WorldWideScience

Sample records for public databases including

  1. Database Publication Practices

    DEFF Research Database (Denmark)

    Bernstein, P.A.; DeWitt, D.; Heuer, A.

    2005-01-01

    There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems.......There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems....

  2. Database Publication Practices

    DEFF Research Database (Denmark)

    Bernstein, P.A.; DeWitt, D.; Heuer, A.

    2005-01-01

    There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems....

  3. Public chemical compound databases.

    Science.gov (United States)

    Williams, Anthony J

    2008-05-01

    The internet has rapidly become the first port of call for all information searches. The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data. This review discusses the types of public compound databases that are available online and provides a series of examples. Focus is also given to the benefits and disruptions associated with the increased availability of such data and the integration of technologies to data mine this information.

  4. A Decade of Database Research Publications

    CERN Document Server

    Sakr, Sherif

    2011-01-01

    We analyze the database research publications of four major core database technology conferences (SIGMOD, VLDB, ICDE, EDBT), two main theoretical database conferences (PODS, ICDT) and three database journals (TODS, VLDB Journal, TKDE) over a period of 10 years (2001 - 2010). Our analysis considers only regular papers as we do not include short papers, demo papers, posters, tutorials or panels into our statistics. We rank the research scholars according to their number of publication in each conference/journal separately and in combined. We also report about the growth in the number of research publications and the size of the research community in the last decade.

  5. Database Support for Research in Public Administration

    Science.gov (United States)

    Tucker, James Cory

    2005-01-01

    This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases…

  6. FEEDBACK ON A PUBLICLY DISTRIBUTED IMAGE DATABASE: THE MESSIDOR DATABASE

    Directory of Open Access Journals (Sweden)

    Etienne Decencière

    2014-08-01

    Full Text Available The Messidor database, which contains hundreds of eye fundus images, has been publicly distributed since 2008. It was created by the Messidor project in order to evaluate automatic lesion segmentation and diabetic retinopathy grading methods. Designing, producing and maintaining such a database entails significant costs. By publicly sharing it, one hopes to bring a valuable resource to the public research community. However, the real interest and benefit of the research community is not easy to quantify. We analyse here the feedback on the Messidor database, after more than 6 years of diffusion. This analysis should apply to other similar research databases.

  7. Public Opinion Poll Question Databases: An Evaluation

    Science.gov (United States)

    Woods, Stephen

    2007-01-01

    This paper evaluates five polling resource: iPOLL, Polling the Nations, Gallup Brain, Public Opinion Poll Question Database, and Polls and Surveys. Content was evaluated on disclosure standards from major polling organizations, scope on a model for public opinion polls, and presentation on a flow chart discussing search limitations and usability.

  8. Implementing database system for LHCb publications page

    CERN Document Server

    Abdullayev, Fakhriddin

    2017-01-01

    The LHCb is one of the main detectors of Large Hadron Collider, where physicists and scientists work together on high precision measurements of matter-antimatter asymmetries and searches for rare and forbidden decays, with the aim of discovering new and unexpected forces. The work does not only consist of analyzing data collected from experiments but also in publishing the results of those analyses. The LHCb publications are gathered on LHCb publications page to maximize their availability to both LHCb members and to the high energy community. In this project a new database system was implemented for LHCb publications page. This will help to improve access to research papers for scientists and better integration with current CERN library website and others.

  9. Digital Equipment Corporation's CRDOM Software and Database Publications.

    Science.gov (United States)

    Adams, Michael Q.

    1986-01-01

    Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

  10. Gene and protein nomenclature in public databases

    Directory of Open Access Journals (Sweden)

    Zimmer Ralf

    2006-08-01

    Full Text Available Abstract Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of

  11. A publication database for optical long baseline interferometry

    CERN Document Server

    Malbet, Fabien; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

    2010-01-01

    Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

  12. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  13. USAID Public-Private Partnerships Database

    Data.gov (United States)

    US Agency for International Development — This dataset brings together information collected since 2001 on PPPs that have been supported by USAID. For the purposes of this dataset a Public-Private...

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

    Science.gov (United States)

    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...

  15. Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity.

    Science.gov (United States)

    Machado, Helena; Silva, Susana

    2015-10-01

    The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of 'solidarity', traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system.

  16. Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity

    Science.gov (United States)

    Machado, Helena; Silva, Susana

    2015-01-01

    The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of ‘solidarity’, traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system. PMID:26139851

  17. Exploring public databases to characterize urban flood risks in Amsterdam

    Science.gov (United States)

    Gaitan, Santiago; ten Veldhuis, Marie-claire; van de Giesen, Nick

    2015-04-01

    Cities worldwide are challenged by increasing urban flood risks. Precise and realistic measures are required to decide upon investment to reduce their impacts. Obvious flooding factors affecting flood risk include sewer systems performance and urban topography. However, currently implemented sewer and topographic models do not provide realistic predictions of local flooding occurrence during heavy rain events. Assessing other factors such as spatially distributed rainfall and socioeconomic characteristics may help to explain probability and impacts of urban flooding. Several public databases were analyzed: complaints about flooding made by citizens, rainfall depths (15 min and 100 Ha spatio-temporal resolution), grids describing number of inhabitants, income, and housing price (1Ha and 25Ha resolution); and buildings age. Data analysis was done using Python and GIS programming, and included spatial indexing of data, cluster analysis, and multivariate regression on the complaints. Complaints were used as a proxy to characterize flooding impacts. The cluster analysis, run for all the variables except the complaints, grouped part of the grid-cells of central Amsterdam into a highly differentiated group, covering 10% of the analyzed area, and accounting for 25% of registered complaints. The configuration of the analyzed variables in central Amsterdam coincides with a high complaint count. Remaining complaints were evenly dispersed along other groups. An adjusted R2 of 0.38 in the multivariate regression suggests that explaining power can improve if additional variables are considered. While rainfall intensity explained 4% of the incidence of complaints, population density and building age significantly explained around 20% each. Data mining of public databases proved to be a valuable tool to identify factors explaining variability in occurrence of urban pluvial flooding, though additional variables must be considered to fully explain flood risk variability.

  18. The Mouse SAGE Site: database of public mouse SAGE libraries.

    Science.gov (United States)

    Divina, Petr; Forejt, Jirí

    2004-01-01

    The Mouse SAGE Site is a web-based database of all available public libraries generated by the Serial Analysis of Gene Expression (SAGE) from various mouse tissues and cell lines. The database contains mouse SAGE libraries organized in a uniform way and provides web-based tools for browsing, comparing and searching SAGE data with reliable tag-to-gene identification. A modified approach based on the SAGEmap database is used for reliable tag identification. The Mouse SAGE Site is maintained on an ongoing basis at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic and is accessible at the internet address http://mouse.biomed.cas.cz/sage/.

  19. Restructuring the Public School Curriculum To Include Parenting Education Classes.

    Science.gov (United States)

    Tyree, Carolyn L.; And Others

    Although the current educational climate stresses a back-to-basics approach, there is nonetheless overwhelming evidence of a need for an appropriately structured parenting education program in the public school curriculum. Reasons for this need include the large number of teenage pregnancies and abortions. These lead teens to miss high school…

  20. NCI at Frederick Scientific Library Reintroduces Scientific Publications Database | Poster

    Science.gov (United States)

    A 20-year-old database of scientific publications by NCI at Frederick, FNLCR, and affiliated employees has gotten a significant facelift. Maintained by the Scientific Library, the redesigned database—which is linked from each of the Scientific Library’s web pages—offers features that were not available in previous versions, such as additional search limits and non-traditional metrics for scholarly and scientific publishing known as altmetrics.

  1. Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): a database of permitted public-supply wells, surface-water intakes, and systems in the United States

    Science.gov (United States)

    Price, Curtis V.; Maupin, Molly A.

    2014-01-01

    The U.S. Geological Survey (USGS) has developed a database containing information about wells, surface-water intakes, and distribution systems that are part of public water systems across the United States, its territories, and possessions. Programs of the USGS such as the National Water Census, the National Water Use Information Program, and the National Water-Quality Assessment Program all require a complete and current inventory of public water systems, the sources of water used by those systems, and the size of populations served by the systems across the Nation. Although the U.S. Environmental Protection Agency’s Safe Drinking Water Information System (SDWIS) database already exists as the primary national Federal database for information on public water systems, the Public-Supply Database (PSDB) was developed to add value to SDWIS data with enhanced location and ancillary information, and to provide links to other databases, including the USGS’s National Water Information System (NWIS) database.

  2. Community Assessment Tool for Public Health Emergencies Including Pandemic Influenza

    Energy Technology Data Exchange (ETDEWEB)

    ORAU' s Oak Ridge Institute for Science Education (HCTT-CHE)

    2011-04-14

    The Community Assessment Tool (CAT) for Public Health Emergencies Including Pandemic Influenza (hereafter referred to as the CAT) was developed as a result of feedback received from several communities. These communities participated in workshops focused on influenza pandemic planning and response. The 2008 through 2011 workshops were sponsored by the Centers for Disease Control and Prevention (CDC). Feedback during those workshops indicated the need for a tool that a community can use to assess its readiness for a disaster - readiness from a total healthcare perspective, not just hospitals, but the whole healthcare system. The CAT intends to do just that - help strengthen existing preparedness plans by allowing the healthcare system and other agencies to work together during an influenza pandemic. It helps reveal each core agency partners (sectors) capabilities and resources, and highlights cases of the same vendors being used for resource supplies (e.g., personal protective equipment [PPE] and oxygen) by the partners (e.g., public health departments, clinics, or hospitals). The CAT also addresses gaps in the community's capabilities or potential shortages in resources. This tool has been reviewed by a variety of key subject matter experts from federal, state, and local agencies and organizations. It also has been piloted with various communities that consist of different population sizes, to include large urban to small rural communities.

  3. Community Assessment Tool for Public Health Emergencies Including Pandemic Influenza

    Energy Technology Data Exchange (ETDEWEB)

    HCTT-CHE

    2011-04-14

    The Community Assessment Tool (CAT) for Public Health Emergencies Including Pandemic Influenza (hereafter referred to as the CAT) was developed as a result of feedback received from several communities. These communities participated in workshops focused on influenza pandemic planning and response. The 2008 through 2011 workshops were sponsored by the Centers for Disease Control and Prevention (CDC). Feedback during those workshops indicated the need for a tool that a community can use to assess its readiness for a disaster—readiness from a total healthcare perspective, not just hospitals, but the whole healthcare system. The CAT intends to do just that—help strengthen existing preparedness plans by allowing the healthcare system and other agencies to work together during an influenza pandemic. It helps reveal each core agency partners' (sectors) capabilities and resources, and highlights cases of the same vendors being used for resource supplies (e.g., personal protective equipment [PPE] and oxygen) by the partners (e.g., public health departments, clinics, or hospitals). The CAT also addresses gaps in the community's capabilities or potential shortages in resources. While the purpose of the CAT is to further prepare the community for an influenza pandemic, its framework is an extension of the traditional all-hazards approach to planning and preparedness. As such, the information gathered by the tool is useful in preparation for most widespread public health emergencies. This tool is primarily intended for use by those involved in healthcare emergency preparedness (e.g., community planners, community disaster preparedness coordinators, 9-1-1 directors, hospital emergency preparedness coordinators). It is divided into sections based on the core agency partners, which may be involved in the community's influenza pandemic influenza response.

  4. Portfolio of prospective clinical trials including brachytherapy: an analysis of the ClinicalTrials.gov database

    OpenAIRE

    Cihoric, Nikola; Tsikkinis, Alexandros; Miguelez, Cristina Gutierrez; Strnad, Vratislav; Soldatovic, Ivan; Ghadjar, Pirus; Jeremic, Branislav; Dal Pra, Alan; Aebersold, Daniel M; Lössl, Kristina

    2016-01-01

    Background To evaluate the current status of prospective interventional clinical trials that includes brachytherapy (BT) procedures. Methods The records of 175,538 (100 %) clinical trials registered at ClinicalTrials.gov were downloaded on September 2014 and a database was established. Trials using BT as an intervention were identified for further analyses. The selected trials were manually categorized according to indication(s), BT source, applied dose rate, primary sponsor type, location, p...

  5. Portfolio of prospective clinical trials including brachytherapy: an analysis of the ClinicalTrials.gov database

    OpenAIRE

    Cihoric, Nikola; Tsikkinis, Alexandros; Gutierrez Miguelez, Cristina; Strnad, Vratislav; Soldatovic, Ivan; Ghadjar, Pirus; Jeremic, Branislav; Dal Pra, Alan; Aebersold, Daniel M; Lössl, Kristina

    2016-01-01

    Background To evaluate the current status of prospective interventional clinical trials that includes brachytherapy (BT) procedures. Methods The records of 175,538 (100 %) clinical trials registered at ClinicalTrials.gov were downloaded on September 2014 and a database was established. Trials using BT as an intervention were identified for further analyses. The selected trials were manually categorized according to indication(s), BT source, applied dose rate, primary sponsor type,...

  6. LBVS: an online platform for ligand-based virtual screening using publicly accessible databases.

    Science.gov (United States)

    Zheng, Minghao; Liu, Zhihong; Yan, Xin; Ding, Qianzhi; Gu, Qiong; Xu, Jun

    2014-11-01

    Abundant data on compound bioactivity and publicly accessible chemical databases increase opportunities for ligand-based drug discovery. In order to make full use of the data, an online platform for ligand-based virtual screening (LBVS) using publicly accessible databases has been developed. LBVS adopts Bayesian learning approach to create virtual screening models because of its noise tolerance, speed, and efficiency in extracting knowledge from data. LBVS currently includes data derived from BindingDB and ChEMBL. Three validation approaches have been employed to evaluate the virtual screening models created from LBVS. The tenfold cross validation results of twenty different LBVS models demonstrate that LBVS achieves an average AUC value of 0.86. Our internal and external testing results indicate that LBVS is predictive for lead identifications. LBVS can be publicly accessed at http://rcdd.sysu.edu.cn/lbvs.

  7. Extending the Intermediate Data Structure (IDS for longitudinal historical databases to include geographic data

    Directory of Open Access Journals (Sweden)

    Finn Hedefalk

    2014-09-01

    Full Text Available The Intermediate Data Structure (IDS is a standardised database structure for longitudinal historical databases. Such a common structure facilitates data sharing and comparative research. In this study, we propose an extended version of IDS, named IDS-Geo, that also includes geographic data. The geographic data that will be stored in IDS-Geo are primarily buildings and/or property units, and the purpose of these geographic data is mainly to link individuals to places in space. When we want to assign such detailed spatial locations to individuals (in times before there were any detailed house addresses available, we often have to create tailored geographic datasets. In those cases, there are benefits of storing geographic data in the same structure as the demographic data. Moreover, we propose the export of data from IDS-Geo using an eXtensible Markup Language (XML Schema. IDS-Geo is implemented in a case study using historical property units, for the period 1804 to 1913, stored in a geographically extended version of the Scanian Economic Demographic Database (SEDD. To fit into the IDS-Geo data structure, we included an object lifeline representation of all of the property units (based on the snapshot time representation of single historical maps and poll-tax registers. The case study verifies that the IDS-Geo model is capable of handling geographic data that can be linked to demographic data.

  8. Information Technologies in Public Health Management: A Database on Biocides to Improve Quality of Life

    Directory of Open Access Journals (Sweden)

    A Grigoriu

    2012-05-01

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

  9. ScafBank: a public comprehensive Scaffold database to support molecular hopping

    Institute of Scientific and Technical Information of China (English)

    Bibo YAN; Mengzhu XUE; Bing XIONG; Ke LIU; Dingyu HU; Jingkang SHEN

    2009-01-01

    Aim:The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years.Our goal is to provide a publi-cally searchable database of scaffolds out from a large collection of existing chemical molecules.Results: Although a number of in silico methods have emerged to facilitate this process,which has become known as "scaffold hopping" or "molecular hopping",there is an urgent need for a database system to provide such valuable data in the drug design field.Here we have systematically analyzed a collection of commercially available small molecule databases and a bioactive compound database to identify unique scaffolds and we have built apublically searchable database.The analysis of approximately 4 800 000 of these compounds identified 241 824 unique scaffolds,which are stored in a relational database (http://202.127.30.184:8080/db.html).Each entry in the database is associated with a molecular occurrence and includes its distribution of molecular properties,such as molecular weight,logP,hydrogen bond acceptor number,hydrogen bond donor number,rotatable bond number and ring number.More importantly,for scaffolds derived from the bioactive compounds database,it also contains the original compounds and their target information.Conclusion: This Web-based database system could help researchers in the fields of medicinal and organic chemistry to design novel molecules with properties similar to the original compounds,but built on novel scaffolds.

  10. Why education in public schools should include religious ideals

    NARCIS (Netherlands)

    de Ruyter, D.J.; Merry, M.S.

    2009-01-01

    This article aims to open a new line of debate about religion in public schools by focusing on religious ideals. The article begins with an elucidation of the concept ‘religious ideals’ and an explanation of the notion of reasonable pluralism, in order to be able to explore the dangers and positive

  11. The final COS-B database now publicly available

    Science.gov (United States)

    Mayer-Hasselwander, H. A.; Bennett, K.; Bignami, G. F.; Bloemen, J. B. G. M.; Buccheri, R.; Caraveo, P. A.; Hermsen, W.; Kanbach, G.; Lebrun, F.; Paul, J. A.

    1985-01-01

    The data obtained by the gamma ray satellite COS-B was processed, condensed and integrated together with the relevant mission and experiment parameters into the Final COS-B Database. The database contents and the access programs available with the database are outlined. The final sky coverage and a presentation of the large scale distribution of the observed Milky Way emission are given. The database is announced to be available through the European Space Agency.

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

    Directory of Open Access Journals (Sweden)

    Kara A Livingston

    Full Text Available 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.(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.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.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.

  13. Genomics and Public Health Research: Can the State Allow Access to Genomic Databases?

    Directory of Open Access Journals (Sweden)

    M Stanton Jean

    2012-04-01

    Full Text Available Because many diseases are multifactorial disorders,the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State's role and authority on matters related to public health,in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec. Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec,as examples of key tools framing public health decision-making process.We observed that State powers in public health, are not,in Quebec,well adapted to the expansion of genomics research.We propose that the scope of the concept of research in public health should be clear and include the following characteristics:a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up,consent, etc..We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters.

  14. The EpiSLI Database: A Publicly Available Database on Speech and Language

    Science.gov (United States)

    Tomblin, J. Bruce

    2010-01-01

    Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

  15. A novel comprehensive wheat miRNA database, including related bioinformatics software

    Directory of Open Access Journals (Sweden)

    Mohamed Amine Remita

    2016-11-01

    Full Text Available MicroRNAs (miRNAs are emerging as important post-transcriptional regulators that may regulate key genes responsible for agronomic traits such as grain yield and stress tolerance. Several studies identified species and clades specific miRNA families associated with plant stress regulated genes. Here, we propose a novel resource that provides data related to the expression of abiotic stress responsive miRNAs in wheat, one of the most important staple food crops. This database allows the query of small RNA libraries, including in silico predicted wheat miRNA sequences and the expression profiles of small RNAs identified from those libraries. Our database also provides a direct access to online miRNA prediction software tuned to de novo miRNA detection in wheat, in monocotyledon clades, as well as in other plant species. These data and software will facilitate multiple comparative analyses and reproducible studies on small RNAs and miRNA families in plants. Our web portal is available at: http://wheat.bioinfo.uqam.ca.

  16. Including the public in pandemic planning: a deliberative approach

    Directory of Open Access Journals (Sweden)

    Braunack-Mayer Annette J

    2010-08-01

    Full Text Available Abstract Background Against a background of pandemic threat posed by SARS and avian H5N1 influenza, this study used deliberative forums to elucidate informed community perspectives on aspects of pandemic planning. Methods Two deliberative forums were carried out with members of the South Australian community. The forums were supported by a qualitative study with adults and youths, systematic reviews of the literature and the involvement of an extended group of academic experts and policy makers. The forum discussions were recorded with simultaneous transcription and analysed thematically. Results Participants allocated scarce resources of antiviral drugs and pandemic vaccine based on a desire to preserve society function in a time of crisis. Participants were divided on the acceptability of social distancing and quarantine measures. However, should such measures be adopted, they thought that reasonable financial, household and psychological support was essential. In addition, provided such support was present, the participants, in general, were willing to impose strict sanctions on those who violated quarantine and social distancing measures. Conclusions The recommendations from the forums suggest that the implementation of pandemic plans in a severe pandemic will be challenging, but not impossible. Implementation may be more successful if the public is engaged in pandemic planning before a pandemic, effective communication of key points is practiced before and during a pandemic and if judicious use is made of supportive measures to assist those in quarantine or affected by social isolation measures.

  17. 75 FR 41180 - Notice of Order: Revisions to Enterprise Public Use Database

    Science.gov (United States)

    2010-07-15

    ... purpose of loan data field in these two databases. 4. Single-family Data Field 27 and Multifamily Data... AGENCY Notice of Order: Revisions to Enterprise Public Use Database AGENCY: Federal Housing Finance... use database (PUDB) for such mortgage data was transferred to FHFA from the U.S. Department of...

  18. Data mining of public SNP databases for the selection of intragenic SNPs

    NARCIS (Netherlands)

    Aerts, J.; Wetzels, Y.; Cohen, N.; Aerssens, J.

    2002-01-01

    Different strategies to search public single nucleotide polymorphism (SNP) databases for intragenic SNPs were evaluated. First, we assembled a strategy to annotate SNPs onto candidate genes based on a BLAST search of public SNP databases (Intragenic SNP Annotation by BLAST, ISAB). Only BLAST hits th

  19. Lignan contents of Dutch plant foods: a database including lariciresinol, pinoresinol, secoisolariciresinol and matairesinol.

    Science.gov (United States)

    Milder, Ivon E J; Arts, Ilja C W; van de Putte, Betty; Venema, Dini P; Hollman, Peter C H

    2005-03-01

    Enterolignans (enterodiol and enterolactone) can potentially reduce the risk of certain cancers and cardiovascular diseases. Enterolignans are formed by the intestinal microflora after the consumption of plant lignans. Until recently, only secoisolariciresinol and matairesinol were considered enterolignan precursors, but now several new precursors have been identified, of which lariciresinol and pinoresinol have a high degree of conversion. Quantitative data on the contents in foods of these new enterolignan precursors are not available. Thus, the aim of this study was to compile a lignan database including all four major enterolignan precursors. Liquid chromatography-tandem mass spectrometry was used to quantify lariciresinol, pinoresinol, secoisolariciresinol and matairesinol in eighty-three solid foods and twenty-six beverages commonly consumed in The Netherlands. The richest source of lignans was flaxseed (301,129 microg/100 g), which contained mainly secoisolariciresinol. Also, lignan concentrations in sesame seeds (29,331 microg/100 g, mainly pinoresinol and lariciresinol) were relatively high. For grain products, which are known to be important sources of lignan, lignan concentrations ranged from 7 to 764 microg/100 g. However, many vegetables and fruits had similar concentrations, because of the contribution of lariciresinol and pinoresinol. Brassica vegetables contained unexpectedly high levels of lignans (185-2321 microg/100 g), mainly pinoresinol and lariciresinol. Lignan levels in beverages varied from 0 (cola) to 91 microg/100 ml (red wine). Only four of the 109 foods did not contain a measurable amount of lignans, and in most cases the amount of lariciresinol and pinoresinol was larger than that of secoisolariciresinol and matairesinol. Thus, available databases largely underestimate the amount of enterolignan precursors in foods.

  20. Including public perspectives in industrial biotechnology and the biobased economy.

    Science.gov (United States)

    Paula, Lino; Birrer, Frans

    2006-01-01

    Industrial ("white") biotechnology promises to contribute to a more sustainable future. Compared to current production processes, cases have been identified where industrial biotechnology can decrease the amount of energy and raw materials used to make products and also reduce the amount of emissions and waste produced during production. However, switching from products based on chemical production processes and fossil fuels towards "biobased" products is at present not necessarily economically viable. This is especially true for bulk products, for example ethanol production from biomass. Therefore, scientists are also turning to genetic modification as a means to develop organisms that can produce at lower costs. These include not only micro-organisms, but also organisms used in agriculture for food and feed. The use of genetic modification for "deliberate release" purposes, in particular, has met great opposition in Europe. Many industrial biotechnology applications may, due to their scale, entail deliberate releases of GM organisms. Thus, the biobased economy brings back a familiar question; is it ethically justifiable, and acceptable to citizens, to expose the environment and society to the risks associated with GM, in order to protect that same environment and to sustain our affluent way of life? For a successful innovation towards a biobased economy, its proponents, especially producers, need to take into account (take responsibility for) such issues when developing new products and processes. These issues, and how scientists can interact with citizens about them in a timely way, are further explored in projects at Delft University and Leiden University, also in collaboration with Utrecht University.

  1. 76 FR 77533 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Science.gov (United States)

    2011-12-13

    ... AGENCY Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family... matrices to include certain data fields for high-cost single-family loans purchased and securitized by the... rate spread field has been corrected in the Single Family Census Tract Data Set. Both files...

  2. Biogas composition and engine performance, including database and biogas property model

    NARCIS (Netherlands)

    Bruijstens, A.J.; Beuman, W.P.H.; Molen, M. van der; Rijke, J. de; Cloudt, R.P.M.; Kadijk, G.; Camp, O.M.G.C. op den; Bleuanus, W.A.J.

    2008-01-01

    In order to enable this evaluation of the current biogas quality situation in the EU; results are presented in a biogas database. Furthermore the key gas parameter Sonic Bievo Index (influence on open loop A/F-ratio) is defined and other key gas parameters like the Methane Number (knock resistance)

  3. Biogas composition and engine performance, including database and biogas property model

    NARCIS (Netherlands)

    Bruijstens, A.J.; Beuman, W.P.H.; Molen, M. van der; Rijke, J. de; Cloudt, R.P.M.; Kadijk, G.; Camp, O.M.G.C. op den; Bleuanus, W.A.J.

    2008-01-01

    In order to enable this evaluation of the current biogas quality situation in the EU; results are presented in a biogas database. Furthermore the key gas parameter Sonic Bievo Index (influence on open loop A/F-ratio) is defined and other key gas parameters like the Methane Number (knock resistance)

  4. Editorial: AAS Will Be Included in the SCI Database in 2009

    Institute of Scientific and Technical Information of China (English)

    Guoxiong Wu; Huijun Wang; Da-Lin Zhang

    2008-01-01

    @@ We are very pleased to announce that our jour-nal of Advances in Atmospheric Sciences(AAS)has been accepted for inclusion in the"Science Citation Index"(SCI)database beginning with its 2009 volume,as recently informed by Mr.Rodney Chonka,Editor of Pysical.Chemical & Earth Sciences of Thomson Reuters.

  5. Big bad data: law, public health, and biomedical databases.

    Science.gov (United States)

    Hoffman, Sharona; Podgurski, Andy

    2013-03-01

    The accelerating adoption of electronic health record (EHR) systems will have far-reaching implications for public health research and surveillance, which in turn could lead to changes in public policy, statutes, and regulations. The public health benefits of EHR use can be significant. However, researchers and analysts who rely on EHR data must proceed with caution and understand the potential limitations of EHRs. Because of clinicians' workloads, poor user-interface design, and other factors, EHR data can be erroneous, miscoded, fragmented, and incomplete. In addition, public health findings can be tainted by the problems of selection bias, confounding bias, and measurement bias. These flaws may become all the more troubling and important in an era of electronic "big data," in which a massive amount of information is processed automatically, without human checks. Thus, we conclude the paper by outlining several regulatory and other interventions to address data analysis difficulties that could result in invalid conclusions and unsound public health policies. © 2013 American Society of Law, Medicine & Ethics, Inc.

  6. Using Bibliographic Knowledge for Ranking in Scientific Publication Databases

    CERN Document Server

    Vesely, Martin; Le Meur, Jean-Yves

    2008-01-01

    Document ranking for scientific publications involves a variety of specialized resources (e.g. author or citation indexes) that are usually difficult to use within standard general purpose search engines that usually operate on large-scale heterogeneous document collections for which the required specialized resources are not always available for all the documents present in the collections. Integrating such resources into specialized information retrieval engines is therefore important to cope with community-specific user expectations that strongly influence the perception of relevance within the considered community. In this perspective, this paper extends the notion of ranking with various methods exploiting different types of bibliographic knowledge that represent a crucial resource for measuring the relevance of scientific publications. In our work, we experimentally evaluated the adequacy of two such ranking methods (one based on freshness, i.e. the publication date, and the other on a novel index, the ...

  7. Databases

    Data.gov (United States)

    National Aeronautics and Space Administration — The databases of computational and experimental data from the first Aeroelastic Prediction Workshop are located here. The databases file names tell their contents by...

  8. Personal Publications Lists Serve as a Reliable Calibration Parameter to Compare Coverage in Academic Citation Databases with Scientific Social Media

    Directory of Open Access Journals (Sweden)

    Emma Hughes

    2017-03-01

    Full Text Available A Review of: Hilbert, F., Barth, J., Gremm, J., Gros, D., Haiter, J., Henkel, M., Reinhardt, W., & Stock, W.G. (2015. Coverage of academic citation databases compared with coverage of scientific social media: personal publication lists as calibration parameters. Online Information Review 39(2: 255-264. http://dx.doi.org/10.1108/OIR-07-2014-0159 Objective – The purpose of this study was to explore coverage rates of information science publications in academic citation databases and scientific social media using a new method of personal publication lists as a calibration parameter. The research questions were: How many publications are covered in different databases, which has the best coverage, and what institutions are represented and how does the language of the publication play a role? Design – Bibliometric analysis. Setting – Academic citation databases (Web of Science, Scopus, Google Scholar and scientific social media (Mendeley, CiteULike, Bibsonomy. Subjects – 1,017 library and information science publications produced by 76 information scientists at 5 German-speaking universities in Germany and Austria. Methods – Only documents which were published between 1 January 2003 and 31 December 2012 were included. In that time the 76 information scientists had produced 1,017 documents. The information scientists confirmed that their publication lists were complete and these served as the calibration parameter for the study. The citations from the publication lists were searched in three academic databases: Google Scholar, Web of Science (WoS, and Scopus; as well as three social media citation sites: Mendeley, CiteULike, and BibSonomy and the results were compared. The publications were searched for by author name and words from the title. Main results – None of the databases investigated had 100% coverage. In the academic databases, Google Scholar had the highest amount of coverage with an average of 63%, Scopus an average of 31%, and

  9. 75 FR 29155 - Publicly Available Consumer Product Safety Information Database

    Science.gov (United States)

    2010-05-24

    ... information, such as where the product was purchased, price paid, model, serial number, date of manufacture... considered as verification including sales, promotion, marketing or warranty activities or...

  10. Autism genetic database (AGD: a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites

    Directory of Open Access Journals (Sweden)

    Talebizadeh Zohreh

    2009-09-01

    Full Text Available Abstract Background Autism is a highly heritable complex neurodevelopmental disorder, therefore identifying its genetic basis has been challenging. To date, numerous susceptibility genes and chromosomal abnormalities have been reported in association with autism, but most discoveries either fail to be replicated or account for a small effect. Thus, in most cases the underlying causative genetic mechanisms are not fully understood. In the present work, the Autism Genetic Database (AGD was developed as a literature-driven, web-based, and easy to access database designed with the aim of creating a comprehensive repository for all the currently reported genes and genomic copy number variations (CNVs associated with autism in order to further facilitate the assessment of these autism susceptibility genetic factors. Description AGD is a relational database that organizes data resulting from exhaustive literature searches for reported susceptibility genes and CNVs associated with autism. Furthermore, genomic information about human fragile sites and noncoding RNAs was also downloaded and parsed from miRBase, snoRNA-LBME-db, piRNABank, and the MIT/ICBP siRNA database. A web client genome browser enables viewing of the features while a web client query tool provides access to more specific information for the features. When applicable, links to external databases including GenBank, PubMed, miRBase, snoRNA-LBME-db, piRNABank, and the MIT siRNA database are provided. Conclusion AGD comprises a comprehensive list of susceptibility genes and copy number variations reported to-date in association with autism, as well as all known human noncoding RNA genes and fragile sites. Such a unique and inclusive autism genetic database will facilitate the evaluation of autism susceptibility factors in relation to known human noncoding RNAs and fragile sites, impacting on human diseases. As a result, this new autism database offers a valuable tool for the research

  11. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  12. Literature curation of protein interactions: measuring agreement across major public databases

    Science.gov (United States)

    Turinsky, Andrei L.; Razick, Sabry; Turner, Brian; Wodak, Shoshana J.

    2010-01-01

    Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15 471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL: http://wodaklab.org/iRefWeb PMID:21183497

  13. Genes (including RNA editing information) - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Genes... (including RNA editing information) Data detail Data name Genes (including RNA editing information...ase Site Policy | Contact Us Genes (including RNA editing information) - RMG | LSDB Archive ...

  14. AraPheno: a public database for Arabidopsis thaliana phenotypes

    Science.gov (United States)

    Seren, Ümit; Grimm, Dominik; Fitz, Joffrey; Weigel, Detlef; Nordborg, Magnus; Borgwardt, Karsten; Korte, Arthur

    2017-01-01

    Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype–phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for more than 1000 different natural inbred lines are available, and this has encouraged the distributed generation of many types of phenotypic data. To leverage these data for meta analyses, AraPheno (https://arapheno.1001genomes.org) provide a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype–phenotype map. PMID:27924043

  15. Including non-public data and studies in systematic reviews and systematic maps.

    Science.gov (United States)

    Haddaway, Neal R; Collins, Alexandra M; Coughlin, Deborah; Kohl, Christian

    2017-02-01

    Systematic reviews and maps should be based on the best available evidence, and reviewers should make all reasonable efforts to source and include potentially relevant studies. However, reviewers may not be able to consider all existing evidence, since some data and studies may not be publicly available. Including non-public studies in reviews provides a valuable opportunity to increase systematic review/map comprehensiveness, potentially mitigating negative impacts of publication bias. Studies may be non-public for many reasons: some may still be in the process of being published (publication can take a long time); some may not be published due to author/publisher restrictions; publication bias may make it difficult to publish non-significant or negative results. Here, we consider what forms these non-public studies may take and the implications of including them in systematic reviews and maps. Reviewers should carefully consider the advantages and disadvantages of including non-public studies, weighing risks of bias against benefits of increased comprehensiveness. As with all systematic reviews and maps, reviewers must be transparent about methods used to obtain data and avoid risks of bias in their synthesis. We make tentative suggestions for reviewers in situations where non-public data may be present in an evidence base.

  16. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

    Directory of Open Access Journals (Sweden)

    Alexandra M Schnoes

    2009-12-01

    Full Text Available Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families; the two other protein sequence databases (GenBank NR and TrEMBL and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.

  17. Molecular scaffold analysis of natural products databases in the public domain.

    Science.gov (United States)

    Yongye, Austin B; Waddell, Jacob; Medina-Franco, José L

    2012-11-01

    Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery.

  18. The 2008 Public Release of the International Multi-tokamak Confinement Profile Database

    NARCIS (Netherlands)

    Roach, C. M.; Walters, M.; Budny, R. V.; Imbeaux, F.; Fredian, T. W.; Greenwald, M.; Stillerman, J. A.; Alexander, D. A.; Carlsson, J.; Cary, J. R.; Ryter, F.; Stober, J.; Gohil, P.; Greenfield, C.; Murakami, M.; Bracco, G.; Esposito, B.; Romanelli, M.; Parail, V.; Stubberfield, P.; Voitsekhovitch, I.; Brickley, C.; Field, A. R.; Sakamoto, Y.; Fujita, T.; Fukuda, T.; Hayashi, N.; Hogeweij, G. M. D.; Chudnovskiy, A.; Kinerva, N. A.; Kessel, C. E.; Aniel, T.; Hoang, G. T.; Ongena, J.; Doyle, E. J.; Houlberg, W. A.; Polevoi, A. R.

    2008-01-01

    This paper documents the public release PR08 of the International Tokamak Physics Activity (ITPA) profile database, which should be of particular interest to the magnetic confinement fusion community. Data from a wide variety of interesting discharges from many of the world's leading tokamak ex

  19. Towards a public analysis database for LHC new physics searches using MadAnalysis 5

    CERN Document Server

    Dumont, B; Kraml, S; Bein, S; Chalons, G; Conte, E; Kulkarni, S; Sengupta, D; Wymant, C

    2015-01-01

    We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

  20. STANDARDIZATION AND STRUCTURAL ANNOTATION OF PUBLIC TOXICITY DATABASES: IMPROVING SAR CAPABILITIES AND LINKAGE TO 'OMICS DATA

    Science.gov (United States)

    Standardization and structural annotation of public toxicity databases: Improving SAR capabilities and linkage to 'omics data Ann M. Richard', ClarLynda Williams', Jamie Burch2'Nat Health & Environ Res Lab, US EPA, RTP, NC 27711; 2EPA/NC Central Univ Student COOP Trainee<...

  1. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

    Science.gov (United States)

    Gilson, Michael K; Liu, Tiqing; Baitaluk, Michael; Nicola, George; Hwang, Linda; Chong, Jenny

    2016-01-04

    BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.

  2. On the level of coverage and citation of publications by mechanicians of the national academy of sciences of Ukraine in the Scopus database

    Science.gov (United States)

    Guz, A. N.; Rushchitsky, J. J.

