WorldWideScience

Sample records for public chemical databases

  1. 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.

  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.......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. 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....

  4. 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.

  5. 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....

  6. 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).

  7. 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.

  8. 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...

  9. A novel approach: chemical relational databases, and the role of the ISSCAN database on assessing chemical carcinogenicity.

    Science.gov (United States)

    Benigni, Romualdo; Bossa, Cecilia; Richard, Ann M; Yang, Chihae

    2008-01-01

    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 not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

  10. 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…

  11. 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.

  12. Predictive toxicology of chemicals and database mining

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The toxic chemicals from the database Registry of Toxic Effects of Chemical Substances (RTECS) were analyzed by structural similarity comparison, which shows that the structure patterns or characteristics of toxic chemicals exist in a sufficiently large database. Then, a two-step strategy was proposed to explore noncongeneric toxic chemicals in the database: the screening of structure patterns by similarity comparison and the derivation of detailed relationship between structure and activity by using comparative molecular field analysis (CoMFA) of Quantitative Structure-Activity Relationship (QSAR) technologies. From the performance of the procedure, such a stepwise scheme is demonstrated to be feasible and effective to mine a database of toxic chemicals. It can be anticipated that database mining of toxic chemicals will be a new area for predictive toxicology of chemicals.

  13. 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.

  14. The CARLSBAD database: a confederated database of chemical bioactivities.

    Science.gov (United States)

    Mathias, Stephen L; Hines-Kay, Jarrett; Yang, Jeremy J; Zahoransky-Kohalmi, Gergely; Bologa, Cristian G; Ursu, Oleg; Oprea, Tudor I

    2013-01-01

    Many bioactivity databases offer information regarding the biological activity of small molecules on protein targets. Information in these databases is often hard to resolve with certainty because of subsetting different data in a variety of formats; use of different bioactivity metrics; use of different identifiers for chemicals and proteins; and having to access different query interfaces, respectively. Given the multitude of data sources, interfaces and standards, it is challenging to gather relevant facts and make appropriate connections and decisions regarding chemical-protein associations. The CARLSBAD database has been developed as an integrated resource, focused on high-quality subsets from several bioactivity databases, which are aggregated and presented in a uniform manner, suitable for the study of the relationships between small molecules and targets. In contrast to data collection resources, CARLSBAD provides a single normalized activity value of a given type for each unique chemical-protein target pair. Two types of scaffold perception methods have been implemented and are available for datamining: HierS (hierarchical scaffolds) and MCES (maximum common edge subgraph). The 2012 release of CARLSBAD contains 439 985 unique chemical structures, mapped onto 1,420 889 unique bioactivities, and annotated with 277 140 HierS scaffolds and 54 135 MCES chemical patterns, respectively. Of the 890 323 unique structure-target pairs curated in CARLSBAD, 13.95% are aggregated from multiple structure-target values: 94 975 are aggregated from two bioactivities, 14 544 from three, 7 930 from four and 2214 have five bioactivities, respectively. CARLSBAD captures bioactivities and tags for 1435 unique chemical structures of active pharmaceutical ingredients (i.e. 'drugs'). CARLSBAD processing resulted in a net 17.3% data reduction for chemicals, 34.3% reduction for bioactivities, 23% reduction for HierS and 25% reduction for MCES, respectively. The CARLSBAD database

  15. 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.

  16. 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…

  17. Chemical Accident Prevention Publications

    Science.gov (United States)

    These include chemical safety alerts, emergency preparedness and prevention advisories, and topical backgrounders. Excess flow valves, protecting workers in ethylene oxide sterilization facilities, reactivity hazards, and delayed coker units are covered.

  18. 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.

  19. 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

  20. How to add chemical abstracts service registry numbers and structures to databases via chemical names comparison

    Science.gov (United States)

    Krebs; Jordis

    2000-03-01

    For the conversion of nonstructural chemical databases to structure databases, a series of algorithms to find the closest match between existing names to names in a reference database are described. On the basis of the best match, new fields such as the Chemical Abstracts Service Registry Number (CASRN) or structures were added to the database.

  1. Development of a consumer product ingredient database for chemical exposure screening and prioritization.

    Science.gov (United States)

    Goldsmith, M-R; Grulke, C M; Brooks, R D; Transue, T R; Tan, Y M; Frame, A; Egeghy, P P; Edwards, R; Chang, D T; Tornero-Velez, R; Isaacs, K; Wang, A; Johnson, J; Holm, K; Reich, M; Mitchell, J; Vallero, D A; Phillips, L; Phillips, M; Wambaugh, J F; Judson, R S; Buckley, T J; Dary, C C

    2014-03-01

    Consumer products are a primary source of chemical exposures, yet little structured information is available on the chemical ingredients of these products and the concentrations at which ingredients are present. To address this data gap, we created a database of chemicals in consumer products using product Material Safety Data Sheets (MSDSs) publicly provided by a large retailer. The resulting database represents 1797 unique chemicals mapped to 8921 consumer products and a hierarchy of 353 consumer product "use categories" within a total of 15 top-level categories. We examine the utility of this database and discuss ways in which it will support (i) exposure screening and prioritization, (ii) generic or framework formulations for several indoor/consumer product exposure modeling initiatives, (iii) candidate chemical selection for monitoring near field exposure from proximal sources, and (iv) as activity tracers or ubiquitous exposure sources using "chemical space" map analyses. Chemicals present at high concentrations and across multiple consumer products and use categories that hold high exposure potential are identified. Our database is publicly available to serve regulators, retailers, manufacturers, and the public for predictive screening of chemicals in new and existing consumer products on the basis of exposure and risk.

  2. Database for Safety-Oriented Tracking of Chemicals

    Science.gov (United States)

    Stump, Jacob; Carr, Sandra; Plumlee, Debrah; Slater, Andy; Samson, Thomas M.; Holowaty, Toby L.; Skeete, Darren; Haenz, Mary Alice; Hershman, Scot; Raviprakash, Pushpa

    2010-01-01

    SafetyChem is a computer program that maintains a relational database for tracking chemicals and associated hazards at Johnson Space Center (JSC) by use of a Web-based graphical user interface. The SafetyChem database is accessible to authorized users via a JSC intranet. All new chemicals pass through a safety office, where information on hazards, required personal protective equipment (PPE), fire-protection warnings, and target organ effects (TOEs) is extracted from material safety data sheets (MSDSs) and recorded in the database. The database facilitates real-time management of inventory with attention to such issues as stability, shelf life, reduction of waste through transfer of unused chemicals to laboratories that need them, quantification of chemical wastes, and identification of chemicals for which disposal is required. Upon searching the database for a chemical, the user receives information on physical properties of the chemical, hazard warnings, required PPE, a link to the MSDS, and references to the applicable International Standards Organization (ISO) 9000 standard work instructions and the applicable job hazard analysis. Also, to reduce the labor hours needed to comply with reporting requirements of the Occupational Safety and Health Administration, the data can be directly exported into the JSC hazardous- materials database.

  3. 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...

  4. Ethical guidelines to publication of chemical research. American Chemical Society.

    Science.gov (United States)

    1994-01-01

    The guidelines embodied in this document were revised by the editors of the Publication Division of the American Chemical Society in January 1994 and endorsed by the Society Committee on Publications.

  5. ChemProt: a disease chemical biology database

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine Marie Laure

    2011-01-01

    Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network...... biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30...... evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram...

  6. Relational database driven two-dimensional chemical graph analysis.

    Science.gov (United States)

    Wilkens, Steven J

    2006-09-01

    This manuscript presents a method for pre-computing and storing molecular features or ''scaffolds'' that can be used for rapid clustering of diverse compound sets within the context of a relational database based on hierarchies of scaffold structures. In addition, a method for rapid structure-based profiling of a large compound collection is demonstrated. Pre-organizing compounds by shared structural features in this way facilitates the merger of chemical features and biological data within a relational database.

  7. 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/.

  8. Validation of metabolic pathway databases based on chemical substructure search.

    Science.gov (United States)

    Félix, Liliana; Valiente, Gabriel

    2007-09-01

    Metabolic pathway databases such as KEGG contain information on thousands of biochemical reactions drawn from the biomedical literature. Ensuring consistency of such large metabolic pathways is essential to their proper use. In this paper, we present a new method to determine consistency of an important class of biochemical reactions. Our method exploits the knowledge of the atomic rearrangement pattern in biochemical reactions, to reduce the automatic atom mapping problem to a series of chemical substructure searches between the substrate and the product of a biochemical reaction. As an illustrative application, we describe the exhaustive validation of a substantial portion from the latest release of the KEGG LIGAND database.

  9. 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.

  10. A database for chemical proteomics: ChEBI.

    Science.gov (United States)

    de Matos, Paula; Adams, Nico; Hastings, Janna; Moreno, Pablo; Steinbeck, Christoph

    2012-01-01

    Chemical proteomics is concerned with the identification of protein targets interacting with small molecules. Hence, the availability of a high quality and free resource storing small molecules is essential for the future development of the field. The Chemical Entities of Biological Interest (ChEBI) database is one such database. The scope of ChEBI includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. These entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. In addition, ChEBI contains a chemical ontology which relates the small molecules with each other thereby making it easier for users to discover data. The ontology also describes the biological roles that the small molecules are active in. The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures.

  11. SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery.

    Directory of Open Access Journals (Sweden)

    Paul A Novick

    Full Text Available In the face of drastically rising drug discovery costs, strategies promising to reduce development timelines and expenditures are being pursued. Computer-aided virtual screening and repurposing approved drugs are two such strategies that have shown recent success. Herein, we report the creation of a highly-curated in silico database of chemical structures representing approved drugs, chemical isolates from traditional medicinal herbs, and regulated chemicals, termed the SWEETLEAD database. The motivation for SWEETLEAD stems from the observance of conflicting information in publicly available chemical databases and the lack of a highly curated database of chemical structures for the globally approved drugs. A consensus building scheme surveying information from several publicly accessible databases was employed to identify the correct structure for each chemical. Resulting structures are filtered for the active pharmaceutical ingredient, standardized, and differing formulations of the same drug were combined in the final database. The publically available release of SWEETLEAD (https://simtk.org/home/sweetlead provides an important tool to enable the successful completion of computer-aided repurposing and drug discovery campaigns.

  12. 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.

  13. The PubChemQC project: A large chemical database from the first principle calculations

    Science.gov (United States)

    Maho, Nakata

    2015-12-01

    In this research, we have been constructing a large database of molecules by ab initio calculations. Currently, we have over 1.53 million entries of 6-31G* B3LYP optimized geometries and ten excited states by 6-31+G* TDDFT calculations. To calculate molecules, we only refer the InChI (International Chemical Identifier) representation of chemical formula by the International Union of Pure and Applied Chemistry (IUPAC), thus, no reference to experimental data. These results are open to public at http://pubchemqc.riken.jp/. The molecular data have been taken from the PubChem Project (http://pubchem.ncbi.nlm.nih.gov/) which is one of the largest in the world (approximately 63 million molecules are listed) and free (public domain) database. Our final goal is, using these data, to develop a molecular search engine or molecular expert system to find molecules which have desired properties.

  14. The PubChemQC Project: a large chemical database from the first principle calculations

    CERN Document Server

    Nakata, Maho

    2015-01-01

    In this research, we have been constructing a large database of molecules by {\\it ab initio} calculations. Currently, we have over 1.53 million entries of 6-31G* B3LYP optimized geometries and ten excited states by 6-31+G* TDDFT calculations. To calculate molecules, we only refer the InChI (International Chemical Identifier) representation of chemical formula by the International Union of Pure and Applied Chemistry (IUPAC), thus, no reference to experimental data. These results are open to public at http://pubchemqc.riken.jp/. The molecular data have been taken from the PubChem Project (http://pubchem.ncbi.nlm.nih.gov/) which is one of the largest in the world (approximately 63 million molecules are listed) and free (public domain) database. Our final goal is, using these data, to develop a molecular search engine or molecular expert system to find molecules which have desired properties.

  15. Exploring Chemical Space for Drug Discovery Using the Chemical Universe Database

    Science.gov (United States)

    2012-01-01

    Herein we review our recent efforts in searching for bioactive ligands by enumeration and virtual screening of the unknown chemical space of small molecules. Enumeration from first principles shows that almost all small molecules (>99.9%) have never been synthesized and are still available to be prepared and tested. We discuss open access sources of molecules, the classification and representation of chemical space using molecular quantum numbers (MQN), its exhaustive enumeration in form of the chemical universe generated databases (GDB), and examples of using these databases for prospective drug discovery. MQN-searchable GDB, PubChem, and DrugBank are freely accessible at www.gdb.unibe.ch. PMID:23019491

  16. 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...

  17. 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.

  18. Ambiguity of non-systematic chemical identifiers within and between small-molecule databases

    NARCIS (Netherlands)

    S.A. Akhondi (Saber); C. Muresan (Cornelia); A.J. Williams (Antony); J.A. Kors (Jan)

    2015-01-01

    textabstractBackground: A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers can query these chemical databases using non-systematic identifiers. These are source-dependent identifiers (e.

  19. Mining the Chemical Abstracts database with pharmacophore-based queries.

    Science.gov (United States)

    Bremner, John B; Castle, Kao; Griffith, Renate; Keller, Paul A; Ridley, Damon D

    2002-12-01

    A method is described to convert 3D patterns of pharmacophoric groups into 2D queries for molecular substructure searches of the Chemical Abstracts database with SciFinder Scholar. The results of such searches and the options for refinement of the hit lists are presented using a rigid tetrahydroisoquinoline-carbazole (IQC) hybrid molecule fitted onto previously developed pharmacophores for subtype-selective alpha1-adrenergic receptor antagonists as an example. The compounds retrieved were further analysed by limiting their physical properties to 'drug-like' ranges and by enumerating the ring skeletons they contain. Selected ring skeletons were evaluated by fitting them on to the original pharmacophores. Several structurally novel rigid ring skeletons were found with this new database mining technique which are potentially useful as leads in the design of alpha1B selective adrenergic receptor antagonists.

  20. 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.

  1. Accelerating chemical database searching using graphics processing units.

    Science.gov (United States)

    Liu, Pu; Agrafiotis, Dimitris K; Rassokhin, Dmitrii N; Yang, Eric

    2011-08-22

    The utility of chemoinformatics systems depends on the accurate computer representation and efficient manipulation of chemical compounds. In such systems, a small molecule is often digitized as a large fingerprint vector, where each element indicates the presence/absence or the number of occurrences of a particular structural feature. Since in theory the number of unique features can be exceedingly large, these fingerprint vectors are usually folded into much shorter ones using hashing and modulo operations, allowing fast "in-memory" manipulation and comparison of molecules. There is increasing evidence that lossless fingerprints can substantially improve retrieval performance in chemical database searching (substructure or similarity), which have led to the development of several lossless fingerprint compression algorithms. However, any gains in storage and retrieval afforded by compression need to be weighed against the extra computational burden required for decompression before these fingerprints can be compared. Here we demonstrate that graphics processing units (GPU) can greatly alleviate this problem, enabling the practical application of lossless fingerprints on large databases. More specifically, we show that, with the help of a ~$500 ordinary video card, the entire PubChem database of ~32 million compounds can be searched in ~0.2-2 s on average, which is 2 orders of magnitude faster than a conventional CPU. If multiple query patterns are processed in batch, the speedup is even more dramatic (less than 0.02-0.2 s/query for 1000 queries). In the present study, we use the Elias gamma compression algorithm, which results in a compression ratio as high as 0.097.

  2. 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.

  3. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  4. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  5. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  6. Applications of the Cambridge Structural Database in chemical education1

    Science.gov (United States)

    Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

    2010-01-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  7. 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.

  8. NOAA's Office of Response and Restoration: Historical Oil and Chemical Spill Incidents Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Historical Incidents database contains reports and images from oil and chemical spills that occurred between 1968 and 2002. The database includes reports on...

  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. Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

    Science.gov (United States)

    Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

    2016-01-01

    Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

  11. Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

    Science.gov (United States)

    Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

    2016-01-01

    Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

  12. 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.

  13. 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…

  14. Identification of environmentally relevant chemicals in bibliographic databases: a comparative analysis

    DEFF Research Database (Denmark)

    Ellegaard, Ole; Wallin, Johan Albert

    2013-01-01

    takes as its starting point environmentally important chemicals and the retrieval of selectively chosen substances in the four databases: SciFinder, Web of Science (WoS), Scopus and Google Scholar. The way chemical data are stored in the databases plays a major role in the recovery process...

  15. Identification of environmentally relevant chemicals in bibliographic databases: a comparative analysis

    DEFF Research Database (Denmark)

    Ellegaard, Ole; Wallin, Johan Albert

    2013-01-01

    takes as its starting point environmentally important chemicals and the retrieval of selectively chosen substances in the four databases: SciFinder, Web of Science (WoS), Scopus and Google Scholar. The way chemical data are stored in the databases plays a major role in the recovery process...

  16. 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...

  17. 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.

  18. 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

  19. 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

  20. Chemical Risk Assessment: Traditional vs Public Health Perspectives

    Science.gov (United States)

    Preventing adverse health impacts from exposures to environmental chemicals is fundamental to protecting individual and public health. When done efficiently and properly, chemical risk assessment enables risk management actions that minimize the incidence and impacts of environme...

  1. Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database

    Science.gov (United States)

    Grondin, Cynthia J.; Davis, Allan Peter; Wiegers, Thomas C.; King, Benjamin L.; Wiegers, Jolene A.; Reif, David M.; Hoppin, Jane A.; Mattingly, Carolyn J.

    2016-01-01

    Background: Exposure science studies the interactions and outcomes between environmental stressors and human or ecological receptors. To augment its role in understanding human health and the exposome, we aimed to centralize and integrate exposure science data into the broader biological framework of the Comparative Toxicogenomics Database (CTD), a public resource that promotes understanding of environmental chemicals and their effects on human health. Objectives: We integrated exposure data within the CTD to provide a centralized, freely available resource that facilitates identification of connections between real-world exposures, chemicals, genes/proteins, diseases, biological processes, and molecular pathways. Methods: We developed a manual curation paradigm that captures exposure data from the scientific literature using controlled vocabularies and free text within the context of four primary exposure concepts: stressor, receptor, exposure event, and exposure outcome. Using data from the Agricultural Health Study, we have illustrated the benefits of both centralization and integration of exposure information with CTD core data. Results: We have described our curation process, demonstrated how exposure data can be accessed and analyzed in the CTD, and shown how this integration provides a broad biological context for exposure data to promote mechanistic understanding of environmental influences on human health. Conclusions: Curation and integration of exposure data within the CTD provides researchers with new opportunities to correlate exposures with human health outcomes, to identify underlying potential molecular mechanisms, and to improve understanding about the exposome. Citation: Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. 2016. Advancing exposure science through chemical data curation and integration in the Comparative Toxicogenomics Database. Environ Health Perspect 124:1592–1599; http://dx.doi.org/10

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

    Science.gov (United States)

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

    2012-10-01

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

  3. Ambiguity of non-systematic chemical identifiers within and between small-molecule databases.

    Science.gov (United States)

    Akhondi, Saber A; Muresan, Sorel; Williams, Antony J; Kors, Jan A

    2015-01-01

    A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers can query these chemical databases using non-systematic identifiers. These are source-dependent identifiers (e.g., brand names, generic names), which are usually assigned to the compound at the point of registration. The correctness of non-systematic identifiers (i.e., whether an identifier matches the associated structure) can only be assessed manually, which is cumbersome, but it is possible to automatically check their ambiguity (i.e., whether an identifier matches more than one structure). In this study we have quantified the ambiguity of non-systematic identifiers within and between eight widely used chemical databases. We also studied the effect of chemical structure standardization on reducing the ambiguity of non-systematic identifiers. The ambiguity of non-systematic identifiers within databases varied from 0.1 to 15.2 % (median 2.5 %). Standardization reduced the ambiguity only to a small extent for most databases. A wide range of ambiguity existed for non-systematic identifiers that are shared between databases (17.7-60.2 %, median of 40.3 %). Removing stereochemistry information provided the largest reduction in ambiguity across databases (median reduction 13.7 percentage points). Ambiguity of non-systematic identifiers within chemical databases is generally low, but ambiguity of non-systematic identifiers that are shared between databases, is high. Chemical structure standardization reduces the ambiguity to a limited extent. Our findings can help to improve database integration, curation, and maintenance.

  4. 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.

  5. 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 ...

  6. 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...

  7. ChemProt: A disease chemical biology database

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    2013-01-01

    The integration of chemistry, biology, and informatics to study drug actions across multiple biological targets, pathways, and biological systems is an emerging paradigm in drug discovery. Rather than reducing a complex system to simplistic models, fields such as chemogenomics and translational...... chemical biology, drug repurposing, and off-target effects prediction....

  8. ChemProt: A disease chemical biology database

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    2013-01-01

    The integration of chemistry, biology, and informatics to study drug actions across multiple biological targets, pathways, and biological systems is an emerging paradigm in drug discovery. Rather than reducing a complex system to simplistic models, fields such as chemogenomics and translational...... chemical biology, drug repurposing, and off-target effects prediction....

  9. 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.

  10. Strategies for chemically healthy public swimming pools

    DEFF Research Database (Denmark)

    Hansen, Kamilla Marie Speht

    of the strategies which can be used to achieve microbiological safe water with low levels of DBPs to ensure healthy environment for bathers. There are different approaches to achieve healthy environment in public swimming pools which in this thesis are divided into three strategies: alternatives to chlorination...

  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. Ethical Standards for Publication in Chinese Journal of Chemical Engineering

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@Chinese Journal of Chemical Engineering is a publication of the Chemical Industry and Engineering Society of China (CIESC) dedicated to present the original contributions of knowledge with permanent value from chemical engineering researcher and technical staff in processing industries in China and the world. The Editors-in-Chief, Associate Editors-in-Chief and Editorial Staff of the journal share the responsibility to maintain the CJChE ethical standards for paper reviewing and handling process.

