A method to implement fine-grained access control for personal health records through standard relational database queries.

PubMed

Sujansky, Walter V; Faus, Sam A; Stone, Ethan; Brennan, Patricia Flatley

2010-10-01

Online personal health records (PHRs) enable patients to access, manage, and share certain of their own health information electronically. This capability creates the need for precise access-controls mechanisms that restrict the sharing of data to that intended by the patient. The authors describe the design and implementation of an access-control mechanism for PHR repositories that is modeled on the eXtensible Access Control Markup Language (XACML) standard, but intended to reduce the cognitive and computational complexity of XACML. The authors implemented the mechanism entirely in a relational database system using ANSI-standard SQL statements. Based on a set of access-control rules encoded as relational table rows, the mechanism determines via a single SQL query whether a user who accesses patient data from a specific application is authorized to perform a requested operation on a specified data object. Testing of this query on a moderately large database has demonstrated execution times consistently below 100ms. The authors include the details of the implementation, including algorithms, examples, and a test database as Supplementary materials. Copyright © 2010 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Database in Artificial Intelligence.

ERIC Educational Resources Information Center

Wilkinson, Julia

1986-01-01

Describes a specialist bibliographic database of literature in the field of artificial intelligence created by the Turing Institute (Glasgow, Scotland) using the BRS/Search information retrieval software. The subscription method for end-users--i.e., annual fee entitles user to unlimited access to database, document provision, and printed awareness…

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

PubMed

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

2015-01-01

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

Libraries of Peptide Fragmentation Mass Spectra Database

National Institute of Standards and Technology Data Gateway

SRD 1C NIST Libraries of Peptide Fragmentation Mass Spectra Database (Web, free access)   The purpose of the library is to provide peptide reference data for laboratories employing mass spectrometry-based proteomics methods for protein analysis. Mass spectral libraries identify these compounds in a more sensitive and robust manner than alternative methods. These databases are freely available for testing and development of new applications.

An SQL query generator for CLIPS

NASA Technical Reports Server (NTRS)

Snyder, James; Chirica, Laurian

1990-01-01

As expert systems become more widely used, their access to large amounts of external information becomes increasingly important. This information exists in several forms such as statistical, tabular data, knowledge gained by experts and large databases of information maintained by companies. Because many expert systems, including CLIPS, do not provide access to this external information, much of the usefulness of expert systems is left untapped. The scope of this paper is to describe a database extension for the CLIPS expert system shell. The current industry standard database language is SQL. Due to SQL standardization, large amounts of information stored on various computers, potentially at different locations, will be more easily accessible. Expert systems should be able to directly access these existing databases rather than requiring information to be re-entered into the expert system environment. The ORACLE relational database management system (RDBMS) was used to provide a database connection within the CLIPS environment. To facilitate relational database access a query generation system was developed as a CLIPS user function. The queries are entered in a CLlPS-like syntax and are passed to the query generator, which constructs and submits for execution, an SQL query to the ORACLE RDBMS. The query results are asserted as CLIPS facts. The query generator was developed primarily for use within the ICADS project (Intelligent Computer Aided Design System) currently being developed by the CAD Research Unit in the California Polytechnic State University (Cal Poly). In ICADS, there are several parallel or distributed expert systems accessing a common knowledge base of facts. Expert system has a narrow domain of interest and therefore needs only certain portions of the information. The query generator provides a common method of accessing this information and allows the expert system to specify what data is needed without specifying how to retrieve it.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Ontology-based geospatial data query and integration

USGS Publications Warehouse

Zhao, T.; Zhang, C.; Wei, M.; Peng, Z.-R.

2008-01-01

Geospatial data sharing is an increasingly important subject as large amount of data is produced by a variety of sources, stored in incompatible formats, and accessible through different GIS applications. Past efforts to enable sharing have produced standardized data format such as GML and data access protocols such as Web Feature Service (WFS). While these standards help enabling client applications to gain access to heterogeneous data stored in different formats from diverse sources, the usability of the access is limited due to the lack of data semantics encoded in the WFS feature types. Past research has used ontology languages to describe the semantics of geospatial data but ontology-based queries cannot be applied directly to legacy data stored in databases or shapefiles, or to feature data in WFS services. This paper presents a method to enable ontology query on spatial data available from WFS services and on data stored in databases. We do not create ontology instances explicitly and thus avoid the problems of data replication. Instead, user queries are rewritten to WFS getFeature requests and SQL queries to database. The method also has the benefits of being able to utilize existing tools of databases, WFS, and GML while enabling query based on ontology semantics. ?? 2008 Springer-Verlag Berlin Heidelberg.

Improved Information Retrieval Performance on SQL Database Using Data Adapter

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Integrating RFID technique to design mobile handheld inventory management system

NASA Astrophysics Data System (ADS)

Huang, Yo-Ping; Yen, Wei; Chen, Shih-Chung

2008-04-01

An RFID-based mobile handheld inventory management system is proposed in this paper. Differing from the manual inventory management method, the proposed system works on the personal digital assistant (PDA) with an RFID reader. The system identifies electronic tags on the properties and checks the property information in the back-end database server through a ubiquitous wireless network. The system also provides a set of functions to manage the back-end inventory database and assigns different levels of access privilege according to various user categories. In the back-end database server, to prevent improper or illegal accesses, the server not only stores the inventory database and user privilege information, but also keeps track of the user activities in the server including the login and logout time and location, the records of database accessing, and every modification of the tables. Some experimental results are presented to verify the applicability of the integrated RFID-based mobile handheld inventory management system.

Five years of poisons information on the internet: the UK experience of TOXBASE

PubMed Central

Bateman, D N; Good, A M

2006-01-01

Introduction In 1999, the UK adopted a policy of using TOXBASE, an internet service available free to registered National Health Service (NHS) departments and professionals, as the first point of information on poisoning. This was the first use worldwide of the internet for provision of clinical advice at a national level. We report the impact on database usage and NPIS telephone call loads. Methods Trends in the pattern of TOXBASE usage from 2000–2004 are reported by user category. Information on the monographs accessed most frequently was also extracted from the webserver and sorted by user category. The numbers of telephone calls to the National Poisons Information Service (NPIS) were extracted from NPIS annual reports. Results Numbers of database logons increased 3.5 fold from 102 352 in 2000 to 368 079 in 2004, with a total of 789 295 accesses to product monographs in 2004. Registered users increased almost tenfold, with approximately half accessing the database at least once a year. Telephone calls to the NPIS dropped by over half. Total contacts with NPIS (web and telephone) increased 50%. Major users in 2004 were hospital emergency departments (60.5% of logons) and NHS public access helplines (NHS Direct and NHS24) (29.4%). Different user groups access different parts of the database. Emergency departments access printable fact sheets for about 10% of monographs they access. Conclusion Provision of poisons information by the internet has been successful in reducing NPIS call loads. Provision of basic poisons information by this method appears to be acceptable to different professional groups, and to be effective in reducing telephone call loads and increasing service cost effectiveness. PMID:16858093

Development of a database of instruments for resource-use measurement: purpose, feasibility, and design.

PubMed

Ridyard, Colin H; Hughes, Dyfrig A

2012-01-01

Health economists frequently rely on methods based on patient recall to estimate resource utilization. Access to questionnaires and diaries, however, is often limited. This study examined the feasibility of establishing an open-access Database of Instruments for Resource-Use Measurement, identified relevant fields for data extraction, and outlined its design. An electronic survey was sent to authors of full UK economic evaluations listed in the National Health Service Economic Evaluation Database (2008-2010), authors of monographs of Health Technology Assessments (1998-2010), and subscribers to the JISCMail health economics e-mailing list. The survey included questions on piloting, validation, recall period, and data capture method. Responses were analyzed and data extracted to generate relevant fields for the database. A total of 143 responses to the survey provided data on 54 resource-use instruments for inclusion in the database. All were reliant on patient or carer recall, and a majority (47) were questionnaires. Thirty-seven were designed for self-completion by the patient, carer, or guardian, and the remainder were designed for completion by researchers or health care professionals while interviewing patients. Methods of development were diverse, particularly in areas such as the planning of resource itemization (evident in 25 instruments), piloting (25), and validation (29). On the basis of the present analysis, we developed a Web-enabled Database of Instruments for Resource-Use Measurement, accessible via www.DIRUM.org. This database may serve as a practical resource for health economists, as well as a means to facilitate further research in the area of resource-use data collection. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.

PubMed

Jeffryes, James G; Colastani, Ricardo L; Elbadawi-Sidhu, Mona; Kind, Tobias; Niehaus, Thomas D; Broadbelt, Linda J; Hanson, Andrew D; Fiehn, Oliver; Tyo, Keith E J; Henry, Christopher S

2015-01-01

In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography-mass spectrometry (LC-MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC-MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. Furthermore, MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures. Graphical abstractMINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.

Molecular Identification and Databases in Fusarium

USDA-ARS?s Scientific Manuscript database

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

NESDIS OSPO Data Access Policy and CRM

NASA Astrophysics Data System (ADS)

Seybold, M. G.; Donoho, N. A.; McNamara, D.; Paquette, J.; Renkevens, T.

2012-12-01

The Office of Satellite and Product Operations (OSPO) is the NESDIS office responsible for satellite operations, product generation, and product distribution. Access to and distribution of OSPO data was formally established in a Data Access Policy dated February, 2011. An extension of the data access policy is the OSPO Customer Relationship Management (CRM) Database, which has been in development since 2008 and is reaching a critical level of maturity. This presentation will provide a summary of the data access policy and standard operating procedure (SOP) for handling data access requests. The tangential CRM database will be highlighted including the incident tracking system, reporting and notification capabilities, and the first comprehensive portfolio of NESDIS satellites, instruments, servers, applications, products, user organizations, and user contacts. Select examples of CRM data exploitation will show how OSPO is utilizing the CRM database to more closely satisfy the user community's satellite data needs with new product promotions, as well as new data and imagery distribution methods in OSPO's Environmental Satellite Processing Center (ESPC). In addition, user services and outreach initiatives from the Satellite Products and Services Division will be highlighted.

Overview of open resources to support automated structure verification and elucidation

EPA Science Inventory

Cheminformatics methods form an essential basis for providing analytical scientists with access to data, algorithms and workflows. There are an increasing number of free online databases (compound databases, spectral libraries, data repositories) and a rich collection of software...

Indexing and retrieving point and region objects

NASA Astrophysics Data System (ADS)

Ibrahim, Azzam T.; Fotouhi, Farshad A.

1996-03-01

R-tree and its variants are examples of spatial data structures for paged-secondary memory. To process a query, these structures require multiple path traversals. In this paper, we present a new image access method, SB+-tree which requires a single path traversal to process a query. Also, SB+-tree will allow commercial databases an access method for spatial objects without a major change, since most commercial databases already support B+-tree as an access method for text data. The SB+-tree can be used for zero and non-zero size data objects. Non-zero size objects are approximated by their minimum bounding rectangles (MBRs). The number of SB+-trees generated is dependent upon the number of dimensions of the approximation of the object. The structure supports efficient spatial operations such as regions-overlap, distance and direction. In this paper, we experimentally and analytically demonstrate the superiority of SB+-tree over R-tree.

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

PubMed

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

2015-01-01

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

Reflective Database Access Control

ERIC Educational Resources Information Center

Olson, Lars E.

2009-01-01

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

External access to ALICE controls conditions data

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

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

Alternative treatment technology information center computer database system

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

Sullivan, D.

1995-10-01

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

Observational database for studies of nearby universe

NASA Astrophysics Data System (ADS)

Kaisina, E. I.; Makarov, D. I.; Karachentsev, I. D.; Kaisin, S. S.

2012-01-01

We present the description of a database of galaxies of the Local Volume (LVG), located within 10 Mpc around the Milky Way. It contains more than 800 objects. Based on an analysis of functional capabilities, we used the PostgreSQL DBMS as a management system for our LVG database. Applying semantic modelling methods, we developed a physical ER-model of the database. We describe the developed architecture of the database table structure, and the implemented web-access, available at http://www.sao.ru/lv/lvgdb.

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

PubMed Central

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

2015-01-01

Background Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Method Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases’ characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Results Forty databases– 20 from Thailand and 20 from Japan—were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Conclusion Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed. PMID:26560127

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

PubMed

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

2010-06-14

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

Vital Business Educators' Perceptions about the Usefulness of Business Education Periodicals: Making the Relevant Literature More Accessible

ERIC Educational Resources Information Center

Scott, James Calvert; Blaszczynski, Carol; Green, Diana J.; Fagerheim, Britt Anna

2008-01-01

Problem: The business education literature isn't accessible. Research Questions: Which business education periodicals do vital business educators perceive to be more useful? In which databases and/or indices are they found? How much literature is fugitive? What strategies might increase literature accessibility? Research Method: Delphi technique.…

A kind of improved fingerprinting indoor location method based on WiFi

NASA Astrophysics Data System (ADS)

Zeng, Xi; Lin, Wei

2017-08-01

In the prior inventions, because of the complexity of the indoor environment, it is hard to guarantee position precision. In this paper provides an improved method that can be adopted to increase the indoor positioning accuracy of handheld positioning device. This method will be the direction of the handheld device position Angle and number of access points two characteristics to join the fingerprint. The two parameters make our normal fingerprint database more abundant. The positioning test results from comparing the normal fingerprint database with the improved fingerprint database prove the later positioning more accurate.

DataHub knowledge based assistance for science visualization and analysis using large distributed databases

NASA Technical Reports Server (NTRS)

Handley, Thomas H., Jr.; Collins, Donald J.; Doyle, Richard J.; Jacobson, Allan S.

1991-01-01

Viewgraphs on DataHub knowledge based assistance for science visualization and analysis using large distributed databases. Topics covered include: DataHub functional architecture; data representation; logical access methods; preliminary software architecture; LinkWinds; data knowledge issues; expert systems; and data management.

75 FR 57437 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-21

... a Food Safety Education and Training Materials Database. The Database is a centralized gateway to... creating previously available education materials) (2) provide a central gateway to access the education materials (3) create a systematic and efficient method of collecting data from USDA grantees and (4) promote...

78 FR 69040 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-18

... a Food Safety Education and Training Materials Database. The Database is a centralized gateway to... creating previously available education materials), (2) provide a central gateway to access the education materials, (3) create a systematic and efficient method of collecting data from USDA grantees, and (4...

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

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

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

PubMed

Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general.

Multi-Resolution Playback of Network Trace Files

DTIC Science & Technology

2015-06-01

a com- plete MySQL database, C++ developer tools and the libraries utilized in the development of the system (Boost and Libcrafter), and Wireshark...XE suite has a limit to the allowed size of each database. In order to be scalable, the project had to switch to the MySQL database suite. The...programs that access the database use the MySQL C++ connector, provided by Oracle, and the supplied methods and libraries. 4.4 Flow Generator Chapter 3

Direct access midwifery booking for prenatal care and its role in Down syndrome screening.

PubMed

Nawaz, Tariq S; Tringham, Gillian M; Holding, Stephen; McFarlane, Jane; Lindow, Stephen W

2011-10-01

To compare the uptake of Down syndrome screening by women following referral by direct access and general practitioner (GP) modes. The method of referral by either GP or direct access, for women who booked into prenatal care in Hull and East Yorkshire in 2010, was analysed using data collected from the Protos database at the Women and Children's Hospital, Hull. Subsequently, the uptake of first and second trimester screening for Down syndrome was reviewed by combining the Protos database to the screening data collected by the Clinical Biochemistry Laboratory at Hull Royal Infirmary, Hull. Women booked into prenatal care significantly earlier when referred by GP in comparison to direct access with a significant difference in screening uptake of 49.5 and 42.7%, respectively. The ratio of uptake between first and second trimester screening was not significantly different. Further research on the new direct access method of referral is required, as it may have a role in the uptake of prenatal screening for Down syndrome. More time is needed to show a definitive effect. Copyright © 2011 John Wiley & Sons, Ltd.

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

PubMed

Sorokin, Anatoly; Selkov, Gene; Goryanin, Igor

2012-07-16

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

Balancing Your Database Network Licenses against Your Budget.

ERIC Educational Resources Information Center

Bauer, Benjamin F.

1995-01-01

Discussion of choosing database access to satisfy users and budgetary constraints highlights a method to make educated estimates of simultaneous usage levels. Topics include pricing; advances in networks and CD-ROM technology; and two networking scenarios, one in an academic library and one in a corporate research facility. (LRW)

Using the TIGR gene index databases for biological discovery.

PubMed

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

Mapping the literature of nursing: 1996–2000

PubMed Central

Allen, Margaret (Peg); Jacobs, Susan Kaplan; Levy, June R.

2006-01-01

Introduction: This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Method: Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Results: Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Discussion: Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. Conclusion: For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered. PMID:16636714

Allelic database and accession divergence of a Brazilian mango collection based on microsatellite markers.

PubMed

Dos Santos Ribeiro, I C N; Lima Neto, F P; Santos, C A F

2012-12-19

Allelic patterns and genetic distances were examined in a collection of 103 foreign and Brazilian mango (Mangifera indica) accessions in order to develop a reference database to support cultivar protection and breeding programs. An UPGMA dendrogram was generated using Jaccard's coefficients from a distance matrix based on 50 alleles of 12 microsatellite loci. The base pair number was estimated by the method of inverse mobility. The cophenetic correlation was 0.8. The accessions had a coefficient of similarity from 30 to 100%, which reflects high genetic variability. Three groups were observed in the UPGMA dendrogram; the first group was formed predominantly by foreign accessions, the second group was formed by Brazilian accessions, and the Dashehari accession was isolated from the others. The 50 microsatellite alleles did not separate all 103 accessions, indicating that there are duplicates in this mango collection. These 12 microsatellites need to be validated in order to establish a reliable set to identify mango cultivars.

Standardization of search methods for guideline development: an international survey of evidence-based guideline development groups.

PubMed

Deurenberg, Rikie; Vlayen, Joan; Guillo, Sylvie; Oliver, Thomas K; Fervers, Beatrice; Burgers, Jako

2008-03-01

Effective literature searching is particularly important for clinical practice guideline development. Sophisticated searching and filtering mechanisms are needed to help ensure that all relevant research is reviewed. To assess the methods used for the selection of evidence for guideline development by evidence-based guideline development organizations. A semistructured questionnaire assessing the databases, search filters and evaluation methods used for literature retrieval was distributed to eight major organizations involved in evidence-based guideline development. All of the organizations used search filters as part of guideline development. The medline database was the primary source accessed for literature retrieval. The OVID or SilverPlatter interfaces were used in preference to the freely accessed PubMed interface. The Cochrane Library, embase, cinahl and psycinfo databases were also frequently used by the organizations. All organizations reported the intention to improve and validate their filters for finding literature specifically relevant for guidelines. In the first international survey of its kind, eight major guideline development organizations indicated a strong interest in identifying, improving and standardizing search filters to improve guideline development. It is to be hoped that this will result in the standardization of, and open access to, search filters, an improvement in literature searching outcomes and greater collaboration among guideline development organizations.

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases

PubMed Central

Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general. PMID:26038727

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

PubMed

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

2012-11-01

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

Integrated Substrate and Thin Film Design Methods

DTIC Science & Technology

1999-02-01

Proper Representation Once the required chemical databases had been converted to the Excel format, VBA macros were written to convert chemical...ternary systems databases were imported from MS Excel to MS Access to implement SQL queries. Further, this database was connected via an ODBC model, to the... VBA macro, corresponding to each of the elements A, B, and C, respectively. The B loop began with the next alphabetical choice of element symbols

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

PubMed

Li, Feng; Li, Maoyu; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Chen, Zhuchu

2006-01-11

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Web based information on clinical toxicology for the United Kingdom: uptake and utilization of TOXBASE in 2000

PubMed Central

Nicholas Bateman, D; Good, Alison M; Kelly, Catherine A; Laing, William J

2002-01-01

Aims To examine the use and uptake of TOXBASE, an Internet database for point of care provision of poisons information in the United Kingdom during its first calendar year of web-based access. Methods Interrogation of the database software to examine: use by different types of user and geographical origin; profile of ingredient and product access; time of access to the system; profile of access to other parts of the database. Results Registered users of the system increased in the first full year of operation (1224 new users) and usage of the system increased to 111 410 sessions with 190 223 product monograph accesses in 2000. Major users were hospitals, in particular accident and emergency departments. NHS Direct, a public access information service staffed by nurses, also made increasing use of the system. Usage per head of population was highest in Northern Ireland and Scotland, and least in southern England. Ingredients accessed most frequently were similar in all four countries of the UK. Times of use of the system reflect clinical activity, with hospitals making many accesses during night-time hours. The most popular parts of the database other than poisons information were those dealing with childhood poisoning, information on decontamination procedures, teratology information and slang terms for drugs of abuse. Conclusions This Internet system has been widely used in its first full year of operation. The provision of clinically relevant, up to date, information at the point of delivery of patient care is now possible using this approach. It has wide implications for the provision of other types of therapeutic information in clinical areas. Web-based technology represents an opportunity for clinical pharmacologists to provide therapeutic information for clinical colleagues at the bedside. PMID:12100219

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

PubMed

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

2007-12-11

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

Method of preliminary localization of the iris in biometric access control systems

NASA Astrophysics Data System (ADS)

Minacova, N.; Petrov, I.

2015-10-01

This paper presents a method of preliminary localization of the iris, based on the stable brightness features of the iris in images of the eye. In tests on images of eyes from publicly available databases method showed good accuracy and speed compared to existing methods preliminary localization.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

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

2006-04-01

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

The STEP database through the end-users eyes--USABILITY STUDY.

PubMed

Salunke, Smita; Tuleu, Catherine

2015-08-15

The user-designed database of Safety and Toxicity of Excipients for Paediatrics ("STEP") is created to address the shared need of drug development community to access the relevant information of excipients effortlessly. Usability testing was performed to validate if the database satisfies the need of the end-users. Evaluation framework was developed to assess the usability. The participants performed scenario based tasks and provided feedback and post-session usability ratings. Failure Mode Effect Analysis (FMEA) was performed to prioritize the problems and improvements to the STEP database design and functionalities. The study revealed several design vulnerabilities. Tasks such as limiting the results, running complex queries, location of data and registering to access the database were challenging. The three critical attributes identified to have impact on the usability of the STEP database included (1) content and presentation (2) the navigation and search features (3) potential end-users. Evaluation framework proved to be an effective method for evaluating database effectiveness and user satisfaction. This study provides strong initial support for the usability of the STEP database. Recommendations would be incorporated into the refinement of the database to improve its usability and increase user participation towards the advancement of the database. Copyright © 2015 Elsevier B.V. All rights reserved.

A Data Analysis Expert System For Large Established Distributed Databases

NASA Astrophysics Data System (ADS)

Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

1987-05-01

The purpose of this work is to analyze the applicability of artificial intelligence techniques for developing a user-friendly, parallel interface to large isolated, incompatible NASA databases for the purpose of assisting the management decision process. To carry out this work, a survey was conducted to establish the data access requirements of several key NASA user groups. In addition, current NASA database access methods were evaluated. The results of this work are presented in the form of a design for a natural language database interface system, called the Deductively Augmented NASA Management Decision Support System (DANMDS). This design is feasible principally because of recently announced commercial hardware and software product developments which allow cross-vendor compatibility. The goal of the DANMDS system is commensurate with the central dilemma confronting most large companies and institutions in America, the retrieval of information from large, established, incompatible database systems. The DANMDS system implementation would represent a significant first step toward this problem's resolution.

MEDLINE: the options for health professionals.

PubMed

Wood, E H

1994-01-01

The bibliographic database MEDLINE, produced by the National Library of Medicine (NLM), is a computerized index to the world's biomedical literature. The database can be searched back to 1966 and contains 6.8 million records. The various means of access are divided, for the purposes of this article, into three categories: logging onto a remote host computer by telephone and modem or by the Internet; subscribing to part or all of the database on compact disc (CD-ROM); and leasing the data on a transport medium such as magnetic tape or CDs for loading on a local host computer. Decisions about which method is preferable in a given situation depend on cost, availability of hardware and software, local expertise, and the size of the intended user population. Trends include increased access to the Internet by health professionals, increased network speed, links from MEDLINE records to full-text databases or online journals, and integration of MEDLINE into wider health information systems.

Automating testbed documentation and database access using World Wide Web (WWW) tools

NASA Technical Reports Server (NTRS)

Ames, Charles; Auernheimer, Brent; Lee, Young H.

1994-01-01

A method for providing uniform transparent access to disparate distributed information systems was demonstrated. A prototype testing interface was developed to access documentation and information using publicly available hypermedia tools. The prototype gives testers a uniform, platform-independent user interface to on-line documentation, user manuals, and mission-specific test and operations data. Mosaic was the common user interface, and HTML (Hypertext Markup Language) provided hypertext capability.

Challenges in Database Design with Microsoft Access

ERIC Educational Resources Information Center

Letkowski, Jerzy

2014-01-01

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

Five years of poisons information on the internet: the UK experience of TOXBASE.

PubMed

Bateman, D N; Good, A M

2006-08-01

In 1999, the UK adopted a policy of using TOXBASE, an internet service available free to registered National Health Service (NHS) departments and professionals, as the first point of information on poisoning. This was the first use worldwide of the internet for provision of clinical advice at a national level. We report the impact on database usage and NPIS telephone call loads. Trends in the pattern of TOXBASE usage from 2000-2004 are reported by user category. Information on the monographs accessed most frequently was also extracted from the webserver and sorted by user category. The numbers of telephone calls to the National Poisons Information Service (NPIS) were extracted from NPIS annual reports. Numbers of database logons increased 3.5 fold from 102,352 in 2000 to 368,079 in 2004, with a total of 789,295 accesses to product monographs in 2004. Registered users increased almost tenfold, with approximately half accessing the database at least once a year. Telephone calls to the NPIS dropped by over half. Total contacts with NPIS (web and telephone) increased 50%. Major users in 2004 were hospital emergency departments (60.5% of logons) and NHS public access helplines (NHS Direct and NHS24) (29.4%). Different user groups access different parts of the database. Emergency departments access printable fact sheets for about 10% of monographs they access. Provision of poisons information by the internet has been successful in reducing NPIS call loads. Provision of basic poisons information by this method appears to be acceptable to different professional groups, and to be effective in reducing telephone call loads and increasing service cost effectiveness.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Security and health research databases: the stakeholders and questions to be addressed.

PubMed

Stewart, Sara

2006-01-01

Health research database security issues abound. Issues include subject confidentiality, data ownership, data integrity and data accessibility. There are also various stakeholders in database security. Each of these stakeholders has a different set of concerns and responsibilities when dealing with security issues. There is an obvious need for training in security issues, so that these issues may be addressed and health research will move on without added obstacles based on misunderstanding security methods and technologies.

Thermodynamics of Enzyme-Catalyzed Reactions Database

National Institute of Standards and Technology Data Gateway

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.

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

Implementing the EuroFIR Document and Data Repositories as accessible resources of food composition information.

PubMed

Unwin, Ian; Jansen-van der Vliet, Martine; Westenbrink, Susanne; Presser, Karl; Infanger, Esther; Porubska, Janka; Roe, Mark; Finglas, Paul

2016-02-15

The EuroFIR Document and Data Repositories are being developed as accessible collections of source documents, including grey literature, and the food composition data reported in them. These Repositories will contain source information available to food composition database compilers when selecting their nutritional data. The Document Repository was implemented as searchable bibliographic records in the Europe PubMed Central database, which links to the documents online. The Data Repository will contain original data from source documents in the Document Repository. Testing confirmed the FoodCASE food database management system as a suitable tool for the input, documentation and quality assessment of Data Repository information. Data management requirements for the input and documentation of reported analytical results were established, including record identification and method documentation specifications. Document access and data preparation using the Repositories will provide information resources for compilers, eliminating duplicated work and supporting unambiguous referencing of data contributing to their compiled data. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

Construction of a database for published phase II/III drug intervention clinical trials for the period 2009-2014 comprising 2,326 records, 90 disease categories, and 939 drug entities.

PubMed

Jeong, Sohyun; Han, Nayoung; Choi, Boyoon; Sohn, Minji; Song, Yun-Kyoung; Chung, Myeon-Woo; Na, Han-Sung; Ji, Eunhee; Kim, Hyunah; Rhew, Ki Yon; Kim, Therasa; Kim, In-Wha; Oh, Jung Mi

2016-06-01

To construct a database of published clinical drug trials suitable for use 1) as a research tool in accessing clinical trial information and 2) in evidence-based decision-making by regulatory professionals, clinical research investigators, and medical practitioners. Comprehensive information obtained from a search of design elements and results of clinical trials in peer reviewed journals using PubMed (http://www.ncbi.nlm.ih.gov/pubmed). The methodology to develop a structured database was devised by a panel composed of experts in medical, pharmaceutical, information technology, and members of Ministry of Food and Drug Safety (MFDS) using a step by step approach. A double-sided system consisting of user mode and manager mode served as the framework for the database; elements of interest from each trial were entered via secure manager mode enabling the input information to be accessed in a user-friendly manner (user mode). Information regarding methodology used and results of drug treatment were extracted as detail elements of each data set and then inputted into the web-based database system. Comprehensive information comprising 2,326 clinical trial records, 90 disease states, and 939 drugs entities and concerning study objectives, background, methods used, results, and conclusion could be extracted from published information on phase II/III drug intervention clinical trials appearing in SCI journals within the last 10 years. The extracted data was successfully assembled into a clinical drug trial database with easy access suitable for use as a research tool. The clinically most important therapeutic categories, i.e., cancer, cardiovascular, respiratory, neurological, metabolic, urogenital, gastrointestinal, psychological, and infectious diseases were covered by the database. Names of test and control drugs, details on primary and secondary outcomes and indexed keywords could also be retrieved and built into the database. The construction used in the database enables the user to sort and download targeted information as a Microsoft Excel spreadsheet. Because of the comprehensive and standardized nature of the clinical drug trial database and its ease of access it should serve as valuable information repository and research tool for accessing clinical trial information and making evidence-based decisions by regulatory professionals, clinical research investigators, and medical practitioners.