    2009-11-01

    The paper analyzes the level of coverage and citation of publications by mechanicians of the National Academy of Sciences of Ukraine (NASU) in the Scopus database. Two groups of mechanicians are considered. One group includes 66 doctors of sciences of the S. P. Timoshenko Institute of Mechanics as representatives of the oldest institute of the NASU. The other group includes 34 members (academicians and corresponding members) of the Division of Mechanics of the NASU as representatives of the authoritative community of mechanicians in Ukraine. The results are presented for each scientist in the form of two indices—the total number of publications accessible in the database as the level of coverage of the scientist's publications in this database and the h-index as the citation level of these publications. This paper may be considered to continue the papers [6-12] published in Prikladnaya Mekhanika (International Applied Mechanics) in 2005-2009

  3. Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

    Science.gov (United States)

    Weirick, Tyler; John, David; Uchida, Shizuka

    2017-03-01

    Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' sequence from one reference annotation could be annotated in another. Furthermore, relationships to nearby or overlapping annotated transcripts are even more complicated when using different genome assemblies. To better understand these problems, we surveyed current and previous versions of genomic assemblies and annotations across a number of public databases containing long noncoding RNA. We identified numerous discrepancies of transcripts regarding their genomic locations, transcript lengths and identifiers. Further investigation showed that the positional differences between reference annotations of essentially the same transcript could lead to differences in its measured expression at the RNA level. To aid in resolving these problems, we present the algorithm 'Universal Genomic Accession Hash (UGAHash)' and created an open source web tool to encourage the usage of the UGAHash algorithm. The UGAHash web tool (http://ugahash.uni-frankfurt.de) can be accessed freely without registration. The web tool allows researchers to generate Universal Genomic Accessions for genomic features or to explore annotations deposited in the public databases of the past and present versions. We anticipate that the UGAHash web tool will be a valuable tool to check for the existence of transcripts before judging the newly discovered transcripts as novel. © The Author 2016. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  4. Extent of non-publication in cohorts of studies approved by research ethics committees or included in trial registries.

    Directory of Open Access Journals (Sweden)

    Christine Schmucker

    Full Text Available BACKGROUND: The synthesis of published research in systematic reviews is essential when providing evidence to inform clinical and health policy decision-making. However, the validity of systematic reviews is threatened if journal publications represent a biased selection of all studies that have been conducted (dissemination bias. To investigate the extent of dissemination bias we conducted a systematic review that determined the proportion of studies published as peer-reviewed journal articles and investigated factors associated with full publication in cohorts of studies (i approved by research ethics committees (RECs or (ii included in trial registries. METHODS AND FINDINGS: Four bibliographic databases were searched for methodological research projects (MRPs without limitations for publication year, language or study location. The searches were supplemented by handsearching the references of included MRPs. We estimated the proportion of studies published using prediction intervals (PI and a random effects meta-analysis. Pooled odds ratios (OR were used to express associations between study characteristics and journal publication. Seventeen MRPs (23 publications evaluated cohorts of studies approved by RECs; the proportion of published studies had a PI between 22% and 72% and the weighted pooled proportion when combining estimates would be 46.2% (95% CI 40.2%-52.4%, I2 = 94.4%. Twenty-two MRPs (22 publications evaluated cohorts of studies included in trial registries; the PI of the proportion published ranged from 13% to 90% and the weighted pooled proportion would be 54.2% (95% CI 42.0%-65.9%, I2 = 98.9%. REC-approved studies with statistically significant results (compared with those without statistically significant results were more likely to be published (pooled OR 2.8; 95% CI 2.2-3.5. Phase-III trials were also more likely to be published than phase II trials (pooled OR 2.0; 95% CI 1.6-2.5. The probability of publication within two

  5. Government databases and public health research: facilitating access in the public interest.

    Science.gov (United States)

    Adams, Carolyn; Allen, Judy

    2014-06-01

    Access to datasets of personal health information held by government agencies is essential to support public health research and to promote evidence-based public health policy development. Privacy legislation in Australia allows the use and disclosure of such information for public health research. However, access is not always forthcoming in a timely manner and the decision-making process undertaken by government data custodians is not always transparent. Given the public benefit in research using these health information datasets, this article suggests that it is time to recognise a right of access for approved research and that the decisions, and decision-making processes, of government data custodians should be subject to increased scrutiny. The article concludes that researchers should have an avenue of external review where access to information has been denied or unduly delayed.

  6. Potential translational targets revealed by linking mouse grooming behavioral phenotypes to gene expression using public databases.

    Science.gov (United States)

    Roth, Andrew; Kyzar, Evan J; Cachat, Jonathan; Stewart, Adam Michael; Green, Jeremy; Gaikwad, Siddharth; O'Leary, Timothy P; Tabakoff, Boris; Brown, Richard E; Kalueff, Allan V

    2013-01-10

    Rodent self-grooming is an important, evolutionarily conserved behavior, highly sensitive to pharmacological and genetic manipulations. Mice with aberrant grooming phenotypes are currently used to model various human disorders. Therefore, it is critical to understand the biology of grooming behavior, and to assess its translational validity to humans. The present in-silico study used publicly available gene expression and behavioral data obtained from several inbred mouse strains in the open-field, light-dark box, elevated plus- and elevated zero-maze tests. As grooming duration differed between strains, our analysis revealed several candidate genes with significant correlations between gene expression in the brain and grooming duration. The Allen Brain Atlas, STRING, GoMiner and Mouse Genome Informatics databases were used to functionally map and analyze these candidate mouse genes against their human orthologs, assessing the strain ranking of their expression and the regional distribution of expression in the mouse brain. This allowed us to identify an interconnected network of candidate genes (which have expression levels that correlate with grooming behavior), display altered patterns of expression in key brain areas related to grooming, and underlie important functions in the brain. Collectively, our results demonstrate the utility of large-scale, high-throughput data-mining and in-silico modeling for linking genomic and behavioral data, as well as their potential to identify novel neural targets for complex neurobehavioral phenotypes, including grooming.

  7. Databases of publications and observations - as a part of the Crimean Astronomical Virtual Observatory

    CERN Document Server

    Shlyapnikov, A; Gorbunov, M

    2015-01-01

    The paper presents the basic principles of formation of a database (DB) with information about objects and their physical characteristics from observations carried out at the Crimean Astrophysical Observatory (CrAO) and published in "Izvestiya Krymskoi Astrofizicheskoi Observatorii" and other publications. The emphasis is placed on DBs that are not present in the most complete global library catalogs and data tables - VizieR (supported by the Strasbourg ADC). Separately, we consider the formation of a digital archive of observational data obtained at CrAO - as the interactive DB related to the DB of objects and publications. Examples of all the above DB as elements integrated into the Crimean Astronomical Virtual Observatory are presented in the paper. The operation with CrAO database is illustrated using tools of the International Virtual Observatory - Aladin, VOPlot, VOSpec jointly with VizieR DB and Simbad.

  8. ScafBank: a public comprehensive Scaffold database to support molecular hopping

    OpenAIRE

    2009-01-01

    Aim: The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years. Our goal is to provide a publically searchable database of scaffolds out from a large collection of existing chemical molecules. Results: Although a number of in silico methods have emerged to facilitate this process, which has become known as ”scaffold hopping” or “molecular hoppin...

  9. Large-scale annotation of small-molecule libraries using public databases.

    Science.gov (United States)

    Zhou, Yingyao; Zhou, Bin; Chen, Kaisheng; Yan, S Frank; King, Frederick J; Jiang, Shumei; Winzeler, Elizabeth A

    2007-01-01

    While many large publicly accessible databases provide excellent annotation for biological macromolecules, the same is not true for small chemical compounds. Commercial data sources also fail to encompass an annotation interface for large numbers of compounds and tend to be cost prohibitive to be widely available to biomedical researchers. Therefore, using annotation information for the selection of lead compounds from a modern day high-throughput screening (HTS) campaign presently occurs only under a very limited scale. The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological databases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. Using the 2.5 million compound collection at the Genomics Institute of the Novartis Research Foundation (GNF) as a model, we determined that approximately 4% of the library contained compounds with potential annotation in such databases as PubChem and the World Drug Index (WDI) as well as related databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and ChemIDplus. Furthermore, the exact structure match analysis showed 32% of GNF compounds can be linked to third party databases via PubChem. We also showed annotations such as MeSH (medical subject headings) terms can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest as well as expediting the assay validation process. The automated annotation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.

  10. Assessment of Residential History Generation Using a Public-Record Database

    Directory of Open Access Journals (Sweden)

    David C. Wheeler

    2015-09-01

    Full Text Available In studies of disease with potential environmental risk factors, residential location is often used as a surrogate for unknown environmental exposures or as a basis for assigning environmental exposures. These studies most typically use the residential location at the time of diagnosis due to ease of collection. However, previous residential locations may be more useful for risk analysis because of population mobility and disease latency. When residential histories have not been collected in a study, it may be possible to generate them through public-record databases. In this study, we evaluated the ability of a public-records database from LexisNexis to provide residential histories for subjects in a geographically diverse cohort study. We calculated 11 performance metrics comparing study-collected addresses and two address retrieval services from LexisNexis. We found 77% and 90% match rates for city and state and 72% and 87% detailed address match rates with the basic and enhanced services, respectively. The enhanced LexisNexis service covered 86% of the time at residential addresses recorded in the study. The mean match rate for detailed address matches varied spatially over states. The results suggest that public record databases can be useful for reconstructing residential histories for subjects in epidemiologic studies.

  11. Designing and recruiting to UK autism spectrum disorder research databases: do they include representative children with valid ASD diagnoses?

    Science.gov (United States)

    Warnell, F; George, B; McConachie, H; Johnson, M; Hardy, R; Parr, J R

    2015-09-04

    (1) Describe how the Autism Spectrum Database-UK (ASD-UK) was established; (2) investigate the representativeness of the first 1000 children and families who participated, compared to those who chose not to; (3) investigate the reliability of the parent-reported Autism Spectrum Disorder (ASD) diagnoses, and present evidence about the validity of diagnoses, that is, whether children recruited actually have an ASD; (4) present evidence about the representativeness of the ASD-UK children and families, by comparing their characteristics with the first 1000 children and families from the regional Database of children with ASD living in the North East (Dasl(n)e), and children and families identified from epidemiological studies. Recruitment through a network of 50 UK child health teams and self-referral. Parents/carers with a child with ASD, aged 2-16 years, completed questionnaires about ASD and some gave professionals' reports about their children. 1000 families registered with ASD-UK in 30 months. Children of families who participated, and of the 208 who chose not to, were found to be very similar on: gender ratio, year of birth, ASD diagnosis and social deprivation score. The reliability of parent-reported ASD diagnoses of children was very high when compared with clinical reports (over 96%); no database child without ASD was identified. A comparison of gender, ASD diagnosis, age at diagnosis, school placement, learning disability, and deprivation score of children and families from ASD-UK with 1084 children and families from Dasl(n)e, and families from population studies, showed that ASD-UK families are representative of families of children with ASD overall. ASD-UK includes families providing parent-reported data about their child and family, who appear to be broadly representative of UK children with ASD. Families continue to join the databases and more than 3000 families can now be contacted by researchers about UK autism research. Published by the BMJ

  12. Tocilizumab use in pregnancy: Analysis of a global safety database including data from clinical trials and post-marketing data.

    Science.gov (United States)

    Hoeltzenbein, Maria; Beck, Evelin; Rajwanshi, Richa; Gøtestam Skorpen, Carina; Berber, Erhan; Schaefer, Christof; Østensen, Monika

    2016-10-01

    Analyze the cumulative evidence for pregnancy outcomes after maternal exposure to tocilizumab, an anti-interleukin-6-receptor monoclonal antibody used for the treatment of rheumatoid arthritis and juvenile idiopathic arthritis. At present, published experience on tocilizumab use during pregnancy is very limited. We have analyzed all pregnancy-related reports documented in the Roche Global Safety Database until December 31, 2014 (n = 501). After exclusion of ongoing pregnancies, duplicates, and cases retrieved from the literature, 399 women were found to have been exposed to tocilizumab shortly before or during pregnancy, with pregnancy outcomes being reported in 288 pregnancies (72.2%). Of these 288 pregnancies, 180 were prospectively reported resulting in 109 live births (60.6%), 39 spontaneous abortions (21.7%), 31 elective terminations of pregnancy (17.2%), and 1 stillbirth. The rate of malformations was 4.5%. Co-medications included methotrexate in 21.1% of the prospectively ascertained cases. Compared to the general population, an increased rate of preterm birth (31.2%) was observed. Retrospectively reported pregnancies (n = 108) resulted in 55 live births (50.9%), 31 spontaneous abortions (28.7%), and 22 elective terminations (20.4%). Three infants/fetuses with congenital anomalies were reported in this group. No increased risks for adverse pregnancy outcomes were observed after paternal exposure in 13 pregnancies with known outcome. No indication for a substantially increased malformation risk was observed. Considering the limitations of global safety databases, the data do not yet prove safety, but provide information for physicians and patients to make informed decisions. This is particularly important after inadvertent exposure to tocilizumab, shortly before or during early pregnancy. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. BIBLIOMETRIC ANALYSIS OF PUBLICATIONS ON WINE TOURISM IN THE DATABASES Scopus and WoS

    Directory of Open Access Journals (Sweden)

    Durán Sánchez, Amador

    2017-01-01

    on the results of the comparative study, we conclude that WoS and Scopus databases differ in scope, data volume and coverage policies with a high degree of unique sources and articles, resulting both of them complementary and not mutually exclusive. Scopus covers the area of wine tourism better, by including a greater number of journals, papers and signatures."

  14. DOE's Public Database for Green Building Case Studies: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Torcellini, P. A.; Crawley, D. B.

    2003-11-01

    To help capture valuable information on''green building'' case studies, the U.S. Department of Energy has created an online database for collecting, standardizing, and disseminating information about high-performance, green projects. Type of information collected includes green features, design processes, energy performance, and comparison to other high-performance, green buildings.

  15. The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis.

    Science.gov (United States)

    Pierson, Kawika; Hand, Michael L; Thompson, Fred

    2015-01-01

    Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available.

  16. Near real-time operation of public image database for ground vehicle navigation

    Science.gov (United States)

    Ali, E.; Kozaitis, S. P.

    2015-02-01

    An effective color night vision system for ground vehicle navigation should operate in near real-time to be practical. We described a system that uses a public database as a source of color information to colorize night vision imagery. Such an approach presents several problems due to differences between acquired and reference imagery. Our system performed registration, colorizing, and reference updating in near real-time in an effort to help drivers of ground vehicles during night to see a colored view of a scene.

  17. Novel statistical tools for management of public databases facilitate community-wide replicability and control of false discovery.

    Science.gov (United States)

    Rosset, Saharon; Aharoni, Ehud; Neuvirth, Hani

    2014-07-01

    Issues of publication bias, lack of replicability, and false discovery have long plagued the genetics community. Proper utilization of public and shared data resources presents an opportunity to ameliorate these problems. We present an approach to public database management that we term Quality Preserving Database (QPD). It enables perpetual use of the database for testing statistical hypotheses while controlling false discovery and avoiding publication bias on the one hand, and maintaining testing power on the other hand. We demonstrate it on a use case of a replication server for GWAS findings, underlining its practical utility. We argue that a shift to using QPD in managing current and future biological databases will significantly enhance the community's ability to make efficient and statistically sound use of the available data resources. © 2014 WILEY PERIODICALS, INC.

  18. Computer-aided detection of pulmonary nodules: a comparative study using the public LIDC/IDRI database

    NARCIS (Netherlands)

    Jacobs, C.; Rikxoort, E.M. van; Murphy, K.; Prokop, M.; Schaefer-Prokop, C.M.; Ginneken, B. van

    2016-01-01

    To benchmark the performance of state-of-the-art computer-aided detection (CAD) of pulmonary nodules using the largest publicly available annotated CT database (LIDC/IDRI), and to show that CAD finds lesions not identified by the LIDC's four-fold double reading process.The LIDC/IDRI database

  19. 41 CFR 102-38.140 - What must we include in the public notice on sale of personal property?

    Science.gov (United States)

    2010-07-01

    ... REGULATION PERSONAL PROPERTY 38-SALE OF PERSONAL PROPERTY Sales Process Advertising § 102-38.140 What must we include in the public notice on sale of personal property? In the public notice, you must provide... the public notice on sale of personal property? 102-38.140 Section 102-38.140 Public Contracts and...

  20. A public turbulence database cluster and applications to study Lagrangian evolution of velocity increments in turbulence

    CERN Document Server

    Li, Yi; Wan, Minping; Yang, Yunke; Meneveau, Charles; Burns, Randal; Chen, Shiyi; Szalay, Alexander; Eyink, Gregory

    2008-01-01

    A public database system archiving a direct numerical simulation (DNS) data set of isotropic, forced turbulence is described in this paper. The data set consists of the DNS output on $1024^3$ spatial points and 1024 time-samples spanning about one large-scale turn-over timescale. This complete $1024^4$ space-time history of turbulence is accessible to users remotely through an interface that is based on the Web-services model. Users may write and execute analysis programs on their host computers, while the programs make subroutine-like calls that request desired parts of the data over the network. The users are thus able to perform numerical experiments by accessing the 27 Terabytes of DNS data using regular platforms such as laptops. The architecture of the database is explained, as are some of the locally defined functions, such as differentiation and interpolation. Test calculations are performed to illustrate the usage of the system and to verify the accuracy of the methods. The database is then used to a...

  1. FISH REPRODUCTION: BIBLIOMETRIC ANALYSIS OF WORLDWIDE AND BRAZILIAN PUBLICATIONS IN SCOPUS DATABASE

    Directory of Open Access Journals (Sweden)

    Marcella Costa RADAEL

    2015-12-01

    Full Text Available Reproduction is a fundamental part of life being and studies related to fish reproduction have been much accessed. The aim of this study was to perform a bibliometric analysis in intend to identify trends in this kind of publication. During June 2013, were performed searches on Scopus Database, using the term “fish reproduction”, being compiled and presented information related to the number of publications per year, number of publications by country, publications by author, by journal, by institution and most used keywords. Based on the study, it was possible to obtain the following results: Brazil occupies a highlight position in number of papers, being that the Brazilian participation compared to worldwide publishing production is having an exponential increase; in Brazil, there is a high concentration of articles when concerning the top 10 authors and institutions. The present study allows verifying that the term “fish reproduction” has been focused by many scientific papers, being that in Brazil there is a special research effort related to this subject, especially in the last few years. The main contribution concerns to the use of bibliometric methods to describe the growth and concentration of researches in the area of fishfarm and reproduction.

  2. The Molecular Biology Database Collection: 2008 update.

    Science.gov (United States)

    Galperin, Michael Y

    2008-01-01

    The Nucleic Acids Research online Molecular Biology Database Collection is a public repository that lists more than 1000 databases described in this and previous Nucleic Acids Research annual database issues, as well as a selection of molecular biology databases described in other journals. All databases included in this Collection are freely available to the public. The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list. The complete database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oxfordjournals.org/.

  3. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. The need to include obstetric nurses in prenatal care visits in the public health system

    Directory of Open Access Journals (Sweden)

    Selma Aparecida Lagrosa Garcia

    2010-06-01

    Full Text Available Objective: To investigate, with a qualitative approach, the role of Obstetric Nurses at the primary level of care given to women’s health as a vital component of the multidisciplinary team, which today is fundamental for providing care, prevention as well as health education and promotion, especially in programs whose activities are geared towards primary care of pregnant, parturient, and puerpera women. Methods: Brazilian laws and the determinations of Nursing Councils in reference to the activities of the obstetric nurse were researched, including the nurse’s responsibilities and limits. The bibliographic search was conducted in health-related journals, lay publications, and the Internet. Results: The conflicts between professional physicians and nurses were discussed. Conclusions: It was concluded that the activities of the nurse, conducting low-risk prenatal clinical visits in the basic healthcare network, has legal and ethical support and provides true benefit to the clients.

  5. Introducing a Public Stereoscopic 3D High Dynamic Range (SHDR) Video Database

    Science.gov (United States)

    Banitalebi-Dehkordi, Amin

    2017-03-01

    High dynamic range (HDR) displays and cameras are paving their ways through the consumer market at a rapid growth rate. Thanks to TV and camera manufacturers, HDR systems are now becoming available commercially to end users. This is taking place only a few years after the blooming of 3D video technologies. MPEG/ITU are also actively working towards the standardization of these technologies. However, preliminary research efforts in these video technologies are hammered by the lack of sufficient experimental data. In this paper, we introduce a Stereoscopic 3D HDR database of videos that is made publicly available to the research community. We explain the procedure taken to capture, calibrate, and post-process the videos. In addition, we provide insights on potential use-cases, challenges, and research opportunities, implied by the combination of higher dynamic range of the HDR aspect, and depth impression of the 3D aspect.

  6. Identifying Useful Terms to Retrieve Survival Data Meta-Analyses Publications for Bibliographic Databases Search Strategies

    Directory of Open Access Journals (Sweden)

    Daniel Corneliu LEUCUŢA

    2009-12-01

    Full Text Available Introduction: Quality research and quality evidence based medicine practice has an important pillar in a solid bibliographic documentation. Quality bibliographic documentation makes use of search strategies to retrieve articles from search engines of bibliographic databases. The AIM of this study was the identification of useful search terms to be used in search strategies that try to find meta-analyses of survival data. Materials and methods: A qualitative study based on text analysis was undertaken to identify useful terms for search strategies in abstracts of scientific papers. Survival analysis meta-analyses publication type studies, published between 1996 and 2005, were searched in Medline bibliographic database through Pubmed web interface. Each abstract was analysed and each important terms were noted down if they were considered to be useful in the creation of search strategies for analysis of survival data, or meta-analyses. Results: Pubmed search yielded 773 results. From these search results 401 (52% fulfilled inclusion criteria. The terms that were identified as useful in search strategies for meta-analyses of survival data are presented in the paper.

  7. Including Public Health Content in a Bioethics and Law Course: Vaccine Exemptions, Tort Liability, and Public Health.

    Science.gov (United States)

    Crossley, Mary

    2015-01-01

    Incorporating public health content in a bioethics and law course can prompt rich discussions. This set of materials on mandatory vaccinations, nonmedical exemptions, and potential tort liability for nonvaccination explores the roles of public health law and tort law in advancing social goals and protecting individual rights and interests. © 2015 American Society of Law, Medicine & Ethics, Inc.

  8. Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

    Directory of Open Access Journals (Sweden)

    Bányai László

    2008-08-01

    Full Text Available Abstract Background Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of incomplete, abnormal or mispredicted entries are not annotated as such, these errors seriously affect the reliability of these databases. Here we describe the MisPred approach that may provide an efficient means for the quality control of databases. The current version of the MisPred approach uses five distinct routines for identifying abnormal, incomplete or mispredicted entries based on the principle that a sequence is likely to be incorrect if some of its features conflict with our current knowledge about protein-coding genes and proteins: (i conflict between the predicted subcellular localization of proteins and the absence of the corresponding sequence signals; (ii presence of extracellular and cytoplasmic domains and the absence of transmembrane segments; (iii co-occurrence of extracellular and nuclear domains; (iv violation of domain integrity; (v chimeras encoded by two or more genes located on different chromosomes. Results Analyses of predicted EnsEMBL protein sequences of nine deuterostome (Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Fugu rubripes, Danio rerio and Ciona intestinalis and two protostome species (Caenorhabditis elegans and Drosophila melanogaster have revealed that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. Analyses of sequences predicted by NCBI's GNOMON annotation pipeline show that the rates of mispredictions are comparable to those of EnsEMBL. Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON

  9. Public Management and Administration Studies. Should we Include Marketind in Our Curricula?

    OpenAIRE

    José L. VÁZQUEZ; Dan LAZAR; Gutiérrez, Pablo; José L. PLACER

    2006-01-01

    As a consequence of continuous adaptation of public institutions to requirements of framing where they perform day by day, Public Management and Administration is behaving once and again as a “reinvented” discipline, aiming a new kind of rational, innovative public entities that focus their activities towards an effective achievement of their intended results and benefits. Concepts such as those of “efficiency”, “effectiveness”, “responsibility”, “organizational culture”, etc. are now not onl...

  10. Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas assembled into a publicly accessible database: the GigasDatabase

    Directory of Open Access Journals (Sweden)

    Klopp Christophe

    2009-07-01

    Full Text Available Abstract Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit

  11. Reflections on a decade of research by ASEAN dental faculties: analysis of publications from ISI-WOS databases from 2000 to 2009.

    Science.gov (United States)

    Sirisinha, Stitaya; Koontongkaew, Sittichai; Phantumvanit, Prathip; Wittayawuttikul, Ruchareka

    2011-05-01

    This communication analyzed research publications in dentistry in the Institute of Scientific Information Web of Science databases of 10 dental faculties in the Association of South-East Asian Nations (ASEAN) from 2000 to 2009. The term used for the "all-document types" search was "Faculty of Dentistry/College of Dentistry." Abstracts presented at regional meetings were also included in the analysis. The Times Higher Education System QS World University Rankings showed that universities in the region fare poorly in world university rankings. Only the National University of Singapore and Nanyang Technological University appeared in the top 100 in 2009; 19 universities in the region, including Indonesia, Malaysia, the Philippines, Singapore, and Thailand, appeared in the top 500. Data from the databases showed that research publications by dental institutes in the region fall short of their Asian counterparts. Singapore and Thailand are the most active in dental research of the ASEAN countries.

  12. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions

    Science.gov (United States)

    Creighton, Chad J.; Nagaraja, Ankur K.; Hanash, Samir M.; Matzuk, Martin M.; Gunaratne, Preethi H.

    2008-01-01

    MicroRNAs are short (∼22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA–mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs—above what could be observed in randomly generated gene lists—suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net. PMID:18812437

  13. A curated public database for multilocus sequence typing (MLST) and analysis of Haemophilus parasuis based on an optimized typing scheme.

    Science.gov (United States)

    Mullins, Michael A; Register, Karen B; Brunelle, Brian W; Aragon, Virginia; Galofré-Mila, Nuria; Bayles, Darrell O; Jolley, Keith A

    2013-03-23

    Haemophilus parasuis causes Glässer's disease and pneumonia in swine. Serotyping is often used to classify isolates but requires reagents that are costly to produce and not standardized or widely available. Sequence-based methods, such as multilocus sequence typing (MLST), offer many advantages over serotyping. An MLST scheme was previously proposed for H. parasuis but genome sequence data only recently available reveals the primers recommended, based on sequences of related bacteria, are not optimal. Here we report modifications to enhance the original method, including primer redesign to eliminate mismatches with H. parasuis sequences and to avoid regions of high sequence heterogeneity, standardization of primer T(m)s and identification of universal PCR conditions that result in robust and reproducible amplification of all targets. The modified typing method was applied to a collection of 127 isolates from North and South America, Europe and Asia. An alignment of the concatenated sequences obtained from seven target housekeeping genes identified 278 variable nucleotide sites that define 116 unique sequence types. A comparison of the original and modified methods using a subset of 86 isolates indicates little difference in overall locus diversity, discriminatory power or in the clustering of strains within Neighbor-Joining trees. Data from the optimized MLST were used to populate a newly created and publicly available H. parasuis database. An accompanying database designed to capture provenance and epidemiological information for each isolate was also created. The modified MLST scheme is highly discriminatory but more robust, reproducible and user-friendly than the original. The MLST database provides a novel resource for investigation of H. parasuis outbreaks and for tracking strain evolution.

  14. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.

    Science.gov (United States)

    Creighton, Chad J; Nagaraja, Ankur K; Hanash, Samir M; Matzuk, Martin M; Gunaratne, Preethi H

    2008-11-01

    MicroRNAs are short (approximately 22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA-mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs-above what could be observed in randomly generated gene lists-suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net.

  15. Disaster Debris Recovery Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 3,500 composting facilities, demolition contractors, haulers, transfer...

  16. Public Management and Administration Studies. Should we Include Marketind in Our Curricula?

    Directory of Open Access Journals (Sweden)

    José L. VÁZQUEZ

    2006-06-01

    Full Text Available As a consequence of continuous adaptation of public institutions to requirements of framing where they perform day by day, Public Management and Administration is behaving once and again as a “reinvented” discipline, aiming a new kind of rational, innovative public entities that focus their activities towards an effective achievement of their intended results and benefits. Concepts such as those of “efficiency”, “effectiveness”, “responsibility”, “organizational culture”, etc. are now not only applied to business disciplines, but also to Public Management and Administration. At this point, Marketing has proved to be an useful subject in PMA curricula, not only being in demand by students and syllabi designers, but also by experts in the public field. However, applying marketing techniques and procedures in the same way as used in private business is clearly nonsense. We must consider a proper “public marketing” or “public sector marketing” development. In this paper we debate on these issues, as well as present an overview into the situation of Spanish public universities offering PMA studies, just when they are facing the Bologna adaptation requirements. As a conclusion, some comments for reflection are suggested.

  17. Including public-health benefits of trees in urban-forestry decision making

    Science.gov (United States)

    Geoffrey H. Donovan

    2017-01-01

    Research demonstrating the biophysical benefits of urban trees are often used to justify investments in urban forestry. Far less emphasis, however, is placed on the non-bio-physical benefits such as improvements in public health. Indeed, the public-health benefits of trees may be significantly larger than the biophysical benefits, and, therefore, failure to account for...

  18. 78 FR 77096 - Newspapers Used for Publication of Legal Notices in the Southwestern Region, Which Includes...

    Science.gov (United States)

    2013-12-20

    ... Forest Service Newspapers Used for Publication of Legal Notices in the Southwestern Region, Which.... SUMMARY: This notice lists the newspapers that will be used by all Ranger Districts, Grasslands, Forests... public which newspapers the Forest Service will use to publish notices of proposed actions, notices of...

  19. 77 FR 73412 - Newspapers Used for Publication of Legal Notices in the Southwestern Region, Which Includes...

    Science.gov (United States)

    2012-12-10

    ... Forest Service Newspapers Used for Publication of Legal Notices in the Southwestern Region, Which.... SUMMARY: This notice lists the newspapers that will be used by all Ranger Districts, Grasslands, Forests... public which newspapers the Forest Service will use to publish notices of proposed actions and notices of...

  20. Data-driven public transport ridership prediction approach including comfort aspects

    NARCIS (Netherlands)

    Van Oort, N.; Drost, M.; Brands, T.; Yap, M.

    2015-01-01

    The most important aspects on which passengers base their choice whether to travel by public transport are the perceived travel time, costs, reliability and comfort. Despite its importance, comfort is often not explicitly considered when predicting demand for public transport. In this paper, we incl

  1. Data-driven public transport ridership prediction approach including comfort aspects

    NARCIS (Netherlands)

    Van Oort, N.; Drost, M.; Brands, T.; Yap, M.

    2015-01-01

    The most important aspects on which passengers base their choice whether to travel by public transport are the perceived travel time, costs, reliability and comfort. Despite its importance, comfort is often not explicitly considered when predicting demand for public transport. In this paper, we incl

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

    Science.gov (United States)

    Granitto, Matthew; Schmidt, Jeanine M.; 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

  3. E-SovTox: An online database of the main publicly-available sources of toxicity data concerning REACH-relevant chemicals published in the Russian language.

    Science.gov (United States)

    Sihtmäe, Mariliis; Blinova, Irina; Aruoja, Villem; Dubourguier, Henri-Charles; Legrand, Nicolas; Kahru, Anne

    2010-08-01

    A new open-access online database, E-SovTox, is presented. E-SovTox provides toxicological data for substances relevant to the EU Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) system, from publicly-available Russian language data sources. The database contains information selected mainly from scientific journals published during the Soviet Union era. The main information source for this database - the journal, Gigiena Truda i Professional'nye Zabolevania [Industrial Hygiene and Occupational Diseases], published between 1957 and 1992 - features acute, but also chronic, toxicity data for numerous industrial chemicals, e.g. for rats, mice, guinea-pigs and rabbits. The main goal of the abovementioned toxicity studies was to derive the maximum allowable concentration limits for industrial chemicals in the occupational health settings of the former Soviet Union. Thus, articles featured in the database include mostly data on LD50 values, skin and eye irritation, skin sensitisation and cumulative properties. Currently, the E-SovTox database contains toxicity data selected from more than 500 papers covering more than 600 chemicals. The user is provided with the main toxicity information, as well as abstracts of these papers in Russian and in English (given as provided in the original publication). The search engine allows cross-searching of the database by the name or CAS number of the compound, and the author of the paper. The E-SovTox database can be used as a decision-support tool by researchers and regulators for the hazard assessment of chemical substances.

  4. Public Land Survey (Township, Range, and Section) for northern Arizona, including Grand Canyon National Park.

    Data.gov (United States)

    National Park Service, Department of the Interior — This ALRIS (Arizona Land Resource Information System) coverage contains Public Land Survey gridding and labels for Townships, Ranges, and Sections for Northern Arizona

  5. Possible Solution to Publication Bias Through Bayesian Statistics, Including Proper Null Hypothesis Testing

    NARCIS (Netherlands)

    Konijn, Elly A.; van de Schoot, Rens; Winter, Sonja D.; Ferguson, Christopher J.

    2015-01-01

    The present paper argues that an important cause of publication bias resides in traditional frequentist statistics forcing binary decisions. An alternative approach through Bayesian statistics provides various degrees of support for any hypothesis allowing balanced decisions and proper null hypothes

  6. Defining new criteria for selection of cell-based intestinal models using publicly available databases

    Directory of Open Access Journals (Sweden)

    Christensen Jon

    2012-06-01

    Full Text Available Abstract Background The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. Results We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. Conclusions This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models

  7. Complementary Value of Databases for Discovery of Scholarly Literature: A User Survey of Online Searching for Publications in Art History

    Science.gov (United States)

    Nemeth, Erik

    2010-01-01

    Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside academic presses and peer-reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars…

  8. Coverage and quality: A comparison of Web of Science and Scopus databases for reporting faculty nursing publication metrics.

    Science.gov (United States)

    Powell, Kimberly R; Peterson, Shenita R

    2017-03-11

    Web of Science and Scopus are the leading databases of scholarly impact. Recent studies outside the field of nursing report differences in journal coverage and quality. A comparative analysis of nursing publications reported impact. Journal coverage by each database for the field of nursing was compared. Additionally, publications by 2014 nursing faculty were collected in both databases and compared for overall coverage and reported quality, as modeled by Scimajo Journal Rank, peer review status, and MEDLINE inclusion. Individual author impact, modeled by the h-index, was calculated by each database for comparison. Scopus offered significantly higher journal coverage. For 2014 faculty publications, 100% of journals were found in Scopus, Web of Science offered 82%. No significant difference was found in the quality of reported journals. Author h-index was found to be higher in Scopus. When reporting faculty publications and scholarly impact, academic nursing programs may be better represented by Scopus, without compromising journal quality. Programs with strong interdisciplinary work should examine all areas of strength to ensure appropriate coverage. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Segmentation of anatomical structures in chest radiographs using supervised methods: a comparative study on a public database

    DEFF Research Database (Denmark)

    van Ginneken, Bram; Stegmann, Mikkel Bille; Loog, Marco

    2006-01-01

    classification method that employs a multi-scale filter bank of Gaussian derivatives and a k-nearest-neighbors classifier. The methods have been tested on a publicly available database of 247 chest radiographs, in which all objects have been manually segmented by two human observers. A parameter optimization...

  10. 76 FR 60031 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Science.gov (United States)

    2011-09-28

    ... AGENCY Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family... contains Enterprise single-family and multifamily mortgage loan-level data reported to FHFA by the... data characteristics of single-family high-cost loans purchased and securitized by the Enterprises...

  11. Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.

    Science.gov (United States)

    Thai, Quan Ke; Chung, Dung Anh; Tran, Hoang-Dung

    2017-06-26

    Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.

  12. 76 FR 75866 - Newspapers Used for Publication of Legal Notices in the Southwestern Region, Which Includes...

    Science.gov (United States)

    2011-12-05

    ... Forest Service Newspapers Used for Publication of Legal Notices in the Southwestern Region, Which.... SUMMARY: This notice lists the newspapers that will be used by all Ranger Districts, Grasslands, Forests... reduction projects under 36 CFR 218.4. This notice also lists newspapers of record for notices pertaining to...

  13. Further Research is Required to Determine Which Database Products Best Support Research in Public Administration. A review of: Tucker, James, Corey. “Database Support for Research in Public Administration.” Behavioral & Social Sciences Librarian 24.1 (2005: 47-60.

    Directory of Open Access Journals (Sweden)

    David Hook

    2006-06-01

    Full Text Available Objective – To examine the extent to which six commercial database products support student and faculty research in the area of public administration. Design – Bibliometric study. Setting – Academic library in the United States. Subjects – Six commercial business‐related database products were examined: Proquest’s ABI/INFORM Global edition (ABI, EBSCO’s Business Source Premier (BSP, Gale’s General BusinessFile ASAP (GBF, EBSCO’s Academic Search Premier (ASP, EBSCO’s Expanded Academic Index (EAI and Proquest’s International Academic Research Library (ARL. Three of the databases (ABI, BSP, GBF were chosen because they address the management, human resource, and financing elements of public administration. The other three (ASP, EAI, ARL were included because of their multidisciplinary coverage. Methods – A list of journal titles covering public administration was assembled from the Institute of Scientific Information’s Social Sciences Citation Index and previously published lists of recommended journals in the field. The author then compared the compiled list of journal titles against the journal titles indexed by the six database products. He further analyzed the results by level of journal coverage (abstract only, full‐text, and full‐text with embargo and subject area based on categories described in Ulrich’s Periodicals Directory. Main Results – The study found that three of the six database products ‐‐EAI, BSP, and ARL ‐‐ provide indexing for the greatest number of public administration journals contained in the compiled list. EIA and ARL cover the greatest number of those that are full‐text journals, while BSP and ASP cover the greatest number of those full‐text journals limited by publisher embargoes. Conclusion – The author concludes that of the six databases examined, EAI, BSP, and ARL are the best for public administration research, based on their strength in the subject areas of public

  14. DMPD: TLR3: interferon induction by double-stranded RNA including poly(I:C). [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18262679 TLR3: interferon induction by double-stranded RNA including poly(I:C). Mat...sumoto M, Seya T. Adv Drug Deliv Rev. 2008 Apr 29;60(7):805-12. Epub 2008 Jan 2. (.png) (.svg) (.html) (.csml) Show TLR3: inter...feron induction by double-stranded RNA including poly(I:C). PubmedID 18262679 Title TLR3: inter

  15. Characterization and compilation of polymorphic simple sequence repeat (SSR markers of peanut from public database

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-07-01

    Full Text Available Abstract Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L. genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5% within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5% was the most abundant followed by AAG (12.1%, AAT (10.9%, and AT (10.3%.The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

  16. Reclamation research database

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2007-07-01

    A reclamation research database was compiled to help stakeholders search publications and research related to the reclamation of Alberta's oil sands region. New publications are added to the database by the Cumulative Environmental Management Association (CEMA), a nonprofit association whose mandate is to develop frameworks and guidelines for the management of cumulative environmental effects in the oil sands region. A total of 514 research papers have been compiled in the database to date. Topics include recent research on hydrology, aquatic and terrestrial ecosystems, laboratory studies on biodegradation, and the effects of oil sands processing on micro-organisms. The database includes a wide variety of studies related to reconstructed wetlands as well as the ecological effects of hydrocarbons on phytoplankton and other organisms. The database format included information on research format availability, as well as information related to the author's affiliations. Links to external abstracts were provided where available, as well as details of source information.