  14. Ethical Standards for Publication in Chinese Journal of Chemical Engineering

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Chinese Journal of Chemical Engineering (CJChE) is a publication of the Chemical Industry and Engineering Society of China (CIESC) dedicated to present the original contributions of knowledge with permanent value from chemical engineering researchers and technical staff of process industries in China and the world. The editors-in-chief, associate editors-in-chief and editorial staff of the journal share the responsibility to maintain the CJChE ethical standards for paper reviewing and handling process. The following ethical standards are thought important to the contributors from Chinese and international chemical engineering communities.

  15. 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.

  16. [Qualitative analysis of chemical constituents in Si-Wu Decoction based on TCM component database].

    Science.gov (United States)

    Wang, Zhen-fang; Zhao, Yang; Fan, Zi-quan; Kang, Li-ping; Qiao, Li-rui; Zhang, Jie; Gao, Yue; Ma, Bai-ping

    2015-10-01

    In order to clarify the chemical constituents of Si-Wu Decoction rapidly and holistically, we analyzed the ethanol extract of Si-Wu Decoction by UPLC/Q-TOF-MSE and UNIFI which based on traditional Chinese medicine database, the probable structures of 113 compounds were identified. The results show that this method can rapidly and effectively characterize the chemical compounds of Si-Wu Decoction and provide a new solution for identification of components from complex TCM extract.

  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. A scalable machine-learning approach to recognize chemical names within large text databases

    Directory of Open Access Journals (Sweden)

    Wren Jonathan D

    2006-09-01

    Full Text Available Abstract Motivation The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. Results A first-order Markov Model (MM was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid.

  19. EPAs DSSTox Chemical Database: A Resource for the Non-Targeted Testing Community (EPA NTA workshop)

    Science.gov (United States)

    EPA’s DSSTox database project, which includes coverage of the ToxCast and Tox21 high-throughput testing inventories, provides high-quality chemical-structure files for inventories of toxicological and environmental relevance. A feature of the DSSTox project, which differentiates ...

  20. 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

  1. 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.

  2. 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<...

  3. Entering new publication territory in chemoinformatics and chemical information science.

    Science.gov (United States)

    Bajorath, Jürgen

    2015-01-01

    The F1000Research publishing platform offers the opportunity to launch themed article collections as a part of its dynamic publication environment. The idea of article collections is further expanded through the generation of publication channels that focus on specific scientific areas or disciplines. This editorial introduces the Chemical Information Science channel of F1000Research designed to collate high-quality publications and foster a culture of open peer review. Articles will be selected by guest editor(s) and a group of experts, the channel Editorial Board, and subjected to open peer review.

  4. Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining.

    Science.gov (United States)

    Singh, S B; Sheridan, R P; Fluder, E M; Hull, R D

    2001-05-10

    In this study we use a novel similarity search technique called latent semantic structure indexing (LaSSI) with joint chemical probes as queries to mine the MDL drug data report database. LaSSI is based on latent semantic indexing developed for searching textual databases. We use atom pair and topological torsion descriptors in our calculations. The results obtained with LaSSI are compared with another in-house similarity search technique TOPOSIM. The results from the similarity searches using joint chemical probes are significantly better than searches using single chemical probes for both LaSSI and TOPOSIM. The selected molecules are closely related in activity to their queries and are ranked among the top 300 scoring molecules of the 82 860 entries in the database. Our implementation of LaSSI is very fast and efficient in finding active compounds. The results also show that LaSSI consistently retrieves more diverse chemical structures representative of the joint chemical probes in comparison to TOPOSIM. The use of multimolecule topological probes to identify compounds complements the use of searching databases with 3D pharmacophore hypotheses.

  5. The Chemical Aquatic Fate and Effects database (CAFE), a tool that supports assessments of chemical spills in aquatic environments.

    Science.gov (United States)

    Bejarano, Adriana C; Farr, James K; Jenne, Polly; Chu, Valerie; Hielscher, Al

    2016-06-01

    The Chemical Aquatic Fate and Effects (CAFE) database is a centralized repository that allows for rapid and unrestricted access to data. Information in CAFE is integrated into a user-friendly tool with modules containing fate and effects data for 32 377 and 4498 chemicals, respectively. Toxicity data are summarized in the form of species sensitivity distributions (SSDs) with associated 1st and 5th percentile hazard concentrations (HCs). An assessment of data availability relative to reported chemical incidents showed that CAFE had fate and toxicity data for 32 and 20 chemicals, respectively, of 55 chemicals reported in the US National Response Center database (2000-2014), and fate and toxicity data for 86 and 103, respectively, of 205 chemicals reported by the National Oceanic and Atmospheric Administration (2003-2014). Modeled environmental concentrations of 2 hypothetical spills (acrylonitrile, 625 barrels; and denatured ethanol, 857 barrels) were used to demonstrate CAFE's practical application. Most species in the 24-h SSD could be potentially impacted by acrylonitrile and denatured ethanol during the first 35 min and 15 h post spill, respectively, with concentrations falling below their HC5s (17 mg/L and 2676 mg/L) at 45 min and 60 h post spill, respectively. Comparisons of CAFE-based versus published HC5 values for 100 chemicals showed that nearly half of values were within a 2-fold difference, with a relatively small number of comparisons exceeding a 10-fold difference. The development of CAFE facilitates access to relevant environmental information, with potential uses likely expanding beyond those related to assessment of spills in aquatic environments. Environ Toxicol Chem 2016;35:1576-1586. © 2015 SETAC.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Structuring Chemical Space: Similarity-Based Characterization of the PubChem Database.

    Science.gov (United States)

    Cincilla, Giovanni; Thormann, Michael; Pons, Miquel

    2010-01-12

    The ensemble of conceivable molecules is referred to as the Chemical Space. In this article we describe a hierarchical version of the Affinity Propagation (AP) clustering algorithm and apply it to analyze the LINGO-based similarity matrix of a 500 000-molecule subset of the PubChem database, which contains more than 19 million compounds. The combination of two highly efficient methods, namely the AP clustering algorithm and LINGO-based molecular similarity calculations, allows the unbiased analysis of large databases. Hierarchical clustering generates a numerical diagonalization of the similarity matrix. The target-independent, intrinsic structure of the database , derived without any previous information on the physical or biological properties of the compounds, maps together molecules experimentally shown to bind the same biological target or to have similar physical properties.

  12. The Northwest Infrared (NWIR) gas-phase spectral database of industrial and environmental chemicals: Recent updates

    Energy Technology Data Exchange (ETDEWEB)

    Brauer, Carolyn S.; Johnson, Timothy J.; Blake, Thomas A.; Sharpe, Steven W.; Sams, Robert L.; Tonkyn, Russell G.

    2014-05-22

    With continuing improvements in both standoff- and point-sensing techniques, there is an ongoing need for high-quality infrared spectral databases. The Northwest Infrared Database (NWIR) contains quantitative, gas-phase infrared spectra of nearly 500 pure chemical species that can be used for a variety of applications such as atmospheric monitoring, biomass burning studies, etc. The data, recorded at 0.1 cm-1 resolution, are pressure broadened to one atmosphere (N2) in order to mimic atmospheric conditions. Each spectrum is a composite composed of multiple individual measurements. Recent updates to the database include over 60 molecules that are known or suspected biomass-burning effluents. Examples from this set of measurements will be presented and experimental details will be discussed in the context of the utility of NWIR for environmental applications.

  13. 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.

  14. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    Science.gov (United States)

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  15. 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.

  16. Public Health Risk Conditioned by Chemical Composition of Ground Water

    Science.gov (United States)

    Yankovich, E.; Osipova, N.; Yankovich, K.; Matveenko, I.

    2016-03-01

    The article studies the public health potential risk originated from water consumption and estimated on the basis of the groundwater chemical composition. We have processed the results of chemical groundwater analysis in different aquifers of Tomsk district (Tomsk Oblast, Russia). More than 8400 samples of chemical groundwater analyses were taken during long-term observation period. Human health risk assessment of exposure to contaminants in drinking water was performed in accordance with the risk assessment guidance for public health concerning chemical pollution of the environment (Russian reference number: 2.1.10.1920-04-M, 2004). Identified potential risks were estimated for consuming water of each aquifer. The comparative analysis of water quality of different aquifers was performed on the basis of the risk coefficient of the total non-carcinogenic effects. The non-carcinogenic risk for the health of the Tomsk district population due to groundwater consumption without prior sanitary treatment was admitted acceptable. A rather similar picture is observed for all aquifers, although deeper aquifers show lower hazard coefficients.

  17. GaussDal: An open source database management system for quantum chemical computations

    Science.gov (United States)

    Alsberg, Bjørn K.; Bjerke, Håvard; Navestad, Gunn M.; Åstrand, Per-Olof

    2005-09-01

    An open source software system called GaussDal for management of results from quantum chemical computations is presented. Chemical data contained in output files from different quantum chemical programs are automatically extracted and incorporated into a relational database (PostgreSQL). The Structural Query Language (SQL) is used to extract combinations of chemical properties (e.g., molecules, orbitals, thermo-chemical properties, basis sets etc.) into data tables for further data analysis, processing and visualization. This type of data management is particularly suited for projects involving a large number of molecules. In the current version of GaussDal, parsers for Gaussian and Dalton output files are supported, however future versions may also include parsers for other quantum chemical programs. For visualization and analysis of generated data tables from GaussDal we have used the locally developed open source software SciCraft. Program summaryTitle of program: GaussDal Catalogue identifier: ADVT Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVT Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Any Operating system under which the system has been tested: Linux Programming language used: Python Memory required to execute with typical data: 256 MB No. of bits in word: 32 or 64 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of lines in distributed program, including test data, etc: 543 531 No. of bytes in distribution program, including test data, etc: 7 718 121 Distribution format: tar.gzip file Nature of physical problem: Handling of large amounts of data from quantum chemistry computations. Method of solution: Use of SQL based database and quantum chemistry software specific parsers. Restriction on the complexity of the problem: Program is currently limited to Gaussian and Dalton output, but expandable to other formats. Generates subsets of multiple data tables from

  18. Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database.

    Directory of Open Access Journals (Sweden)

    Benjamin L King

    Full Text Available Exposure to chemicals in the environment is believed to play a critical role in the etiology of many human diseases. To enhance understanding about environmental effects on human health, the Comparative Toxicogenomics Database (CTD; http://ctdbase.org provides unique curated data that enable development of novel hypotheses about the relationships between chemicals and diseases. CTD biocurators read the literature and curate direct relationships between chemicals-genes, genes-diseases, and chemicals-diseases. These direct relationships are then computationally integrated to create additional inferred relationships; for example, a direct chemical-gene statement can be combined with a direct gene-disease statement to generate a chemical-disease inference (inferred via the shared gene. In CTD, the number of inferences has increased exponentially as the number of direct chemical, gene and disease interactions has grown. To help users navigate and prioritize these inferences for hypothesis development, we implemented a statistic to score and rank them based on the topology of the local network consisting of the chemical, disease and each of the genes used to make an inference. In this network, chemicals, diseases and genes are nodes connected by edges representing the curated interactions. Like other biological networks, node connectivity is an important consideration when evaluating the CTD network, as the connectivity of nodes follows the power-law distribution. Topological methods reduce the influence of highly connected nodes that are present in biological networks. We evaluated published methods that used local network topology to determine the reliability of protein-protein interactions derived from high-throughput assays. We developed a new metric that combines and weights two of these methods and uniquely takes into account the number of common neighbors and the connectivity of each entity involved. We present several CTD inferences as case

  19. Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

    Science.gov (United States)

    Davis, Allan Peter; Wiegers, Thomas C; Johnson, Robin J; Lay, Jean M; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J

    2013-01-01

    The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency.

  20. Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

    Directory of Open Access Journals (Sweden)

    Allan Peter Davis

    Full Text Available The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/ is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS, wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel. Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency.

  1. The needs for chemistry standards, database tools and data curation at the chemical-biology interface (SLAS meeting)

    Science.gov (United States)

    This presentation will highlight known challenges with the production of high quality chemical databases and outline recent efforts made to address these challenges. Specific examples will be provided illustrating these challenges within the U.S. Environmental Protection Agency ...

  2. Use of detailed thermochemical databases to model chemical interactions in the Severe Accident codes

    Energy Technology Data Exchange (ETDEWEB)

    Barrachin, M. [IPSN/DRS, CEA Cadarache (France)

    2001-07-01

    For the prevention, mitigation and management of severe accidents, many problems related to core melt have to be solved: fuel degradation, melting and relocation, convection in the core melt(s), coolability of the core melt(s), fission product release, hydrogen production, behavior of the materials of the protective layers, ex-vessel spreading of the core melt(s).. To solve these problems such properties like thermal conductivity, heat capacity, density, viscosity, evaporation or sublimation of melts, the solidification behavior (solid/liquid fraction), the tendency to trap or to release the fission products, the stratification of melts notably metallic and oxide, must be known. However most of these properties are delicate to measure directly at high temperature and/or in the radio-active environment produced by the fission products. Therefore some of them must be derived by calculations from the physical-chemical description of the melt: number of phases, phase compositions, proportions of solids and liquids and their respective oxidation state, miscibility of the liquids, solubility of one phase in another, etc. This information is given by the phase diagrams of the materials in presence. Since more than ten years, IPSN has developed in collaboration with THERMODATA (Grenoble, France) a very detailed thermochemical database for the complex system U-O-Zr-Fe-Ni-La-Ba-Ru-Sr-Si-Mg-Ca-Al-(H-Ar). The direct coupling between the severe accident (SA) Codes and a thermochemical code with its database is not actually possible because of the computer time consuming and the size of the database. For this reason, most of the Severe Accident codes usually have a very simplified description for the phase diagrams which are not in agreement with the status of the art. In this presentation, alternative methodologies are detailed with their respective difficulties, the goal being to build an interface between a thermochemical database and a SA Code and to get a fast, accurate and

  3. 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.

  4. 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.

  5. 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.

  6. BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.

    Science.gov (United States)

    Howe, E A; de Souza, A; Lahr, D L; Chatwin, S; Montgomery, P; Alexander, B R; Nguyen, D-T; Cruz, Y; Stonich, D A; Walzer, G; Rose, J T; Picard, S C; Liu, Z; Rose, J N; Xiang, X; Asiedu, J; Durkin, D; Levine, J; Yang, J J; Schürer, S C; Braisted, J C; Southall, N; Southern, M R; Chung, T D Y; Brudz, S; Tanega, C; Schreiber, S L; Bittker, J A; Guha, R; Clemons, P A

    2015-01-01

    BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.

  7. 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

  8. Public concerns and the public role in siting nuclear and chemical waste facilities

    Science.gov (United States)

    Johnson, Branden B.

    1987-09-01

    Nuclear and chemical waste facilities can be successfully sited, despite nimby responses, if siting programs account for the sources of public concern. Irrational fear is not the main source; instead, waste managers must deal with perceived inequities in the distribution of benefits and costs, and concern about facility safety. Benefit-cost inequities may be dealt with in part by keeping wastes where they are generated, through political restrictions, or by providing economic compensation and political incentives (for example, a local veto). Assuring people of facility safety includes allowing local control (monitoring, health assessment, regulation), and enhancing trust of facility managers through such means as rectifying past mistakes, individual-oriented education campaigns, and negotiation of compensation packages with local residents. These means should reduce —without eliminating—public opposition to local siting of nuclear and chemical waste facilities.

  9. 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...

  10. Database proton NMR chemical shifts for RNA signal assignment and validation

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

    2013-01-15

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4{sup 3} possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA {sup 1}H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

  11. Identification of "Known Unknowns" Utilizing Accurate Mass Data and Chemical Abstracts Service Databases

    Science.gov (United States)

    Little, James L.; Cleven, Curtis D.; Brown, Stacy D.

    2011-02-01

    In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others.

  12. Identification of "known unknowns" utilizing accurate mass data and chemical abstracts service databases.

    Science.gov (United States)

    Little, James L; Cleven, Curtis D; Brown, Stacy D

    2011-02-01

    In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others. © American Society for Mass Spectrometry, 2011

  13. 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.

  14. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD).

    Science.gov (United States)

    Wiegers, Thomas C; Davis, Allan Peter; Cohen, K Bretonnel; Hirschman, Lynette; Mattingly, Carolyn J

    2009-10-08

    The Comparative Toxicogenomics Database (CTD) is a publicly available resource that promotes understanding about the etiology of environmental diseases. It provides manually curated chemical-gene/protein interactions and chemical- and gene-disease relationships from the peer-reviewed, published literature. The goals of the research reported here were to establish a baseline analysis of current CTD curation, develop a text-mining prototype from readily available open source components, and evaluate its potential value in augmenting curation efficiency and increasing data coverage. Prototype text-mining applications were developed and evaluated using a CTD data set consisting of manually curated molecular interactions and relationships from 1,600 documents. Preliminary results indicated that the prototype found 80% of the gene, chemical, and disease terms appearing in curated interactions. These terms were used to re-rank documents for curation, resulting in increases in mean average precision (63% for the baseline vs. 73% for a rule-based re-ranking), and in the correlation coefficient of rank vs. number of curatable interactions per document (baseline 0.14 vs. 0.38 for the rule-based re-ranking). This text-mining project is unique in its integration of existing tools into a single workflow with direct application to CTD. We performed a baseline assessment of the inter-curator consistency and coverage in CTD, which allowed us to measure the potential of these integrated tools to improve prioritization of journal articles for manual curation. Our study presents a feasible and cost-effective approach for developing a text mining solution to enhance manual curation throughput and efficiency.

  15. Chemical composition of suspended sediments in World Rivers: New insights from a new database.

    Science.gov (United States)

    Viers, Jérôme; Dupré, Bernard; Gaillardet, Jérôme

    2009-01-01

    The aim of this paper is to present a new database on the chemical composition of suspended matter in World Rivers, together with the associated elemental fluxes. There is a lack of any recent attempt in the literature to update the pioneering work of Martin and Meybeck [Martin, J.-M., Meybeck, M., 1979. Elemental mass balance of material carried by major world rivers. Mar. Chem. 7, 173-206.] and Martin and Whitfield [Martin, J.-M., Whitfield, M., 1983. The significance of the river input of chemical elements to the ocean. Trace metals in sea water Wong, Boyle, Bruland, Burton, Goldberg (Eds) Plenum Publishing Corporation.] regarding the worldwide average major and trace element chemistry of riverine particulate matter. Apart from compiling a new database on particulate matter, this paper also aims to give a "snap-shot" of elemental fluxes for each continent. This approach should allow us to obtain new insights on weathering conditions in different environments and assess the influence of human activities on natural geochemical cycles. Finally, this study demonstrates the large uncertainties currently associated with estimating the flux of sediments transported by rivers. By comparing the riverine suspended sediment fluxes of some metals (Cd, Zn, Ni, Cu, Cr and Pb) given in this study with estimates of the anthropogenic fluxes of these metals to the atmosphere, soils and waters (natural ecosystems) [Nriagu, J.O., 1988. A silent epidemic of environmental poisoning. Environ. Pollut. 50, 139-161.], we can see that riverine fluxes are similar to anthropogenic fluxes. This casts light on the effect of human activities on the cycles of trace elements at the Earth's surface.

  16. 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.

  17. 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.

  18. 75 FR 4402 - Notice of National Conversation on Public Health and Chemical Exposures Leadership Council...

    Science.gov (United States)

    2010-01-27

    ... Health and Chemical Exposures Leadership Council Conference Call Time and Date: 1 p.m.-3 p.m., Friday... National Conversation on Public Health and Chemical Exposures Leadership Council. The National Conversation... protecting the public's health from harmful chemical exposures. The Leadership Council provides...

  19. 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

  20. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    OpenAIRE

    2015-01-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ([superscript 13]C–[superscript 13]C, [superscript 15]N–[superscript 13]C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 [superscript 13]C chemical shifts and >3 million chemical...

  1. 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

  2. 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

  3. 78 FR 34377 - Trichloroethylene TSCA Chemical Risk Assessment; Notice of Public Meetings and Opportunity to...

    Science.gov (United States)

    2013-06-07

    ... information contact: The TSCA-Hotline, ABVI-Goodwill, 422 South Clinton Ave., Rochester, NY 14620; telephone... assessment, the chemical industry, chemical users, consumer product companies, and members of the public...

  4. Definition and detection of data-based uniqueness in evaluating bilinear (two-way) chemical measurements.

    Science.gov (United States)

    Rajkó, Róbert; Abdollahi, Hamid; Beyramysoltan, Samira; Omidikia, Nematollah

    2015-01-15

    Multivariate curve resolution methods, frequently used in analyzing bilinear data sets, result in ambiguous decomposition in general. Implementing the adequate constraints may lead to reduce the so-called rotational ambiguity drastically, and in the most favorable cases to the unique solution. However, in some special cases, non-negativity constraint as minimal information of the system is a sufficient condition to resolve profiles uniquely. Although, several studies on exploring the uniqueness of the bilinear non-negatively constrained multivariate curve resolution methods have been made in the literature, it has still remained a mysterious question. In 1995, Manne published his profile-based theorems giving the necessary and sufficient conditions of the unique resolution. In this study, a new term, i.e., data-based uniqueness is defined and investigated in details, and a general procedure is suggested for detection of uniquely recovered profile(s) on the basis of data set structure in the abstract space. Close inspection of Borgen plots of these data sets leads to realize the comprehensive information of local rank, and these argumentations furnish a basis for data-based uniqueness theorem. The reported phenomenon and its exploration is a new stage (it can be said fundament) in understanding and describing the bilinear (matrix-type) chemical data in general. Our proposed detection tool is restricted to three-component systems because of the visual limitations of the Borgen plot, but the theorem is universal for systems with more than three components. A recently published experimental four-component system is used for illustrating this theorem in the case of systems with more than three components.

