniel; Harte, Nicola; Hulo, Nicolas; Kahn, Daniel; Kanapin, Alexander; Krestyaninova, Maria; Lopez, Rodrigo; Letunic, Ivica; Lonsdale, David; Silventoinen, Ville; Orchard, Sandra E; Pagni, Marco; Peyruc, David; Ponting, Chris P; Selengut, Jeremy D; Servant, Florence; Sigrist, Christian J A; Vaughan, Robert; Zdobnov, Evgueni M

    2003-01-01

    InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). PMID:12520011

  9. The InterPro Database, 2003 brings increased coverage and new features

    PubMed Central

    Mulder, Nicola J.; Apweiler, Rolf; Attwood, Teresa K.; Bairoch, Amos; Barrell, Daniel; Bateman, Alex; Binns, David; Biswas, Margaret; Bradley, Paul; Bork, Peer; Bucher, Phillip; Copley, Richard R.; Courcelle, Emmanuel; Das, Ujjwal; Durbin, Richard; Falquet, Laurent; Fleischmann, Wolfgang; Griffiths-Jones, Sam; Haft, Daniel; Harte, Nicola; Hulo, Nicolas; Kahn, Daniel; Kanapin, Alexander; Krestyaninova, Maria; Lopez, Rodrigo; Letunic, Ivica; Lonsdale, David; Silventoinen, Ville; Orchard, Sandra E.; Pagni, Marco; Peyruc, David; Ponting, Chris P.; Selengut, Jeremy D.; Servant, Florence; Sigrist, Christian J. A.; Vaughan, Robert; Zdobnov, Evgueni M.

    2003-01-01

    InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). PMID:12520011

  10. 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. PMID:24990533

  11. ORNL RAIL & BARGE DB. Network Database

    SciTech Connect

    Johnson, P.

    1991-07-01

    The Oak Ridge National Laboratory (ORNL) Rail and Barge Network Database is a representation of the rail and barge system of the United States. The network is derived from the Federal Rail Administration (FRA) rail database. The database consists of 96 subnetworks. Each of the subnetworks represent an individual railroad, a waterway system, or a composite group of small railroads. Two subnetworks represent waterways; one being barge/intercoastal, and the other coastal merchant marine with access through the Great Lakes/Saint Lawrence Seaway, Atlantic and Gulf Coasts, the Panama Canal, and Pacific Coast. Two other subnetworks represent small shortline railroads and terminal railroad operations. One subnetwork is maintained for the representation of Amtrak operations. The remaining 91 subnetworks represent individual or corporate groups of railroads. Coordinate locations are included as part of the database. The rail portion of the database is similar to the original FRA rail network. The waterway coordinates are greatly enhanced in the current release. Inland waterway representation was extracted from the 1:2,000,000 United States Geological Survey data. An important aspect of the database is the transfer file. This file identifies where two railroads interline traffic between their systems. Also included are locations where rail/waterway intermodal transfers could occur. Other files in the database include a translation table between Association of American Railroad (AAR) codes to the 96 subnetworks in the database, a list of names of the 96 subnetworks, and a file of names for a large proportion of the nodes in the network.

  12. ORNL RAIL & BARGE DB. Network Database

    SciTech Connect

    Johnson, P.

    1992-03-16

    The Oak Ridge National Laboratory (ORNL) Rail and Barge Network Database is a representation of the rail and barge system of the United States. The network is derived from the Federal Rail Administration (FRA) rail database. The database consists of 96 subnetworks. Each of the subnetworks represent an individual railroad, a waterway system, or a composite group of small railroads. Two subnetworks represent waterways; one being barge/intercoastal, and the other coastal merchant marine with access through the Great Lakes/Saint Lawrence Seaway, Atlantic and Gulf Coasts, the Panama Canal, and Pacific Coast. Two other subnetworks represent small shortline railroads and terminal railroad operations. One subnetwork is maintained for the representation of Amtrak operations. The remaining 91 subnetworks represent individual or corporate groups of railroads. Coordinate locations are included as part of the database. The rail portion of the database is similar to the original FRA rail network. The waterway coordinates are greatly enhanced in the current release. Inland waterway representation was extracted from the 1:2,000,000 United States Geological Survey data. An important aspect of the database is the transfer file. This file identifies where two railroads interline traffic between their systems. Also included are locations where rail/waterway intermodal transfers could occur. Other files in the database include a translation table between Association of American Railroad (AAR) codes to the 96 subnetworks in the database, a list of names of the 96 subnetworks, and a file of names for a large proportion of the nodes in the network.