  17. Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes.

    Science.gov (United States)

    Kikuchi, Akira; Nakazato, Takeru; Ito, Katsuhiko; Nojima, Yosui; Yokoyama, Takeshi; Iwabuchi, Kikuo; Bono, Hidemasa; Toyoda, Atsushi; Fujiyama, Asao; Sato, Ryoichi; Tabunoki, Hiroko

    2017-01-13

    Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. Enolase is an important glycolytic enzyme in all organisms. We used a combination of dry and wet bench processes to identify functional enolases in the silkworm Bombyx mori (BmEno). First, we detected five annotated enolases from public databases using a Hidden Markov Model (HMM) search, and then through cDNA cloning, Northern blotting, and RNA-seq analysis, we revealed three functional enolases in B. mori: BmEno1, BmEno2, and BmEnoC. BmEno1 contained a conserved key amino acid residue for metal binding and substrate binding in other species. However, BmEno2 and BmEnoC showed a change in this key amino acid. Phylogenetic analysis showed that BmEno2 and BmEnoC were distinct from BmEno1 and other enolases, and were distributed only in lepidopteran clusters. BmEno1 was expressed in all of the tissues used in our study. In contrast, BmEno2 was mainly expressed in the testis with some expression in the ovary and suboesophageal ganglion. BmEnoC was weakly expressed in the testis. Quantitative RT-PCR showed that the mRNA expression of BmEno2 and BmEnoC correlated with testis development; thus, BmEno2 and BmEnoC may be related to lepidopteran-specific spermiogenesis. We identified and characterized three functional enolases from public databases with a combination of dry and wet bench processes in the silkworm B. mori. In addition, we determined that BmEno2 and BmEnoC had species-specific functions. Our strategy could be helpful for the detection of minor genes and functional genes in non-model organisms from public databases.

  18. Exploration of Preterm Birth Rates Using the Public Health Exposome Database and Computational Analysis Methods

    Directory of Open Access Journals (Sweden)

    Anne D. Kershenbaum

    2014-11-01

    Full Text Available Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother’s age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%. Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births.

  19. Predicting 30-day Hospital Readmission with Publicly Available Administrative Database. A Conditional Logistic Regression Modeling Approach.

    Science.gov (United States)

    Zhu, K; Lou, Z; Zhou, J; Ballester, N; Kong, N; Parikh, P

    2015-01-01

    more than 10% over the standard classification models, which can be translated to correct labeling of additional 400 - 500 readmissions for heart failure patients in the state of California over a year. Lastly, several key predictor identified from the HCUP data include the disposition location from discharge, the number of chronic conditions, and the number of acute procedures. It would be beneficial to apply simple decision rules obtained from the decision tree in an ad-hoc manner to guide the cohort stratification. It could be potentially beneficial to explore the effect of pairwise interactions between influential predictors when building the logistic regression models for different data strata. Judicious use of the ad-hoc CLR models developed offers insights into future development of prediction models for hospital readmissions, which can lead to better intuition in identifying high-risk patients and developing effective post-discharge care strategies. Lastly, this paper is expected to raise the awareness of collecting data on additional markers and developing necessary database infrastructure for larger-scale exploratory studies on readmission risk prediction.

  20. Disaster Debris Recovery Database - Recovery

    Data.gov (United States)

    U.S. Environmental Protection Agency — The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 6,000 composting facilities, demolition contractors, transfer stations,...

  1. Disaster Debris Recovery Database - Landfills

    Data.gov (United States)

    U.S. Environmental Protection Agency — The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 6,000 composting facilities, demolition contractors, transfer stations,...

  2. NPL-PAD (National Priorities List Publication Assistance Database) for Region 7

    Data.gov (United States)

    U.S. Environmental Protection Agency — THIS DATA ASSET NO LONGER ACTIVE: This is metadata documentation for the National Priorities List (NPL) Publication Assistance Databsae (PAD), a Lotus Notes...

  3. The Impact of Including Immigrants without Permanent Residence Status in the Public Health Insurance System in the Czech Republic

    Directory of Open Access Journals (Sweden)

    Tepperová Jana

    2016-03-01

    Full Text Available Whether an individual can or cannot participate in the Czech public health insurance system depends on several characteristics, one of which is whether he/she has permanent residence status in the Czech Republic, and a second whether he/she is employed. This means that those without permanent residence status, including self-employed migrants from third countries, their dependent relatives, and the dependent relatives of third country employees in the Czech Republic, cannot participate in the public health insurance system. Some argue that such migrants should be included in the system, since commercial health insurance is disadvantageous and the contributions they would pay into the public health insurance system would increase the public health insurance agencies’ income. We estimate the value of the contributions to public health insurance that would be paid by third country self-employed and non-working immigrants, if they were insured based on data from 2011 to 2013, and compare this to the assumed costs of their medical care. To calculate the contributions for self-employed migrants we use data on the distribution of the tax base for self-employed persons from personal income tax returns. Our estimation results in an overall negative balance of 22 million CZK on the data for 2012 and 2013. In the current system this deficit would be covered by the state, which would pay contributions to the system for certain (state insured persons amounting to 97 million CZK; overall therefore the inclusion of these immigrants would result in a positive balance of 75 million CZK.

  4. Application of Optical Disc Databases and Related Technology to Public Access Settings

    Science.gov (United States)

    1992-03-01

    Librarian 5, no 6: 23. Nelson, Nancy Melin. 1991. CD-ROM growth: unleashing the potential. Library Journal 116, no. 2: 51-53. Nicholls, Paul Travis...1991. The impact of CD-ROM on online. Library Journal 116, no. 2: 61-62. Tenopir, Carol, and Ralph Neufang. 1991. CD-ROM, online and databases on...primer. PC Magazine, 17 December, 44. Zink, Steven D. 1990. Planning for the perils of CD-ROM. Library Journal 115, no. 2: 51-55. 211 INITIAL

  5. De-identifying a public use microdata file from the Canadian national discharge abstract database.

    Science.gov (United States)

    El Emam, Khaled; Paton, David; Dankar, Fida; Koru, Gunes

    2011-08-23

    The Canadian Institute for Health Information (CIHI) collects hospital discharge abstract data (DAD) from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF) was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression. The strategies we used to maximize data utility and

  6. De-identifying a public use microdata file from the Canadian national discharge abstract database

    Directory of Open Access Journals (Sweden)

    Paton David

    2011-08-01

    Full Text Available Abstract Background The Canadian Institute for Health Information (CIHI collects hospital discharge abstract data (DAD from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Methods Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Results Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression

  7. Seabird databases and the new paradigm for scientific publication and attribution

    Science.gov (United States)

    Hatch, Scott A.

    2010-01-01

    For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

  8. 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

    Directory of Open Access Journals (Sweden)

    Barfod Charlotte

    2012-04-01

    Full Text Available Abstract 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 7.45. 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 28 days after admission

  9. [Public scientific knowledge distribution in health information, communication and information technology indexed in MEDLINE and LILACS databases].

    Science.gov (United States)

    Packer, Abel Laerte; Tardelli, Adalberto Otranto; Castro, Regina Célia Figueiredo

    2007-01-01

    This study explores the distribution of international, regional and national scientific output in health information and communication, indexed in the MEDLINE and LILACS databases, between 1996 and 2005. A selection of articles was based on the hierarchical structure of Information Science in MeSH vocabulary. Four specific domains were determined: health information, medical informatics, scientific communications on healthcare and healthcare communications. The variables analyzed were: most-covered subjects and journals, author affiliation and publication countries and languages, in both databases. The Information Science category is represented in nearly 5% of MEDLINE and LILACS articles. The four domains under analysis showed a relative annual increase in MEDLINE. The Medical Informatics domain showed the highest number of records in MEDLINE, representing about half of all indexed articles. The importance of Information Science as a whole is more visible in publications from developed countries and the findings indicate the predominance of the United States, with significant growth in scientific output from China and South Korea and, to a lesser extent, Brazil.

  10. Development of a panel of unigene-derived polymorphic EST-SSR markers in lentil using public database information

    Institute of Scientific and Technical Information of China (English)

    Debjyoti Sen Gupta; Peng Cheng; Gaurav Sablok; Dil Thavarajah; Pushparajah Thavarajah; Clarice J Coyne; Shiv Kumar; Michael Baum; Rebecca J McGee

    2016-01-01

    Lentil (Lens culinaris Medik.), a diploid (2n=14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information (ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information (NCBI) database to develop unigene-based simple sequence repeat (SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches (using E-value 1 × 10−5) against the public UniProt (http://www.uniprot.org/) and NCBI (http://www.ncbi.nlh.nih.gov/) data-bases were performed. Further functional annotation was performed using PLAZA (version 3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.

  11. Automatic detection of lung nodules in computed tomography images: training and validation of algorithms using public research databases

    Science.gov (United States)

    Camarlinghi, Niccolò

    2013-09-01

    Lung cancer is one of the main public health issues in developed countries. Lung cancer typically manifests itself as non-calcified pulmonary nodules that can be detected reading lung Computed Tomography (CT) images. To assist radiologists in reading images, researchers started, a decade ago, the development of Computer Aided Detection (CAD) methods capable of detecting lung nodules. In this work, a CAD composed of two CAD subprocedures is presented: , devoted to the identification of parenchymal nodules, and , devoted to the identification of the nodules attached to the pleura surface. Both CADs are an upgrade of two methods previously presented as Voxel Based Neural Approach CAD . The novelty of this paper consists in the massive training using the public research Lung International Database Consortium (LIDC) database and on the implementation of new features for classification with respect to the original VBNA method. Finally, the proposed CAD is blindly validated on the ANODE09 dataset. The result of the validation is a score of 0.393, which corresponds to the average sensitivity of the CAD computed at seven predefined false positive rates: 1/8, 1/4, 1/2, 1, 2, 4, and 8 FP/CT.

  12. Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases?

    Science.gov (United States)

    Maldonado, Carla; Molina, Carlos I.; Zizka, Alexander; Persson, Claes; Taylor, Charlotte M.; Albán, Joaquina; Chilquillo, Eder; Antonelli, Alexandre

    2015-01-01

    Abstract Aim Massive digitalization of natural history collections is now leading to a steep accumulation of publicly available species distribution data. However, taxonomic errors and geographical uncertainty of species occurrence records are now acknowledged by the scientific community – putting into question to what extent such data can be used to unveil correct patterns of biodiversity and distribution. We explore this question through quantitative and qualitative analyses of uncleaned versus manually verified datasets of species distribution records across different spatial scales. Location The American tropics. Methods As test case we used the plant tribe Cinchoneae (Rubiaceae). We compiled four datasets of species occurrences: one created manually and verified through classical taxonomic work, and the rest derived from GBIF under different cleaning and filling schemes. We used new bioinformatic tools to code species into grids, ecoregions, and biomes following WWF's classification. We analysed species richness and altitudinal ranges of the species. Results Altitudinal ranges for species and genera were correctly inferred even without manual data cleaning and filling. However, erroneous records affected spatial patterns of species richness. They led to an overestimation of species richness in certain areas outside the centres of diversity in the clade. The location of many of these areas comprised the geographical midpoint of countries and political subdivisions, assigned long after the specimens had been collected. Main conclusion Open databases and integrative bioinformatic tools allow a rapid approximation of large‐scale patterns of biodiversity across space and altitudinal ranges. We found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties, often leading to false positives, i.e. overestimating species richness in relatively species poor regions. Public databases for species distribution are valuable and should be

  13. Clinical profile of 266 Filipino patients with rheumatoid arthritis included in the rheumatoid arthritis database and registry (RADAR) of the Philippine General Hospital.

    Science.gov (United States)

    Penserga, Ester G; Natividad, Therese Aileen L; Salido, Evelyn S

    2015-05-01

    To describe Filipino patients with rheumatoid arthritis (RA) entered in the Rheumatoid arthritis database and registry (RADAR) of the Philippine General Hospital. Cases entered to RADAR from 2010-2012 were included. All fulfilled the 1987 American College of Rheumatology criteria for classification of RA. Included cases gave written infomed consent. Data extracted were demographics, clinical presentation, laboratory tests, treatment and disease course. Means and proportions were used for population characteristics. Two hundred and sixty-six cases were included. Mean age was 44 years, with 9 : 1 female preponderance and mean diagnosis time of 5 years. There was symmetrical polyarthritis with high tender and swollen joint count and mean Disease Activity Score of 28 joints, erythrocyte sedimentation rate of 5.27 (3.39, 8.13). Rheumatoid factor was positive in 2/3 of cases. Hypertension, tuberculosis and diabetes were important co-morbidities. Treatment included prednisone, non-steroidal anti-inflammatory drugs and methotrexate. At 12 months of treatment, evaluable cases (arthritis unit whose disease characteristics are similar to what is reported worldwide. This cohort differs from most studies in having a high female to male ratio, a long delay in diagnosis, and high attrition rate. Mean methotrexate dose was low and there was less access to biologic disease-modifying anti-rheumatic drugs. © 2014 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

  14. Towards development of a high quality public domain global roads database

    Directory of Open Access Journals (Sweden)

    Andrew Nelson

    2006-12-01

    Full Text Available There is clear demand for a global spatial public domain roads data set with improved geographic and temporal coverage, consistent coding of road types, and clear documentation of sources. The currently best available global public domain product covers only one-quarter to one-third of the existing road networks, and this varies considerably by region. Applications for such a data set span multiple sectors and would be particularly valuable for the international economic development, disaster relief, and biodiversity conservation communities, not to mention national and regional agencies and organizations around the world. The building blocks for such a global product are available for many countries and regions, yet thus far there has been neither strategy nor leadership for developing it. This paper evaluates the best available public domain and commercial data sets, assesses the gaps in global coverage, and proposes a number of strategies for filling them. It also identifies stakeholder organizations with an interest in such a data set that might either provide leadership or funding for its development. It closes with a proposed set of actions to begin the process.

  15. Ethical implications of including children in a large biobank for genetic-epidemiologic research: a qualitative study of public opinion.

    Science.gov (United States)

    Kaufman, David; Geller, Gail; Leroy, Lisa; Murphy, Juli; Scott, Joan; Hudson, Kathy

    2008-02-15

    The National Institutes of Health and other federal agencies are considering initiating a cohort study of 500,000 people, including 120,000 children, to measure genetic and environmental influences on common diseases. A community engagement pilot study was conducted to identify public attitudes and concerns about the proposed cohort study, including the ethics of involving children. The pilot included 15 focus groups where the inclusion of children in the proposed cohort study was discussed. Focus groups, conducted in six cities, included 141 adults of different ages, incomes, genders, ethnicities, and races. Many of the concerns expressed by participants mirrored those addressed in pediatric research guidelines. These concerns included minimizing children's fear, pain, and burdens; whether to include young children; and how to obtain children's assent. There was little agreement about which children can assent. Some voiced concern about children's privacy, but most expected that parents would have access to children's study results. Some believed children would not benefit from participating, while others identified personal and societal benefits that might accrue. A few people believed that children's participation would not advance the study's goals. To successfully include children, proposed cohort study would need to address children's changing capabilities and rights as they grow and reach the age of consent.

  16. Attitudes regarding the national forensic DNA database: Survey data from the general public, prison inmates and prosecutors' offices in the Republic of Serbia.

    Science.gov (United States)

    Teodorović, Smilja; Mijović, Dragan; Radovanović Nenadić, Una; Savić, Marina

    2017-01-21

    Worldwide, the establishment of national forensic DNA databases has transformed personal identification in the criminal justice system over the past two decades. It has also stimulated much debate centering on ethical issues, human rights, individual privacy, lack of safeguards and other standards. Therefore, a balance between effectiveness and intrusiveness of a national DNA repository is an imperative and needs to be achieved through a suitable legal framework. On its path to the European Union (EU), the Republic of Serbia is required to harmonize its national policies and legislation with the EU. Specifically, Chapter 24 of the EU acquis communautaire (Justice, Freedom and Security) stipulates the compulsory creation of a forensic DNA registry and adoption of corresponding legislation. This process is expected to occur in 2016. Thus, in light of launching the national DNA database, the goal of this work is to instigate a consultation with the Serbian public regarding their views on various aspects of the forensic DNA databank. Importantly, this study specifically assessed the opinions of distinct categories of citizens, including the general public, the prosecutors' offices staff, prisoners, prison guards, and students majoring in criminalistics. Our findings set a baseline for Serbian attitudes towards DNA databank custody, DNA sample and profile inclusion and retention criteria, ethical issues and concerns. Furthermore, results clearly demonstrate a permissive outlook of the respondents who are professional "beneficiaries" of genetic profiling and a restrictive position taken by the respondents whose genetic material has been acquired by the government. We believe that this opinion poll will be essential in discussions regarding a national DNA database, as well as in motivating further research on the reasons behind the observed views and subsequent development of educational strategies. All of these are, in turn, expected to aid the creation of suitable

  17. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  18. Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

    Directory of Open Access Journals (Sweden)

    Ryberg Martin

    2005-07-01

    Full Text Available Abstract Background During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. Results A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service http://emerencia.math.chalmers.se, users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches publication-wise, are also available. Discussion The ever-increasing use of DNA sequences for identification purposes

  19. Sustainability Initiatives and Organizational Performance: An Analysis of Publications in the WEB of SCIENCE DATABASE

    Directory of Open Access Journals (Sweden)

    Eduardo Luís Hepper

    2016-07-01

    Full Text Available Brazil is going through a time of reflection about the preservation of natural resources, an issue that is increasingly considered in its agenda. The search for balance between environmental, social and economic aspects has been a challenge for business survival over the years and has led companies to adopt initiatives focused on sustainability. The objective of this article is to analyse how the international scientific production addresses sustainable practices and initiatives and their relationship with organizational performance. Considering this scope, a bibliometric study of the publications located on Web of Science - Social Sciences Citation Index (WoS-SSCI was developed. There were 33 articles identified and selected on the subject. Journals that stand out in quantity of articles and number of citations are the Journal of Cleaner Production and Strategic Management Journal, respectively. Analysing the results, a growing concern about this issue and the increase in publications was noticed after the 2000s. The results found, in general, associate sustainable practices to positive organizational performance, such as increased profit on the product sold, quality improvement, improved reputation, and waste reduction, among others gains identified.

  20. Datasets will not be made accessible to the public due to the fact that they include household level data with PII.

    Data.gov (United States)

    U.S. Environmental Protection Agency — Datasets will not be made accessible to the public due to the fact that they include household level data with PII. This dataset is not publicly accessible because:...

  1. Creating a data exchange strategy for radiotherapy research: towards federated databases and anonymised public datasets.

    Science.gov (United States)

    Skripcak, Tomas; Belka, Claus; Bosch, Walter; Brink, Carsten; Brunner, Thomas; Budach, Volker; Büttner, Daniel; Debus, Jürgen; Dekker, Andre; Grau, Cai; Gulliford, Sarah; Hurkmans, Coen; Just, Uwe; Krause, Mechthild; Lambin, Philippe; Langendijk, Johannes A; Lewensohn, Rolf; Lühr, Armin; Maingon, Philippe; Masucci, Michele; Niyazi, Maximilian; Poortmans, Philip; Simon, Monique; Schmidberger, Heinz; Spezi, Emiliano; Stuschke, Martin; Valentini, Vincenzo; Verheij, Marcel; Whitfield, Gillian; Zackrisson, Björn; Zips, Daniel; Baumann, Michael

    2014-12-01

    Disconnected cancer research data management and lack of information exchange about planned and ongoing research are complicating the utilisation of internationally collected medical information for improving cancer patient care. Rapidly collecting/pooling data can accelerate translational research in radiation therapy and oncology. The exchange of study data is one of the fundamental principles behind data aggregation and data mining. The possibilities of reproducing the original study results, performing further analyses on existing research data to generate new hypotheses or developing computational models to support medical decisions (e.g. risk/benefit analysis of treatment options) represent just a fraction of the potential benefits of medical data-pooling. Distributed machine learning and knowledge exchange from federated databases can be considered as one beyond other attractive approaches for knowledge generation within "Big Data". Data interoperability between research institutions should be the major concern behind a wider collaboration. Information captured in electronic patient records (EPRs) and study case report forms (eCRFs), linked together with medical imaging and treatment planning data, are deemed to be fundamental elements for large multi-centre studies in the field of radiation therapy and oncology. To fully utilise the captured medical information, the study data have to be more than just an electronic version of a traditional (un-modifiable) paper CRF. Challenges that have to be addressed are data interoperability, utilisation of standards, data quality and privacy concerns, data ownership, rights to publish, data pooling architecture and storage. This paper discusses a framework for conceptual packages of ideas focused on a strategic development for international research data exchange in the field of radiation therapy and oncology.

  2. Risk of Mortality (Including Sudden Cardiac Death and Major Cardiovascular Events in Atypical and Typical Antipsychotic Users: A Study with the General Practice Research Database

    Directory of Open Access Journals (Sweden)

    Tarita Murray-Thomas

    2013-01-01

    Full Text Available Objective. Antipsychotics have been associated with increased cardiac events including mortality. This study assessed cardiac events including mortality among antipsychotic users relative to nonusers. Methods. The General Practice Research Database (GPRD was used to identify antipsychotic users, matched general population controls, and psychiatric diseased nonusers. Outcomes included cardiac mortality, sudden cardiac death (SCD, all-cause mortality (excluding suicide, coronary heart disease (CHD, and ventricular arrhythmias (VA. Sensitivity analyses were conducted for age, dose, duration, antipsychotic type, and psychiatric disease. Results. 183,392 antipsychotic users (115,491 typical and 67,901 atypical, 544,726 general population controls, and 193,920 psychiatric nonusers were identified. Nonusers with schizophrenia, dementia, or bipolar disorder had increased risks of all-cause mortality compared to general population controls, while nonusers with major depression had comparable risks. Relative to psychiatric nonusers, the adjusted relative ratios (aRR of all-cause mortality in antipsychotic users was 1.75 (95% CI: 1.64–1.87; cardiac mortality 1.72 (95% CI: 1.42–2.07; SCD primary definition 5.76 (95% CI: 2.90–11.45; SCD secondary definition 2.15 (95% CI: 1.64–2.81; CHD 1.16 (95% CI: 0.94–1.44; and VA 1.16 (95% CI: 1.02–1.31. aRRs of the various outcomes were lower for atypical versus typical antipsychotics (all-cause mortality 0.83 (95% CI: 0.80–0.85; cardiac mortality 0.89 (95% CI: 0.82–0.97; and SCD secondary definition 0.76 (95% CI: 0.55–1.04. Conclusions. Antipsychotic users had an increased risk of cardiac mortality, all-cause mortality, and SCD compared to a psychiatric nonuser cohort.

  3. Alaska Geochemical Database Version 2.0 (AGDB2) - Including "Best Value" Data Compilations for Geochemical Data for Rock, Sediment, Soil, Mineral, and Concentrate Sample Media

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Alaska Geochemical Database Version 2.0 (AGDB2) contains new geochemical data compilations in which each geologic material sample has one "best value"...

  4. Databases and their application

    NARCIS (Netherlands)

    E.C. Grimm; R.H.W Bradshaw; S. Brewer; S. Flantua; T. Giesecke; A.M. Lézine; H. Takahara; J.W.,Jr Williams

    2013-01-01

    During the past 20 years, several pollen database cooperatives have been established. These databases are now constituent databases of the Neotoma Paleoecology Database, a public domain, multiproxy, relational database designed for Quaternary-Pliocene fossil data and modern surface samples. The poll

  5. African-American and Latina Women Seeking Public Health Services: Cultural Beliefs regarding Pregnancy, including Medication-taking Behavior

    Directory of Open Access Journals (Sweden)

    Luz Dalia Sanchez, MD, MCP, MHA, PhD

    2011-01-01

    Full Text Available Objective: to describe cultural beliefs and medication-taking-behavior about pregnancy in African-American and Latina women. Design: qualitative study using phenomenological methodology; face-to-face, semi structured interviews and focus group. Thematic analysis was done to obtain themes consistent with the research objective. Setting: Maricopa County, Arizona, Department of Public-health Programs, November 2008 through April 2009.Participants: women seeking public-health services in the greater Phoenix, Arizona.Results: fifteen adult women representing two ethnic groups (seven African-Americans and eight Latinas participated. Themes derived from the interview data included: “The Dilemma: To Become or Not to Become Pregnant;” “The Ideal Stress-free World: Support System;” “Changing Worlds: Wanting Dependency;” and “The Health care System: Disconnection from Pregnancy to Postpartum.”Conclusions: based on the cultural themes: 1. pregnancies were not planned; 2. healthy life-style changes were not likely to occur during pregnancy; 3. basic facts about the biology of sexual intercourse and pregnancy were not understood, and there was no usage of any preconceptional or prenatal medications; and 4. professional health care was not desired or considered necessary (except during delivery. These cultural beliefs can contribute to negative birth outcomes, and need to be considered by pharmacists and other health-care providers. The information gained from this study can guide the implementation of educational programs developed by pharmacists that are more sensitive to the cultural beliefs and points of view of these particular women. Such programs would thus be more likely to be favorably received and utilized.

  6. USGS Dam Removal Science Database

    Science.gov (United States)

    Bellmore, J. Ryan; Vittum, Katherine; Duda, Jeff J.; Greene, Samantha L.

    2015-01-01

    This database is the result of an extensive literature search aimed at identifying documents relevant to the emerging field of dam removal science. In total the database contains 179 citations that contain empirical monitoring information associated with 130 different dam removals across the United States and abroad. Data includes publications through 2014 and supplemented with the U.S. Army Corps of Engineers National Inventory of Dams database, U.S. Geological Survey National Water Information System and aerial photos to estimate locations when coordinates were not provided. Publications were located using the Web of Science, Google Scholar, and Clearinghouse for Dam Removal Information.

  7. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  8. The post-millennium development goals agenda: include 'end to all wars' as a public health goal!

    Science.gov (United States)

    Jayasinghe, Saroj

    2014-09-01

    The process of identifying global post-millennium development goals (post-MDGs) has begun in earnest. Consensus is emerging in certain areas (e.g. eliminating poverty) and conflicts and violence are recognized as key factors that retard human development. However, current discussions focus on tackling intra-state conflicts and individual-based violence and hardly mention eliminating wars as a goal. Wars create public health catastrophes. They kill, maim, displace and affect millions. Inter-state wars fuel intra-state conflicts and violence. The peace agenda should not be the monopoly of the UN Security Council, and the current consensus-building process setting the post-MDG agenda is a rallying point for the global community. The human rights approach will not suffice to eliminate wars, because few are fought to protect human rights. The development agenda should therefore commit to eliminating all wars by 2030. Targets to reduce tensions and discourage wars should be included. We should act now.

  9. Database of recent tsunami deposits

    Science.gov (United States)

    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.

  10. The Exoplanet Orbit Database

    CERN Document Server

    Wright, Jason T; Marcy, Geoffrey W; Han, Eunkyu; Feng, Ying; Johnson, John Asher; Howard, Andrew W; Valenti, Jeff A; Anderson, Jay; Piskunov, Nikolai

    2010-01-01

    We present a database of well determined orbital parameters of exoplanets. This database comprises spectroscopic orbital elements measured for 421 planets orbiting 357 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 on the Web at http://exoplanets.org through the Exoplanets Data Explorer Table, and the data can be plotted and explored through the Exoplanets 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 selection different biase...

  11. International scientific seminar «Chronicle of Nature – a common database for scientific analysis and joint planning of scientific publications»

    Directory of Open Access Journals (Sweden)

    Juri P. Kurhinen

    2016-05-01

    Full Text Available Provides information about the results of the international scienti fic seminar «Сhronicle of Nature – a common database for scientific analysis and joint planning of scientific publications», held at Findland-Russian project «Linking environmental change to biodiversity change: large scale analysis оf Eurasia ecosystem».

  12. Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database

    Directory of Open Access Journals (Sweden)

    Nicolas Aurélie

    2012-07-01

    Full Text Available Abstract Background Dystrophin is a large essential protein of skeletal and heart muscle. It is a filamentous scaffolding protein with numerous binding domains. Mutations in the DMD gene, which encodes dystrophin, mostly result in the deletion of one or several exons and cause Duchenne (DMD and Becker (BMD muscular dystrophies. The most common DMD mutations are frameshift mutations resulting in an absence of dystrophin from tissues. In-frame DMD mutations are less frequent and result in a protein with partial wild-type dystrophin function. The aim of this study was to highlight structural and functional modifications of dystrophin caused by in-frame mutations. Methods and results We developed a dedicated database for dystrophin, the eDystrophin database. It contains 209 different non frame-shifting mutations found in 945 patients from a French cohort and previous studies. Bioinformatics tools provide models of the three-dimensional structure of the protein at deletion sites, making it possible to determine whether the mutated protein retains the typical filamentous structure of dystrophin. An analysis of the structure of mutated dystrophin molecules showed that hybrid repeats were reconstituted at the deletion site in some cases. These hybrid repeats harbored the typical triple coiled-coil structure of native repeats, which may be correlated with better function in muscle cells. Conclusion This new database focuses on the dystrophin protein and its modification due to in-frame deletions in BMD patients. The observation of hybrid repeat reconstitution in some cases provides insight into phenotype-genotype correlations in dystrophin diseases and possible strategies for gene therapy. The eDystrophin database is freely available: http://edystrophin.genouest.org/.

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

    Science.gov (United States)

    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.

  14. Glycoproteomic and glycomic databases.

    Science.gov (United States)

    Baycin Hizal, Deniz; Wolozny, Daniel; Colao, Joseph; Jacobson, Elena; Tian, Yuan; Krag, Sharon S; Betenbaugh, Michael J; Zhang, Hui

    2014-01-01

    Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.

  15. Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software.

    Science.gov (United States)

    Peach, Megan L; Zakharov, Alexey V; Liu, Ruifeng; Pugliese, Angelo; Tawa, Gregory; Wallqvist, Anders; Nicklaus, Marc C

    2012-10-01

    Metabolism has been identified as a defining factor in drug development success or failure because of its impact on many aspects of drug pharmacology, including bioavailability, half-life and toxicity. In this article, we provide an outline and descriptions of the resources for metabolism-related property predictions that are currently either freely or commercially available to the public. These resources include databases with data on, and software for prediction of, several end points: metabolite formation, sites of metabolic transformation, binding to metabolizing enzymes and metabolic stability. We attempt to place each tool in historical context and describe, wherever possible, the data it was based on. For predictions of interactions with metabolizing enzymes, we show a typical set of results for a small test set of compounds. Our aim is to give a clear overview of the areas and aspects of metabolism prediction in which the currently available resources are useful and accurate, and the areas in which they are inadequate or missing entirely.

  16. Survey of the situation of technology succession. Databases of articles including in industrial technology museums; Gijutsu keisho jokyo chosa. Sangyo gijutsu hakubutsukan shuzohin D.B. hen

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    To promote the succession of history of and the creative use of industrial science technologies, the paper made lists and databases of the articles of industrial technology museums and material halls in Japan. Record/preservation and collection/systematization of history of the industrial technology is useful for forming bases necessary for promotion of future research/development and international contribution. Museums and material halls are the fields for making comprehensive and practical activities. The data were made as one of the basic databases as the first step for promoting activities for examining the technical succession situation in a long term range continuously and systematically. In the classification of the data, the energy relation was divided into electric power, nuclear power, oil, coal, gas and energy in general. Others were classified into metal/mine, electricity/electronics/communication, chemistry/food, ship building/heavy machinery, printing/precision instrument, and textile/spinning. Moreover, the traffic relation was classified into railroad, automobiles/two-wheeled vehicles, airline/space, and ships. Items were also set of life relation, civil engineering/architecture, and general. The total number of the museums for the survey reached 208.

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

    Science.gov (United States)

    Friedman, Debra; Hoffman, Phillip

    2001-01-01

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

  18. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  19. Native Health Research Database

    Science.gov (United States)

    ... APP WITH JAVASCRIPT TURNED OFF. THE NATIVE HEALTH DATABASE REQUIRES JAVASCRIPT IN ORDER TO FUNCTION. PLEASE ENTER ... To learn more about searching the Native Health Database, click here. Keywords Title Author Source of Publication ...

  20. Library Instruction and Online Database Searching.

    Science.gov (United States)

    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;…

  1. 基于PDA的知识库与数据库集成和通用推理算法%PDA-oriented Integration of Knowledge Base and Database and Public Inference

    Institute of Scientific and Technical Information of China (English)

    欧阳建权; 钱跃良; 李锦涛; 刘任任

    2002-01-01

    This paper studies the correspondence relation between the knowledge and the database to combine the synthetic knowledge representation[1] and the relation database;defines the fields in the database as the feature in the knowledge base such as rule,weight and result for integrating the knowledge base and database.At alst,the paper introduces a public PDA-oriented inference algorism.

  2. FishTraits Database

    Science.gov (United States)

    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.

  3. USAID Anticorruption Projects Database

    Data.gov (United States)

    US Agency for International Development — The Anticorruption Projects Database (Database) includes information about USAID projects with anticorruption interventions implemented worldwide between 2007 and...

  4. Performance contracting for small fry -- Including individually owned multi-family buildings in a public/private sector partnership

    Energy Technology Data Exchange (ETDEWEB)

    Burger, M.; Jensen, V.

    1998-07-01

    Performance contracting has worked well in large multi-family buildings markets, such as public housing authorities. As equally deserving a market are assisted housing developments, which tend to be smaller scale in terms of size and ownership. This scale discourages energy service companies (ESO's) from approaching these developments because marketing and other transaction costs may be considered prohibitive. One answer to this barrier is a partnership that may act as an umbrella and aggregator for this market. The Illinois Housing Development Authority, assisted by the US Department of Energy's Chicago Regional Support office, is piloting such a partnership for developments that has its mortgages. Working with ESCO Landis and Staefa, Inc., this ongoing initiative is expanding performance contracting into the assisted housing market.

  5. 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

    DEFF Research Database (Denmark)

    Barfod, Charlotte; Lauritzen, Marlene Mp; Danker, Jakob K

    2012-01-01

    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......ABSTRACT: BACKGROUND: Management and care of the acutely ill patient have 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...... (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 28 days after admission. CONCLUSIONS: Despite challenges of data registration, we succeeded in creating a database...

  6. MetIDB: A Publicly Accessible Database of Predicted and Experimental 1H NMR Spectra of Flavonoids

    NARCIS (Netherlands)

    Mihaleva, V.V.; Beek, te T.A.; Zimmeren, van F.; Moco, S.I.A.; Laatikainen, R.; Niemitz, M.; Korhonen, S.P.; Driel, van M.A.; Vervoort, J.

    2013-01-01

    Identification of natural compounds, especially secondary metabolites, has been hampered by the lack of easy to use and accessible reference databases. Nuclear magnetic resonance (NMR) spectroscopy is the most selective technique for identification of unknown metabolites. High quality 1H NMR (proton

  7. Reducing the probability of false positive research findings by pre-publication validation – Experience with a large multiple sclerosis database

    Directory of Open Access Journals (Sweden)

    Heinz Moritz

    2008-04-01

    Full Text Available Abstract Background Published false positive research findings are a major problem in the process of scientific discovery. There is a high rate of lack of replication of results in clinical research in general, multiple sclerosis research being no exception. Our aim was to develop and implement a policy that reduces the probability of publishing false positive research findings. We have assessed the utility to work with a pre-publication validation policy after several years of research in the context of a large multiple sclerosis database. Methods The large database of the Sylvia Lawry Centre for Multiple Sclerosis Research was split in two parts: one for hypothesis generation and a validation part for confirmation of selected results. We present case studies from 5 finalized projects that have used the validation policy and results from a simulation study. Results In one project, the "relapse and disability" project as described in section II (example 3, findings could not be confirmed in the validation part of the database. The simulation study showed that the percentage of false positive findings can exceed 20% depending on variable selection. Conclusion We conclude that the validation policy has prevented the publication of at least one research finding that could not be validated in an independent data set (and probably would have been a "true" false-positive finding over the past three years, and has led to improved data analysis, statistical programming, and selection of hypotheses. The advantages outweigh the lost statistical power inherent in the process.