  5. An analysis of Chemical Stockpile Emergency Preparedness Program exercise results. Volume 1: The CSEPP Exercise Results Database

    Energy Technology Data Exchange (ETDEWEB)

    Hewett, P.L. Jr.; Mitrani, J.E.; Absil-Mills, M.J.G.; Tallarovic, P.; Molsen, J.; Vercellone, J.; Madore, M.A.

    1998-06-01

    The primary focus of the Chemical Stockpile Emergency Preparedness Program (CSEPP) is to enhance the response capabilities of the eight US Army installations that store chemical weapons agent and of the communities immediately surrounding each Army storage installation. Exercises are a major component of the program and are conducted annually at each of the eight installations. Following each exercise, a report summarizing the results of the exercise is produced. To gain a better perspective on the site-specific and program-wide results of these exercises, the Project Manager for Chemical Stockpile Emergency Preparedness requested that Argonne National Laboratory develop a database containing the results of exercises held through June 1996. This document provides a summary of the process used to develop the CSEPP Exercise Results Database. The database provides CSEPP managers in the Department of the Army and the Federal Emergency Management Agency a method for tracking and analyzing exercise results. The report discusses the collection and coding of exercise data and provides tables to guide coding of future exercise results. An electronic copy of the database (CD-ROM) accompanies the report. This report focuses only on methods used to collect exercise data and develop the database; Volume 2 discusses the analysis of the data collected.

  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. 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.

  8. 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…

  9. 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.

  10. 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...

  11. 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...

  12. 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...

  13. 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.

  14. Colour quantitation for chemical spot tests for a controlled substances presumptive test database.

    Science.gov (United States)

    Elkins, Kelly M; Weghorst, Alex C; Quinn, Alicia A; Acharya, Subrata

    2017-02-01

    Crime scene investigators (CSIs) often encounter unknown powders, capsules, tablets, and liquids at crime scenes, many of which are controlled substances. Because most drugs are white powders, however, visual determination of the chemical identity is difficult. Colourimetric tests are a well-established method of presumptive drug identification. Positive tests are often reported differently, however, because two analysts may perceive colour or record colourimetric results in different ways. In addition to perceiving colour differently, it is very common for there to be poor visibility conditions (e.g. rain, darkness) while performing these tests, further obscuring the results. In order to address these concerns and to create uniformity in the reporting of on-site colourimetric test results, this study has evaluated two of the state-of-the-art apps (ColorAssist® and Colorimeter®) for reporting the colour test results quantitatively in red-green-blue (RGB) format. The compiled library database of presumptive test results contains over 3300 data points including over 800 unique drug/test combinations. Variations observed between test replicates, from performing a test on different days, recording with a different device type (e.g. iPod Touch, iPhone models 4, 5c, 5s, or 6), and using different quantities of drug are discussed. Overall, the least variation in Euclidian norm was observed using ColorAssist® with the camera light (25.1±22.1) while the variation between replicates and data recorded using different devices was similar. The resulting library is uploaded to a smartphone application aimed to aid in identifying and interpreting suspected controlled substance evidence. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  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. Journal Coverage by the Major Chemical Title and Abstract Publications

    Science.gov (United States)

    Kiehlmann, Eberhard

    1972-01-01

    The journal coverage provided by Chemical Titles,'' Current Contents,'' Science Citation Index,'' Chemischer Informationsdienst,'' and Index Chemicus'' is discussed and compared with the CASSI list of the thousand primary journals most frequently cited by Chemical Abstracts.'' (10 references) (Author/NH)

  17. Navigating public health chemicals policy in Australia: a policy maker's and practitioner's guide.

    Science.gov (United States)

    Capon, Adam; Smith, Wayne; Gillespie, James A

    2013-03-01

    Chemicals are ubiquitous in everyday life. Environmental health practitioners rely on a complex web of regulators and policy bodies to ensure the protection of public health, yet few understand the full extent of this web. A lack of understanding can hamper public health response and impede policy development. In this paper we map the public health chemicals policy landscape in Australia and conclude that an understanding of this system is essential for effective environmental health responses and policy development.

  18. Reality theory: A means to control the public`s fear of chemical weapons use. Research report

    Energy Technology Data Exchange (ETDEWEB)

    Pate, B.E.

    1997-04-01

    On 20 March 1995 terrorists released the chemical nerve agent sarin into the Tokyo subway system, killing 10 commuters and changing the public`s attitude about the most basic aspect of their lives: the air they breathe and the daily ritual of their commute to work. This is the new threat the United States must face: terrorism and its attack on the will of the people forcing governments to yield to the terrorists` position. Yet there is a different public response in warfare compared with a peacetime terrorist attack. This paper examines the psychological response of people in wartime and applies this description to chemical weapons use in war and in peace. The public`s response can be predicted if one uses reality theory, a concept leaders can use to mitigate responses that would prevent the execution of national strategy.

  19. New agents with potential leishmanicidal activity identified by virtual screening of chemical databases: New agents with potential leishmanicidal activity

    Directory of Open Access Journals (Sweden)

    Juan Rebollo

    2013-04-01

    Full Text Available Introduction and Objectives: Leishmaniosis, a disease caused by a protozoan parasite, remains a serious public health problem threatening about 350 million people around the world, of which 12 million are believed to be currently infected (WHO 2010. To date, there are no vaccines against the species of parasites and the treatment is based only on chemotherapy with toxic-, expensive- and inefficient- drugs. There is an urgent need for better drugs against Leishmania, the etiological agent of the disease. The main anti-leishmanial drug used in Colombia is meglumineantimoniate [chemical name according to the International Union of Pure and Applied Chemistry (IUPAC: Hydroxy-dioxostiborane; (2R,3R,4R,5S- 6-methylaminohexane-1,2,3,4,5-pentol, (C7H17NO5], which is not efficient in the treatment of infections caused by Leishmania braziliensis, the most prevalent specie in the Caribbean coast of Colombia. Methods: We performed an in silico virtual screening of several datasets including ChemBridge and Pubchem. We virtually screened a total of 28.755 compounds against a 3D model of 6-phosphoglucono -lactonase (6-PGL from Leishmania braziliensis to identify novel inhibitors.Molecular docking of databases was performed using the software Sybyl 8.0 and AutoDockVina. Results: The initial virtual screening using a structure-based method identified 10 compounds, which were later tested with AutodockVina and classified according to their docking scores. Conclusions: These novel and potential inhibitors constitute new drug candidates that must be biologically tested to define their value as an alternative chemotherapeutic agent in the treatment of these protozoan infections. Salud UIS 2013; 45 (1: 33-40

  20. 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.

  1. Endocrine-disrupting chemicals and public health protection

    DEFF Research Database (Denmark)

    Zoeller, R Thomas; Brown, T R; Doan, L L

    2012-01-01

    exposures to have potent and irreversible effects. Finally, with regard to the current program designed to detect putative EDC, namely, the Endocrine Disruptor Screening Program, we offer recommendations for strengthening this program through the incorporation of basic endocrine principles to promote......An endocrine-disrupting chemical (EDC) is an exogenous chemical, or mixture of chemicals, that can interfere with any aspect of hormone action. The potential for deleterious effects of EDC must be considered relative to the regulation of hormone synthesis, secretion, and actions and the variability...... in regulation of these events across the life cycle. The developmental age at which EDC exposures occur is a critical consideration in understanding their effects. Because endocrine systems exhibit tissue-, cell-, and receptor-specific actions during the life cycle, EDC can produce complex, mosaic effects...

  2. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2016-02-15

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra

  3. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria.

    Science.gov (United States)

    Fritzsching, Keith J; Hong, Mei; Schmidt-Rohr, Klaus

    2016-02-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided

  4. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  5. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  6. Quantum Isostere Database: a web-based tool using quantum chemical topology to predict bioisosteric replacements for drug design.

    Science.gov (United States)

    Devereux, Mike; Popelier, Paul L A; McLay, Iain M

    2009-06-01

    This paper introduces the 'Quantum Isostere Database' (QID), a Web-based tool designed to find bioisosteric fragment replacements for lead optimization using stored ab initio data. A wide range of original geometric, electronic, and calculated physical properties are stored for each fragment. Physical descriptors with clear meaning are chosen, such as distribution of electrostatic potential energy values across a fragment surface and geometric parameters to describe fragment conformation and shape from ab initio structures. Further fundamental physical properties are linked to broader chemical characteristics relevant to biological activity, such as H-bond donor and acceptor strengths. Additional properties with less easily interpretable links to biological activity are also stored to allow future development of QSAR/QSPR models for quantities such as pK(a) and solubility. Conformational dependence of the ab initio descriptors is explicitly dealt with by storing properties for a variety of low-energy conformers of each fragment. Capping groups are used in ab initio calculations to represent different chemical environments, based on background research into transferability of electronic descriptors [J. Comput. Chem. 2009, 30, 1300-1318]. The resulting database has a Web interface that allows medicinal chemists to enter a query fragment, select important chemical features, and retrieve a list of suggested replacements with similar chemical characteristics. Examples of known bioisosteric replacements correctly identified by the QID tool are given.

  7. 78 FR 14299 - Notification of a Public Meeting of the Science Advisory Board Chemical Assessment Advisory...

    Science.gov (United States)

    2013-03-05

    ... chemicals. The SAB Staff Office previously requested public nominations of experts to serve on the SAB..., or Rich Text files in IBM-PC/Windows 98/2000/XP format). It is the SAB Staff Office general policy to...

  8. 78 FR 52525 - Dichloromethane and N-Methylpyrrolidone TSCA Chemical Risk Assessment; Notice of Public Meetings...

    Science.gov (United States)

    2013-08-23

    ... address: SWARNER@scgcorp.com . For general information contact: The TSCA-Hotline, ABVI-Goodwill, 422 South... product companies, and members of the public interested in the assessment of chemical risks. Since others...

  9. 78 FR 59679 - Antimony Trioxide TSCA Chemical Risk Assessment; Notice of Public Meetings and Opportunity To...

    Science.gov (United States)

    2013-09-27

    ... address: SWARNER@scgcorp.com . For general information contact: The TSCA-Hotline, ABVI-Goodwill, 422 South... product companies, and members of the public interested in the assessment of chemical risks. Since others...

  10. 75 FR 52355 - Draft National Conversation on Public Health and Chemical Exposures Work Group Reports...

    Science.gov (United States)

    2010-08-25

    ... Prevention Draft National Conversation on Public Health and Chemical Exposures Work Group Reports... exposures. This notice announces the availability of draft National Conversation work group reports for... National Conversation Leadership Council and facilitating the work group process. DATES: Draft work...

  11. 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."

  12. 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.

  13. Using Patent Classification to Discover Chemical Information in a Free Patent Database: Challenges and Opportunities

    Science.gov (United States)

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

    Developing skills for searching the patent literature is an essential element of chemical information literacy programs at the university level. The present article creates awareness of patents as a rich source of chemical information. Patent classification is introduced as a key-component in comprehensive search strategies. The free Espacenet…

  14. Chemical industry: Government regulations. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-05-01

    The bibliography contains citations concerning government regulation effects on the chemical industry. Regulations pertaining to industrial wastes, energy consumption and conservation, and industrial emissions are discussed. Emission standards and control, toxic substances control, and economic impacts of regulations affecting the chemical industry are considered.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  15. Database development of chemical thermodynamics of protactinium for performance assessment of HLW geological disposal system

    Energy Technology Data Exchange (ETDEWEB)

    Shibutani, Tomoki; Shibutani, Sanae; Yui, Mikazu [Power Reactor and Nuclear Fuel Development Corp., Tokai, Ibaraki (Japan). Tokai Works

    1998-03-01

    In the performance analysis of geological disposal system of high-level radioactive waste (HLW), solubilities of radioactive elements are estimated by thermodynamic calculation. The reliable thermodynamic database (TDB) is needed for solubility estimation. In this report, thermodynamic data for protactinium solid and aqueous species for performance assessment were selected. For the refinement of previous PNC in house thermodynamic database (PNC-TDB), existing literatures data were surveyed and reliable thermodynamic data were selected under consideration of the scientific defensibility and the consistency with the whole PNC-TDB. The estimated solubility using refined PNC-TDB was higher than measured value. We have confirmed the refined data-set of Pa to be conservative for solubility estimation of performance assessment. (author)

  16. 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...

  17. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

    2015-09-15

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

  18. 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

  19. ChemProt-2.0: visual navigation in a disease chemical biology database

    DEFF Research Database (Denmark)

    Kjærulff, Sonny Kim; Wich, Louis; Kringelum, Jens Vindahl

    2013-01-01

    measurements for 15 290 proteins. Each protein is linked to quality-scored human protein-protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO terms) through protein complexes. In ChemProt-2.0, therapeutic effects...... of proteins, which can help in the prediction of off-target effects. Finally, the database was integrated into a visual interface that enables navigation of the pharmacological space for small molecules. Filtering options were included in order to facilitate and to guide dynamic search of specific queries....

  20. Development of a Biomedical Database on the Medical Aspects of Chemical Defense

    Science.gov (United States)

    1988-12-01

    databases: Eric Biosis 1981 NTIS Social Scisearch Agricola 79 Psycinfo Chem Ind Notes Federal Index Claims/U.S. Patent Claims/U.S. Patent A Scisearch 84...CAT Enviro Perio Bib Intl Pharm ABS Life Sciences Collection Conf Papers Index PTS A/DM&T Scisearch 81-81 USPSD Scisearch 78-80 CIS Agricola 70-78... Business World Patents Index World Patents Index Remarc 1900-1939 Remarc 1940-1959 Remarc 1960-1969 Remarc 1970+ LC Marc Books in Print Wiley Catalog Online

  1. 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.

  2. [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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. The need for better public health decisions on chemicals released into our environment.

    Science.gov (United States)

    Woodruff, Tracey J; Burke, Thomas A; Zeise, Lauren

    2011-05-01

    Protecting the health of the public-particularly the most vulnerable groups, such as children-requires rethinking current approaches to reducing environmental risks. We review the evolving understanding of the relationship between exposure to chemicals in the environment and disease, as well as the current state of managing those chemicals. We present recommendations to improve current approaches, including changing the burden of proof so that chemicals are not presumed safe in the absence of scientific data. We also propose modernizing approaches to assessing health risks.

  8. Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

    Directory of Open Access Journals (Sweden)

    Diana Fusco

    Full Text Available X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. An analysis of Chemical Stockpile Emergency Preparedness Program exercise results. Volume 2: Preliminary evaluation and analysis of CSEPP exercise database

    Energy Technology Data Exchange (ETDEWEB)

    Wernette, D.; Lerner, K.

    1998-06-01

    This study investigated the quality and usefulness of the information in the Chemical Stockpile Emergency Preparedness Program (CSEPP) exercise database. It incorporates the results of two separate analytical efforts. The first effort investigated the process of assigning standardized codes to issues identified in CSEPP exercise reports. A small group of issues was coded independently by each of several individuals, and the results of the individual codings were compared. Considerable differences were found among the individuals` codings. The second effort consisted of a statistical multivariate analysis, to investigate whether exercise issues are evenly distributed among exercise tabs, sites, and objectives. It was found that certain tabs, sites, and objectives were disproportionately associated with problem areas in exercises. In some cases, these problem areas have persisted over time, but in other cases they have undergone significant shifts over the time span of the investigation. The study concludes that the database can be a useful resource for analyzing problem areas and setting priorities for CSEPP program resources. However, some further analyses should be performed in order to more fully explore the data and increase confidence in the results.

  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.

    2008-01-01

    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

  15. 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.

  16. 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.

  17. 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.

  18. The Matthew effect in environmental science publication: A bibliometric analysis of chemical substances in journal articles

    Directory of Open Access Journals (Sweden)

    Grandjean Philippe

    2011-11-01

    Full Text Available Abstract Background While environmental research addresses scientific questions of possible societal relevance, it is unclear to what degree research focuses on environmental chemicals in need of documentation for risk assessment purposes. Methods In a bibliometric analysis, we used SciFinder to extract Chemical Abstract Service (CAS numbers for chemicals addressed by publications in the 78 major environmental science journals during 2000-2009. The Web of Science was used to conduct title searches to determine long-term trends for prominent substances and substances considered in need of research attention. Results The 119,636 journal articles found had 760,056 CAS number links during 2000-2009. The top-20 environmental chemicals consisted of metals, (chlorinated biphenyls, polyaromatic hydrocarbons, benzene, and ethanol and contributed 12% toward the total number of links- Each of the top-20 substances was covered by 2,000-10,000 articles during the decade. The numbers for the 10-year period were similar to the total numbers of pre-2000 articles on the same chemicals. However, substances considered a high priority from a regulatory viewpoint, due to lack of documentation, showed very low publication rates. The persistence in the scientific literature of the top-20 chemicals was only weakly related to their publication in journals with a high impact factor, but some substances achieved high citation rates. Conclusions The persistence of some environmental chemicals in the scientific literature may be due to a 'Matthew' principle of maintaining prominence for the very reason of having been well researched. Such bias detracts from the societal needs for documentation on less well known environmental hazards, and it may also impact negatively on the potentials for innovation and discovery in research.

  19. The Matthew effect in environmental science publication: A bibliometric analysis of chemical substances in journal articles

    Science.gov (United States)

    2011-01-01

    Background While environmental research addresses scientific questions of possible societal relevance, it is unclear to what degree research focuses on environmental chemicals in need of documentation for risk assessment purposes. Methods In a bibliometric analysis, we used SciFinder to extract Chemical Abstract Service (CAS) numbers for chemicals addressed by publications in the 78 major environmental science journals during 2000-2009. The Web of Science was used to conduct title searches to determine long-term trends for prominent substances and substances considered in need of research attention. Results The 119,636 journal articles found had 760,056 CAS number links during 2000-2009. The top-20 environmental chemicals consisted of metals, (chlorinated) biphenyls, polyaromatic hydrocarbons, benzene, and ethanol and contributed 12% toward the total number of links- Each of the top-20 substances was covered by 2,000-10,000 articles during the decade. The numbers for the 10-year period were similar to the total numbers of pre-2000 articles on the same chemicals. However, substances considered a high priority from a regulatory viewpoint, due to lack of documentation, showed very low publication rates. The persistence in the scientific literature of the top-20 chemicals was only weakly related to their publication in journals with a high impact factor, but some substances achieved high citation rates. Conclusions The persistence of some environmental chemicals in the scientific literature may be due to a 'Matthew' principle of maintaining prominence for the very reason of having been well researched. Such bias detracts from the societal needs for documentation on less well known environmental hazards, and it may also impact negatively on the potentials for innovation and discovery in research. PMID:22074398

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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».

  5. Consumer Product Category Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Chemical and Product Categories database (CPCat) catalogs the use of over 40,000 chemicals and their presence in different consumer products. The chemical use...

  6. The Realization of Chemical Web Database in Web%化学网络数据库在WEB中的实现

    Institute of Scientific and Technical Information of China (English)

    周翠松; 李梦龙; 李工兵; 刘冀昆

    2003-01-01

      对化学网络数据库的结构和工作原理进行了介绍,对如何建立全面完整的化学网络数据库做了深入总结。以MySQL 作为数据库管理系统,选用中药数据(天然药物)为数据源,采用PERL为CGI开发工具,利用化学计量学算法和三维结构搜索开发了化学软件包,建立了WEB中的化学网络数据库。%  The structure and the principle of chemical web database were introduced and a deep sum-up on how to establish a comprehensive and complete chemical web database was also made in this paper. During the establishment of chemical web database, we chose MySQL as our DBMS and Chinese traditional medicine (natural medicament) as database resources, used PERL to develop the CGI and produced software packages by 3D structure research and chemometrics arithmetic.

  7. An isomer-specific high-energy collision-induced dissociation MS/MS database for forensic applications: a proof-of-concept on chemical warfare agent markers.

    Science.gov (United States)

    Subramaniam, Raja; Östin, Anders; Nygren, Yvonne; Juhlin, Lars; Nilsson, Calle; Åstot, Crister

    2011-09-01

    Spectra database search has become the most popular technique for the identification of unknown chemicals, minimizing the need for authentic reference chemicals. In the present study, an isomer-specific high-energy collision-induced dissociation (CID) MS/MS spectra database of 12 isomeric O-hexyl methylphosphonic acids (degradation markers of nerve agents) was created. Phosphonate anions were produced by the electrospray ionization of phosphonic acids or negative-ion chemical ionization of their fluorinated derivatives and were analysed in a hybrid magnetic-sector-time-of-flight tandem mass spectrometer. A centre-of-mass energy (E(com)) of 65 eV led to an optimal sequential carbon-carbon bond breakage, which was interpreted in terms of charge remote fragmentation. The proposed mechanism is discussed in comparison with the routinely used low-energy CID MS/MS. Even-mass (odd-electron) charge remote fragmentation ion series were diagnostic of the O-alkyl chain structure and can be used to interpret unknown spectra. Together with the odd-mass ion series, they formed highly reproducible, isomer-specific spectra that gave significantly higher database matches and probability factors (by 1.5 times) than did the EI MS spectra of the trimethylsilyl derivatives of the same isomers. In addition, ionization by negative-ion chemical ionization and electrospray ionization resulted in similar spectra, which further highlights the general potential of the high-energy CID MS/MS technique.

  8. 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…

  9. 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.