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

PubMed

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

2013-09-01

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

BNDB - the Biochemical Network Database.

PubMed

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

2007-10-02

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

The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

PubMed

Harb, Omar S; Roos, David S

2015-01-01

Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

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

USGS Publications Warehouse

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

2012-01-01

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

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

PubMed

Jiang, Keyuan; Cao, Xiang

2011-10-01

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

Fermilab Security Site Access Request Database

Science.gov Websites

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

47 CFR 54.410 - Subscriber eligibility determination and certification.

Code of Federal Regulations, 2012 CFR

2012-10-01

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

47 CFR 54.410 - Subscriber eligibility determination and certification.

Code of Federal Regulations, 2013 CFR

2013-10-01

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

47 CFR 54.410 - Subscriber eligibility determination and certification.

Code of Federal Regulations, 2014 CFR

2014-10-01

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

Open access intrapartum CTG database.

PubMed

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

2014-01-13

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

Automating Reference Desk Files with Microcomputers in a Public Library: An Exploration of Data Resources, Methods, and Software.

ERIC Educational Resources Information Center

Miley, David W.

Many reference librarians still rely on manual searches to access vertical files, ready reference files, and other information stored in card files, drawers, and notebooks scattered around the reference department. Automated access to these materials via microcomputers using database management software may speed up the process. This study focuses…

Changes in the Use of Contraception at First Intercourse: A Comparison of the National Survey of Family Growth 1995 and 2006-2010 Databases.

PubMed

Patel, Pooja R; Lee, Jinhyung; Hirth, Jacqueline; Berenson, Abbey B; Smith, Peggy B

2016-08-01

To determine trends in characteristics associated with contraceptive use at coitarche from 1995 to 2006-2010. The National Survey of Family Growth (NSFG) 1995 and 2006-2010 databases were used to abstract variables of interest. Generalized linear models (GLM) were applied to examine the association between the use of contraceptive methods at coitarche and variables abstracted for each database. Of the 9599 women from the 1995 database included in this study, 3885 (40%) used contraception at coitarche in comparison to 4860 (82%) out of 5931 women assessed in 2006-2010. For both time periods, Hispanic women were significantly less likely to use contraception at coitarche when compared to White women. In the 1995 database, only women from families with incomes >$50,000 were more likely to use contraception at coitarche, while women from families with income > $20,000 were more likely to use contraception at coitarche in 2006-2010. There were some differences noted in the association between age at coitarche and contraception use at coitarche, but in general, women who had a higher age at coitarche were more likely to use contraception. For both time periods, women were more likely to use contraception at coitarche if they used barrier methods as their first form of contraception or if they obtained their first contraceptive method from a spouse, partner, or friend. Our results suggest that access to contraception may be associated with use of a contraceptive method at coitarche. Innovative measures need to be investigated so that this young population has increased access to more reliable methods before their first sexual experience.

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

PubMed

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

2005-01-01

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

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

PubMed

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

2015-01-01

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

LexisNexis

EPA Pesticide Factsheets

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

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Development and implementation of a custom integrated database with dashboards to assist with hematopathology specimen triage and traffic

PubMed Central

Azzato, Elizabeth M.; Morrissette, Jennifer J. D.; Halbiger, Regina D.; Bagg, Adam; Daber, Robert D.

2014-01-01

Background: At some institutions, including ours, bone marrow aspirate specimen triage is complex, with hematopathology triage decisions that need to be communicated to downstream ancillary testing laboratories and many specimen aliquot transfers that are handled outside of the laboratory information system (LIS). We developed a custom integrated database with dashboards to facilitate and streamline this workflow. Methods: We developed user-specific dashboards that allow entry of specimen information by technologists in the hematology laboratory, have custom scripting to present relevant information for the hematopathology service and ancillary laboratories and allow communication of triage decisions from the hematopathology service to other laboratories. These dashboards are web-accessible on the local intranet and accessible from behind the hospital firewall on a computer or tablet. Secure user access and group rights ensure that relevant users can edit or access appropriate records. Results: After database and dashboard design, two-stage beta-testing and user education was performed, with the first focusing on technologist specimen entry and the second on downstream users. Commonly encountered issues and user functionality requests were resolved with database and dashboard redesign. Final implementation occurred within 6 months of initial design; users report improved triage efficiency and reduced need for interlaboratory communications. Conclusions: We successfully developed and implemented a custom database with dashboards that facilitates and streamlines our hematopathology bone marrow aspirate triage. This provides an example of a possible solution to specimen communications and traffic that are outside the purview of a standard LIS. PMID:25250187

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

PubMed

Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

2013-07-01

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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

PubMed

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

2018-05-07

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

Construction of 3-D Earth Models for Station Specific Path Corrections by Dynamic Ray Tracing

DTIC Science & Technology

2001-10-01

the numerical eikonal solution method of Vidale (1988) being used by the MIT led consortium. The model construction described in this report relies...assembled. REFERENCES Barazangi, M., Fielding, E., Isacks, B. & Seber, D., (1996), Geophysical And Geological Databases And Ctbt...preprint download6). Fielding, E., Isacks, B.L., and Baragangi. M. (1992), A Network Accessible Geological and Geophysical Database for

Correlates of Access to Business Research Databases

ERIC Educational Resources Information Center

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.…

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

Code of Federal Regulations, 2011 CFR

2011-10-01

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

3DSDSCAR--a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation.

PubMed

Veluraja, Kasinadar; Selvin, Jeyasigamani F A; Venkateshwari, Selvakumar; Priyadarzini, Thanu R K

2010-09-23

The inherent flexibility and lack of strong intramolecular interactions of oligosaccharides demand the use of theoretical methods for their structural elucidation. In spite of the developments of theoretical methods, not much research on glycoinformatics is done so far when compared to bioinformatics research on proteins and nucleic acids. We have developed three dimensional structural database for a sialic acid-containing carbohydrates (3DSDSCAR). This is an open-access database that provides 3D structural models of a given sialic acid-containing carbohydrate. At present, 3DSDSCAR contains 60 conformational models, belonging to 14 different sialic acid-containing carbohydrates, deduced through 10 ns molecular dynamics (MD) simulations. The database is available at the URL: http://www.3dsdscar.org. Copyright 2010 Elsevier Ltd. All rights reserved.

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

PubMed

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

2016-01-01

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

Mapping the literature of transcultural nursing*

PubMed Central

Murphy, Sharon C.

2006-01-01

Overview: No bibliometric studies of the literature of the field of transcultural nursing have been published. This paper describes a citation analysis as part of the project undertaken by the Nursing and Allied Health Resources Section of the Medical Library Association to map the literature of nursing. Objective: The purpose of this study was to identify the core literature and determine which databases provided the most complete access to the transcultural nursing literature. Methods: Cited references from essential source journals were analyzed for a three-year period. Eight major databases were compared for indexing coverage of the identified core list of journals. Results: This study identifies 138 core journals. Transcultural nursing relies on journal literature from associated health sciences fields in addition to nursing. Books provide an important format. Nearly all cited references were from the previous 18 years. In comparing indexing coverage among 8 major databases, 3 databases rose to the top. Conclusions: No single database can claim comprehensive indexing coverage for this broad field. It is essential to search multiple databases. Based on this study, PubMed/MEDLINE, Social Sciences Citation Index, and CINAHL provide the best coverage. Collections supporting transcultural nursing require robust access to literature beyond nursing publications. PMID:16710461

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

NASA Astrophysics Data System (ADS)

Jin, Peiquan; Wan, Shouhong; Yue, Lihua

2009-12-01

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

Design and implementation of a fault-tolerant and dynamic metadata database for clinical trials

NASA Astrophysics Data System (ADS)

Lee, J.; Zhou, Z.; Talini, E.; Documet, J.; Liu, B.

2007-03-01

In recent imaging-based clinical trials, quantitative image analysis (QIA) and computer-aided diagnosis (CAD) methods are increasing in productivity due to higher resolution imaging capabilities. A radiology core doing clinical trials have been analyzing more treatment methods and there is a growing quantity of metadata that need to be stored and managed. These radiology centers are also collaborating with many off-site imaging field sites and need a way to communicate metadata between one another in a secure infrastructure. Our solution is to implement a data storage grid with a fault-tolerant and dynamic metadata database design to unify metadata from different clinical trial experiments and field sites. Although metadata from images follow the DICOM standard, clinical trials also produce metadata specific to regions-of-interest and quantitative image analysis. We have implemented a data access and integration (DAI) server layer where multiple field sites can access multiple metadata databases in the data grid through a single web-based grid service. The centralization of metadata database management simplifies the task of adding new databases into the grid and also decreases the risk of configuration errors seen in peer-to-peer grids. In this paper, we address the design and implementation of a data grid metadata storage that has fault-tolerance and dynamic integration for imaging-based clinical trials.

Federated or cached searches: Providing expected performance from multiple invasive species databases

NASA Astrophysics Data System (ADS)

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-06-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Federated or cached searches: providing expected performance from multiple invasive species databases

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-01-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

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

PubMed

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

2013-01-01

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

Databases and Associated Tools for Glycomics and Glycoproteomics.

PubMed

Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide; Rudd, Pauline M; Abrahams, Jodie L; Campbell, Matthew P; Packer, Nicolle H; Ståhle, Jonas; Widmalm, Göran; Mullen, Elaine; Adamczyk, Barbara; Rojas-Macias, Miguel A; Jin, Chunsheng; Karlsson, Niclas G

2017-01-01

The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).

Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs

NASA Astrophysics Data System (ADS)

Munekawa, Yuma; Ino, Fumihiko; Hagihara, Kenichi

This paper presents a fast method capable of accelerating the Smith-Waterman algorithm for biological database search on a cluster of graphics processing units (GPUs). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. As compared with previous methods, our method has four major contributions. (1) The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip video memory and processing elements in the GPU. (2) It also reduces the number of data fetches by applying a data reuse technique to query and database sequences. (3) A pipelined method is also implemented to overlap GPU execution with database access. (4) Finally, a master/worker paradigm is employed to accelerate hundreds of database searches on a cluster system. In experiments, the peak performance on a GeForce GTX 280 card reaches 8.32 giga cell updates per second (GCUPS). We also find that our method reduces the amount of data fetches to 1/140, achieving approximately three times higher performance than a previous CUDA-based method. Our 32-node cluster version is approximately 28 times faster than a single GPU version. Furthermore, the effective performance reaches 75.6 giga instructions per second (GIPS) using 32 GeForce 8800 GTX cards.

An Algorithm for Building an Electronic Database.

PubMed

Cohen, Wess A; Gayle, Lloyd B; Patel, Nima P

2016-01-01

We propose an algorithm on how to create a prospectively maintained database, which can then be used to analyze prospective data in a retrospective fashion. Our algorithm provides future researchers a road map on how to set up, maintain, and use an electronic database to improve evidence-based care and future clinical outcomes. The database was created using Microsoft Access and included demographic information, socioeconomic information, and intraoperative and postoperative details via standardized drop-down menus. A printed out form from the Microsoft Access template was given to each surgeon to be completed after each case and a member of the health care team then entered the case information into the database. By utilizing straightforward, HIPAA-compliant data input fields, we permitted data collection and transcription to be easy and efficient. Collecting a wide variety of data allowed us the freedom to evolve our clinical interests, while the platform also permitted new categories to be added at will. We have proposed a reproducible method for institutions to create a database, which will then allow senior and junior surgeons to analyze their outcomes and compare them with others in an effort to improve patient care and outcomes. This is a cost-efficient way to create and maintain a database without additional software.

Mapping Norway - a Method to Register and Survey the Status of Accessibility

NASA Astrophysics Data System (ADS)

Michaelis, Sven; Bögelsack, Kathrin

2018-05-01

The Norwegian mapping authority has developed a standard method for mapping accessibility mostly for people with limited or no walking abilities in urban and recreational areas. We choose an object-orientated approach where points, lines and polygons represents objects in the environment. All data are stored in a geospatial database, so they can be presented as web map and analyzed using GIS software. By the end of 2016 more than 160 municipalities are mapped using that method. The aim of this project is to establish a national standard for mapping and to provide a geodatabase that shows the status of accessibility throughout Norway. The data provide a useful tool for national statistics, local planning authorities and private users. First results show that accessibility is low and Norway still faces many challenges to meet the government's goals for Universal Design.

In-Memory Graph Databases for Web-Scale Data

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

Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++more » compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.« less

TOXBASE: Poisons information on the internet

PubMed Central

Bateman, D; Good, A; Laing, W; Kelly, C

2002-01-01

Objectives: To assess the uptake, usage and acceptability of TOXBASE, the National Poisons Information Service internet toxicology information service. Methods: An observational study of database usage, and a questionnaire of users were undertaken involving users of TOXBASE within the UK between August 1999, when the internet site was launched, and May 2000. The main outcome measures were numbers of registered users, usage patterns on the database, responses to user satisfaction questionnaire. Results: The number of registered users increased from 567 to 1500. There was a 68% increase in accident and emergency departments registered, a 159% increase in general practitioners, but a 324% increase in other hospital departments. Between January 2000 and the end of May there had been 60 281 accesses to the product database, the most frequent to the paracetamol entry (7291 accesses). Ecstasy was the seventh most frequent entry accessed. Altogether 165 of 330 questionnaires were returned. The majority came from accident and emergency departments, the major users of the system. Users were generally well (>95%) satisfied with ease and speed of access. A number of suggestions for improvements were put forward. Conclusions: TOXBASE has been extensively accessed since being placed on the internet (http://www.spib.axl.co.uk). The pattern of enquiries mirrors clinical presentation with poisoning. The system seems to be easily used. It is a model for future delivery of treatment guidelines at the point of patient care. PMID:11777868

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

PubMed

Ramirez-Gonzalez, Ricardo; Caccamo, Mario; MacLean, Daniel

2011-10-01

Scientists now use high-throughput sequencing technologies and short-read assembly methods to create draft genome assemblies in just days. Tools and pipelines like the assembler, and the workflow management environments make it easy for a non-specialist to implement complicated pipelines to produce genome assemblies and annotations very quickly. Such accessibility results in a proliferation of assemblies and associated files, often for many organisms. These assemblies get used as a working reference by lots of different workers, from a bioinformatician doing gene prediction or a bench scientist designing primers for PCR. Here we describe Gee Fu, a database tool for genomic assembly and feature data, including next-generation sequence alignments. Gee Fu is an instance of a Ruby-On-Rails web application on a feature database that provides web and console interfaces for input, visualization of feature data via AnnoJ, access to data through a web-service interface, an API for direct data access by Ruby scripts and access to feature data stored in BAM files. Gee Fu provides a platform for storing and sharing different versions of an assembly and associated features that can be accessed and updated by bench biologists and bioinformaticians in ways that are easy and useful for each. http://tinyurl.com/geefu dan.maclean@tsl.ac.uk.

ARIANE: integration of information databases within a hospital intranet.

PubMed

Joubert, M; Aymard, S; Fieschi, D; Volot, F; Staccini, P; Robert, J J; Fieschi, M

1998-05-01

Large information systems handle massive volume of data stored in heterogeneous sources. Each server has its own model of representation of concepts with regard to its aims. One of the main problems end-users encounter when accessing different servers is to match their own viewpoint on biomedical concepts with the various representations that are made in the databases servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet and to propose a method to realize it. This method is based on the knowledge sources provided by the Unified Medical Language System (UMLS) project of the US National Library of Medicine. Experiments concern queries to three different information servers: PubMed, a Medline server of the NLM; Thériaque, a French database on drugs implemented in the Hospital Intranet; and a Web site dedicated to Internet resources in gastroenterology and nutrition, located at the Faculty of Medicine of Nice (France). Accessing to each of these servers is different according to the kind of information delivered and according to the technology used to query it. Dealing with health care professional workstation, the authors introduced in the ARIANE project quality criteria in order to attempt a homogeneous and efficient way to build a query system able to be integrated in existing information systems and to integrate existing and new information sources.

The new interactive CESAR

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

Fox, P.B.; Yatabe, M.

1987-01-01

In this report the Nuclear Criticality Safety Analytical Methods Resource Center describes a new interactive version of CESAR, a critical experiments storage and retrieval program available on the Nuclear Criticality Information System (NCIS) database at Lawrence Livermore National Laboratory. The original version of CESAR did not include interactive search capabilities. The CESAR database was developed to provide a convenient, readily accessible means of storing and retrieving code input data for the SCALE Criticality Safety Analytical Sequences and the codes comprising those sequences. The database includes data for both cross section preparation and criticality safety calculations. 3 refs., 1 tab.

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

DTIC Science & Technology

2016-05-04

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

Automated grading of homework assignments and tests in introductory and intermediate statistics courses using active server pages.

PubMed

Stockburger, D W

1999-05-01

Active server pages permit a software developer to customize the Web experience for users by inserting server-side script and database access into Web pages. This paper describes applications of these techniques and provides a primer on the use of these methods. Applications include a system that generates and grades individualized homework assignments and tests for statistics students. The student accesses the system as a Web page, prints out the assignment, does the assignment, and enters the answers on the Web page. The server, running on NT Server 4.0, grades the assignment, updates the grade book (on a database), and returns the answer key to the student.

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

DTIC Science & Technology

2014-06-01

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

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

ERIC Educational Resources Information Center

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

2016-01-01

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

A development and integration of database code-system with a compilation of comparator, k0 and absolute methods for INAA using microsoft access

NASA Astrophysics Data System (ADS)

Hoh, Siew Sin; Rapie, Nurul Nadiah; Lim, Edwin Suh Wen; Tan, Chun Yuan; Yavar, Alireza; Sarmani, Sukiman; Majid, Amran Ab.; Khoo, Kok Siong

2013-05-01

Instrumental Neutron Activation Analysis (INAA) is often used to determine and calculate the elemental concentrations of a sample at The National University of Malaysia (UKM) typically in Nuclear Science Programme, Faculty of Science and Technology. The objective of this study was to develop a database code-system based on Microsoft Access 2010 which could help the INAA users to choose either comparator method, k0-method or absolute method for calculating the elemental concentrations of a sample. This study also integrated k0data, Com-INAA, k0Concent, k0-Westcott and Abs-INAA to execute and complete the ECC-UKM database code-system. After the integration, a study was conducted to test the effectiveness of the ECC-UKM database code-system by comparing the concentrations between the experiments and the code-systems. 'Triple Bare Monitor' Zr-Au and Cr-Mo-Au were used in k0Concent, k0-Westcott and Abs-INAA code-systems as monitors to determine the thermal to epithermal neutron flux ratio (f). Calculations involved in determining the concentration were net peak area (Np), measurement time (tm), irradiation time (tirr), k-factor (k), thermal to epithermal neutron flux ratio (f), parameters of the neutron flux distribution epithermal (α) and detection efficiency (ɛp). For Com-INAA code-system, certified reference material IAEA-375 Soil was used to calculate the concentrations of elements in a sample. Other CRM and SRM were also used in this database codesystem. Later, a verification process to examine the effectiveness of the Abs-INAA code-system was carried out by comparing the sample concentrations between the code-system and the experiment. The results of the experimental concentration values of ECC-UKM database code-system were performed with good accuracy.

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

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

PubMed Central

Efthimiadis, E N; Afifi, M

1996-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2002-12-01

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

Fungal genome resources at NCBI.

PubMed

Robbertse, B; Tatusova, T

2011-09-01

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

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

PubMed

Taylor, Merwyn

2002-06-01

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

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

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

2013-01-01

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

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

PubMed

Silva, Ikaro; Moody, George B

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

DianaHealth.com, an On-Line Database Containing Appraisals of the Clinical Value and Appropriateness of Healthcare Interventions: Database Development and Retrospective Analysis

PubMed Central

Bonfill, Xavier; Osorio, Dimelza; Solà, Ivan; Pijoan, Jose Ignacio; Balasso, Valentina; Quintana, Maria Jesús; Puig, Teresa; Bolibar, Ignasi; Urrútia, Gerard; Zamora, Javier; Emparanza, José Ignacio; Gómez de la Cámara, Agustín; Ferreira-González, Ignacio

2016-01-01

Objective To describe the development of a novel on-line database aimed to serve as a source of information concerning healthcare interventions appraised for their clinical value and appropriateness by several initiatives worldwide, and to present a retrospective analysis of the appraisals already included in the database. Methods and Findings Database development and a retrospective analysis. The database DianaHealth.com is already on-line and it is regularly updated, independent, open access and available in English and Spanish. Initiatives are identified in medical news, in article references, and by contacting experts in the field. We include appraisals in the form of clinical recommendations, expert analyses, conclusions from systematic reviews, and original research that label any health care intervention as low-value or inappropriate. We obtain the information necessary to classify the appraisals according to type of intervention, specialties involved, publication year, authoring initiative, and key words. The database is accessible through a search engine which retrieves a list of appraisals and a link to the website where they were published. DianaHealth.com also provides a brief description of the initiatives and a section where users can report new appraisals or suggest new initiatives. From January 2014 to July 2015, the on-line database included 2940 appraisals from 22 initiatives: eleven campaigns gathering clinical recommendations from scientific societies, five sets of conclusions from literature review, three sets of recommendations from guidelines, two collections of articles on low clinical value in medical journals, and an initiative of our own. Conclusions We have developed an open access on-line database of appraisals about healthcare interventions considered of low clinical value or inappropriate. DianaHealth.com could help physicians and other stakeholders make better decisions concerning patient care and healthcare systems sustainability. Future efforts should be focused on assessing the impact of these appraisals in the clinical practice. PMID:26840451

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

PubMed

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

2016-10-18

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

ChEMBL web services: streamlining access to drug discovery data and utilities

PubMed Central

Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P.

2015-01-01

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. PMID:25883136

Access Control based on Attribute Certificates for Medical Intranet Applications

PubMed Central

Georgiadis, Christos; Pangalos, George; Khair, Marie

2001-01-01

Background Clinical information systems frequently use intranet and Internet technologies. However these technologies have emphasized sharing and not security, despite the sensitive and private nature of much health information. Digital certificates (electronic documents which recognize an entity or its attributes) can be used to control access in clinical intranet applications. Objectives To outline the need for access control in distributed clinical database systems, to describe the use of digital certificates and security policies, and to propose the architecture for a system using digital certificates, cryptography and security policy to control access to clinical intranet applications. Methods We have previously developed a security policy, DIMEDAC (Distributed Medical Database Access Control), which is compatible with emerging public key and privilege management infrastructure. In our implementation approach we propose the use of digital certificates, to be used in conjunction with DIMEDAC. Results Our proposed access control system consists of two phases: the ways users gain their security credentials; and how these credentials are used to access medical data. Three types of digital certificates are used: identity certificates for authentication; attribute certificates for authorization; and access-rule certificates for propagation of access control policy. Once a user is identified and authenticated, subsequent access decisions are based on a combination of identity and attribute certificates, with access-rule certificates providing the policy framework. Conclusions Access control in clinical intranet applications can be successfully and securely managed through the use of digital certificates and the DIMEDAC security policy. PMID:11720951

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

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

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

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

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

PubMed

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

2017-11-21

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

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

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

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

Database of Geoscientific References Through 2007 for Afghanistan, Version 2

USGS Publications Warehouse

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

2007-01-01

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

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

Physical Oceanography Program Science Abstracts.

DTIC Science & Technology

1985-04-01

substantial part of the database used by the U.S. Navy and the U.S. National Weather Service to generate, in real-time, subsurface tempera- ture maps...quality, 1ST database which incorporates GTS bathymessagss and on-sbip recordings from the Pacific for the period 1979 through 1983. Access to these data...Investigator: Stanley M. FlattE Frank S. Henyey INTERNAL-WAVE NONLINEAR INTERACTIONS BY THE EIKONAL METHOD We have been involved in the study of

X-ray Photoelectron Spectroscopy Database (Version 4.1)

National Institute of Standards and Technology Data Gateway

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

Criteria for Comparing Children's Web Search Tools.

ERIC Educational Resources Information Center

Kuntz, Jerry

1999-01-01

Presents criteria for evaluating and comparing Web search tools designed for children. Highlights include database size; accountability; categorization; search access methods; help files; spell check; URL searching; links to alternative search services; advertising; privacy policy; and layout and design. (LRW)

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

NASA Technical Reports Server (NTRS)

Lulla, Kamlesh

1994-01-01

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

Antidepressants for depressive disorder in children and adolescents: a database of randomised controlled trials.

PubMed

Zhang, Yuqing; Zhou, Xinyu; Pu, Juncai; Zhang, Hanping; Yang, Lining; Liu, Lanxiang; Zhou, Chanjuan; Yuan, Shuai; Jiang, Xiaofeng; Xie, Peng

2018-05-31

In recent years, whether, when and how to use antidepressants to treat depressive disorder in children and adolescents has been hotly debated. Relevant evidence on this topic has increased rapidly. In this paper, we present the construction and content of a database of randomised controlled trials of antidepressants to treat depressive disorder in children and adolescents. This database can be freely accessed via our website and will be regularly updated. Major bibliographic databases (PubMed, the Cochrane Library, Web of Science, Embase, CINAHL, PsycINFO and LiLACS), international trial registers and regulatory agencies' websites were systematically searched for published and unpublished studies up to April 30, 2017. We included randomised controlled trials in which the efficacy or tolerability of any oral antidepressant was compared with that of a control group or any other treatment. In total, 7377 citations from bibliographical databases and 3289 from international trial registers and regulatory agencies' websites were identified. Of these, 53 trials were eligible for inclusion in the final database. Selected data were extracted from each study, including characteristics of the participants (the study population, setting, diagnostic criteria, type of depression, age, sex, and comorbidity), characteristics of the treatment conditions (the treatment conditions, general information, and detail of pharmacotherapy and psychotherapy) and study characteristics (the sponsor, country, number of sites, blinding method, sample size, treatment duration, depression scales, other scales, and primary outcome measure used, and side-effect monitoring method). Moreover, the risk of bias for each trial were assessed. This database provides information on nearly all randomised controlled trials of antidepressants in children and adolescents. By using this database, researchers can improve research efficiency, avoid inadvertent errors and easily focus on the targeted subgroups in which they are interested. For authors of subsequent reviews, they could only use this database to insure that they have completed a comprehensive review, rather than relied solely on the data from this database. We expect this database could help to promote research on evidence-based practice in the treatment of depressive disorder in children and adolescents. The database could be freely accessed in our website: http://xiepengteam.cn/research/evidence-based-medicine .

Documentation of the U.S. Geological Survey Oceanographic Time-Series Measurement Database

USGS Publications Warehouse

Montgomery, Ellyn T.; Martini, Marinna A.; Lightsom, Frances L.; Butman, Bradford

2008-01-02

This report describes the instrumentation and platforms used to make the measurements; the methods used to process, apply quality-control criteria, and archive the data; the data storage format, and how the data are released and distributed. The report also includes instructions on how to access the data from the online database at http://stellwagen.er.usgs.gov/. As of 2016, the database contains about 5,000 files, which may include observations of current velocity, wave statistics, ocean temperature, conductivity, pressure, and light transmission at one or more depths over some duration of time.

ThermoBuild: Online Method Made Available for Accessing NASA Glenn Thermodynamic Data

NASA Technical Reports Server (NTRS)

McBride, Bonnie; Zehe, Michael J.

2004-01-01

The new Web site program "ThermoBuild" allows users to easily access and use the NASA Glenn Thermodynamic Database of over 2000 solid, liquid, and gaseous species. A convenient periodic table allows users to "build" the molecules of interest and designate the temperature range over which thermodynamic functions are to be displayed. ThermoBuild also allows users to build custom databases for use with NASA's Chemical Equilibrium with Applications (CEA) program or other programs that require the NASA format for thermodynamic properties. The NASA Glenn Research Center has long been a leader in the compilation and dissemination of up-to-date thermodynamic data, primarily for use with the NASA CEA program, but increasingly for use with other computer programs.

Pathway Distiller - multisource biological pathway consolidation

PubMed Central

2012-01-01

Background One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. Methods After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. Results We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods. Conclusions By combining several pathway systems, implementing different, but complementary pathway consolidation methods, and providing a user-friendly web-accessible tool, we have enabled users the ability to extract functional explanations of their genome wide experiments. PMID:23134636

Heterogeneous distributed query processing: The DAVID system

NASA Technical Reports Server (NTRS)

Jacobs, Barry E.

1985-01-01

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

Evidence generation from healthcare databases: recommendations for managing change.