  8. The Danish Depression Database

    Directory of Open Access Journals (Sweden)

    Videbech P

    2016-10-01

    Full Text Available Poul Videbech,1 Anette Deleuran2 1Mental Health Centre Glostrup, Department of Clinical Medicine, University of Copenhagen, Glostrup, 2Psychiatric Centre Amager, Copenhagen S, Denmark Aim of database: The purpose of the Danish Depression Database (DDD is to monitor and facilitate the improvement of the quality of the treatment of depression in Denmark. Furthermore, the DDD has been designed to facilitate research. Study population: Inpatients as well as outpatients with depression, aged above 18 years, and treated in the public psychiatric hospital system were enrolled. Main variables: Variables include whether the patient has been thoroughly somatically examined and has been interviewed about the psychopathology by a specialist in psychiatry. The Hamilton score as well as an evaluation of the risk of suicide are measured before and after treatment. Whether psychiatric aftercare has been scheduled for inpatients and the rate of rehospitalization are also registered. Descriptive data: The database was launched in 2011. Every year since then ~5,500 inpatients and 7,500 outpatients have been registered annually in the database. A total of 24,083 inpatients and 29,918 outpatients have been registered. The DDD produces an annual report published on the Internet. Conclusion: The DDD can become an important tool for quality improvement and research, when the reporting is more complete. Keywords: quality assurance, suicide, somatic diseases, national database

  9. The Chandra Bibliography Database

    Science.gov (United States)

    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.

  10. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. [Open access to academic scholarship as a public policy resource: a study of the Capes database on Brazilian theses and dissertations].

    Science.gov (United States)

    da Silva Rosa, Teresa; Carneiro, Maria José

    2010-12-01

    Access to scientific knowledge is a valuable resource than can inform and validate positions taken in formulating public policy. But access to this knowledge can be challenging, given the diversity and breadth of available scholarship. Communication between the fields of science and of politics requires the dissemination of scholarship and access to it. We conducted a study using an open-access search tool in order to map existent knowledge on a specific topic: agricultural contributions to the preservation of biodiversity. The present article offers a critical view of access to the information available through the Capes database on Brazilian theses and dissertations.

  12. An Interoperable Cartographic Database

    OpenAIRE

    Slobodanka Ključanin; Zdravko Galić

    2007-01-01

    The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on t...

  13. A Chronostratigraphic Relational Database Ontology

    Science.gov (United States)

    Platon, E.; Gary, A.; Sikora, P.

    2005-12-01

    A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide

  14. Family medicine publications in Taiwan: An analysis of the Web of Science database from 1993 to 2012

    Directory of Open Access Journals (Sweden)

    Ming-Hwai Lin

    2014-11-01

    Conclusion: Publications from departments/institutes of family medicine in Taiwan increased rapidly from 1993 to 2012. However, the trends of decreased citation number of articles and journal impact factor, as well as the small amount of articles published in the Primary Health Care Category, deserve further attention and effort.

  15. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

    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.

  16. Protein Model Database

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Psychiatric inpatient expenditures and public health insurance programmes: analysis of a national database covering the entire South Korean population

    Directory of Open Access Journals (Sweden)

    Chung Woojin

    2010-09-01

    Full Text Available Abstract Background Medical spending on psychiatric hospitalization has been reported to impose a tremendous socio-economic burden on many developed countries with public health insurance programmes. However, there has been no in-depth study of the factors affecting psychiatric inpatient medical expenditures and differentiated these factors across different types of public health insurance programmes. In view of this, this study attempted to explore factors affecting medical expenditures for psychiatric inpatients between two public health insurance programmes covering the entire South Korean population: National Health Insurance (NHI and National Medical Care Aid (AID. Methods This retrospective, cross-sectional study used a nationwide, population-based reimbursement claims dataset consisting of 1,131,346 claims of all 160,465 citizens institutionalized due to psychiatric diagnosis between January 2005 and June 2006 in South Korea. To adjust for possible correlation of patients characteristics within the same medical institution and a non-linearity structure, a Box-Cox transformed, multilevel regression analysis was performed. Results Compared with inpatients 19 years old or younger, the medical expenditures of inpatients between 50 and 64 years old were 10% higher among NHI beneficiaries but 40% higher among AID beneficiaries. Males showed higher medical expenditures than did females. Expenditures on inpatients with schizophrenia as compared to expenditures on those with neurotic disorders were 120% higher among NHI beneficiaries but 83% higher among AID beneficiaries. Expenditures on inpatients of psychiatric hospitals were greater on average than expenditures on inpatients of general hospitals. Among AID beneficiaries, institutions owned by private groups treated inpatients with 32% higher costs than did government institutions. Among NHI beneficiaries, inpatients medical expenditures were positively associated with the proportion of

  18. Protected Areas Database of the United States (PAD-US)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Protected Areas Database of the United States (PAD-US) is the nation's inventory of protected areas, including public open space and voluntarily provided,...

  19. World-wide ocean optics database WOOD (NODC Accession 0092528)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — WOOD was developed to be a comprehensive publicly-available oceanographic bio-optical database providing global coverage. It includes nearly 250 major data sources...

  20. Quality Control of EUVE Databases

    Science.gov (United States)

    John, Linda M.

    1993-01-01

    The publicly accessible databases for the Extreme Ultraviolet Explorer (EUVE) include: the EUVE Archive Mailserver, the Center for EUV Astrophysics 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 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 paper, we describe the quality assurance (QA) procedures we have developed from approaching QA as a service organization; this approach reflects the overall EUVE philosophy of QA integrated into normal operating procedures, rather than imposed as an external, post-facto, control mechanism.

  1. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Intended Use of a Building in Terms of Updating the Cadastral Database and Harmonizing the Data with other Public Records

    Directory of Open Access Journals (Sweden)

    Buśko Małgorzata

    2017-06-01

    Full Text Available According to the original wording of the Regulation on the register of land and buildings of 2001, in the real estate cadastre there was one attribute associated with the use of a building structure - its intended use, which was applicable until the amendment to the Regulation was introduced in 2013. Then, additional attributes were added, i.e. the type of the building according to the Classification of Fixed Assets (KST, the class of the building according to the Polish Classification of Types of Constructions (PKOB and, at the same time, the main functional use and other functions of the building remained in the Regulation as well. The record data on buildings are captured for the real estate cadastre from other data sets, for example those maintained by architectural and construction authorities. At the same time, the data contained in the cadastre, after they have been entered or changed in the database, are transferred to other registers, such as tax records, or land and mortgage court registers. This study is the result of the analysis of the laws applicable to the specific units and registers. A list of discrepancies in the attributes occurring in the different registers was prepared. The practical part of the study paid particular attention to the legal bases and procedures for entering the function of a building in the real estate cadastre, which is extremely significant, as it is the attribute determining the property tax basis.

  3. Legume and Lotus japonicus Databases

    DEFF Research Database (Denmark)

    Hirakawa, Hideki; Mun, Terry; Sato, Shusei

    2014-01-01

    Since the genome sequence of Lotus japonicus, a model plant of family Fabaceae, was determined in 2008 (Sato et al. 2008), the genomes of other members of the Fabaceae family, soybean (Glycine max) (Schmutz et al. 2010) and Medicago truncatula (Young et al. 2011), have been sequenced. In this sec....... In this section, we introduce representative, publicly accessible online resources related to plant materials, integrated databases containing legume genome information, and databases for genome sequence and derived marker information of legume species including L. japonicus...

  4. How important is Overdiagnosis to members of the public offered the chance to include it in an online multi-criteria decision aid for prostate cancer screening?

    DEFF Research Database (Denmark)

    Kaltoft, Mette Kjer; Nielsen, Jesper Bo; Salkeld, Glenn;

    Objectives To establish the proportion of men who chose to include Overdiagnosis as a criterion in an online multi-criteria decision aid for the prostate cancer screening decision; and to determine the relative importance assigned to Overdiagnosis by those who included it in their personalised aid...... was 33%. Conclusions Overdiagnosis was prominent among the criteria selected from a menu by male members of the public participating in a trial of online multi-criteria decision aids for prostate cancer. Notably, over 40% of those who excluded 4 to 6 of the 10 criteria included Overdiagnosis in their aid....... Methods The data are from the 'Pick Your Own' arm of an Australian community panel-based trial involving men aged 40-69 years without diagnosed prostate cancer. The 720 participants were asked to choose between 1 and 10 criteria for inclusion in their aid. With only Overdiagnosis spelled out here...

  5. The AMMA database

    Science.gov (United States)

    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

  6. Validation of White-Matter Lesion Change Detection Methods on a Novel Publicly Available MRI Image Database.

    Science.gov (United States)

    Lesjak, Žiga; Pernuš, Franjo; Likar, Boštjan; Špiclin, Žiga

    2016-10-01

    Changes of white-matter lesions (WMLs) are good predictors of the progression of neurodegenerative diseases like multiple sclerosis (MS). Based on longitudinal magnetic resonance (MR) imaging the changes can be monitored, while the need for their accurate and reliable quantification led to the development of several automated MR image analysis methods. However, an objective comparison of the methods is difficult, because publicly unavailable validation datasets with ground truth and different sets of performance metrics were used. In this study, we acquired longitudinal MR datasets of 20 MS patients, in which brain regions were extracted, spatially aligned and intensity normalized. Two expert raters then delineated and jointly revised the WML changes on subtracted baseline and follow-up MR images to obtain ground truth WML segmentations. The main contribution of this paper is an objective, quantitative and systematic evaluation of two unsupervised and one supervised intensity based change detection method on the publicly available datasets with ground truth segmentations, using common pre- and post-processing steps and common evaluation metrics. Besides, different combinations of the two main steps of the studied change detection methods, i.e. dissimilarity map construction and its segmentation, were tested to identify the best performing combination.

  7. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  8. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries.

    Science.gov (United States)

    Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

    2002-01-01

    In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  9. Cell Centred Database (CCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging.

  10. A High Energy Nuclear Database Proposal

    CERN Document Server

    Brown, D A; Brown, David A.; Vogt, Ramona

    2005-01-01

    We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interace. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from the Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for intertial confinement fusion and target a...

  11. Proposal for a High Energy Nuclear Database

    CERN Document Server

    Vogt, D A B R

    2005-01-01

    We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and ...

  12. Scientific publications and research groups on alcohol consumption and related problems worldwide: authorship analysis of papers indexed in PubMed and Scopus databases (2005 to 2009).

    Science.gov (United States)

    González-Alcaide, Gregorio; Castelló-Cogollos, Lourdes; Castellano-Gómez, Miguel; Agullo-Calatayud, Víctor; Aleixandre-Benavent, Rafael; Alvarez, Francisco Javier; Valderrama-Zurián, Juan Carlos

    2013-01-01

    The research of alcohol consumption-related problems is a multidisciplinary field. The aim of this study is to analyze the worldwide scientific production in the area of alcohol-drinking and alcohol-related problems from 2005 to 2009. A MEDLINE and Scopus search on alcohol (alcohol-drinking and alcohol-related problems) published from 2005 to 2009 was carried out. Using bibliometric indicators, the distribution of the publications was determined within the journals that publish said articles, specialty of the journal (broad subject terms), article type, language of the publication, and country where the journal is published. Also, authorship characteristics were assessed (collaboration index and number of authors who have published more than 9 documents). The existing research groups were also determined. About 24,100 documents on alcohol, published in 3,862 journals, and authored by 69,640 authors were retrieved from MEDLINE and Scopus between the years 2005 and 2009. The collaboration index of the articles was 4.83 ± 3.7. The number of consolidated research groups in the field was identified as 383, with 1,933 authors. Documents on alcohol were published mainly in journals covering the field of "Substance-Related Disorders," 23.18%, followed by "Medicine," 8.7%, "Psychiatry," 6.17%, and "Gastroenterology," 5.25%. Research on alcohol is a consolidated field, with an average of 4,820 documents published each year between 2005 and 2009 in MEDLINE and Scopus. Alcohol-related publications have a marked multidisciplinary nature. Collaboration was common among alcohol researchers. There is an underrepresentation of alcohol-related publications in languages other than English and from developing countries, in MEDLINE and Scopus databases. Copyright © 2012 by the Research Society on Alcoholism.

  13. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

    Cain, J.M. (Calm (James M.), Great Falls, VA (United States))

    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.

  14. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

    Cain, J.M. [Calm (James M.), Great Falls, VA (United States)

    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.

  15. Databases of the marine metagenomics

    KAUST Repository

    Mineta, Katsuhiko

    2015-10-28

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.

  16. Databases of the marine metagenomics.

    Science.gov (United States)

    Mineta, Katsuhiko; Gojobori, Takashi

    2016-02-01

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.

  17. Online Information. Selected Databases at the New York State Library.

    Science.gov (United States)

    New York State Library, Albany. Database Services.

    This brochure describes the online information services at the New York State Library, which has online access to over 250 databases covering a broad range of subject areas, including current events, law, science, medicine, public affairs, grants, business, computer technology, education, social welfare, and humanities. Many of these databases are…

  18. Global Volcano Locations Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NGDC maintains a database of over 1,500 volcano locations obtained from the Smithsonian Institution Global Volcanism Program, Volcanoes of the World publication. The...

  19. HS3D, A Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database

    Science.gov (United States)

    Pollastro, Pasquale; Rampone, Salvatore

    The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D - Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT-AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT-AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: http://www.sci.unisannio.it/docenti/rampone/.

  20. DMTB: the magnetotactic bacteria database

    Science.gov (United States)

    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.

  1. Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.

    Science.gov (United States)

    Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

    2012-06-01

    We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology.

  2. Interactive bibliographical database on color

    Science.gov (United States)

    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.

  3. The Cambridge Structural Database.

    Science.gov (United States)

    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.

  4. Putative Vitis vinifera Rop- and Rab-GAP-, GEF-, and GDI-interacting proteins uncovered with novel methods for public genomic and EST database analysis.

    Science.gov (United States)

    Abbal, Philippe; Tesniere, Catherine

    2010-01-01

    To understand how grapevine Rop and Rab proteins achieve their functional versatility in signalling, identification of the putative VvRop- and VvRab-interacting proteins was performed using newly designed tools. In this study, sequences encoding eight full-length proteins for VvRop GTPase-activating proteins (GAPs), five for VvRabGAPs, six for VvRop guanine nucleotide exchange factors (GEFs), one for VvRabGEF, five for VvRop GDP dissociation inhibitors (GDIs), and three for VvRabGDIs were identified. These proteins had a CRIB motif or PH domain, a TBC domain, a PRONE domain, a DENN domain, or GDI signatures, respectively. By bootstrap analysis, an unrooted consensus phylogenetic tree was constructed which indicated that VvRopGDIs and VvRopGEFs--but not VvRopGAP--belonged to the same clade, and that VvRabGEF1 protein was more closely related to VvRopGAPs than to the other putative VvRab-interacting proteins. Twenty-two genes out of 28 encoding putative VvRop- and VvRab-interacting proteins could be located on identified grapevine chromosomes. Generally one gene was anchored on one chromosome, but in some cases up to four genes were located on the same chromosome. Expression patterns of the genes encoding putative VvRop- and VvRab-interacting proteins were also examined using a newly developed tool based on public expressed sequence tag (EST) database analysis. Expression patterns were sometimes found to be specific to an organ or a developmental stage. Although some limitations exist, the use of EST database analysis is stressed, in particular in the case of species where expression data are obtained at high costs in terms of time and effort.

  5. Scopus database: a review.

    Science.gov (United States)

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  6. SENTRA, a database of signal transduction proteins.

    Energy Technology Data Exchange (ETDEWEB)

    D' Souza, M.; Romine, M. F.; Maltsev, N.; Mathematics and Computer Science; PNNL

    2000-01-01

    SENTRA, available via URL http://wit.mcs.anl.gov/WIT2/Sentra/, is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and methyl-accepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction systems that are modulated by phosphorylation or methylation reactions. Although the majority of database entries are from prokaryotic systems, eukaroytic proteins with bacterial-like signal transduction domains are also included. Currently SENTRA contains signal transduction proteins in 34 complete and almost completely sequenced prokaryotic genomes, as well as sequences from 243 organisms available in public databases (SWISS-PROT and EMBL). The analysis was carried out within the framework of the WIT2 system, which is designed and implemented to support genetic sequence analysis and comparative analysis of sequenced genomes.

  7. An Interoperable Cartographic Database

    Directory of Open Access Journals (Sweden)

    Slobodanka Ključanin

    2007-05-01

    Full Text Available The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on the Internet. 

  8. Plant databases and data analysis tools

    Science.gov (United States)

    It is anticipated that the coming years will see the generation of large datasets including diagnostic markers in several plant species with emphasis on crop plants. To use these datasets effectively in any plant breeding program, it is essential to have the information available via public database...

  9. Quantitative Study and Structure Visualization of Scientific Publications in the Field of Information Management in Web of Science Database during 1988-2009

    Directory of Open Access Journals (Sweden)

    Afshin Hamdipour

    2012-12-01

    Full Text Available The present study endeavored to analysis the scientific publications that were indexed in the Web of Science database as the information management records and the visualization of science structure in this field during 1988-2009. The research method was scientometrics. During the study period, 1120 records in the field of information management have been published. These records were extracted in the form of plain text files and stored in a PC. Then they were analyzed by ISI.exe and HistCite softwares. Author's coefficient collaboration (CC was grown from zero in 1988 to 0.33 in 2009. Average coefficient collaboration between the authors was 0.22 which confirmed low authors collaboration in this area. The records have been published in 63 languages. Among these records the English language with 93.8 % possessed the highest proportion. City University London and the University of Sheffield in England had the most common publications in information management field. Based on the number of published records, T.D. Wilson with 13 records and 13 citations ranked as the first. The average number of global citations to 112 documents has been equal to 8.78. Despite the participation of different countries in the production of documents, more than 28.9% of records have been produced in the United States. According to results, 10 countries have published more than 72.4 percent of the records. City University London and the University of Sheffield have had highest frequency in this area. 15 journals have published 564 records (50.4% of the total productions. Finally, by implementation of scientific software HistCite map drawing clustered and authors, articles and four effective specific subjects were introduced..

  10. Accessing and using chemical databases

    DEFF Research Database (Denmark)

    Nikolov, Nikolai Georgiev; Pavlov, Todor; Niemelä, Jay Russell

    2013-01-01

    Computer-based representation of chemicals makes it possible to organize data in chemical databases-collections of chemical structures and associated properties. Databases are widely used wherever efficient processing of chemical information is needed, including search, storage, retrieval......, and dissemination. Structure and functionality of chemical databases are considered. The typical kinds of information found in a chemical database are considered-identification, structural, and associated data. Functionality of chemical databases is presented, with examples of search and access types. More details...... are included about the OASIS database and platform and the Danish (Q)SAR Database online. Various types of chemical database resources are discussed, together with a list of examples....

  11. Danish Colorectal Cancer Group Database

    Directory of Open Access Journals (Sweden)

    Ingeholm P

    2016-10-01

    Full Text Available Peter Ingeholm,1,2 Ismail Gögenur,1,3 Lene H Iversen1,4 1Danish Colorectal Cancer Group Database, Copenhagen, 2Department of Pathology, Herlev University Hospital, Herlev, 3Department of Surgery, Roskilde University Hospital, Roskilde, 4Department of Surgery P, Aarhus University Hospital, Aarhus C, Denmark Aim of database: The aim of the database, which has existed for registration of all patients with colorectal cancer in Denmark since 2001, is to improve the prognosis for this patient group. Study population: All Danish patients with newly diagnosed colorectal cancer who are either diagnosed or treated in a surgical department of a public Danish hospital. Main variables: The database comprises an array of surgical, radiological, oncological, and pathological variables. The surgeons record data such as diagnostics performed, including type and results of radiological examinations, lifestyle factors, comorbidity and performance, treatment including the surgical procedure, urgency of surgery, and intra- and postoperative complications within 30 days after surgery. The pathologists record data such as tumor type, number of lymph nodes and metastatic lymph nodes, surgical margin status, and other pathological risk factors. Descriptive data: The database has had >95% completeness in including patients with colorectal adenocarcinoma with >54,000 patients registered so far with approximately one-third rectal cancers and two-third colon cancers and an overrepresentation of men among rectal cancer patients. The stage distribution has been more or less constant until 2014 with a tendency toward a lower rate of stage IV and higher rate of stage I after introduction of the national screening program in 2014. The 30-day mortality rate after elective surgery has been reduced from >7% in 2001–2003 to <2% since 2013. Conclusion: The database is a national population-based clinical database with high patient and data completeness for the perioperative period

  12. 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

    Science.gov (United States)

    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.

  13. Using a relational database to index infectious disease information.

    Science.gov (United States)

    Brown, Jay A

    2010-05-01

    Mapping medical knowledge into a relational database became possible with the availability of personal computers and user-friendly database software in the early 1990s. To create a database of medical knowledge, the domain expert works like a mapmaker to first outline the domain and then add the details, starting with the most prominent features. The resulting "intelligent database" can support the decisions of healthcare professionals. The intelligent database described in this article contains profiles of 275 infectious diseases. Users can query the database for all diseases matching one or more specific criteria (symptom, endemic region of the world, or epidemiological factor). Epidemiological factors include sources (patients, water, soil, or animals), routes of entry, and insect vectors. Medical and public health professionals could use such a database as a decision-support software tool.

  14. Biofuel Database

    Science.gov (United States)

    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.

  15. Onzekere databases

    NARCIS (Netherlands)

    van Keulen, Maurice

    Een recente ontwikkeling in het databaseonderzoek betret zogenaamde 'onzekere databases'. Dit artikel beschrijft wat onzekere databases zijn, hoe ze gebruikt kunnen worden en welke toepassingen met name voordeel zouden kunnen hebben van deze technologie.

  16. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  17. Database Administrator

    Science.gov (United States)

    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…

  18. Database Administrator

    Science.gov (United States)

    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…

  19. The Danish Fetal Medicine database

    DEFF Research Database (Denmark)

    Ekelund, Charlotte; Kopp, Tine Iskov; Tabor, Ann

    2016-01-01

    trimester ultrasound scan performed at all public hospitals in Denmark are registered in the database. Main variables/descriptive data: Data on maternal characteristics, ultrasonic, and biochemical variables are continuously sent from the fetal medicine units’Astraia databases to the central database via...... analyses are sent to the database. Conclusion: It has been possible to establish a fetal medicine database, which monitors first-trimester screening for chromosomal abnormalities and second-trimester screening for major fetal malformations with the input from already collected data. The database...

  20. The NCBI Taxonomy database.

    Science.gov (United States)

    Federhen, Scott

    2012-01-01

    The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.

  1. Hawaii bibliographic database

    Science.gov (United States)

    Wright, Thomas L.; Takahashi, Taeko Jane

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and s or (if no ) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  2. Trends in performance indicators of neuroimaging anatomy research publications: a bibliometric study of major neuroradiology journal output over four decades based on web of science database.

    Science.gov (United States)

    Wing, Louise; Massoud, Tarik F

    2015-01-01

    Quantitative, qualitative, and innovative application of bibliometric research performance indicators to anatomy and radiology research and education can enhance cross-fertilization between the two disciplines. We aim to use these indicators to identify long-term trends in dissemination of publications in neuroimaging anatomy (including both productivity and citation rates), which has subjectively waned in prestige during recent years. We examined publications over the last 40 years in two neuroradiological journals, AJNR and Neuroradiology, and selected and categorized all neuroimaging anatomy research articles according to theme and type. We studied trends in their citation activity over time, and mathematically analyzed these trends for 1977, 1987, and 1997 publications. We created a novel metric, "citation half-life at 10 years postpublication" (CHL-10), and used this to examine trends in the skew of citation numbers for anatomy articles each year. We identified 367 anatomy articles amongst a total of 18,110 in these journals: 74.2% were original articles, with study of normal anatomy being the commonest theme (46.7%). We recorded a mean of 18.03 citations for each anatomy article, 35% higher than for general neuroradiology articles. Graphs summarizing the rise (upslope) in citation rates after publication revealed similar trends spanning two decades. CHL-10 trends demonstrated that more recently published anatomy articles were likely to take longer to reach peak citation rate. Bibliometric analysis suggests that anatomical research in neuroradiology is not languishing. This novel analytical approach can be applied to other aspects of neuroimaging research, and within other subspecialties in radiology and anatomy, and also to foster anatomical education. © 2014 Wiley Periodicals, Inc.

  3. The Danish Melanoma Database

    DEFF Research Database (Denmark)

    Hölmich, Lisbet Rosenkrantz; Klausen, Siri; Spaun, Eva

    2016-01-01

    AIM OF DATABASE: The aim of the database is to monitor and improve the treatment and survival of melanoma patients. STUDY POPULATION: All Danish patients with cutaneous melanoma and in situ melanomas must be registered in the Danish Melanoma Database (DMD). In 2014, 2,525 patients with invasive......, nature, and treatment hereof is registered. In case of death, the cause and date are included. Currently, all data are entered manually; however, data catchment from the existing registries is planned to be included shortly. DESCRIPTIVE DATA: The DMD is an old research database, but new as a clinical...

  4. The Gun Violence Database

    OpenAIRE

    Pavlick, Ellie; Callison-Burch, Chris

    2016-01-01

    We describe the Gun Violence Database (GVDB), a large and growing database of gun violence incidents in the United States. The GVDB is built from the detailed information found in local news reports about gun violence, and is constructed via a large-scale crowdsourced annotation effort through our web site, http://gun-violence.org/. We argue that centralized and publicly available data about gun violence can facilitate scientific, fact-based discussion about a topic that is often dominated by...

  5. TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico.

    Science.gov (United States)

    Chen, Calvin Yu-Chian

    2011-01-06

    Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine.

  6. Three Dendromonocotyle species (Monogenea: Monocotylidae) reported from captive rays, including D. lotteri sp. n. from Himantura gerrardi (Elasmobranchii: Dasyatidae) in the public aquarium at the Atlantis resort, Dubai.

    Science.gov (United States)

    Vaughan, David B; Chisholm, Leslie A

    2009-06-01

    Dendromonocotyle lotteri sp. n. is described from the dorsal skin surface of the stingray Himantura gerrardi (Gray) on exhibit in the public aquarium at the Atlantis resort in Dubai. It is differentiated from all other Dendromonocotyle species by the unique morphology of the distal portion of the sclerotised male copulatory organ. Dendromonocotyle lotteri is the second representative in the genus with 56 marginal haptoral papillae having a papillae to loculus association represented numerically as 6-6-8-8. We found Dendromonocotyle colorni Chisholm, Whittington et Kearn, 2001 on the same host specimens at the Atlantis resort public aquarium and Dendromonocotyle kuhlii Young, 1967 on Neotrygon kuhlii (Müller et Henle) kept at Burgers' Zoo Aquarium in Arnhem, The Netherlands. Supplemental information is provided for both D. colorni and D. kuhlii. The presence of Dendromonocotyle infections in public aquaria and host specificity are discussed. A key to the 17 species of Dendromonocotyle is also provided.

  7. The Danish Nonmelanoma Skin Cancer Dermatology Database

    DEFF Research Database (Denmark)

    Lamberg, Anna Lei; Sølvsten, Henrik; Lei, Ulrikke

    2016-01-01

    AIM OF DATABASE: The Danish Nonmelanoma Skin Cancer Dermatology Database was established in 2008. The aim of this database was to collect data on nonmelanoma skin cancer (NMSC) treatment and improve its treatment in Denmark. NMSC is the most common malignancy in the western countries and represents...... a significant challenge in terms of public health management and health care costs. However, high-quality epidemiological and treatment data on NMSC are sparse. STUDY POPULATION: The NMSC database includes patients with the following skin tumors: basal cell carcinoma (BCC), squamous cell carcinoma, Bowen......'s disease, and keratoacanthoma diagnosed by the participating office-based dermatologists in Denmark. MAIN VARIABLES: Clinical and histological diagnoses, BCC subtype, localization, size, skin cancer history, skin phototype, and evidence of metastases and treatment modality are the main variables...

  8. Plant Genome Duplication Database.

    Science.gov (United States)

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  9. National Database of Geriatrics

    DEFF Research Database (Denmark)

    Kannegaard, Pia Nimann; Vinding, Kirsten L; Hare-Bruun, Helle

    2016-01-01

    AIM OF DATABASE: The aim of the National Database of Geriatrics is to monitor the quality of interdisciplinary diagnostics and treatment of patients admitted to a geriatric hospital unit. STUDY POPULATION: The database population consists of patients who were admitted to a geriatric hospital unit....... Geriatric patients cannot be defined by specific diagnoses. A geriatric patient is typically a frail multimorbid elderly patient with decreasing functional ability and social challenges. The database includes 14-15,000 admissions per year, and the database completeness has been stable at 90% during the past......, percentage of discharges with a rehabilitation plan, and the part of cases where an interdisciplinary conference has taken place. Data are recorded by doctors, nurses, and therapists in a database and linked to the Danish National Patient Register. DESCRIPTIVE DATA: Descriptive patient-related data include...

  10. Implications of Public Reporting of Risk-Adjusted Mortality Following Percutaneous Coronary Intervention: Misperceptions and Potential Consequences for High-Risk Patients Including Nonsurgical Patients.

    Science.gov (United States)

    Gupta, Anuj; Yeh, Robert W; Tamis-Holland, Jacqueline E; Patel, Shalin H; Guyton, Robert A; Klein, Lloyd W; Rab, Tanveer; Kirtane, Ajay J

    2016-10-24

    Assessment of clinical outcomes such as 30-day mortality following coronary revascularization procedures has historically been used to spur quality improvement programs. Public reporting of risk-adjusted outcomes is already mandated in several states, and proposals to further expand public reporting have been put forward as a means of increasing transparency and potentially incentivizing high quality care. However, for public reporting of outcomes to be considered a useful surrogate of procedural quality of care, several prerequisites must be met. First, the reporting measure must be truly representative of the quality of the procedure itself, rather than be dominated by other underlying factors, such as the overall level of illness of a patient. Second, to foster comparisons among physicians and institutions, the metric requires accurate ascertainment of and adjustment for differences in patient risk profiles. This is particularly relevant for high-risk clinical patient scenarios. Finally, the potential deleterious consequences of public reporting of a quality metric should be considered prior to expanding the use of public reporting more broadly. In this viewpoint, the authors review in particular the characterization of high-risk patients currently treated by percutaneous coronary interventional procedures, assessing the adequacy of clinical risk models used in this population. They then expand upon the limitations of 30-day mortality as a quality metric for percutaneous coronary intervention, addressing the strengths and limitations of this metric, as well as offering suggestions to enhance its future use in public reporting. Copyright © 2016 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  11. Searching Databases with Keywords

    Institute of Scientific and Technical Information of China (English)

    Shan Wang; Kun-Long Zhang

    2005-01-01

    Traditionally, SQL query language is used to search the data in databases. However, it is inappropriate for end-users, since it is complex and hard to learn. It is the need of end-user, searching in databases with keywords, like in web search engines. This paper presents a survey of work on keyword search in databases. It also includes a brief introduction to the SEEKER system which has been developed.

  12. Public Lands, Other, This would include all counties owned by Chippewa County that are not Forest or Park. Most lands obtained through tax deed., Published in 2013, Not Applicable scale, Chippewa County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Public Lands, Other dataset current as of 2013. This would include all counties owned by Chippewa County that are not Forest or Park. Most lands obtained through tax...

  13. ECMDB: the E. coli Metabolome Database.

    Science.gov (United States)

    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.

  14. A review of drug-induced liver injury databases.

    Science.gov (United States)

    Luo, Guangwen; Shen, Yiting; Yang, Lizhu; Lu, Aiping; Xiang, Zheng

    2017-07-17

    Drug-induced liver injuries have been a major focus of current research in drug development, and are also one of the major reasons for the failure and withdrawal of drugs in development. Drug-induced liver injuries have been systematically recorded in many public databases, which have become valuable resources in this field. In this study, we provide an overview of these databases, including the liver injury-specific databases LiverTox, LTKB, Open TG-GATEs, LTMap and Hepatox, and the general databases, T3DB, DrugBank, DITOP, DART, CTD and HSDB. The features and limitations of these databases are summarized and discussed in detail. Apart from their powerful functions, we believe that these databases can be improved in several ways: by providing the data about the molecular targets involved in liver toxicity, by incorporating information regarding liver injuries caused by drug interactions, and by regularly updating the data.

  15. Hadoop NoSQL database

    OpenAIRE

    2015-01-01

    The theme of this work is database storage Hadoop Hbase. The main goal is to demonstrate the principles of its function and show the main usage. The entire text assumes that the reader is already familiar with the basic principles of NoSQL databases. The theoretical part briefly describes the basic concepts of databases then mostly covers Hadoop and its properties. This work also includes the practical part which describes how to install a database repository and illustrates basic database op...

  16. A Quality System Database

    Science.gov (United States)

    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.

  17. Database Manager

    Science.gov (United States)

    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…

  18. Database Copyright Issues in the Integration of Public Digital Cultural Resources%公共数字文化资源整合中的数据库版权问题

    Institute of Scientific and Technical Information of China (English)

    高峰

    2015-01-01

    公共文化机构存在三种不同类型的数据库:开放存取数据库、自建数据库和商业数据库,在资源整合的过程中,它们分别涉及不同的版权问题.需要规划好资源整合的版权策略,包括强化版权意识,注意保护被整合的数据库的知识产权;充分利用版权例外,最大限度实现资源整合;加强与数据库商的协商,利用约定许可规避整合的版权风险;加强版权法规建设,赋予公共文化机构更多权利以利资源整合;在整合中注意保护自身数据库资源的知识产权等,从而推动公共数字文化资源整合.%There are three different types of databases in public cultural institutions: open access databases, self-built databases, and commercial databases. In the process of resources integration, they are involved in different copyright issues. The copyright strategies of resources integration are needed to be well planned: we should strengthen the copyright awareness, pay attention to the protection of copyrights of the integrated databases and make full use of copyright exceptions to maximize the integration of resources. Meanwhile, it's also recommended to strengthen consultation with the database providers to avoid the copyright risk of resource integration by using the agreed licensing, to strengthen the construction of copyright laws and regulations, and to give the public cultural institutions more rights to facilitate the resources integration and to protect the intellectual property rights of their own database resources, etc. All these measures serve the purpose of the promotion of the integration of public digital cultural resources.

  19. Proposal for a High Energy Nuclear Database

    Energy Technology Data Exchange (ETDEWEB)

    Brown, David A.; Vogt, Ramona

    2005-03-31

    We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac and AGS to RHIC to CERN-LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, we propose periodically performing evaluations of the data and summarizing the results in topical reviews.

  20. The Danish Urogynaecological Database

    DEFF Research Database (Denmark)

    Guldberg, Rikke; Brostrøm, Søren; Hansen, Jesper Kjær

    2013-01-01

    INTRODUCTION AND HYPOTHESIS: The Danish Urogynaecological Database (DugaBase) is a nationwide clinical database established in 2006 to monitor, ensure and improve the quality of urogynaecological surgery. We aimed to describe its establishment and completeness and to validate selected variables....... This is the first study based on data from the DugaBase. METHODS: The database completeness was calculated as a comparison between urogynaecological procedures reported to the Danish National Patient Registry and to the DugaBase. Validity was assessed for selected variables from a random sample of 200 women...... in the DugaBase from 1 January 2009 to 31 October 2010, using medical records as a reference. RESULTS: A total of 16,509 urogynaecological procedures were registered in the DugaBase by 31 December 2010. The database completeness has increased by calendar time, from 38.2 % in 2007 to 93.2 % in 2010 for public...

  1. Cascadia Tsunami Deposit Database

    Science.gov (United States)

    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.

  2. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  3. Probabilistic Databases

    CERN Document Server

    Suciu, Dan; Koch, Christop

    2011-01-01

    Probabilistic databases are databases where the value of some attributes or the presence of some records are uncertain and known only with some probability. Applications in many areas such as information extraction, RFID and scientific data management, data cleaning, data integration, and financial risk assessment produce large volumes of uncertain data, which are best modeled and processed by a probabilistic database. This book presents the state of the art in representation formalisms and query processing techniques for probabilistic data. It starts by discussing the basic principles for rep

  4. Fine Arts Database (FAD)

    Data.gov (United States)

    General Services Administration — The Fine Arts Database records information on federally owned art in the control of the GSA; this includes the location, current condition and information on artists.

  5. Phase Equilibria Diagrams Database

    Science.gov (United States)

    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.

  6. The Danish Nonmelanoma Skin Cancer Dermatology Database

    Science.gov (United States)

    Lamberg, Anna Lei; Sølvsten, Henrik; Lei, Ulrikke; Vinding, Gabrielle Randskov; Stender, Ida Marie; Jemec, Gregor Borut Ernst; Vestergaard, Tine; Thormann, Henrik; Hædersdal, Merete; Dam, Tomas Norman; Olesen, Anne Braae

    2016-01-01

    Aim of database The Danish Nonmelanoma Skin Cancer Dermatology Database was established in 2008. The aim of this database was to collect data on nonmelanoma skin cancer (NMSC) treatment and improve its treatment in Denmark. NMSC is the most common malignancy in the western countries and represents a significant challenge in terms of public health management and health care costs. However, high-quality epidemiological and treatment data on NMSC are sparse. Study population The NMSC database includes patients with the following skin tumors: basal cell carcinoma (BCC), squamous cell carcinoma, Bowen’s disease, and keratoacanthoma diagnosed by the participating office-based dermatologists in Denmark. Main variables Clinical and histological diagnoses, BCC subtype, localization, size, skin cancer history, skin phototype, and evidence of metastases and treatment modality are the main variables in the NMSC database. Information on recurrence, cosmetic results, and complications are registered at two follow-up visits at 3 months (between 0 and 6 months) and 12 months (between 6 and 15 months) after treatment. Descriptive data In 2014, 11,522 patients with 17,575 tumors were registered in the database. Of tumors with a histological diagnosis, 13,571 were BCCs, 840 squamous cell carcinomas, 504 Bowen’s disease, and 173 keratoakanthomas. Conclusion The NMSC database encompasses detailed information on the type of tumor, a variety of prognostic factors, treatment modalities, and outcomes after treatment. The database has revealed that overall, the quality of care of NMSC in Danish dermatological clinics is high, and the database provides the necessary data for continuous quality assurance. PMID:27822110

  7. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May 1,...