  10. Lessons learned from process incident databases and the process safety incident database (PSID) approach sponsored by the Center for Chemical Process Safety

    Energy Technology Data Exchange (ETDEWEB)

    Sepeda, Adrian L. [American Institute of Chemical Engineers, Center for Chemical Process Safety, A.L. Sepeda Consulting Inc., P.O. Box 250183, Plano, TX 75025-0183 (United States)]. E-mail: Adrian_L@swbell.net

    2006-03-17

    Learning from the experiences of others has long been recognized as a valued and relatively painless process. In the world of process safety, this learning method is an essential tool since industry has neither the time and resources nor the willingness to experience an incident before taking corrective or preventative steps. This paper examines the need for and value of process safety incident databases that collect incidents of high learning value and structure them so that needed information can be easily and quickly extracted. It also explores how they might be used to prevent incidents by increasing awareness and by being a tool for conducting PHAs and incident investigations. The paper then discusses how the CCPS PSID meets those requirements, how PSID is structured and managed, and its attributes and features.

  11. 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 ...

  12. Evidence of Coal-Fly-Ash Toxic Chemical Geoengineering in the Troposphere: Consequences for Public Health

    Directory of Open Access Journals (Sweden)

    J. Marvin Herndon

    2015-08-01

    Full Text Available The widespread, intentional and increasingly frequent chemical emplacement in the troposphere has gone unidentified and unremarked in the scientific literature for years. The author presents evidence that toxic coal combustion fly ash is the most likely aerosolized particulate sprayed by tanker-jets for geoengineering, weather-modification and climate-modification purposes and describes some of the multifold consequences on public health. Two methods are employed: (1 Comparison of 8 elements analyzed in rainwater, leached from aerosolized particulates, with corresponding elements leached into water from coal fly ash in published laboratory experiments, and (2 Comparison of 14 elements analyzed in dust collected outdoors on a high-efficiency particulate air (HEPA filter with corresponding elements analyzed in un-leached coal fly ash material. The results show: (1 the assemblage of elements in rainwater and in the corresponding experimental leachate are essentially identical. At a 99% confidence interval, they have identical means (T-test and identical variances (F-test; and (2 the assemblage of elements in the HEPA dust and in the corresponding average un-leached coal fly ash are likewise essentially identical. The consequences on public health are profound, including exposure to a variety of toxic heavy metals, radioactive elements, and neurologically-implicated chemically mobile aluminum released by body moisture in situ after inhalation or through transdermal induction.

  13. Evidence of Coal-Fly-Ash Toxic Chemical Geoengineering in the Troposphere: Consequences for Public Health.

    Science.gov (United States)

    Herndon, J Marvin

    2015-08-11

    The widespread, intentional and increasingly frequent chemical emplacement in the troposphere has gone unidentified and unremarked in the scientific literature for years. The author presents evidence that toxic coal combustion fly ash is the most likely aerosolized particulate sprayed by tanker-jets for geoengineering, weather-modification and climate-modification purposes and describes some of the multifold consequences on public health. Two methods are employed: (1) Comparison of 8 elements analyzed in rainwater, leached from aerosolized particulates, with corresponding elements leached into water from coal fly ash in published laboratory experiments, and (2) Comparison of 14 elements analyzed in dust collected outdoors on a high-efficiency particulate air (HEPA) filter with corresponding elements analyzed in un-leached coal fly ash material. The results show: (1) the assemblage of elements in rainwater and in the corresponding experimental leachate are essentially identical. At a 99% confidence interval, they have identical means (T-test) and identical variances (F-test); and (2) the assemblage of elements in the HEPA dust and in the corresponding average un-leached coal fly ash are likewise essentially identical. The consequences on public health are profound, including exposure to a variety of toxic heavy metals, radioactive elements, and neurologically-implicated chemically mobile aluminum released by body moisture in situ after inhalation or through transdermal induction.

  14. 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.

  15. 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.

  16. Chemical and biological warfare: Biology, chemistry, and toxicology. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning the physiological effects, physicochemical effects, and toxicology of chemical and biological warfare agents. Citations discuss toxic chemicals, chemical agent simulants, detoxification and decontamination, environmental toxicity, and land pollution. Detection techniques and warning systems are examined in a separate bibliography. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  17. Chemical and biological warfare: Biology, chemistry, and toxicology. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning the physiological effects, physicochemical effects, and toxicology of chemical and biological warfare agents. Citations discuss toxic chemicals, chemical agent simulants, detoxification and decontamination, environmental toxicity, and land pollution. Detection techniques and warning systems are examined in a separate bibliography. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. Chemical and biological warfare: Detection and warning systems. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning the detection, identification, verification, and warning systems of chemical and biological warfare agents. Citations discuss agents sampling, monitoring, and assessment. Techniques include chromotography, biosensing, chemical analysis, and DNA probes. Land pollution, soil tests, and skin protection are examined. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  3. Exploring consumer exposure pathways and patterns of use for chemicals in the environment

    OpenAIRE

    Dionisio, Kathie L.; Alicia M. Frame; Goldsmith, Michael-Rock; Wambaugh, John F.; Liddell, Alan; Cathey, Tommy; Smith, Doris; Vail, James; Ernstoff, Alexi; Fantke, Peter; Jolliet, Olivier; Judson, Richard S.

    2015-01-01

    Humans are exposed to thousands of chemicals in the workplace, home, and via air, water, food, and soil. A major challenge in estimating chemical exposures is to understand which chemicals are present in these media and microenvironments. Here we describe the Chemical/Product Categories Database (CPCat), a new, publically available (http://actor.epa.gov/cpcat) database of information on chemicals mapped to “use categories” describing the usage or function of the chemical. CPCat was created by...

  4. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

    Science.gov (United States)

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

  5. Chemical and biological warfare: Protection, decontamination, and disposal. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning the means to defend against chemical and biological agents used in military operations, and to eliminate the effects of such agents on personnel, equipment, and grounds. Protection is accomplished through protective clothing and masks, and in buildings and shelters through filtration. Elimination of effects includes decontamination and removal of the agents from clothing, equipment, buildings, grounds, and water, using chemical deactivation, incineration, and controlled disposal of material in injection wells and ocean dumping. Other Published Searches in this series cover chemical warfare detection; defoliants; general studies; biochemistry and therapy; and biology, chemistry, and toxicology associated with chemical warfare agents.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  6. Chemical and biological warfare: Protection, decontamination, and disposal. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning the means to defend against chemical and biological agents used in military operations, and to eliminate the effects of such agents on personnel, equipment, and grounds. Protection is accomplished through protective clothing and masks, and in buildings and shelters through filtration. Elimination of effects includes decontamination and removal of the agents from clothing, equipment, buildings, grounds, and water, using chemical deactivation, incineration, and controlled disposal of material in injection wells and ocean dumping. Other Published Searches in this series cover chemical warfare detection; defoliants; general studies; biochemistry and therapy; and biology, chemistry, and toxicology associated with chemical warfare agents. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  7. [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.

  8. Pool chemical-associated health events in public and residential settings - United States, 2003-2012, and Minnesota, 2013.

    Science.gov (United States)

    Hlavsa, Michele C; Robinson, Trisha J; Collier, Sarah A; Beach, Michael J

    2014-05-16

    Pool chemicals are added to treated recreational water venues (e.g., pools, hot tubs/spas, and interactive fountains) primarily to protect public health by inactivating pathogens and maximizing the effectiveness of disinfection by controlling pH. However, pool chemicals also can cause injuries when handled or stored improperly. To estimate the number of emergency department (ED) visits for injuries associated with pool chemicals in the United States per year during 2003-2012, CDC analyzed data from the U.S. Consumer Product Safety Commission's National Electronic Injury Surveillance System (NEISS). This report summarizes the results of that analysis. In 2012 alone, an estimated 4,876 persons (95% confidence interval [CI] = 2,821-6,930) visited an ED for injuries associated with pool chemicals. Almost half of the patients were aged pool chemical-associated health event that occurred in Minnesota in 2013, which sent seven children and one adult to an ED. An investigation by the Minnesota Department of Health (MDH) determined the cause to be poor monitoring of or response to pool chemistry. Pool chemical-associated health events are preventable. CDC's Model Aquatic Health Code (MAHC) (1) is a resource that state and local agencies can use to optimize prevention of injuries and illnesses associated with public treated recreational water venues, including pool chemical-associated health events.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress

    Science.gov (United States)

    A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate and aggregate such information by chemical, and broad data coverage within...

  15. Chemical and microbiological analysis of public school water in Uberaba Municipality

    Directory of Open Access Journals (Sweden)

    Sérgio Marcos Sanches

    2015-07-01

    Full Text Available This study evaluated the quality of water consumed by schoolchildren in the city of Uberaba, relying upon chemical analyzes to determine the levels of free-residual chlorine and levels of chromium, copper, manganese, lead and cadmium. Microbiological analysis was also performed in order to determine total coliforms and Escherichia coli, using the values established by Ordinance n0 . 2914 of 2011 of the Ministry of Health as parameters for safe drinking water. Water samples were analyzed from the drinking fountains and kitchen faucets of eight public schools that serve children aged 0-5 years. Sampling was conducted quarterly from December 2011 to September 2012, resulting in four collections. The results revealed the presence of Escherichia coli and total coliforms above the valued permitted by legislation in more than 50% of the samples. It was also observed that concentrations of free-residual chlorine were below the minimum value required by law in nearly half of the samples analyzed. In relation to the concentration of metals, some samples had water contents of copper, cadmium, chromium, manganese and lead above the permissible levels. Statistical tests revealed that when analyzing the period of sampling, only the values for the concentrations of free-residual chlorine, chromium and lead showed no significant difference (p> 0.05. The results show the need for corrective actions at the water supply point for the school population, in addition to monitoring and controlling the quality of water for human consumption.

  16. The High-Throughput Stochastic Human Exposure and Dose Simulation Model (SHEDS-HT) & The Chemical and Products Database (CPDat)

    Science.gov (United States)

    The Stochastic Human Exposure and Dose Simulation Model – High-Throughput (SHEDS-HT) is a U.S. Environmental Protection Agency research tool for predicting screening-level (low-tier) exposures to chemicals in consumer products. This course will present an overview of this m...

  17. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical s...

  18. Development of databases for use in validation studies of probabilistic models of dietary exposure to food chemicals and nutrients

    NARCIS (Netherlands)

    Leclerq, C.; Arcella, D.; Armentia, A.; Boon, P.E.; Kruizinga, A.G.; Gilsenan, M.B.; Thompson, R.L.

    2003-01-01

    The data currently available in the European Union in terms of food consumption and of food chemical and nutrient concentration data present many limitations when used for estimating intake. The most refined techniques currently available were used within the European Union FP5 Monte Carlo project t

  19. 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.

  20. 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

  1. CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

    Science.gov (United States)

    Waters, Michael; Stasiewicz, Stanley; Merrick, B Alex; Tomer, Kenneth; Bushel, Pierre; Paules, Richard; Stegman, Nancy; Nehls, Gerald; Yost, Kenneth J; Johnson, C Harris; Gustafson, Scott F; Xirasagar, Sandhya; Xiao, Nianqing; Huang, Cheng-Cheng; Boyer, Paul; Chan, Denny D; Pan, Qinyan; Gong, Hui; Taylor, John; Choi, Danielle; Rashid, Asif; Ahmed, Ayazaddin; Howle, Reese; Selkirk, James; Tennant, Raymond; Fostel, Jennifer

    2008-01-01

    CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis. Scope of CEBS: CEBS currently holds 22 studies of rats, four studies of mice and one study of Caenorhabditis elegans. CEBS can also accommodate data from studies of human subjects. Toxicogenomics studies currently in CEBS comprise over 4000 microarray hybridizations, and 75 2D gel images annotated with protein identification performed by MALDI and MS/MS. CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Additionally, clinical chemistry and histopathology findings from over 1500 animals are included in CEBS. CEBS/BID: The BID (Biomedical Investigation Database) is another component of the CEBS system. BID is a relational database used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee (in preparation). BID has been shared with Health Canada and the US Environmental Protection Agency. CEBS is available at http://cebs.niehs.nih.gov. BID can be accessed via the user interface from https://dir-apps.niehs.nih.gov/arc/. Requests for a copy of BID and for depositing data into CEBS or BID are available at http://www.niehs.nih.gov/cebs-df/.

  2. Organization and Efficient Manual Searching of the Major Chemical Title and Abstract Publications

    Science.gov (United States)

    Kiehlmann, Eberhard

    1973-01-01

    Science Citation Index'' and several new Chemical Abstracts''' indexes are discussed as effective tools for retrospective literature work and a comparison is made of the features of Chemischer Informationsdienst,'' Index Chemicus,'' Chemical Titles,'' and Current Contents'' as the main sources of current chemical information. (9 references)…

  3. Understanding public responses to chemical, biological, radiological and nuclear incidents--driving factors, emerging themes and research gaps.

    Science.gov (United States)

    Krieger, Kristian; Amlôt, Richard; Rogers, M Brooke

    2014-11-01

    This paper discusses the management of public responses to incidents involving chemical, biological, radiological and nuclear materials (CBRN). Given the extraordinary technical and operational challenges of a response to a CBRN release including, but not limited to, hazard detection and identification, casualty decontamination and multi-agency co-ordination, it is not surprising that public psychological and behavioural responses to such incidents have received limited attention by scholars and practitioners alike. As a result, a lack of understanding about the role of the public in effective emergency response constitutes a major gap in research and practice. This limitation must be addressed as a CBRN release has the potential to have wide-reaching psychological and behavioural impacts which, in turn, impact upon public morbidity and mortality rates. This paper addresses a number of key issues: why public responses matter; how responses have been conceptualised by practitioners; what factors have been identified as influencing public responses to a CBRN release and similar extreme events, and what further analysis is needed in order to generate a better understanding of public responses to inform the management of public responses to a CBRN release. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. 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

  5. Exploring Natural Products from the Biodiversity of Pakistan for Computational Drug Discovery Studies: Collection, Optimization, Design and Development of A Chemical Database (ChemDP).

    Science.gov (United States)

    Mirza, Shaher Bano; Bokhari, Habib; Fatmi, Muhammad Qaiser

    2015-01-01

    Pakistan possesses a rich and vast source of natural products (NPs). Some of these secondary metabolites have been identified as potent therapeutic agents. However, the medicinal usage of most of these compounds has not yet been fully explored. The discoveries for new scaffolds of NPs as inhibitors of certain enzymes or receptors using advanced computational drug discovery approaches are also limited due to the unavailability of accurate 3D structures of NPs. An organized database incorporating all relevant information, therefore, can facilitate to explore the medicinal importance of the metabolites from Pakistani Biodiversity. The Chemical Database of Pakistan (ChemDP; release 01) is a fully-referenced, evolving, web-based, virtual database which has been designed and developed to introduce natural products (NPs) and their derivatives from the biodiversity of Pakistan to Global scientific communities. The prime aim is to provide quality structures of compounds with relevant information for computer-aided drug discovery studies. For this purpose, over 1000 NPs have been identified from more than 400 published articles, for which 2D and 3D molecular structures have been generated with a special focus on their stereochemistry, where applicable. The PM7 semiempirical quantum chemistry method has been used to energy optimize the 3D structure of NPs. The 2D and 3D structures can be downloaded as .sdf, .mol, .sybyl, .mol2, and .pdb files - readable formats by many chemoinformatics/bioinformatics software packages. Each entry in ChemDP contains over 100 data fields representing various molecular, biological, physico-chemical and pharmacological properties, which have been properly documented in the database for end users. These pieces of information have been either manually extracted from the literatures or computationally calculated using various computational tools. Cross referencing to a major data repository i.e. ChemSpider has been made available for overlapping

  6. Chemical and isotopic provenance tracers in ancient copper and bronze artifacts: a geochemical database of copper mines

    Science.gov (United States)

    Giunti, I.; Artioli, G.; Giussani, B.; Marelli, M.; Recchia, S.; Angelini, I.; Baumgarten, B.; Omenetto, P.; Villa, I. M.

    2009-04-01

    The provenance of ore minerals used in prehistoric and historic times for copper smelting and extraction is one of the basic questions that archaeologists pose to modern analytical archaeometry [1]. To aid metal provenancing studies, a database of fully characterized Alpine copper mineralisations is being developed as the fundamental reference frame for metal extraction and diffusion in the past. In the early stages of the project, some of the most well known copper deposits in the Western Alps were selected and compared with very different minerogenetic deposits from the French Queyras (Saint Veran) and the Ligurian Apennines (Libiola, Monte Loreto). The fully characterized samples were then analysed by ICP-QMS (inductively coupled plasma-quadrupolar mass spectrometry). The abundances of about 60 minor and trace elements, including most transition metals and chalcophile elements, and the rare earths were measured in all samples. Furthermore, the feasibility of the routine reliable measurement of the 65Cu/63Cu isotope ratio [2] and its eventual use as a possible ore tracer was tested. Multicollector ICP-Mass Spectrometry was used to determine precise Pb isotopic ratios (206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb) and is being used for 65Cu/63Cu ratios as well. Advanced strategies based on multivariate analysis were then used to discriminate the ore mineral provenance. Data were treated with the chemometric software "The Unscrambler Version 9.5" (CAMO AS, Trondheim, Norway). Data pre-treatment, PCA [3] and PLS-DA [4,5] models were performed as implemented in the software. The availability of such unprecedented and complete amount of data of Alpine copper deposits also yields information relevant for the geochemical and minerogenetic intepretation of the deposits themselves. Application of PCA and PLS-DA to the geochemical and isotopic database proved to be a very powerful tool to discriminate the ore source areas with very little ambiguity. The applications to

  7. Chemical and biological warfare: Biochemistry, therapy, and treatment. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-01

    The bibliography contains citations concerning biochemistry, therapy, and treatment of the effects of military chemical and biological warfare agents. References include surveys and studies of immunizing agents and drugs, the efficacy of these drugs, and the effect of the drugs on the patient. Also included are biochemical studies, assay techniques, and antidote development, some of which is supported by animal studies. Citations concerning detection and warning, defoliants, protection, biology and toxicology, and general studies are covered in separate bibliographies.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  8. Chemical and biological warfare: Biochemistry, therapy, and treatment. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning biochemistry, therapy, and treatment of the effects of military chemical and biological warfare agents. References include surveys and studies of immunizing agents and drugs, the efficacy of these drugs, and the effect of the drugs on the patient. Also included are biochemical studies, assay techniques, and antidote development, some of which is supported by animal studies. Citations concerning detection and warning, defoliants, protection, biology and toxicology, and general studies are covered in separate bibliographies.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  9. 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.

  10. Modeling of The hERG K+ Channel Blockage Using Online Chemical Database and Modeling Environment (OCHEM).

    Science.gov (United States)

    Li, Xiao; Zhang, Yuan; Li, Huanhuan; Zhao, Yong

    2017-08-30

    Human ether-a-go-go related gene (hERG) K+ channel plays an important role in cardiac action potential. Blockage of hERG channel may result in long QT syndrome (LQTS), even cause sudden cardiac death. Many drugs have been withdrawn from the market because of the serious hERG-related cardiotoxicity. Therefore, it is quite essential to estimate the chemical blockage of hERG in the early stage of drug discovery. In this study, a diverse set of 3721 compounds with hERG inhibition data was assembled from literature. Then, we make full use of the Online Chemical Modeling Environment (OCHEM), which supplies rich machine learning methods and descriptor sets, to build a series of classification models for hERG blockage. We also generated two consensus models based on the top-performing individual models. The consensus models performed much better than the individual models both on 5-fold cross validation and external validation. Especially, consensus model II yielded the prediction accuracy of 89.5 % and MCC of 0.670 on external validation. This result indicated that the predictive power of consensus model II should be stronger than most of the previously reported models. The 17 top-performing individual models and the consensus models and the data sets used for model development are available at https://ochem.eu/article/103592. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-05-27

    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.

  16. 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

  17. Preview of DATACHOA Ver. 1.0: Database for Chemical and Physical Properties of Molten Chloride Salts Comprising Actinide and Lanthanide Chloride Salts

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong-Yun; Lee, Jin-Hong; Park, Tae-Hong; Bae, Sang-Eun; Cho, Young Hwan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-10-15

    International Atomic Energy Agency (IAEA) provides molten salt database based on a world-wide-web (WWW) server. However, many data useful for the pyroprocess under development in Korea are missing. We have developed various measurement techniques for obtaining the chemical and physical data of the molten salts over the last four years: absorption spectra, emission spectra, molar absorptivity, Gibbs free energy, apparent potential, activity coefficient, exchange current density, solubility, electrical conductivity, density, surface tension, viscosity, melting point, diffusion coefficient, etc, which have been of our current interests. Those property data are essential in the understanding and the operation of the pyrochemical system. Some properties are intercorrelated, and multi-component molten salt systems can be understood by using a multivariate chemometric data analysis. Our final goal is to establish the 'Expert System', which is defined as a system that emulates the decision-making ability of a human expert. Although expert systems have been successful in the artificial intelligence, they are not known to chemists or chemical engineers for many years. The DATACHOA is the first step forward to the 'Expert System', although the amount of our property data is not currently enough to build up the 'Expert System'. DATACHOA is our first attempt to collect extensive basic and fundamental properties of molten salts of interest to pyroprocess chemists and engineers in Korea. DATACHOA ver. 1.0 will be released to the pyroprocess engineers within a few months.

  18. 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.

  19. 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...

  20. 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...

  1. MACiE: A Database of Enzyme Reaction Mechanisms

    Science.gov (United States)

    Holliday, Gemma L.; Bartlett, Gail J.; Almonacid, Daniel E.; O’Boyle, Noel M.; Murray-Rust, Peter; Thornton, Janet M.; Mitchell, John B. O.