PubMed

Bourke, Alison; Bate, Andrew; Sauer, Brian C; Brown, Jeffrey S; Hall, Gillian C

2016-07-01

There is an increasing reliance on databases of healthcare records for pharmacoepidemiology and other medical research, and such resources are often accessed over a long period of time so it is vital to consider the impact of changes in data, access methodology and the environment. The authors discuss change in communication and management, and provide a checklist of issues to consider for both database providers and users. The scope of the paper is database research, and changes are considered in relation to the three main components of database research: the data content itself, how it is accessed, and the support and tools needed to use the database. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The NOAO Data Lab PHAT Photometry Database

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Assessing barriers to health insurance and threats to equity in comparative perspective: The Health Insurance Access Database

PubMed Central

2012-01-01

Background Typologies traditionally used for international comparisons of health systems often conflate many system characteristics. To capture policy changes over time and by service in health systems regulation of public and private insurance, we propose a database containing explicit, standardized indicators of policy instruments. Methods The Health Insurance Access Database (HIAD) will collect policy information for ten OECD countries, over a range of eight health services, from 1990–2010. Policy indicators were selected through a comprehensive literature review which identified policy instruments most likely to constitute barriers to health insurance, thus potentially posing a threat to equity. As data collection is still underway, we present here the theoretical bases and methodology adopted, with a focus on the rationale underpinning the study instruments. Results These harmonized data will allow the capture of policy changes in health systems regulation of public and private insurance over time and by service. The standardization process will permit international comparisons of systems’ performance with regards to health insurance access and equity. Conclusion This research will inform and feed the current debate on the future of health care in developed countries and on the role of the private sector in these changes. PMID:22551599

A Model Based Mars Climate Database for the Mission Design

NASA Technical Reports Server (NTRS)

2005-01-01

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

A data skimming service for locally resident analysis data

NASA Astrophysics Data System (ADS)

Cranshaw, J.; Gardner, R. W.; Gieraltowski, J.; Malon, D.; Mambelli, M.; May, E.

2008-07-01

A Data Skimming Service (DSS) is a site-level service for rapid event filtering and selection from locally resident datasets based on metadata queries to associated 'tag' databases. In US ATLAS, we expect most if not all of the AOD-based datasets to be replicated to each of the five Tier 2 regional facilities in the US Tier 1 'cloud' coordinated by Brookhaven National Laboratory. Entire datasets will consist of on the order of several terabytes of data, and providing easy, quick access to skimmed subsets of these data will be vital to physics working groups. Typically, physicists will be interested in portions of the complete datasets, selected according to event-level attributes (number of jets, missing Et, etc) and content (specific analysis objects for subsequent processing). In this paper we describe methods used to classify data (metadata tag generation) and to store these results in a local database. Next we discuss a general framework which includes methods for accessing this information, defining skims, specifying event output content, accessing locally available storage through a variety of interfaces (SRM, dCache/dccp, gridftp), accessing remote storage elements as specified, and user job submission tools through local or grid schedulers. The advantages of the DSS are the ability to quickly 'browse' datasets and design skims, for example, pre-adjusting cuts to get to a desired skim level with minimal use of compute resources, and to encode these analysis operations in a database for re-analysis and archival purposes. Additionally the framework has provisions to operate autonomously in the event that external, central resources are not available, and to provide, as a reduced package, a minimal skimming service tailored to the needs of small Tier 3 centres or individual users.

EZQUERY

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

Holcomb, F.; Kroes, J.; Jessen, T.

1973-10-18

EZQUERY is a generalized information retrieval and reporting system developed by the Data Processing Services Department to provide a method of accessing and displaying information from common types of data-base files. By eliminating the costs and delays associated with coding and debugging special purpose programs, it produces simple reports. It was designed with the user in mind, and may be used by programmers and nonprogrammers to access data base files and obtain reports in a reasonably brief period of time. (auth)

An Approach for Selecting a Theoretical Framework for the Evaluation of Training Programs

ERIC Educational Resources Information Center

Tasca, Jorge Eduardo; Ensslin, Leonardo; Ensslin, Sandra Rolim; Alves, Maria Bernardete Martins

2010-01-01

Purpose: This research paper proposes a method for selecting references related to a research topic, and seeks to exemplify it for the case of a study evaluating training programs. The method is designed to identify references with high academic relevance in databases accessed via the internet, using a bibliometric analysis to sift the selected…

A practical approach for inexpensive searches of radiology report databases.

PubMed

Desjardins, Benoit; Hamilton, R Curtis

2007-06-01

We present a method to perform full text searches of radiology reports for the large number of departments that do not have this ability as part of their radiology or hospital information system. A tool written in Microsoft Access (front-end) has been designed to search a server (back-end) containing the indexed backup weekly copy of the full relational database extracted from a radiology information system (RIS). This front end-/back-end approach has been implemented in a large academic radiology department, and is used for teaching, research and administrative purposes. The weekly second backup of the 80 GB, 4 million record RIS database takes 2 hours. Further indexing of the exported radiology reports takes 6 hours. Individual searches of the indexed database typically take less than 1 minute on the indexed database and 30-60 minutes on the nonindexed database. Guidelines to properly address privacy and institutional review board issues are closely followed by all users. This method has potential to improve teaching, research, and administrative programs within radiology departments that cannot afford more expensive technology.

Pathway Distiller - multisource biological pathway consolidation.

PubMed

Doderer, Mark S; Anguiano, Zachry; Suresh, Uthra; Dashnamoorthy, Ravi; Bishop, Alexander J R; Chen, Yidong

2012-01-01

One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods. By combining several pathway systems, implementing different, but complementary pathway consolidation methods, and providing a user-friendly web-accessible tool, we have enabled users the ability to extract functional explanations of their genome wide experiments.

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

EPA Science Inventory

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

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

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

NASA Technical Reports Server (NTRS)

Morusiewicz, Linda; Bristow, John

1992-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Using glycome databases for drug discovery.

PubMed

Aoki-Kinoshita, Kiyoko F

2008-08-01

The glycomics field has made great advancements in the last decade due to technologies for their synthesis and analysis including carbohydrate microarrays. Accordingly, databases for glycomics research have also emerged and been made publicly available by many major institutions worldwide. This review introduces these and other useful databases on which new methods for drug discovery can be developed. The scope of this review covers current documented and accessible databases and resources pertaining to glycomics. These were selected with the expectation that they may be useful for drug discovery research. There is a plethora of glycomics databases that have much potential for drug discovery. This may seem daunting at first but this review helps to put some of these resources into perspective. Additionally, some thoughts on how to integrate these resources to allow more efficient research are presented.

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

ERIC Educational Resources Information Center

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

2002-01-01

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

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

USGS Publications Warehouse

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

2008-01-01

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

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

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

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

2003-11-01

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

A service-oriented data access control model

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Methodologies and Methods for User Behavioral Research.

ERIC Educational Resources Information Center

Wang, Peiling

1999-01-01

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

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

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

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

PubMed

Oswal, Sushil K

2014-01-01

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

Atomic Spectra Database (ASD)

National Institute of Standards and Technology Data Gateway

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

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

PubMed

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

2011-01-01

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

A web-based 3D geological information visualization system

NASA Astrophysics Data System (ADS)

Song, Renbo; Jiang, Nan

2013-03-01

Construction of 3D geological visualization system has attracted much more concern in GIS, computer modeling, simulation and visualization fields. It not only can effectively help geological interpretation and analysis work, but also can it can help leveling up geosciences professional education. In this paper, an applet-based method was introduced for developing a web-based 3D geological information visualization system. The main aims of this paper are to explore a rapid and low-cost development method for constructing a web-based 3D geological system. First, the borehole data stored in Excel spreadsheets was extracted and then stored in SQLSERVER database of a web server. Second, the JDBC data access component was utilized for providing the capability of access the database. Third, the user interface was implemented with applet component embedded in JSP page and the 3D viewing and querying functions were implemented with PickCanvas of Java3D. Last, the borehole data acquired from geological survey were used for test the system, and the test results has shown that related methods of this paper have a certain application values.

Electronic Reference Library: Silverplatter's Database Networking Solution.

ERIC Educational Resources Information Center

Millea, Megan

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

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

USDA-ARS?s Scientific Manuscript database

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

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

Code of Federal Regulations, 2010 CFR

2010-10-01

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

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

Code of Federal Regulations, 2011 CFR

2011-10-01

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

High-Performance Secure Database Access Technologies for HEP Grids

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

Matthew Vranicar; John Weicher

2006-04-17

The Large Hadron Collider (LHC) at the CERN Laboratory will become the largest scientific instrument in the world when it starts operations in 2007. Large Scale Analysis Computer Systems (computational grids) are required to extract rare signals of new physics from petabytes of LHC detector data. In addition to file-based event data, LHC data processing applications require access to large amounts of data in relational databases: detector conditions, calibrations, etc. U.S. high energy physicists demand efficient performance of grid computing applications in LHC physics research where world-wide remote participation is vital to their success. To empower physicists with data-intensive analysismore » capabilities a whole hyperinfrastructure of distributed databases cross-cuts a multi-tier hierarchy of computational grids. The crosscutting allows separation of concerns across both the global environment of a federation of computational grids and the local environment of a physicist’s computer used for analysis. Very few efforts are on-going in the area of database and grid integration research. Most of these are outside of the U.S. and rely on traditional approaches to secure database access via an extraneous security layer separate from the database system core, preventing efficient data transfers. Our findings are shared by the Database Access and Integration Services Working Group of the Global Grid Forum, who states that "Research and development activities relating to the Grid have generally focused on applications where data is stored in files. However, in many scientific and commercial domains, database management systems have a central role in data storage, access, organization, authorization, etc, for numerous applications.” There is a clear opportunity for a technological breakthrough, requiring innovative steps to provide high-performance secure database access technologies for grid computing. We believe that an innovative database architecture where the secure authorization is pushed into the database engine will eliminate inefficient data transfer bottlenecks. Furthermore, traditionally separated database and security layers provide an extra vulnerability, leaving a weak clear-text password authorization as the only protection on the database core systems. Due to the legacy limitations of the systems’ security models, the allowed passwords often can not even comply with the DOE password guideline requirements. We see an opportunity for the tight integration of the secure authorization layer with the database server engine resulting in both improved performance and improved security. Phase I has focused on the development of a proof-of-concept prototype using Argonne National Laboratory’s (ANL) Argonne Tandem-Linac Accelerator System (ATLAS) project as a test scenario. By developing a grid-security enabled version of the ATLAS project’s current relation database solution, MySQL, PIOCON Technologies aims to offer a more efficient solution to secure database access.« less

Barriers related to prenatal care utilization among women

PubMed Central

Roozbeh, Nasibeh; Nahidi, Fatemeh; Hajiyan, Sepideh

2016-01-01

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

TransAtlasDB: an integrated database connecting expression data, metadata and variants

PubMed Central

Adetunji, Modupeore O; Lamont, Susan J; Schmidt, Carl J

2018-01-01

Abstract High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful functionalities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis. Database URL: https://modupeore.github.io/TransAtlasDB/ PMID:29688361

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

PubMed

Jha, Ashish Kumar

2015-01-01

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

Modern Hardware Technologies and Software Techniques for On-Line Database Storage and Access.

DTIC Science & Technology

1985-12-01

of the information in a message narrative. This method employs artificial intelligence techniques to extract information, In simalest terms, an...disf ribif ion (tape replacemenf) systemns Database distribution On-fine mass storage Videogame ROM (luke-box I Media Cost Mt $2-10/438 $10-SO/G38...trajninq ot tne great intelligence for the analyst would be required. If, on’ the other hand, a sentence analysis scneme siTole enouq,. for the low-level

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

PubMed

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

2015-03-01

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

Integration of NASA/GSFC and USGS Rock Magnetic Databases.

NASA Astrophysics Data System (ADS)

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

2004-05-01

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

Increasing access to Latin American social medicine resources: a preliminary report*

PubMed Central

Buchanan, Holly Shipp; Waitzkin, Howard; Eldredge, Jonathan; Davidson, Russ; Iriart, Celia; Teal, Janis

2003-01-01

Purpose: This preliminary report describes the development and implementation of a project to improve access to literature in Latin American social medicine (LASM). Methods: The University of New Mexico project team collaborated with participants from Argentina, Brazil, Chile, and Ecuador to identify approximately 400 articles and books in Latin American social medicine. Structured abstracts were prepared, translated into English, Spanish, and Portuguese, assigned Medical Subject Headings (MeSH), and loaded into a Web-based database for public searching. The project has initiated Web-based publication for two LASM journals. Evaluation included measures of use and content. Results: The LASM Website (http://hsc.unm.edu/lasm) and database create access to formerly little-known literature that addresses problems relevant to current medicine and public health. This Website offers a unique resource for researchers, practitioners, and teachers who seek to understand the links between socioeconomic conditions and health. The project provides a model for collaboration between librarians and health care providers. Challenges included procurement of primary material; preparation of concise abstracts; working with trilingual translations of abstracts, metadata, and indexing; and the work processes of the multidisciplinary team. Conclusions: The literature of Latin American social medicine has become more readily available to researchers worldwide. The LASM project serves as a collaborative model for the creation of sustainable solutions for disseminating information that is difficult to access through traditional methods. PMID:14566372

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

PubMed

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

2018-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

The PMDB Protein Model Database

PubMed Central

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

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

PubMed

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

1998-01-01

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

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2012 CFR

2012-04-01

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

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2013 CFR

2013-04-01

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

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2014 CFR

2014-04-01

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

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

ERIC Educational Resources Information Center

Jack, Robert F.

1984-01-01

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

ChEMBL web services: streamlining access to drug discovery data and utilities.

PubMed

Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P

2015-07-01

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

PubMed Central

Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.

2014-01-01

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR—the JASPAR CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods. PMID:24194598

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

PubMed

Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

2014-01-01

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.

Microcomputer-Based Access to Machine-Readable Numeric Databases.

ERIC Educational Resources Information Center

Wenzel, Patrick

1988-01-01

Describes the use of microcomputers and relational database management systems to improve access to numeric databases by the Data and Program Library Service at the University of Wisconsin. The internal records management system, in-house reference tools, and plans to extend these tools to the entire campus are discussed. (3 references) (CLB)

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

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

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

Code of Federal Regulations, 2012 CFR

2012-10-01

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

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

Code of Federal Regulations, 2014 CFR

2014-10-01

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

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

Code of Federal Regulations, 2013 CFR

2013-10-01

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

Tao of Gateway: Providing Internet Access to Licensed Databases.

ERIC Educational Resources Information Center

McClellan, Gregory A.; Garrison, William V.

1997-01-01

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

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

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

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

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

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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

PubMed

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

2018-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

The CoFactor database: organic cofactors in enzyme catalysis.

PubMed

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

2010-10-01

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

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

PubMed

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

2017-08-01

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

Documentation of the U.S. Geological Survey Stress and Sediment Mobility Database

USGS Publications Warehouse

Dalyander, P. Soupy; Butman, Bradford; Sherwood, Christopher R.; Signell, Richard P.

2012-01-01

The U.S. Geological Survey Sea Floor Stress and Sediment Mobility Database contains estimates of bottom stress and sediment mobility for the U.S. continental shelf. This U.S. Geological Survey database provides information that is needed to characterize sea floor ecosystems and evaluate areas for human use. The estimates contained in the database are designed to spatially and seasonally resolve the general characteristics of bottom stress over the U.S. continental shelf and to estimate sea floor mobility by comparing critical stress thresholds based on observed sediment texture data to the modeled stress. This report describes the methods used to make the bottom stress and mobility estimates, statistics used to characterize stress and mobility, data validation procedures, and the metadata for each dataset and provides information on how to access the database online.

Towards pathogenomics: a web-based resource for pathogenicity islands

PubMed Central

Yoon, Sung Ho; Park, Young-Kyu; Lee, Soohyun; Choi, Doil; Oh, Tae Kwang; Hur, Cheol-Goo; Kim, Jihyun F.

2007-01-01

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at . PMID:17090594

Magnetic Fields for All: The GPIPS Community Web-Access Portal

NASA Astrophysics Data System (ADS)

Carveth, Carol; Clemens, D. P.; Pinnick, A.; Pavel, M.; Jameson, K.; Taylor, B.

2007-12-01

The new GPIPS website portal provides community users with an intuitive and powerful interface to query the data products of the Galactic Plane Infrared Polarization Survey. The website, which was built using PHP for the front end and MySQL for the database back end, allows users to issue queries based on galactic or equatorial coordinates, GPIPS-specific identifiers, polarization information, magnitude information, and several other attributes. The returns are presented in HTML tables, with the added option of either downloading or being emailed an ASCII file including the same or more information from the database. Other functionalities of the website include providing details of the status of the Survey (which fields have been observed or are planned to be observed), techniques involved in data collection and analysis, and descriptions of the database contents and names. For this initial launch of the website, users may access the GPIPS polarization point source catalog and the deep coadd photometric point source catalog. Future planned developments include a graphics-based method for querying the database, as well as tools to combine neighboring GPIPS images into larger image files for both polarimetry and photometry. This work is partially supported by NSF grant AST-0607500.

Proteome reference map and regulation network of neonatal rat cardiomyocyte

PubMed Central

Li, Zi-jian; Liu, Ning; Han, Qi-de; Zhang, You-yi

2011-01-01

Aim: To study and establish a proteome reference map and regulation network of neonatal rat cardiomyocyte. Methods: Cultured cardiomyocytes of neonatal rats were used. All proteins expressed in the cardiomyocytes were separated and identified by two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Biological networks and pathways of the neonatal rat cardiomyocytes were analyzed using the Ingenuity Pathway Analysis (IPA) program (www.ingenuity.com). A 2-DE database was made accessible on-line by Make2ddb package on a web server. Results: More than 1000 proteins were separated on 2D gels, and 148 proteins were identified. The identified proteins were used for the construction of an extensible markup language-based database. Biological networks and pathways were constructed to analyze the functions associate with cardiomyocyte proteins in the database. The 2-DE database of rat cardiomyocyte proteins can be accessed at http://2d.bjmu.edu.cn. Conclusion: A proteome reference map and regulation network of the neonatal rat cardiomyocytes have been established, which may serve as an international platform for storage, analysis and visualization of cardiomyocyte proteomic data. PMID:21841810

Collecting and Using Student Information for School Improvement.

ERIC Educational Resources Information Center

Riegel, N. Blyth

This paper suggests methods for collecting and using student information for school improvement by describing how the Richardson Independent School District (RISD), Texas, determines data for effective school management decisionmaking. RISD readily accesses student information via a networked database on line with the central office's IBM…

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

Wireless access to a pharmaceutical database: A demonstrator for data driven Wireless Application Protocol applications in medical information processing

PubMed Central

Hansen, Michael Schacht

2001-01-01

Background The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. Objectives To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. Methods We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. Results A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. Conclusions We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control. PMID:11720946

Erectile Dysfunction Herbs: A Natural Treatment for ED?

MedlinePlus

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

Authentication Based on Pole-zero Models of Signature Velocity

PubMed Central

Rashidi, Saeid; Fallah, Ali; Towhidkhah, Farzad

2013-01-01

With the increase of communication and financial transaction through internet, on-line signature verification is an accepted biometric technology for access control and plays a significant role in authenticity and authorization in modernized society. Therefore, fast and precise algorithms for the signature verification are very attractive. The goal of this paper is modeling of velocity signal that pattern and properties is stable for persons. With using pole-zero models based on discrete cosine transform, precise method is proposed for modeling and then features is founded from strokes. With using linear, parzen window and support vector machine classifiers, the signature verification technique was tested with a large number of authentic and forgery signatures and has demonstrated the good potential of this technique. The signatures are collected from three different database include a proprietary database, the SVC2004 and the Sabanci University signature database benchmark databases. Experimental results based on Persian, SVC2004 and SUSIG databases show that our method achieves an equal error rate of 5.91%, 5.62% and 3.91% in the skilled forgeries, respectively. PMID:24696797

ERMes: Open Source Simplicity for Your E-Resource Management

ERIC Educational Resources Information Center

Doering, William; Chilton, Galadriel

2009-01-01

ERMes, the latest version of electronic resource management system (ERM), is a relational database; content in different tables connects to, and works with, content in other tables. ERMes requires Access 2007 (Windows) or Access 2008 (Mac) to operate as the database utilizes functionality not available in previous versions of Microsoft Access. The…

Databases and Electronic Resources - Betty Petersen Memorial Library

Science.gov Websites

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

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

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

PubMed Central

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

2009-01-01

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

DynAstVO : a Europlanet database of NEA orbits

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Perspectives in astrophysical databases

NASA Astrophysics Data System (ADS)

Frailis, Marco; de Angelis, Alessandro; Roberto, Vito

2004-07-01

Astrophysics has become a domain extremely rich of scientific data. Data mining tools are needed for information extraction from such large data sets. This asks for an approach to data management emphasizing the efficiency and simplicity of data access; efficiency is obtained using multidimensional access methods and simplicity is achieved by properly handling metadata. Moreover, clustering and classification techniques on large data sets pose additional requirements in terms of computation and memory scalability and interpretability of results. In this study we review some possible solutions.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

Slushie World: An In-Class Access Database Tutorial

ERIC Educational Resources Information Center

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

2015-01-01

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

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

EPA Science Inventory

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

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Automated Assistance in the Formulation of Search Statements for Bibliographic Databases.

ERIC Educational Resources Information Center

Oakes, Michael P.; Taylor, Malcolm J.

1998-01-01

Reports on the design of an automated query system to help pharmacologists access the Derwent Drug File (DDF). Topics include knowledge types; knowledge representation; role of the search intermediary; vocabulary selection, thesaurus, and user input in natural language; browsing; evaluation methods; and search statement generation for the World…

Parallel Processable Cryptographic Methods with Unbounded Practical Security.

ERIC Educational Resources Information Center

Rothstein, Jerome

Addressing the problem of protecting confidential information and data stored in computer databases from access by unauthorized parties, this paper details coding schemes which present such astronomical work factors to potential code breakers that security breaches are hopeless in any practical sense. Two procedures which can be used to encode for…

What's Lost Can Be Found.

ERIC Educational Resources Information Center

Barre, Nancy

1989-01-01

The ways in which alumni associations trace missing alumni are described. Methods vary from listing lost names in alumni periodicals to paying credit bureaus to trace alumni by Social Security number. The U.S. Postal Service, which runs National Change of Address, sells access to its database of forwarding addresses. (MLW)

[Establishement for regional pelvic trauma database in Hunan Province].

PubMed

Cheng, Liang; Zhu, Yong; Long, Haitao; Yang, Junxiao; Sun, Buhua; Li, Kanghua

2017-04-28

To establish a database for pelvic trauma in Hunan Province, and to start the work of multicenter pelvic trauma registry.
 Methods: To establish the database, literatures relevant to pelvic trauma were screened, the experiences from the established trauma database in China and abroad were learned, and the actual situations for pelvic trauma rescue in Hunan Province were considered. The database for pelvic trauma was established based on the PostgreSQL and the advanced programming language Java 1.6.
 Results: The complex procedure for pelvic trauma rescue was described structurally. The contents for the database included general patient information, injurious condition, prehospital rescue, conditions in admission, treatment in hospital, status on discharge, diagnosis, classification, complication, trauma scoring and therapeutic effect. The database can be accessed through the internet by browser/servicer. The functions for the database include patient information management, data export, history query, progress report, video-image management and personal information management.
 Conclusion: The database with whole life cycle pelvic trauma is successfully established for the first time in China. It is scientific, functional, practical, and user-friendly.

CERES Search and Subset Tool

Atmospheric Science Data Center

2016-06-24

... data granules using a high resolution spatial metadata database and directly accessing the archived data granules. Subset results are ... data granules using a high resolution spatial metadata database and directly accessing the archived data granules. Subset results are ...

VIEWCACHE: An incremental pointer-base access method for distributed databases. Part 1: The universal index system design document. Part 2: The universal index system low-level design document. Part 3: User's guide. Part 4: Reference manual. Part 5: UIMS test suite

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos

1992-01-01

The goal of the Universal Index System (UIS), is to provide an easy-to-use and reliable interface to many different kinds of database systems. The impetus for this system was to simplify database index management for users, thus encouraging the use of indexes. As the idea grew into an actual system design, the concept of increasing database performance by facilitating the use of time-saving techniques at the user level became a theme for the project. This Final Report describes the Design, the Implementation of UIS, and its Language Interfaces. It also includes the User's Guide and the Reference Manual.

WaveNet: A Web-Based Metocean Data Access, Processing, and Analysis Tool. Part 3 - CDIP Database

DTIC Science & Technology

2014-06-01

and Analysis Tool; Part 3 – CDIP Database by Zeki Demirbilek, Lihwa Lin, and Derek Wilson PURPOSE: This Coastal and Hydraulics Engineering...Technical Note (CHETN) describes coupling of the Coastal Data Information Program ( CDIP ) database to WaveNet, the first module of MetOcnDat (Meteorological...provides a step-by-step procedure to access, process, and analyze wave and wind data from the CDIP database. BACKGROUND: WaveNet addresses a basic

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

PubMed Central

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

1997-01-01

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

NNDC Data Services

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

Tuli, J.K.; Sonzogni,A.

The National Nuclear Data Center has provided remote access to some of its resources since 1986. The major databases and other resources available currently through NNDC Web site are summarized. The National Nuclear Data Center (NNDC) has provided remote access to the nuclear physics databases it maintains and to other resources since 1986. With considerable innovation access is now mostly through the Web. The NNDC Web pages have been modernized to provide a consistent state-of-the-art style. The improved database services and other resources available from the NNOC site at www.nndc.bnl.govwill be described.

Secure, web-accessible call rosters for academic radiology departments.

PubMed

Nguyen, A V; Tellis, W M; Avrin, D E

2000-05-01

Traditionally, radiology department call rosters have been posted via paper and bulletin boards. Frequently, changes to these lists are made by multiple people independently, but often not synchronized, resulting in confusion among the house staff and technical staff as to who is on call and when. In addition, multiple and disparate copies exist in different sections of the department, and changes made would not be propagated to all the schedules. To eliminate such difficulties, a paperless call scheduling application was developed. Our call scheduling program allowed Java-enabled web access to a database by designated personnel from each radiology section who have privileges to make the necessary changes. Once a person made a change, everyone accessing the database would see the modification. This eliminates the chaos resulting from people swapping shifts at the last minute and not having the time to record or broadcast the change. Furthermore, all changes to the database were logged. Users are given a log-in name and password and can only edit their section; however, all personnel have access to all sections' schedules. Our applet was written in Java 2 using the latest technology in database access. We access our Interbase database through the DataExpress and DB Swing (Borland, Scotts Valley, CA) components. The result is secure access to the call rosters via the web. There are many advantages to the web-enabled access, mainly the ability for people to make changes and have the changes recorded and propagated in a single virtual location and available to all who need to know.

The Challenges of Plasma Modeling: Current Status and Future Plans

NASA Astrophysics Data System (ADS)

Foster, A. R.; Smith, R. K.; Brickhouse, N. S.; Kallman, T. R.; Witthoeft, M. C.

2010-12-01

Successfully modeling X-ray emission from astrophysical plasmas requires a wide range of atomic data to be rapidly accessible by modeling codes, enabling calculation of synthetic spectra for fitting with observations. Over many years the astrophysical databases have roughly kept pace with the advances in detector and spectrometer technology. We outline here the basic atomic processes contributing to the emission from different types of plasmas and briefly touch on the difference between the methods used to calculate this data. We then discuss in more detail the different issues addressed by atomic databases in regards to what data to store and how to make it accessible. Finally, the question of the effect of uncertainties in atomic data is explored, as a reminder to observers that atomic data is not known to infinite precision, and should not be treated as such.

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

PubMed Central

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

2011-01-01

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

Kingfisher: a system for remote sensing image database management

NASA Astrophysics Data System (ADS)

Bruzzo, Michele; Giordano, Ferdinando; Dellepiane, Silvana G.

2003-04-01

At present retrieval methods in remote sensing image database are mainly based on spatial-temporal information. The increasing amount of images to be collected by the ground station of earth observing systems emphasizes the need for database management with intelligent data retrieval capabilities. The purpose of the proposed method is to realize a new content based retrieval system for remote sensing images database with an innovative search tool based on image similarity. This methodology is quite innovative for this application, at present many systems exist for photographic images, as for example QBIC and IKONA, but they are not able to extract and describe properly remote image content. The target database is set by an archive of images originated from an X-SAR sensor (spaceborne mission, 1994). The best content descriptors, mainly texture parameters, guarantees high retrieval performances and can be extracted without losses independently of image resolution. The latter property allows DBMS (Database Management System) to process low amount of information, as in the case of quick-look images, improving time performance and memory access without reducing retrieval accuracy. The matching technique has been designed to enable image management (database population and retrieval) independently of dimensions (width and height). Local and global content descriptors are compared, during retrieval phase, with the query image and results seem to be very encouraging.

Representing inequities in the distribution of socio-economic benefits and environmental risk.

PubMed

Louis, Garric E; Magpili, Luna M

2002-10-01

There is currently no standard method for analyzing claims of environmental inequity. Neither is there a database of statistics on the extent of relationship between regional indicators of environmental quality, likely sources of pollution, and the demographic characteristics of affected populations. The resolution of environmental disputes is often hampered by inadequate communication between stakeholder groups about their perceptions and prioritization of the issues in dispute and by differential access to information about the issues by each stakeholder group. This paper describes a web-based tool, ICEP, that uses multi-layered GIS maps to establish a standard method for analyzing claims of environmental inequity and establish a database of correlation coefficients between environmental indicators, industry type by SIC code, and demographic characteristics of the population in proximity to noxious facilities. The maps are generated from stakeholder reports of environmental quality and are designed to be accessible via the Internet. This provides stakeholders with direct access to graphical displays of the perceptions of their co-stakeholders and provides all groups with links to relevant information sources about the issues in dispute. ICEP enhances existing community environmental websites like Scorecard and Envirofacts by providing displays of median household income as a measure of the distribution of benefits accrued within an area.

Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.

PubMed

Krystkowiak, Izabella; Lenart, Jakub; Debski, Konrad; Kuterba, Piotr; Petas, Michal; Kaminska, Bozena; Dabrowski, Michal

2013-01-01

We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql -h database.nencki-genomics.org -u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface.

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs

PubMed Central

Krystkowiak, Izabella; Lenart, Jakub; Debski, Konrad; Kuterba, Piotr; Petas, Michal; Kaminska, Bozena; Dabrowski, Michal

2013-01-01

We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql –h database.nencki-genomics.org –u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface. Database URL: http://www.nencki-genomics.org. PMID:24089456

[The opening of the French national health database: Opportunities and difficulties. The experience of the Gazel and Constances cohorts].

PubMed

Goldberg, M; Carton, M; Gourmelen, J; Genreau, M; Montourcy, M; Le Got, S; Zins, M

2016-09-01

In France, the national health database (SNIIRAM) is an administrative health database that collects data on hospitalizations and healthcare consumption for more than 60 million people. Although it does not record behavioral and environmental data, these data have a major interest for epidemiology, surveillance and public health. One of the most interesting uses of SNIIRAM is its linkage with surveys collecting data directly from persons. Access to the SNIIRAM data is currently relatively limited, but in the near future changes in regulations will largely facilitate open access. However, it is a huge and complex database and there are some important methodological and technical difficulties for using it due to its volume and architecture. We are developing tools for facilitating the linkage of the Gazel and Constances cohorts to the SNIIRAM: interactive documentation on the SNIIRAM database, software for the verification of the completeness and validity of the data received from the SNIIRAM, methods for constructing indicators from the raw data in order to flag the presence of certain events (specific diagnosis, procedure, drug…), standard queries for producing a set of variables on a specific area (drugs, diagnoses during a hospital stay…). Moreover, the REDSIAM network recently set up aims to develop, evaluate and make available algorithms to identify pathologies in SNIIRAM. In order to fully benefit from the exceptional potential of the SNIIRAM database, it is essential to develop tools to facilitate its use. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Selected Geochemical Data for Modeling Near-Surface Processes in Mineral Systems

USGS Publications Warehouse

Giles, Stuart A.; Granitto, Matthew; Eppinger, Robert G.

2009-01-01

The database herein was initiated, designed, and populated to collect and integrate geochemical, geologic, and mineral deposit data in an organized manner to facilitate geoenvironmental mineral deposit modeling. The Microsoft Access database contains data on a variety of mineral deposit types that have variable environmental effects when exposed at the ground surface by mining or natural processes. The data tables describe quantitative and qualitative geochemical analyses determined by 134 analytical laboratory and field methods for over 11,000 heavy-mineral concentrate, rock, sediment, soil, vegetation, and water samples. The database also provides geographic information on geology, climate, ecoregion, and site contamination levels for over 3,000 field sites in North America.

Advanced technologies for scalable ATLAS conditions database access on the grid

NASA Astrophysics Data System (ADS)

Basset, R.; Canali, L.; Dimitrov, G.; Girone, M.; Hawkings, R.; Nevski, P.; Valassi, A.; Vaniachine, A.; Viegas, F.; Walker, R.; Wong, A.

2010-04-01

During massive data reprocessing operations an ATLAS Conditions Database application must support concurrent access from numerous ATLAS data processing jobs running on the Grid. By simulating realistic work-flow, ATLAS database scalability tests provided feedback for Conditions Db software optimization and allowed precise determination of required distributed database resources. In distributed data processing one must take into account the chaotic nature of Grid computing characterized by peak loads, which can be much higher than average access rates. To validate database performance at peak loads, we tested database scalability at very high concurrent jobs rates. This has been achieved through coordinated database stress tests performed in series of ATLAS reprocessing exercises at the Tier-1 sites. The goal of database stress tests is to detect scalability limits of the hardware deployed at the Tier-1 sites, so that the server overload conditions can be safely avoided in a production environment. Our analysis of server performance under stress tests indicates that Conditions Db data access is limited by the disk I/O throughput. An unacceptable side-effect of the disk I/O saturation is a degradation of the WLCG 3D Services that update Conditions Db data at all ten ATLAS Tier-1 sites using the technology of Oracle Streams. To avoid such bottlenecks we prototyped and tested a novel approach for database peak load avoidance in Grid computing. Our approach is based upon the proven idea of pilot job submission on the Grid: instead of the actual query, an ATLAS utility library sends to the database server a pilot query first.

Are There Any Natural Remedies That Reduce Chronic Fatigue Associated with Chronic Fatigue Syndrome?

MedlinePlus

... management of chronic fatigue syndrome. Natural Medicines Comprehensive Database. http://www.naturaldatabase.com. Accessed Feb. 23, 2015. Magnesium. Natural Medicines Comprehensive Database. http://www.naturaldatabase.com. Accessed Feb. 24, 2015. ...

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

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

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

2002-01-01

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

Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

PubMed

Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

2014-01-01

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

BIRS - Bioterrorism Information Retrieval System.

PubMed

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. The database is freely available at http://www.bioterrorism.biowaves.org.

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

PubMed Central

Levy, C.; Beauchamp, C.

1996-01-01

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

Migration of legacy mumps applications to relational database servers.

PubMed

O'Kane, K C

2001-07-01

An extended implementation of the Mumps language is described that facilitates vendor neutral migration of legacy Mumps applications to SQL-based relational database servers. Implemented as a compiler, this system translates Mumps programs to operating system independent, standard C code for subsequent compilation to fully stand-alone, binary executables. Added built-in functions and support modules extend the native hierarchical Mumps database with access to industry standard, networked, relational database management servers (RDBMS) thus freeing Mumps applications from dependence upon vendor specific, proprietary, unstandardized database models. Unlike Mumps systems that have added captive, proprietary RDMBS access, the programs generated by this development environment can be used with any RDBMS system that supports common network access protocols. Additional features include a built-in web server interface and the ability to interoperate directly with programs and functions written in other languages.

Correspondence: World Wide Web access to the British Universities Human Embryo Database

PubMed Central

AITON, JAMES F.; MCDONOUGH, ARIANA; MCLACHLAN, JOHN C.; SMART, STEVEN D.; WHITEN, SUSAN C.

1997-01-01

The British Universities Human Embryo Database has been created by merging information from the Walmsley Collection of Human Embryos at the School of Biological and Medical Sciences, University of St Andrews and from the Boyd Collection of Human Embryos at the Department of Anatomy, University of Cambridge. The database has been made available electronically on the Internet and World Wide Web browsers can be used to implement interactive access to the information stored in the British Universities Human Embryo Database. The database can, therefore, be accessed and searched from remote sites and specific embryos can be identified in terms of their location, age, developmental stage, plane of section, staining technique, and other parameters. It is intended to add information from other similar collections in the UK as it becomes available. PMID:9034891

Patenting of University and Non-University Public Research Organisations in Germany: Evidence from Patent Applications for Medical Research Results

PubMed Central

Tinnemann, Peter; Özbay, Jonas; Saint, Victoria A.; Willich, Stefan N.

2010-01-01

Background Patents are one of the most important forms of intellectual property. They grant a time-limited exclusivity on the use of an invention allowing the recuperation of research costs. The use of patents is fiercely debated for medical innovation and especially controversial for publicly funded research, where the patent holder is an institution accountable to public interest. Despite this controversy, for the situation in Germany almost no empirical information exists. The purpose of this study is to examine the amount, types and trends of patent applications for health products submitted by German public research organisations. Methods/Principal Findings We conducted a systematic search for patent documents using the publicly accessible database search interface of the German Patent and Trademark Office. We defined keywords and search criteria and developed search patterns for the database request. We retrieved documents with application date between 1988 and 2006 and processed the collected data stepwise to compile the most relevant documents in patent families for further analysis. We developed a rationale and present individual steps of a systematic method to request and process patent data from a publicly accessible database. We retrieved and processed 10194 patent documents. Out of these, we identified 1772 relevant patent families, applied for by 193 different universities and non-university public research organisations. 827 (47%) of these patent families contained granted patents. The number of patent applications submitted by universities and university-affiliated institutions more than tripled since the introduction of legal reforms in 2002, constituting almost half of all patent applications and accounting for most of the post-reform increase. Patenting of most non-university public research organisations remained stable. Conclusions We search, process and analyse patent applications from publicly accessible databases. Internationally mounting evidence questions the viability of policies to increase commercial exploitation of publicly funded research results. To evaluate the outcome of research policies a transparent evidence base for public debate is needed in Germany. PMID:21124982

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

PubMed

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

2011-10-01

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

A DICOM based radiotherapy plan database for research collaboration and reporting

NASA Astrophysics Data System (ADS)

Westberg, J.; Krogh, S.; Brink, C.; Vogelius, I. R.

2014-03-01

Purpose: To create a central radiotherapy (RT) plan database for dose analysis and reporting, capable of calculating and presenting statistics on user defined patient groups. The goal is to facilitate multi-center research studies with easy and secure access to RT plans and statistics on protocol compliance. Methods: RT institutions are able to send data to the central database using DICOM communications on a secure computer network. The central system is composed of a number of DICOM servers, an SQL database and in-house developed software services to process the incoming data. A web site within the secure network allows the user to manage their submitted data. Results: The RT plan database has been developed in Microsoft .NET and users are able to send DICOM data between RT centers in Denmark. Dose-volume histogram (DVH) calculations performed by the system are comparable to those of conventional RT software. A permission system was implemented to ensure access control and easy, yet secure, data sharing across centers. The reports contain DVH statistics for structures in user defined patient groups. The system currently contains over 2200 patients in 14 collaborations. Conclusions: A central RT plan repository for use in multi-center trials and quality assurance was created. The system provides an attractive alternative to dummy runs by enabling continuous monitoring of protocol conformity and plan metrics in a trial.

Viral genome analysis and knowledge management.

PubMed

Kuiken, Carla; Yoon, Hyejin; Abfalterer, Werner; Gaschen, Brian; Lo, Chienchi; Korber, Bette

2013-01-01

One of the challenges of genetic data analysis is to combine information from sources that are distributed around the world and accessible through a wide array of different methods and interfaces. The HIV database and its footsteps, the hepatitis C virus (HCV) and hemorrhagic fever virus (HFV) databases, have made it their mission to make different data types easily available to their users. This involves a large amount of behind-the-scenes processing, including quality control and analysis of the sequences and their annotation. Gene and protein sequences are distilled from the sequences that are stored in GenBank; to this end, both submitter annotation and script-generated sequences are used. Alignments of both nucleotide and amino acid sequences are generated, manually curated, distilled into an alignment model, and regenerated in an iterative cycle that results in ever better new alignments. Annotation of epidemiological and clinical information is parsed, checked, and added to the database. User interfaces are updated, and new interfaces are added based upon user requests. Vital for its success, the database staff are heavy users of the system, which enables them to fix bugs and find opportunities for improvement. In this chapter we describe some of the infrastructure that keeps these heavily used analysis platforms alive and vital after nearly 25 years of use. The database/analysis platforms described in this chapter can be accessed at http://hiv.lanl.gov http://hcv.lanl.gov http://hfv.lanl.gov.

PmiRExAt: plant miRNA expression atlas database and web applications

PubMed Central

Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

2016-01-01

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

A survey of commercial object-oriented database management systems

NASA Technical Reports Server (NTRS)

Atkins, John

1992-01-01

The object-oriented data model is the culmination of over thirty years of database research. Initially, database research focused on the need to provide information in a consistent and efficient manner to the business community. Early data models such as the hierarchical model and the network model met the goal of consistent and efficient access to data and were substantial improvements over simple file mechanisms for storing and accessing data. However, these models required highly skilled programmers to provide access to the data. Consequently, in the early 70's E.F. Codd, an IBM research computer scientists, proposed a new data model based on the simple mathematical notion of the relation. This model is known as the Relational Model. In the relational model, data is represented in flat tables (or relations) which have no physical or internal links between them. The simplicity of this model fostered the development of powerful but relatively simple query languages that now made data directly accessible to the general database user. Except for large, multi-user database systems, a database professional was in general no longer necessary. Database professionals found that traditional data in the form of character data, dates, and numeric data were easily represented and managed via the relational model. Commercial relational database management systems proliferated and performance of relational databases improved dramatically. However, there was a growing community of potential database users whose needs were not met by the relational model. These users needed to store data with data types not available in the relational model and who required a far richer modelling environment than that provided by the relational model. Indeed, the complexity of the objects to be represented in the model mandated a new approach to database technology. The Object-Oriented Model was the result.

EMAGE mouse embryo spatial gene expression database: 2010 update

PubMed Central

Richardson, Lorna; Venkataraman, Shanmugasundaram; Stevenson, Peter; Yang, Yiya; Burton, Nicholas; Rao, Jianguo; Fisher, Malcolm; Baldock, Richard A.; Davidson, Duncan R.; Christiansen, Jeffrey H.

2010-01-01

EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (∼19 000 gene) ‘EURExpress’ dataset into EMAGE. PMID:19767607

System of end-to-end symmetric database encryption

NASA Astrophysics Data System (ADS)

Galushka, V. V.; Aydinyan, A. R.; Tsvetkova, O. L.; Fathi, V. A.; Fathi, D. V.

2018-05-01

The article is devoted to the actual problem of protecting databases from information leakage, which is performed while bypassing access control mechanisms. To solve this problem, it is proposed to use end-to-end data encryption, implemented at the end nodes of an interaction of the information system components using one of the symmetric cryptographic algorithms. For this purpose, a key management method designed for use in a multi-user system based on the distributed key representation model, part of which is stored in the database, and the other part is obtained by converting the user's password, has been developed and described. In this case, the key is calculated immediately before the cryptographic transformations and is not stored in the memory after the completion of these transformations. Algorithms for registering and authorizing a user, as well as changing his password, have been described, and the methods for calculating parts of a key when performing these operations have been provided.

78 FR 48177 - Submission for OMB Review; 30-day Comment Request: National Institute of Mental Health Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-07

... Access Request and Use Certification (previously National Database for Autism Research Data Access... approval for use of the National Database for Autism Research (NDAR) Data Use Certification (DUC) Form...

Interactive, Automated Management of Icing Data

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.

2009-01-01

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

The "GeneTrustee": a universal identification system that ensures privacy and confidentiality for human genetic databases.

PubMed

Burnett, Leslie; Barlow-Stewart, Kris; Proos, Anné L; Aizenberg, Harry

2003-05-01

This article describes a generic model for access to samples and information in human genetic databases. The model utilises a "GeneTrustee", a third-party intermediary independent of the subjects and of the investigators or database custodians. The GeneTrustee model has been implemented successfully in various community genetics screening programs and has facilitated research access to genetic databases while protecting the privacy and confidentiality of research subjects. The GeneTrustee model could also be applied to various types of non-conventional genetic databases, including neonatal screening Guthrie card collections, and to forensic DNA samples.

An Introduction to Database Structure and Database Machines.

ERIC Educational Resources Information Center

Detweiler, Karen

1984-01-01

Enumerates principal management objectives of database management systems (data independence, quality, security, multiuser access, central control) and criteria for comparison (response time, size, flexibility, other features). Conventional database management systems, relational databases, and database machines used for backend processing are…

QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors.

PubMed

Tarasova, Olga A; Urusova, Aleksandra F; Filimonov, Dmitry A; Nicklaus, Marc C; Zakharov, Alexey V; Poroikov, Vladimir V

2015-07-27

Large-scale databases are important sources of training sets for various QSAR modeling approaches. Generally, these databases contain information extracted from different sources. This variety of sources can produce inconsistency in the data, defined as sometimes widely diverging activity results for the same compound against the same target. Because such inconsistency can reduce the accuracy of predictive models built from these data, we are addressing the question of how best to use data from publicly and commercially accessible databases to create accurate and predictive QSAR models. We investigate the suitability of commercially and publicly available databases to QSAR modeling of antiviral activity (HIV-1 reverse transcriptase (RT) inhibition). We present several methods for the creation of modeling (i.e., training and test) sets from two, either commercially or freely available, databases: Thomson Reuters Integrity and ChEMBL. We found that the typical predictivities of QSAR models obtained using these different modeling set compilation methods differ significantly from each other. The best results were obtained using training sets compiled for compounds tested using only one method and material (i.e., a specific type of biological assay). Compound sets aggregated by target only typically yielded poorly predictive models. We discuss the possibility of "mix-and-matching" assay data across aggregating databases such as ChEMBL and Integrity and their current severe limitations for this purpose. One of them is the general lack of complete and semantic/computer-parsable descriptions of assay methodology carried by these databases that would allow one to determine mix-and-matchability of result sets at the assay level.

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

Bikakis, Nikos; Gioldasis, Nektarios; Tsinaraki, Chrisa; Christodoulakis, Stavros

SPARQL is today the standard access language for Semantic Web data. In the recent years XML databases have also acquired industrial importance due to the widespread applicability of XML in the Web. In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases. Our approach assumes that fairly generic mappings between ontology constructs and XML Schema constructs have been automatically derived or manually specified. The mappings are used to automatically translate SPARQL queries to semantically equivalent XQuery queries which are used to access the XML databases. We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.

Second-Tier Database for Ecosystem Focus, 2003-2004 Annual Report.

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

University of Washington, Columbia Basin Research, DART Project Staff,

2004-12-01

The Second-Tier Database for Ecosystem Focus (Contract 00004124) provides direct and timely public access to Columbia Basin environmental, operational, fishery and riverine data resources for federal, state, public and private entities essential to sound operational and resource management. The database also assists with juvenile and adult mainstem passage modeling supporting federal decisions affecting the operation of the FCRPS. The Second-Tier Database known as Data Access in Real Time (DART) integrates public data for effective access, consideration and application. DART also provides analysis tools and performance measures for evaluating the condition of Columbia Basin salmonid stocks. These services are critical tomore » BPA's implementation of its fish and wildlife responsibilities under the Endangered Species Act (ESA).« less

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

PubMed

Chang, Hsien-Tsung; Lin, Tsai-Huei

2016-01-01

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

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

PubMed Central

Lin, Tsai-Huei

2016-01-01

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

Developing methods for systematic reviewing in health services delivery and organization: an example from a review of access to health care for people with learning disabilities. Part 2. Evaluation of the literature--a practical guide.

PubMed

Alborz, Alison; McNally, Rosalind

2004-12-01

To develop methods to facilitate the 'systematic' review of evidence from a range of methodologies on diffuse or 'soft' topics, as exemplified by 'access to health care'. Twenty-eight bibliographic databases, research registers, organizational websites or library catalogues. Reference lists from identified studies. Contact with experts and service users. Current awareness and contents alerting services in the area of learning disabilities. Inclusion criteria were English language literature from 1980 onwards, relating to people with learning disabilities of any age and all study designs. The main criteria for assessment was relevance to Guillifords' model of access to health care which was adapted to the circumstances of people with learning disabilities. Selected studies were evaluated for scientific rigour then data was extracted and the results synthesized. Quality assessment was by an initial set of 'generic' quality indicators. This enabled further evidence selection before evaluation of findings according to specific criteria for qualitative, quantitative or mixed-method studies. Eighty-two studies were fully evaluated. Five studies were rated 'highly rigorous', 22 'rigorous', 46 'less rigorous' and nine 'poor' papers were retained as the sole evidence covering aspects of the guiding model. The majority of studies were quantitative but used only descriptive statistics. Most evidence lacked methodological detail, which often lowered final quality ratings. The application of a consistent structure to quality evaluation can facilitate data appraisal, extraction and synthesis across a range of methodologies in diffuse or 'soft' topics. Synthesis can be facilitated further by using software, such as the microsoft 'access' database, for managing information.

Virus Database and Online Inquiry System Based on Natural Vectors.

PubMed

Dong, Rui; Zheng, Hui; Tian, Kun; Yau, Shek-Chung; Mao, Weiguang; Yu, Wenping; Yin, Changchuan; Yu, Chenglong; He, Rong Lucy; Yang, Jie; Yau, Stephen St

2017-01-01

We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.

EMEN2: An Object Oriented Database and Electronic Lab Notebook

PubMed Central

Rees, Ian; Langley, Ed; Chiu, Wah; Ludtke, Steven J.

2013-01-01

Transmission electron microscopy and associated methods such as single particle analysis, 2-D crystallography, helical reconstruction and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments, and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source. PMID:23360752

The Génolevures database.

PubMed

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

2011-01-01

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

Comparison of Online Agricultural Information Services.

ERIC Educational Resources Information Center

Reneau, Fred; Patterson, Richard

1984-01-01

Outlines major online agricultural information services--agricultural databases, databases with agricultural services, educational databases in agriculture--noting services provided, access to the database, and costs. Benefits of online agricultural database sources (availability of agricultural marketing, weather, commodity prices, management…

Enhanced DIII-D Data Management Through a Relational Database

NASA Astrophysics Data System (ADS)

Burruss, J. R.; Peng, Q.; Schachter, J.; Schissel, D. P.; Terpstra, T. B.

2000-10-01

A relational database is being used to serve data about DIII-D experiments. The database is optimized for queries across multiple shots, allowing for rapid data mining by SQL-literate researchers. The relational database relates different experiments and datasets, thus providing a big picture of DIII-D operations. Users are encouraged to add their own tables to the database. Summary physics quantities about DIII-D discharges are collected and stored in the database automatically. Meta-data about code runs, MDSplus usage, and visualization tool usage are collected, stored in the database, and later analyzed to improve computing. Documentation on the database may be accessed through programming languages such as C, Java, and IDL, or through ODBC compliant applications such as Excel and Access. A database-driven web page also provides a convenient means for viewing database quantities through the World Wide Web. Demonstrations will be given at the poster.

NATIONAL URBAN DATABASE AND ACCESS PROTAL TOOL

EPA Science Inventory

Current mesoscale weather prediction and microscale dispersion models are limited in their ability to perform accurate assessments in urban areas. A project called the National Urban Database with Access Portal Tool (NUDAPT) is beginning to provide urban data and improve the para...

Hermes, the Information Messenger, Integrating Information Services and Delivering Them to the End User.

ERIC Educational Resources Information Center

Coello-Coutino, Gerardo; Ainsworth, Shirley; Escalante-Gonzalbo, Ana Marie

2002-01-01

Describes Hermes, a research tool that uses specially designed acquisition, parsing and presentation methods to integrate information resources on the Internet, from searching in disparate bibliographic databases, to accessing full text articles online, and developing a web of information associated with each reference via one common interface.…

Social Work Literature Searching: Current Issues with Databases and Online Search Engines

ERIC Educational Resources Information Center

McGinn, Tony; Taylor, Brian; McColgan, Mary; McQuilkan, Janice

2016-01-01

Objectives: To compare the performance of a range of search facilities; and to illustrate the execution of a comprehensive literature search for qualitative evidence in social work. Context: Developments in literature search methods and comparisons of search facilities help facilitate access to the best available evidence for social workers.…

Pathfinding in the Research Forest: The Pearl Harvesting Method for Effective Information Retrieval

ERIC Educational Resources Information Center

Sandieson, Robert

2006-01-01

Knowledge of empirical research has become important for everyone involved in education and special education. Policy, practice, and informed reporting rely on locating and understanding unfiltered, original source material. Although access to vast amounts of research has been greatly facilitated by online databases, such as ERIC and PsychInfo,…

Waterpipe Smoking among College Students in the United States: A Review of the Literature

ERIC Educational Resources Information Center

Grekin, Emily R.; Ayna, Dinah

2012-01-01

Objective: To review the literature on college student waterpipe use with a focus on undergraduates in the United States. Participants: Undergraduate students. Methods: Studies were accessed using the databases PubMed, MEDLINE, PsycINFO, and Academic Search Premier. Searches included combinations of the following keywords: "waterpipe," "hookah,"…

Scientific Journal Publishing: Yearly Volume and Open Access Availability

ERIC Educational Resources Information Center

Bjork, Bo-Christer; Roos, Annikki; Lauri, Mari

2009-01-01

Introduction: We estimate the total yearly volume of peer-reviewed scientific journal articles published world-wide as well as the share of these articles available openly on the Web either directly or as copies in e-print repositories. Method: We rely on data from two commercial databases (ISI and Ulrich's Periodicals Directory) supplemented by…

Obesity and Intellectual Disability in New Zealand

ERIC Educational Resources Information Center

Stedman, Kurstyn V.; Leland, Louis S., Jr.

2010-01-01

Background: The international literature suggests that obesity is likely to be more pronounced in the population of people with intellectual disability (ID). However, there are no published New Zealand data for this population. Method: We accessed a database containing anonymous data for a New Zealand ID population. Ninety-eight people of 141 had…

Literature Review: Update on Amphetamine Neurotoxicity and Its Relevance to the Treatment of ADHD

ERIC Educational Resources Information Center

Advokat, Claire

2007-01-01

Objective: A review of amphetamine treatment for attention-deficit/hyperactivity disorder (ADHD) was conducted, to obtain information on the long-term neurological consequences of this therapy. Method: Several databases were accessed for research articles on the effects of amphetamine in the brain of laboratory animals and ADHD diagnosed…

When Questions Are Answers: Using a Survey to Achieve Faculty Awareness of the Library's Electronic Resources.

ERIC Educational Resources Information Center

Weingart, Sandra J.; Anderson, Janet A.

2000-01-01

Describes a study conducted at the Utah State University library that investigated electronic database awareness and use by 856 administrators and teaching faculty. Responses to a survey revealed the need for greater publicity regarding new electronic acquisitions, training opportunities, and methods of remote access. (Author/LRW)

Virtual OPACs versus Union Database: Two Models of Union Catalogue Provision.

ERIC Educational Resources Information Center

Cousins, Shirley

1999-01-01

Considers some of the major technical and organizational issues involved in virtual-catalog production, contrasting them with the traditional union catalog approach exemplified by COPAC, an online public-access catalog composed of academic libraries in the United Kingdom. Suggest a method of integrating these two models of the union catalog.…

A Locally Created ERM: How and Why We Did It

ERIC Educational Resources Information Center

Doering, William; Chilton, Galadriel

2008-01-01

The University of Wisconsin-La Crosse's Murphy Library provides access to approximately 200 subscription databases. As with many academic libraries, methods and tools for managing these resources were sorely needed. However, the budget has been cut repeatedly over the past few years--thus the possibility of purchasing a commercial electronic…

System and method for integrating and accessing multiple data sources within a data warehouse architecture

DOEpatents

Musick, Charles R [Castro Valley, CA; Critchlow, Terence [Livermore, CA; Ganesh, Madhaven [San Jose, CA; Slezak, Tom [Livermore, CA; Fidelis, Krzysztof [Brentwood, CA

2006-12-19

A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including "get" and "set" methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take "distinguished" high-level objects as input and traverse their data structures and enter information into the data warehouse.

Designing a Multi-Petabyte Database for LSST

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

Becla, Jacek; Hanushevsky, Andrew; Nikolaev, Sergei

2007-01-10

The 3.2 giga-pixel LSST camera will produce approximately half a petabyte of archive images every month. These data need to be reduced in under a minute to produce real-time transient alerts, and then added to the cumulative catalog for further analysis. The catalog is expected to grow about three hundred terabytes per year. The data volume, the real-time transient alerting requirements of the LSST, and its spatio-temporal aspects require innovative techniques to build an efficient data access system at reasonable cost. As currently envisioned, the system will rely on a database for catalogs and metadata. Several database systems are beingmore » evaluated to understand how they perform at these data rates, data volumes, and access patterns. This paper describes the LSST requirements, the challenges they impose, the data access philosophy, results to date from evaluating available database technologies against LSST requirements, and the proposed database architecture to meet the data challenges.« less

Accurate palm vein recognition based on wavelet scattering and spectral regression kernel discriminant analysis

NASA Astrophysics Data System (ADS)

Elnasir, Selma; Shamsuddin, Siti Mariyam; Farokhi, Sajad

2015-01-01

Palm vein recognition (PVR) is a promising new biometric that has been applied successfully as a method of access control by many organizations, which has even further potential in the field of forensics. The palm vein pattern has highly discriminative features that are difficult to forge because of its subcutaneous position in the palm. Despite considerable progress and a few practical issues, providing accurate palm vein readings has remained an unsolved issue in biometrics. We propose a robust and more accurate PVR method based on the combination of wavelet scattering (WS) with spectral regression kernel discriminant analysis (SRKDA). As the dimension of WS generated features is quite large, SRKDA is required to reduce the extracted features to enhance the discrimination. The results based on two public databases-PolyU Hyper Spectral Palmprint public database and PolyU Multi Spectral Palmprint-show the high performance of the proposed scheme in comparison with state-of-the-art methods. The proposed approach scored a 99.44% identification rate and a 99.90% verification rate [equal error rate (EER)=0.1%] for the hyperspectral database and a 99.97% identification rate and a 99.98% verification rate (EER=0.019%) for the multispectral database.

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

PubMed

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

2013-01-01

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

Scrubchem: Building Bioactivity Datasets from Pubchem ...

EPA Pesticide Factsheets

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

Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas.