  8. An online database of nuclear electromagnetic moments

    Science.gov (United States)

    Mertzimekis, T. J.; Stamou, K.; Psaltis, A.

    2016-01-01

    Measurements of nuclear magnetic dipole and electric quadrupole moments are considered quite important for the understanding of nuclear structure both near and far from the valley of stability. The recent advent of radioactive beams has resulted in a plethora of new, continuously flowing, experimental data on nuclear structure - including nuclear moments - which hinders the information management. A new, dedicated, public and user friendly online database

  9. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  10. Human Exposure Database System (HEDS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Human Exposure Database System (HEDS) provides public access to data sets, documents, and metadata from EPA on human exposure. It is primarily intended for...

  11. PADB : Published Association Database

    Directory of Open Access Journals (Sweden)

    Lee Jin-Sung

    2007-09-01

    Full Text Available Abstract 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; http://www.medclue.com/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.

  12. EPIC-DB: a proteomics database for studying Apicomplexan organisms

    Directory of Open Access Journals (Sweden)

    Angeletti Ruth

    2009-01-01

    Full Text Available Abstract Background High throughput proteomics experiments are useful for analyzing the protein expression of an organism, identifying the correct gene structure of a genome, or locating possible post-translational modifications within proteins. High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data. Description EPICDB is a publicly accessible, queryable, relational database that organizes and displays experimental, high throughput proteomics data for Toxoplasma gondii and Cryptosporidium parvum. Along with detailed information on mass spectrometry experiments, the database also provides antibody experimental results and analysis of functional annotations, comparative genomics, and aligned expressed sequence tag (EST and genomic open reading frame (ORF sequences. The database contains all available alternative gene datasets for each organism, which comprises a complete theoretical proteome for the respective organism, and all data is referenced to these sequences. The database is structured around clusters of protein sequences, which allows for the evaluation of redundancy, protein prediction discrepancies, and possible splice variants. The database can be expanded to include genomes of other organisms for which proteome-wide experimental data are available. Conclusion EPICDB is a comprehensive database of genome-wide T. gondii and C. parvum proteomics data and incorporates many features that allow for the analysis of the entire proteomes and/or annotation of specific protein sequences. EPICDB is complementary to other -genomics- databases of these organisms by offering complete mass spectrometry analysis on a comprehensive set of all available protein sequences.

  13. The Danish Anaesthesia Database

    Directory of Open Access Journals (Sweden)

    Antonsen K

    2016-10-01

    Full Text Available Kristian Antonsen,1 Charlotte Vallentin Rosenstock,2 Lars Hyldborg Lundstrøm2 1Board of Directors, Copenhagen University Hospital, Bispebjerg and Frederiksberg Hospital, Capital Region of Denmark, Denmark; 2Department of Anesthesiology, Copenhagen University Hospital, Nordsjællands Hospital-Hillerød, Capital Region of Denmark, Denmark Aim of database: The aim of the Danish Anaesthesia Database (DAD is the nationwide collection of data on all patients undergoing anesthesia. Collected data are used for quality assurance, quality development, and serve as a basis for research projects. Study population: The DAD was founded in 2004 as a part of Danish Clinical Registries (Regionernes Kliniske Kvalitetsudviklings Program [RKKP]. Patients undergoing general anesthesia, regional anesthesia with or without combined general anesthesia as well as patients under sedation are registered. Data are retrieved from public and private anesthesia clinics, single-centers as well as multihospital corporations across Denmark. In 2014 a total of 278,679 unique entries representing a national coverage of ~70% were recorded, data completeness is steadily increasing. Main variable: Records are aggregated for determining 13 defined quality indicators and eleven defined complications all covering the anesthetic process from the preoperative assessment through anesthesia and surgery until the end of the postoperative recovery period. Descriptive data: Registered variables include patients' individual social security number (assigned to all Danes and both direct patient-related lifestyle factors enabling a quantification of patients' comorbidity as well as variables that are strictly related to the type, duration, and safety of the anesthesia. Data and specific data combinations can be extracted within each department in order to monitor patient treatment. In addition, an annual DAD report is a benchmark for departments nationwide. Conclusion: The DAD is covering the

  14. The Danish Testicular Cancer database

    DEFF Research Database (Denmark)

    Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel

    2016-01-01

    AIM: The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC......) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. STUDY POPULATION: All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data...

  15. The Danish Nonmelanoma Skin Cancer Dermatology Database

    DEFF Research Database (Denmark)

    Lamberg, Anna Lei; Sølvsten, Henrik; Lei, Ulrikke;

    2016-01-01

    a significant challenge in terms of public health management and health care costs. However, high-quality epidemiological and treatment data on NMSC are sparse. STUDY POPULATION: The NMSC database includes patients with the following skin tumors: basal cell carcinoma (BCC), squamous cell carcinoma, Bowen......'s disease, and keratoacanthoma diagnosed by the participating office-based dermatologists in Denmark. MAIN VARIABLES: Clinical and histological diagnoses, BCC subtype, localization, size, skin cancer history, skin phototype, and evidence of metastases and treatment modality are the main variables...... in the database. Of tumors with a histological diagnosis, 13,571 were BCCs, 840 squamous cell carcinomas, 504 Bowen's disease, and 173 keratoakanthomas. CONCLUSION: The NMSC database encompasses detailed information on the type of tumor, a variety of prognostic factors, treatment modalities, and outcomes after...

  16. Computational Tools and Resources for Metabolism-Related Property Predictions. 1. Overview of Publicly Available (Free and Commercial) Databases and Software

    Science.gov (United States)

    2012-01-01

    models described in the literature have been developed by pharmaceutical companies, on large propri- etary datasets, using proprietary descriptors and...Suite, was created in 2009 with the merger of Pharma Algorithms with ACD/Labs. Initially, the only available metabolism-related model, which had...set of screening hits, or for database filtering prior to sample acquisition or synthesis. Ideally, one would like to be able to predict the rate of

  17. Database machine performance

    Energy Technology Data Exchange (ETDEWEB)

    Cesarini, F.; Salza, S.

    1987-01-01

    This book is devoted to the important problem of database machine performance evaluation. The book presents several methodological proposals and case studies, that have been developed within an international project supported by the European Economic Community on Database Machine Evaluation Techniques and Tools in the Context of the Real Time Processing. The book gives an overall view of the modeling methodologies and the evaluation strategies that can be adopted to analyze the performance of the database machine. Moreover, it includes interesting case studies and an extensive bibliography.

  18. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  19. Biological Databases

    Directory of Open Access Journals (Sweden)

    Kaviena Baskaran

    2013-12-01

    Full Text Available Biology has entered a new era in distributing information based on database and this collection of database become primary in publishing information. This data publishing is done through Internet Gopher where information resources easy and affordable offered by powerful research tools. The more important thing now is the development of high quality and professionally operated electronic data publishing sites. To enhance the service and appropriate editorial and policies for electronic data publishing has been established and editors of article shoulder the responsibility.

  20. CERCLIS (Superfund) ASCII Text Format - CPAD Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database (CPAD) contains a selected set...

  1. Distributed Structure-Searchable Toxicity Database Network

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Distributed Structure-Searchable Toxicity (DSSTox) Database Network provides a public forum for search and publishing downloadable, structure-searchable,...

  2. A database of antimalarial drug resistance

    Directory of Open Access Journals (Sweden)

    Ringwald Pascal

    2006-06-01

    Full Text Available Abstract A large investment is required to develop, license and deploy a new antimalarial drug. Too often, that investment has been rapidly devalued by the selection of parasite populations resistant to the drug action. To understand the mechanisms of selection, detailed information on the patterns of drug use in a variety of environments, and the geographic and temporal patterns of resistance is needed. Currently, there is no publically-accessible central database that contains information on the levels of resistance to antimalaria drugs. This paper outlines the resources that are available and the steps that might be taken to create a dynamic, open access database that would include current and historical data on clinical efficacy, in vitro responses and molecular markers related to drug resistance in Plasmodium falciparum and Plasmodium vivax. The goal is to include historical and current data on resistance to commonly used drugs, like chloroquine and sulfadoxine-pyrimethamine, and on the many combinations that are now being tested in different settings. The database will be accessible to all on the Web. The information in such a database will inform optimal utilization of current drugs and sustain the longest possible therapeutic life of newly introduced drugs and combinations. The database will protect the valuable investment represented by the development and deployment of novel therapies for malaria.

  3. Working with Documents in Databases

    Directory of Open Access Journals (Sweden)

    Marian DARDALA

    2008-01-01

    Full Text Available Using on a larger and larger scale the electronic documents within organizations and public institutions requires their storage and unitary exploitation by the means of databases. The purpose of this article is to present the way of loading, exploitation and visualization of documents in a database, taking as example the SGBD MSSQL Server. On the other hand, the modules for loading the documents in the database and for their visualization will be presented through code sequences written in C#. The interoperability between averages will be carried out by the means of ADO.NET technology of database access.

  4. SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

    Science.gov (United States)

    Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

    2014-08-15

    Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

  5. The Danish Testicular Cancer database

    DEFF Research Database (Denmark)

    Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel

    2016-01-01

    AIM: The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC......) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. STUDY POPULATION: All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data...... survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database...

  6. The Gene Expression Omnibus database

    Science.gov (United States)

    Clough, Emily; Barrett, Tanya

    2016-01-01

    The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome–protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/. PMID:27008011

  7. A database of charged cosmic rays

    Science.gov (United States)

    Maurin, D.; Melot, F.; Taillet, R.

    2014-09-01

    Aims: This paper gives a description of a new online database and associated online tools (data selection, data export, plots, etc.) for charged cosmic-ray measurements. The experimental setups (type, flight dates, techniques) from which the data originate are included in the database, along with the references to all relevant publications. Methods: The database relies on the MySQL5 engine. The web pages and queries are based on PHP, AJAX and the jquery, jquery.cluetip, jquery-ui, and table-sorter third-party libraries. Results: In this first release, we restrict ourselves to Galactic cosmic rays with Z ≤ 30 and a kinetic energy per nucleon up to a few tens of TeV/n. This corresponds to more than 200 different sub-experiments (i.e., different experiments, or data from the same experiment flying at different times) in as many publications. Conclusions: We set up a cosmic-ray database (CRDB) and provide tools to sort and visualise the data. New data can be submitted, providing the community with a collaborative tool to archive past and future cosmic-ray measurements. http://lpsc.in2p3.fr/crdb; Contact: crdatabase@lpsc.in2p3.fr

  8. ECOTOX database; new additions and future direction

    Science.gov (United States)

    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...

  9. ECOTOX database; new additions and future direction

    Science.gov (United States)

    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...

  10. A few problems in the generic nomenclature of insects and amphibians, with recommendations for the publication of new generic nomina in zootaxonomy and comments on taxonomic and nomenclatural databases and websites.

    Science.gov (United States)

    Dubois, Alain

    2017-02-26

    Dahanukar et al. (2016a) proposed the nomen Walkerana for a new genus of amphibians, but shortly after (2016b) they replaced it by the new nomen Sallywalkerana, believing that their nomen Walkerana was preoccupied by a generic nomen of orthopterans. This was unjustified because the orthopteran nomen 'Walkerella' Otte & Perez-Gelabert, 2009a and its new replacement nomen 'Walkerana' Otte & Perez-Gelabert, 2009b were both nomina nuda. These recent examples of nomenclatural errors in generic nomenclature are just a few among many in recent zootaxonomic publications. This opportunity is taken to make some general methodological recommendations, in several domains (availability, homonymy, synonymy, neonymy, length and palatability of nomina), for the publication of new generic nomina in zootaxonomy. However, the absence of a comprehensive database and website providing all the relevant information necessary to establish the nomenclatural status of all zoological generic and subgeneric nomina is a brake on the efforts that can be made to avoid nomenclatural errors in zoological generic nomenclature. The international community of taxonomists should seek at establishing such a database and website.

  11. Enhanced Publications Linking Publications and Research Data in Digital Repositories

    CERN Document Server

    Vernooy-Gerritsen, Marjan

    2009-01-01

    The traditional publication will be overhauled by the 'Enhanced Publication'. This is a publication that is enhanced with research data, extra materials, post publication data, and database records. It has an object-based structure with explicit l

  12. Chemical Kinetics Database

    Science.gov (United States)

    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.

  13. USDA food and nutrient databases provide the infrastructure for food and nutrition research, policy, and practice.

    Science.gov (United States)

    Ahuja, Jaspreet K C; Moshfegh, Alanna J; Holden, Joanne M; Harris, Ellen

    2013-02-01

    The USDA food and nutrient databases provide the basic infrastructure for food and nutrition research, nutrition monitoring, policy, and dietary practice. They have had a long history that goes back to 1892 and are unique, as they are the only databases available in the public domain that perform these functions. There are 4 major food and nutrient databases released by the Beltsville Human Nutrition Research Center (BHNRC), part of the USDA's Agricultural Research Service. These include the USDA National Nutrient Database for Standard Reference, the Dietary Supplement Ingredient Database, the Food and Nutrient Database for Dietary Studies, and the USDA Food Patterns Equivalents Database. The users of the databases are diverse and include federal agencies, the food industry, health professionals, restaurants, software application developers, academia and research organizations, international organizations, and foreign governments, among others. Many of these users have partnered with BHNRC to leverage funds and/or scientific expertise to work toward common goals. The use of the databases has increased tremendously in the past few years, especially the breadth of uses. These new uses of the data are bound to increase with the increased availability of technology and public health emphasis on diet-related measures such as sodium and energy reduction. Hence, continued improvement of the databases is important, so that they can better address these challenges and provide reliable and accurate data.

  14. A user-friendly phytoremediation database: creating the searchable database, the users, and the broader implications.

    Science.gov (United States)

    Famulari, Stevie; Witz, Kyla

    2015-01-01

    Designers, students, teachers, gardeners, farmers, landscape architects, architects, engineers, homeowners, and others have uses for the practice of phytoremediation. This research looks at the creation of a phytoremediation database which is designed for ease of use for a non-scientific user, as well as for students in an educational setting ( http://www.steviefamulari.net/phytoremediation ). During 2012, Environmental Artist & Professor of Landscape Architecture Stevie Famulari, with assistance from Kyla Witz, a landscape architecture student, created an online searchable database designed for high public accessibility. The database is a record of research of plant species that aid in the uptake of contaminants, including metals, organic materials, biodiesels & oils, and radionuclides. The database consists of multiple interconnected indexes categorized into common and scientific plant name, contaminant name, and contaminant type. It includes photographs, hardiness zones, specific plant qualities, full citations to the original research, and other relevant information intended to aid those designing with phytoremediation search for potential plants which may be used to address their site's need. The objective of the terminology section is to remove uncertainty for more inexperienced users, and to clarify terms for a more user-friendly experience. Implications of the work, including education and ease of browsing, as well as use of the database in teaching, are discussed.

  15. Annotation of novel neuropeptide precursors in the migratory locust based on transcript screening of a public EST database and mass spectrometry

    Directory of Open Access Journals (Sweden)

    De Loof Arnold

    2006-08-01

    Full Text Available Abstract Background For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, have been far less studied. The migratory locust Locusta migratoria, a heterometabolous insect, is one of the most infamous agricultural pests. They undergo a well-known and profound phase transition from the relatively harmless solitary form to a ferocious gregarious form. The underlying regulatory mechanisms of this phase transition are not fully understood, but it is undoubtedly that neuropeptides are involved. However, neuropeptide research in locusts is hampered by the absence of genomic information. Results Recently, EST (Expressed Sequence Tag databases from Locusta migratoria were constructed. Using bioinformatical tools, we searched these EST databases specifically for neuropeptide precursors. Based on known locust neuropeptide sequences, we confirmed the sequence of several previously identified neuropeptide precursors (i.e. pacifastin-related peptides, which consolidated our method. In addition, we found two novel neuroparsin precursors and annotated the hitherto unknown tachykinin precursor. Besides one of the known tachykinin peptides, this EST contained an additional tachykinin-like sequence. Using neuropeptide precursors from Drosophila melanogaster as a query, we succeeded in annotating the Locusta neuropeptide F, allatostatin-C and ecdysis-triggering hormone precursor, which until now had not been identified in locusts or in any other heterometabolous insect. For the tachykinin precursor, the ecdysis-triggering hormone precursor and the allatostatin-C precursor, translation of the predicted neuropeptides in neural tissues was confirmed with mass spectrometric techniques. Conclusion In this study we describe the annotation of 6 novel neuropeptide precursors and the neuropeptides they encode from the

  16. Comprehensive resource: Skeletal gene database.

    Science.gov (United States)

    Jia, L; Ho, N C; Park, S S; Powell, J; Francomano, C A

    2001-01-01

    The Skeletal Gene Database (SGD) is an integrated resource that provides comprehensive information about bone-related genes, mRNA, and proteins expressed in human and mouse, with rich links to numerous other electronic tools. SGD contains expressed sequence tag (EST) data from all the skeletal-related cDNA libraries that are available to the public. It supplies the query/data access analytic tools for users to search and compare each gene expressed in skeletal tissue(s). The results derived from EST tissue expression profiling will allow users to get the data on the mRNA copy numbers of each gene expressed in each tissue and its normalized value. From the SGD, researchers can obtain information regarding the name, symbol, size, exon/intron number, chromosomal location, LocusLink, and related disease (if any is known) of each gene. This electronic compendium also furnishes information on the protein of the corresponding gene including the protein size (amino acid number and molecular weight). It provides swift and ready access to other useful databases including OMIM, UniGene and PUBMED. The data will be updated regularly in step with current and future research, thereby providing what we hope will serve as a highly useful source of information and a powerful analytic tool to the scientific community.

  17. The RIKEN integrated database of mammals.

    Science.gov (United States)

    Masuya, Hiroshi; Makita, Yuko; Kobayashi, Norio; Nishikata, Koro; Yoshida, Yuko; Mochizuki, Yoshiki; Doi, Koji; Takatsuki, Terue; Waki, Kazunori; Tanaka, Nobuhiko; Ishii, Manabu; Matsushima, Akihiro; Takahashi, Satoshi; Hijikata, Atsushi; Kozaki, Kouji; Furuichi, Teiichi; Kawaji, Hideya; Wakana, Shigeharu; Nakamura, Yukio; Yoshiki, Atsushi; Murata, Takehide; Fukami-Kobayashi, Kaoru; Mohan, Sujatha; Ohara, Osamu; Hayashizaki, Yoshihide; Mizoguchi, Riichiro; Obata, Yuichi; Toyoda, Tetsuro

    2011-01-01

    The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

  18. Analysis of Coordinating Acquisition of Multimedia Database and Audiovisual Publication%浅析多媒体数据库与音像出版物协调采访

    Institute of Scientific and Technical Information of China (English)

    刘薇

    2012-01-01

    After the newborn multimedia database came into appearance,it has had a great attack on traditional audiovisual publication industry;however,it still cannot take the place of those multimedia publications seeing in the long run.Based on a comparison of multimedia database and audiovisual publication,the author discussed the necessities and feasibilities of coordinate acquisition for these two types of resources;besides,this essay introduced some exploration and achievements of coordinate acquisition in National Library of China,and finally provides some strategies for coordinate acquisition in library,from the angle of library status,technology,user types and human resources.%多媒体数据库这一新的资源类型出现后,对传统的音像出版物造成了一定的冲击,但在相当长一段时间内还无法替代音像出版物。在对比多媒体数据库和音像出版物这两种载体资源特点的基础上,论述了二者协调采访的必要性和可行性,并结合国家图书馆在协调采访方面的探索和成效,从馆情、技术条件、用户、人才等方面提出图书馆多媒体数据库与音像出版物协调采访的策略。

  19. Comparing public and private sector switchers

    DEFF Research Database (Denmark)

    Frederiksen, Anders; Hansen, Jesper Rosenberg; Bozeman, Barry

    are related to sector switching and the pattern of sector switch, public to private versus private to public. We propose a life stage model arguing that people's needs change in different life stages of their lives. We further suggest that this can help explain why they switch sector. We use unique Danish...... labor market data that include information on all employees in Denmark (both private and public sector). The data are for the period 1980 to 2006, and this longitudinal database includes abundant information about job changes, including sector switching. Our findings indicate mixed support....... Finally, we find that people with more education are likely to switch from private to public sector....

  20. The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database

    OpenAIRE

    Okba Selama; Phillip James; Farida Nateche; Wellington, Elizabeth M. H.; Hocine Hacène

    2013-01-01

    Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geog...

  1. MetaBase—the wiki-database of biological databases

    Science.gov (United States)

    Bolser, Dan M.; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Dominguez Del; Swan, Dan; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J.; Clements, Dave; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

    2012-01-01

    Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. PMID:22139927

  2. Developing, evaluating and maintaining a standardized stormwater BMP effectiveness database.

    Science.gov (United States)

    Clary, J; Urbonas, B; Jones, J; Strecker, E; Quigley, M; O'Brien, J

    2002-01-01

    The Urban Water Resources Research Council of the American Society of Civil Engineers, under a cooperative agreement with the US Environmental Protection Agency, released Version 1.0 of the National Stormwater Best Management Practices (BMP) Database to the stormwater management community in 1999. The product included a loaded database of 71 BMPs, as well as data entry software for standardized reporting of BMP test data. In conjunction with the database, the project team developed BMP performance evaluation protocols and applied them to the data contained in the initial database. Since the initial database release, 42 new BMP data sets have been added to the database, which is now accessible via the Internet at www.bmpdatabase.org along with associated data evaluation reports and other project documentation. A national stormwater BMP data clearinghouse continues to screen and post new BMP data to the database, as well as respond to inquiries from the public. An overview of both of the database software and results of the data evaluation are provided in this paper.

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

    Science.gov (United States)

    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.

  4. Musical Structural Analysis Database Based on GTTM

    OpenAIRE

    Hamanaka, Masatoshi; Hirata, Keiji; Tojo, Satoshi

    2014-01-01

    This paper, we present the publication of our analysis data and analyzing tool based on the generative theory of tonal music (GTTM). Musical databases such as score databases, instrument sound databases, and musical pieces with standard MIDI files and annotated data are key to advancements in the field of music information technology. We started implementing the GTTM on a computer in 2004 and ever since have collected and publicized test data by musicologists in a step-by-step manner. In our ...

  5. Hanford Site technical baseline database

    Energy Technology Data Exchange (ETDEWEB)

    Porter, P.E.

    1996-09-30

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of September 30, 1996. The cassette tape also includes the delta files that dellinate the differences between this revision and revision 4 (May 10, 1996) of the Hanford Site Technical Baseline Database.

  6. Hanford Site technical baseline database

    Energy Technology Data Exchange (ETDEWEB)

    Porter, P.E., Westinghouse Hanford

    1996-05-10

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of May 10, 1996. The cassette tape also includes the delta files that delineate the differences between this revision and revision 3 (April 10, 1996) of the Hanford Site Technical Baseline Database.

  7. Database Vs Data Warehouse

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Data warehouse technology includes a set of concepts and methods that offer the users useful information for decision making. The necessity to build a data warehouse arises from the necessity to improve the quality of information in the organization. The date proceeding from different sources, having a variety of forms - both structured and unstructured, are filtered according to business rules and are integrated in a single large data collection. Using informatics solutions, managers have understood that data stored in operational systems - including databases, are an informational gold mine that must be exploited. Data warehouses have been developed to answer the increasing demands for complex analysis, which could not be properly achieved with operational databases. The present paper emphasizes some of the criteria that information application developers can use in order to choose between a database solution or a data warehouse one.

  8. The Danish Melanoma Database

    DEFF Research Database (Denmark)

    Hölmich, Lisbet Rosenkrantz; Klausen, Siri; Spaun, Eva;

    2016-01-01

    AIM OF DATABASE: The aim of the database is to monitor and improve the treatment and survival of melanoma patients. STUDY POPULATION: All Danish patients with cutaneous melanoma and in situ melanomas must be registered in the Danish Melanoma Database (DMD). In 2014, 2,525 patients with invasive...... melanoma and 780 with in situ tumors were registered. The coverage is currently 93% compared with the Danish Pathology Register. MAIN VARIABLES: The main variables include demographic, clinical, and pathological characteristics, including Breslow's tumor thickness, ± ulceration, mitoses, and tumor...... quality register. The coverage is high, and the performance in the five Danish regions is quite similar due to strong adherence to guidelines provided by the Danish Melanoma Group. The list of monitored indicators is constantly expanding, and annual quality reports are issued. Several important scientific...

  9. Danish Gynecological Cancer Database

    DEFF Research Database (Denmark)

    Sørensen, Sarah Mejer; Bjørn, Signe Frahm; Jochumsen, Kirsten Marie;

    2016-01-01

    AIM OF DATABASE: The Danish Gynecological Cancer Database (DGCD) is a nationwide clinical cancer database and its aim is to monitor the treatment quality of Danish gynecological cancer patients, and to generate data for scientific purposes. DGCD also records detailed data on the diagnostic measures...... for gynecological cancer. STUDY POPULATION: DGCD was initiated January 1, 2005, and includes all patients treated at Danish hospitals for cancer of the ovaries, peritoneum, fallopian tubes, cervix, vulva, vagina, and uterus, including rare histological types. MAIN VARIABLES: DGCD data are organized within separate...... Danish personal identification number (CPR number). DESCRIPTIVE DATA: Data from DGCD and registers are available online in the Statistical Analysis Software portal. The DGCD forms cover almost all possible clinical variables used to describe gynecological cancer courses. The only limitation...

  10. Cloud Database Management System (CDBMS

    Directory of Open Access Journals (Sweden)

    Snehal B. Shende

    2015-10-01

    Full Text Available Cloud database management system is a distributed database that delivers computing as a service. It is sharing of web infrastructure for resources, software and information over a network. The cloud is used as a storage location and database can be accessed and computed from anywhere. The large number of web application makes the use of distributed storage solution in order to scale up. It enables user to outsource the resource and services to the third party server. This paper include, the recent trend in cloud service based on database management system and offering it as one of the services in cloud. The advantages and disadvantages of database as a service will let you to decide either to use database as a service or not. This paper also will highlight the architecture of cloud based on database management system.

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

    Science.gov (United States)

    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.

  12. The International Nucleotide Sequence Database Collaboration

    Science.gov (United States)

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Takagi, Toshihisa; Sequence Database Collaboration, International Nucleotide

    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

  13. Patent Database : A Methodology of Information Retrieval From PDF

    Directory of Open Access Journals (Sweden)

    Pawan Sharma

    2013-10-01

    Full Text Available Patent document holds wealth of information in itself. A brief detail of Indian patent applicationinformation is published as eighteen month publication by Indian patent Office, in electronic gazetteweekly. To date, a proper database of Indian patents specifically for research determination has not beenavailable, making it complicated for researcher to use this data for measuring any kind of researchactivities in terms of patents in India. To facilitate this, we constructed a comprehensive patent databasewhich incorporates the information presented in the electronic gazette. This database includes informationsuch as technology class, applicant, inventor, country of origin etc., of the patent submitted. We present themethodology for the creation of this database, its basic features along with its accuracy and reliability inthis research paper. Patent based database has been developed and can be used for various innovationresearches and activities.

  14. Data Preparation Process for the Buildings Performance Database

    Energy Technology Data Exchange (ETDEWEB)

    Walter, Travis; Dunn, Laurel; Mercado, Andrea; Brown, Richard E.; Mathew, Paul

    2014-06-30

    The Buildings Performance Database (BPD) includes empirically measured data from a variety of data sources with varying degrees of data quality and data availability. The purpose of the data preparation process is to maintain data quality within the database and to ensure that all database entries have sufficient data for meaningful analysis and for the database API. Data preparation is a systematic process of mapping data into the Building Energy Data Exchange Specification (BEDES), cleansing data using a set of criteria and rules of thumb, and deriving values such as energy totals and dominant asset types. The data preparation process takes the most amount of effort and time therefore most of the cleansing process has been automated. The process also needs to adapt as more data is contributed to the BPD and as building technologies over time. The data preparation process is an essential step between data contributed by providers and data published to the public in the BPD.

  15. Journalism, database and the construction of a connected public sphere NEOFLUXO: Jornalismo, base de dados e a construção da esfera pública interconectada

    Directory of Open Access Journals (Sweden)

    Walter Teixeira Lima Junior

    2011-07-01

    Full Text Available The paper aims to reveal the results of researched project research project applied in Conected Social Media Observatory, called Neofluxo. It was approved by the National Council for Scientific and Technological Development (CNPq and its main objective is to identify the behavior of informational flow in social networks during the majority electoral processs in Brazil, in 2010 and demonstrate the possibility to produce Journalism through the intersection and data visualization using APIs. The project stored more than 20,2 million of mentions of candidates, and keywords defined by the researchers. For this, it was elaborated a specific computer program based on an open source that is able to track entries from Twitter users from keywords, collecting and storing them in the database. The Neofluxo also recorded data from official social networks of candidates Jose Serra, Dilma Rousseff and Marina Silva, in order to identify –by these starting points - the informational flows until they have reached Twitter.O presente trabalho visa expor os resultados preliminares do projeto de pesquisa aplicada Observatório de Mídias Sociais Conectadas, batizado de Neofluxo. Aprovado em edital do CNPq, o projeto possui a duração de dois anos, devendo desenvolver-se até junho de 2012. O objetivo principal é identificar o comportamento do fluxo informacional nas redes sociais durante o processo eleitoral majoritário no Brasil, em 2010, e demonstrar a possibilidade de produzir Jornalismo por intermédio do cruzamento e visualização de dados utilizando APIs. O projeto armazenou mais de 20,2 milhões de menções aos candidatos e palavras-chave definidas pelos pesquisadores. Para isso foi elaborado um programa computacional espe¬cífico, baseado em software aberto, capaz de rastrear participações de usuários do Twitter segundo palavras-chave, coletando-as e armazenando-as em banco de dados. Também foram gravados dados das redes sociais oficiais dos

  16. The Danish Testicular Cancer database

    Directory of Open Access Journals (Sweden)

    Daugaard G

    2016-10-01

    Full Text Available Gedske Daugaard,1 Maria Gry Gundgaard Kier,1 Mikkel Bandak,1 Mette Saksø Mortensen,1 Heidi Larsson,2 Mette Søgaard,2 Birgitte Groenkaer Toft,3 Birte Engvad,4 Mads Agerbæk,5 Niels Vilstrup Holm,6 Jakob Lauritsen1 1Department of Oncology 5073, Copenhagen University Hospital, Rigshospitalet, Copenhagen, 2Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, 3Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, 4Department of Pathology, Odense University Hospital, Odense, 5Department of Oncology, Aarhus University Hospital, Aarhus, 6Department of Oncology, Odense University Hospital, Odense, Denmark Aim: The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database. The aim is to improve the quality of care for patients with testicular cancer (TC in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. Study population: All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. Main variables and descriptive data: The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions

  17. CORE-Hom: a powerful and exhaustive database of clinical trials in homeopathy.

    Science.gov (United States)

    Clausen, Jürgen; Moss, Sian; Tournier, Alexander; Lüdtke, Rainer; Albrecht, Henning

    2014-10-01

    The CORE-Hom database was created to answer the need for a reliable and publicly available source of information in the field of clinical research in homeopathy. As of May 2014 it held 1048 entries of clinical trials, observational studies and surveys in the field of homeopathy, including second publications and re-analyses. 352 of the trials referenced in the database were published in peer reviewed journals, 198 of which were randomised controlled trials. The most often used remedies were Arnica montana (n = 103) and Traumeel(®) (n = 40). The most studied medical conditions were respiratory tract infections (n = 126) and traumatic injuries (n = 110). The aim of this article is to introduce the database to the public, describing and explaining the interface, features and content of the CORE-Hom database.

  18. Mouse genome database 2016.

    Science.gov (United States)

    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.

  19. The Danish Sarcoma Database

    DEFF Research Database (Denmark)

    Jørgensen, Peter Holmberg; Lausten, Gunnar Schwarz; Pedersen, Alma B

    2016-01-01

    AIM: The aim of the database is to gather information about sarcomas treated in Denmark in order to continuously monitor and improve the quality of sarcoma treatment in a local, a national, and an international perspective. STUDY POPULATION: Patients in Denmark diagnosed with a sarcoma, both...... skeletal and ekstraskeletal, are to be registered since 2009. MAIN VARIABLES: The database contains information about appearance of symptoms; date of receiving referral to a sarcoma center; date of first visit; whether surgery has been performed elsewhere before referral, diagnosis, and treatment; tumor...... of Diseases - tenth edition codes and TNM Classification of Malignant Tumours, and date of death (after yearly coupling to the Danish Civil Registration System). Data quality and completeness are currently secured. CONCLUSION: The Danish Sarcoma Database is population based and includes sarcomas occurring...

  20. Harmonization of Databases

    DEFF Research Database (Denmark)

    Charlifue, Susan; Tate, Denise; Biering-Sorensen, Fin

    2016-01-01

    The objectives of this article are to (1) provide an overview of existing spinal cord injury (SCI) clinical research databases-their purposes, characteristics, and accessibility to users; and (2) present a vision for future collaborations required for cross-cutting research in SCI. This vision...... strengths and weaknesses. Efforts to provide a uniform approach to data collection are also reviewed. The databases reviewed offer different approaches to capture important clinical information on SCI. They vary on size, purpose, data points, inclusion of standard outcomes, and technical requirements. Each...... highlights the need for validated and relevant data for longitudinal clinical trials and observational and epidemiologic SCI-related studies. Three existing SCI clinical research databases/registries are reviewed and summarized with regard to current formats, collection methods, and uses, including major...

  1. ADANS database specification

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  2. Multicenter neonatal databases: Trends in research uses.

    Science.gov (United States)

    Creel, Liza M; Gregory, Sean; McNeal, Catherine J; Beeram, Madhava R; Krauss, David R

    2017-01-13

    In the US, approximately 12.7% of all live births are preterm, 8.2% of live births were low birth weight (LBW), and 1.5% are very low birth weight (VLBW). Although technological advances have improved mortality rates among preterm and LBW infants, improving overall rates of prematurity and LBW remains a national priority. Monitoring short- and long-term outcomes is critical for advancing medical treatment and minimizing morbidities associated with prematurity or LBW; however, studying these infants can be challenging. Several large, multi-center neonatal databases have been developed to improve research and quality improvement of treatments for and outcomes of premature and LBW infants. The purpose of this systematic review was to describe three multi-center neonatal databases. We conducted a literature search using PubMed and Google Scholar over the period 1990 to August 2014. Studies were included in our review if one of the databases was used as a primary source of data or comparison. Included studies were categorized by year of publication; study design employed, and research focus. A total of 343 studies published between 1991 and 2014 were included. Studies of premature and LBW infants using these databases have increased over time, and provide evidence for both neonatology and community-based pediatric practice. Research into treatment and outcomes of premature and LBW infants is expanding, partially due to the availability of large, multicenter databases. The consistency of clinical conditions and neonatal outcomes studied since 1990 demonstrates that there are dedicated research agendas and resources that allow for long-term, and potentially replicable, studies within this population.

  3. Imago Mundi Included in the Thomson Reuters Databases

    Directory of Open Access Journals (Sweden)

    Nedjeljko Frančula

    2012-06-01

    Full Text Available Imago Mundi – The International Journal for the History of Cartography is dedicated exclusively to the research of early maps in all of their aspects. It publishes papers related to the history and interpretation of those maps and their production in any part of the world.

  4. FAO/INFOODS Guidelines for Checking Food Composition Data Prior to the Publication of a User Table/Database, Version 1.0

    Science.gov (United States)

    Food composition data play an essential role in many sectors, including nutrition, health, agriculture, environment, food labeling and trade. Over the last 25 years, International Network of Food Data Systems (INFOODS) has developed many international standards, guidelines and tools to obtain harmo...

  5. Wisconsin Inventors` Network Database final report

    Energy Technology Data Exchange (ETDEWEB)

    1991-12-04

    The Wisconsin Innovation Service Center at UW-Whitewater received a DOE grant to create an Inventor`s Network Database to assist independent inventors and entrepreneurs with new product development. Since 1980, the Wisconsin Innovation Service Center (WISC) at the University of Wisconsin-Whitewater has assisted independent and small business inventors in estimating the marketability of their new product ideas and inventions. The purpose of the WISC as an economic development entity is to encourage inventors who appear to have commercially viable inventions, based on preliminary market research, to invest in the next stages of development, perhaps investigating prototype development, legal protection, or more in-depth market research. To address inventor`s information needs, WISC developed on electronic database with search capabilities by geographic region and by product category/industry. It targets both public and private resources capable of, and interested in, working with individual and small business inventors. At present, the project includes resources in Wisconsin only.

  6. Open Geoscience Database

    Science.gov (United States)

    Bashev, A.