  13. IPShocks: Database of Interplanetary Shock Waves

    NASA Astrophysics Data System (ADS)

    Isavnin, Alexey; Lumme, Erkka; Kilpua, Emilia; Lotti, Mikko; Andreeova, Katerina; Koskinen, Hannu; Nikbakhsh, Shabnam

    2016-04-01

    Fast collisionless shocks are one of the key interplanetary structures, which have also paramount role for solar-terrestrial physics. In particular, coronal mass ejection driven shocks accelerate particles to high energies and turbulent post-shock flows may drive intense geomagnetic storms. We present comprehensive Heliospheric Shock Database (ipshocks.fi) developed and hosted at University of Helsinki. The database contains currently over 2000 fast forward and fast reverse shocks observed by Wind, ACE, STEREO, Helios, Ulysses and Cluster spacecraft. In addition, the database has search and sort tools based on the spacecraft, time range, and several key shock parameters (e.g., shock type, shock strength, shock angle), data plots for each shock and data download options. These features allow easy access to shocks and quick statistical analyses. All current shocks are identified visually and analysed using the same procedure.

  14. SCOP: a structural classification of proteins database.

    PubMed Central

    Hubbard, T J; Murzin, A G; Brenner, S E; Chothia, C

    1997-01-01

    The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/ PMID:9016544

  15. The CATDAT damaging earthquakes database

    NASA Astrophysics Data System (ADS)

    Daniell, J. E.; Khazai, B.; Wenzel, F.; Vervaeck, A.

    2011-08-01

    The global CATDAT damaging earthquakes and secondary effects (tsunami, fire, landslides, liquefaction and fault rupture) database was developed to validate, remove discrepancies, and expand greatly upon existing global databases; and to better understand the trends in vulnerability, exposure, and possible future impacts of such historic earthquakes. Lack of consistency and errors in other earthquake loss databases frequently cited and used in analyses was a major shortcoming in the view of the authors which needed to be improved upon. Over 17 000 sources of information have been utilised, primarily in the last few years, to present data from over 12 200 damaging earthquakes historically, with over 7000 earthquakes since 1900 examined and validated before insertion into the database. Each validated earthquake includes seismological information, building damage, ranges of social losses to account for varying sources (deaths, injuries, homeless, and affected), and economic losses (direct, indirect, aid, and insured). Globally, a slightly increasing trend in economic damage due to earthquakes is not consistent with the greatly increasing exposure. The 1923 Great Kanto (214 billion USD damage; 2011 HNDECI-adjusted dollars) compared to the 2011 Tohoku (>300 billion USD at time of writing), 2008 Sichuan and 1995 Kobe earthquakes show the increasing concern for economic loss in urban areas as the trend should be expected to increase. Many economic and social loss values not reported in existing databases have been collected. Historical GDP (Gross Domestic Product), exchange rate, wage information, population, HDI (Human Development Index), and insurance information have been collected globally to form comparisons. This catalogue is the largest known cross-checked global historic damaging earthquake database and should have far-reaching consequences for earthquake loss estimation, socio-economic analysis, and the global reinsurance field.

  16. MannDB: A microbial annotation database for protein characterization

    SciTech Connect

    Zhou, C; Lam, M; Smith, J; Zemla, A; Dyer, M; Kuczmarski, T; Vitalis, E; Slezak, T

    2006-05-19

    MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high

  17. HDACiDB: a database for histone deacetylase inhibitors

    PubMed Central

    Murugan, Kasi; Sangeetha, Shanmugasamy; Ranjitha, Shanmugasamy; Vimala, Antony; Al-Sohaibani, Saleh; Rameshkumar, Gopal

    2015-01-01

    An histone deacetylase (HDAC) inhibitor database (HDACiDB) was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi]), helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski’s rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http://hdacidb.bioinfo.au-kbc.org.in/hdacidb/website. PMID:25945037

  18. HDACiDB: a database for histone deacetylase inhibitors.

    PubMed

    Murugan, Kasi; Sangeetha, Shanmugasamy; Ranjitha, Shanmugasamy; Vimala, Antony; Al-Sohaibani, Saleh; Rameshkumar, Gopal