    2009-01-01

    Summary MACiE (Mechanism, Annotation and Classification in Enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. PMID:16188925

  2. The Colorful Chemical Bottle Experiment Kit: From School Laboratory To Public Demonstration

    OpenAIRE

    Limpanuparb, Taweetham; Hsu, Suphattra

    2015-01-01

    The blue bottle experiment was first introduced to the chemical education literature as a simple demonstration on kinetics. Its original formulation contains only glucose, NaOH and small amount of methylene blue. The solution turns blue when shaken and fades to colorless upon standing. This bluing/de-bluing cycle may be repeated and may be compared to blood colors in animal's respiratory cycle. Inspired by the blue bottle experiment, the colorful chemical bottle experiment kit was commerciall...

  3. 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.

  4. CHEMICALS

    CERN Document Server

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  5. 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.

  6. The Colorful Chemical Bottle Experiment Kit: From School Laboratory To Public Demonstration

    CERN Document Server

    Limpanuparb, Taweetham

    2015-01-01

    The blue bottle experiment was first introduced to the chemical education literature as a simple demonstration on kinetics. Its original formulation contains only glucose, NaOH and small amount of methylene blue. The solution turns blue when shaken and fades to colorless upon standing. This bluing/de-bluing cycle may be repeated and may be compared to blood colors in animal's respiratory cycle. Inspired by the blue bottle experiment, the colorful chemical bottle experiment kit was commercially developed in 2006. The kit is a versatile pedagogical tool, not only for physical chemistry but also for analytical, biological and organic chemistry. It also helps teaching concepts in scientific method and laboratory safety. This manuscript contains four parts, brief review on literature relating to the blue bottle experiment, description of the colorful chemical bottle experiment kit, pedagogical discussion of the experiments and preliminary evaluation from students.

  7. 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.

  8. The Matthew effect in environmental science publication: A bibliometric analysis of chemical substances in journal articles

    DEFF Research Database (Denmark)

    Grandjean, Philippe; Eriksen, Mette Lindholm; Ellegaard, Ole

    2011-01-01

    Background While environmental research addresses scientific questions of possible societal relevance, it is unclear to what degree research focuses on environmental chemicals in need of documentation for risk assessment purposes. Methods In a bibliometric analysis, we used SciFinder to extract...

  9. 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/.

  10. 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..

  11. Key aspects of a Flemish system to safeguard public health interests in case of chemical release incidents.

    Science.gov (United States)

    Smolders, Roel; Colles, Ann; Cornelis, Christa; Van Holderbeke, Mirja; Chovanova, Hana; Wildemeersch, Dirk; Mampaey, Maja; Van Campenhout, Karen

    2014-12-15

    Although well-established protocols are available for emergency services and first-responders in case of chemical release incidents, a well-developed system to monitor and safeguard public health was, until recently, lacking in Flanders. We therefore developed a decision support system (DSS) to aid public health officials in identifying the appropriate actions in case of incidents. Although the DSS includes human biomonitoring as one of its key instruments, it also goes well beyond this instrument alone. Also other, complementary, approaches that focus more on effect assessment using in vitro toxicity testing, indirect exposures through the food chain, and parallel means of data collection (e.g. through ecosurveillance or public consultation), are integrated in the Flemish approach. Even though the DSS is set up to provide a flexible and structured decision tree, the value of expert opinion is deemed essential to account for the many uncertainties associated with the early phases of technological incidents. When the DSS and the associated instruments will be fully operational, it will provide a valuable addition to the already available protocols, and will specifically safeguard public health interests.

  12. Reconnaissance of Volatile Synthetic Organic Chemicals at Public Water Supply Wells Throughout Puerto Rico, November 1984-May 1985

    Science.gov (United States)

    Guzman-Rios, Senen; Garcia, Rene; Aviles, Ada

    1987-01-01

    INTRODUCTION Ground water is the principal source of drinking water for about 850,000 people in Puerto Rico (National Water Summary, 1985). Ground-water withdrawals for public supply, agricultural, and industrial water uses in Puerto Rico are about 250 million gallons per day (Mgal/d) (Torres-Sierra and Aviles, 1985). The development of the most accessible surface water supplies will result in an increasing demand for ground water. Recent investigations conducted by the U. S. Geological Survey, WRD (USGS) have shown the presence of toxic synthetic organic chemicals in ground water throughout Puerto Rico (Gomez-Gomez and Guzman-Rios, 1982). Volatile synthetic organic chemicals (VOC's) have been detected in water from public water supply wells in concentrations ranging from 1 to 500 micrograms per liter (Guzman-Rios and Quinones-Marquez, 1984 and Guzman-Rios and Quinones-Marquez, 1985). As result of these findings, pumpage was discontinued at 6 wells operated by the Puerto Rico Aqueduct and Sewer Authority (PRASA), the Commonwealth of Puerto Rico agency responsible for public-water supply. Monitoring of 10 additional wells in the vicinity of those wells is being conducted by the USGS in cooperation with PRASA. In 1985, the USGS began a comprehensive islandwide study of VOC's in drinking water. The study was conducted in cooperation with the Puerto Rico Department of Health (PRDOH) and PRASA. Samples were collected from 243 public-water supply wells operated by PRASA (flgure 1). The authors wish to acknowledge the support, assistance and cooperation of the PRASA staff throughout Puerto Rico in the sample collection effort. The authors are especially grateful to Engineer Carlos Garcia-Troche from the PRASA main office in San Juan.

  13. 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.

  14. Toxicity of the Organophosphate Chemical Warfare Agents GA, GB, and VX: Implications for Public Protection.

    OpenAIRE

    Munro, N

    1994-01-01

    The nerve agents, GA, GB, and VX are organophosphorus esters that form a major portion of the total agent volume contained in the U.S. stockpile of unitary chemical munitions. Congress has mandated the destruction of these agents, which is currently slated for completion in 2004. The acute, chronic, and delayed toxicity of these agents is reviewed in this analysis. The largely negative results from studies of genotoxicity, carcinogenicity, developmental, and reproductive toxicity are also pre...

  15. Final Technical Report - Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web

    Energy Technology Data Exchange (ETDEWEB)

    Ostlund, Neil [Chemical Semantics, Inc.,Gainesville, FL (United States)

    2017-07-20

    This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giant Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.

  16. 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

  17. 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.

  18. 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.

  19. 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...

  20. 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…

  1. 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…

  2. 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...

  3. CAMEO Chemicals Software

    Science.gov (United States)

    CAMEO Chemicals is an extensive chemical database, available for download, with critical response information for thousands of chemicals, and a tool that tells you what reactions might occur if chemicals were mixed together.

  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. 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/.

  6. 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

  7. The Database Research of Sudden Chemical Poisoning in Gaolan Port of Zhuhai City%珠海市高栏港区突发化学中毒数据库研究

    Institute of Scientific and Technical Information of China (English)

    胡俊; 吴兆伦; 陈杏云; 罗浮亮

    2015-01-01

    目的:建立一个动态地数据应用系统,包括化学泄露隐患、危害因素识别和应急救援以及应急减灾方法数据库,目的是提高应对突发性化学中毒事件的能力。方法搜集港区化学品数据,采用PHP 5.2语言、mysq l5.5数据库以及apache2.46 Web服务器软件作为应用技术服务器平台构建数据库,提供快速检索功能。结果建立了高栏港区突发化学中毒应急数据库,可通过多种途径检索、查询并迅速识别化学毒物的名称、理化性能以及应急救治方法和脱毒减毒方法。结论通过网页浏览方式查询毒物信息,有助于突发中毒事故中危害因素的快速识别。%Objective To establish a dynamically data application system,including chemical leakage hidden trouble database,hazard identification and emergency rescue database,and emergency relief method database. The system was to improve the the ability of response time and the ability to respond to sudden chemical poisoning events.MethodsColecting the chemical data of Gaolan port,use PHP 5.2 language,mysq l5.5 database and apache 2.46 Web server software to build database,and provides a rapid retrieval function.Results The sudden chemical poisoning emergency database of Gaolan is established. Through the database We can quickly identify the poison,retrieve the name of poison,the performance of poison,the contingency approach and treatment method of poison,and the detoxification attenuated method of poison.Conclusion Searching the poison information through the web browser, it is helpful for the rapid identification of the harmful factors in the sudden poisoning accident.

  8. Exploring consumer exposure pathways and patterns of use for chemicals in the environment

    DEFF Research Database (Denmark)

    Dionisio, Kathie L.; Frame, Alicia M.; Goldsmith, Michael-Rock

    2015-01-01

    (CPCat), a new, publically available (http://actor.epa.gov/cpcat) database of information on chemicals mapped to “use categories” describing the usage or function of the chemical. CPCat was created by combining multiple and diverse sources of data on consumer- and industrial-process based chemical uses...

  9. The CAPEC Database

    DEFF Research Database (Denmark)

    Nielsen, Thomas Lund; Abildskov, Jens; Harper, Peter Mathias

    2001-01-01

    The Computer-Aided Process Engineering Center (CAPEC) database of measured data was established with the aim to promote greater data exchange in the chemical engineering community. The target properties are pure component properties, mixture properties, and special drug solubility data. The datab......The Computer-Aided Process Engineering Center (CAPEC) database of measured data was established with the aim to promote greater data exchange in the chemical engineering community. The target properties are pure component properties, mixture properties, and special drug solubility data....... The database divides pure component properties into primary, secondary, and functional properties. Mixture properties are categorized in terms of the number of components in the mixture and the number of phases present. The compounds in the database have been classified on the basis of the functional groups...... in the compound. This classification makes the CAPEC database a very useful tool, for example, in the development of new property models, since properties of chemically similar compounds are easily obtained. A program with efficient search and retrieval functions of properties has been developed....

  10. 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.

  11. 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…

  12. 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.

  13. ACToR Chemical Structure processing using Open Source ...

    Science.gov (United States)

    ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

  14. 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...

  15. 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...

  16. Self-reported household impacts of large-scale chemical contamination of the public water supply, Charleston, West Virginia, USA.

    Directory of Open Access Journals (Sweden)

    Charles P Schade

    Full Text Available A January 2014 industrial accident contaminated the public water supply of approximately 300,000 homes in and near Charleston, West Virginia (USA with low levels of a strongly-smelling substance consisting principally of 4-methylcyclohexane methanol (MCHM. The ensuing state of emergency closed schools and businesses. Hundreds of people sought medical care for symptoms they related to the incident. We surveyed 498 households by telephone to assess the episode's health and economic impact as well as public perception of risk communication by responsible officials. Thirty two percent of households (159/498 reported someone with illness believed to be related to the chemical spill, chiefly dermatological or gastrointestinal symptoms. Respondents experienced more frequent symptoms of psychological distress during and within 30 days of the emergency than 90 days later. Sixty-seven respondent households (13% had someone miss work because of the crisis, missing a median of 3 days of work. Of 443 households reporting extra expenses due to the crisis, 46% spent less than $100, while 10% spent over $500 (estimated average about $206. More than 80% (401/485 households learned of the spill the same day it occurred. More than 2/3 of households complied fully with "do not use" orders that were issued; only 8% reported drinking water against advice. Household assessments of official communications varied by source, with local officials receiving an average "B" rating, whereas some federal and water company communication received a "D" grade. More than 90% of households obtained safe water from distribution centers or stores during the emergency. We conclude that the spill had major economic impact with substantial numbers of individuals reporting incident-related illnesses and psychological distress. Authorities were successful supplying emergency drinking water, but less so with risk communication.

  17. Self-reported household impacts of large-scale chemical contamination of the public water supply, Charleston, West Virginia, USA.

    Science.gov (United States)

    Schade, Charles P; Wright, Nasandra; Gupta, Rahul; Latif, David A; Jha, Ayan; Robinson, John

    2015-01-01

    A January 2014 industrial accident contaminated the public water supply of approximately 300,000 homes in and near Charleston, West Virginia (USA) with low levels of a strongly-smelling substance consisting principally of 4-methylcyclohexane methanol (MCHM). The ensuing state of emergency closed schools and businesses. Hundreds of people sought medical care for symptoms they related to the incident. We surveyed 498 households by telephone to assess the episode's health and economic impact as well as public perception of risk communication by responsible officials. Thirty two percent of households (159/498) reported someone with illness believed to be related to the chemical spill, chiefly dermatological or gastrointestinal symptoms. Respondents experienced more frequent symptoms of psychological distress during and within 30 days of the emergency than 90 days later. Sixty-seven respondent households (13%) had someone miss work because of the crisis, missing a median of 3 days of work. Of 443 households reporting extra expenses due to the crisis, 46% spent less than $100, while 10% spent over $500 (estimated average about $206). More than 80% (401/485) households learned of the spill the same day it occurred. More than 2/3 of households complied fully with "do not use" orders that were issued; only 8% reported drinking water against advice. Household assessments of official communications varied by source, with local officials receiving an average "B" rating, whereas some federal and water company communication received a "D" grade. More than 90% of households obtained safe water from distribution centers or stores during the emergency. We conclude that the spill had major economic impact with substantial numbers of individuals reporting incident-related illnesses and psychological distress. Authorities were successful supplying emergency drinking water, but less so with risk communication.

  18. 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

  19. 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

  20. Expansion of ARAC for chemical releases

    Energy Technology Data Exchange (ETDEWEB)

    Baskett, R.L.; Blair, M.D.; Foster, C.S.; Taylor, A.G.

    1997-07-01

    In 1996 the Atmospheric Release Advisory Capability (ARAC) at Lawrence Livermore National Laboratory (LLNL) completed an effort to expand its national emergency response modeling system for chemical releases. Key components of the new capability include the integration of (1) an extensive chemical property database, (2) source modeling for tanks and evaporating pools, (3) denser-than-air dispersion, (4) public exposure guidelines, and (5) an interactive graphical user interface (GUI). Recent use and the future of the new capability are also discussed.

  1. Progress and Prospect of Chemical Accident Databases at Home and Abroad%国内外化学事故数据库的发展现状与展望

    Institute of Scientific and Technical Information of China (English)

    付靖春; 袁纪武; 翟良云

    2011-01-01

    为完善我国化学事故数据库,充分发挥其在预防事故中的作用,通过研究美国、欧洲和日本等国家化学事故数据库的发展现状及其特点,分析我国化学事故数据库目前存在的问题.研究表明:国外化学事故数据库发展较完善,其数据结构设计较合理,且事故信息全面、准确,事故数量多;而我国化学事故数据库建设还比较落后,存在数据结构设计简单、标准不统一、数据可靠性差,很多事故信息也未能共享等问题.因此,在发展我国化学事故数据库时,应确保事故数据的数量、质量和多样性,重视未遂事故信息的收集,设计合理的数据结构,并实现数据共享,使其为事故原因分析、事故研究、安全评价和安全培训提供数据支持.%To improve China's chemical accident database and play its full role in prevention of accidents , the development and features of chemical accident databases in America, Europe and Japan were researched, and the problems of Chinas databases were analyzed. The study shows that the development of foreign chemical accidents is perfect, design of data structure is reasonable, accident information is comprehensive and reliable, and accident numbers are numerous. The problems in Chinas databases are simple design of data structure, standard discrepancy, data fallibility, and lack of data sharing. Therefore, when developing Chinas chemical accident database, the quantity, quality and diversity of accident data should be ensured, near miss should be paid attention to, reasonable data structure should be designed and data should be shared, so as to provide data for accident cause analysis, accident research, safety evaluation and safety training.

  2. Mathematical Notation in Bibliographic Databases.

    Science.gov (United States)

    Pasterczyk, Catherine E.

    1990-01-01

    Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

  3. Exploratory Study on Occupational Health Exposure to Chemical Agents, in a Public Hospital in Valencia, Venezuela. Preliminar Assessment

    Directory of Open Access Journals (Sweden)

    Maritza Rojas

    2008-07-01

    Full Text Available Descriptive study that identified chemicalagents (AQ use and training on risk managementand waste disposal techniques in a publicHospital in Valencia. A questionnaire wasanswered by 48 workers. Information obtainedwas: personal data, occupational history, AQused; knowledge of risk management and wastedisposal. There were 16 occupations from 12“High Risk” areas. “Adult emergency” was theone with more workers (11 individuals, followedby “sterilization” and “clinical laboratory”(7 each and oncology (5. The remained areashad less than 8.3% workers. The most usedanesthetic agents were: Halothane, Enfluoraneand Isofluorane 4.17% each and main antineoplasticsused were: Doxorubicin 16.67% andPaclitaxel, 5-Fluoracil and Etoposide, 8.33%each. The most mentioned substances were:alcohol (70.8% and Chlorine (64.6%. None ofthe answers regarding knowledge of AQ’ riskmanagement and waste disposal was satisfactory.Statistical associations between trainingand several variables such as age, time in theirjob and being or not a professional, resultednon-significant. The correlation between trainingand the knowledge of AQ’s managementwas significant (p < 0.001. Participants showedthat their knowledge about chemical occupationalrisk factors they are exposed to is stillinsufficient. Therefore, this theme should beincluded in graduate course curricula. Theseresults provide important data and will serveas a pilot research for the follow up Phase IIstudy that will include clinical aspects and environmentaland biological monitoring.

  4. 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,...

  5. 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...

  6. Expansion of DSSTox: Leveraging public data to create a semantic cheminformatics resource with quality annotations for support of U.S. EPA applications. (American Chemical Society)

    Science.gov (United States)

    The expansion of chemical-bioassay data in the public domain is a boon to science; however, the difficulty in establishing accurate linkages from CAS registry number (CASRN) to structure, or for properly annotating names and synonyms for a particular structure is well known. DSS...

  7. 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....

  8. 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.

  9. 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,...

  10. 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,...

  11. 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...

  12. 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

  13. Molecular Quantum Similarity, Chemical Reactivity and Database Screening of 3D Pharmacophores of the Protein Kinases A, B and G from Mycobacterium tuberculosis.

    Science.gov (United States)

    Morales-Bayuelo, Alejandro

    2017-06-21

    Mycobacterium tuberculosis remains one of the world's most devastating pathogens. For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity. Using the Molecular Quantum Similarity field and reactivity descriptors supported in the Density Functional Theory, it was possible to measure the quantification of the steric and electrostatic effects through the Overlap and Coulomb quantitative convergence (alpha and beta) scales. In addition, an analysis of reactivity indices using global and local descriptors was developed, identifying the binding sites and selectivity on these anti-tuberculosis compounds in the active sites. Finally, the reported pharmacophores to PKn A, B and G, were used to carry out database screening, using a database with anti-tuberculosis drugs from the Kelly Chibale research group (http://www.kellychibaleresearch.uct.ac.za/), to find the compounds with affinity for the specific protein targets associated with PKn A, B and G. In this regard, this hybrid methodology (Molecular Mechanic/Quantum Chemistry) shows new insights into drug design that may be useful in the tuberculosis treatment today.

  14. 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.

  15. 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...

  16. 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,...

  17. 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.

  18. 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.

  19. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M.

    1996-11-15

    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 alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  20. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M.

    1996-07-01

    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 alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  1. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-01-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilities access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers 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.

  2. Chemical mixtures: considering the evolution of toxicology and chemical assessment.

    Science.gov (United States)

    Monosson, Emily

    2005-04-01

    The assessment of chemical mixtures is a complex topic for toxicologists, regulators, and the public. In this article the linkage between the science of toxicology and the needs of governmental regulatory agencies in the United States is explored through an overview of environmental regulations enacted over the past century and a brief history of modern toxicology. One of the goals of this overview is to encourage both regulators and scientists to consider the benefits and limitations of this science-regulatory relationship as they tackle existing issues such as chemical mixtures. It is clear that a) over the past 100 years chemical regulation and toxicologic research, have in large part, shared a common emphasis on characterization and regulation of individual chemicals. But chemical mixtures have been, and continue to be, evaluated at hazardous waste sites around the United States. For this reason the current U.S. Environmental Protection Agency guidelines for chemical mixtures assessment are also reviewed. These guidelines highlight the current practice of mixtures assessment, which relies primarily on the existing single-chemical database. It is also clear that b) the science and assessment of chemical mixtures are moving forward through the combined efforts of regulatory agencies and scientists from a broad range of disciplines, including toxicology. Because toxicology is at this exciting crossroads, particular attention should be paid to the forces (e.g., public demands, regulatory needs, funding, academic interests) that both promote and limit the growth of this expanding discipline.

  3. Research on security access control model of the Web-based database of nonfer-rous metal physical & chemical properties%基于Web有色金属物性数据库安全访问控制模型

    Institute of Scientific and Technical Information of China (English)

    李尚勇; 谢刚; 俞小花; 周明

    2009-01-01

    针对基于Web的有色金属物性数据库的访问特点,分析了有色金属物性数据库在多层架构体系中存在的非法入侵、越权访问、信息重放攻击等安全性问题,提出了适应其软件架构要求的安全访问控制模型.并对所提出的安全模型分别进行了访问性能和安全性测试,测试结果表明,访问模型安全性较好,性能稳定.%According to accessing characteristic of the Web-based database of non-ferrous metal physical & chemical properties, the se-curity issues are discussed in Multi-tier Application Architecture of database of non-ferrous metal physical & chemical properties, such as illegal invasion, unauthorized access, and information replay attack. The security access control model which is adaptive to charac-teristic of Multi-tier Application Architecture is proposed and tested in accessing performance and security. The test results show that the model is better in accessing performance and stability.

  4. Automatic sorting of toxicological information into the IUCLID (International Uniform Chemical Information Database) endpoint-categories making use of the semantic search engine Go3R.