    2012-04-01

    Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data

  7. 新立法对公共设施经营机构的数据库设计和维护的影响(英文)%Impact of Legislation on Database Design and Maintenance in Public Administration and Utilities

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    正如在其它欧洲国家所发生的一样,目前欧共体关于经济和货币一体化的政策对意大利的公共设施运营机构产生了戏剧性的影响.一方面,这些机构必须提供有效的服务,甚至通过互联网来提供给公民和企业,另一方面,市场的不合常规目的是促进更强的竞争:如今那些垄断的行业,如能源、汽油、水和电信,不得不进行竞争.这个新的范型需要组织方式的变化,它对信息系统以及其中最为重要的部分--数据库将产生重大的影响.通过两个案例研究来说明欧洲的政策对数据库所产生的影响.这两个案例分别是,一个坐落在意大利米兰的地方性的公共设施经营机构Regione Lombardia,另一个是在意大利罗马的能源企业ACEA.关于新立法对数据库设计和维护的影响,将介绍一些基本的观点.还将特别讨论,作为新法律环境下的一个产物,数据库重新设计所进行联合和分裂的一些问题.%Analogously to what occurs in other European Countries,the current policy of the European Union concerning the economic and monetary union is having a dramatic impact on Public Administration and utilities in Italy.As for Public Administrations,efficient services have to be provided,and even distributed via the Internet,to citizens and enterprises.On the other hand,the deregulation of the market is aimed at promoting a higher level of competitiveness:today also "natural" monopolies (like energy,gas,water,and telecommunications) are forced to competition.This new paradigm requires an organizational change which has a significant impact on information systems and on their most valuable component:the database.In this paper,the authors present the impact of the European policy on databases in two case studies:Regione Lombardia,an Italian Local Public Administration located in Milan,and ACEA,an Italian Energy Undertaking located in Rome.The authors show common issues related to the impact of the

  8. The Danish Nonmelanoma Skin Cancer Dermatology Database

    Directory of Open Access Journals (Sweden)

    Lamberg AL

    2016-10-01

    Full Text Available Anna Lei Lamberg,1 Henrik Sølvsten,2 Ulrikke Lei,3 Gabrielle Randskov Vinding,3 Ida Marie Stender,4 Gregor Borut Ernst Jemec,5 Tine Vestergaard,6 Henrik Thormann,7 Merete Hædersdal,8 Tomas Norman Dam,9 Anne Braae Olesen10 1Dermatology Clinic, Grenaa, Central Denmark Region, 2Dermatology Clinic, Aalborg, North Denmark Region, 3Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, Gentofte, 4Dermatology Clinic, Charlottenlund, Capital Region of Denmark, 5Department of Dermatology, Roskilde Hospital, Health Sciences Faculty, University of Copenhagen, Roskilde, Zealand Region, 6Department of Dermatology, Odense University Hospital, Odense, 7Dermatology Clinic, Vejle, Region of Southern Denmark, 8Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Capital Region of Denmark, 9Dermatology Clinic, Nykøbing Falster, Zealand Region, 10Department of Dermatology, University Hospital of Aarhus, Aarhus, Central Denmark Region, Denmark Aim of database: The Danish Nonmelanoma Skin Cancer Dermatology Database was established in 2008. The aim of this database was to collect data on nonmelanoma skin cancer (NMSC treatment and improve its treatment in Denmark. NMSC is the most common malignancy in the western countries and represents a significant challenge in terms of public health management and health care costs. However, high-quality epidemiological and treatment data on NMSC are sparse. Study population: The NMSC database includes patients with the following skin tumors: basal cell carcinoma (BCC, squamous cell carcinoma, Bowen's disease, and keratoacanthoma diagnosed by the participating office-based dermatologists in Denmark. Main variables: Clinical and histological diagnoses, BCC subtype, localization, size, skin cancer history, skin phototype, and evidence of metastases and treatment modality are the main variables in the NMSC database. Information on recurrence, cosmetic results, and

  9. Database of osmoregulated proteins in mammalian cells.

    Science.gov (United States)

    Grady, Cameron R; Knepper, Mark A; Burg, Maurice B; Ferraris, Joan D

    2014-10-28

    Biological information, even in highly specialized fields, is increasing at a volume that no single investigator can assimilate. The existence of this vast knowledge base creates the need for specialized computer databases to store and selectively sort the information. We have developed a manually curated database of the effects of hypertonicity on target proteins. Effects include changes in mRNA abundance and protein abundance, activity, phosphorylation state, binding, and cellular compartment. The biological information used in this database was derived from three research approaches: transcriptomic, proteomic, and reductionist (hypothesis-driven). The data are presented in the form of grammatical triplets consisting of subject, verb phrase, and object. The purpose of this format is to allow the data to be read from left to right as an English sentence. It is readable either by humans or by computers using natural language processing algorithms. An example of a data entry reads "Hypertonicity increases activity of ABL1 in HEK293." This database was created to provide access to a wealth of information on the effects of hypertonicity in a format that can be selectively sorted. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

  10. Atomic Spectra Bibliography Databases at NIST

    Science.gov (United States)

    Kramida, Alexander

    2008-05-01

    NIST's Atomic Spectroscopy Data Center maintains three online Bibliographic Databases (BD) containing references to papers with atomic data for controlled fusion research, modeling and diagnostics of astrophysical and terrestrial plasmas, and fundamental properties of electronic spectra of atoms and ions. The NIST Atomic Energy Levels and Spectra BD [http://physics.nist.gov/elevbib] now includes about 11500 references, mostly for years 1967--2007. The NIST Atomic Transition Probability BD, v. 8.1 [http://physics.nist.gov/fvalbib] with its 7500 references mainly covers years 1964--2007. The NIST Spectral Line Broadening BD, v. 2.0 [http://physics.nist.gov/linebrbib] has 3670 references, mostly for 1978--2006. All three databases are maintained in a unified database management system that allows us to quickly update the contents. Updates become available to users on the next day. An automated Data Entry module makes it easy to enter and categorize the data. The system allows us to keep the contents of all BDs up to date. A number of enhancements made since last year greatly increased public usability of the databases. This work is supported in part by the Office of Fusion Energy Sciences of the U.S. Department of Energy and by the National Aeronautics and Space Administration.

  11. Semantic web services for web databases

    CERN Document Server

    Ouzzani, Mourad

    2011-01-01

    Semantic Web Services for Web Databases introduces an end-to-end framework for querying Web databases using novel Web service querying techniques. This includes a detailed framework for the query infrastructure for Web databases and services. Case studies are covered in the last section of this book. Semantic Web Services For Web Databases is designed for practitioners and researchers focused on service-oriented computing and Web databases.

  12. BBGD: an online database for blueberry genomic data

    Directory of Open Access Journals (Sweden)

    Matthews Benjamin F

    2007-01-01

    Full Text Available Abstract Background Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry. Description BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure. Conclusion By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.

  13. BBGD: an online database for blueberry genomic data.

    Science.gov (United States)

    Alkharouf, Nadim W; Dhanaraj, Anik L; Naik, Dhananjay; Overall, Chris; Matthews, Benjamin F; Rowland, Lisa J

    2007-01-30

    Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG) was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry. BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure. By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.

  14. Application of China's National Forest Continuous Inventory Database

    Science.gov (United States)

    Xie, Xiaokui; Wang, Qingli; Dai, Limin; Su, Dongkai; Wang, Xinchuang; Qi, Guang; Ye, Yujing

    2011-12-01

    The maintenance of a timely, reliable and accurate spatial database on current forest ecosystem conditions and changes is essential to characterize and assess forest resources and support sustainable forest management. Information for such a database can be obtained only through a continuous forest inventory. The National Forest Continuous Inventory (NFCI) is the first level of China's three-tiered inventory system. The NFCI is administered by the State Forestry Administration; data are acquired by five inventory institutions around the country. Several important components of the database include land type, forest classification and ageclass/ age-group. The NFCI database in China is constructed based on 5-year inventory periods, resulting in some of the data not being timely when reports are issued. To address this problem, a forest growth simulation model has been developed to update the database for years between the periodic inventories. In order to aid in forest plan design and management, a three-dimensional virtual reality system of forest landscapes for selected units in the database (compartment or sub-compartment) has also been developed based on Virtual Reality Modeling Language. In addition, a transparent internet publishing system for a spatial database based on open source WebGIS (UMN Map Server) has been designed and utilized to enhance public understanding and encourage free participation of interested parties in the development, implementation, and planning of sustainable forest management.

  15. Very large database of lipids: rationale and design.

    Science.gov (United States)

    Martin, Seth S; Blaha, Michael J; Toth, Peter P; Joshi, Parag H; McEvoy, John W; Ahmed, Haitham M; Elshazly, Mohamed B; Swiger, Kristopher J; Michos, Erin D; Kwiterovich, Peter O; Kulkarni, Krishnaji R; Chimera, Joseph; Cannon, Christopher P; Blumenthal, Roger S; Jones, Steven R

    2013-11-01

    Blood lipids have major cardiovascular and public health implications. Lipid-lowering drugs are prescribed based in part on categorization of patients into normal or abnormal lipid metabolism, yet relatively little emphasis has been placed on: (1) the accuracy of current lipid measures used in clinical practice, (2) the reliability of current categorizations of dyslipidemia states, and (3) the relationship of advanced lipid characterization to other cardiovascular disease biomarkers. To these ends, we developed the Very Large Database of Lipids (NCT01698489), an ongoing database protocol that harnesses deidentified data from the daily operations of a commercial lipid laboratory. The database includes individuals who were referred for clinical purposes for a Vertical Auto Profile (Atherotech Inc., Birmingham, AL), which directly measures cholesterol concentrations of low-density lipoprotein, very low-density lipoprotein, intermediate-density lipoprotein, high-density lipoprotein, their subclasses, and lipoprotein(a). Individual Very Large Database of Lipids studies, ranging from studies of measurement accuracy, to dyslipidemia categorization, to biomarker associations, to characterization of rare lipid disorders, are investigator-initiated and utilize peer-reviewed statistical analysis plans to address a priori hypotheses/aims. In the first database harvest (Very Large Database of Lipids 1.0) from 2009 to 2011, there were 1 340 614 adult and 10 294 pediatric patients; the adult sample had a median age of 59 years (interquartile range, 49-70 years) with even representation by sex. Lipid distributions closely matched those from the population-representative National Health and Nutrition Examination Survey. The second harvest of the database (Very Large Database of Lipids 2.0) is underway. Overall, the Very Large Database of Lipids database provides an opportunity for collaboration and new knowledge generation through careful examination of granular lipid data on

  16. Wind turbine reliability database update.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Alternative treatment technology information center computer database system

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, D. [Environmental Protection Agency, Edison, NJ (United States)

    1995-10-01

    The Alternative Treatment Technology Information Center (ATTIC) computer database system was developed pursuant to the 1986 Superfund law amendments. It provides up-to-date information on innovative treatment technologies to clean up hazardous waste sites. ATTIC v2.0 provides access to several independent databases as well as a mechanism for retrieving full-text documents of key literature. It can be accessed with a personal computer and modem 24 hours a day, and there are no user fees. ATTIC provides {open_quotes}one-stop shopping{close_quotes} for information on alternative treatment options by accessing several databases: (1) treatment technology database; this contains abstracts from the literature on all types of treatment technologies, including biological, chemical, physical, and thermal methods. The best literature as viewed by experts is highlighted. (2) treatability study database; this provides performance information on technologies to remove contaminants from wastewaters and soils. It is derived from treatability studies. This database is available through ATTIC or separately as a disk that can be mailed to you. (3) underground storage tank database; this presents information on underground storage tank corrective actions, surface spills, emergency response, and remedial actions. (4) oil/chemical spill database; this provides abstracts on treatment and disposal of spilled oil and chemicals. In addition to these separate databases, ATTIC allows immediate access to other disk-based systems such as the Vendor Information System for Innovative Treatment Technologies (VISITT) and the Bioremediation in the Field Search System (BFSS). The user may download these programs to their own PC via a high-speed modem. Also via modem, users are able to download entire documents through the ATTIC system. Currently, about fifty publications are available, including Superfund Innovative Technology Evaluation (SITE) program documents.

  18. The Danish Sarcoma Database

    Directory of Open Access Journals (Sweden)

    Jorgensen PH

    2016-10-01

    Full Text Available Peter Holmberg Jørgensen,1 Gunnar Schwarz Lausten,2 Alma B Pedersen3 1Tumor Section, Department of Orthopedic Surgery, Aarhus University Hospital, Aarhus, 2Tumor Section, Department of Orthopedic Surgery, Rigshospitalet, Copenhagen, 3Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark Aim: The aim of the database is to gather information about sarcomas treated in Denmark in order to continuously monitor and improve the quality of sarcoma treatment in a local, a national, and an international perspective. Study population: Patients in Denmark diagnosed with a sarcoma, both skeletal and ekstraskeletal, are to be registered since 2009. Main variables: The database contains information about appearance of symptoms; date of receiving referral to a sarcoma center; date of first visit; whether surgery has been performed elsewhere before referral, diagnosis, and treatment; tumor characteristics such as location, size, malignancy grade, and growth pattern; details on treatment (kind of surgery, amount of radiation therapy, type and duration of chemotherapy; complications of treatment; local recurrence and metastases; and comorbidity. In addition, several quality indicators are registered in order to measure the quality of care provided by the hospitals and make comparisons between hospitals and with international standards. Descriptive data: Demographic patient-specific data such as age, sex, region of living, comorbidity, World Health Organization's International Classification of Diseases – tenth edition codes and TNM Classification of Malignant Tumours, and date of death (after yearly coupling to the Danish Civil Registration System. Data quality and completeness are currently secured. Conclusion: The Danish Sarcoma Database is population based and includes sarcomas occurring in Denmark since 2009. It is a valuable tool for monitoring sarcoma incidence and quality of treatment and its improvement, postoperative

  19. Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research.

    Science.gov (United States)

    Saokaew, Surasak; Sugimoto, Takashi; Kamae, Isao; Pratoomsoot, Chayanin; Chaiyakunapruk, Nathorn

    2015-01-01

    Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases' characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Forty databases- 20 from Thailand and 20 from Japan-were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed.

  20. The Danish Melanoma Database

    Directory of Open Access Journals (Sweden)

    Hölmich Lr

    2016-10-01

    Full Text Available Lisbet Rosenkrantz Hölmich,1 Siri Klausen,2 Eva Spaun,3 Grethe Schmidt,4 Dorte Gad,5 Inge Marie Svane,6,7 Henrik Schmidt,8 Henrik Frank Lorentzen,9 Else Helene Ibfelt10 1Department of Plastic Surgery, 2Department of Pathology, Herlev-Gentofte Hospital, University of Copenhagen, Herlev, 3Institute of Pathology, Aarhus University Hospital, Aarhus, 4Department of Plastic and Reconstructive Surgery, Breast Surgery and Burns, Rigshospitalet – Glostrup, University of Copenhagen, Copenhagen, 5Department of Plastic Surgery, Odense University Hospital, Odense, 6Center for Cancer Immune Therapy, Department of Hematology, 7Department of Oncology, Herlev-Gentofte Hospital, University of Copenhagen, Herlev, 8Department of Oncology, 9Department of Dermatology, Aarhus University Hospital, Aarhus, 10Registry Support Centre (East – Epidemiology and Biostatistics, Research Centre for Prevention and Health, Glostrup – Rigshospitalet, University of Copenhagen, Glostrup, Denmark Aim of database: The aim of the database is to monitor and improve the treatment and survival of melanoma patients.Study population: All Danish patients with cutaneous melanoma and in situ melanomas must be registered in the Danish Melanoma Database (DMD. In 2014, 2,525 patients with invasive melanoma and 780 with in situ tumors were registered. The coverage is currently 93% compared with the Danish Pathology Register.Main variables: The main variables include demographic, clinical, and pathological characteristics, including Breslow’s tumor thickness, ± ulceration, mitoses, and tumor–node–metastasis stage. Information about the date of diagnosis, treatment, type of surgery, including safety margins, results of lymphoscintigraphy in patients for whom this was indicated (tumors > T1a, results of sentinel node biopsy, pathological evaluation hereof, and follow-up information, including recurrence, nature, and treatment hereof is registered. In case of death, the cause and date

  1. SoyDB: a knowledge database of soybean transcription factors

    Directory of Open Access Journals (Sweden)

    Valliyodan Babu

    2010-01-01

    Full Text Available Abstract Background Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. Description The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB, protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models. Conclusions A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.

  2. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    Directory of Open Access Journals (Sweden)

    Andronescu Mirela

    2008-08-01

    Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

  3. Database systems for knowledge-based discovery.

    Science.gov (United States)

    Jagarlapudi, Sarma A R P; Kishan, K V Radha

    2009-01-01

    Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

  4. Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture.

    Science.gov (United States)

    Tanca, Alessandro; Palomba, Antonio; Deligios, Massimo; Cubeddu, Tiziana; Fraumene, Cristina; Biosa, Grazia; Pagnozzi, Daniela; Addis, Maria Filippa; Uzzau, Sergio

    2013-01-01

    Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and

  5. Computerized comprehensive data analysis of Lung Imaging Database Consortium (LIDC)

    OpenAIRE

    Tan, Jun; Pu, Jiantao; Zheng, Bin; Wang, Xingwei; Leader, Joseph K.

    2010-01-01

    Purpose: Lung Image Database Consortium (LIDC) is the largest public CT image database of lung nodules. In this study, the authors present a comprehensive and the most updated analysis of this dynamically growing database under the help of a computerized tool, aiming to assist researchers to optimally use this database for lung cancer related investigations.

  6. Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species.

    Science.gov (United States)

    Arbefeville, S; Harris, A; Ferrieri, P

    2017-09-01

    Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. Our results indicated that the MicroSEQ® D2 LSU r

  7. Database development and management

    CERN Document Server

    Chao, Lee

    2006-01-01

    Introduction to Database Systems Functions of a DatabaseDatabase Management SystemDatabase ComponentsDatabase Development ProcessConceptual Design and Data Modeling Introduction to Database Design Process Understanding Business ProcessEntity-Relationship Data Model Representing Business Process with Entity-RelationshipModelTable Structure and NormalizationIntroduction to TablesTable NormalizationTransforming Data Models to Relational Databases .DBMS Selection Transforming Data Models to Relational DatabasesEnforcing ConstraintsCreating Database for Business ProcessPhysical Design and Database

  8. Immune epitope database analysis resource

    DEFF Research Database (Denmark)

    Kim, Yohan; Ponomarenko, Julia; Zhu, Zhanyang

    2012-01-01

    The immune epitope database analysis resource (IEDB-AR: http://tools.iedb.org) is a collection of tools for prediction and analysis of molecular targets of T- and B-cell immune responses (i.e. epitopes). Since its last publication in the NAR webserver issue in 2008, a new generation of peptide:MH...

  9. The COMPADRE Plant Matrix Database

    DEFF Research Database (Denmark)

    2014-01-01

    COMPADRE contains demographic information on hundreds of plant species. The data in COMPADRE are in the form of matrix population models and our goal is to make these publicly available to facilitate their use for research and teaching purposes. COMPADRE is an open-access database. We only request...

  10. The COMPADRE Plant Matrix Database

    DEFF Research Database (Denmark)

    2014-01-01

    COMPADRE contains demographic information on hundreds of plant species. The data in COMPADRE are in the form of matrix population models and our goal is to make these publicly available to facilitate their use for research and teaching purposes. COMPADRE is an open-access database. We only request...

  11. A Quaternary Fault Database for Central Asia

    Directory of Open Access Journals (Sweden)

    S. Mohadjer

    2015-09-01

    Full Text Available Earthquakes represent the highest risk in terms of potential loss of lives and economic damage for Central Asian countries. Knowledge of fault location and behavior is essential in calculating and mapping seismic hazard. Previous efforts in compiling fault information for Central Asia have generated a large amount of data that are published in limited-access journals with no digital maps publicly available, or are limited in their description of important fault parameters such as slip rates. This study builds on previous work by improving access to fault information through a web-based interactive map and an online database with search capabilities that allow users to organize data by different fields. The data presented in this compilation include fault location, its geographic, seismic and structural characteristics, short descriptions, narrative comments and references to peer-reviewed publications. The interactive map displays 1196 fault segments and 34 000 earthquake locations on a shaded-relief map. The online database contains attributes for 122 faults mentioned in the literature, with Quaternary and geodetic slip rates reported for 38 and 26 faults respectively, and earthquake history reported for 39 faults. This work has implications for seismic hazard studies in Central Asia as it summarizes important fault parameters, and can reduce earthquake risk by enhancing public access to information. It also allows scientists and hazard assessment teams to identify structures and regions where data gaps exist and future investigations are needed.

  12. A Quaternary Fault Database for Central Asia

    Science.gov (United States)

    Mohadjer, S.; Ehlers, T. A.; Bendick, R.; Stübner, K.; Strube, T.

    2015-09-01

    Earthquakes represent the highest risk in terms of potential loss of lives and economic damage for Central Asian countries. Knowledge of fault location and behavior is essential in calculating and mapping seismic hazard. Previous efforts in compiling fault information for Central Asia have generated a large amount of data that are published in limited-access journals with no digital maps publicly available, or are limited in their description of important fault parameters such as slip rates. This study builds on previous work by improving access to fault information through a web-based interactive map and an online database with search capabilities that allow users to organize data by different fields. The data presented in this compilation include fault location, its geographic, seismic and structural characteristics, short descriptions, narrative comments and references to peer-reviewed publications. The interactive map displays 1196 fault segments and 34 000 earthquake locations on a shaded-relief map. The online database contains attributes for 122 faults mentioned in the literature, with Quaternary and geodetic slip rates reported for 38 and 26 faults respectively, and earthquake history reported for 39 faults. This work has implications for seismic hazard studies in Central Asia as it summarizes important fault parameters, and can reduce earthquake risk by enhancing public access to information. It also allows scientists and hazard assessment teams to identify structures and regions where data gaps exist and future investigations are needed.

  13. A Quaternary fault database for central Asia

    Science.gov (United States)

    Mohadjer, Solmaz; Ehlers, Todd Alan; Bendick, Rebecca; Stübner, Konstanze; Strube, Timo

    2016-02-01

    Earthquakes represent the highest risk in terms of potential loss of lives and economic damage for central Asian countries. Knowledge of fault location and behavior is essential in calculating and mapping seismic hazard. Previous efforts in compiling fault information for central Asia have generated a large amount of data that are published in limited-access journals with no digital maps publicly available, or are limited in their description of important fault parameters such as slip rates. This study builds on previous work by improving access to fault information through a web-based interactive map and an online database with search capabilities that allow users to organize data by different fields. The data presented in this compilation include fault location, its geographic, seismic, and structural characteristics, short descriptions, narrative comments, and references to peer-reviewed publications. The interactive map displays 1196 fault traces and 34 000 earthquake locations on a shaded-relief map. The online database contains attributes for 123 faults mentioned in the literature, with Quaternary and geodetic slip rates reported for 38 and 26 faults respectively, and earthquake history reported for 39 faults. All data are accessible for viewing and download via http://www.geo.uni-tuebingen.de/faults/. This work has implications for seismic hazard studies in central Asia as it summarizes important fault parameters, and can reduce earthquake risk by enhancing public access to information. It also allows scientists and hazard assessment teams to identify structures and regions where data gaps exist and future investigations are needed.

  14. Information Literacy Skills: Comparing and Evaluating Databases

    Science.gov (United States)

    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. Factors impacting time to acceptance and publication for peer-reviewed publications.

    Science.gov (United States)

    Toroser, Dikran; Carlson, Janice; Robinson, Micah; Gegner, Julie; Girard, Victoria; Smette, Lori; Nilsen, Jon; O'Kelly, James

    2017-07-01

    Timely publication of data is important for the medical community and provides a valuable contribution to data disclosure. The objective of this study was to identify and evaluate times to acceptance and publication for peer-reviewed manuscripts, reviews, and letters to the editor. Key publication metrics for published manuscripts, reviews, and letters to the editor were identified by eight Amgen publications professionals. Data for publications submitted between 1 January 2013 and 1 November 2015 were extracted from a proprietary internal publication-tracking database. Variables included department initiating the study, publication type, number of submissions per publication, and the total number of weeks from first submission to acceptance, online publication, and final publication. A total of 337 publications were identified, of which 300 (89%) were manuscripts. Time from submission to acceptance and publication was generally similar between clinical and real-world evidence (e.g. observational and health economics studies) publications. Median (range) time from first submission to acceptance was 23.4 (0.2-226.2) weeks. Median (range) time from first submission to online (early-release) publication was 29.7 (2.4-162.6) weeks. Median (range) time from first submission to final (print) publication was 36.2 (2.8-230.8) weeks. Time from first submission to acceptance, online publication, and final publication increased accordingly with number of submissions required for acceptance, with similar times noted between each subsequent submission. Analysis of a single-company publication database showed that the median time for manuscripts to be fully published after initial submission was 36.2 weeks, and time to publication increased accordingly with the number of submissions. Causes for multiple submissions and time from clinical trial completion to first submission were not assessed; these were limitations of the study. Nonetheless, publication planners should consider

  16. SAMMD: Staphylococcus aureus Microarray Meta-Database

    Directory of Open Access Journals (Sweden)

    Elasri Mohamed O

    2007-10-01

    Full Text Available Abstract Background Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL. Conclusion SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. Currently there are over 9500 entries for regulated genes, from 67 microarray

  17. Core Data of Yeast Interacting Proteins Database (Annotation Updated Version) - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nteractions are required. Several sources including YPD (Yeast Proteome Database, Costanzo, M. C., Hogan, J....erse direction. *1 The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources

  18. 77 FR 67341 - Fisheries of the South Atlantic; Southeast Data, Assessment and Review (SEDAR); Public Meeting

    Science.gov (United States)

    2012-11-09

    ... Data, Assessment and Review (SEDAR); Public Meeting AGENCY: National Marine Fisheries Service (NMFS... Management Councils, in conjunction with NOAA Fisheries and the Atlantic and Gulf States Marine Fisheries... include: Data collectors and database managers; stock assessment scientists, biologists, and researchers...

  19. Java Web Simulation (JWS); a web based database of kinetic models.

    Science.gov (United States)

    Snoep, J L; Olivier, B G

    2002-01-01

    Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

  20. Should we search Chinese biomedical databases when performing systematic reviews?

    Science.gov (United States)

    Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M

    2015-03-06

    Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.

  1. InterAction Database (IADB)

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. Addition of a breeding database in the Genome Database for Rosaceae.

    Science.gov (United States)

    Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

    2013-01-01

    Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will

  4. Practical database programming with Java

    CERN Document Server

    Bai, Ying

    2011-01-01

    "This important resource offers a detailed description about the practical considerations and applications in database programming using Java NetBeans 6.8 with authentic examples and detailed explanations. This book provides readers with a clear picture as to how to handle the database programming issues in the Java NetBeans environment. The book is ideal for classroom and professional training material. It includes a wealth of supplemental material that is available for download including Powerpoint slides, solution manuals, and sample databases"--

  5. PLANEX: the plant co-expression database

    OpenAIRE

    Yim, Won Cheol; Yu, YongBin; Song, Kitae; Jang, Cheol Seong; Lee, Byung-Moo

    2013-01-01

    Background The PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org) contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization...

  6. Public Budget Database - Governmental receipts 1962-Current

    Data.gov (United States)

    Executive Office of the President — This file contains governmental receipts for 1962 through the current budget year, as well as four years of projections. It can be used to reproduce many of the...

  7. Maize microarray annotation database

    Directory of Open Access Journals (Sweden)

    Berger Dave K

    2011-10-01

    Full Text Available Abstract Background Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a reporter - gene model match, (b number of reporters per gene model, (c potential for cross hybridization, (d sense/antisense orientation of reporters, (e position of reporter on B73 genome sequence (for eQTL studies, and (f functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database. Description Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i "annotation by sense gene model" (23,668 reporters, (ii "annotation by antisense gene model" (4,330; (iii "annotation by gDNA" without a WGS transcript hit (1,549; (iv "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390; (v "ambiguous annotation" (2,608; and (vi "inconclusive annotation" (6,489. Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank. The annotations are available in the Maize Microarray Annotation Database http://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to

  8. A Comparative Analysis Among the SRS M&M, NIS, and KID Databases for the Adolescent Idiopathic Scoliosis.

    Science.gov (United States)

    Lee, Nathan J; Guzman, Javier Z; Kim, Jun; Skovrlj, Branko; Martin, Christopher T; Pugely, Andrew J; Gao, Yubo; Caridi, John M; Mendoza-Lattes, Sergio; Cho, Samuel K

    2016-11-01

    Retrospective cohort analysis. A growing number of publications have utilized the Scoliosis Research Society (SRS) Morbidity and Mortality (M&M) database, but none have compared it to other large databases. The objective of this study was to compare SRS complications with those in administrative databases. The Nationwide Inpatient Sample (NIS) and Kid's Inpatient Database (KID) captured a greater number of overall complications while the SRS M&M data provided a greater incidence of spine-related complications following adolescent idiopathic scoliosis (AIS) surgery. Chi-square was used to obtain statistical significance, with p databases were analyzed for AIS patients who underwent fusion. Comparable variables were queried in all three databases, including patient demographics, surgical variables, and complications. Patients undergoing AIS in the SRS database were slightly older (SRS 14.4 years vs. NIS 13.8 years, p database. The SRS database reported fewer overall complications (SRS 3.9% vs. NIS 7.3%, p databases. In contrast, SRS reported higher spine-specific complication rates. Mortality rates were similar between SRS versus NIS (p = .280) and SRS versus KID (p = .08) databases. There are similarities and differences between the three databases. These discrepancies are likely due to the varying data-gathering methods each organization uses to collect their morbidity data. Level IV. Copyright © 2016 Scoliosis Research Society. Published by Elsevier Inc. All rights reserved.

  9. World Ocean Database 2013 (NCEI Accession 0117075)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The World Ocean Database (WOD) is the World’s largest publicly available uniform format quality controlled ocean profile dataset. Ocean profile data are sets of...

  10. Protected Areas Database for New Mexico

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The Protected Areas Database of the United States (PAD-US) is a geodatabase, managed by USGS GAP, that illustrates and describes public land ownership, management...

  11. Pacific Northwest Salmon Habitat Project Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In the Pacific Northwest Salmon Habitat Project Database Across the Pacific Northwest, both public and private agents are working to improve riverine habitat for a...

  12. A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity

    Science.gov (United States)

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

  13. Investigating students’ attitude towards the importance of factors included in the teaching evaluation forms of School of Public Health of Shahid Sadoughi University of Medical Sciences in 2010-2011

    Directory of Open Access Journals (Sweden)

    M. H Dehghani Tafti

    2012-11-01

    Full Text Available Introduction: students’ attitudes about teaching methodology have been widely recognised as a valid tool of evaluating teaching activities of faculty members. This study aims to determine the importance of the factors included in the teaching evaluation, from the students’ point of view. Methods: This is a cross-sectional study. Using a random cluster sampling, 332 students of the school of public health of Shahid Sadoughi University were selected .To collect data, a questionnaire containing three partswere used. These were demographic items, teachers’ evaluation (14 items and self-evaluation (4 items. Results: The students (80% scoredpersonal characteristics more. Among different fields of study, those studying occupational health scored the factorsless than others, and those studying at masters level scored them more than others.   The results indicated that there are significant correlation between age, marital status, and employment status of the students and the total average score.   The students scored the self-evaluation items more than 60%, There was a significant correlation between the average scores of evaluation and self-evaluation items. The students at bachelor level scored the factor more than masters students. Conclusion: The students’ focus on personal characteristics of teachers was remarkable. There is a need to revise the process of academics’ recruitment based on these findings. There is also a need to review the items included in evaluation forms of the school.

  14. Correlates of Access to Business Research Databases

    Science.gov (United States)

    Gottfried, John C.

    2010-01-01

    This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

  15. Managing Multiuser Database Buffers Using Data Mining Techniques

    NARCIS (Netherlands)

    Feng, L.; Lu, H.J.

    2004-01-01

    In this paper, we propose a data-mining-based approach to public buffer management for a multiuser database system, where database buffers are organized into two areas – public and private. While the private buffer areas contain pages to be updated by particular users, the public buffe

  16. The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts.

    Science.gov (United States)

    Hudson, Lawrence N; Newbold, Tim; Contu, Sara; Hill, Samantha L L; Lysenko, Igor; De Palma, Adriana; Phillips, Helen R P; Senior, Rebecca A; Bennett, Dominic J; Booth, Hollie; Choimes, Argyrios; Correia, David L P; Day, Julie; Echeverría-Londoño, Susy; Garon, Morgan; Harrison, Michelle L K; Ingram, Daniel J; Jung, Martin; Kemp, Victoria; Kirkpatrick, Lucinda; Martin, Callum D; Pan, Yuan; White, Hannah J; Aben, Job; Abrahamczyk, Stefan; Adum, Gilbert B; Aguilar-Barquero, Virginia; Aizen, Marcelo A; Ancrenaz, Marc; Arbeláez-Cortés, Enrique; Armbrecht, Inge; Azhar, Badrul; Azpiroz, Adrián B; Baeten, Lander; Báldi, András; Banks, John E; Barlow, Jos; Batáry, Péter; Bates, Adam J; Bayne, Erin M; Beja, Pedro; Berg, Åke; Berry, Nicholas J; Bicknell, Jake E; Bihn, Jochen H; Böhning-Gaese, Katrin; Boekhout, Teun; Boutin, Céline; Bouyer, Jérémy; Brearley, Francis Q; Brito, Isabel; Brunet, Jörg; Buczkowski, Grzegorz; Buscardo, Erika; Cabra-García, Jimmy; Calviño-Cancela, María; Cameron, Sydney A; Cancello, Eliana M; Carrijo, Tiago F; Carvalho, Anelena L; Castro, Helena; Castro-Luna, Alejandro A; Cerda, Rolando; Cerezo, Alexis; Chauvat, Matthieu; Clarke, Frank M; Cleary, Daniel F R; Connop, Stuart P; D'Aniello, Biagio; da Silva, Pedro Giovâni; Darvill, Ben; Dauber, Jens; Dejean, Alain; Diekötter, Tim; Dominguez-Haydar, Yamileth; Dormann, Carsten F; Dumont, Bertrand; Dures, Simon G; Dynesius, Mats; Edenius, Lars; Elek, Zoltán; Entling, Martin H; Farwig, Nina; Fayle, Tom M; Felicioli, Antonio; Felton, Annika M; Ficetola, Gentile F; Filgueiras, Bruno K C; Fonte, Steven J; Fraser, Lauchlan H; Fukuda, Daisuke; Furlani, Dario; Ganzhorn, Jörg U; Garden, Jenni G; Gheler-Costa, Carla; Giordani, Paolo; Giordano, Simonetta; Gottschalk, Marco S; Goulson, Dave; Gove, Aaron D; Grogan, James; Hanley, Mick E; Hanson, Thor; Hashim, Nor R; Hawes, Joseph E; Hébert, Christian; Helden, Alvin J; Henden, John-André; Hernández, Lionel; Herzog, Felix; Higuera-Diaz, Diego; Hilje, Branko; Horgan, Finbarr G; Horváth, Roland; Hylander, Kristoffer; Isaacs-Cubides, Paola; Ishitani, Masahiro; Jacobs, Carmen T; Jaramillo, Víctor J; Jauker, Birgit; Jonsell, Mats; Jung, Thomas S; Kapoor, Vena; Kati, Vassiliki; Katovai, Eric; Kessler, Michael; Knop, Eva; Kolb, Annette; Kőrösi, Ádám; Lachat, Thibault; Lantschner, Victoria; Le Féon, Violette; LeBuhn, Gretchen; Légaré, Jean-Philippe; Letcher, Susan G; Littlewood, Nick A; López-Quintero, Carlos A; Louhaichi, Mounir; Lövei, Gabor L; Lucas-Borja, Manuel Esteban; Luja, Victor H; Maeto, Kaoru; Magura, Tibor; Mallari, Neil Aldrin; Marin-Spiotta, Erika; Marshall, E J P; Martínez, Eliana; Mayfield, Margaret M; Mikusinski, Grzegorz; Milder, Jeffrey C; Miller, James R; Morales, Carolina L; Muchane, Mary N; Muchane, Muchai; Naidoo, Robin; Nakamura, Akihiro; Naoe, Shoji; Nates-Parra, Guiomar; Navarrete Gutierrez, Dario A; Neuschulz, Eike L; Noreika, Norbertas; Norfolk, Olivia; Noriega, Jorge Ari; Nöske, Nicole M; O'Dea, Niall; Oduro, William; Ofori-Boateng, Caleb; Oke, Chris O; Osgathorpe, Lynne M; Paritsis, Juan; Parra-H, Alejandro; Pelegrin, Nicolás; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Phalan, Ben; Philips, T Keith; Poveda, Katja; Power, Eileen F; Presley, Steven J; Proença, Vânia; Quaranta, Marino; Quintero, Carolina; Redpath-Downing, Nicola A; Reid, J Leighton; Reis, Yana T; Ribeiro, Danilo B; Richardson, Barbara A; Richardson, Michael J; Robles, Carolina A; Römbke, Jörg; Romero-Duque, Luz Piedad; Rosselli, Loreta; Rossiter, Stephen J; Roulston, T'ai H; Rousseau, Laurent; Sadler, Jonathan P; Sáfián, Szabolcs; Saldaña-Vázquez, Romeo A; Samnegård, Ulrika; Schüepp, Christof; Schweiger, Oliver; Sedlock, Jodi L; Shahabuddin, Ghazala; Sheil, Douglas; Silva, Fernando A B; Slade, Eleanor M; Smith-Pardo, Allan H; Sodhi, Navjot S; Somarriba, Eduardo J; Sosa, Ramón A; Stout, Jane C; Struebig, Matthew J; Sung, Yik-Hei; Threlfall, Caragh G; Tonietto, Rebecca; Tóthmérész, Béla; Tscharntke, Teja; Turner, Edgar C; Tylianakis, Jason M; Vanbergen, Adam J; Vassilev, Kiril; Verboven, Hans A F; Vergara, Carlos H; Vergara, Pablo M; Verhulst, Jort; Walker, Tony R; Wang, Yanping; Watling, James I; Wells, Konstans; Williams, Christopher D; Willig, Michael R; Woinarski, John C Z; Wolf, Jan H D; Woodcock, Ben A; Yu, Douglas W; Zaitsev, Andrey S; Collen, Ben; Ewers, Rob M; Mace, Georgina M; Purves, Drew W; Scharlemann, Jörn P W; Purvis, Andy

    2014-12-01

    Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

  17. The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

    Science.gov (United States)