PubMed

Chu, Philip; Peck, Joshua; Brumberg, Joshua C

2015-01-01

Laboratory instruction of neuroscience is often limited by the lack of physical resources and supplies (e.g., brains specimens, dissection kits, physiological equipment). Online databases can serve as supplements to material labs by providing professionally collected images of brain specimens and their underlying cellular populations with resolution and quality that is extremely difficult to access for strictly pedagogical purposes. We describe a method using two online databases, the Neuromorpho.org and the Allen Brain Atlas (ABA), that freely provide access to data from working brain scientists that can be modified for laboratory instruction/exercises. Neuromorpho.org is the first neuronal morphology database that provides qualitative and quantitative data from reconstructed cells analyzed in published scientific reports. The Neuromorpho.org database contains cross species and multiple neuronal phenotype datasets which allows for comparative examinations. The ABA provides modules that allow students to study the anatomy of the rodent brain, as well as observe the different cellular phenotypes that exist using histochemical labeling. Using these tools in conjunction, advanced students can ask questions about qualitative and quantitative neuronal morphology, then examine the distribution of the same cell types across the entire brain to gain a full appreciation of the magnitude of the brain's complexity.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

Allelic database and divergence among Psidium accessions by using microsatellite markers.

PubMed

da Costa, S R; Santos, C A F

2013-12-16

This study aimed to investigate the genetic variability among guava accessions and wild Psidium species of the Embrapa Semiárido germplasm collection by using microsatellite loci to guide genetic resources and breeding programs, emphasizing crosses between guava and other Psidium species. DNA was extracted using the 2X CTAB method, and polymerase chain reaction products were analyzed on 6% denatured polyacrylamide gels stained with silver nitrate. The unweighted pair-group method using arithmetic average dendrogram generated from the distance matrix of the Jaccard coefficient for 183 alleles of 13 microsatellite loci was used for visualization of genetic similarity. The number of base pairs was estimated using inverse mobility method based on the regression of known-size products. Analysis of molecular variance was performed using total decomposition between and within guava accessions. The accessions showed similarity from 0.75 to 1.00, with the dendrogram presenting cophenetic value of 0.85. Five groups were observed: the first included guava accessions; the second, P. guineense accessions; the third, one accession of P. friedrichsthalianum; and the last 2 groups, P. cattleianum. The genetic similarity among P. guineense and some guava accessions were above 80%, suggesting greater possibility to obtain interspecies hybrids between these 2 species. The genetic variability between the accessions was considered to be high (ΦST = 0.238), indicating that guava genetic variability is not uniformly distributed among the 9 Brazilian states from where the accession were obtained. Obtaining a greater number of accessions by Brazilian states is recommended in order to have greater diversity among the species.

Evaluation models and criteria of the quality of hospital websites: a systematic review study

PubMed Central

Jeddi, Fatemeh Rangraz; Gilasi, Hamidreza; Khademi, Sahar

2017-01-01

Introduction Hospital websites are important tools in establishing communication and exchanging information between patients and staff, and thus should enjoy an acceptable level of quality. The aim of this study was to identify proper models and criteria to evaluate the quality of hospital websites. Methods This research was a systematic review study. The international databases such as Science Direct, Google Scholar, PubMed, Proquest, Ovid, Elsevier, Springer, and EBSCO together with regional database such as Magiran, Scientific Information Database, Persian Journal Citation Report (PJCR) and IranMedex were searched. Suitable keywords including website, evaluation, and quality of website were used. Full text papers related to the research were included. The criteria and sub criteria of the evaluation of website quality were extracted and classified. Results To evaluate the quality of the websites, various models and criteria were presented. The WEB-Q-IM, Mile, Minerva, Seruni Luci, and Web-Qual models were the designed models. The criteria of accessibility, content and apparent features of the websites, the design procedure, the graphics applied in the website, and the page’s attractions have been mentioned in the majority of studies. Conclusion The criteria of accessibility, content, design method, security, and confidentiality of personal information are the essential criteria in the evaluation of all websites. It is suggested that the ease of use, graphics, attractiveness and other apparent properties of websites are considered as the user-friendliness sub criteria. Further, the criteria of speed and accessibility of the website should be considered as sub criterion of efficiency. When determining the evaluation criteria of the quality of websites, attention to major differences in the specific features of any website is essential. PMID:28465807

Chemical and isotopic database of water and gas from hydrothermal systems with an emphasis for the western United States

USGS Publications Warehouse

Mariner, R.H.; Venezky, D.Y.; Hurwitz, S.

2006-01-01

Chemical and isotope data accumulated by two USGS Projects (led by I. Barnes and R. Mariner) over a time period of about 40 years can now be found using a basic web search or through an image search (left). The data are primarily chemical and isotopic analyses of waters (thermal, mineral, or fresh) and associated gas (free and/or dissolved) collected from hot springs, mineral springs, cold springs, geothermal wells, fumaroles, and gas seeps. Additional information is available about the collection methods and analysis procedures.The chemical and isotope data are stored in a MySQL database and accessed using PHP from a basic search form below. Data can also be accessed using an Open Source GIS called WorldKit by clicking on the image to the left. Additional information is available about WorldKit including the files used to set up the site.

libChEBI: an API for accessing the ChEBI database.

PubMed

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

2016-01-01

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

Open-access databases as unprecedented resources and drivers of cultural change in fisheries science

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

McManamay, Ryan A; Utz, Ryan

2014-01-01

Open-access databases with utility in fisheries science have grown exponentially in quantity and scope over the past decade, with profound impacts to our discipline. The management, distillation, and sharing of an exponentially growing stream of open-access data represents several fundamental challenges in fisheries science. Many of the currently available open-access resources may not be universally known among fisheries scientists. We therefore introduce many national- and global-scale open-access databases with applications in fisheries science and provide an example of how they can be harnessed to perform valuable analyses without additional field efforts. We also discuss how the development, maintenance, and utilizationmore » of open-access data are likely to pose technical, financial, and educational challenges to fisheries scientists. Such cultural implications that will coincide with the rapidly increasing availability of free data should compel the American Fisheries Society to actively address these problems now to help ease the forthcoming cultural transition.« less

SORTEZ: a relational translator for NCBI's ASN.1 database.

PubMed

Hart, K W; Searls, D B; Overton, G C

1994-07-01

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

The ISO Data Archive and Interoperability with Other Archives

NASA Astrophysics Data System (ADS)

Salama, Alberto; Arviset, Christophe; Hernández, José; Dowson, John; Osuna, Pedro

The ESA's Infrared Space Observatory (ISO), an unprecedented observatory for infrared astronomy launched in November 1995, successfully made nearly 30,000 scientific observations in its 2.5-year mission. The ISO data can be retrieved from the ISO Data Archive, available at ISO Data Archive , and comprised of about 150,000 observations, including parallel and serendipity mode observations. A user-friendly Java interface permits queries to the database and data retrieval. The interface currently offers a wide variety of links to other archives, such as name resolution with NED and SIMBAD, access to electronic articles from ADS and CDS/VizieR, and access to IRAS data. In the past year development has been focused on improving the IDA interoperability with other astronomical archives, either by accessing other relevant archives or by providing direct access to the ISO data for external services. A mechanism of information transfer has been developed, allowing direct query to the IDA via a Java Server Page, returning quick look ISO images and relevant, observation-specific information embedded in an HTML page. This method has been used to link from the CDS/Vizier Data Centre and ADS, and work with IPAC to allow access to the ISO Archive from IRSA, including display capabilities of the observed sky regions onto other mission images, is in progress. Prospects for further links to and from other archives and databases are also addressed.

[Status of libraries and databases for natural products at abroad].

PubMed

Zhao, Li-Mei; Tan, Ning-Hua

2015-01-01

For natural products are one of the important sources for drug discovery, libraries and databases of natural products are significant for the development and research of natural products. At present, most of compound libraries at abroad are synthetic or combinatorial synthetic molecules, resulting to access natural products difficult; for information of natural products are scattered with different standards, it is difficult to construct convenient, comprehensive and large-scale databases for natural products. This paper reviewed the status of current accessing libraries and databases for natural products at abroad and provided some important information for the development of libraries and database for natural products.

FRED, a Front End for Databases.

ERIC Educational Resources Information Center

Crystal, Maurice I.; Jakobson, Gabriel E.

1982-01-01

FRED (a Front End for Databases) was conceived to alleviate data access difficulties posed by the heterogeneous nature of online databases. A hardware/software layer interposed between users and databases, it consists of three subsystems: user-interface, database-interface, and knowledge base. Architectural alternatives for this database machine…

The Marshall Islands Data Management Program

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

Stoker, A.C.; Conrado, C.L.

1995-09-01

This report is a resource document of the methods and procedures used currently in the Data Management Program of the Marshall Islands Dose Assessment and Radioecology Project. Since 1973, over 60,000 environmental samples have been collected. Our program includes relational database design, programming and maintenance; sample and information management; sample tracking; quality control; and data entry, evaluation and reduction. The usefulness of scientific databases involves careful planning in order to fulfill the requirements of any large research program. Compilation of scientific results requires consolidation of information from several databases, and incorporation of new information as it is generated. The successmore » in combining and organizing all radionuclide analysis, sample information and statistical results into a readily accessible form, is critical to our project.« less

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

PubMed Central

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

2015-01-01

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

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

Village Green Project: Web-accessible Database

EPA Science Inventory

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

47 CFR 64.623 - Administrator requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... administrator of the TRS User Registration Database, the administrator of the VRS Access Technology Reference... parties with a vested interest in the outcome of TRS-related numbering administration and activities. (4) None of the administrator of the TRS User Registration Database, the administrator of the VRS Access...

47 CFR 64.623 - Administrator requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... administrator of the TRS User Registration Database, the administrator of the VRS Access Technology Reference... parties with a vested interest in the outcome of TRS-related numbering administration and activities. (4) None of the administrator of the TRS User Registration Database, the administrator of the VRS Access...

Designing a multi-petabyte database for LSST

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

Becla, J; Hanushevsky, A

2005-12-21

The 3.2 giga-pixel LSST camera will produce over half a petabyte of raw images every month. This data needs to be reduced in under a minute to produce real-time transient alerts, and then cataloged and indexed to allow efficient access and simplify further analysis. The indexed catalogs alone are expected to grow at a speed of about 600 terabytes per year. The sheer volume of data, the real-time transient alerting requirements of the LSST, and its spatio-temporal aspects require cutting-edge techniques to build an efficient data access system at reasonable cost. As currently envisioned, the system will rely on amore » database for catalogs and metadata. Several database systems are being evaluated to understand how they will scale and perform at these data volumes in anticipated LSST access patterns. This paper describes the LSST requirements, the challenges they impose, the data access philosophy, and the database architecture that is expected to be adopted in order to meet the data challenges.« less

MitiGate; an online meta-analysis database for quantification of mitigation strategies for enteric methane emissions.

PubMed

Veneman, Jolien B; Saetnan, Eli R; Clare, Amanda J; Newbold, Charles J

2016-12-01

The body of peer-reviewed papers on enteric methane mitigation strategies in ruminants is rapidly growing and allows for better estimation of the true effect of each strategy though the use of meta-analysis methods. Here we present the development of an online database of measured methane mitigation strategies called MitiGate, currently comprising 412 papers. The database is accessible through an online user-friendly interface that allows data extraction with various levels of aggregation on one hand and data-uploading for submission to the database allowing for future refinement and updates of mitigation estimates as well as providing easy access to relevant data for integration into modelling efforts or policy recommendations. To demonstrate and verify the usefulness of the MitiGate database those studies where methane emissions were expressed per unit of intake (293 papers resulting in 845 treatment comparisons) were used in a meta-analysis. The meta-analysis of the current database estimated the effect size of each of the mitigation strategies as well as the associated variance and measure of heterogeneity. Currently, under-representation of certain strategies, geographic regions and long term studies are the main limitations in providing an accurate quantitative estimation of the mitigation potential of each strategy under varying animal production systems. We have thus implemented the facility for researchers to upload meta-data of their peer reviewed research through a simple input form in the hope that MitiGate will grow into a fully inclusive resource for those wishing to model methane mitigation strategies in ruminants. Copyright © 2016 Elsevier B.V. All rights reserved.

Assesment of access to bibliographic databases and telemetry databases in Astronomy: A groundswell for development.

NASA Astrophysics Data System (ADS)

Diaz-Merced, Wanda Liz; Casado, Johanna; Garcia, Beatriz; Aarnio, Alicia; Knierman, Karen; Monkiewicz, Jacqueline; Alicia Aarnio.

2018-01-01

Big Data" is a subject that has taken special relevance today, particularly in Astrophysics, where continuous advances in technology are leading to ever larger data sets. A multimodal approach in perception of astronomical data data (achieved through sonification used for the processing of data) increases the detection of signals in very low signal-to-noise ratio limits and is of special importance to achieve greater inclusion in the field of Astronomy. In the last ten years, different software tools have been developed that perform the sonification of astronomical data from tables or databases, among them the best known and in multiplatform development are Sonification Sandbox, MathTrack, and xSonify.In order to determine the accessibility of software we propose to start carrying out a conformity analysis of ISO (International Standard Organization) 9241-171171: 2008. This standard establishes the general guidelines that must be taken into account for accessibility in software design, and it is applied to software used in work, public places, and at home. To analyze the accessibility of web databases, we take into account the "Web Content Content Accessibility Guidelines (WCAG) 2.0", accepted and published by ISO in the ISO / IEC 40500: 2012 standard.In this poster, we present a User Centered Design (UCD), Human Computer Interaction (HCI), and User Experience (UX) framework to address a non-segregational provision of access to bibliographic databases and telemetry databases in Astronomy. Our framework is based on an ISO evaluation on a selection of data bases such as ADS, Simbad and SDSS. The WCAG 2.0 and ISO 9241-171171: 2008 should not be taken as absolute accessibility standards: these guidelines are very general, are not absolute, and do not address particularities. They are not to be taken as a substitute for UCD, HCI, UX design and evaluation. Based on our results, this research presents the framework for a focus group and qualitative data analysis aimed to lay the foundations for the employment of UCD functionalities on astronomical databases.

Recent improvements in the NASA technical report server

NASA Technical Reports Server (NTRS)

Maa, Ming-Hokng; Nelson, Michael L.

1995-01-01

The NASA Technical Report Server (NTRS), a World Wide Web (WWW) report distribution service, has been modified to allow parallel database queries, significantly decreasing user access time by an average factor of 2.3, access from clients behind firewalls and/or proxies which truncate excessively long Uniform Resource Locators (URL's), access to non-Wide Area Information Server (WAIS) databases, and compatibility with the Z39-50.3 protocol.

Taiwan Biobank: making cross-database convergence possible in the Big Data era

PubMed Central

Lin, Jui-Chu; Fan, Chien-Te; Liao, Chia-Cheng; Chen, Yao-Sheng

2018-01-01

Abstract The Taiwan Biobank (TWB) is a biomedical research database of biopsy data from 200 000 participants. Access to this database has been granted to research communities taking part in the development of precision medicines; however, this has raised issues surrounding TWB’s access to electronic medical records (EMRs). The Personal Data Protection Act of Taiwan restricts access to EMRs for purposes not covered by patients’ original consent. This commentary explores possible legal solutions to help ensure that the access TWB has to EMR abides with legal obligations, and with governance frameworks associated with ethical, legal, and social implications. We suggest utilizing “hash function” algorithms to create nonretrospective, anonymized data for the purpose of cross-transmission and/or linkage with EMR. PMID:29149267

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

PubMed

Snoep, J L; Olivier, B G

2002-01-01

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

Toward an open-access global database for mapping, control, and surveillance of neglected tropical diseases.

PubMed

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F L; Utzinger, Jürg; Kristensen, Thomas K; Vounatsou, Penelope

2011-12-01

After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and 'grey literature'), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay.

Finding alternatives when a major database is gone*

PubMed Central

Hu, Estelle

2016-01-01

Question What to do when a major database ceases publication? Setting An urban, academic health sciences library with four campuses serves a university health sciences system, a college of medicine, and five other health sciences colleges. Methods Usage statistics of each e-book title in the resource were carefully analyzed. Purchase decisions were made based on the assessment of usage. Results Sustainable resources were acquired from other vendors, with perpetual access for library users. Conclusion This systematic process of finding alternative resources is an example of librarians' persistence in acquiring perpetual electronic resources when a major resource is cancelled. PMID:27076804

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

EPA Science Inventory

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

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

PubMed

Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

2008-11-27

The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

Received Signal Strength Database Interpolation by Kriging for a Wi-Fi Indoor Positioning System

PubMed Central

Jan, Shau-Shiun; Yeh, Shuo-Ju; Liu, Ya-Wen

2015-01-01

The main approach for a Wi-Fi indoor positioning system is based on the received signal strength (RSS) measurements, and the fingerprinting method is utilized to determine the user position by matching the RSS values with the pre-surveyed RSS database. To build a RSS fingerprint database is essential for an RSS based indoor positioning system, and building such a RSS fingerprint database requires lots of time and effort. As the range of the indoor environment becomes larger, labor is increased. To provide better indoor positioning services and to reduce the labor required for the establishment of the positioning system at the same time, an indoor positioning system with an appropriate spatial interpolation method is needed. In addition, the advantage of the RSS approach is that the signal strength decays as the transmission distance increases, and this signal propagation characteristic is applied to an interpolated database with the Kriging algorithm in this paper. Using the distribution of reference points (RPs) at measured points, the signal propagation model of the Wi-Fi access point (AP) in the building can be built and expressed as a function. The function, as the spatial structure of the environment, can create the RSS database quickly in different indoor environments. Thus, in this paper, a Wi-Fi indoor positioning system based on the Kriging fingerprinting method is developed. As shown in the experiment results, with a 72.2% probability, the error of the extended RSS database with Kriging is less than 3 dBm compared to the surveyed RSS database. Importantly, the positioning error of the developed Wi-Fi indoor positioning system with Kriging is reduced by 17.9% in average than that without Kriging. PMID:26343673

Received Signal Strength Database Interpolation by Kriging for a Wi-Fi Indoor Positioning System.

PubMed

Jan, Shau-Shiun; Yeh, Shuo-Ju; Liu, Ya-Wen

2015-08-28

The main approach for a Wi-Fi indoor positioning system is based on the received signal strength (RSS) measurements, and the fingerprinting method is utilized to determine the user position by matching the RSS values with the pre-surveyed RSS database. To build a RSS fingerprint database is essential for an RSS based indoor positioning system, and building such a RSS fingerprint database requires lots of time and effort. As the range of the indoor environment becomes larger, labor is increased. To provide better indoor positioning services and to reduce the labor required for the establishment of the positioning system at the same time, an indoor positioning system with an appropriate spatial interpolation method is needed. In addition, the advantage of the RSS approach is that the signal strength decays as the transmission distance increases, and this signal propagation characteristic is applied to an interpolated database with the Kriging algorithm in this paper. Using the distribution of reference points (RPs) at measured points, the signal propagation model of the Wi-Fi access point (AP) in the building can be built and expressed as a function. The function, as the spatial structure of the environment, can create the RSS database quickly in different indoor environments. Thus, in this paper, a Wi-Fi indoor positioning system based on the Kriging fingerprinting method is developed. As shown in the experiment results, with a 72.2% probability, the error of the extended RSS database with Kriging is less than 3 dBm compared to the surveyed RSS database. Importantly, the positioning error of the developed Wi-Fi indoor positioning system with Kriging is reduced by 17.9% in average than that without Kriging.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

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

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

Enabling Self-Directed Computer Use for Individuals with Cerebral Palsy: A Systematic Review of Assistive Devices and Technologies

ERIC Educational Resources Information Center

Davies, T. Claire; Mudge, Suzie; Ameratunga, Shanthi; Stott, N. Susan

2010-01-01

Aim: The purpose of this study was to systematically review published evidence on the development, use, and effectiveness of devices and technologies that enable or enhance self-directed computer access by individuals with cerebral palsy (CP). Methods: Nine electronic databases were searched using keywords "computer", "software", "spastic",…

ELT Research in Turkey: A Content Analysis of Selected Features of Published Articles

ERIC Educational Resources Information Center

Yagiz, Oktay; Aydin, Burcu; Akdemir, Ahmet Selçuk

2016-01-01

This study reviews a selected sample of 274 research articles on ELT, published between 2005 and 2015 in Turkish contexts. In the study, 15 journals in ULAKBIM database and articles from national and international journals accessed according to convenience sampling method were surveyed and relevant articles were obtained. A content analysis was…

Using the CREW Method to Enhance Public and School Library Collections

ERIC Educational Resources Information Center

Boon, Belinda

2009-01-01

Now, more than ever, public and school libraries struggle to main- tain their relevance in the age of instant access, electronic databases, and Google. While print collections continue to grow, many collections are drowning in obsolete, unused, and unwanted materials. And while most libraries keep up with deselection in an intelligent manner, many…

Fast fingerprint database maintenance for indoor positioning based on UGV SLAM.

PubMed

Tang, Jian; Chen, Yuwei; Chen, Liang; Liu, Jingbin; Hyyppä, Juha; Kukko, Antero; Kaartinen, Harri; Hyyppä, Hannu; Chen, Ruizhi

2015-03-04

Indoor positioning technology has become more and more important in the last two decades. Utilizing Received Signal Strength Indicator (RSSI) fingerprints of Signals of OPportunity (SOP) is a promising alternative navigation solution. However, as the RSSIs vary during operation due to their physical nature and are easily affected by the environmental change, one challenge of the indoor fingerprinting method is maintaining the RSSI fingerprint database in a timely and effective manner. In this paper, a solution for rapidly updating the fingerprint database is presented, based on a self-developed Unmanned Ground Vehicles (UGV) platform NAVIS. Several SOP sensors were installed on NAVIS for collecting indoor fingerprint information, including a digital compass collecting magnetic field intensity, a light sensor collecting light intensity, and a smartphone which collects the access point number and RSSIs of the pre-installed WiFi network. The NAVIS platform generates a map of the indoor environment and collects the SOPs during processing of the mapping, and then the SOP fingerprint database is interpolated and updated in real time. Field tests were carried out to evaluate the effectiveness and efficiency of the proposed method. The results showed that the fingerprint databases can be quickly created and updated with a higher sampling frequency (5Hz) and denser reference points compared with traditional methods, and the indoor map can be generated without prior information. Moreover, environmental changes could also be detected quickly for fingerprint indoor positioning.

Providing accurate near real-time fire alerts for Protected Areas through NASA FIRMS: Opportunities and Challenges

NASA Astrophysics Data System (ADS)

Ilavajhala, S.; Davies, D.; Schmaltz, J. E.; Wong, M.; Murphy, K. J.

2013-12-01

The NASA Fire Information for Resource Management System (FIRMS) is at the forefront of providing global near real-time (NRT) MODIS thermal anomalies / hotspot location data to end-users . FIRMS serves the data via an interactive Web GIS named Web Fire Mapper, downloads of NRT active fire, archive data downloads for MODIS hotspots dating back to 1999 and a hotspot email alert system The FIRMS Email Alerts system has been successfully alerting users of fires in their area of interest in near real-time and/or via daily and weekly email summaries, with an option to receive MODIS hotspot data as a text file (CSV) attachment. Currently, there are more than 7000 email alert subscriptions from more than 100 countries. Specifically, the email alerts system is designed to generate and send an email alert for any region or area on the globe, with a special focus on providing alerts for protected areas worldwide. For many protected areas, email alerts are particularly useful for early fire detection, monitoring on going fires, as well as allocating resources to protect wildlife and natural resources of particular value. For protected areas, FIRMS uses the World Database on Protected Areas (WDPA) supplied by United Nations Environment Program - World Conservation Monitoring Centre (UNEP-WCMC). Maintaining the most up-to-date, accurate boundary geometry for the protected areas for the email alerts is a challenge as the WDPA is continuously updated due to changing boundaries, merging or delisting of certain protected areas. Because of this dynamic nature of the protected areas database, the FIRMS protected areas database is frequently out-of-date with the most current version of WDPA database. To maintain the most up-to-date boundary information for protected areas and to be in compliance with the WDPA terms and conditions, FIRMS needs to constantly update its database of protected areas. Currently, FIRMS strives to keep its database up to date by downloading the most recent WDPA database at regular intervals, processing it, and ingesting it into the FIRMS spatial database. However, due to the large size of database, the process to download, process and ingest the database is quite time consuming. The FIRMS team is currently working on developing a method to update the protected areas database via web at regular intervals or on-demand. Using such a solution, FIRMS will be able access the most up-to-date extents of any protected area and the corresponding spatial geometries in real time. As such, FIRMS can utilize such a service to access the protected areas and their associated geometries to keep users' protected area boundaries in sync with those of the most recent WDPA database, and thus serve a more accurate email alert to the users. Furthermore, any client accessing the WDPA protected areas database could potentially use the solution of real-time access to the protected areas database. This talk primarily focuses on the challenges for FIRMS in sending accurate email alerts for protected areas, along with the solution the FIRMS team is developing. This talk also introduces the FIRMS fire information system and its components, with a special emphasis on the FIRMS email alerts system.

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

PubMed

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.

Generation of comprehensive thoracic oncology database--tool for translational research.

PubMed

Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

2011-01-22

The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation.

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

MaizeGDB: enabling access to basic, translational, and applied research information

USDA-ARS?s Scientific Manuscript database

MaizeGDB is the Maize Genetics and Genomics Database (available online at http://www.maizegdb.org). The MaizeGDB project is not simply an online database and website but rather an information service to maize researchers that supports customized data access and analysis needs to individual research...

Customizable tool for ecological data entry, assessment, monitoring, and interpretation

USDA-ARS?s Scientific Manuscript database

The Database for Inventory, Monitoring and Assessment (DIMA) is a highly customizable tool for data entry, assessment, monitoring, and interpretation. DIMA is a Microsoft Access database that can easily be used without Access knowledge and is available at no cost. Data can be entered for common, nat...

Database Access Manager for the Software Engineering Laboratory (DAMSEL) user's guide

NASA Technical Reports Server (NTRS)

1990-01-01

Operating instructions for the Database Access Manager for the Software Engineering Laboratory (DAMSEL) system are presented. Step-by-step instructions for performing various data entry and report generation activities are included. Sample sessions showing the user interface display screens are also included. Instructions for generating reports are accompanied by sample outputs for each of the reports. The document groups the available software functions by the classes of users that may access them.

MEIMAN: Database exploring Medicinal and Edible insects of Manipur

PubMed Central

Shantibala, Tourangbam; Lokeshwari, Rajkumari; Thingnam, Gourshyam; Somkuwar, Bharat Gopalrao

2012-01-01

We have developed MEIMAN, a unique database on medicinal and edible insects of Manipur which comprises 51 insects species collected through extensive survey and questionnaire for two years. MEIMAN provides integrated access to insect species thorough sophisticated web interface which has following capabilities a) Graphical interface of seasonality, b) Method of preparation, c) Form of use - edible and medicinal, d) habitat, e) medicinal uses, f) commercial importance and g) economic status. This database will be useful for scientific validations and updating of traditional wisdom in bioprospecting aspects. It will be useful in analyzing the insect biodiversity for the development of virgin resources and their industrialization. Further, the features will be suited for detailed investigation on potential medicinal and edible insects that make MEIMAN a powerful tool for sustainable management. Availability The database is available for free at www.ibsd.gov.in/meiman PMID:22715305

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

PubMed Central

Lomatch, Diane; Truax, Terry; Savage, Peter

1981-01-01

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

HLLV avionics requirements study and electronic filing system database development

NASA Technical Reports Server (NTRS)

1994-01-01

This final report provides a summary of achievements and activities performed under Contract NAS8-39215. The contract's objective was to explore a new way of delivering, storing, accessing, and archiving study products and information and to define top level system requirements for Heavy Lift Launch Vehicle (HLLV) avionics that incorporate Vehicle Health Management (VHM). This report includes technical objectives, methods, assumptions, recommendations, sample data, and issues as specified by DPD No. 772, DR-3. The report is organized into two major subsections, one specific to each of the two tasks defined in the Statement of Work: the Index Database Task and the HLLV Avionics Requirements Task. The Index Database Task resulted in the selection and modification of a commercial database software tool to contain the data developed during the HLLV Avionics Requirements Task. All summary information is addressed within each task's section.

The BioImage Database Project: organizing multidimensional biological images in an object-relational database.

PubMed

Carazo, J M; Stelzer, E H

1999-01-01

The BioImage Database Project collects and structures multidimensional data sets recorded by various microscopic techniques relevant to modern life sciences. It provides, as precisely as possible, the circumstances in which the sample was prepared and the data were recorded. It grants access to the actual data and maintains links between related data sets. In order to promote the interdisciplinary approach of modern science, it offers a large set of key words, which covers essentially all aspects of microscopy. Nonspecialists can, therefore, access and retrieve significant information recorded and submitted by specialists in other areas. A key issue of the undertaking is to exploit the available technology and to provide a well-defined yet flexible structure for dealing with data. Its pivotal element is, therefore, a modern object relational database that structures the metadata and ameliorates the provision of a complete service. The BioImage database can be accessed through the Internet. Copyright 1999 Academic Press.

GenBank.

PubMed

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

2008-01-01

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

GenBank

PubMed Central

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

2008-01-01

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

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

PubMed Central

Levy, Christine; Rogers, Elizabeth

1995-01-01

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

A Ruby API to query the Ensembl database for genomic features.

PubMed

Strozzi, Francesco; Aerts, Jan

2011-04-01

The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases. Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.