    Science.gov (United States)

    Sauer, Ursula G; Wächter, Thomas; Hareng, Lars; Wareing, Britta; Langsch, Angelika; Zschunke, Matthias; Alvers, Michael R; Landsiedel, Robert

    2014-06-01

    The knowledge-based search engine Go3R, www.Go3R.org, has been developed to assist scientists from industry and regulatory authorities in collecting comprehensive toxicological information with a special focus on identifying available alternatives to animal testing. The semantic search paradigm of Go3R makes use of expert knowledge on 3Rs methods and regulatory toxicology, laid down in the ontology, a network of concepts, terms, and synonyms, to recognize the contents of documents. Search results are automatically sorted into a dynamic table of contents presented alongside the list of documents retrieved. This table of contents allows the user to quickly filter the set of documents by topics of interest. Documents containing hazard information are automatically assigned to a user interface following the endpoint-specific IUCLID5 categorization scheme required, e.g. for REACH registration dossiers. For this purpose, complex endpoint-specific search queries were compiled and integrated into the search engine (based upon a gold standard of 310 references that had been assigned manually to the different endpoint categories). Go3R sorts 87% of the references concordantly into the respective IUCLID5 categories. Currently, Go3R searches in the 22 million documents available in the PubMed and TOXNET databases. However, it can be customized to search in other databases including in-house databanks.

  5. 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.

  6. 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

  7. 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.

  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. Consequences arising from the activities of the Mining and Chemical Enterprise, a defense production association, and influence of the public opinion on decision-making

    Energy Technology Data Exchange (ETDEWEB)

    Lazarev, L.N.; Kuznetsov, Yu.V. [Khlopin Radium Inst., St. Petersburg (Russian Federation); Zhidkov, V.V. [Mining and Chemical Enterprise, Zheleznogorsk (Russian Federation); Mel`nikov, G.Y. [Central Medical Office 51, Zheleznogorsk (Russian Federation)

    1995-12-31

    Mining and Chemical Enterprise was created during the Cold War in Russia to produce plutonium for defense purposes. Now, when these activities are stopped, prime attention is given to the evaluation of impacts caused by the execution of the defense program and to the conversion possibilities of the enterprise for provisions of the nuclear fuel cycle. The role of public opinion in solving these problems is considered.

  13. US Army Public Health Command’s (Prov) (Formly USACHPPM) Process to Screen Chemicals in Support of DoD’s CMRM Emerging Contaminants Program

    Science.gov (United States)

    2010-06-01

    US Army Public Health Command’s (Prov) (Formly USACHPPM) Process to Screen Chemicals in Support of DoD’s CMRM Emerging Contaminants Program...CMRM Emerging Contaminants Program 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER...Occupational Health • DoD Instruction 5000.2 Operation of the Defense Acquisition System • DoD Instruction 4715.18 Emerging Contaminants (EC

  14. Nutritional composition, assessed by chemical analyses, of prepared foods available for primary-school children: a comparison of public and private schools.

    Science.gov (United States)

    Weber, Márcia L; Morais, Tania B

    2010-11-01

    To assess the nutritional quality of prepared foods available to primary-school children. Prepared foods available in a public and private school were sampled daily for 4 weeks (a total of forty-five samples) and chemically analysed for protein, fat, carbohydrate, iron, salt and sodium. The results were compared to the nutritional standards for children aged 7-10 years. Alfenas, south-eastern Brazil. The concentration of protein, lipid, iron and sodium and the energy values of the foods at the private school were significantly higher than those at the public school. No differences were seen in the carbohydrate and salt values. The range of macronutrients was more balanced at the public school in relation to fat and protein. Foods at the private school were, in general, energy-dense. At both the public and private school, they provided the minimum energy and iron. Salt content was over twice the maximum amount, and that for sodium was over three times the amount, in both the public and private school. Overall, foods prepared at the public school were better nutritional quality than those at the private school and those offered in public schools in some developed countries. This finding can probably be explained by the fact that a nutritionist, as required by law, was responsible for planning the menus at the public school. However, corrective action is needed to adjust for the wide variability in energy and nutrient content during weekdays and in the sodium content of prepared foods available in both the public and private school.

  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. 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. 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.

  18. 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.

  19. 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。

  20. Fullerene data mining using bibliometrics and database tomography

    Science.gov (United States)

    Kostoff; Braun; Schubert; Toothman; Humenik

    2000-01-01

    Database tomography (DT) is a textual database analysis system consisting of two major components: (1) algorithms for extracting multiword phrase frequencies and phrase proximities (physical closeness of the multiword technical phrases) from any type of large textual database, to augment (2) interpretative capabilities of the expert human analyst. DT was used to derive technical intelligence from a fullerenes database derived from the Science Citation Index and the Engineering Compendex. Phrase frequency analysis by the technical domain experts provided the pervasive technical themes of the fullerenes database, and phrase proximity analysis provided the relationships among the pervasive technical themes. Bibliometric analysis of the fullerenes literature supplemented the DT results with author/journal/institution publication and citation data. Comparisons of fullerenes results with past analyses of similarly structured near-earth space, chemistry, hypersonic/supersonic flow, aircraft, and ship hydrodynamics databases are made. One important finding is that many of the normalized bibliometric distribution functions are extremely consistent across these diverse technical domains and could reasonably be expected to apply to broader chemical topics than fullerenes that span multiple structural classes. Finally, lessons learned about integrating the technical domain experts with the data mining tools are presented.

  1. 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...

  2. 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

  3. 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 ...

  4. Malaria Parasite Metabolic Pathways (MPMP) Upgraded with Targeted Chemical Compounds

    KAUST Repository

    Ginsburg, Hagai

    2015-10-31

    Malaria Parasite Metabolic Pathways (MPMP) is the website for the functional genomics of intraerythrocytic Plasmodium falciparum. All the published information about targeted chemical compounds has now been added. Users can find the drug target and publication details linked to a drug database for further information about the medicinal properties of each compound.

  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. The comet assay with multiple mouse organs: comparison of comet assay results and carcinogenicity with 208 chemicals selected from the IARC monographs and U.S. NTP Carcinogenicity Database.

    Science.gov (United States)

    Sasaki, Y F; Sekihashi, K; Izumiyama, F; Nishidate, E; Saga, A; Ishida, K; Tsuda, S

    2000-11-01

    The comet assay is a microgel electrophoresis technique for detecting DNA damage at the level of the single cell. When this technique is applied to detect genotoxicity in experimental animals, the most important advantage is that DNA lesions can be measured in any organ, regardless of the extent of mitotic activity. The purpose of this article is to summarize the in vivo genotoxicity in eight organs of the mouse of 208 chemicals selected from International Agency for Research on Cancer (IARC) Groups 1, 2A, 2B, 3, and 4, and from the U.S. National Toxicology Program (NTP) Carcinogenicity Database, and to discuss the utility of the comet assay in genetic toxicology. Alkylating agents, amides, aromatic amines, azo compounds, cyclic nitro compounds, hydrazines, halides having reactive halogens, and polycyclic aromatic hydrocarbons were chemicals showing high positive effects in this assay. The responses detected reflected the ability of this assay to detect the fragmentation of DNA molecules produced by DNA single strand breaks induced chemically and those derived from alkali-labile sites developed from alkylated bases and bulky base adducts. The mouse or rat organs exhibiting increased levels of DNA damage were not necessarily the target organs for carcinogenicity. It was rare, in contrast, for the target organs not to show DNA damage. Therefore, organ-specific genotoxicity was necessary but not sufficient for the prediction of organ-specific carcinogenicity. It would be expected that DNA crosslinkers would be difficult to detect by this assay, because of the resulting inhibition of DNA unwinding. The proportion of 10 DNA crosslinkers that was positive, however, was high in the gastrointestinal mucosa, stomach, and colon, but less than 50% in the liver and lung. It was interesting that the genotoxicity of DNA crosslinkers could be detected in the gastrointestinal organs even though the agents were administered intraperitoneally. Chemical carcinogens can be classified

  7. OECD/NEA thermochemical database

    Energy Technology Data Exchange (ETDEWEB)

    Byeon, Kee Hoh; Song, Dae Yong; Shin, Hyun Kyoo; Park, Seong Won; Ro, Seung Gy

    1998-03-01

    This state of the art report is to introduce the contents of the Chemical Data-Service, OECD/NEA, and the results of survey by OECD/NEA for the thermodynamic and kinetic database currently in use. It is also to summarize the results of Thermochemical Database Projects of OECD/NEA. This report will be a guide book for the researchers easily to get the validate thermodynamic and kinetic data of all substances from the available OECD/NEA database. (author). 75 refs.

  8. The New version of Danish food composition database FRIDA including a case study on recipe calculation compared to a chemical analysis

    DEFF Research Database (Denmark)

    Objective: Constantly updated food data that reflect the food supply, such as the recently published http://frida.fooddata.dk, is essential for recipe calculation in dietary assessment. The objective of this study was to compare the content of selected nutrients estimated by recipe calculation...... and chemical analysis of fast food based on data from http://frida.fooddata.dk. Materials and methods: New fast food data in http://frida.fooddata.dk was based on 135 samples of ready to eat fast foods as burgers and sandwiches collected from fast food outlets, separated into their recipe components which were...... weighed. Typical components were bread, French fries, vegetables, meat, and dressings. The fast foods were analyzed and the content of energy, protein, saturated fat, iron, thiamin, potassium and sodium were compared to recipe calculation. Wilcoxon Signed Rank test, Spearman correlation coefficients...

  9. The New version of Danish food composition database FRIDA including a case study on recipe calculation compared to a chemical analysis

    DEFF Research Database (Denmark)

    Biltoft-Jensen, Anja Pia; Saxholt, Erling; Knuthsen, Pia

    weighed. Typical components were bread, French fries, vegetables, meat, and dressings. The fast foods were analyzed and the content of energy, protein, saturated fat, iron, thiamin, potassium and sodium were compared to recipe calculation. Wilcoxon Signed Rank test, Spearman correlation coefficients...... and Bland-Altman plots were used for comparing the two methods. Results: Overall there were differences between the chemical and recipe analysis for energy, protein, saturated fat and iron (P0.05). The error percentage was largest for saturated fat (28......%). Correlations ranged from 0.49 for iron to 0.75 for energy. Bland-Altman plots showed larger differences for higher contents for thiamin and potassium. Results depended on the type of fast food. For burgers (n=36) there was no significant difference for any of the nutrients between the two methods. Meat...

  10. The DIPPR® databases

    Science.gov (United States)

    Thomson, G. H.

    1996-01-01

    The Design Institute for Physical Property Data® (DIPPR), one of the Sponsored Research groups of the American Institute of Chemical Engineers (AIChE), has been in existence for 15 years and has supported a total of 14 projects, some completed, some ongoing. Four of these projects are “database” projects for which the primary product is a database of carefully evaluated property data. These projects are Data Compilation; Evaluated Data on Mixtures; Environmental, Safety, and Health Data Compilation; and Difusivities and Thermal Properties of Polymer Solutions. This paper lists the existing DIPPR projects; discusses DIPPR's structure and modes of dissemination of results; describes DIPPR's supporters and its unique characteristics; and finally, discusses the origin, nature, and content of the four database projects.

  11. Using publicly available information to create exposure and risk-based ranking of chemicals used in the workplace and consumer products.

    Science.gov (United States)

    Jayjock, Michael A; Chaisson, Christine F; Franklin, Claire A; Arnold, Susan; Price, Paul S

    2009-07-01

    Mandates that require the estimation of exposure and human health risk posed by large numbers of chemicals present regulatory managers with a significant challenge. Although these issues have been around for some time, the estimation of human exposure to chemicals from use of products in the workplace and by the consumer has been generally hindered by the lack of good tools. Logically and in the interest of cost-effective resource allocation and regulation one would typically and naturally first attempt to rank-order or prioritize the chemicals according to the human exposure potential that each might pose. We have developed an approach and systematic modeling construct that accomplishes this critical task by providing a quantitative estimate of human exposure for as many as several hundred chemicals initially; however, it could ultimately do this for any number of regulated chemicals starting only with the identity (Chemical Abstract Service number) for each chemical under consideration. These exposure estimates can then be readily linked to toxicological benchmarks for each item to estimate and rank the human health risk for the chemicals under consideration in a "worst things first" listing. This modeling construct, entitled Complex Exposure Tool (ComET) was developed by The LifeLine Group as a proof of concept under the sponsorship of Health Canada. ComET considers multiple routes of exposure, multiple subpopulations and different possible durations of exposure. A beta-version of ComET was issued and demonstrated in which users can change the assumptions in the model and see the impacts of these changes and the quality of information as they relate to the predicted exposure potential. We have advanced the operational elements of ComET into a tool entitled the Chemical Exposure Priority Setting Tool (CEPST) designed to provide quantitative estimation of the exposure potential of large groups of chemicals with little data and possibly multiple exposure scenarios

  12. 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.

  13. 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.

  14. 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.

  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. A New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data-Mining and Modeling

    Science.gov (United States)

    A new XML-based query language, CSRML, has been developed for representing chemical substructures, molecules, reaction rules, and reactions. CSRML queries are capable of integrating additional forms of information beyond the simple substructure (e.g., SMARTS) or reaction transfor...

  17. Chemical information science coverage in Chemical Abstracts.

    Science.gov (United States)

    Wiggins, G

    1987-02-01

    For many years Chemical Abstracts has included in its coverage publications on chemical documentation or chemical information science. Although the bulk of those publications can be found in section 20 of Chemical Abstracts, many relevant articles were found scattered among 39 other sections of CA in 1984-1985. In addition to the scattering of references in CA, the comprehensiveness of Chemical Abstracts as a secondary source for chemical information science is called into question. Data are provided on the journals that contributed the most references on chemical information science and on the languages of publication of relevant articles.

  18. 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.

  19. 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

  20. 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

  1. 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

  2. Microbiological and chemical quality of ground water used as a source of public supply in southern Missouri : Phase II, April-July, 1998

    Science.gov (United States)

    Femmer, Suzanne R.

    2000-01-01

    The protection of public health through quality public ground-water systems is the responsibility of the U. S. Environmental Protection Agency and the State of Missouri, through the Missouri Department of Natural Resources, Public Drinking Water Program. Approximately 95 percent of the public-water supplies in Missouri use ground water as their source of drinking water through more than 3,700 public wells. Karst terrain, intensive agricultural operations, extensive numbers of on-site sewage systems, and poor well construction can lead to chemical and microbiological contamination of the contributing aquifers. Sitespecific studies and routine regulatory monitoring have produced information on the overall quality and potability of the State's public-drinking-water supplies, but little is known about the presence of viruses. The U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources, sampled 109 public-water supplies to characterize the physical, chemical, bacterial, and viral conditions in southern Missouri. During April to July 1998, these wells were sampled for nutrients, total organic carbon, optical brighteners, indicator bacteria, enteric viruses, and ribonucleic acid and somatic coli phages. These constituents indicate possible surface contamination of the sampled aquifer. Selection of the wells to be sampled depended on the age of the well (pre-1970), land use, geohydrology, and well construction. None of the physical or chemical constituents measured or analyzed exceeded Missouri's Drinking Water Standards set by the Public Drinking Water Program of the Missouri Department of Natural Resources. The majority of ammonia plus organic nitrogen, nitrite, and phosphorus concentrations were below the laboratory's minimum reporting levels. There were a greater number of detects above the minimum reporting level with respect to the nitrite plus nitrate, ammonia, orthophosphate, and total organic carbon concentrations. Analyses

  3. 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.

  4. Exploring consumer exposure pathways and patterns of use for chemicals in the environment

    Directory of Open Access Journals (Sweden)

    Kathie L. Dionisio

    Full Text Available •To assign use-related information to chemicals to help prioritize which will be given more scrutiny relative to human exposure potential.•Categorical chemical use and functional information are presented through the Chemical/Product Categories Database (CPCat.•CPCat contains information on >43,000 unique chemicals mapped to ∼800 terms categorizing their usage or function.•The CPCat database is useful for modeling and prioritizing human chemical exposures.Humans are exposed to thousands of chemicals in the workplace, home, and via air, water, food, and soil. A major challenge in estimating chemical exposures is to understand which chemicals are present in these media and microenvironments. Here we describe the Chemical/Product Categories Database (CPCat, a new, publically available (http://actor.epa.gov/cpcat database of information on chemicals mapped to “use categories” describing the usage or function of the chemical. CPCat was created by combining multiple and diverse sources of data on consumer- and industrial-process based chemical uses from regulatory agencies, manufacturers, and retailers in various countries. The database uses a controlled vocabulary of 833 terms and a novel nomenclature to capture and streamline descriptors of chemical use for 43,596 chemicals from the various sources. Examples of potential applications of CPCat are provided, including identifying chemicals to which children may be exposed and to support prioritization of chemicals for toxicity screening. CPCat is expected to be a valuable resource for regulators, risk assessors, and exposure scientists to identify potential sources of human exposures and exposure pathways, particularly for use in high-throughput chemical exposure assessment. keywords: ACToR,Aggregated Computational Toxicology Resource,AICS,Australian Inventory of Chemical Substances,CAS RN,Chemical Abstracts Service Registry Number,CDR,Chemical Data Reporting Rule,CPCat,Chemical

  5. Idaho Chemical Processing Plant safety document ICPP hazardous chemical evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, B.J.

    1993-01-01

    This report presents the results of a hazardous chemical evaluation performed for the Idaho Chemical Processing Plant (ICPP). ICPP tracks chemicals on a computerized database, Haz Track, that contains roughly 2000 individual chemicals. The database contains information about each chemical, such as its form (solid, liquid, or gas); quantity, either in weight or volume; and its location. The Haz Track database was used as the primary starting point for the chemical evaluation presented in this report. The chemical data and results presented here are not intended to provide limits, but to provide a starting point for nonradiological hazards analysis.

  6. Effective responder communication improves efficiency and psychological outcomes in a mass decontamination field experiment: implications for public behaviour in the event of a chemical incident.

    Science.gov (United States)

    Carter, Holly; Drury, John; Amlôt, Richard; Rubin, G James; Williams, Richard

    2014-01-01

    The risk of incidents involving mass decontamination in response to a chemical, biological, radiological, or nuclear release has increased in recent years, due to technological advances, and the willingness of terrorists to use unconventional weapons. Planning for such incidents has focused on the technical issues involved, rather than on psychosocial concerns. This paper presents a novel experimental study, examining the effect of three different responder communication strategies on public experiences and behaviour during a mass decontamination field experiment. Specifically, the research examined the impact of social identity processes on the relationship between effective responder communication, and relevant outcome variables (e.g. public compliance, public anxiety, and co-operative public behaviour). All participants (n = 111) were asked to visualise that they had been involved in an incident involving mass decontamination, before undergoing the decontamination process, and receiving one of three different communication strategies: 1) 'Theory-based communication': Health-focused explanations about decontamination, and sufficient practical information; 2) 'Standard practice communication': No health-focused explanations about decontamination, sufficient practical information; 3) 'Brief communication': No health-focused explanations about decontamination, insufficient practical information. Four types of data were collected: timings of the decontamination process; observational data; and quantitative and qualitative self-report data. The communication strategy which resulted in the most efficient progression of participants through the decontamination process, as well as the fewest observations of non-compliance and confusion, was that which included both health-focused explanations about decontamination and sufficient practical information. Further, this strategy resulted in increased perceptions of responder legitimacy and increased identification with

  7. Effective Responder Communication Improves Efficiency and Psychological Outcomes in a Mass Decontamination Field Experiment: Implications for Public Behaviour in the Event of a Chemical Incident

    Science.gov (United States)

    Carter, Holly; Drury, John; Amlôt, Richard; Rubin, G. James; Williams, Richard

    2014-01-01

    The risk of incidents involving mass decontamination in response to a chemical, biological, radiological, or nuclear release has increased in recent years, due to technological advances, and the willingness of terrorists to use unconventional weapons. Planning for such incidents has focused on the technical issues involved, rather than on psychosocial concerns. This paper presents a novel experimental study, examining the effect of three different responder communication strategies on public experiences and behaviour during a mass decontamination field experiment. Specifically, the research examined the impact of social identity processes on the relationship between effective responder communication, and relevant outcome variables (e.g. public compliance, public anxiety, and co-operative public behaviour). All participants (n = 111) were asked to visualise that they had been involved in an incident involving mass decontamination, before undergoing the decontamination process, and receiving one of three different communication strategies: 1) ‘Theory-based communication’: Health-focused explanations about decontamination, and sufficient practical information; 2) ‘Standard practice communication’: No health-focused explanations about decontamination, sufficient practical information; 3) ‘Brief communication’: No health-focused explanations about decontamination, insufficient practical information. Four types of data were collected: timings of the decontamination process; observational data; and quantitative and qualitative self-report data. The communication strategy which resulted in the most efficient progression of participants through the decontamination process, as well as the fewest observations of non-compliance and confusion, was that which included both health-focused explanations about decontamination and sufficient practical information. Further, this strategy resulted in increased perceptions of responder legitimacy and increased

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Candidates Profile in FUVEST Exams from 2004 to 2013: Private and Public School Distribution, FUVEST Average Performance and Chemical Equilibrium Tasks Performance

    Directory of Open Access Journals (Sweden)

    R.S.A.P. Oliveira

    2014-08-01

    Full Text Available INTRODUCTION. Chemical equilibrium is recognized as a topic of several misconceptions. Its origins must be tracked from previous scholarship. Its impact on biochemistry learning is not fully described. A possible bulk of data is the FUVEST exam. OBJECTIVES: Identify students’ errors profile on chemical equilibrium tasks using public data from FUVEST exam. MATERIAL AND METHODS: Data analysis from FUVEST were: i Private and Public school distribution in Elementary and Middle School, and High School candidates of Pharmacy-Biochemistry course and total USP careers until the last call for enrollment (2004-2013; ii Average performance in 1st and 2nd parts of FUVEST exam of Pharmacy-Biochemistry, Chemistry, Engineering, Biological Sciences, Languages and Medicine courses and total enrolled candidates until 1st call for enrollment (2008- 2013; iii Performance of candidates of Pharmacy-Biochemistry, Chemistry, Engineering, Biological Sciences, Languages and Medicine courses and total USP careers in chemical equilibrium issues from 1st part of FUVEST (2011-2013. RESULTS AND DISCUSSION: i 66.2% of candidates came from private Elementary-Middle School courses and 71.8%, came from High School courses; ii Average grade over the period for 1st and 2nd FUVEST parts are respectively (in 100 points: Pharmacy-Biochemistry 66.7 and 61.2, Chemistry 65.9 and 58.9, Engineering 75.9 and 71.9, Biological Sciences 65.6 and 54.6, Languages 49.9 and 43.3, Medicine 83.5 and 79.5, total enrolled candidates 51,5 and 48.9; iii Four chemical equilibrium issues were found during 2011-2013 and the analysis of multiplechoice percentage distribution over the courses showed that there was a similar performance of students among them, except for Engineering and Medicine with higher grades, but the same proportional distribution among choices. CONCLUSION: Approved students came majorly from private schools. There was a different average performance among courses and similar on

  13. 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...