    Hudson, Lawrence N; Newbold, Tim; Contu, Sara; Hill, Samantha L L; Lysenko, Igor; De Palma, Adriana; Phillips, Helen R P; Senior, Rebecca A; Bennett, Dominic J; Booth, Hollie; Choimes, Argyrios; Correia, David L P; Day, Julie; Echeverría-Londoño, Susy; Garon, Morgan; Harrison, Michelle L K; Ingram, Daniel J; Jung, Martin; Kemp, Victoria; Kirkpatrick, Lucinda; Martin, Callum D; Pan, Yuan; White, Hannah J; Aben, Job; Abrahamczyk, Stefan; Adum, Gilbert B; Aguilar-Barquero, Virginia; Aizen, Marcelo A; Ancrenaz, Marc; Arbeláez-Cortés, Enrique; Armbrecht, Inge; Azhar, Badrul; Azpiroz, Adrián B; Baeten, Lander; Báldi, András; Banks, John E; Barlow, Jos; Batáry, Péter; Bates, Adam J; Bayne, Erin M; Beja, Pedro; Berg, Åke; Berry, Nicholas J; Bicknell, Jake E; Bihn, Jochen H; Böhning-Gaese, Katrin; Boekhout, Teun; Boutin, Céline; Bouyer, Jérémy; Brearley, Francis Q; Brito, Isabel; Brunet, Jörg; Buczkowski, Grzegorz; Buscardo, Erika; Cabra-García, Jimmy; Calviño-Cancela, María; Cameron, Sydney A; Cancello, Eliana M; Carrijo, Tiago F; Carvalho, Anelena L; Castro, Helena; Castro-Luna, Alejandro A; Cerda, Rolando; Cerezo, Alexis; Chauvat, Matthieu; Clarke, Frank M; Cleary, Daniel F R; Connop, Stuart P; D'Aniello, Biagio; da Silva, Pedro Giovâni; Darvill, Ben; Dauber, Jens; Dejean, Alain; Diekötter, Tim; Dominguez-Haydar, Yamileth; Dormann, Carsten F; Dumont, Bertrand; Dures, Simon G; Dynesius, Mats; Edenius, Lars; Elek, Zoltán; Entling, Martin H; Farwig, Nina; Fayle, Tom M; Felicioli, Antonio; Felton, Annika M; Ficetola, Gentile F; Filgueiras, Bruno K C; Fonte, Steven J; Fraser, Lauchlan H; Fukuda, Daisuke; Furlani, Dario; Ganzhorn, Jörg U; Garden, Jenni G; Gheler-Costa, Carla; Giordani, Paolo; Giordano, Simonetta; Gottschalk, Marco S; Goulson, Dave; Gove, Aaron D; Grogan, James; Hanley, Mick E; Hanson, Thor; Hashim, Nor R; Hawes, Joseph E; Hébert, Christian; Helden, Alvin J; Henden, John-André; Hernández, Lionel; Herzog, Felix; Higuera-Diaz, Diego; Hilje, Branko; Horgan, Finbarr G; Horváth, Roland; Hylander, Kristoffer; Isaacs-Cubides, Paola; Ishitani, Masahiro; Jacobs, Carmen T; Jaramillo, Víctor J; Jauker, Birgit; Jonsell, Mats; Jung, Thomas S; Kapoor, Vena; Kati, Vassiliki; Katovai, Eric; Kessler, Michael; Knop, Eva; Kolb, Annette; Kőrösi, Ádám; Lachat, Thibault; Lantschner, Victoria; Le Féon, Violette; LeBuhn, Gretchen; Légaré, Jean-Philippe; Letcher, Susan G; Littlewood, Nick A; López-Quintero, Carlos A; Louhaichi, Mounir; Lövei, Gabor L; Lucas-Borja, Manuel Esteban; Luja, Victor H; Maeto, Kaoru; Magura, Tibor; Mallari, Neil Aldrin; Marin-Spiotta, Erika; Marshall, E J P; Martínez, Eliana; Mayfield, Margaret M; Mikusinski, Grzegorz; Milder, Jeffrey C; Miller, James R; Morales, Carolina L; Muchane, Mary N; Muchane, Muchai; Naidoo, Robin; Nakamura, Akihiro; Naoe, Shoji; Nates-Parra, Guiomar; Navarrete Gutierrez, Dario A; Neuschulz, Eike L; Noreika, Norbertas; Norfolk, Olivia; Noriega, Jorge Ari; Nöske, Nicole M; O'Dea, Niall; Oduro, William; Ofori-Boateng, Caleb; Oke, Chris O; Osgathorpe, Lynne M; Paritsis, Juan; Parra-H, Alejandro; Pelegrin, Nicolás; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Phalan, Ben; Philips, T Keith; Poveda, Katja; Power, Eileen F; Presley, Steven J; Proença, Vânia; Quaranta, Marino; Quintero, Carolina; Redpath-Downing, Nicola A; Reid, J Leighton; Reis, Yana T; Ribeiro, Danilo B; Richardson, Barbara A; Richardson, Michael J; Robles, Carolina A; Römbke, Jörg; Romero-Duque, Luz Piedad; Rosselli, Loreta; Rossiter, Stephen J; Roulston, T'ai H; Rousseau, Laurent; Sadler, Jonathan P; Sáfián, Szabolcs; Saldaña-Vázquez, Romeo A; Samnegård, Ulrika; Schüepp, Christof; Schweiger, Oliver; Sedlock, Jodi L; Shahabuddin, Ghazala; Sheil, Douglas; Silva, Fernando A B; Slade, Eleanor M; Smith-Pardo, Allan H; Sodhi, Navjot S; Somarriba, Eduardo J; Sosa, Ramón A; Stout, Jane C; Struebig, Matthew J; Sung, Yik-Hei; Threlfall, Caragh G; Tonietto, Rebecca; Tóthmérész, Béla; Tscharntke, Teja; Turner, Edgar C; Tylianakis, Jason M; Vanbergen, Adam J; Vassilev, Kiril; Verboven, Hans A F; Vergara, Carlos H; Vergara, Pablo M; Verhulst, Jort; Walker, Tony R; Wang, Yanping; Watling, James I; Wells, Konstans; Williams, Christopher D; Willig, Michael R; Woinarski, John C Z; Wolf, Jan H D; Woodcock, Ben A; Yu, Douglas W; Zaitsev, Andrey S; Collen, Ben; Ewers, Rob M; Mace, Georgina M; Purves, Drew W; Scharlemann, Jörn P W; Purvis, Andy

    2014-01-01

    Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015. PMID:25558364

  18. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.

    Science.gov (United States)

    Galperin, Michael Y; Cochrane, Guy R

    2009-01-01

    The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  19. Dietary Supplement Ingredient Database

    Science.gov (United States)

    ... and US Department of Agriculture Dietary Supplement Ingredient Database Toggle navigation Menu Home About DSID Mission Current ... values can be saved to build a small database or add to an existing database for national, ...

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

    Science.gov (United States)

    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.

  1. Gis and public health

    CERN Document Server

    Cromley, Ellen K

    2011-01-01

    Authoritative and comprehensive, this is the leading text and professional resource on using geographic information systems (GIS) to analyze and address public health problems. Basic GIS concepts and tools are explained, including ways to access and manage spatial databases. The book presents state-of-the-art methods for mapping and analyzing data on population, health events, risk factors, and health services, and for incorporating geographical knowledge into planning and policy. Numerous maps, diagrams, and real-world applications are featured. The companion Web page provides lab exercises w

  2. The Danish Inguinal Hernia Database

    Directory of Open Access Journals (Sweden)

    Friis-Andersen H

    2016-10-01

    Full Text Available Hans Friis-Andersen1,2, Thue Bisgaard2,3 1Surgical Department, Horsens Regional Hospital, Horsens, Denmark; 2Steering Committee, Danish Hernia Database, 3Surgical Gastroenterological Department 235, Copenhagen University Hospital, Hvidovre, Denmark Aim of database: To monitor and improve nation-wide surgical outcome after groin hernia repair based on scientific evidence-based surgical strategies for the national and international surgical community. Study population: Patients ≥18 years operated for groin hernia. Main variables: Type and size of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. Descriptive data: According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time. All institutions have continuous access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles the medical management of the database. Results: The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015. A total of 49 peer-reviewed national and international publications have been published from the database (June 2015. Conclusion: The Danish Inguinal Hernia Database is fully active monitoring surgical quality and contributes to the national and international surgical society to improve outcome after groin hernia repair. Keywords: nation-wide, recurrence, chronic pain, femoral hernia, surgery, quality improvement

  3. The Danish National Database for Obstructive Sleep Apnea

    DEFF Research Database (Denmark)

    Jennum, Poul Jørgen; Larsen, Preben; Cerqueira, Charlotte

    2016-01-01

    National Patient Registry. STUDY POPULATION: All patients diagnosed with obstructive sleep apnea or obesity hypoventilation syndrome at public and private in- and out-hospital departments in Denmark were included. MAIN VARIABLES: The NDOSA contains information about baseline characteristics, comorbidity......AIM: The aim of the Danish National Database for Obstructive Sleep Apnea (NDOSA) was to evaluate the clinical quality (diagnostic, treatment, and management) for obstructive sleep apnea and obesity hypoventilation syndrome in Denmark using a real-time national database reporting to the Danish...... departments was involved in the management of sleep apnea in Denmark for the purpose of quality improvement. CONCLUSION: The NDOSA has proven to be a real-time national database using diagnostic and treatment procedures reported to the Danish National Patient Registry....

  4. A Consolidated Online Database of Galactic Planetary Nebulae

    CERN Document Server

    Miszalski, B; Ochsenbein, F; Parker, Q A

    2011-01-01

    Since the unifying Strasbourg-ESO Catalogue of Galactic Planetary Nebulae (SECGPN) a large number of new discoveries have been made thanks to improved surveys and discovery techniques. The increasingly heterogeneous published population of Galactic PNe, that we have determined totals < 2850 PNe, is becoming more difficult to study on the whole without a centralised repository. We introduce a consolidated and interactive online database with object classifications that reflect the latest multi-wavelength data and the most recent results. The extensible database, hosted by the Centre de Donnees astronomique de Strasbourg (CDS), will contain a wealth of observed data for large, well-defined samples of PNe including coordinates, multi-wavelength images, spectroscopy, line intensities, radial velocities and central star information. It is anticipated that the database will be publicly released early 2012.

  5. NoSQL Databases

    OpenAIRE

    2013-01-01

    This thesis deals with database systems referred to as NoSQL databases. In the second chapter, I explain basic terms and the theory of database systems. A short explanation is dedicated to database systems based on the relational data model and the SQL standardized query language. Chapter Three explains the concept and history of the NoSQL databases, and also presents database models, major features and the use of NoSQL databases in comparison with traditional database systems. In the fourth ...

  6. Collecting Taxes Database

    Data.gov (United States)

    US Agency for International Development — The Collecting Taxes Database contains performance and structural indicators about national tax systems. The database contains quantitative revenue performance...

  7. Rule-based deduplication of article records from bibliographic databases.

    Science.gov (United States)

    Jiang, Yu; Lin, Can; Meng, Weiyi; Yu, Clement; Cohen, Aaron M; Smalheiser, Neil R

    2014-01-01

    We recently designed and deployed a metasearch engine, Metta, that sends queries and retrieves search results from five leading biomedical databases: PubMed, EMBASE, CINAHL, PsycINFO and the Cochrane Central Register of Controlled Trials. Because many articles are indexed in more than one of these databases, it is desirable to deduplicate the retrieved article records. This is not a trivial problem because data fields contain a lot of missing and erroneous entries, and because certain types of information are recorded differently (and inconsistently) in the different databases. The present report describes our rule-based method for deduplicating article records across databases and includes an open-source script module that can be deployed freely. Metta was designed to satisfy the particular needs of people who are writing systematic reviews in evidence-based medicine. These users want the highest possible recall in retrieval, so it is important to err on the side of not deduplicating any records that refer to distinct articles, and it is important to perform deduplication online in real time. Our deduplication module is designed with these constraints in mind. Articles that share the same publication year are compared sequentially on parameters including PubMed ID number, digital object identifier, journal name, article title and author list, using text approximation techniques. In a review of Metta searches carried out by public users, we found that the deduplication module was more effective at identifying duplicates than EndNote without making any erroneous assignments.

  8. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  9. The Astrobiology Habitable Environments Database (AHED)

    Science.gov (United States)

    Lafuente, B.; Stone, N.; Downs, R. T.; Blake, D. F.; Bristow, T.; Fonda, M.; Pires, A.

    2015-12-01

    The Astrobiology Habitable Environments Database (AHED) is a central, high quality, long-term searchable repository for archiving and collaborative sharing of astrobiologically relevant data, including, morphological, textural and contextural images, chemical, biochemical, isotopic, sequencing, and mineralogical information. The aim of AHED is to foster long-term innovative research by supporting integration and analysis of diverse datasets in order to: 1) help understand and interpret planetary geology; 2) identify and characterize habitable environments and pre-biotic/biotic processes; 3) interpret returned data from present and past missions; 4) provide a citable database of NASA-funded published and unpublished data (after an agreed-upon embargo period). AHED uses the online open-source software "The Open Data Repository's Data Publisher" (ODR - http://www.opendatarepository.org) [1], which provides a user-friendly interface that research teams or individual scientists can use to design, populate and manage their own database according to the characteristics of their data and the need to share data with collaborators or the broader scientific community. This platform can be also used as a laboratory notebook. The database will have the capability to import and export in a variety of standard formats. Advanced graphics will be implemented including 3D graphing, multi-axis graphs, error bars, and similar scientific data functions together with advanced online tools for data analysis (e. g. the statistical package, R). A permissions system will be put in place so that as data are being actively collected and interpreted, they will remain proprietary. A citation system will allow research data to be used and appropriately referenced by other researchers after the data are made public. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, Mars Science Laboratory Investigations. [1] Nate et al. (2015) AGU, submitted.

  10. Mammalian Mitochondrial ncRNA Database.

    Science.gov (United States)

    Anandakumar, Shanmugam; Vijayakumar, Saravanan; Arumugam, Nagarajan; Gromiha, M Michael

    2015-01-01

    Mammalian Mitochondrial ncRNA is a web-based database, which provides specific information on non-coding RNA in mammals. This database includes easy searching, comparing with BLAST and retrieving information on predicted structure and its function about mammalian ncRNAs. The database is available for free at http://www.iitm.ac.in/bioinfo/mmndb/.

  11. Bisphosphonate adverse effects, lessons from large databases

    DEFF Research Database (Denmark)

    Abrahamsen, Bo

    2010-01-01

    PURPOSE OF REVIEW: To review the latest findings on bisphosphonate safety from health databases, in particular sources that can provide incidence rates for stress fractures, osteonecrosis of the jaw (ONJ), atrial fibrillation and gastrointestinal lesions including esophageal cancer. The main focus...... health databases. However, database studies have limited specificity and sensitivity for atypical fractures and ONJ. Clinical case control studies are recommended....

  12. Tourism through Travel Club: A Database Project

    Science.gov (United States)

    Pratt, Renée M. E.; Smatt, Cindi T.; Wynn, Donald E.

    2017-01-01

    This applied database exercise utilizes a scenario-based case study to teach the basics of Microsoft Access and database management in introduction to information systems and introduction to database course. The case includes background information on a start-up business (i.e., Carol's Travel Club), description of functional business requirements,…

  13. A Principled Approach to Online Publication Listings and Scientific Resource Sharing

    Directory of Open Access Journals (Sweden)

    Jacquelijn Ringersma

    2010-03-01

    Full Text Available The Max Planck Institute (MPI for Psycholinguistics has developed a service to manage and present the scholarly output of their researchers. The PubMan database manages publication metadata and full-texts of publications published by their scholars. All relevant information regarding a researcher's work is brought together in this database, including supplementary materials and links to the MPI database for primary research data. The PubMan metadata is harvested into the MPI website CMS (Plone. The system developed for the creation of the publication lists, allows the researcher to create a selection of the harvested data in a variety of formats.

  14. SinEx DB: a database for single exon coding sequences in mammalian genomes.

    Science.gov (United States)

    Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

    2016-01-01

    Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.

  15. Genomic Database Searching.

    Science.gov (United States)

    Hutchins, James R A

    2017-01-01

    The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

  16. ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

    Directory of Open Access Journals (Sweden)

    Moss Gerard P

    2007-07-01

    Full Text Available Abstract Background We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. Description The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. Conclusion ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

  17. Danish Colorectal Cancer Group Database

    DEFF Research Database (Denmark)

    Ingeholm, Peter; Gögenur, Ismail; Iversen, Lene H

    2016-01-01

    , and other pathological risk factors. DESCRIPTIVE DATA: The database has had >95% completeness in including patients with colorectal adenocarcinoma with >54,000 patients registered so far with approximately one-third rectal cancers and two-third colon cancers and an overrepresentation of men among rectal......-term survivals since it started in 2001 for both patients with colon and rectal cancers.......AIM OF DATABASE: The aim of the database, which has existed for registration of all patients with colorectal cancer in Denmark since 2001, is to improve the prognosis for this patient group. STUDY POPULATION: All Danish patients with newly diagnosed colorectal cancer who are either diagnosed...

  18. Security Research on Engineering Database System

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Engine engineering database system is an oriented C AD applied database management system that has the capability managing distributed data. The paper discusses the security issue of the engine engineering database management system (EDBMS). Through studying and analyzing the database security, to draw a series of securi ty rules, which reach B1, level security standard. Which includes discretionary access control (DAC), mandatory access control (MAC) and audit. The EDBMS implem ents functions of DAC, ...

  19. Database Marketing In Travel And Tourism

    OpenAIRE

    Alford, Philip

    1999-01-01

    An increasing number of organisations are developing customer databases in a bid to get closer to their customers and gain competitive advantage. This report investigates the practice of database marketing among different travel and tourism sectors, including airlines, hotels, museums and tour operators, and draws on UK and international examples. It compares direct marketing and database marketing and examines the different levels of sophistication at which database marketing can be practice...

  20. The Danish Smoking Cessation Database

    DEFF Research Database (Denmark)

    Rasmussen, Mette; Tønnesen, Hanne

    2016-01-01

    , place or person working with a preventive aim. There are no age limits for registering a smoker in the database. Data collection: The SCDB contains prospectively collected baseline and outcome data on SC clinics, interventions, and individual smokers. Baseline data include socio-economic, demographic......Background: The Danish Smoking Cessation Database (SCDB) was established in 2001 as the first national healthcare register within the field of health promotion. Aim of the database: The aim of the SCDB is to document and evaluate smoking cessation (SC) interventions to assess and improve...... their quality. The database was also designed to function as a basis for register-based research projects. Study population The population includes smokers in Denmark who have been receiving a face-to-face SC intervention offered by an SC clinic affiliated with the SCDB. SC clinics can be any organisation...

  1. Fish Karyome: A karyological information network database of Indian Fishes.

    Science.gov (United States)

    Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra

    2012-01-01

    'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

  2. The GLENDAMA Database

    CERN Document Server

    Goicoechea, Luis J; Gil-Merino, Rodrigo

    2015-01-01

    This is the first version (v1) of the Gravitational LENses and DArk MAtter (GLENDAMA) database accessible at http://grupos.unican.es/glendama/database. The new database contains more than 6000 ready-to-use (processed) astronomical frames corresponding to 15 objects that fall into three classes: (1) lensed QSO (8 objects), (2) binary QSO (3 objects), and (3) accretion-dominated radio-loud QSO (4 objects). Data are also divided into two categories: freely available and available upon request. The second category includes observations related to our yet unpublished analyses. Although this v1 of the GLENDAMA archive incorporates an X-ray monitoring campaign for a lensed QSO in 2010, the rest of frames (imaging, polarimetry and spectroscopy) were taken with NUV, visible and NIR facilities over the period 1999$-$2014. The monitorings and follow-up observations of lensed QSOs are key tools for discussing the accretion flow in distant QSOs, the redshift and structure of intervening (lensing) galaxies, and the physica...

  3. CMD: a Cotton Microsatellite Database resource for Gossypium genomics

    Directory of Open Access Journals (Sweden)

    Liu Shaolin

    2006-05-01

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

  4. Accessing and using chemical property databases.

    Science.gov (United States)

    Hastings, Janna; Josephs, Zara; Steinbeck, Christoph

    2012-01-01

    Chemical compounds participate in all the processes of life. Understanding the complex interactions of small molecules such as metabolites and drugs and the biological macromolecules that consume and produce them is key to gaining a wider understanding in a systemic context. Chemical property databases collect information on the biological effects and physicochemical properties of chemical entities. Accessing and using such databases is key to understanding the chemistry of toxic molecules. In this chapter, we present methods to search, understand, download, and manipulate the wealth of information available in public chemical property databases, with particular focus on the database of Chemical Entities of Biological Interest (ChEBI).

  5. The Danish Inguinal Hernia database

    DEFF Research Database (Denmark)

    Friis-Andersen, Hans; Bisgaard, Thue

    2016-01-01

    of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. DESCRIPTIVE DATA: According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time). All institutions have continuous...... access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles...... the medical management of the database. RESULTS: The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015). A total of 49 peer-reviewed national and international publications have been published from the database (June 2015). CONCLUSION: The Danish Inguinal Hernia...

  6. Searching NCBI Databases Using Entrez.

    Science.gov (United States)

    Gibney, Gretchen; Baxevanis, Andreas D

    2011-10-01

    One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  7. Quantifying the consistency of scientific databases

    CERN Document Server

    Šubelj, Lovro; Boshkoska, Biljana Mileva; Kastrin, Andrej; Levnajić, Zoran

    2015-01-01

    Science is a social process with far-reaching impact on our modern society. In the recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific publications that is increasingly becoming available. The data is contained in several databases such as Web of Science or PubMed, maintained by various public and private entities. Unfortunately, these databases are not always consistent, which considerably hinders this study. Relying on the powerful framework of complex networks, we conduct a systematic analysis of the consistency among six major scientific databases. We found that identifying a single "best" database is far from easy. Nevertheless, our results indicate appreciable differences in mutual consistency of different databases, which we interpret as recipes for future bibliometric studies.

  8. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

    Energy Technology Data Exchange (ETDEWEB)

    Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

    2005-08-13

    HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan

  9. The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection.

    Science.gov (United States)

    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/).

  10. Cloud Databases: A Paradigm Shift in Databases

    Directory of Open Access Journals (Sweden)

    Indu Arora

    2012-07-01

    Full Text Available Relational databases ruled the Information Technology (IT industry for almost 40 years. But last few years have seen sea changes in the way IT is being used and viewed. Stand alone applications have been replaced with web-based applications, dedicated servers with multiple distributed servers and dedicated storage with network storage. Cloud computing has become a reality due to its lesser cost, scalability and pay-as-you-go model. It is one of the biggest changes in IT after the rise of World Wide Web. Cloud databases such as Big Table, Sherpa and SimpleDB are becoming popular. They address the limitations of existing relational databases related to scalability, ease of use and dynamic provisioning. Cloud databases are mainly used for data-intensive applications such as data warehousing, data mining and business intelligence. These applications are read-intensive, scalable and elastic in nature. Transactional data management applications such as banking, airline reservation, online e-commerce and supply chain management applications are write-intensive. Databases supporting such applications require ACID (Atomicity, Consistency, Isolation and Durability properties, but these databases are difficult to deploy in the cloud. The goal of this paper is to review the state of the art in the cloud databases and various architectures. It further assesses the challenges to develop cloud databases that meet the user requirements and discusses popularly used Cloud databases.

  11. 78 FR 15706 - Fisheries of the Gulf of Mexico; Southeast Data, Assessment, and Review (SEDAR); Public Meetings

    Science.gov (United States)

    2013-03-12

    ... Data, Assessment, and Review (SEDAR); Public Meetings AGENCY: National Marine Fisheries Service (NMFS... Management Councils, in conjunction with NOAA Fisheries and the Atlantic and Gulf States Marine Fisheries.... Participants include: data collectors and database managers; stock assessment scientists, biologists, and...

  12. Database tomography for commercial application

    Science.gov (United States)

    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.

  13. NORPERM, the Norwegian Permafrost Database - a TSP NORWAY IPY legacy

    Science.gov (United States)

    Juliussen, H.; Christiansen, H. H.; Strand, G. S.; Iversen, S.; Midttømme, K.; Rønning, J. S.

    2010-10-01

    NORPERM, the Norwegian Permafrost Database, was developed at the Geological Survey of Norway during the International Polar Year (IPY) 2007-2009 as the main data legacy of the IPY research project Permafrost Observatory Project: A Contribution to the Thermal State of Permafrost in Norway and Svalbard (TSP NORWAY). Its structural and technical design is described in this paper along with the ground temperature data infrastructure in Norway and Svalbard, focussing on the TSP NORWAY permafrost observatory installations in the North Scandinavian Permafrost Observatory and Nordenskiöld Land Permafrost Observatory, being the primary data providers of NORPERM. Further developments of the database, possibly towards a regional database for the Nordic area, are also discussed. The purpose of NORPERM is to store ground temperature data safely and in a standard format for use in future research. The IPY data policy of open, free, full and timely release of IPY data is followed, and the borehole metadata description follows the Global Terrestrial Network for Permafrost (GTN-P) standard. NORPERM is purely a temperature database, and the data is stored in a relation database management system and made publically available online through a map-based graphical user interface. The datasets include temperature time series from various depths in boreholes and from the air, snow cover, ground-surface or upper ground layer recorded by miniature temperature data-loggers, and temperature profiles with depth in boreholes obtained by occasional manual logging. All the temperature data from the TSP NORWAY research project is included in the database, totalling 32 temperature time series from boreholes, 98 time series of micrometeorological temperature conditions, and 6 temperature depth profiles obtained by manual logging in boreholes. The database content will gradually increase as data from previous and future projects are added. Links to near real-time permafrost temperatures, obtained

  14. Logical database design principles

    CERN Document Server

    Garmany, John; Clark, Terry

    2005-01-01

    INTRODUCTION TO LOGICAL DATABASE DESIGNUnderstanding a Database Database Architectures Relational Databases Creating the Database System Development Life Cycle (SDLC)Systems Planning: Assessment and Feasibility System Analysis: RequirementsSystem Analysis: Requirements Checklist Models Tracking and Schedules Design Modeling Functional Decomposition DiagramData Flow Diagrams Data Dictionary Logical Structures and Decision Trees System Design: LogicalSYSTEM DESIGN AND IMPLEMENTATION The ER ApproachEntities and Entity Types Attribute Domains AttributesSet-Valued AttributesWeak Entities Constraint

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

    Science.gov (United States)

    Vihinen, Mauno

    2016-10-01

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

  16. On-Line Databases in Mexico.

    Science.gov (United States)

    Molina, Enzo

    1986-01-01

    Use of online bibliographic databases in Mexico is provided through Servicio de Consulta a Bancos de Informacion, a public service that provides information retrieval, document delivery, translation, technical support, and training services. Technical infrastructure is based on a public packet-switching network and institutional users may receive…

  17. Village Green Project: Web-accessible Database

    Science.gov (United States)

    The purpose of this web-accessible database is for the public to be able to view instantaneous readings from a solar-powered air monitoring station located in a public location (prototype pilot test is outside of a library in Durham County, NC). The data are wirelessly transmitte...

  18. The Danish Inguinal Hernia database

    Science.gov (United States)

    Friis-Andersen, Hans; Bisgaard, Thue

    2016-01-01

    Aim of database To monitor and improve nation-wide surgical outcome after groin hernia repair based on scientific evidence-based surgical strategies for the national and international surgical community. Study population Patients ≥18 years operated for groin hernia. Main variables Type and size of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. Descriptive data According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time). All institutions have continuous access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles the medical management of the database. Results The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015). A total of 49 peer-reviewed national and international publications have been published from the database (June 2015). Conclusion The Danish Inguinal Hernia Database is fully active monitoring surgical quality and contributes to the national and international surgical society to improve outcome after groin hernia repair. PMID:27822094

  19. Relationship between public subsidies and vaccination rates with the 23-valent pneumococcal vaccine in elderly persons, including the influence of the free vaccination campaign after the Great East Japan Earthquake.

    Science.gov (United States)

    Naito, Toshio; Matsuda, Naoto; Tanei, Mika; Watanabe, Yukiko; Watanabe, Akira

    2014-07-01

    Low vaccination rates with pneumococcal vaccine in elderly persons in Japan are thought to be related to low levels of public subsidy. To identify strategies to increase future pneumococcal vaccination rates, we examined the relationship between public subsidies and vaccination rates. We also investigated the influence of free vaccinations after the 2011 Great East Japan Earthquake on vaccination rates in the three Tohoku prefectures of Japan. We surveyed a total of 1742 municipalities in Japan about whether public subsidies were available and their monetary amount. Vaccination rates with the 23-valent pneumococcal vaccine were calculated as the "cumulative amount shipped to each municipality divided by the population aged ≥65 years." There were no subsidies in 773 municipalities (44.4%). In those municipalities with public subsidies, larger subsidies were significantly associated with elevated vaccination rates (p Japan, the vaccination rate was 52.1% in municipalities where the full cost was subsidized. The three prefectures (Iwate, Miyagi, and Fukushima) most affected by the Great East Japan Earthquake ranked as the top three prefectures for vaccination rates in Japan, presumably as a result of the free vaccination campaign for disaster victims. Our findings show that public subsidies play an important role in increasing the vaccination rate. The free vaccinations given to disaster victims after the Great East Japan Earthquake helped to achieve extremely high vaccination rates in the three Tohoku prefectures. We suggest that such public subsidies should be promoted throughout Japan.

  20. Publication misrepresentation among anesthesiology residency applicants.

    Science.gov (United States)

    Neuman, Stephanie A; Long, Timothy R; Rose, Steven H

    2011-03-01

    Publication misrepresentation has been documented among applicants for residency positions in several specialties. However, these data are not available for anesthesiology applicants. Our purpose in this study was to document the prevalence of publication misrepresentation among applicants to a single anesthesiology residency, to compare anesthesiology publication misrepresentation data with similar data in other specialties, and to determine how often publication misrepresentation leads to an unfair competitive advantage in the application process. Applications to the Mayo School of Graduate Medical Education anesthesiology core residency in Rochester, Minnesota, were reviewed for publication misrepresentations using Medline and PubMed databases, Mayo Clinic library databases, and/or review by a qualified medical librarian. Misrepresented publications underwent further review to identify fraudulent publications and/or citation errors that provide an unfair competitive advantage. The authors found that 2.4% of the applications (13 of 532) included fraudulent publications, 6.6% of the applications with at least 1 publication (13 of 197) included ≥1 that was fraudulent, and 2.9% of all cited publications (15 of 522) were fraudulent. In addition, 0.9% of the applications (5 of 532) contained a citation error that, although not grossly fraudulent, could have favorably affected the applicant's competitiveness for a residency position. Misrepresented publications were fairly common among anesthesiology residency applicants. However, only a small percentage of applicants listed misrepresented publications that were clearly fraudulent or contained a citation error that conferred a competitive advantage. Identification of fraudulent publications on Electronic Residency Application Service applications is important to maintain the integrity of the application process.

  1. Overview of selected molecular biological databases

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. SoyFN: a knowledge database of soybean functional networks.

    Science.gov (United States)

    Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

    2014-01-01

    Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

  3. National Administrative Databases in Adult Spinal Deformity Surgery: A Cautionary Tale.

    Science.gov (United States)

    Buckland, Aaron J; Poorman, Gregory; Freitag, Robert; Jalai, Cyrus; Klineberg, Eric O; Kelly, Michael; Passias, Peter G

    2017-08-15

    Comparison between national administrative databases and a prospective multicenter physician managed database. This study aims to assess the applicability of National Administrative Databases (NADs) in adult spinal deformity (ASD). Our hypothesis is that NADs do not include comparable patients as in a physician-managed database (PMD) for surgical outcomes in adult spinal deformity. NADs such as National Inpatient Sample (NIS) and National Surgical Quality Improvement Program (NSQIP) provide large numbers of publications owing to ease of data access and lack of IRB approval requirement. These databases utilize billing codes, not clinical inclusion criteria, and have not been validated against PMDs in ASD surgery. The NIS was searched for years 2002 to 2012 and NSQIP for years 2006 to 2013 using validated spinal deformity diagnostic codes. Procedural codes (ICD-9 and CPT) were then applied to each database. A multicenter PMD including years 2008 to 2015 was used for comparison. Databases were assessed for levels fused, osteotomies, decompressed levels, and invasiveness. Database comparisons for surgical details were made in all patients, and also for patients with ≥ 5 level spinal fusions. Approximately, 37,368 NIS, 1291 NSQIP, and 737 PMD patients were identified. NADs showed an increased use of deformity billing codes over the study period (NIS doubled, 68x NSQIP, P databases (6.4-12.7) compared with PMD (27.5-32.3). When limited to patients with ≥5 levels, invasiveness, levels fused, and use of 3-CO remained significantly higher in the PMD compared with NADs (P databases NIS and NSQIP do not capture the same patient population as is captured in PMDs in ASD. Physicians should remain cautious in interpreting conclusions drawn from these databases. 4.

  4. SmallSat Database

    Science.gov (United States)

    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

  5. Database Description - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RMOS Database Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...e Microarray Opening Site is a database of comprehensive information for Rice Mic...es and manner of utilization of database You can refer to the information of the

  6. 40 CFR 1400.13 - Read-only database.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of...

  7. Building Database-Powered Mobile Applications

    Directory of Open Access Journals (Sweden)

    Paul POCATILU

    2012-01-01

    Full Text Available Almost all mobile applications use persistency for their data. A common way for complex mobile applications is to store data in local relational databases. Almost all major mobile platforms include a relational database engine. These databases engines expose specific API (Application Programming Interface to be used by mobile applications developers for data definition and manipulation. This paper focus on database-based application models for several mobile platforms (Android, Symbian, Windows CE/Mobile and Windows Phone. For each selected platform the API and specific database operations are presented.

  8. Database design and SQL for DB2

    CERN Document Server

    Cooper, James

    2013-01-01

    Thorough and updated coverage of database design and SQL for DB2 are the focus of this guide for the relational database-management system used on IBM i computer systems. Suitable for classroom instruction or self-study, this book explains the most widely used database language and the way that language is implemented on a variety of computer platforms. Topics covered include database concepts, SQL inquiries, web applications, and database security, and the material is reinforced by numerous illustrations, examples, and exercises.

  9. Creating databases for biological information: an introduction.

    Science.gov (United States)

    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.

  10. Advancements in web-database applications for rabies surveillance

    Directory of Open Access Journals (Sweden)

    Bélanger Denise

    2011-08-01

    Full Text Available Abstract Background Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. Results RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include 1 automatic integration of multi-agency data and diagnostic results on a daily basis; 2 a web-based data editing interface that enables authorized users to add, edit and extract data; and 3 an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. Conclusions RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from

  11. Network and Database Security: Regulatory Compliance, Network, and Database Security - A Unified Process and Goal

    Directory of Open Access Journals (Sweden)

    Errol A. Blake

    2007-12-01

    Full Text Available Database security has evolved; data security professionals have developed numerous techniques and approaches to assure data confidentiality, integrity, and availability. This paper will show that the Traditional Database Security, which has focused primarily on creating user accounts and managing user privileges to database objects are not enough to protect data confidentiality, integrity, and availability. This paper is a compilation of different journals, articles and classroom discussions will focus on unifying the process of securing data or information whether it is in use, in storage or being transmitted. Promoting a change in Database Curriculum Development trends may also play a role in helping secure databases. This paper will take the approach that if one make a conscientious effort to unifying the Database Security process, which includes Database Management System (DBMS selection process, following regulatory compliances, analyzing and learning from the mistakes of others, Implementing Networking Security Technologies, and Securing the Database, may prevent database breach.

  12. Danish Palliative Care Database

    Directory of Open Access Journals (Sweden)

    Groenvold M

    2016-10-01

    Full Text Available Mogens Groenvold,1,2 Mathilde Adsersen,1 Maiken Bang Hansen1 1The Danish Palliative Care Database (DPD Secretariat, Research Unit, Department of Palliative Medicine, Bispebjerg Hospital, 2Department of Public Health, University of Copenhagen, Copenhagen, Denmark Aims: The aim of the Danish Palliative Care Database (DPD is to monitor, evaluate, and improve the clinical quality of specialized palliative care (SPC (ie, the activity of hospital-based palliative care teams/departments and hospices in Denmark. Study population: The study population is all patients in Denmark referred to and/or in contact with SPC after January 1, 2010. Main variables: The main variables in DPD are data about referral for patients admitted and not admitted to SPC, type of the first SPC contact, clinical and sociodemographic factors, multidisciplinary conference, and the patient-reported European Organisation for Research and Treatment of Cancer Quality of Life Questionaire-Core-15-Palliative Care questionnaire, assessing health-related quality of life. The data support the estimation of currently five quality of care indicators, ie, the proportions of 1 referred and eligible patients who were actually admitted to SPC, 2 patients who waited <10 days before admission to SPC, 3 patients who died from cancer and who obtained contact with SPC, 4 patients who were screened with European Organisation for Research and Treatment of Cancer Quality of Life Questionaire-Core-15-Palliative Care at admission to SPC, and 5 patients who were discussed at a multidisciplinary conference. Descriptive data: In 2014, all 43 SPC units in Denmark reported their data to DPD, and all 9,434 cancer patients (100% referred to SPC were registered in DPD. In total, 41,104 unique cancer patients were registered in DPD during the 5 years 2010–2014. Of those registered, 96% had cancer. Conclusion: DPD is a national clinical quality database for SPC having clinically relevant variables and high data

  13. Curation accuracy of model organism databases.

    Science.gov (United States)

    Keseler, Ingrid M; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C; Mladinich, Katherine M; Chow, Edmond D; Sherlock, Gavin; Karp, Peter D

    2014-01-01

    Manual extraction of information from the biomedical literature-or biocuration-is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org//

  14. Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)

    Energy Technology Data Exchange (ETDEWEB)

    Timothy R. Carr; Scott W. White

    2002-06-01

    This annual report describes progress of the project entitled ''Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)''. This project, funded by the Department of Energy, is a cooperative project that assembles a consortium of five states (Indiana, Illinois, Kansas, Kentucky and Ohio) to construct an online distributed Relational Database Management System (RDBMS) and Geographic Information System (GIS) covering aspects of carbon dioxide geologic sequestration (http://www.midcarb.org). The system links the five states in the consortium into a coordinated regional database system consisting of datasets useful to industry, regulators and the public. The project is working to provide advanced distributed computing solutions to link database servers across the five states into a single system where data is maintained at the local level but is accessed through a single Web portal and can be queried, assembled, analyzed and displayed. Each individual state has strengths in data gathering, data manipulation and data display, including GIS mapping, custom application development, web development, and database design. Sharing of expertise provides the critical mass of technical expertise to improve CO{sub 2} databases and data access in all states. This project improves the flow of data across servers in the five states and increases the amount and quality of available digital data. The MIDCARB project is developing improved online tools to provide real-time display and analyze CO{sub 2} sequestration data. The system links together data from sources, sinks and transportation within a spatial database that can be queried online. Visualization of high quality and current data can assist decision makers by providing access to common sets of high quality data in a consistent manner.