BIRS – Bioterrorism Information Retrieval System

PubMed Central

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. Availability The database is freely available at http://www.bioterrorism.biowaves.org PMID:23390356

Footprint Database and web services for the Herschel space observatory

NASA Astrophysics Data System (ADS)

Verebélyi, Erika; Dobos, László; Kiss, Csaba

2015-08-01

Using all telemetry and observational meta-data, we created a searchable database of Herschel observation footprints. Data from the Herschel space observatory is freely available for everyone but no uniformly processed catalog of all observations has been published yet. As a first step, we unified the data model for all three Herschel instruments in all observation modes and compiled a database of sky coverage information. As opposed to methods using a pixellation of the sphere, in our database, sky coverage is stored in exact geometric form allowing for precise area calculations. Indexing of the footprints allows for very fast search among observations based on pointing, time, sky coverage overlap and meta-data. This enables us, for example, to find moving objects easily in Herschel fields. The database is accessible via a web site and also as a set of REST web service functions which makes it usable from program clients like Python or IDL scripts. Data is available in various formats including Virtual Observatory standards.

The UBIRIS.v2: a database of visible wavelength iris images captured on-the-move and at-a-distance.

PubMed

Proença, Hugo; Filipe, Sílvio; Santos, Ricardo; Oliveira, João; Alexandre, Luís A

2010-08-01

The iris is regarded as one of the most useful traits for biometric recognition and the dissemination of nationwide iris-based recognition systems is imminent. However, currently deployed systems rely on heavy imaging constraints to capture near infrared images with enough quality. Also, all of the publicly available iris image databases contain data correspondent to such imaging constraints and therefore are exclusively suitable to evaluate methods thought to operate on these type of environments. The main purpose of this paper is to announce the availability of the UBIRIS.v2 database, a multisession iris images database which singularly contains data captured in the visible wavelength, at-a-distance (between four and eight meters) and on on-the-move. This database is freely available for researchers concerned about visible wavelength iris recognition and will be useful in accessing the feasibility and specifying the constraints of this type of biometric recognition.

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

Riemer, R.L.

The Panel on Basic Nuclear Data Compilations believes that it is important to provide the user with an evaluated nuclear database of the highest quality, dependability, and currency. It is also important that the evaluated nuclear data are easily accessible to the user. In the past the panel concentrated its concern on the cycle time for the publication of A-chain evaluations. However, the panel now recognizes that publication cycle time is no longer the appropriate goal. Sometime in the future, publication of the evaluated A-chains will evolve from the present hard-copy Nuclear Data Sheets on library shelves to purely electronicmore » publication, with the advent of universal access to terminals and the nuclear databases. Therefore, the literature cut-off date in the Evaluated Nuclear Structure Data File (ENSDF) is rapidly becoming the only important measure of the currency of an evaluated A-chain. Also, it has become exceedingly important to ensure that access to the databases is as user-friendly as possible and to enable electronic publication of the evaluated data files. Considerable progress has been made in these areas: use of the on-line systems has almost doubled in the past year, and there has been initial development of tools for electronic evaluation, publication, and dissemination. Currently, the nuclear data effort is in transition between the traditional and future methods of dissemination of the evaluated data. Also, many of the factors that adversely affect the publication cycle time simultaneously affect the currency of the evaluated nuclear database. Therefore, the panel continues to examine factors that can influence cycle time: the number of evaluators, the frequency with which an evaluation can be updated, the review of the evaluation, and the production of the evaluation, which currently exists as a hard-copy issue of Nuclear Data Sheets.« less

Teaching Case: Adapting the Access Northwind Database to Support a Database Course

ERIC Educational Resources Information Center

Dyer, John N.; Rogers, Camille

2015-01-01

A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

76 FR 41792 - Information Collection Being Submitted for Review and Approval to the Office of Management and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

... administrator from the private sector to create and operate TV band databases. The TV band database... database administrator will be responsible for operation of their database and coordination of the overall functioning of the database with other administrators, and will provide database access to TVBDs. The...

[A Terahertz Spectral Database Based on Browser/Server Technique].

PubMed

Zhang, Zhuo-yong; Song, Yue

2015-09-01

With the solution of key scientific and technical problems and development of instrumentation, the application of terahertz technology in various fields has been paid more and more attention. Owing to the unique characteristic advantages, terahertz technology has been showing a broad future in the fields of fast, non-damaging detections, as well as many other fields. Terahertz technology combined with other complementary methods can be used to cope with many difficult practical problems which could not be solved before. One of the critical points for further development of practical terahertz detection methods depends on a good and reliable terahertz spectral database. We developed a BS (browser/server) -based terahertz spectral database recently. We designed the main structure and main functions to fulfill practical requirements. The terahertz spectral database now includes more than 240 items, and the spectral information was collected based on three sources: (1) collection and citation from some other abroad terahertz spectral databases; (2) collected from published literatures; and (3) spectral data measured in our laboratory. The present paper introduced the basic structure and fundament functions of the terahertz spectral database developed in our laboratory. One of the key functions of this THz database is calculation of optical parameters. Some optical parameters including absorption coefficient, refractive index, etc. can be calculated based on the input THz time domain spectra. The other main functions and searching methods of the browser/server-based terahertz spectral database have been discussed. The database search system can provide users convenient functions including user registration, inquiry, displaying spectral figures and molecular structures, spectral matching, etc. The THz database system provides an on-line searching function for registered users. Registered users can compare the input THz spectrum with the spectra of database, according to the obtained correlation coefficient one can perform the searching task very fast and conveniently. Our terahertz spectral database can be accessed at http://www.teralibrary.com. The proposed terahertz spectral database is based on spectral information so far, and will be improved in the future. We hope this terahertz spectral database can provide users powerful, convenient, and high efficient functions, and could promote the broader applications of terahertz technology.

A Mixed Methods Analysis of a Library Based Handheld Intervention with Rural Clinicians

PubMed Central

Wallace, Richard L.; Woodward, Nakia J.; Wolf, Katherine M.

2014-01-01

Background The East Tennessee State University Quillen College of Medicine Library has participated for several years in projects to provide rural clinicians with health information resources. Objectives To determine if a strategy of handheld devices with a best-evidence point-of-care disease tool and a drug database paired with access to a medical library for full-text articles and training to use the tools would be an affordable way to meet the information needs of rural underserved clinicians. Methods This study is a mixed methods methodology. The first project was evaluated using a randomized controlled trial (RCT) methodology. The second was evaluated qualitatively using interviews and focus groups. Results The quantitative findings discovered that clinicians equipped with a handheld device with evidence-based software more frequently found answers to clinical questions, found answers more quickly, were more satisfied with information they found, and use expensive resources such as continuing medical education, online databases, and textbooks less than the group that did not have access to online technology. Qualitative results supported the quantitative findings. Conclusion Librarians can implement a three-pronged strategy of the secondary literature via a handheld, the primary literature via LoansomeDoc, and quality training to meet basic information needs of rural clinicians. PMID:25155980

Unified Access Architecture for Large-Scale Scientific Datasets

NASA Astrophysics Data System (ADS)

Karna, Risav

2014-05-01

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

Protein Solvent-Accessibility Prediction by a Stacked Deep Bidirectional Recurrent Neural Network.

PubMed

Zhang, Buzhong; Li, Linqing; Lü, Qiang

2018-05-25

Residue solvent accessibility is closely related to the spatial arrangement and packing of residues. Predicting the solvent accessibility of a protein is an important step to understand its structure and function. In this work, we present a deep learning method to predict residue solvent accessibility, which is based on a stacked deep bidirectional recurrent neural network applied to sequence profiles. To capture more long-range sequence information, a merging operator was proposed when bidirectional information from hidden nodes was merged for outputs. Three types of merging operators were used in our improved model, with a long short-term memory network performing as a hidden computing node. The trained database was constructed from 7361 proteins extracted from the PISCES server using a cut-off of 25% sequence identity. Sequence-derived features including position-specific scoring matrix, physical properties, physicochemical characteristics, conservation score and protein coding were used to represent a residue. Using this method, predictive values of continuous relative solvent-accessible area were obtained, and then, these values were transformed into binary states with predefined thresholds. Our experimental results showed that our deep learning method improved prediction quality relative to current methods, with mean absolute error and Pearson's correlation coefficient values of 8.8% and 74.8%, respectively, on the CB502 dataset and 8.2% and 78%, respectively, on the Manesh215 dataset.

Applications of Database Machines in Library Systems.

ERIC Educational Resources Information Center

Salmon, Stephen R.

1984-01-01

Characteristics and advantages of database machines are summarized and their applications to library functions are described. The ability to attach multiple hosts to the same database and flexibility in choosing operating and database management systems for different functions without loss of access to common database are noted. (EJS)

SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

Smiles2Monomers: a link between chemical and biological structures for polymers.

PubMed

Dufresne, Yoann; Noé, Laurent; Leclère, Valérie; Pupin, Maude

2015-01-01

The monomeric composition of polymers is powerful for structure comparison and synthetic biology, among others. Many databases give access to the atomic structure of compounds but the monomeric structure of polymers is often lacking. We have designed a smart algorithm, implemented in the tool Smiles2Monomers (s2m), to infer efficiently and accurately the monomeric structure of a polymer from its chemical structure. Our strategy is divided into two steps: first, monomers are mapped on the atomic structure by an efficient subgraph-isomorphism algorithm ; second, the best tiling is computed so that non-overlapping monomers cover all the structure of the target polymer. The mapping is based on a Markovian index built by a dynamic programming algorithm. The index enables s2m to search quickly all the given monomers on a target polymer. After, a greedy algorithm combines the mapped monomers into a consistent monomeric structure. Finally, a local branch and cut algorithm refines the structure. We tested this method on two manually annotated databases of polymers and reconstructed the structures de novo with a sensitivity over 90 %. The average computation time per polymer is 2 s. s2m automatically creates de novo monomeric annotations for polymers, efficiently in terms of time computation and sensitivity. s2m allowed us to detect annotation errors in the tested databases and to easily find the accurate structures. So, s2m could be integrated into the curation process of databases of small compounds to verify the current entries and accelerate the annotation of new polymers. The full method can be downloaded or accessed via a website for peptide-like polymers at http://bioinfo.lifl.fr/norine/smiles2monomers.jsp.Graphical abstract:.

Integrated radiologist's workstation enabling the radiologist as an effective clinical consultant

NASA Astrophysics Data System (ADS)

McEnery, Kevin W.; Suitor, Charles T.; Hildebrand, Stan; Downs, Rebecca; Thompson, Stephen K.; Shepard, S. Jeff

2002-05-01

Since February 2000, radiologists at the M. D. Anderson Cancer Center have accessed clinical information through an internally developed radiologist's clinical interpretation workstation called RadStation. This project provides a fully integrated digital dictation workstation with clinical data review. RadStation enables the radiologist as an effective clinical consultant with access to pertinent sources of clinical information at the time of dictation. Data sources not only include prior radiology reports from the radiology information system (RIS) but access to pathology data, laboratory data, history and physicals, clinic notes, and operative reports. With integrated clinical information access, a radiologists's interpretation not only comments on morphologic findings but also can enable evaluation of study findings in the context of pertinent clinical presentation and history. Image access is enabled through the integration of an enterprise image archive (Stentor, San Francisco). Database integration is achieved by a combination of real time HL7 messaging and queries to SQL-based legacy databases. A three-tier system architecture accommodates expanding access to additional databases including real-time patient schedule as well as patient medications and allergies.

Heterogeneous database integration in biomedicine.

PubMed

Sujansky, W

2001-08-01

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins.

PubMed

Varadi, Mihaly; Kosol, Simone; Lebrun, Pierre; Valentini, Erica; Blackledge, Martin; Dunker, A Keith; Felli, Isabella C; Forman-Kay, Julie D; Kriwacki, Richard W; Pierattelli, Roberta; Sussman, Joel; Svergun, Dmitri I; Uversky, Vladimir N; Vendruscolo, Michele; Wishart, David; Wright, Peter E; Tompa, Peter

2014-01-01

The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states.

Biofuel Database

National Institute of Standards and Technology Data Gateway

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

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.

PubMed

Gromiha, M Michael; Anoosha, P; Huang, Liang-Tsung

2016-01-01

Protein stability is the free energy difference between unfolded and folded states of a protein, which lies in the range of 5-25 kcal/mol. Experimentally, protein stability is measured with circular dichroism, differential scanning calorimetry, and fluorescence spectroscopy using thermal and denaturant denaturation methods. These experimental data have been accumulated in the form of a database, ProTherm, thermodynamic database for proteins and mutants. It also contains sequence and structure information of a protein, experimental methods and conditions, and literature information. Different features such as search, display, and sorting options and visualization tools have been incorporated in the database. ProTherm is a valuable resource for understanding/predicting the stability of proteins and it can be accessed at http://www.abren.net/protherm/ . ProTherm has been effectively used to examine the relationship among thermodynamics, structure, and function of proteins. We describe the recent progress on the development of methods for understanding/predicting protein stability, such as (1) general trends on mutational effects on stability, (2) relationship between the stability of protein mutants and amino acid properties, (3) applications of protein three-dimensional structures for predicting their stability upon point mutations, (4) prediction of protein stability upon single mutations from amino acid sequence, and (5) prediction methods for addressing double mutants. A list of online resources for predicting has also been provided.

The IRHUM (Isotopic Reconstruction of Human Migration) database - bioavailable strontium isotope ratios for geochemical fingerprinting in France

NASA Astrophysics Data System (ADS)

Willmes, M.; McMorrow, L.; Kinsley, L.; Armstrong, R.; Aubert, M.; Eggins, S.; Falguères, C.; Maureille, B.; Moffat, I.; Grün, R.

2013-11-01

Strontium isotope ratios (87Sr/86Sr) are a key geochemical tracer used in a wide range of fields including archaeology, ecology, food and forensic sciences. These applications are based on the principle that the Sr isotopic ratios of natural materials reflect the sources of strontium available during their formation. A major constraint for current studies is the lack of robust reference maps to evaluate the source of strontium isotope ratios measured in the samples. Here we provide a new dataset of bioavailable Sr isotope ratios for the major geologic units of France, based on plant and soil samples (Pangaea data repository doi:10.1594/PANGAEA.819142). The IRHUM (Isotopic Reconstruction of Human Migration) database is a web platform to access, explore and map our dataset. The database provides the spatial context and metadata for each sample, allowing the user to evaluate the suitability of the sample for their specific study. In addition, it allows users to upload and share their own datasets and data products, which will enhance collaboration across the different research fields. This article describes the sampling and analytical methods used to generate the dataset and how to use and access of the dataset through the IRHUM database. Any interpretation of the isotope dataset is outside the scope of this publication.

Mapping the literature of maternal-child/gynecologic nursing

PubMed Central

Jacobs, Susan Kaplan

2006-01-01

Objectives: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. Methods: Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. Results: Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. Conclusion: The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles. PMID:16710464

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2013 CFR

2013-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2014 CFR

2014-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2012 CFR

2012-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... fully evaluate evidence, all spreadsheets must be fully accessible and manipulable. Electronic databases... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...

Achievable Rate Estimation of IEEE 802.11ad Visual Big-Data Uplink Access in Cloud-Enabled Surveillance Applications.

PubMed

Kim, Joongheon; Kim, Jong-Kook

2016-01-01

This paper addresses the computation procedures for estimating the impact of interference in 60 GHz IEEE 802.11ad uplink access in order to construct visual big-data database from randomly deployed surveillance camera sensing devices. The acquired large-scale massive visual information from surveillance camera devices will be used for organizing big-data database, i.e., this estimation is essential for constructing centralized cloud-enabled surveillance database. This performance estimation study captures interference impacts on the target cloud access points from multiple interference components generated by the 60 GHz wireless transmissions from nearby surveillance camera devices to their associated cloud access points. With this uplink interference scenario, the interference impacts on the main wireless transmission from a target surveillance camera device to its associated target cloud access point with a number of settings are measured and estimated under the consideration of 60 GHz radiation characteristics and antenna radiation pattern models.

Mandatory and Location-Aware Access Control for Relational Databases

NASA Astrophysics Data System (ADS)

Decker, Michael

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

Design of Knowledge Bases for Plant Gene Regulatory Networks.

PubMed

Mukundi, Eric; Gomez-Cano, Fabio; Ouma, Wilberforce Zachary; Grotewold, Erich

2017-01-01

Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary information and resources, and outline the methods for obtaining data. The second stage consists of designing the schema, which involves defining the entire arrangement of the database in a systematic plan. The third stage is the implementation, defined by actualization of the database by using software according to a predefined schema. The final stage is development, where the database is made available to users in a web-accessible system. The result is a knowledgebase that integrates all the information pertaining to gene regulation, and which is easily expandable and transferable.

Outreach and online training services at the Saccharomyces Genome Database.

PubMed

MacPherson, Kevin A; Starr, Barry; Wong, Edith D; Dalusag, Kyla S; Hellerstedt, Sage T; Lang, Olivia W; Nash, Robert S; Skrzypek, Marek S; Engel, Stacia R; Cherry, J Michael

2017-01-01

The Saccharomyces Genome Database (SGD; www.yeastgenome.org ), the primary genetics and genomics resource for the budding yeast S. cerevisiae , provides free public access to expertly curated information about the yeast genome and its gene products. As the central hub for the yeast research community, SGD engages in a variety of social outreach efforts to inform our users about new developments, promote collaboration, increase public awareness of the importance of yeast to biomedical research, and facilitate scientific discovery. Here we describe these various outreach methods, from networking at scientific conferences to the use of online media such as blog posts and webinars, and include our perspectives on the benefits provided by outreach activities for model organism databases. http://www.yeastgenome.org. © The Author(s) 2017. Published by Oxford University Press.

Online access to international aerospace science and technology

NASA Technical Reports Server (NTRS)

Lahr, Thomas F.; Harrison, Laurie K.

1993-01-01

The NASA Aerospace Database contains over 625,000 foreign R&D documents from 1962 to the present from over 60 countries worldwide. In 1991 over 26,000 new non-U.S. entries were added from a variety of innovative exchange programs. An active international acquisitions effort by the NASA STI Program seeks to increase the percentage of foreign data in the coming years, focusing on Japan, the Commonwealth of Independent States, Western Europe, Australia, and Canada. It also has plans to target China, India, Brazil, and Eastern Europe in the future. The authors detail the resources the NASA Aerospace Database offers in the international arena, the methods used to gather this information, and the STI Program's initiatives for maintaining and expanding the percentage of international information in this database.

A probabilistic approach to information retrieval in heterogeneous databases

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

Chatterjee, A.; Segev, A.

During the post decade, organizations have increased their scope and operations beyond their traditional geographic boundaries. At the same time, they have adopted heterogeneous and incompatible information systems independent of each other without a careful consideration that one day they may need to be integrated. As a result of this diversity, many important business applications today require access to data stored in multiple autonomous databases. This paper examines a problem of inter-database information retrieval in a heterogeneous environment, where conventional techniques are no longer efficient. To solve the problem, broader definitions for join, union, intersection and selection operators are proposed.more » Also, a probabilistic method to specify the selectivity of these operators is discussed. An algorithm to compute these probabilities is provided in pseudocode.« less

Human Connectome Project Informatics: quality control, database services, and data visualization

PubMed Central

Marcus, Daniel S.; Harms, Michael P.; Snyder, Abraham Z.; Jenkinson, Mark; Wilson, J Anthony; Glasser, Matthew F.; Barch, Deanna M.; Archie, Kevin A.; Burgess, Gregory C.; Ramaratnam, Mohana; Hodge, Michael; Horton, William; Herrick, Rick; Olsen, Timothy; McKay, Michael; House, Matthew; Hileman, Michael; Reid, Erin; Harwell, John; Coalson, Timothy; Schindler, Jon; Elam, Jennifer S.; Curtiss, Sandra W.; Van Essen, David C.

2013-01-01

The Human Connectome Project (HCP) has developed protocols, standard operating and quality control procedures, and a suite of informatics tools to enable high throughput data collection, data sharing, automated data processing and analysis, and data mining and visualization. Quality control procedures include methods to maintain data collection consistency over time, to measure head motion, and to establish quantitative modality-specific overall quality assessments. Database services developed as customizations of the XNAT imaging informatics platform support both internal daily operations and open access data sharing. The Connectome Workbench visualization environment enables user interaction with HCP data and is increasingly integrated with the HCP's database services. Here we describe the current state of these procedures and tools and their application in the ongoing HCP study. PMID:23707591

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

PubMed

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

2016-12-01

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

Understanding How Principals Use Data Dashboards to Inform Systemic School Improvement

ERIC Educational Resources Information Center

Marker, Kathryn Christner

2016-01-01

Because data access may be perceived by principals as overwhelming or irrelevant rather than helpful (Wayman, Spikes, & Volonnino, 2013), data access does not guarantee effective data use. The data-based decision making literature has largely focused on teacher use of data, considering less often data-based organizational improvements for the…

FACILITATING ADVANCED URBAN METEOROLOGY AND AIR QUALITY MODELING CAPABILITIES WITH HIGH RESOLUTION URBAN DATABASE AND ACCESS PORTAL TOOLS

EPA Science Inventory

Information of urban morphological features at high resolution is needed to properly model and characterize the meteorological and air quality fields in urban areas. We describe a new project called National Urban Database with Access Portal Tool, (NUDAPT) that addresses this nee...

EVALIDatorReports: Reporting beyond the FIADB

Treesearch

Patrick D. Miles

2009-01-01

Tools for analyzing data collected by the U.S. Forest Service's Forest Inventory and Analysis (FIA) program are available in Microsoft Access© format. Databases have been created for every state, except Hawaii, and are available for downloading. EVALIDatorReports is a Visual Basic Application that is stored within each Microsoft Access© database...

Microcomputer Database Management Systems that Interface with Online Public Access Catalogs.

ERIC Educational Resources Information Center

Rice, James

1988-01-01

Describes a study that assessed the availability and use of microcomputer database management interfaces to online public access catalogs. The software capabilities needed to effect such an interface are identified, and available software packages are evaluated by these criteria. A directory of software vendors is provided. (4 notes with…

The GraVent DDT database

NASA Astrophysics Data System (ADS)

Boeck, Lorenz R.; Katzy, Peter; Hasslberger, Josef; Kink, Andreas; Sattelmayer, Thomas

2016-09-01

An open-access online platform containing data from experiments on deflagration-to-detonation transition conducted at the Institute of Thermodynamics, Technical University of Munich, has been developed and is accessible at http://www.td.mw.tum.de/ddt. The database provides researchers working on explosion dynamics with data for theoretical analyses and for the validation of numerical simulations.

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY (DSSTOX) DATABASE NETWORK: MAKING PUBLIC TOXICITY DATA RESOURCES MORE ACCESSIBLE AND USABLE FOR DATA EXPLORATION AND SAR DEVELOPMENT

EPA Science Inventory

Distributed Structure-Searchable Toxicity (DSSTox) Database Network: Making Public Toxicity Data Resources More Accessible and U sable for Data Exploration and SAR Development

Many sources of public toxicity data are not currently linked to chemical structure, are not ...

Online Public Access Catalogs. ERIC Fact Sheet.

ERIC Educational Resources Information Center

Cochrane, Pauline A.

A listing is presented of 17 documents in the ERIC database concerning the Online Catalog (sometimes referred to as OPAC or Online Public Access Catalog), a computer-based and supported library catalog designed for patron use. The database usually represents recent acquisitions and often contains information about books on order and items in…

Extending the Online Public Access Catalog into the Microcomputer Environment.

ERIC Educational Resources Information Center

Sutton, Brett

1990-01-01

Describes PCBIS, a database program for MS-DOS microcomputers that features a utility for automatically converting online public access catalog search results stored as text files into structured database files that can be searched, sorted, edited, and printed. Topics covered include the general features of the program, record structure, record…

Childhood immunization rates in rural Intibucá, Honduras: an analysis of a local database tool and community health center records for assessing and improving vaccine coverage

PubMed Central

2012-01-01

Background Vaccines are highly effective at preventing infectious diseases in children, and prevention is especially important in resource-limited countries where treatment is difficult to access. In Honduras, the World Health Organization (WHO) reports very high immunization rates in children. To determine whether or not these estimates accurately depict the immunization coverage in non-urban regions of the country, we compared the WHO data to immunization rates obtained from a local database tool and community health center records in rural Intibucá, Honduras. Methods We used data from two sources to comprehensively evaluate immunization rates in the area: 1) census data from a local database and 2) immunization data collected at health centers. We compared these rates using logistic regression, and we compared them to publicly available WHO-reported estimates using confidence interval inclusion. Results We found that mean immunization rates for each vaccine were high (range 84.4 to 98.8 percent), but rates recorded at the health centers were significantly higher than those reported from the census data (p≤0.001). Combining the results from both databases, the mean rates of four out of five vaccines were less than WHO-reported rates (p <0.05). Overall immunization rates were significantly different between townships (p=0.03). The rates by individual vaccine were similar across townships (p >0.05), except for diphtheria/tetanus/pertussis vaccine (p=0.02) and oral polio vaccine (p <0.01). Conclusions Immunization rates in Honduras were high across data sources, though most of the rates recorded in rural Honduras were less than WHO-reported rates. Despite geographical difficulties and barriers to access, the local database and Honduran community health workers have developed a thorough system for ensuring that children receive their immunizations on time. The successful integration of community health workers and a database within the Honduran decentralized health system may serve as a model for other immunization programs in resource-limited countries where health care is less accessible. PMID:23216801

OLIO+: an osteopathic medicine database.

PubMed

Woods, S E

1991-01-01

OLIO+ is a bibliographic database designed to meet the information needs of the osteopathic medical community. Produced by the American Osteopathic Association (AOA), OLIO+ is devoted exclusively to the osteopathic literature. The database is available only by subscription through AOA and may be accessed from any data terminal with modem or IBM-compatible personal computer with telecommunications software that can emulate VT100 or VT220. Apple access is also available, but some assistance from OLIO+ support staff may be necessary to modify the Apple keyboard.

Breach Risk Magnitude: A Quantitative Measure of Database Security.

PubMed

Yasnoff, William A

2016-01-01

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

Karst database development in Minnesota: Design and data assembly

USGS Publications Warehouse

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

2005-01-01

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

GenBank

PubMed Central

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

2007-01-01

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

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

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

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

Use of Data Mining to Reveal Body Mass Index (BMI): Patterns among Pennsylvania Schoolchildren, Pre-K to Grade 12

ERIC Educational Resources Information Center

YoussefAgha, Ahmed H.; Lohrmann, David K.; Jayawardene, Wasantha P.

2013-01-01

Background: Health eTools for Schools was developed to assist school nurses with routine entries, including height and weight, on student health records, thus providing a readily accessible data base. Data-mining techniques were applied to this database to determine if clinically signi?cant results could be generated. Methods: Body mass index…

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

PubMed Central

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

2018-01-01

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

Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

2013-12-01

The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

Inequities in access to inpatient rehabilitation after stroke: an international scoping review.

PubMed

Lynch, Elizabeth A; Cadilhac, Dominique A; Luker, Julie A; Hillier, Susan L

2017-12-01

Background Inequities in accessing inpatient rehabilitation after stroke have been reported in many countries and impact on patient outcomes. Objective To explore variation in international recommendations regarding which patients should receive inpatient rehabilitation after stroke and to describe reported access to rehabilitation. Methods A scoping review was conducted to identify clinical guidelines with recommendations regarding which patients should access inpatient rehabilitation after stroke, and data regarding the proportion of patients accessing stroke rehabilitation. Four bibliographic databases and grey literature were searched. Results Twenty-eight documents were included. Selection criteria for post-acute inpatient rehabilitation were identified for 14 countries or regions and summary data on the proportion of patients receiving inpatient rehabilitation were identified for 14 countries. In Australia, New Zealand, and the United Kingdom, it is recommended that all patients with stroke symptoms should access rehabilitation, whereas guidelines from the United States, Canada, and Europe did not consistently recommend rehabilitation for people with severe stroke. Access to inpatient rehabilitation ranged from 13% in Sweden to 57% in Israel. Differences in availability of early supported discharge/home rehabilitation programs and variations in reporting methods may influence the ability to reliably compare access to rehabilitation between regions. Conclusion Recommendations regarding which patients with moderate and severe strokes should access ongoing rehabilitation are inconsistent. Clinical practice guidelines from different countries regarding post-stroke rehabilitation do not always reflect the evidence regarding the likely benefits to people with stroke. Inequity in access to rehabilitation after stroke is an international issue.

NSWC Crane Aerospace Cell Test History Database

NASA Technical Reports Server (NTRS)

Brown, Harry; Moore, Bruce

1994-01-01

The Aerospace Cell Test History Database was developed to provide project engineers and scientists ready access to the data obtained from testing of aerospace cell designs at Naval Surface Warfare Center, Crane Division. The database is intended for use by all aerospace engineers and scientists involved in the design of power systems for satellites. Specifically, the database will provide a tool for project engineers to review the progress of their test at Crane and to have ready access to data for evaluation. Additionally, the database will provide a history of test results that designers can draw upon to answer questions about cell performance under certain test conditions and aid in selection of a cell for a satellite battery. Viewgraphs are included.

Beyond relevance and recall: testing new user-centred measures of database performance.