  14. 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...

  15. 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...

  16. 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…

  17. Are we safe? NLM's household products database.

    Science.gov (United States)

    Bronson Fitzpatrick, Roberta

    2004-01-01

    This column features an overview of the Division of Specialized Information Services, National Library of Medicine Household Products Database. Basic searching techniques are presented, as well as a brief overview of the data contained in this file. The Household Products Database contains information on chemical ingredients in various products used in U.S. homes.

  18. 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.

  19. 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...

  20. 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.

  1. 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.

  2. 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...

  3. New free Danish online (Q)SAR predictions database with >600,000 substances

    DEFF Research Database (Denmark)

    Wedebye, Eva Bay; Dybdahl, Marianne; Reffstrup, Trine Klein

    by regulators and industry. A lot of progress in (Q)SAR model development, application and documentation has been made since the publication in 2005. A new and completely rebuild online (Q)SAR predictions database was therefore published in November 2015 at http://qsar.food.dtu.dk. The number of chemicals...... in the database has been expanded from 185,000 to >600,000. As far as possible all organic single constituent substances that were pre-registered under REACH have been included in the new structure set. The new Danish (Q)SAR Database includes estimates from more than 200 (Q)SARs covering a wide range of hazardous......-scale screenings. The online interface to the database allows for advanced combination of searches as well as sorting functions on chemical similarity. Negotiations are underway with the OECD to integrate the new database with the OECD (Q)SAR Application Toolbox. The database was developed by the DTU National Food...

  4. 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

  5. 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...

  6. 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...

  7. 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...

  8. 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;…

  9. 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.…

  10. 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

  11. chemical safety and chemical security overview

    African Journals Online (AJOL)

    IICBA01

    expert in chemical security and work hard to safeguard the communities. Items discussed in this ... the public from injury, fire or other damage. In order to achieve these ..... 10.8 Transportation of hazardous chemicals and wastes? ... Chemical Security Engagement Program: https://chemsecurity.sandia.gov/. Chemical Safety.

  12. 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, ...

  13. Exploring consumer exposure pathways and patterns of use for chemicals in the environment.

    Science.gov (United States)

    Dionisio, Kathie L; Frame, Alicia M; Goldsmith, Michael-Rock; Wambaugh, John F; Liddell, Alan; Cathey, Tommy; Smith, Doris; Vail, James; Ernstoff, Alexi S; Fantke, Peter; Jolliet, Olivier; Judson, Richard S

    2015-01-01

    Humans are exposed to thousands of chemicals in the workplace, home, and via air, water, food, and soil. A major challenge in estimating chemical exposures is to understand which chemicals are present in these media and microenvironments. Here we describe the Chemical/Product Categories Database (CPCat), a new, publically available (http://actor.epa.gov/cpcat) database of information on chemicals mapped to "use categories" describing the usage or function of the chemical. CPCat was created by combining multiple and diverse sources of data on consumer- and industrial-process based chemical uses from regulatory agencies, manufacturers, and retailers in various countries. The database uses a controlled vocabulary of 833 terms and a novel nomenclature to capture and streamline descriptors of chemical use for 43,596 chemicals from the various sources. Examples of potential applications of CPCat are provided, including identifying chemicals to which children may be exposed and to support prioritization of chemicals for toxicity screening. CPCat is expected to be a valuable resource for regulators, risk assessors, and exposure scientists to identify potential sources of human exposures and exposure pathways, particularly for use in high-throughput chemical exposure assessment.

  14. 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...

  15. 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.

  16. 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

  17. 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 ...

  18. 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...

  19. 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...

  20. 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

  1. 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.

  2. Chemical reageants management in laboratories of the Universidad Nacional

    Directory of Open Access Journals (Sweden)

    José Carlos Mora Barrantes

    2013-03-01

    Full Text Available During years 2008-2009, a diagnostic regarding chemical reagents management (aspects related with; regulations, safety procedures, handle and storage conditions, etc in teaching and research laboratories of the Universidad Nacional, was carried out. In order to collect such information different strategies/methodologies were used: 1 application of an interview and questionnaire to the laboratories’ personnel, 2an inspection of the laboratories, 3 generation of chemical reagents database 4 work sessions with university management authorities and 5 interview with chemical products management personnel of public and private institutions .This study allowed to identify the actual conditions for the chemical reagents management at Universidad Nacional, for example; the different procedures for the segregation, storage, labeling and use of the chemicals, as well as the aspects related with; chemical database generation, material and safety equipment control, use of safety procedures, etc. Also, the study allowed to evaluate the existing management procedures executed by university authorities for handling them appropriately. As a conclusion, in order to conduct an adequate chemical reagents management at Universidad Nacional it is necessary to formulate and implement regulation (institutional procedures, protocols, etc and the establishment of an university office in charge of all the chemical reagents management activities and procedures. Also is necessary to generate national regulations focused on university activities (chemical reagents management as well as the existing for the industry chemical products control and regulation.

  3. Acidentes químicos ampliados: um desafio para a saúde pública The increase in chemical accidents: a challenge for public health

    Directory of Open Access Journals (Sweden)

    Carlos M. de Freitas

    1995-12-01

    Full Text Available Os acidentes envolvendo substâncias perigosas nas atividades de transporte, armazenamento e produção industrial de produtos químicos constituem um sério risco à saúde e ao meio ambiente. Objetiva-se discutir, no âmbito da saúde pública, alguns dos desafios que esses tipos de acidentes colocam, principalmente para os países de economia periférica. Através da combinação de informações quantitativas e qualitativas, foram definidos e caracterizados esses tipos de acidentes e seus diversos riscos. Esses acidentes têm se apresentado com a maior gravidade nos países de economia periférica, embora a maioria deles venha ocorrendo sem o adequado registro de informações básicas para a avaliação e vigilância, como é demonstrado no caso do Rio de Janeiro (Brasil. Além da tarefa de se avaliar as conseqüências de eventos, por vezes extremamente complexos, coloca-se também, a de formular estratégias de controle e prevenção em realidades sociais que configuram um terreno fértil para a ocorrência e agravamento dos mesmos.Chemical accidents involving explosions, large fires and leakages of hazardous substances occuring during transport, storage and industrial production of chemicals constitute a real challeng to health, environmental and industrial safety professionals. The aim of this article is to discuss the main questions that this kind of accident provokes, in terms of public helth, particularly in developing countries such as Brazil. The paper defines and characterises these accidents and the various health risk they involve excluding the leakages of hazardous substances during "normal" production in industry - through the combination of quantitative and qualitative information drawn from the international literature on the subject. From some examples of chemical accidents such as occurred in Bophal (Índia, Vila Socó (Brazil, São Paulo (México and data of the World Health Organization (WHO, the authors seek to show

  4. 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...

  5. 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.

  6. 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.

  7. Understanding genetic toxicity through data mining: the process of building knowledge by integrating multiple genetic toxicity databases.

    Science.gov (United States)

    Yang, C; Hasselgren, C H; Boyer, S; Arvidson, K; Aveston, S; Dierkes, P; Benigni, R; Benz, R D; Contrera, J; Kruhlak, N L; Matthews, E J; Han, X; Jaworska, J; Kemper, R A; Rathman, J F; Richard, A M

    2008-01-01

    ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed database using the ToxML schema. The public database sources include the U.S. Food and Drug Administration (FDA) submission data from approved new drug applications, food contact notifications, generally recognized as safe food ingredients, and chemicals from the NTP and CCRIS databases. The data from public sources were then combined with data from private industry according to ToxML criteria. The resulting "integrated" database, enriched in pharmaceuticals, was used for data mining analysis. Structural features describing the database were used to differentiate the chemical spaces of drugs/candidates, food ingredients, and industrial chemicals. In general, structures for drugs/candidates and food ingredients are associated with lower frequencies of mutagenicity and clastogenicity, whereas industrial chemicals as a group contain a much higher proportion of positives. Structural features were selected to analyze endpoint outcomes of the genetic toxicity studies. Although most of the well-known genotoxic carcinogenic alerts were identified, some discrepancies from the classic Ashby-Tennant alerts were observed. Using these influential features as the independent variables, the results of four types of genotoxicity studies were correlated. High Pearson correlations were found between the results of Salmonella mutagenicity and mouse lymphoma assay testing as well as those from in vitro chromosome aberration studies. This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies.

  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. 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.

  10. 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.

  11. 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

  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. 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…

  14. 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...

  15. 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

  16. X-ray Photoelectron Spectroscopy Database (Version 4.1)

    Science.gov (United States)

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

  17. Historical reconstruction of wastewater and land use impacts to groundwater used for public drinking water: exposure assessment using chemical data and GIS.

    Science.gov (United States)

    Swartz, Christopher H; Rudel, Ruthann A; Kachajian, Jennifer R; Brody, Julia G

    2003-09-01

    Land use in geographic areas that replenish groundwater and surface water resources is increasingly recognized as an important factor affecting drinking water quality. Efforts to understand the implications for health, particularly outcomes with long latency or critical exposure windows, have been hampered by lack of historical exposure data for unregulated pollutants. This limitation has hindered studies of the possible links between breast cancer risk and drinking water impacted by endocrine disrupting compounds and mammary carcinogens, for example. This paper describes a methodology to assess potential historical exposure to a broad range of chemicals associated with wastewater and land use impacts to 132 groundwater wells and one surface water body supplying drinking water to 18 public distribution systems on Cape Cod, MA. We calculated annual measures of impact to each distribution system and used the measures as exposure estimates for the residential addresses of control women in the Cape Cod Breast Cancer and Environment Study (Cape Cod Study). Impact was assessed using (1) historical chemical measurements of nitrate at the water supply sources (performed as required by the Safe Water Drinking Act) and (2) a geographic information system analysis of land use within the zones of contribution (ZOCs) delineated for each well in a state-mandated wellhead protection program. The period for which these impact estimates were developed (1972-1995) was constrained by the availability of chemical measurements and land use data and consideration of time required for groundwater transport of contaminants to the water supply wells. Trends in these estimates for Cape Cod suggest increasing impact to drinking water quality for land use over the study period. Sensitivity analyses were conducted to assess the effect on the distribution of controls' cumulative exposure estimates from (1) reducing the area of the ZOCs to reflect typical well operating conditions rather than

  18. Property Modelling and Databases in Product-Process Design

    DEFF Research Database (Denmark)

    Gani, Rafiqul; Sansonetti, Sascha

    of the PC-SAFT is used. The developed database and property prediction models have been combined into a properties-software that allows different product-process design related applications. The presentation will also briefly highlight applications of the software for virtual product-process design...... development, however, it is necessary to have a large database of measured property data that has been checked for consistency and accuracy. The presentation will first introduce a database, in terms of its knowledge representation structure, the type and range of properties and chemical systems covered......, and their internal consistency-accuracy checks. The database includes properties of organic chemicals, polymers and ionic liquids. There are also chemical class specific database sections, such as for solvents, aroma-chemicals, surfactants and emulsifiers. The use of this property database for model development...

  19. Property Modelling and Databases in Product-Process Design

    DEFF Research Database (Denmark)

    Gani, Rafiqul; Sansonetti, Sascha

    development, however, it is necessary to have a large database of measured property data that has been checked for consistency and accuracy. The presentation will first introduce a database, in terms of its knowledge representation structure, the type and range of properties and chemical systems covered......, and their internal consistency-accuracy checks. The database includes properties of organic chemicals, polymers and ionic liquids. There are also chemical class specific database sections, such as for solvents, aroma-chemicals, surfactants and emulsifiers. The use of this property database for model development...... of the PC-SAFT is used. The developed database and property prediction models have been combined into a properties-software that allows different product-process design related applications. The presentation will also briefly highlight applications of the software for virtual product-process design...

  20. Non-redundant patent sequence databases with value-added annotations at two levels.

    Science.gov (United States)

    Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

    2010-01-01

    The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.

  1. Non-redundant patent sequence databases with value-added annotations at two levels

    Science.gov (United States)

    Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

    2010-01-01

    The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/. PMID:19884134

  2. Chemical Search Web Utility

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Chemical Search Web Utility is an intuitive web application that allows the public to easily find the chemical that they are interested in using, and which...

  3. 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

  4. 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...

  5. 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

  6. 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

  7. Cosmetics Europe compilation of historical serious eye damage/eye irritation in vivo data analysed by drivers of classification to support the selection of chemicals for development and evaluation of alternative methods/strategies: the Draize eye test Reference Database (DRD).

    Science.gov (United States)

    Barroso, João; Pfannenbecker, Uwe; Adriaens, Els; Alépée, Nathalie; Cluzel, Magalie; De Smedt, Ann; Hibatallah, Jalila; Klaric, Martina; Mewes, Karsten R; Millet, Marion; Templier, Marie; McNamee, Pauline

    2017-02-01

    A thorough understanding of which of the effects assessed in the in vivo Draize eye test are responsible for driving UN GHS/EU CLP classification is critical for an adequate selection of chemicals to be used in the development and/or evaluation of alternative methods/strategies and for properly assessing their predictive capacity and limitations. For this reason, Cosmetics Europe has compiled a database of Draize data (Draize eye test Reference Database, DRD) from external lists that were created to support past validation activities. This database contains 681 independent in vivo studies on 634 individual chemicals representing a wide range of chemical classes. A description of all the ocular effects observed in vivo, i.e. degree of severity and persistence of corneal opacity (CO), iritis, and/or conjunctiva effects, was added for each individual study in the database, and the studies were categorised according to their UN GHS/EU CLP classification and the main effect driving the classification. An evaluation of the various in vivo drivers of classification compiled in the database was performed to establish which of these are most important from a regulatory point of view. These analyses established that the most important drivers for Cat 1 Classification are (1) CO mean ≥ 3 (days 1-3) (severity) and (2) CO persistence on day 21 in the absence of severity, and those for Cat 2 classification are (3) CO mean ≥ 1 and (4) conjunctival redness mean ≥ 2. Moreover, it is shown that all classifiable effects (including persistence and CO = 4) should be present in ≥60 % of the animals to drive a classification. As a consequence, our analyses suggest the need for a critical revision of the UN GHS/EU CLP decision criteria for the Cat 1 classification of chemicals. Finally, a number of key criteria are identified that should be taken into consideration when selecting reference chemicals for the development, evaluation and/or validation of alternative methods and

  8. 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//

  9. Environmental Chemicals in Breast Milk

    Science.gov (United States)

    Most of the information available on environmental chemicals in breast milk is focused on persistent, lipophilic chemicals; the database on levels of these chemicals has expanded substantially since the 1950s. Currently, various types of chemicals are measured in breast milk and ...

  10. Environmental Chemicals in Breast Milk

    Science.gov (United States)

    Most of the information available on environmental chemicals in breast milk is focused on persistent, lipophilic chemicals; the database on levels of these chemicals has expanded substantially since the 1950s. Currently, various types of chemicals are measured in breast milk and ...

  11. DDEC: Dragon database of genes implicated in esophageal cancer

    KAUST Repository

    Essack, Magbubah

    2009-07-06

    Background: Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Description: Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new \\'association hypotheses\\' generated based on the precompiled reports. Conclusion: We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is

  12. 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...

  13. 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...

  14. 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.

  15. 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).

  16. 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

  17. 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.

  18. 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...

  19. 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.

  20. Incorporating Health Impacts from Exposure to Chemicals in Food Packaging in LCA

    DEFF Research Database (Denmark)

    Ernstoff, Alexi; Trier, Xenia; Jolliet, Oliver

    2014-01-01

    Life cycle assessments (LCA) on the environmental and public health impacts of food and beverage packaging materials have found some advantages to plastic over glass. Entirely missing from these evaluations are the health impacts of possible chemical, e.g. endocrine dis-ruptor, exposure through...... migration of chemicals from the packaging into the food product. We build a framework based on a life cycle perspective to predict which chemicals may be in a package that are not intentionally added ingredients, and we apply this approach to the US EPA’s CPCAT database. In total we find 1,154 chemicals...... within the CPCAT database related to food-contact materials; out of these 107 are potential endocrine disruptors according to the TEDX list of endocrine disruptors. We also build a framework in an effort to begin harmonizing LCA to include health impacts of chemical exposure related to food packaging...

  1. 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...

  2. Thermodynamics of Enzyme-Catalyzed Reactions Database

    Science.gov (United States)

    SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

  3. 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

  4. 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

  5. SuperNatural: a searchable database of available natural compounds.

    Science.gov (United States)

    Dunkel, Mathias; Fullbeck, Melanie; Neumann, Stefanie; Preissner, Robert

    2006-01-01

    Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of approximately 50,000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used. The SuperNatural Database is publicly available at http://bioinformatics.charite.de/supernatural. Viewing requires the free Chime-plugin from MDL (Chime) or Java2 Runtime Environment (MView), which is also necessary for using Marvin application for chemical drawing.

  6. A KINETIC DATABASE FOR ASTROCHEMISTRY (KIDA)

    Energy Technology Data Exchange (ETDEWEB)

    Wakelam, V.; Pavone, B.; Hebrard, E.; Hersant, F. [University of Bordeaux, LAB, UMR 5804, F-33270 Floirac (France); Herbst, E. [Departments of Physics, Astronomy, and Chemistry, The Ohio State University, Columbus, OH 43210 (United States); Loison, J.-C.; Chandrasekaran, V.; Bergeat, A. [University of Bordeaux, ISM, CNRS UMR 5255, F-33400 Talence (France); Smith, I. W. M. [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Adams, N. G. [Department of Chemistry, University of Georgia, Athens, GA 30602 (United States); Bacchus-Montabonel, M.-C. [LASIM, CNRS-UMR5579, Universite de Lyon (Lyon I), 43 Bvd. 11 Novembre 1918, F-69622 Villeurbanne Cedex (France); Beroff, K. [Institut des Sciences Moleculaires d' Orsay, CNRS and Universite Paris-Sud, F-91405 Orsay Cedex (France); Bierbaum, V. M. [Department of Chemistry and Biochemistry, Center for Astrophysics and Space Astronomy, University of Colorado, Boulder, CO 80309 (United States); Chabot, M. [Intitut de Physique Nucleaire d' Orsay, IN2P3-CNRS and Universite Paris-Sud, F-91406 Orsay Cedex (France); Dalgarno, A. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Van Dishoeck, E. F. [Leiden Observatory, Leiden University, P.O. Box 9513, NL-2300 RA Leiden (Netherlands); Faure, A. [UJF-Grenoble 1/CNRS, Institut de Planetologie et d' Astrophysique de Grenoble (IPAG) UMR 5274, F-38041 Grenoble (France); Geppert, W. D. [Department of Physics, University of Stockholm, Roslagstullbacken 21, S-10691 Stockholm (Sweden); Gerlich, D. [Technische Universitaet Chemnitz, Department of Physics, D-09107 Chemnitz (Germany); Galli, D. [INAF-Osservatorio Astrofisico di Arcetri, Largo E. Fermi 5, I-50125 Firenze (Italy); and others

    2012-03-01

    We present a novel chemical database for gas-phase astrochemistry. Named the KInetic Database for Astrochemistry (KIDA), this database consists of gas-phase reactions with rate coefficients and uncertainties that will be vetted to the greatest extent possible. Submissions of measured and calculated rate coefficients are welcome, and will be studied by experts before inclusion into the database. Besides providing kinetic information for the interstellar medium, KIDA is planned to contain such data for planetary atmospheres and for circumstellar envelopes. Each year, a subset of the reactions in the database (kida.uva) will be provided as a network for the simulation of the chemistry of dense interstellar clouds with temperatures between 10 K and 300 K. We also provide a code, named Nahoon, to study the time-dependent gas-phase chemistry of zero-dimensional and one-dimensional interstellar sources.

  7. 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

  8. 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. 

  9. 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

  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. 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.

  13. DDESC: Dragon database for exploration of sodium channels in human

    Directory of Open Access Journals (Sweden)

    Radovanovic Aleksandar

    2008-12-01

    Full Text Available Abstract Background Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic disorders such as febrile epilepsy, Brugada syndrome, ventricular fibrillation, long QT syndrome, or channelopathy associated insensitivity to pain. In spite of these significant effects that sodium channel proteins/genes could have on human health, there is no publicly available resource focused on sodium channels that would support exploration of the sodium channel related information. Results We report here Dragon Database for Exploration of Sodium Channels in Human (DDESC, which provides comprehensive information related to sodium channels regarding different entities, such as "genes and proteins", "metabolites and enzymes", "toxins", "chemicals with pharmacological effects", "disease concepts", "human anatomy", "pathways and pathway reactions" and their potential links. DDESC is compiled based on text- and data-mining. It allows users to explore potential associations between different entities related to sodium channels in human, as well as to automatically generate novel hypotheses. Conclusion DDESC is first publicly available resource where the information related to sodium channels in human can be explored at different levels. This database is freely accessible for academic and non-profit users via the worldwide web http://apps.sanbi.ac.za/ddesc.