    2015-01-01

    An histone deacetylase (HDAC) inhibitor database (HDACiDB) was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi]), helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski's rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http://hdacidb.bioinfo.au-kbc.org.in/hdacidb/website. PMID:25945037

  19. MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis

    DOE Data Explorer

    Kaufman, Markus; Pal, Debnath; Eisenberg, David

    Proteins up- and down- regulated in Mycobacterium tuberculosis grown under conditions mimicking infection are included in this database. It also includes information on proteins that are regulated by selected transcription factors or other regulatory proteins. The literature data provided here is complimentary to the databases provided by Michael Strong that include recent TB computational functional linkages and the Prolinks Database by Peter Bowers. The experimental condition, the experimental dataset and a literature reference will be displayed, including links to the computationally linked proteins in the Prolinks Database and the entry in the Mycobacterium tuberculosis Structural Genomics Database.[Copied from information at http://www.doe-mbi.ucla.edu/Services/MTBreg/

  20. Comprehensive Planning To Address Homelessness. City Initiatives.

    ERIC Educational Resources Information Center

    Zawisza, Kris

    This packet contains documents that provide information about the planning and implementation of a comprehensive plan to address homelessness in cities throughout the U.S. Information on the following components of a comprehensive strategy are included: (1) "Task Forces"; (2) "Assessment Studies"; (3) "Emergency Services"; (4) "Transitional…

  1. 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.

  2. CDS - Database Administrator's Guide

    NASA Astrophysics Data System (ADS)

    Day, J. P.

    This guide aims to instruct the CDS database administrator in: o The CDS file system. o The CDS index files. o The procedure for assimilating a new CDS tape into the database. It is assumed that the administrator has read SUN/79.

  3. Ionic Liquids Database- (ILThermo)

    National Institute of Standards and Technology Data Gateway

    SRD 147 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.

  4. Database Searching by Managers.

    ERIC Educational Resources Information Center

    Arnold, Stephen E.

    Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

  5. Morchella MLST database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Welcome to the Morchella MLST database. This dedicated database was set up at the CBS-KNAW Biodiversity Center by Vincent Robert in February 2012, using BioloMICS software (Robert et al., 2011), to facilitate DNA sequence-based identifications of Morchella species via the Internet. The current datab...

  6. First Look: TRADEMARKSCAN Database.

    ERIC Educational Resources Information Center

    Fernald, Anne Conway; Davidson, Alan B.

    1984-01-01

    Describes database produced by Thomson and Thomson and available on Dialog which contains over 700,000 records representing all active federal trademark registrations and applications for registrations filed in United States Patent and Trademark Office. A typical record, special features, database applications, learning to use TRADEMARKSCAN, and…

  7. HIV Structural Database

    National Institute of Standards and Technology Data Gateway

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  8. Biological Macromolecule Crystallization Database

    National Institute of Standards and Technology Data Gateway

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  9. Assignment to database industy

    NASA Astrophysics Data System (ADS)

    Abe, Kohichiroh

    Various kinds of databases are considered to be essential part in future large sized systems. Information provision only by databases is also considered to be growing as the market becomes mature. This paper discusses how such circumstances have been built and will be developed from now on.

  10. BioImaging Database

    Energy Science and Technology Software Center (ESTSC)

    2006-10-25

    The Biolmaging Database (BID) is a relational database developed to store the data and meta-data for the 3D gene expression in early Drosophila embryo development on a cellular level. The schema was written to be used with the MySQL DBMS but with minor modifications can be used on any SQL compliant relational DBMS.

  11. The intelligent database machine

    NASA Technical Reports Server (NTRS)

    Yancey, K. E.

    1985-01-01

    The IDM data base was compared with the data base crack to determine whether IDM 500 would better serve the needs of the MSFC data base management system than Oracle. The two were compared and the performance of the IDM was studied. Implementations that work best on which database are implicated. The choice is left to the database administrator.

  12. Build Your Own Database.

    ERIC Educational Resources Information Center

    Jacso, Peter; Lancaster, F. W.