PubMed

Stokes, Peter; Foster, Allen; Urquhart, Christine

2009-09-01

Measures of the effectiveness of databases have traditionally focused on recall, precision, with some debate on how relevance can be assessed, and by whom. New measures of database performance are required when users are familiar with search engines, and expect full text availability. This research ascertained which of four bibliographic databases (BNI, CINAHL, MEDLINE and EMBASE) could be considered most useful to nursing and midwifery students searching for information for an undergraduate dissertation. Searches on title were performed for dissertation topics supplied by nursing students (n = 9), who made the relevance judgements. Measures of recall and precision were combined with additional factors to provide measures of effectiveness, while efficiency combined measures of novelty and originality and accessibility combined measures for availability and retrievability, based on obtainability. There were significant differences among the databases in precision, originality and availability, but other differences were not significant (Friedman test). Odds ratio tests indicated that BNI, followed by CINAHL were the most effective, CINAHL the most efficient, and BNI the most accessible. The methodology could help library services in purchase decisions as the measure for accessibility, and odds ratio testing helped to differentiate database performance.

High Temperature Superconducting Materials Database

National Institute of Standards and Technology Data Gateway

SRD 62 NIST High Temperature Superconducting Materials Database (Web, free access)   The NIST High Temperature Superconducting Materials Database (WebHTS) provides evaluated thermal, mechanical, and superconducting property data for oxides and other nonconventional superconductors.

Quantum search of a real unstructured database

NASA Astrophysics Data System (ADS)

Broda, Bogusław

2016-02-01

A simple circuit implementation of the oracle for Grover's quantum search of a real unstructured classical database is proposed. The oracle contains a kind of quantumly accessible classical memory, which stores the database.

HOWDY: an integrated database system for human genome research

PubMed Central

Hirakawa, Mika

2002-01-01

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search. PMID:11752279

Optimizing the NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maa, Ming-Hokng

1996-01-01

The NASA Technical Report Server (NTRS), a World Wide Web report distribution NASA technical publications service, is modified for performance enhancement, greater protocol support, and human interface optimization. Results include: Parallel database queries, significantly decreasing user access times by an average factor of 2.3; access from clients behind firewalls and/ or proxies which truncate excessively long Uniform Resource Locators (URLs); access to non-Wide Area Information Server (WAIS) databases and compatibility with the 239-50.3 protocol; and a streamlined user interface.

78 FR 39290 - Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-01

... project, known as the ``National Mortgage Database,'' which is a joint effort of FHFA and the Consumer... a database of timely and otherwise unavailable residential mortgage market information to be made... Mortgage Database. The key purpose of the National Mortgage Database is to make accessible accurate...

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

PubMed

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

2015-03-01

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

Mapping the literature of nursing: 1996-2000.

PubMed

Allen, Margaret Peg; Jacobs, Susan Kaplan; Levy, June R

2006-04-01

This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered.

Simple re-instantiation of small databases using cloud computing.

PubMed

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

2013-01-01

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

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

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

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool; Part 5 - WW3 Database

DTIC Science & Technology

2015-02-01

Program ( CDIP ); and Part 4 for the Great Lakes Observing System/Coastal Forecasting System (GLOS/GLCFS). Using step-by-step instructions, this Part 5...Demirbilek, Z., L. Lin, and D. Wilson. 2014a. WaveNet: A web-based metocean data access, processing, and analysis tool; part 3– CDIP database

100 Colleges Sign Up with Google to Speed Access to Library Resources

ERIC Educational Resources Information Center

Young, Jeffrey R.

2005-01-01

More than 100 colleges and universities have arranged to give people using the Google Scholar search engine on their campuses more-direct access to library materials. Google Scholar is a free tool that searches scholarly materials on the Web and in academic databases. The new arrangements essentially let Google know which online databases the…

GPU-based cloud service for Smith-Waterman algorithm using frequency distance filtration scheme.

PubMed

Lee, Sheng-Ta; Lin, Chun-Yuan; Hung, Che Lun

2013-01-01

As the conventional means of analyzing the similarity between a query sequence and database sequences, the Smith-Waterman algorithm is feasible for a database search owing to its high sensitivity. However, this algorithm is still quite time consuming. CUDA programming can improve computations efficiently by using the computational power of massive computing hardware as graphics processing units (GPUs). This work presents a novel Smith-Waterman algorithm with a frequency-based filtration method on GPUs rather than merely accelerating the comparisons yet expending computational resources to handle such unnecessary comparisons. A user friendly interface is also designed for potential cloud server applications with GPUs. Additionally, two data sets, H1N1 protein sequences (query sequence set) and human protein database (database set), are selected, followed by a comparison of CUDA-SW and CUDA-SW with the filtration method, referred to herein as CUDA-SWf. Experimental results indicate that reducing unnecessary sequence alignments can improve the computational time by up to 41%. Importantly, by using CUDA-SWf as a cloud service, this application can be accessed from any computing environment of a device with an Internet connection without time constraints.

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

PubMed

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

2008-10-10

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

Toward an Open-Access Global Database for Mapping, Control, and Surveillance of Neglected Tropical Diseases

PubMed Central

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F.; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F. L.; Utzinger, Jürg; Kristensen, Thomas K.; Vounatsou, Penelope

2011-01-01

Background After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. Methodology With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and ‘grey literature’), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. Principal Findings At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. Conclusions An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay. PMID:22180793

Fast Fingerprint Database Maintenance for Indoor Positioning Based on UGV SLAM

PubMed Central

Tang, Jian; Chen, Yuwei; Chen, Liang; Liu, Jingbin; Hyyppä, Juha; Kukko, Antero; Kaartinen, Harri; Hyyppä, Hannu; Chen, Ruizhi

2015-01-01

Indoor positioning technology has become more and more important in the last two decades. Utilizing Received Signal Strength Indicator (RSSI) fingerprints of Signals of OPportunity (SOP) is a promising alternative navigation solution. However, as the RSSIs vary during operation due to their physical nature and are easily affected by the environmental change, one challenge of the indoor fingerprinting method is maintaining the RSSI fingerprint database in a timely and effective manner. In this paper, a solution for rapidly updating the fingerprint database is presented, based on a self-developed Unmanned Ground Vehicles (UGV) platform NAVIS. Several SOP sensors were installed on NAVIS for collecting indoor fingerprint information, including a digital compass collecting magnetic field intensity, a light sensor collecting light intensity, and a smartphone which collects the access point number and RSSIs of the pre-installed WiFi network. The NAVIS platform generates a map of the indoor environment and collects the SOPs during processing of the mapping, and then the SOP fingerprint database is interpolated and updated in real time. Field tests were carried out to evaluate the effectiveness and efficiency of the proposed method. The results showed that the fingerprint databases can be quickly created and updated with a higher sampling frequency (5Hz) and denser reference points compared with traditional methods, and the indoor map can be generated without prior information. Moreover, environmental changes could also be detected quickly for fingerprint indoor positioning. PMID:25746096

Publishing SNP genotypes of human embryonic stem cell lines: policy statement of the International Stem Cell Forum Ethics Working Party.

PubMed

Knoppers, Bartha M; Isasi, Rosario; Benvenisty, Nissim; Kim, Ock-Joo; Lomax, Geoffrey; Morris, Clive; Murray, Thomas H; Lee, Eng Hin; Perry, Margery; Richardson, Genevra; Sipp, Douglas; Tanner, Klaus; Wahlström, Jan; de Wert, Guido; Zeng, Fanyi

2011-09-01

Novel methods and associated tools permitting individual identification in publicly accessible SNP databases have become a debatable issue. There is growing concern that current technical and ethical safeguards to protect the identities of donors could be insufficient. In the context of human embryonic stem cell research, there are no studies focusing on the probability that an hESC line donor could be identified by analyzing published SNP profiles and associated genotypic and phenotypic information. We present the International Stem Cell Forum (ISCF) Ethics Working Party's Policy Statement on "Publishing SNP Genotypes of Human Embryonic Stem Cell Lines (hESC)". The Statement prospectively addresses issues surrounding the publication of genotypic data and associated annotations of hESC lines in open access databases. It proposes a balanced approach between the goals of open science and data sharing with the respect for fundamental bioethical principles (autonomy, privacy, beneficence, justice and research merit and integrity).

Oral oncoprevention by phytochemicals - a systematic review disclosing the therapeutic dilemma.

PubMed

Bhavana, Sujana Mulk; Lakshmi, Chintamaneni Raja

2014-10-01

The aim of this article is to emphasize and focus on the preclinical and clinical update on phytochemicals and their role in prevention of oral carcinogenesis. Accordingly, the literature search was made following database: Embase, Medline, Science Citation index, NIH public access, pubmed and Cochrane Database of systematic reviews. Several internet websites were also searched to access publications from major phytochemical research sites and relevant information was obtained with regards to each plant chemical. The authors also spotted different list servers through wignet.com, Stanford cancer research etc: The data base search was made from the inception to 1988 and updated till 2013. A systematic method was obtained for literature search and data collection was critiqued. 60 articles were searched, among which there were only 6 systematic reviews on phytochemicals regarding oral carcinogenesis. Additional articles were obtained on phytochemicals and their mechanism of action in other cancers, which were regarded as background material. The studies done by various authors on each phytochemical has been briefly emphasized.

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

PubMed Central

Henkel, Ron; Wolkenhauer, Olaf; Waltemath, Dagmar

2015-01-01

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

GenBank.

PubMed

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

2010-01-01

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

GenBank.

PubMed

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

2009-01-01

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

Increasing access to Latin American social medicine resources: a preliminary report.

PubMed

Buchanan, Holly Shipp; Waitzkin, Howard; Eldredge, Jonathan; Davidson, Russ; Iriart, Celia; Teal, Janis

2003-10-01

This preliminary report describes the development and implementation of a project to improve access to literature in Latin American social medicine (LASM). The University of New Mexico project team collaborated with participants from Argentina, Brazil, Chile, and Ecuador to identify approximately 400 articles and books in Latin American social medicine. Structured abstracts were prepared, translated into English, Spanish, and Portuguese, assigned Medical Subject Headings (MeSH), and loaded into a Web-based database for public searching. The project has initiated Web-based publication for two LASM journals. Evaluation included measures of use and content. The LASM Website (http://hsc.unm.edu/lasm) and database create access to formerly little-known literature that addresses problems relevant to current medicine and public health. This Website offers a unique resource for researchers, practitioners, and teachers who seek to understand the links between socioeconomic conditions and health. The project provides a model for collaboration between librarians and health care providers. Challenges included procurement of primary material; preparation of concise abstracts; working with trilingual translations of abstracts, metadata, and indexing; and the work processes of the multidisciplinary team. The literature of Latin American social medicine has become more readily available to researchers worldwide. The LASM project serves as a collaborative model for the creation of sustainable solutions for disseminating information that is difficult to access through traditional methods.

Structural Ceramics Database

National Institute of Standards and Technology Data Gateway

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

Towards the Architecture of an Instructional Multimedia Database.

ERIC Educational Resources Information Center

Verhagen, Plin W.; Bestebreurtje, R.

1994-01-01

Discussion of multimedia databases in education focuses on the development of an adaptable database in The Netherlands that uses optical storage media to hold the audiovisual components. Highlights include types of applications; types of users; accessibility; adaptation; an object-oriented approach; levels of the database architecture; and…

Online drug databases: a new method to assess and compare inclusion of clinically relevant information.

PubMed

Silva, Cristina; Fresco, Paula; Monteiro, Joaquim; Rama, Ana Cristina Ribeiro

2013-08-01

Evidence-Based Practice requires health care decisions to be based on the best available evidence. The model "Information Mastery" proposes that clinicians should use sources of information that have previously evaluated relevance and validity, provided at the point of care. Drug databases (DB) allow easy and fast access to information and have the benefit of more frequent content updates. Relevant information, in the context of drug therapy, is that which supports safe and effective use of medicines. Accordingly, the European Guideline on the Summary of Product Characteristics (EG-SmPC) was used as a standard to evaluate the inclusion of relevant information contents in DB. To develop and test a method to evaluate relevancy of DB contents, by assessing the inclusion of information items deemed relevant for effective and safe drug use. Hierarchical organisation and selection of the principles defined in the EGSmPC; definition of criteria to assess inclusion of selected information items; creation of a categorisation and quantification system that allows score calculation; calculation of relative differences (RD) of scores for comparison with an "ideal" database, defined as the one that achieves the best quantification possible for each of the information items; pilot test on a sample of 9 drug databases, using 10 drugs frequently associated in literature with morbidity-mortality and also being widely consumed in Portugal. Main outcome measure Calculate individual and global scores for clinically relevant information items of drug monographs in databases, using the categorisation and quantification system created. A--Method development: selection of sections, subsections, relevant information items and corresponding requisites; system to categorise and quantify their inclusion; score and RD calculation procedure. B--Pilot test: calculated scores for the 9 databases; globally, all databases evaluated significantly differed from the "ideal" database; some DB performed better but performance was inconsistent at subsections level, within the same DB. The method developed allows quantification of the inclusion of relevant information items in DB and comparison with an "ideal database". It is necessary to consult diverse DB in order to find all the relevant information needed to support clinical drug use.

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

PubMed Central

Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

2009-01-01

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

An innovative approach to capability-based emergency operations planning

PubMed Central

Keim, Mark E

2013-01-01

This paper describes the innovative use information technology for assisting disaster planners with an easily-accessible method for writing and improving evidence-based emergency operations plans. This process is used to identify all key objectives of the emergency response according to capabilities of the institution, community or society. The approach then uses a standardized, objective-based format, along with a consensus-based method for drafting capability-based operational-level plans. This information is then integrated within a relational database to allow for ease of access and enhanced functionality to search, sort and filter and emergency operations plan according to user need and technological capacity. This integrated approach is offered as an effective option for integrating best practices of planning with the efficiency, scalability and flexibility of modern information and communication technology. PMID:28228987

An innovative approach to capability-based emergency operations planning.

PubMed

Keim, Mark E

2013-01-01

This paper describes the innovative use information technology for assisting disaster planners with an easily-accessible method for writing and improving evidence-based emergency operations plans. This process is used to identify all key objectives of the emergency response according to capabilities of the institution, community or society. The approach then uses a standardized, objective-based format, along with a consensus-based method for drafting capability-based operational-level plans. This information is then integrated within a relational database to allow for ease of access and enhanced functionality to search, sort and filter and emergency operations plan according to user need and technological capacity. This integrated approach is offered as an effective option for integrating best practices of planning with the efficiency, scalability and flexibility of modern information and communication technology.

CruiseViewer: SIOExplorer Graphical Interface to Metadata and Archives.

NASA Astrophysics Data System (ADS)

Sutton, D. W.; Helly, J. J.; Miller, S. P.; Chase, A.; Clark, D.

2002-12-01

We are introducing "CruiseViewer" as a prototype graphical interface for the SIOExplorer digital library project, part of the overall NSF National Science Digital Library (NSDL) effort. When complete, CruiseViewer will provide access to nearly 800 cruises, as well as 100 years of documents and images from the archives of the Scripps Institution of Oceanography (SIO). The project emphasizes data object accessibility, a rich metadata format, efficient uploading methods and interoperability with other digital libraries. The primary function of CruiseViewer is to provide a human interface to the metadata database and to storage systems filled with archival data. The system schema is based on the concept of an "arbitrary digital object" (ADO). Arbitrary in that if the object can be stored on a computer system then SIOExplore can manage it. Common examples are a multibeam swath bathymetry file, a .pdf cruise report, or a tar file containing all the processing scripts used on a cruise. We require a metadata file for every ADO in an ascii "metadata interchange format" (MIF), which has proven to be highly useful for operability and extensibility. Bulk ADO storage is managed using the Storage Resource Broker, SRB, data handling middleware developed at the San Diego Supercomputer Center that centralizes management and access to distributed storage devices. MIF metadata are harvested from several sources and housed in a relational (Oracle) database. For CruiseViewer, cgi scripts resident on an Apache server are the primary communication and service request handling tools. Along with the CruiseViewer java application, users can query, access and download objects via a separate method that operates through standard web browsers, http://sioexplorer.ucsd.edu. Both provide the functionability to query and view object metadata, and select and download ADOs. For the CruiseViewer application Java 2D is used to add a geo-referencing feature that allows users to select basemap images and have vector shapes representing query results mapped over the basemap in the image panel. The two methods together address a wide range of user access needs and will allow for widespread use of SIOExplorer.

Validated environmental and physiological data from the CELSS Breadboard Projects Biomass Production Chamber. BWT931 (Wheat cv. Yecora Rojo)

NASA Technical Reports Server (NTRS)

Stutte, G. W.; Mackowiak, C. L.; Markwell, G. A.; Wheeler, R. M.; Sager, J. C.

1993-01-01

This KSC database is being made available to the scientific research community to facilitate the development of crop development models, to test monitoring and control strategies, and to identify environmental limitations in crop production systems. The KSC validated dataset consists of 17 parameters necessary to maintain bioregenerative life support functions: water purification, CO2 removal, O2 production, and biomass production. The data are available on disk as either a DATABASE SUBSET (one week of 5-minute data) or DATABASE SUMMARY (daily averages of parameters). Online access to the VALIDATED DATABASE will be made available to institutions with specific programmatic requirements. Availability and access to the KSC validated database are subject to approval and limitations implicit in KSC computer security policies.

Functionally Graded Materials Database

NASA Astrophysics Data System (ADS)

Kisara, Katsuto; Konno, Tomomi; Niino, Masayuki

2008-02-01

Functionally Graded Materials Database (hereinafter referred to as FGMs Database) was open to the society via Internet in October 2002, and since then it has been managed by the Japan Aerospace Exploration Agency (JAXA). As of October 2006, the database includes 1,703 research information entries with 2,429 researchers data, 509 institution data and so on. Reading materials such as "Applicability of FGMs Technology to Space Plane" and "FGMs Application to Space Solar Power System (SSPS)" were prepared in FY 2004 and 2005, respectively. The English version of "FGMs Application to Space Solar Power System (SSPS)" is now under preparation. This present paper explains the FGMs Database, describing the research information data, the sitemap and how to use it. From the access analysis, user access results and users' interests are discussed.

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

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

Organizational context and taxonomy of health care databases.

PubMed

Shatin, D

2001-01-01

An understanding of the organizational context and taxonomy of health care databases is essential to appropriately use these data sources for research purposes. Characteristics of the organizational structure of the specific health care setting, including the model type, financial arrangement, and provider access, have implications for accessing and using this data effectively. Additionally, the benefit coverage environment may affect the utility of health care databases to address specific research questions. Coverage considerations that affect pharmacoepidemiologic research include eligibility, the nature of the pharmacy benefit, and regulatory aspects of the treatment under consideration.

PMAG: Relational Database Definition

NASA Astrophysics Data System (ADS)

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

2002-12-01

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

Creation of the NaSCoRD Database

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

Denman, Matthew R.; Jankovsky, Zachary Kyle; Stuart, William

This report was written as part of a United States Department of Energy (DOE), Office of Nuclear Energy, Advanced Reactor Technologies program funded project to re-create the capabilities of the legacy Centralized Reliability Database Organization (CREDO) database. The CREDO database provided a record of component design and performance documentation across various systems that used sodium as a working fluid. Regaining this capability will allow the DOE complex and the domestic sodium reactor industry to better understand how previous systems were designed and built for use in improving the design and operations of future loops. The contents of this report include:more » overview of the current state of domestic sodium reliability databases; summary of the ongoing effort to improve, understand, and process the CREDO information; summary of the initial efforts to develop a unified sodium reliability database called the Sodium System Component Reliability Database (NaSCoRD); and explain both how potential users can access the domestic sodium reliability databases and the type of information that can be accessed from these databases.« less

MatProps: Material Properties Database and Associated Access Library

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

Durrenberger, J K; Becker, R C; Goto, D M

2007-08-13

Coefficients for analytic constitutive and equation of state models (EOS), which are used by many hydro codes at LLNL, are currently stored in a legacy material database (Steinberg, UCRL-MA-106349). Parameters for numerous materials are available through this database, and include Steinberg-Guinan and Steinberg-Lund constitutive models for metals, JWL equations of state for high explosives, and Mie-Gruniesen equations of state for metals. These constitutive models are used in most of the simulations done by ASC codes today at Livermore. Analytic EOSs are also still used, but have been superseded in many cases by tabular representations in LEOS (http://leos.llnl.gov). Numerous advanced constitutivemore » models have been developed and implemented into ASC codes over the past 20 years. These newer models have more physics and better representations of material strength properties than their predecessors, and therefore more model coefficients. However, a material database of these coefficients is not readily available. Therefore incorporating these coefficients with those of the legacy models into a portable database that could be shared amongst codes would be most welcome. The goal of this paper is to describe the MatProp effort at LLNL to create such a database and associated access library that could be used by codes throughout the DOE complex and beyond. We have written an initial version of the MatProp database and access library and our DOE/ASC code ALE3D (Nichols et. al., UCRL-MA-152204) is able to import information from the database. The database, a link to which exists on the Sourceforge server at LLNL, contains coefficients for many materials and models (see Appendix), and includes material parameters in the following categories--flow stress, shear modulus, strength, damage, and equation of state. Future versions of the Matprop database and access library will include the ability to read and write material descriptions that can be exchanged between codes. It will also include an ability to do unit changes, i.e. have the library return parameters in user-specified unit systems. In addition to these, additional material categories can be added (e.g., phase change kinetics, etc.). The Matprop database and access library is part of a larger set of tools used at LLNL for assessing material model behavior. One of these is MSlib, a shared constitutive material model library. Another is the Material Strength Database (MSD), which allows users to compare parameter fits for specific constitutive models to available experimental data. Together with Matprop, these tools create a suite of capabilities that provide state-of-the-art models and parameters for those models to integrated simulation codes. This document is broken into several appendices. Appendix A contains a code example to retrieve several material coefficients. Appendix B contains the API for the Matprop data access library. Appendix C contains a list of the material names and model types currently available in the Matprop database. Appendix D contains a list of the parameter names for the currently recognized model types. Appendix E contains a full xml description of the material Tantalum.« less

Physiological Information Database (PID)

EPA Science Inventory

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

Center for Nanoscale Science and Technology

National Institute of Standards and Technology Data Gateway

NIST Center for Nanoscale Science and Technology (Program website, free access)   Currently there is no database matching your keyword search, but the NIST Center for Nanoscale Science and Technology website may be of interest. The Center for Nanoscale Science and Technology enables science and industry by providing essential measurement methods, instrumentation, and standards to support all phases of nanotechnology development, from discovery to production.

Beyond Scissors and Glue: Staff Developers Guide Teachers in Piecing Together a Vertically Aligned Curriculum and in Creating a Method to Get This Job Done

ERIC Educational Resources Information Center

Phelps, Vickie

2005-01-01

Layers and layers of curricula stuffed into vinyl binders were the norm in this Texas district until teachers sat down with scissors and glue to create a vertically aligned curriculum. They then created standards-based lessons to support the curriculum and put them into a database readily accessible by all.

MIPS: a database for protein sequences and complete genomes.

PubMed Central

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

1998-01-01

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

Development and Operation of a Database Machine for Online Access and Update of a Large Database.

ERIC Educational Resources Information Center

Rush, James E.

1980-01-01

Reviews the development of a fault tolerant database processor system which replaced OCLC's conventional file system. A general introduction to database management systems and the operating environment is followed by a description of the hardware selection, software processes, and system characteristics. (SW)

Release of ToxCastDB and ExpoCastDB databases

EPA Science Inventory

EPA has released two databases - the Toxicity Forecaster database (ToxCastDB) and a database of chemical exposure studies (ExpoCastDB) - that scientists and the public can use to access chemical toxicity and exposure data. ToxCastDB users can search and download data from over 50...

47 CFR 69.120 - Line information database.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Line information database. 69.120 Section 69...) ACCESS CHARGES Computation of Charges § 69.120 Line information database. (a) A charge that is expressed... from a local exchange carrier database to recover the costs of: (1) The transmission facilities between...

47 CFR 69.120 - Line information database.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Line information database. 69.120 Section 69...) ACCESS CHARGES Computation of Charges § 69.120 Line information database. (a) A charge that is expressed... from a local exchange carrier database to recover the costs of: (1) The transmission facilities between...

47 CFR 69.120 - Line information database.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 3 2014-10-01 2014-10-01 false Line information database. 69.120 Section 69...) ACCESS CHARGES Computation of Charges § 69.120 Line information database. (a) A charge that is expressed... from a local exchange carrier database to recover the costs of: (1) The transmission facilities between...

Tourism through Travel Club: A Database Project

ERIC Educational Resources Information Center

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

2017-01-01

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

47 CFR 69.120 - Line information database.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Line information database. 69.120 Section 69...) ACCESS CHARGES Computation of Charges § 69.120 Line information database. (a) A charge that is expressed... from a local exchange carrier database to recover the costs of: (1) The transmission facilities between...

47 CFR 69.120 - Line information database.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Line information database. 69.120 Section 69...) ACCESS CHARGES Computation of Charges § 69.120 Line information database. (a) A charge that is expressed... from a local exchange carrier database to recover the costs of: (1) The transmission facilities between...

NBIC: Search Ballast Report Database

Science.gov Websites

Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database developed an online database that can be queried through our website. Data are accessible for all coastal Lakes, have been incorporated into the NBIC database as of August 2004. Information on data availability

FIREMON Database

Treesearch

John F. Caratti

2006-01-01

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

Geographic Access to US Neurocritical Care Units Registered with the Neurocritical Care Society

PubMed Central

Shutter, Lori A.; Branas, Charles C.; Adeoye, Opeolu; Albright, Karen C.; Carr, Brendan G.

2018-01-01

Background Neurocritical care provides multidisciplinary, specialized care to critically ill neurological patients, yet an understanding of the proportion of the population able to rapidly access specialized Neurocritical Care Units (NCUs) in the United States is currently unknown. We sought to quantify geographic access to NCUs by state, division, region, and for the US as a whole. In addition, we examined how mode of transportation (ground or air ambulance), and prehospital transport times affected population access to NCUs. Methods Data were obtained from the Neurocritical Care Society (NCS), US Census Bureau and the Atlas and Database of Air Medical Services. Empirically derived prehospital time intervals and validated models estimating prehospital ground and air travel times were used to calculate total prehospital times. A discrete total prehospital time interval was calculated for each small unit of geographic analysis (block group) and block group populations were summed to determine the proportion of Americans able to reach a NCU within discrete time intervals (45, 60, 75, and 90 min). Results are presented for different geographies and for different modes of prehospital transport (ground or air ambulance). Results There are 73 NCUs in the US using ground transportation alone, 12.8, 20.5, 27.4, and 32.6% of the US population are within 45, 60, 75, and 90 min of an NCU, respectively. Use of air ambulances increases access to 36.8, 50.4, 60, and 67.3 within 45, 60, 75, and 90 min, respectively. The Northeast has the highest access rates in the US using ground ambulances and for 45, 60, and 75 min transport times with the addition of air ambulances. At 90 min, the West has the highest access rate. The Southern region has the lowest ground and air access to NCUs access rates for all transport times. Conclusions Using NCUs registered with the NCS, current geographic access to NCUs is limited in the US, and geographic disparities in access to care exist. While additional NCUs may exist beyond those identified by the NCS database, we identify geographies with limited access to NCUs and offer a population-based planning perspective on the further development of the US neurocritical care system. PMID:22045246

Use of the World Wide Web for multisite data collection.

PubMed

Subramanian, A K; McAfee, A T; Getzinger, J P

1997-08-01

As access to the Internet becomes increasingly available, research applications in medicine will increase. This paper describes the use of the Internet, and, more specifically, the World Wide Web (WWW), as a channel of communication between EDs throughout the world and investigators who are interested in facilitating the collection of data from multiple sites. Data entered into user-friendly electronic surveys can be transmitted over the Internet to a database located at the site of the study, rendering geographic separation less of a barrier to the conduction of multisite studies. The electronic format of the data can enable real-time statistical processing while data are stored using existing database technologies. In theory, automated processing of variables within such a database enables early identification of data trends. Methods of ensuring validity, security, and compliance are discussed.

Validity of administrative database code algorithms to identify vascular access placement, surgical revisions, and secondary patency.

PubMed

Al-Jaishi, Ahmed A; Moist, Louise M; Oliver, Matthew J; Nash, Danielle M; Fleet, Jamie L; Garg, Amit X; Lok, Charmaine E

2018-03-01

We assessed the validity of physician billing codes and hospital admission using International Classification of Diseases 10th revision codes to identify vascular access placement, secondary patency, and surgical revisions in administrative data. We included adults (≥18 years) with a vascular access placed between 1 April 2004 and 31 March 2013 at the University Health Network, Toronto. Our reference standard was a prospective vascular access database (VASPRO) that contains information on vascular access type and dates of placement, dates for failure, and any revisions. We used VASPRO to assess the validity of different administrative coding algorithms by calculating the sensitivity, specificity, and positive predictive values of vascular access events. The sensitivity (95% confidence interval) of the best performing algorithm to identify arteriovenous access placement was 86% (83%, 89%) and specificity was 92% (89%, 93%). The corresponding numbers to identify catheter insertion were 84% (82%, 86%) and 84% (80%, 87%), respectively. The sensitivity of the best performing coding algorithm to identify arteriovenous access surgical revisions was 81% (67%, 90%) and specificity was 89% (87%, 90%). The algorithm capturing arteriovenous access placement and catheter insertion had a positive predictive value greater than 90% and arteriovenous access surgical revisions had a positive predictive value of 20%. The duration of arteriovenous access secondary patency was on average 578 (553, 603) days in VASPRO and 555 (530, 580) days in administrative databases. Administrative data algorithms have fair to good operating characteristics to identify vascular access placement and arteriovenous access secondary patency. Low positive predictive values for surgical revisions algorithm suggest that administrative data should only be used to rule out the occurrence of an event.