  14. CREDO: a protein-ligand interaction database for drug discovery.

    Science.gov (United States)

    Schreyer, Adrian; Blundell, Tom

    2009-02-01

    Harnessing data from the growing number of protein-ligand complexes in the Protein Data Bank is an important task in drug discovery. In order to benefit from the abundance of three-dimensional structures, structural data must be integrated with sequence as well as chemical data and the protein-small molecule interactions characterized structurally at the inter-atomic level. In this study, we present CREDO, a new publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its application programming interface. Features of CREDO include implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Selected analyses of these key features are presented to highlight a range of potential applications of CREDO. The CREDO dataset has been released into the public domain together with the application programming interface under a Creative Commons license at http://www-cryst.bioc.cam.ac.uk/credo. We believe that the free availability and numerous features of CREDO database will be useful not only for commercial but also for academia-driven drug discovery programmes.

  15. 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.

  16. A indústria de processamento químico no Brasil: suas motivações para pesquisa e desenvolvimento e suas interfaces com as políticas governamentais The chemical process industry in Brazil: its motivations for research and development and its interfaces with public policies

    Directory of Open Access Journals (Sweden)

    Alberto Ramy Mansur

    2005-12-01

    Full Text Available As the Chemical Science is an experimental one a Chemical Industry require technical people in all its staff level: from Directors and Managers to Operators. This chemical and chemical engineering based education is the foundation of the innovate process and motivation. The paper discusses this and the role of Public Policies to improve the R&D and innovation in the Brazilian Chemical Industry.

  17. The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports.

    Science.gov (United States)

    Wohlgemuth, Gert; Haldiya, Pradeep Kumar; Willighagen, Egon; Kind, Tobias; Fiehn, Oliver

    2010-10-15

    Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed. The software was implemented in Groovy and JAVA, the web frontend was implemented in GRAILS and the database used was PostgreSQL. The source code and an online web interface are freely available. Chemical Translation Service (CTS): http://cts.fiehnlab.ucdavis.edu ofiehn@ucdavis.edu

  18. 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.

  19. 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 ...

  20. 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 ...

  1. 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

  2. Parallel Worlds of Public and Commercial Bioactive Chemistry Data

    Science.gov (United States)

    2014-01-01

    The availability of structures and linked bioactivity data in databases is powerfully enabling for drug discovery and chemical biology. However, we now review some confounding issues with the divergent expansions of public and commercial sources of chemical structures. These are associated with not only expanding patent extraction but also increasingly large vendor collections amassed via different selection criteria between SciFinder from Chemical Abstracts Service (CAS) and major public sources such as PubChem, ChemSpider, UniChem, and others. These increasingly massive collections may include both real and virtual compounds, as well as so-called prophetic compounds from patents. We address a range of issues raised by the challenges faced resolving the NIH probe compounds. In addition we highlight the confounding of prior-art searching by virtual compounds that could impact the composition of matter patentability of a new medicinal chemistry lead. Finally, we propose some potential solutions. PMID:25415348

  3. 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...

  4. 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...

  5. 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...

  6. 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.

  7. 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).

  8. 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.

  9. 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...

  10. Relational database cartridges and their efficiency in chemical sub-structure searching%子结构检索中关系数据库插件的使用和效率

    Institute of Scientific and Technical Information of China (English)

    王玉玲; 吴昊; 温浩

    2011-01-01

    采用关系数据库插件能够实现化合物描述符(FingerPrint)的生成、建立索引和化合物的子结构检索.本文以PubChem 有机化合物Molfile为数据源,在Oracle关系数据库上分别安装插件OrChem(JAVA)和Bingo(C++)构建了化合物分子结构数据库.本文从FingerPrint的构成和索引策略两方面讨论了OrChem和Bingo的主要差异,并选取10个特征化合物进行子结构检索测试.对存储40万种化合物的分子结构数据库的测试结果显示,OrChem可满足用户检索响应,Bingo则更为快捷.对于存储2600万种化合物的分子结构数据库,针对Bingo通过优化Oracle数据库内存管理、数据表结构、子结构预筛选参数,实现了满足用户的高效检索.%Relational database cartridge provides FingerPrint generation, indexing and molecular substructure searching. Two Oracle database cartridges, OrChem (JAVA) and Bingo (C++), are used in this work to develop the molecular structure database and its sub-structure search system with PubChem organic compound Molfile data. Differences between OrChem and Bingo on FingerPrint and Index strategy were discussed for 2-dimensional sub-structure searching. The efficiency of OrChem and Bingo on sub-structure searching was tested by using 10 typical query substructures on molecular structure databases of 400000 compounds and of 26000000 compounds, respectively. For the database of 400000 compounds, either OrChem or Bingo operates well enough for practical service, while Bingo shows higher efficiency. Bingo, for its capability on supporting the operation of larger database, operates successfully on the database of 26000000 compounds by configuration of memory management, table structure and sub-structure pre-screening parameters settings.

  11. 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...

  12. 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...

  13. 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

  14. 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...

  15. 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...

  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. VALD - an atomic and molecular database for astrophysics

    Energy Technology Data Exchange (ETDEWEB)

    Heiter, U; Barklem, P; Kochukhov, O; Piskunov, N [Department of Astronomy and Space Physics, Uppsala University (Sweden); Fossati, L; Obbrugger, M; Stuetz, Ch; Weiss, W W [Institute of Astronomy, University of Vienna (Austria); Kildiyarova, R [Institute of Spectroscopy, Russian Academy of Sciences, Moscow region, Troitsk (Russian Federation); Kupka, F [Max-Planck-Institute for Astrophysics, Garching (Germany); Plez, B [Universite Montpellier II, GRAAL, CNRS - UMR 5024 (France); Ryabchikova, T [Institute of Astronomy, Russian Academy of Sciences, Moscow (Russian Federation); Stempels, H C [School of Physics and Astronomy, University of St Andrews, Scotland (United Kingdom)], E-mail: ulrike@astro.uu.se

    2008-10-15

    The VALD database of atomic and molecular data aims to ensure a robust and consistent analysis of astrophysical spectra. We offer a convenient e-mail and web-based user interface to a vast collection of spectral line parameters for all chemical elements and in the future also for molecules. An international team is working on the following tasks: collecting line parameters from relevant theoretical and experimental publications, computing line parameters, evaluating the data quality by comparison of similar data from different sources and by comparison with astrophysical observations, and incorporating the data into VALD. A unique feature of VALD is its capability to provide the most comprehensive spectral line lists for specific astrophysical plasma conditions defined by the user.

  4. Blending Education and Polymer Science: Semi Automated Creation of a Thermodynamic Property Database.

    Science.gov (United States)

    Tchoua, Roselyne B; Qin, Jian; Audus, Debra J; Chard, Kyle; Foster, Ian T; de Pablo, Juan

    2016-09-13

    Structured databases of chemical and physical properties play a central role in the everyday research activities of scientists and engineers. In materials science, researchers and engineers turn to these databases to quickly query, compare, and aggregate various properties, thereby allowing for the development or application of new materials. The vast majority of these databases have been generated manually, through decades of labor-intensive harvesting of information from the literature; yet, while there are many examples of commonly used databases, a significant number of important properties remain locked within the tables, figures, and text of publications. The question addressed in our work is whether, and to what extent, the process of data collection can be automated. Students of the physical sciences and engineering are often confronted with the challenge of finding and applying property data from the literature, and a central aspect of their education is to develop the critical skills needed to identify such data and discern their meaning or validity. To address shortcomings associated with automated information extraction, while simultaneously preparing the next generation of scientists for their future endeavors, we developed a novel course-based approach in which students develop skills in polymer chemistry and physics and apply their knowledge by assisting with the semi-automated creation of a thermodynamic property database.

  5. SynProt: A Comprehensive Database for Proteins of the Detergent-Resistant Synaptic Junctions Fraction

    Directory of Open Access Journals (Sweden)

    Rainer ePielot

    2012-06-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  7. Blending Education and Polymer Science: Semiautomated Creation of a Thermodynamic Property Database

    Energy Technology Data Exchange (ETDEWEB)

    Tchoua, Roselyne B.; Qin, Jian; Audus, Debra J.; Chard, Kyle; Foster, Ian T.; de Pablo, Juan

    2016-09-13

    Structured databases of chemical and physical properties play a central role in the everyday research activities of scientists and engineers. In materials science, researchers and engineers turn to these databases to quickly query, compare, and aggregate various properties, thereby allowing for the development or application of new materials. The vast majority of these databases have been generated manually, through decades of labor-intensive harvesting of information from the literature, yet while there are many examples of commonly used databases, a significant number of important properties remain locked within the tables, figures, and text of publications. The question addressed in our work is whether and to what extent the process of data collection can be automated. Students of the physical sciences and engineering are often confronted with the challenge of finding and applying property data from the literature, and a central aspect of their education is to develop the critical skills needed to identify such data and discern their meaning or validity. To address shortcomings associated with automated information extraction while simultaneously preparing the next generation of scientists for their future endeavors, we developed a novel course-based approach in which students develop skills in polymer chemistry and physics and apply their knowledge by assisting with the semiautomated creation of a thermodynamic property database.

  8. Chemicals for worldwide aquaculture

    Science.gov (United States)

    Schnick, R.A.

    1991-01-01

    Regulations and therapeutants or other safe chemicals that are approved or acceptable for use in the aquaculture industry in the US, Canada, Europe and Japan are presented, discussing also compounds that are unacceptable for aquaculture. Chemical use practices that could affect public health are considered and details given regarding efforts to increase the number of registered and acceptable chemicals.

  9. Chemical Abstracts Service Chemical Registry System: History, Scope, and Impacts.

    Science.gov (United States)

    Weisgerber, David W.

    1997-01-01

    Describes the history, scope, and applications of the Chemical Abstracts Service Chemical Registry System, a computerized database that uniquely identifies chemical substances on the basis of their molecular structures. Explains searching the system is and discusses its use as an international resource. (66 references) (Author/LRW)

  10. Publicity and public relations

    Science.gov (United States)

    Fosha, Charles E.

    1990-01-01

    This paper addresses approaches to using publicity and public relations to meet the goals of the NASA Space Grant College. Methods universities and colleges can use to publicize space activities are presented.

  11. License - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database License License to Use This Database Last updated : 2014/02/04 You may use this database...pecifies the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons... Attribution-Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database...pan is found here . With regard to this database, you are licensed to: freely access part or whole of this database

  12. A Computational Chemistry Database for Semiconductor Processing

    Science.gov (United States)

    Jaffe, R.; Meyyappan, M.; Arnold, J. O. (Technical Monitor)

    1998-01-01

    The concept of 'virtual reactor' or 'virtual prototyping' has received much attention recently in the semiconductor industry. Commercial codes to simulate thermal CVD and plasma processes have become available to aid in equipment and process design efforts, The virtual prototyping effort would go nowhere if codes do not come with a reliable database of chemical and physical properties of gases involved in semiconductor processing. Commercial code vendors have no capabilities to generate such a database, rather leave the task to the user of finding whatever is needed. While individual investigations of interesting chemical systems continue at Universities, there has not been any large scale effort to create a database. In this presentation, we outline our efforts in this area. Our effort focuses on the following five areas: 1. Thermal CVD reaction mechanism and rate constants. 2. Thermochemical properties. 3. Transport properties.4. Electron-molecule collision cross sections. and 5. Gas-surface interactions.

  13. Prediction methods and databases within chemoinformatics

    DEFF Research Database (Denmark)

    Jónsdóttir, Svava Osk; Jørgensen, Flemming Steen; Brunak, Søren

    2005-01-01

    MOTIVATION: To gather information about available databases and chemoinformatics methods for prediction of properties relevant to the drug discovery and optimization process. RESULTS: We present an overview of the most important databases with 2-dimensional and 3-dimensional structural information...... about drugs and drug candidates, and of databases with relevant properties. Access to experimental data and numerical methods for selecting and utilizing these data is crucial for developing accurate predictive in silico models. Many interesting predictive methods for classifying the suitability...... of chemical compounds as potential drugs, as well as for predicting their physico-chemical and ADMET properties have been proposed in recent years. These methods are discussed, and some possible future directions in this rapidly developing field are described....

  14. IDBD: infectious disease biomarker database.

    Science.gov (United States)

    Yang, In Seok; Ryu, Chunsun; Cho, Ki Joon; Kim, Jin Kwang; Ong, Swee Hoe; Mitchell, Wayne P; Kim, Bong Su; Oh, Hee-Bok; Kim, Kyung Hyun

    2008-01-01

    Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

  15. Neutrosophic Relational Database Decomposition

    OpenAIRE

    Meena Arora; Ranjit Biswas; Dr. U.S.Pandey

    2011-01-01

    In this paper we present a method of decomposing a neutrosophic database relation with Neutrosophic attributes into basic relational form. Our objective is capable of manipulating incomplete as well as inconsistent information. Fuzzy relation or vague relation can only handle incomplete information. Authors are taking the Neutrosophic Relational database [8],[2] to show how imprecise data can be handled in relational schema.

  16. HIV Structural Database

    Science.gov (United States)

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  17. Structural Ceramics Database

    Science.gov (United States)

    SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

  18. Odense Pharmacoepidemiological Database (OPED)

    DEFF Research Database (Denmark)

    Hallas, Jesper; Poulsen, Maja Hellfritzsch; Hansen, Morten Rix

    2017-01-01

    The Odense University Pharmacoepidemiological Database (OPED) is a prescription database established in 1990 by the University of Southern Denmark, covering reimbursed prescriptions from the county of Funen in Denmark and the region of Southern Denmark (1.2 million inhabitants). It is still active...

  19. The Danish Anaesthesia Database

    DEFF Research Database (Denmark)

    Antonsen, Kristian; Rosenstock, Charlotte Vallentin; Lundstrøm, Lars Hyldborg

    2016-01-01

    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...

  20. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1.

  1. Balkan Vegetation Database

    NARCIS (Netherlands)

    Vassilev, Kiril; Pedashenko, Hristo; Alexandrova, Alexandra; Tashev, Alexandar; Ganeva, Anna; Gavrilova, Anna; Gradevska, Asya; Assenov, Assen; Vitkova, Antonina; Grigorov, Borislav; Gussev, Chavdar; Filipova, Eva; Aneva, Ina; Knollová, Ilona; Nikolov, Ivaylo; Georgiev, Georgi; Gogushev, Georgi; Tinchev, Georgi; Pachedjieva, Kalina; Koev, Koycho; Lyubenova, Mariyana; Dimitrov, Marius; Apostolova-Stoyanova, Nadezhda; Velev, Nikolay; Zhelev, Petar; Glogov, Plamen; Natcheva, Rayna; Tzonev, Rossen; Boch, Steffen; Hennekens, Stephan M.; Georgiev, Stoyan; Stoyanov, Stoyan; Karakiev, Todor; Kalníková, Veronika; Shivarov, Veselin; Russakova, Veska; Vulchev, Vladimir

    2016-01-01

    The Balkan Vegetation Database (BVD; GIVD ID: EU-00-019; http://www.givd.info/ID/EU-00- 019) is a regional database that consists of phytosociological relevés from different vegetation types from six countries on the Balkan Peninsula (Albania, Bosnia and Herzegovina, Bulgaria, Kosovo, Montenegro

  2. Balkan Vegetation Database

    NARCIS (Netherlands)

    Vassilev, Kiril; Pedashenko, Hristo; Alexandrova, Alexandra; Tashev, Alexandar; Ganeva, Anna; Gavrilova, Anna; Gradevska, Asya; Assenov, Assen; Vitkova, Antonina; Grigorov, Borislav; Gussev, Chavdar; Filipova, Eva; Aneva, Ina; Knollová, Ilona; Nikolov, Ivaylo; Georgiev, Georgi; Gogushev, Georgi; Tinchev, Georgi; Pachedjieva, Kalina; Koev, Koycho; Lyubenova, Mariyana; Dimitrov, Marius; Apostolova-Stoyanova, Nadezhda; Velev, Nikolay; Zhelev, Petar; Glogov, Plamen; Natcheva, Rayna; Tzonev, Rossen; Boch, Steffen; Hennekens, Stephan M.; Georgiev, Stoyan; Stoyanov, Stoyan; Karakiev, Todor; Kalníková, Veronika; Shivarov, Veselin; Russakova, Veska; Vulchev, Vladimir

    2016-01-01

    The Balkan Vegetation Database (BVD; GIVD ID: EU-00-019; http://www.givd.info/ID/EU-00- 019) is a regional database that consists of phytosociological relevés from different vegetation types from six countries on the Balkan Peninsula (Albania, Bosnia and Herzegovina, Bulgaria, Kosovo, Montenegro

  3. Biological Macromolecule Crystallization Database

    Science.gov (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  4. 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.

  5. An organic database system

    NARCIS (Netherlands)

    M.L. Kersten (Martin); A.P.J.M. Siebes (Arno)

    1999-01-01

    textabstractThe pervasive penetration of database technology may suggest that we have reached the end of the database research era. The contrary is true. Emerging technology, in hardware, software, and connectivity, brings a wealth of opportunities to push technology to a new level of maturity.

  6. Atomic Spectra Database (ASD)

    Science.gov (United States)

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

  7. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1. Bib

  8. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1. Bib

  9. Database Description - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Yeast Interacting Proteins Database Database Description General information of database Database name Yeast... Interacting Proteins Database Alternative name - Creator Creator Name: Takashi Ito* Creator Affiliation: Di...-4-7136-3989 FAX: +81-4-7136-3979 E-mail : Database classification Metabolic and Signaling Pathways - Protei...n-protein interactions Organism Taxonomy Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Database descripti...ive yeast two-hybrid analysis of budding yeast proteins. Features and manner of utilization of database Prot

  10. Internet patent databases: a comparative study.

    Directory of Open Access Journals (Sweden)

    Borja González-Albo Manglano

    2008-02-01

    Full Text Available The patent is an essential document in the evaluation of technological investigation that has been used as approximation of innovation. The patent databases on the Internet are one principal source of information for this kind of analysis. However they are many databases and they are very different; reason why the election of one of them in the accomplishment of bibliometric analysis is a crucial aspect. In this sense, this survey studies some of main free –Esp@cenet, PatentScope, national databases and commercial –Derwent Innovatios Index, Chemical Abstracts Plus, Thomson Delphion Intellectual Property Network– patent databases. The results show that commercial systems provide value-added –data revision, analysis tools, etc.–; althought the free ones are going to become trustworthy resources thanks to the improvements and options that are introduced in them.

  11. The LHCb configuration database

    CERN Document Server

    Abadie, L; Van Herwijnen, Eric; Jacobsson, R; Jost, B; Neufeld, N

    2005-01-01

    The aim of the LHCb configuration database is to store information about all the controllable devices of the detector. The experiment's control system (that uses PVSS ) will configure, start up and monitor the detector from the information in the configuration database. The database will contain devices with their properties, connectivity and hierarchy. The ability to store and rapidly retrieve huge amounts of data, and the navigability between devices are important requirements. We have collected use cases to ensure the completeness of the design. Using the entity relationship modelling technique we describe the use cases as classes with attributes and links. We designed the schema for the tables using relational diagrams. This methodology has been applied to the TFC (switches) and DAQ system. Other parts of the detector will follow later. The database has been implemented using Oracle to benefit from central CERN database support. The project also foresees the creation of tools to populate, maintain, and co...

  12. 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.

  13. Database Description - DGBY | 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 DGBY Database... Description General information of database Database name DGBY Alternative name Database for G...-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan Akira Ando TEL: +81-29-838-8066 E-mail: Database classificati...on Microarray Data and other Gene Expression Databases Organism Taxonomy Name: Sa...ccharomyces cerevisiae Taxonomy ID: 4932 Database description Baker's yeast Saccharomyces cerevisiae is an e

  14. Database Description - RPSD | 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 RPSD Database... Description General information of database Database name RPSD Alternative name Summary inform...n National Institute of Agrobiological Sciences Toshimasa Yamazaki E-mail : Database classification Structure Database...idopsis thaliana Taxonomy ID: 3702 Taxonomy Name: Glycine max Taxonomy ID: 3847 Database description We have...nts such as rice, and have put together the result and related informations. This database contains the basi

  15. Chemical Carcinogenesis Research Information System (CCRIS)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CCRIS database contains chemical records with carcinogenicity, mutagenicity, tumor promotion, and tumor inhibition test results. CCRIS provides historical...

  16. 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...

  17. Native Pig and Chicken Breed Database: NPCDB.

    Science.gov (United States)

    Jeong, Hyeon-Soo; Kim, Dae-Won; Chun, Se-Yoon; Sung, Samsun; Kim, Hyeon-Jeong; Cho, Seoae; Kim, Heebal; Oh, Sung-Jong

    2014-10-01

    Indigenous (native) breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB) which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/) provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed's characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  18. [Total quality management of clinical database].

    Science.gov (United States)

    Okubo, Suguru; Miyata, Hiroaki; Tomotaki, Ai; Motomura, Noboru; Murakami, Arata; Ono, Minoru; Iwanaka, Tadashi

    2013-06-01

    Data entry system should be constructed considering utility, accuracy, propriety, and feasibility. The methods for developing useful and accurate clinical databases are 1)system development based on the concept of "error proofing", 2)system test by real users, 3)guidances for participants, and 4)incentive for accurate data entry. In terms of propriety, to gain patient's consent on data collection and to publicly announce objectives and methods of clinical database are necessary. Confidentiality and anonymization of data are also important. Balancing efficacy and propriety for maximization of patients' and societal benefit is one of the important responsibilities of database management organizations. In addition, assessment of data quality such as audit and feedback is useful for enhancing accuracy and reliability of clinical databases.

  19. 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.

  20. 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...