    This book is intended to help librarians and others to produce databases of better value and quality, especially if they have had little previous experience in database construction. Drawing upon almost 40 years of experience in the field of information retrieval, this book emphasizes basic principles and approaches rather than in-depth and…

  13. Database Reviews: Legal Information.

    ERIC Educational Resources Information Center

    Seiser, Virginia

    Detailed reviews of two legal information databases--"Laborlaw I" and "Legal Resource Index"--are presented in this paper. Each database review begins with a bibliographic entry listing the title; producer; vendor; cost per hour contact time; offline print cost per citation; time period covered; frequency of updates; and size of file. A detailed…

  14. Database in Artificial Intelligence.

    ERIC Educational Resources Information Center

    Wilkinson, Julia

    1986-01-01

    Describes a specialist bibliographic database of literature in the field of artificial intelligence created by the Turing Institute (Glasgow, Scotland) using the BRS/Search information retrieval software. The subscription method for end-users--i.e., annual fee entitles user to unlimited access to database, document provision, and printed awareness…

  15. Structural Ceramics Database

    National Institute of Standards and Technology Data Gateway

    SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

  16. Knowledge Discovery in Databases.

    ERIC Educational Resources Information Center

    Norton, M. Jay

    1999-01-01

    Knowledge discovery in databases (KDD) revolves around the investigation and creation of knowledge, processes, algorithms, and mechanisms for retrieving knowledge from data collections. The article is an introductory overview of KDD. The rationale and environment of its development and applications are discussed. Issues related to database design…

  17. Online Database Searching Workbook.

    ERIC Educational Resources Information Center

    Littlejohn, Alice C.; Parker, Joan M.

    Designed primarily for use by first-time searchers, this workbook provides an overview of online searching. Following a brief introduction which defines online searching, databases, and database producers, five steps in carrying out a successful search are described: (1) identifying the main concepts of the search statement; (2) selecting a…

  18. CPDB: Carcinogenic Potency Database.

    PubMed

    Fitzpatrick, Roberta Bronson

    2008-01-01

    The Carcinogenic Potency Database reports analyses of animal cancer tests on 1,547 chemicals. These tests are used in support of cancer risk assessments for humans. Results are searchable and are made available via the National Library of Medicine's (NLM) TOXNET system. This column will provide background information on the database, as well as present search basics. PMID:19042710

  19. The EXOSAT database and archive

    NASA Technical Reports Server (NTRS)

    Reynolds, A. P.; Parmar, A. N.

    1992-01-01

    The EXOSAT database provides on-line access to the results and data products (spectra, images, and lightcurves) from the EXOSAT mission as well as access to data and logs from a number of other missions (such as EINSTEIN, COS-B, ROSAT, and IRAS). In addition, a number of familiar optical, infrared, and x ray catalogs, including the Hubble Space Telescope (HST) guide star catalog are available. The complete database is located at the EXOSAT observatory at ESTEC in the Netherlands and is accessible remotely via a captive account. The database management system was specifically developed to efficiently access the database and to allow the user to perform statistical studies on large samples of astronomical objects as well as to retrieve scientific and bibliographic information on single sources. The system was designed to be mission independent and includes timing, image processing, and spectral analysis packages as well as software to allow the easy transfer of analysis results and products to the user's own institute. The archive at ESTEC comprises a subset of the EXOSAT observations, stored on magnetic tape. Observations of particular interest were copied in compressed format to an optical jukebox, allowing users to retrieve and analyze selected raw data entirely from their terminals. Such analysis may be necessary if the user's needs are not accommodated by the products contained in the database (in terms of time resolution, spectral range, and the finesse of the background subtraction, for instance). Long-term archiving of the full final observation data is taking place at ESRIN in Italy as part of the ESIS program, again using optical media, and ESRIN have now assumed responsibility for distributing the data to the community. Tests showed that raw observational data (typically several tens of megabytes for a single target) can be transferred via the existing networks in reasonable time.

  20. Spectrum of Physics Comprehension

    ERIC Educational Resources Information Center

    Blasiak, W.; Godlewska, M.; Rosiek, R.; Wcislo, D.

    2012-01-01

    The paper presents the results of research on the relationship between self-assessed comprehension of physics lectures and final grades of junior high school students (aged 13-15), high school students (aged 16-18) and physics students at the Pedagogical University of Cracow, Poland (aged 21). Students' declared level of comprehension was measured…