  15. Medical databases in studies of drug teratogenicity: methodological issues

    Directory of Open Access Journals (Sweden)

    Vera Ehrenstein

    2010-03-01

    Full Text Available Vera Ehrenstein1, Henrik T Sørensen1, Leiv S Bakketeig1,2, Lars Pedersen11Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark; 2Norwegian Institute of Public Health, Oslo, NorwayAbstract: More than half of all pregnant women take prescription medications, raising concerns about fetal safety. Medical databases routinely collecting data from large populations are potentially valuable resources for cohort studies addressing teratogenicity of drugs. These include electronic medical records, administrative databases, population health registries, and teratogenicity information services. Medical databases allow estimation of prevalences of birth defects with enhanced precision, but systematic error remains a potentially serious problem. In this review, we first provide a brief description of types of North American and European medical databases suitable for studying teratogenicity of drugs and then discuss manifestation of systematic errors in teratogenicity studies based on such databases. Selection bias stems primarily from the inability to ascertain all reproductive outcomes. Information bias (misclassification may be caused by paucity of recorded clinical details or incomplete documentation of medication use. Confounding, particularly confounding by indication, can rarely be ruled out. Bias that either masks teratogenicity or creates false appearance thereof, may have adverse consequences for the health of the child and the mother. Biases should be quantified and their potential impact on the study results should be assessed. Both theory and software are available for such estimation. Provided that methodological problems are understood and effectively handled, computerized medical databases are a valuable source of data for studies of teratogenicity of drugs.Keywords: databases, birth defects, epidemiologic methods, pharmacoepidemiology

  16. E3 Staff Database

    Data.gov (United States)

    US Agency for International Development — E3 Staff database is maintained by E3 PDMS (Professional Development & Management Services) office. The database is Mysql. It is manually updated by E3 staff as...

  17. Physiological Information Database (PID)

    Science.gov (United States)

    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...

  18. Database Urban Europe

    NARCIS (Netherlands)

    Sleutjes, B.; de Valk, H.A.G.

    2016-01-01

    Database Urban Europe: ResSegr database on segregation in The Netherlands. Collaborative research on residential segregation in Europe 2014–2016 funded by JPI Urban Europe (Joint Programming Initiative Urban Europe).

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

    Science.gov (United States)

    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…

  20. The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.

    Science.gov (United States)

    Cochrane, Guy R; Galperin, Michael Y

    2010-01-01

    The current issue of Nucleic Acids Research includes descriptions of 58 new and 73 updated data resources. The accompanying online Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, now lists 1230 carefully selected databases covering various aspects of molecular and cell biology. While most data resource descriptions remain very brief, the issue includes several longer papers that highlight recent significant developments in such databases as Pfam, MetaCyc, UniProt, ELM and PDBe. The databases described in the Database Issue and Database Collection, however, are far more than a distinct set of resources; they form a network of connected data, concepts and shared technology. The full content of the Database Issue is available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  1. Future database machine architectures

    OpenAIRE

    Hsiao, David K.

    1984-01-01

    There are many software database management systems available on many general-purpose computers ranging from micros to super-mainframes. Database machines as backened computers can offload the database management work from the mainframe so that we can retain the same mainframe longer. However, the database backend must also demonstrate lower cost, higher performance, and newer functionality. Some of the fundamental architecture issues in the design of high-performance and great-capacity datab...

  2. MPlus Database system

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Multi databases in Health Care Networks

    CERN Document Server

    Salih, Nadir K; Sun, Mingrui

    2011-01-01

    E-Health is a relatively recent term for healthcare practice supported by electronic processes and communication, dating back to at least 1999. E-Health is greatly impacting on information distribution and availability within the health services, hospitals and to the public. E-health was introduced as the death of telemedicine, because - in the context of a broad availability of medical information systems that can interconnect and communicate - telemedicine will no longer exist as a specific field. The same could also be said for any other traditional field in medical informatics, including information systems and electronic patient records. E-health presents itself as a common name for all such technological fields. In this paper we focuses in multi database by determined some sites and distributed it in Homogenous way. This will be followed by an illustrative example as related works. Finally, the paper concludes with general remarks and a statement of further work.

  4. CTD_DATABASE - Cascadia tsunami deposit database

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have...

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

    Science.gov (United States)

    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/).

  6. Asbestos Exposure Assessment Database

    Science.gov (United States)

    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.

  7. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    OpenAIRE

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10...

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

    Science.gov (United States)

    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/).

  9. Steviol glycoside safety: is the genotoxicity database sufficient?

    Science.gov (United States)

    Urban, J D; Carakostas, M C; Brusick, D J

    2013-01-01

    The safety of steviol glycoside sweeteners has been extensively reviewed in the literature. National and international food safety agencies and approximately 20 expert panels have concluded that steviol glycosides, including the widely used sweeteners stevioside and rebaudioside A, are not genotoxic. However, concern has been expressed in recent publications that steviol glycosides may be mutagenic based on select studies representing a small fraction of the overall database, and it has been suggested that further in vivo genotoxicity studies are required to complete their safety profiles. To address the utility of conducting additional in vivo genotoxicity studies, this review evaluates the specific genotoxicity studies that are the sources of concern, and evaluates the adequacy of the database including more recent genotoxicity data not mentioned in those publications. The current database of in vitro and in vivo studies for steviol glycosides is robust and does not indicate that either stevioside or rebaudioside A are genotoxic. This, combined with a lack of evidence for neoplasm development in rat bioassays, establish the safety of all steviol glycosides with respect to their genotoxic/carcinogenic potential.

  10. Database Description - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Trypanosomes Database... Database Description General information of database Database name Trypanosomes Database...rmation and Systems Yata 1111, Mishima, Shizuoka 411-8540, JAPAN E mail: Database... classification Protein sequence databases Organism Taxonomy Name: Trypanosoma Taxonomy ID: 5690 Taxonomy Na...me: Homo sapiens Taxonomy ID: 9606 Database description The Trypanosomes database is a database providing th

  11. Database Description - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PLACE Database... Description General information of database Database name A Database of Plant Cis-acting Regu...araki 305-8602, Japan National Institute of Agrobiological Sciences E-mail : Database classification Plant database...s Organism Taxonomy Name: Tracheophyta Taxonomy ID: 58023 Database description PLACE is a database of... motifs found in plant cis-acting regulatory DNA elements based on previously pub

  12. Specialized microbial databases for inductive exploration of microbial genome sequences

    Directory of Open Access Journals (Sweden)

    Cabau Cédric

    2005-02-01

    Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

  13. Problemas multiplicativos envolvendo combinatória: estratégias de resolução empregadas por alunos do Ensino Fundamental público Multiplicative problems including combinatorics: solving strategies adopted by Public Elementary School students

    Directory of Open Access Journals (Sweden)

    Leny R. M. Teixeira

    2011-01-01

    Full Text Available Neste trabalho apresentamos os dados de uma pesquisa que teve por objetivo verificar o desempenho de alunos do 6.° ao 9.° anos do Ensino Fundamental na resolução de oito problemas multiplicativos, envolvendo raciocínio combinatório. Os problemas diferiam em relação à quantidade de variáveis e à quantidade de algarismos utilizados nos fatores. Para tanto, por meio de uma entrevista clínica levantamos as principais estratégias e erros produzidos por 40 alunos de duas escolas públicas (A e B da cidade de Campo Grande-MS, as quais fizeram parte de uma pesquisa mais ampla realizada anteriormente. Os dados revelam que o desempenho foi melhor nos problemas com duas variáveis e com fatores de valores baixos, não havendo diferença de desempenho entre alunos do 6.° e do 9.° anos. De modo geral, as dificuldades que emergiram estavam relacionadas: 1 aos modelos intuitivos que os alunos têm a respeito da multiplicação (em especial o da soma repetida; 2 a estrutura semântica do problema; 3 as preferências numéricas quanto ao tamanho dos números, formas de representar o problema e interpretação do enunciado verbal. Por ser a multiplicação uma operação bastante complexa envolvendo, em sua resolução, processos cognitivos abstratos, acreditamos que o professor precisa conhecê-los para favorecer a aprendizagem dos alunos.This work presents data from a study which aimed at verifying the performance of Elementary School 6th and 9th graders when solving eight multiplicative problems involving combinatorial thinking. The problems were different concerning the amount of variables and the amount of numerical digits used in factors. Therefore, through a clinical interview, we listed the main strategies and mistakes produced by 40 graders from two public schools (A and B in the municipality of Campo Grande (Mato Grosso do Sul - MS - State which were part of a larger research developed before. The observations reveal that the performance

  14. EuPathDB: the eukaryotic pathogen genomics database resource

    Science.gov (United States)

    Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

    2017-01-01

    The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

  15. EuPathDB: the eukaryotic pathogen genomics database resource.

    Science.gov (United States)

    Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y; Brestelli, John; Brunk, Brian P; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C; Lawrence, Cris; Li, Wei; Pinney, Deborah F; Pulman, Jane A; Roos, David S; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

    2017-01-04

    The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host-pathogen interactions.

  16. The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

    Science.gov (United States)

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

    2015-01-01

    The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  17. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  18. 1962 Satellite High Altitude Radiation Belt Database

    Science.gov (United States)

    2014-03-01

    TR-14-18 1962 Satellite High Altitude Radiation Belt Database Approved for public release; distribution is unlimited. March...the Status of the High Altitude Nuclear Explosion (HANE) Trapped Radiation Belt Database”, AFRL-VS-PS-TR- 2006-1079, Air Force Research Laboratory...Roth, B., “Blue Ribbon Panel and Support Work Assessing the Status of the High Altitude Nuclear Explosion (HANE) Trapped Radiation Belt Database

  19. The Histone Database: an integrated resource for histones and histone fold-containing proteins.

    Science.gov (United States)

    Mariño-Ramírez, Leonardo; Levine, Kevin M; Morales, Mario; Zhang, Suiyuan; Moreland, R Travis; Baxevanis, Andreas D; Landsman, David

    2011-01-01

    Eukaryotic chromatin is composed of DNA and protein components-core histones-that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins.

  20. The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

    Science.gov (United States)

    Galperin, Michael Y; Cochrane, Guy R

    2011-01-01

    The current 18th Database Issue of Nucleic Acids Research features descriptions of 96 new and 83 updated online databases covering various areas of molecular biology. It includes two editorials, one that discusses COMBREX, a new exciting project aimed at figuring out the functions of the 'conserved hypothetical' proteins, and one concerning BioDBcore, a proposed description of the 'minimal information about a biological database'. Papers from the members of the International Nucleotide Sequence Database collaboration (INSDC) describe each of the participating databases, DDBJ, ENA and GenBank, principles of data exchange within the collaboration, and the recently established Sequence Read Archive. A testament to the longevity of databases, this issue includes updates on the RNA modification database, Definition of Secondary Structure of Proteins (DSSP) and Homology-derived Secondary Structure of Proteins (HSSP) databases, which have not been featured here in >12 years. There is also a block of papers describing recent progress in protein structure databases, such as Protein DataBank (PDB), PDB in Europe (PDBe), CATH, SUPERFAMILY and others, as well as databases on protein structure modeling, protein-protein interactions and the organization of inter-protein contact sites. Other highlights include updates of the popular gene expression databases, GEO and ArrayExpress, several cancer gene databases and a detailed description of the UK PubMed Central project. The Nucleic Acids Research online Database Collection, available at: http://www.oxfordjournals.org/nar/database/a/, now lists 1330 carefully selected molecular biology databases. The full content of the Database Issue is freely available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  1. The UCSC Genome Browser Database

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  2. The National Land Cover Database

    Science.gov (United States)

    Homer, Collin H.; Fry, Joyce A.; Barnes, Christopher A.

    2012-01-01

    The National Land Cover Database (NLCD) serves as the definitive Landsat-based, 30-meter resolution, land cover database for the Nation. NLCD provides spatial reference and descriptive data for characteristics of the land surface such as thematic class (for example, urban, agriculture, and forest), percent impervious surface, and percent tree canopy cover. NLCD supports a wide variety of Federal, State, local, and nongovernmental applications that seek to assess ecosystem status and health, understand the spatial patterns of biodiversity, predict effects of climate change, and develop land management policy. NLCD products are created by the Multi-Resolution Land Characteristics (MRLC) Consortium, a partnership of Federal agencies led by the U.S. Geological Survey. All NLCD data products are available for download at no charge to the public from the MRLC Web site: http://www.mrlc.gov.

  3. ASEAN Mineral Database and Information System (AMDIS)

    Science.gov (United States)

    Okubo, Y.; Ohno, T.; Bandibas, J. C.; Wakita, K.; Oki, Y.; Takahashi, Y.

    2014-12-01

    AMDIS has lunched officially since the Fourth ASEAN Ministerial Meeting on Minerals on 28 November 2013. In cooperation with Geological Survey of Japan, the web-based GIS was developed using Free and Open Source Software (FOSS) and the Open Geospatial Consortium (OGC) standards. The system is composed of the local databases and the centralized GIS. The local databases created and updated using the centralized GIS are accessible from the portal site. The system introduces distinct advantages over traditional GIS. Those are a global reach, a large number of users, better cross-platform capability, charge free for users, charge free for provider, easy to use, and unified updates. Raising transparency of mineral information to mining companies and to the public, AMDIS shows that mineral resources are abundant throughout the ASEAN region; however, there are many datum vacancies. We understand that such problems occur because of insufficient governance of mineral resources. Mineral governance we refer to is a concept that enforces and maximizes the capacity and systems of government institutions that manages minerals sector. The elements of mineral governance include a) strengthening of information infrastructure facility, b) technological and legal capacities of state-owned mining companies to fully-engage with mining sponsors, c) government-led management of mining projects by supporting the project implementation units, d) government capacity in mineral management such as the control and monitoring of mining operations, and e) facilitation of regional and local development plans and its implementation with the private sector.

  4. DASHR: database of small human noncoding RNAs.

    Science.gov (United States)

    Leung, Yuk Yee; Kuksa, Pavel P; Amlie-Wolf, Alexandre; Valladares, Otto; Ungar, Lyle H; Kannan, Sampath; Gregory, Brian D; Wang, Li-San

    2016-01-01

    Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs. Here, we present the Database of small human noncoding RNAs (DASHR). DASHR contains the most comprehensive information to date on human sncRNA genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). Currently, DASHR (v1.0) integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data from multiple public sources. DASHR contains annotations for ∼ 48,000 human sncRNA genes and mature sncRNA products, 82% of which are expressed in one or more of the curated tissues. DASHR is available at http://lisanwanglab.org/DASHR.

  5. Continuous Reliability Enhancement for Wind (CREW) database :

    Energy Technology Data Exchange (ETDEWEB)

    Hines, Valerie Ann-Peters; Ogilvie, Alistair B.; Bond, Cody R.

    2013-09-01

    To benchmark the current U.S. wind turbine fleet reliability performance and identify the major contributors to component-level failures and other downtime events, the Department of Energy funded the development of the Continuous Reliability Enhancement for Wind (CREW) database by Sandia National Laboratories. This report is the third annual Wind Plant Reliability Benchmark, to publically report on CREW findings for the wind industry. The CREW database uses both high resolution Supervisory Control and Data Acquisition (SCADA) data from operating plants and Strategic Power Systems ORAPWindª (Operational Reliability Analysis Program for Wind) data, which consist of downtime and reserve event records and daily summaries of various time categories for each turbine. Together, these data are used as inputs into CREWs reliability modeling. The results presented here include: the primary CREW Benchmark statistics (operational availability, utilization, capacity factor, mean time between events, and mean downtime); time accounting from an availability perspective; time accounting in terms of the combination of wind speed and generation levels; power curve analysis; and top system and component contributors to unavailability.

  6. Comprehensive Thematic T-Matrix Reference Database: A 2014-2015 Update

    Science.gov (United States)

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

    2015-01-01

    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.

  7. Comprehensive Thematic T-Matrix Reference Database: A 2015-2017 Update

    Science.gov (United States)

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

    2017-01-01

    The T-matrix method pioneered by Peter C. Waterman is one of the most versatile and efficient numerically exact computer solvers of the time-harmonic macroscopic Maxwell equations. It is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, periodic structures (including metamaterials), and particles in the vicinity of plane or rough interfaces separating media with different refractive indices. This paper is the eighth update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated in 2004 and lists relevant publications that have appeared since 2015. It also references a small number of earlier publications overlooked previously.

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

    Science.gov (United States)

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

    2011-01-01

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

  9. Knowledge discovery from legal databases

    CERN Document Server

    Stranieri, Andrew; Schauer, Frederick

    2006-01-01

    Knowledge Discovery from Legal Databases is the first text to describe data mining techniques as they apply to law. Law students, legal academics and applied information technology specialists are guided thorough all phases of the knowledge discovery from databases process with clear explanations of numerous data mining algorithms including rule induction, neural networks and association rules. Throughout the text, assumptions that make data mining in law quite different to mining other data are made explicit.  Issues such as the selection of commonplace cases, the use of discretion as a form

  10. PDS: A Performance Database Server

    Directory of Open Access Journals (Sweden)

    Michael W. Berry

    1994-01-01

    Full Text Available The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallel benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.

  11. An automated system for terrain database construction

    Science.gov (United States)

    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.

  12. Vector database for vehicle road navigation

    OpenAIRE

    Kenda, Lian

    2007-01-01

    Vehicle navigation devices use vector cartographic view, which is designed as a vector database. Database creation begins by setting up a landscape model which includes all the graphical and descriptive data required for accurate vehicle navigation. This paper presents the creation of a database part called StreetConnect, which is used for road navigation. Data obtained using distinct specifications have been transformed into the format compatible with Garmin GPS devices. Data have been obtai...

  13. UPI: A Primary Index for Uncertain Databases

    OpenAIRE

    Kimura, Hideaki; Madden, Samuel R.; Zdonik, Stanley B.

    2010-01-01

    Uncertain data management has received growing attention from industry and academia. Many efforts have been made to optimize uncertain databases, including the development of special index data structures. However, none of these efforts have explored primary (clustered) indexes for uncertain databases, despite the fact that clustering has the potential to offer substantial speedups for non-selective analytic queries on large uncertain databases. In this paper, we propose a new index called a ...

  14. The Danish Prostate Cancer Database

    DEFF Research Database (Denmark)

    Nguyen-Nielsen, Mary; Høyer, Søren; Friis, Søren

    2016-01-01

    AIM OF DATABASE: The Danish Prostate Cancer Database (DAPROCAdata) is a nationwide clinical cancer database that has prospectively collected data on patients with incident prostate cancer in Denmark since February 2010. The overall aim of the DAPROCAdata is to improve the quality of prostate cancer...... care in Denmark by systematically collecting key clinical variables for the purposes of health care monitoring, quality improvement, and research. STUDY POPULATION: All Danish patients with histologically verified prostate cancer are included in the DAPROCAdata. MAIN VARIABLES: The DAPROCAdata...... registers clinical data and selected characteristics for patients with prostate cancer at diagnosis. Data are collected from the linkage of nationwide health registries and supplemented with online registration of key clinical variables by treating physicians at urological and oncological departments. Main...

  15. Update History of This Database - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Update History of This Database Date Update contents 2017/02/27... Arabidopsis Phenome Database English archive site is opened. - Arabidopsis Phenome Database (http://jphenom...e.info/?page_id=95) is opened. About This Database Database Description Download License Update History of This Database... Site Policy | Contact Us Update History of This Database - Arabidopsis Phenome Database | LSDB Archive ...

  16. Update History of This Database - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SKIP Stemcell Database Update History of This Database Date Update contents 2017/03/13 SKIP Stemcell Database... English archive site is opened. 2013/03/29 SKIP Stemcell Database ( https://www.skip.med.k...eio.ac.jp/SKIPSearch/top?lang=en ) is opened. About This Database Database Description Download License Upda...te History of This Database Site Policy | Contact Us Update History of This Database - SKIP Stemcell Database | LSDB Archive ...

  17. Reference ballistic imaging database performance.

    Science.gov (United States)

    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.

  18. Database Description - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Database... Description General information of database Database name RMG Alternative name Rice Mitochondri...ational Institute of Agrobiological Sciences E-mail : Database classification Nucleotide Sequence Databases ...Organism Taxonomy Name: Oryza sativa Japonica Group Taxonomy ID: 39947 Database description This database co...e of rice mitochondrial genome and information on the analysis results. Features and manner of utilization of database

  19. Multidimensional Databases and Data Warehousing

    DEFF Research Database (Denmark)

    Jensen, Christian S.; Pedersen, Torben Bach; Thomsen, Christian

    techniques that are particularly important to multidimensional databases, including materialized views, bitmap indices, join indices, and star join processing. The book ends with a chapter that presents the literature on which the book is based and offers further readings for those readers who wish to engage......The present book's subject is multidimensional data models and data modeling concepts as they are applied in real data warehouses. The book aims to present the most important concepts within this subject in a precise and understandable manner. The book's coverage of fundamental concepts includes...... data cubes and their elements, such as dimensions, facts, and measures and their representation in a relational setting; it includes architecture-related concepts; and it includes the querying of multidimensional databases. The book also covers advanced multidimensional concepts that are considered...

  20. Bridging radiology and public health: the emerging field of radiologic public health informatics.

    Science.gov (United States)

    Mollura, Daniel J; Carrino, John A; Matuszak, Diane L; Mnatsakanyan, Zaruhi R; Eng, John; Cutchis, Protagoras; Babin, Steven M; Sniegoski, Carol; Lombardo, Joseph S

    2008-03-01

    Radiology and public health have an emerging opportunity to collaborate, in which radiology's vast supply of imaging data can be integrated into public health information systems for epidemiologic assessments and responses to population health problems. Fueling the linkage of radiology and public health include (i) the transition from analog film to digital formats, enabling flexible use of radiologic data; (ii) radiology's role in imaging across nearly all medical and surgical subspecialties, which establishes a foundation for a consolidated and uniform database of images and reports for public health use; and (iii) the use of radiologic data to characterize disease patterns in a population occupying a geographic area at one time and to characterize disease progression over time via follow-up examinations. The backbone for this integration is through informatics projects such as Systematized Nomenclature of Medicine Clinical Terms and RadLex constructing terminology libraries and ontologies, as well as algorithms integrating data from the electronic health record and Digital Imaging and Communications in Medicine Structured Reporting. Radiology's role in public health is being tested in disease surveillance systems for outbreak detection and bioterrorism, such as the Electronic Surveillance System for the Early Notification of Community-based Epidemics. Challenges for radiologic public health informatics include refining the systems and user interfaces, adhering to privacy regulations, and strengthening collaborative relations among stakeholders, including radiologists and public health officials. Linking radiology with public health, radiologic public health informatics is a promising avenue through which radiology can contribute to public health decision making and health policy.

  1. Hazard Analysis Database Report

    CERN Document Server

    Grams, W H

    2000-01-01

    The Hazard Analysis Database was developed in conjunction with the hazard analysis activities conducted in accordance with DOE-STD-3009-94, Preparation Guide for U S . Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports, for HNF-SD-WM-SAR-067, Tank Farms Final Safety Analysis Report (FSAR). The FSAR is part of the approved Authorization Basis (AB) for the River Protection Project (RPP). This document describes, identifies, and defines the contents and structure of the Tank Farms FSAR Hazard Analysis Database and documents the configuration control changes made to the database. The Hazard Analysis Database contains the collection of information generated during the initial hazard evaluations and the subsequent hazard and accident analysis activities. The Hazard Analysis Database supports the preparation of Chapters 3 ,4 , and 5 of the Tank Farms FSAR and the Unreviewed Safety Question (USQ) process and consists of two major, interrelated data sets: (1) Hazard Analysis Database: Data from t...

  2. Conditioning Probabilistic Databases

    CERN Document Server

    Koch, Christoph

    2008-01-01

    Past research on probabilistic databases has studied the problem of answering queries on a static database. Application scenarios of probabilistic databases however often involve the conditioning of a database using additional information in the form of new evidence. The conditioning problem is thus to transform a probabilistic database of priors into a posterior probabilistic database which is materialized for subsequent query processing or further refinement. It turns out that the conditioning problem is closely related to the problem of computing exact tuple confidence values. It is known that exact confidence computation is an NP-hard problem. This has lead researchers to consider approximation techniques for confidence computation. However, neither conditioning nor exact confidence computation can be solved using such techniques. In this paper we present efficient techniques for both problems. We study several problem decomposition methods and heuristics that are based on the most successful search techn...

  3. Full Data of Yeast Interacting Proteins Database (Annotation Updated Version) - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available st proteins and their interactions are required. Several sources including YPD (Yeast Proteome Database, Cos...ome database (WormPD): comprehensive resources for the organization and comparison of model organism protein

  4. Database design and database administration for a kindergarten

    OpenAIRE

    Vítek, Daniel

    2009-01-01

    The bachelor thesis deals with creation of database design for a standard kindergarten, installation of the designed database into the database system Oracle Database 10g Express Edition and demonstration of the administration tasks in this database system. The verification of the database was proved by a developed access application.

  5. ITS-90 Thermocouple Database

    Science.gov (United States)

    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).

  6. Specialist Bibliographic Databases

    OpenAIRE

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

    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 d...

  7. Maternal Deaths Databases Analysis: Ecuador 2003-2013.

    Science.gov (United States)

    Pino, Antonio; Albán, María; Rivas, Alejandra; Rodríguez, Erika

    2016-08-19

    Background: Maternal mortality ratio in Ecuador is the only millennium goal on which national agencies are still making strong efforts to reach 2015 target. The purpose of the study was to process national maternal death databases to identify a specific association pattern of variable included in the death certificate. Design and methods: The study processed mortality databases published yearly by the National Census and Statistics Institute (INEC). Data analysed were exclusively maternal deaths. Data corresponds to the 2003-2013 period, accessible through INEC's website. Comparisons are based on number of deaths and use an ecological approach for geographical coincidences. Results: The study identified variable association into the maternal mortality national databases showing that to die at home or in a different place than a hospital is closely related to women's socioeconomic characteristics; there was an association with the absence of a public health facility. Also, to die in a different place than the usual residence could mean that women and families are searching for or were referred to a higher level of attention when they face complications. Conclusions: Ecuadorian maternal deaths showed Patterns of inequity in health status, health care provision and health risks. A predominant factor seems unclear to explain the variable association found processing national databases; perhaps every pattern of health systems development played a role in maternal mortality or factors different from those registered by the statistics system may remain hidden. Some random influences might not be even considered in an explanatory model yet.

  8. The BioGRID interaction database: 2017 update

    Science.gov (United States)

    Chatr-aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K.; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

    2017-01-01

    The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. PMID:27980099

  9. The BioGRID interaction database: 2017 update.

    Science.gov (United States)

    Chatr-Aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

    2017-01-04

    The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical-protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Maternal deaths databases analysis: Ecuador 2003-2013

    Directory of Open Access Journals (Sweden)

    Antonio Pino

    2016-08-01

    Full Text Available Background: Maternal mortality ratio in Ecuador is the only millennium goal on which national agencies are still making strong efforts to reach 2015 target. The purpose of the study was to process national maternal death databases to identify a specific association pattern of variable included in the death certificate. Design and methods: The study processed mortality databases published yearly by the National Census and Statistics Institute (INEC. Data analysed were exclusively maternal deaths. Data corresponds to the 2003-2013 period, accessible through INEC’s website. Comparisons are based on number of deaths and use an ecological approach for geographical coincidences. Results: The study identified variable association into the maternal mortality national databases showing that to die at home or in a different place than a hospital is closely related to women’s socioeconomic characteristics; there was an association with the absence of a public health facility. Also, to die in a different place than the usual residence could mean that women and families are searching for or were referred to a higher level of attention when they face complications. Conclusions: Ecuadorian maternal deaths showed Patterns of inequity in health status, health care provision and health risks. A predominant factor seems unclear to explain the variable association found processing national databases; perhaps every pattern of health systems development played a role in maternal mortality or factors different from those registered by the statistics system may remain hidden. Some random influences might not be even considered in an explanatory model yet.

  11. Comparing public and private sector switchers

    DEFF Research Database (Denmark)

    Frederiksen, Anders; Hansen, Jesper Rosenberg; Bozeman, Barry

    are related to sector switching and the pattern of sector switch, public to private versus private to public. We propose a life stage model arguing that people's needs change in different life stages of their lives. We further suggest that this can help explain why they switch sector. We use unique Danish......Sector switching is a new rising research area. Little is known about the motives and behaviors of those switching sectors. Using Person-Environment (P-E) fit theory, we seek to determine whether familiar demographic characteristics, including age, gender, having children and length of education...... labor market data that include information on all employees in Denmark (both private and public sector). The data are for the period 1980 to 2006, and this longitudinal database includes abundant information about job changes, including sector switching. Our findings indicate mixed support...

  12. The design and implementation of pedagogical software for multi-backend/multi-lingual database system.

    OpenAIRE

    Little, Craig W.

    1987-01-01

    Approved for public release; distribution is unlimited Traditionally, courses in database systems do not use pedagogical software for the purpose of instructing the database systems, despite the progress made in modem database architecture. In this thesis, we present a working document to assist in the instruction of a new database system, the Multi-Backend Database System (MBDS)-and the Multi-Lingual Database System (MLDS). As the course of instruction describes the creatio...

  13. Smart Location Database - Download

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census block...

  14. Database principles programming performance

    CERN Document Server

    O'Neil, Patrick

    2014-01-01

    Database: Principles Programming Performance provides an introduction to the fundamental principles of database systems. This book focuses on database programming and the relationships between principles, programming, and performance.Organized into 10 chapters, this book begins with an overview of database design principles and presents a comprehensive introduction to the concepts used by a DBA. This text then provides grounding in many abstract concepts of the relational model. Other chapters introduce SQL, describing its capabilities and covering the statements and functions of the programmi

  15. Smart Location Database - Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census block...

  16. Danish Gynecological Cancer Database

    DEFF Research Database (Denmark)

    Sørensen, Sarah Mejer; Bjørn, Signe Frahm; Jochumsen, Kirsten Marie

    2016-01-01

    AIM OF DATABASE: The Danish Gynecological Cancer Database (DGCD) is a nationwide clinical cancer database and its aim is to monitor the treatment quality of Danish gynecological cancer patients, and to generate data for scientific purposes. DGCD also records detailed data on the diagnostic measures...... is the registration of oncological treatment data, which is incomplete for a large number of patients. CONCLUSION: The very complete collection of available data from more registries form one of the unique strengths of DGCD compared to many other clinical databases, and provides unique possibilities for validation...

  17. Transporter Classification Database (TCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Transporter Classification Database details a comprehensive classification system for membrane transport proteins known as the Transporter Classification (TC)...

  18. The Relational Database Dictionary

    CERN Document Server

    J, C

    2006-01-01

    Avoid misunderstandings that can affect the design, programming, and use of database systems. Whether you're using Oracle, DB2, SQL Server, MySQL, or PostgreSQL, The Relational Database Dictionary will prevent confusion about the precise meaning of database-related terms (e.g., attribute, 3NF, one-to-many correspondence, predicate, repeating group, join dependency), helping to ensure the success of your database projects. Carefully reviewed for clarity, accuracy, and completeness, this authoritative and comprehensive quick-reference contains more than 600 terms, many with examples, covering i

  19. IVR EFP Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database contains trip-level reports submitted by vessels participating in Exempted Fishery projects with IVR reporting requirements.

  20. Databases for Microbiologists

    Science.gov (United States)

    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

  1. Veterans Administration Databases

    Science.gov (United States)

    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.

  2. Residency Allocation Database

    Data.gov (United States)

    Department of Veterans Affairs — The Residency Allocation Database is used to determine allocation of funds for residency programs offered by Veterans Affairs Medical Centers (VAMCs). Information...

  3. Data mining in time series databases

    CERN Document Server

    Kandel, Abraham; Bunke, Horst

    2004-01-01

    Adding the time dimension to real-world databases produces Time SeriesDatabases (TSDB) and introduces new aspects and difficulties to datamining and knowledge discovery. This book covers the state-of-the-artmethodology for mining time series databases. The novel data miningmethods presented in the book include techniques for efficientsegmentation, indexing, and classification of noisy and dynamic timeseries. A graph-based method for anomaly detection in time series isdescribed and the book also studies the implications of a novel andpotentially useful representation of time series as strings. Theproblem of detecting changes in data mining models that are inducedfrom temporal databases is additionally discussed.

  4. Sagace: A web-based search engine for biomedical databases in Japan

    Directory of Open Access Journals (Sweden)

    Morita Mizuki

    2012-10-01

    Full Text Available Abstract Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data and biological resource banks (such as mouse models of disease and cell lines. With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/.

  5. The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data

    Directory of Open Access Journals (Sweden)

    Sauvage Thomas

    2009-09-01

    Full Text Available Abstract Background Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS. The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. Description We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. Conclusion The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at http://algae.manoa.hawaii.edu.

  6. The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data.

    Science.gov (United States)

    Wang, Norman; Sherwood, Alison R; Kurihara, Akira; Conklin, Kimberly Y; Sauvage, Thomas; Presting, Gernot G

    2009-09-04

    Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS). The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at http://algae.manoa.hawaii.edu.

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

    Directory of Open Access Journals (Sweden)

    Nozomu Sakurai

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  10. US-LHC Magnet Database and conventions

    CERN Document Server

    Wei, J; Jain, A; Peggs, S; Pilat, F; Bottura, L; Sabbi, G L; MacKay, W W

    1999-01-01

    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. (7 refs).

  11. Reverse engineering of relational database applications

    NARCIS (Netherlands)

    Vermeer, W.W.M.; Apers, P.M.G.

    1995-01-01

    This paper presents techniques for reverse engineering of relational database applications. The target of such an effort is the definition of a fully equipped object-oriented view of the relational database, including methods and constraints. Such views can be seen as a full specification of the dat

  12. Diet History Questionnaire II: Database Utility Program

    Science.gov (United States)

    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.

  13. Diet History Questionnaire: Database Utility Program

    Science.gov (United States)

    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.

  14. The Status of Statewide Subscription Databases

    Science.gov (United States)

    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…

  15. Database Selection in the Life Sciences.

    Science.gov (United States)

    Snow, Bonnie

    1985-01-01

    Focuses on indexing refinements in major life science databases--those specializing in biological/biomedical literature coverage--which influence cross-life searching decisions. Tables included highlight database descriptions, comparisons in coverage, ease of access (indexing of secondary concepts or search modifiers), chemical substance indexing…

  16. Designing Corporate Databases to Support Technology Innovation

    Science.gov (United States)

    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…

  17. Development of a Water Infrastructure Knowledge Database

    Science.gov (United States)

    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...

  18. The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource.

    Science.gov (United States)

    Sherwood, Alison R; Wang, Norman; Carlile, Amy L; Neumann, Jessica M; Wolfgruber, Thomas K; Presting, Gernot G

    2012-10-25

    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. 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. 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 micrographs, and DNA sequences. It is publicly

  19. The Hawaiian Freshwater Algal Database (HfwADB: a laboratory LIMS and online biodiversity resource

    Directory of Open Access Journals (Sweden)

    Sherwood Alison R

    2012-10-01

    Full Text Available Abstract 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

  20. Spatial digital database for the tectonic map of Southeast Arizona

    Science.gov (United States)

    map by Drewes, Harald; digital database by Fields, Robert A.; Hirschberg, Douglas M.; Bolm, Karen S.

    2002-01-01

    A spatial database was created for Drewes' (1980) tectonic map of southeast Arizona: this database supercedes Drewes and others (2001, ver. 1.0). Staff and a contractor at the U.S. Geological Survey in Tucson, Arizona completed an interim digital geologic map database for the east part of the map in 2001, made revisions to the previously released digital data for the west part of the map (Drewes and others, 2001, ver. 1.0), merged data files for the east and west parts, and added additional data not previously captured. Digital base map data files (such as topography, roads, towns, rivers and lakes) are not included: they may be obtained from a variety of commercial and government sources. This digital geospatial database is one of many being created by the U.S. Geological Survey as an ongoing effort to provide geologic information in a geographic information system (GIS) for use in spatial analysis. The resulting digital geologic map database can be queried in many ways to produce a variety of geologic maps and derivative products. Because Drewes' (1980) map sheets include additional text and graphics that were not included in this report, scanned images of his maps (i1109_e.jpg, i1109_w.jpg) are included as a courtesy to the reader. This database should not be used or displayed at any scale larger than 1:125,000 (for example, 1:100,000 or 1:24,000). The digital geologic map plot files (i1109_e.pdf and i1109_w.pdf) that are provided herein are representations of the database (see Appendix A). The map area is located in southeastern Arizona (fig. 1). This report describes the map units (from Drewes, 1980), the methods used to convert the geologic map data into a digital format, the ArcInfo GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. The manuscript and digital data review by Helen Kayser (Information Systems Support, Inc.) is greatly