The AAS Working Group on Accessibility and Disability (WGAD): progress, current projects, and prospects for making astronomy accessible to all

NASA Astrophysics Data System (ADS)

Aarnio, Alicia; Diaz-Merced, Wanda; Monkiewicz, Jacqueline; Knierman, Karen; AAS WGAD

2018-01-01

Representation of astronomers with disabilities is low at the earliest career stages and losses compound with career stage thereafter; single-digit and lower percentage representation statistics are in large part due to systemic barriers to access and failure to accommodate the needs of users of a wide range of abilities. In this presentation, we discuss the barriers currently inhibiting broad access to astronomical publications, databases, and conferences. The WGAD was formed in January of 2016 to work toward removal of these barriers to make our field inclusive of astronomers with disabilities at all career stages. We have productively engaged with publishers and accessibility audits have been performed. Database accessibility evaluation is underway, and we are working with the AAS and other professional organizations on conference accessibility. We are keeping users centrally focused via surveys and user test groups, and holding paramount the overarching idea that meeting present accessibility standards is a necessary but insufficient condition for full access.

The CHARA Array Database

NASA Astrophysics Data System (ADS)

Jones, Jeremy; Schaefer, Gail; ten Brummelaar, Theo; Gies, Douglas; Farrington, Christopher

2018-01-01

We are building a searchable database for the CHARA Array data archive. The Array consists of six telescopes linked together as an interferometer, providing sub-milliarcsecond resolution in the optical and near-infrared. The Array enables a variety of scientific studies, including measuring stellar angular diameters, imaging stellar shapes and surface features, mapping the orbits of close binary companions, and resolving circumstellar environments. This database is one component of an NSF/MSIP funded program to provide open access to the CHARA Array to the broader astronomical community. This archive goes back to 2004 and covers all the beam combiners on the Array. We discuss the current status of and future plans for the public database, and give directions on how to access it.

Mass-Spectrometry Based Structure Identification of "Known-Unknowns" Using the EPA's CompTox Dashboard (ACS Spring National Meeting) 4 of 7

EPA Science Inventory

The CompTox Dashboard is a publicly accessible database provided by the National Center for Computational Toxicology at the US-EPA. The dashboard provides access to a database containing ~720,000 chemicals and integrates a number of our public-facing projects (e.g. ToxCast and Ex...

Ubiquitous Mobile Educational Data Management by Teachers, Students and Parents: Does Technology Change School-Family Communication and Parental Involvement?

ERIC Educational Resources Information Center

Blau, Ina; Hameiri, Mira

2017-01-01

Digital educational data management has become an integral part of school practices. Accessing school database by teachers, students, and parents from mobile devices promotes data-driven educational interactions based on real-time information. This paper analyses mobile access of educational database in a large sample of 429 schools during an…

SciELO, Scientific Electronic Library Online, a Database of Open Access Journals

ERIC Educational Resources Information Center

Meneghini, Rogerio

2013-01-01

This essay discusses SciELO, a scientific journal database operating in 14 countries. It covers over 1000 journals providing open access to full text and table sets of scientometrics data. In Brazil it is responsible for a collection of nearly 300 journals, selected along 15 years as the best Brazilian periodicals in natural and social sciences.…

Using Microsoft Access: A How-To-Do-It Manual for Librarians. How-To-Do-It Manuals for Librarians, Number 76.

ERIC Educational Resources Information Center

Butler, E. Sonny

Much of what librarians do today requires adeptness in creating and manipulating databases. Many new computers bought by libraries every year come packaged with Microsoft Office and include Microsoft Access. This database program features a seamless interface between Microsoft Office's other programs like Word, Excel, and PowerPoint. This book…

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

PubMed

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

2000-01-01

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

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

NASA Astrophysics Data System (ADS)

Trumpy, Eugenio; Manzella, Adele

2017-02-01

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

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

PubMed

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

2018-01-04

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

High-resolution digital brain atlases: a Hubble telescope for the brain.

PubMed

Jones, Edward G; Stone, James M; Karten, Harvey J

2011-05-01

We describe implementation of a method for digitizing at microscopic resolution brain tissue sections containing normal and experimental data and for making the content readily accessible online. Web-accessible brain atlases and virtual microscopes for online examination can be developed using existing computer and internet technologies. Resulting databases, made up of hierarchically organized, multiresolution images, enable rapid, seamless navigation through the vast image datasets generated by high-resolution scanning. Tools for visualization and annotation of virtual microscope slides enable remote and universal data sharing. Interactive visualization of a complete series of brain sections digitized at subneuronal levels of resolution offers fine grain and large-scale localization and quantification of many aspects of neural organization and structure. The method is straightforward and replicable; it can increase accessibility and facilitate sharing of neuroanatomical data. It provides an opportunity for capturing and preserving irreplaceable, archival neurohistological collections and making them available to all scientists in perpetuity, if resources could be obtained from hitherto uninterested agencies of scientific support. © 2011 New York Academy of Sciences.

ReprDB and panDB: minimalist databases with maximal microbial representation.

PubMed

Zhou, Wei; Gay, Nicole; Oh, Julia

2018-01-18

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

Improved Infrastucture for Cdms and JPL Molecular Spectroscopy Catalogues

NASA Astrophysics Data System (ADS)

Endres, Christian; Schlemmer, Stephan; Drouin, Brian; Pearson, John; Müller, Holger S. P.; Schilke, P.; Stutzki, Jürgen

2014-06-01

Over the past years a new infrastructure for atomic and molecular databases has been developed within the framework of the Virtual Atomic and Molecular Data Centre (VAMDC). Standards for the representation of atomic and molecular data as well as a set of protocols have been established which allow now to retrieve data from various databases through one portal and to combine the data easily. Apart from spectroscopic databases such as the Cologne Database for Molecular Spectroscopy (CDMS), the Jet Propulsion Laboratory microwave, millimeter and submillimeter spectral line catalogue (JPL) and the HITRAN database, various databases on molecular collisions (BASECOL, KIDA) and reactions (UMIST) are connected. Together with other groups within the VAMDC consortium we are working on common user tools to simplify the access for new customers and to tailor data requests for users with specified needs. This comprises in particular tools to support the analysis of complex observational data obtained with the ALMA telescope. In this presentation requests to CDMS and JPL will be used to explain the basic concepts and the tools which are provided by VAMDC. In addition a new portal to CDMS will be presented which has a number of new features, in particular meaningful quantum numbers, references linked to data points, access to state energies and improved documentation. Fit files are accessible for download and queries to other databases are possible.

Assessing availability of scientific journals, databases, and health library services in Canadian health ministries: a cross-sectional study

PubMed Central

2013-01-01

Background Evidence-informed health policymaking logically depends on timely access to research evidence. To our knowledge, despite the substantial political and societal pressure to enhance the use of the best available research evidence in public health policy and program decision making, there is no study addressing availability of peer-reviewed research in Canadian health ministries. Objectives To assess availability of (1) a purposive sample of high-ranking scientific journals, (2) bibliographic databases, and (3) health library services in the fourteen Canadian health ministries. Methods From May to October 2011, we conducted a cross-sectional survey among librarians employed by Canadian health ministries to collect information relative to availability of scientific journals, bibliographic databases, and health library services. Availability of scientific journals in each ministry was determined using a sample of 48 journals selected from the 2009 Journal Citation Reports (Sciences and Social Sciences Editions). Selection criteria were: relevance for health policy based on scope note information about subject categories and journal popularity based on impact factors. Results We found that the majority of Canadian health ministries did not have subscription access to key journals and relied heavily on interlibrary loans. Overall, based on a sample of high-ranking scientific journals, availability of journals through interlibrary loans, online and print-only subscriptions was estimated at 63%, 28% and 3%, respectively. Health Canada had a 2.3-fold higher number of journal subscriptions than that of the provincial ministries’ average. Most of the organisations provided access to numerous discipline-specific and multidisciplinary databases. Many organisations provided access to the library resources described through library partnerships or consortia. No professionally led health library environment was found in four out of fourteen Canadian health ministries (i.e. Manitoba Health, Northwest Territories Department of Health and Social Services, Nunavut Department of Health and Social Services and Yukon Department of Health and Social Services). Conclusions There is inequity in availability of peer-reviewed research in the fourteen Canadian health ministries. This inequity could present a problem, as each province and territory is responsible for formulating and implementing evidence-informed health policies and services for the benefit of its population. PMID:23514333

Using a centralised database system and server in the European Union Framework Programme 7 project SEPServer

NASA Astrophysics Data System (ADS)

Heynderickx, Daniel

2012-07-01

The main objective of the SEPServer project (EU FP7 project 262773) is to produce a new tool, which greatly facilitates the investigation of solar energetic particles (SEPs) and their origin: a server providing SEP data, related electromagnetic (EM) observations and analysis methods, a comprehensive catalogue of the observed SEP events, and educational/outreach material on solar eruptions. The project is coordinated by the University of Helsinki. The project will combine data and knowledge from 11 European partners and several collaborating parties from Europe and US. The datasets provided by the consortium partners are collected in a MySQL database (using the ESA Open Data Interface under licence) on a server operated by DH Consultancy, which also hosts a web interface providing browsing, plotting and post-processing and analysis tools developed by the consortium, as well as a Solar Energetic Particle event catalogue. At this stage of the project, a prototype server has been established, which is presently undergoing testing by users inside the consortium. Using a centralized database has numerous advantages, including: homogeneous storage of the data, which eliminates the need for dataset specific file access routines once the data are ingested in the database; a homogeneous set of metadata describing the datasets on both a global and detailed level, allowing for automated access to and presentation of the various data products; standardised access to the data in different programming environments (e.g. php, IDL); elimination of the need to download data for individual data requests. SEPServer will, thus, add value to several space missions and Earth-based observations by facilitating the coordinated exploitation of and open access to SEP data and related EM observations, and promoting correct use of these data for the entire space research community. This will lead to new knowledge on the production and transport of SEPs during solar eruptions and facilitate the development of models for predicting solar radiation storms and calculation of expected fluxes/fluences of SEPs encountered by spacecraft in the interplanetary medium.

Officer Career Development: Longitudinal Sample--Fiscal Year 1982

DTIC Science & Technology

1991-10-01

Those that wish to access the database to conduct additional analyses, link it to or combine it with other databases, enlarge the database for the...link it to or combine it with other databases, enlarge the database for the conduct of trend analyses, etc., will find this data dictionary an...analyses, link it to or combine it with other databases, enlarge the database for the conduct of trend analyses, etc., will find this data dictionary

Scaling Semantic Graph Databases in Size and Performance

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

Morari, Alessandro; Castellana, Vito G.; Villa, Oreste

In this paper we present SGEM, a full software system for accelerating large-scale semantic graph databases on commodity clusters. Unlike current approaches, SGEM addresses semantic graph databases by only employing graph methods at all the levels of the stack. On one hand, this allows exploiting the space efficiency of graph data structures and the inherent parallelism of graph algorithms. These features adapt well to the increasing system memory and core counts of modern commodity clusters. On the other hand, however, these systems are optimized for regular computation and batched data transfers, while graph methods usually are irregular and generate fine-grainedmore » data accesses with poor spatial and temporal locality. Our framework comprises a SPARQL to data parallel C compiler, a library of parallel graph methods and a custom, multithreaded runtime system. We introduce our stack, motivate its advantages with respect to other solutions and show how we solved the challenges posed by irregular behaviors. We present the result of our software stack on the Berlin SPARQL benchmarks with datasets up to 10 billion triples (a triple corresponds to a graph edge), demonstrating scaling in dataset size and in performance as more nodes are added to the cluster.« less

PS1-41: Just Add Data: Implementing an Event-Based Data Model for Clinical Trial Tracking

PubMed Central

Fuller, Sharon; Carrell, David; Pardee, Roy

2012-01-01

Background/Aims Clinical research trials often have similar fundamental tracking needs, despite being quite variable in their specific logic and activities. A model tracking database that can be quickly adapted by a variety of studies has the potential to achieve significant efficiencies in database development and maintenance. Methods Over the course of several different clinical trials, we have developed a database model that is highly adaptable to a variety of projects. Rather than hard-coding each specific event that might occur in a trial, along with its logical consequences, this model considers each event and its parameters to be a data record in its own right. Each event may have related variables (metadata) describing its prerequisites, subsequent events due, associated mailings, or events that it overrides. The metadata for each event is stored in the same record with the event name. When changes are made to the study protocol, no structural changes to the database are needed. One has only to add or edit events and their metadata. Changes in the event metadata automatically determine any related logic changes. In addition to streamlining application code, this model simplifies communication between the programmer and other team members. Database requirements can be phrased as changes to the underlying data, rather than to the application code. The project team can review a single report of events and metadata and easily see where changes might be needed. In addition to benefitting from streamlined code, the front end database application can also implement useful standard features such as automated mail merges and to do lists. Results The event-based data model has proven itself to be robust, adaptable and user-friendly in a variety of study contexts. We have chosen to implement it as a SQL Server back end and distributed Access front end. Interested readers may request a copy of the Access front end and scripts for creating the back end database. Discussion An event-based database with a consistent, robust set of features has the potential to significantly reduce development time and maintenance expense for clinical trial tracking databases.

Direct access to physical therapy for the patient with musculoskeletal disorders, a literature review.

PubMed

Piano, Leonardo; Maselli, Filippo; Viceconti, Antonello; Gianola, Silvia; Ciuro, Aldo

2017-08-01

[Purpose] To present legislation comparing direct and referred access-or other measures-to physical therapy. The focus is on the management of the most burdensome musculoskeletal disorders in terms of regulations, costs, effectiveness, safety and cost-effectiveness. [Methods] Main biomedical databases and gray literature were searched ranging from a global scenario to the analysis of targeted geographical areas and specifically Italy and the Region Piedmont. [Results] legislation on Direct Access highlights inconsistencies among the countries belonging to World Confederation for Physical Therapy. Direct Access could be an effective, safe and efficient organization model for the management of patients with musculoskeletal diseases and seems to be more effective safer and cost effective. [Conclusion] Direct Access is a virtuous model which can help improve the global quality of physical therapy services. Further studies are required to confirm this approach and determine whether the findings of the present overview can be replicated in different countries and healthcare systems.

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

The Danish Inguinal Hernia database.

PubMed

Friis-Andersen, Hans; Bisgaard, Thue

2016-01-01

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. Patients ≥18 years operated for groin hernia. Type and size of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. 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. 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). 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.

Academic medical center libraries on the Web.

PubMed Central

Tannery, N H; Wessel, C B

1998-01-01

Academic medical center libraries are moving towards publishing electronically, utilizing networked technologies, and creating digital libraries. The catalyst for this movement has been the Web. An analysis of academic medical center library Web pages was undertaken to assess the information created and communicated in early 1997. A summary of present uses and suggestions for future applications is provided. A method for evaluating and describing the content of library Web sites was designed. The evaluation included categorizing basic information such as description and access to library services, access to commercial databases, and use of interactive forms. The main goal of the evaluation was to assess original resources produced by these libraries. PMID:9803298

Artificial intelligence techniques for modeling database user behavior

NASA Technical Reports Server (NTRS)

Tanner, Steve; Graves, Sara J.

1990-01-01

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

Annual Review of Database Development: 1992.

ERIC Educational Resources Information Center

Basch, Reva

1992-01-01

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

Report: EPA Needs to Strengthen Financial Database Security Oversight and Monitor Compliance

EPA Pesticide Factsheets

Report #2007-P-00017, March 29, 2007. Weaknesses in how EPA offices monitor databases for known security vulnerabilities, communicate the status of critical system patches, and monitor the access to database administrator accounts and privileges.

GenBank.

PubMed

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

2007-01-01

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

GenBank.

PubMed

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

2005-01-01

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

GenBank.

PubMed

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

2006-01-01

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

CEBS: a comprehensive annotated database of toxicological data

PubMed Central

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

2017-01-01

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

Enabling Scientists: Serving Sci-Tech Library Users with Disabilities.

ERIC Educational Resources Information Center

Coonin, Bryna

2001-01-01

Discusses how librarians in scientific and technical libraries can contribute to an accessible electronic library environment for users with disabilities to ensure independent access to information. Topics include relevant assistive technologies; creating accessible Web pages; monitoring accessibility of electronic databases; preparing accessible…

Charting the complete elastic properties of inorganic crystalline compounds

PubMed Central

de Jong, Maarten; Chen, Wei; Angsten, Thomas; Jain, Anubhav; Notestine, Randy; Gamst, Anthony; Sluiter, Marcel; Krishna Ande, Chaitanya; van der Zwaag, Sybrand; Plata, Jose J; Toher, Cormac; Curtarolo, Stefano; Ceder, Gerbrand; Persson, Kristin A.; Asta, Mark

2015-01-01

The elastic constant tensor of an inorganic compound provides a complete description of the response of the material to external stresses in the elastic limit. It thus provides fundamental insight into the nature of the bonding in the material, and it is known to correlate with many mechanical properties. Despite the importance of the elastic constant tensor, it has been measured for a very small fraction of all known inorganic compounds, a situation that limits the ability of materials scientists to develop new materials with targeted mechanical responses. To address this deficiency, we present here the largest database of calculated elastic properties for inorganic compounds to date. The database currently contains full elastic information for 1,181 inorganic compounds, and this number is growing steadily. The methods used to develop the database are described, as are results of tests that establish the accuracy of the data. In addition, we document the database format and describe the different ways it can be accessed and analyzed in efforts related to materials discovery and design. PMID:25984348

The IRHUM (Isotopic Reconstruction of Human Migration) database - bioavailable strontium isotope ratios for geochemical fingerprinting in France

NASA Astrophysics Data System (ADS)

Willmes, M.; McMorrow, L.; Kinsley, L.; Armstrong, R.; Aubert, M.; Eggins, S.; Falguères, C.; Maureille, B.; Moffat, I.; Grün, R.

2014-03-01

Strontium isotope ratios (87Sr / 86Sr) are a key geochemical tracer used in a wide range of fields including archaeology, ecology, food and forensic sciences. These applications are based on the principle that the Sr isotopic ratios of natural materials reflect the sources of strontium available during their formation. A major constraint for current studies is the lack of robust reference maps to evaluate the source of strontium isotope ratios measured in the samples. Here we provide a new data set of bioavailable Sr isotope ratios for the major geologic units of France, based on plant and soil samples (Pangaea data repository doi:10.1594/PANGAEA.819142). The IRHUM (Isotopic Reconstruction of Human Migration) database is a web platform to access, explore and map our data set. The database provides the spatial context and metadata for each sample, allowing the user to evaluate the suitability of the sample for their specific study. In addition, it allows users to upload and share their own data sets and data products, which will enhance collaboration across the different research fields. This article describes the sampling and analytical methods used to generate the data set and how to use and access the data set through the IRHUM database. Any interpretation of the isotope data set is outside the scope of this publication.

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

PubMed

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.

Analysis Tool Web Services from the EMBL-EBI.

PubMed

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

WMC Database Evaluation. Case Study Report

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

Palounek, Andrea P. T

The WMC Database is ultimately envisioned to hold a collection of experimental data, design information, and information from computational models. This project was a first attempt at using the Database to access experimental data and extract information from it. This evaluation shows that the Database concept is sound and robust, and that the Database, once fully populated, should remain eminently usable for future researchers.

Traditional Medicine Collection Tracking System (TM-CTS): A Database for Ethnobotanically-Driven Drug-Discovery Programs

PubMed Central

Harris, Eric S. J.; Erickson, Sean D.; Tolopko, Andrew N.; Cao, Shugeng; Craycroft, Jane A.; Scholten, Robert; Fu, Yanling; Wang, Wenquan; Liu, Yong; Zhao, Zhongzhen; Clardy, Jon; Shamu, Caroline E.; Eisenberg, David M.

2011-01-01

Aim of the study. Ethnobotanically-driven drug-discovery programs include data related to many aspects of the preparation of botanical medicines, from initial plant collection to chemical extraction and fractionation. The Traditional Medicine-Collection Tracking System (TM-CTS) was created to organize and store data of this type for an international collaborative project involving the systematic evaluation of commonly used Traditional Chinese Medicinal plants. Materials and Methods. The system was developed using domain-driven design techniques, and is implemented using Java, Hibernate, PostgreSQL, Business Intelligence and Reporting Tools (BIRT), and Apache Tomcat. Results. The TM-CTS relational database schema contains over 70 data types, comprising over 500 data fields. The system incorporates a number of unique features that are useful in the context of ethnobotanical projects such as support for information about botanical collection, method of processing, quality tests for plants with existing pharmacopoeia standards, chemical extraction and fractionation, and historical uses of the plants. The database also accommodates data provided in multiple languages and integration with a database system built to support high throughput screening based drug discovery efforts. It is accessed via a web-based application that provides extensive, multi-format reporting capabilities. Conclusions. This new database system was designed to support a project evaluating the bioactivity of Chinese medicinal plants. The software used to create the database is open source, freely available, and could potentially be applied to other ethnobotanically-driven natural product collection and drug-discovery programs. PMID:21420479

Noisy Ocular Recognition Based on Three Convolutional Neural Networks.

PubMed

Lee, Min Beom; Hong, Hyung Gil; Park, Kang Ryoung

2017-12-17

In recent years, the iris recognition system has been gaining increasing acceptance for applications such as access control and smartphone security. When the images of the iris are obtained under unconstrained conditions, an issue of undermined quality is caused by optical and motion blur, off-angle view (the user's eyes looking somewhere else, not into the front of the camera), specular reflection (SR) and other factors. Such noisy iris images increase intra-individual variations and, as a result, reduce the accuracy of iris recognition. A typical iris recognition system requires a near-infrared (NIR) illuminator along with an NIR camera, which are larger and more expensive than fingerprint recognition equipment. Hence, many studies have proposed methods of using iris images captured by a visible light camera without the need for an additional illuminator. In this research, we propose a new recognition method for noisy iris and ocular images by using one iris and two periocular regions, based on three convolutional neural networks (CNNs). Experiments were conducted by using the noisy iris challenge evaluation-part II (NICE.II) training dataset (selected from the university of Beira iris (UBIRIS).v2 database), mobile iris challenge evaluation (MICHE) database, and institute of automation of Chinese academy of sciences (CASIA)-Iris-Distance database. As a result, the method proposed by this study outperformed previous methods.

Retrieving Clinical Evidence: A Comparison of PubMed and Google Scholar for Quick Clinical Searches

PubMed Central

Bejaimal, Shayna AD; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

2013-01-01

Background Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. Objective To compare the performance of searches in PubMed and Google Scholar. Methods We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Results Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; P<.001). Precision was similar in both databases (PubMed: 6%; Google Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; P<.001). Conclusions For quick clinical searches, Google Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles. PMID:23948488

PEP725 Pan European Phenological Database

NASA Astrophysics Data System (ADS)

Koch, E.; Lipa, W.; Ungersböck, M.; Zach-Hermann, S.

2012-04-01

PEP725 is a 5 years project with the main object to promote and facilitate phenological research by delivering a pan European phenological database with an open, unrestricted data access for science, research and education. PEP725 is funded by EUMETNET (the network of European meteorological services), ZAMG and the Austrian ministry for science & research bm:w_f. So far 16 European national meteorological services and 7 partners from different nati-onal phenological network operators have joined PEP725. The data access is very easy via web-access from the homepage www.pep725.eu. Ha-ving accepted the PEP725 data policy and registry the data download can be done by different criteria as for instance the selection of a specific plant or all data from one country. At present more than 300 000 new records are available in the PEP725 data-base coming from 31 European countries and from 8150 stations. For some more sta-tions (154) META data (location and data holder) are provided. Links to the network operators and data owners are also on the webpage in case you have more sophisticated questions about the data. Another objective of PEP725 is to bring together network-operators and scientists by organizing workshops. In April 2012 the second of these workshops will take place on the premises of ZAMG. Invited speakers will give presentations spanning the whole study area of phenology starting from observations to modelling. Quality checking is also a big issue. At the moment we study the literature to find ap-propriate methods.

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.

PubMed

Hardison, Ross C; Chui, David H K; Giardine, Belinda; Riemer, Cathy; Patrinos, George P; Anagnou, Nicholas; Miller, Webb; Wajcman, Henri

2002-03-01

We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci. Copyright 2002 Wiley-Liss, Inc.

Implementation of an interactive database interface utilizing HTML, PHP, JavaScript, and MySQL in support of water quality assessments in the Northeastern North Carolina Pasquotank Watershed

NASA Astrophysics Data System (ADS)

Guion, A., Jr.; Hodgkins, H.

2015-12-01

The Center of Excellence in Remote Sensing Education and Research (CERSER) has implemented three research projects during the summer Research Experience for Undergraduates (REU) program gathering water quality data for local waterways. The data has been compiled manually utilizing pen and paper and then entered into a spreadsheet. With the spread of electronic devices capable of interacting with databases, the development of an electronic method of entering and manipulating the water quality data was pursued during this project. This project focused on the development of an interactive database to gather, display, and analyze data collected from local waterways. The database and entry form was built in MySQL on a PHP server allowing participants to enter data from anywhere Internet access is available. This project then researched applying this data to the Google Maps site to provide labeling and information to users. The NIA server at http://nia.ecsu.edu is used to host the application for download and for storage of the databases. Water Quality Database Team members included the authors plus Derek Morris Jr., Kathryne Burton and Mr. Jeff Wood as mentor.

Database constraints applied to metabolic pathway reconstruction tools.

PubMed

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

2014-01-01

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

Creating Access to Data of Worldwide Volcanic Unrest

NASA Astrophysics Data System (ADS)

Venezky, D. Y.; Newhall, C. G.; Malone, S. D.

2003-12-01

We are creating a pilot database (WOVOdat - the World Organization of Volcano Observatories database) using an open source database and content generation software, allowing web access to data of worldwide volcanic seismicity, ground deformation, fumarolic activity, and other changes within or adjacent to a volcanic system. After three years of discussions with volcano observatories of the WOVO community and institutional databases such as IRIS, UNAVCO, and the Smithsonian's Global Volcanism Program about how to link global data of volcanic unrest for use during crisis situations and for research, we are now developing the pilot database. We already have created the core tables and have written simple queries that access some of the available data using pull-down menus on a website. Over the next year, we plan to complete schema realization, expand querying capabilities, and then open the pilot database for a multi-year data-loading process. Many of the challenges we are encountering are common to multidisciplinary projects and include determining standard data formats, choosing levels of data detail (raw vs. minimally processed data, summary intervals vs. continuous data, etc.), and organizing the extant but variable data into a useable schema. Additionally, we are working on how best to enter the varied data into the database (scripts for digital data and web-entry tools for non-digital data) and what standard sets of queries are most important. An essential during an evolving volcanic crisis would be: `Has any volcano shown the behavior being observed here and what happened?'. We believe that with a systematic aggregation of all datasets on volcanic unrest, we should be able to find patterns that were previously inaccessible or unrecognized. The second WOVOdat workshop in 2002 provided a recent forum for discussion of data formats, database access, and schemas. The formats and units for the discussed parameters can be viewed at http://www.wovo.org/WOVOdat/parameters.htm. Comments, suggestions, and participation in all aspects of the WOVOdat project are welcome and appreciated.

The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource

PubMed Central

2012-01-01

Background Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species. Description The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers (“Isolate Accession”), the first five of which correspond to the collection site (“Environmental Accession”). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages. Conclusions HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/. PMID:23095476

DIMA.Tools: An R package for working with the database for inventory, monitoring, and assessment

USDA-ARS?s Scientific Manuscript database

The Database for Inventory, Monitoring, and Assessment (DIMA) is a Microsoft Access database used to collect, store and summarize monitoring data. This database is used by both local and national monitoring efforts within the National Park Service, the Forest Service, the Bureau of Land Management, ...

The Web-Database Connection Tools for Sharing Information on the Campus Intranet.

ERIC Educational Resources Information Center

Thibeault, Nancy E.

This paper evaluates four tools for creating World Wide Web pages that interface with Microsoft Access databases: DB Gateway, Internet Database Assistant (IDBA), Microsoft Internet Database Connector (IDC), and Cold Fusion. The system requirements and features of each tool are discussed. A sample application, "The Virtual Help Desk"…

Database Systems and Oracle: Experiences and Lessons Learned

ERIC Educational Resources Information Center

Dunn, Deborah

2005-01-01

In a tight job market, IT professionals with database experience are likely to be in great demand. Companies need database personnel who can help improve access to and security of data. The events of September 11 have increased business' awareness of the need for database security, backup, and recovery procedures. It is our responsibility to…

Implementation of a data management software system for SSME test history data

NASA Technical Reports Server (NTRS)

Abernethy, Kenneth

1986-01-01

The implementation of a software system for managing Space Shuttle Main Engine (SSME) test/flight historical data is presented. The software system uses the database management system RIM7 for primary data storage and routine data management, but includes several FORTRAN programs, described here, which provide customized access to the RIM7 database. The consolidation, modification, and transfer of data from the database THIST, to the RIM7 database THISRM is discussed. The RIM7 utility modules for generating some standard reports from THISRM and performing some routine updating and maintenance are briefly described. The FORTRAN accessing programs described include programs for initial loading of large data sets into the database, capturing data from files for database inclusion, and producing specialized statistical reports which cannot be provided by the RIM7 report generator utility. An expert system tutorial, constructed using the expert system shell product INSIGHT2, is described. Finally, a potential expert system, which would analyze data in the database, is outlined. This system could use INSIGHT2 as well and would take advantage of RIM7's compatibility with the microcomputer database system RBase 5000.