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

PubMed

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

1995-01-01

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

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

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

PubMed

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

2012-07-01

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

Building an Integrated Environment for Multimedia

NASA Technical Reports Server (NTRS)

1997-01-01

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

JICST Factual Database(1)

NASA Astrophysics Data System (ADS)

Kurosawa, Shinji

The outline of JICST factual database (JOIS-F), which JICST has started from January, 1988, and its online service are described in this paper. First, the author mentions the circumstances from 1973, when its planning was started, to the present, and its relation to "Project by Special Coordination Founds for Promoting Science and Technology". Secondly, databases, which are now under development aiming to start its services from fiscal 1988 or fiscal 1989, of DNA, metallic material intensity, crystal structure, chemical substance regulations, and so forth, are described. Lastly, its online service is briefly explained.

The CMS DBS query language

NASA Astrophysics Data System (ADS)

Kuznetsov, Valentin; Riley, Daniel; Afaq, Anzar; Sekhri, Vijay; Guo, Yuyi; Lueking, Lee

2010-04-01

The CMS experiment has implemented a flexible and powerful system enabling users to find data within the CMS physics data catalog. The Dataset Bookkeeping Service (DBS) comprises a database and the services used to store and access metadata related to CMS physics data. To this, we have added a generalized query system in addition to the existing web and programmatic interfaces to the DBS. This query system is based on a query language that hides the complexity of the underlying database structure by discovering the join conditions between database tables. This provides a way of querying the system that is simple and straightforward for CMS data managers and physicists to use without requiring knowledge of the database tables or keys. The DBS Query Language uses the ANTLR tool to build the input query parser and tokenizer, followed by a query builder that uses a graph representation of the DBS schema to construct the SQL query sent to underlying database. We will describe the design of the query system, provide details of the language components and overview of how this component fits into the overall data discovery system architecture.

Integrating heterogeneous databases in clustered medic care environments using object-oriented technology

NASA Astrophysics Data System (ADS)

Thakore, Arun K.; Sauer, Frank

1994-05-01

The organization of modern medical care environments into disease-related clusters, such as a cancer center, a diabetes clinic, etc., has the side-effect of introducing multiple heterogeneous databases, often containing similar information, within the same organization. This heterogeneity fosters incompatibility and prevents the effective sharing of data amongst applications at different sites. Although integration of heterogeneous databases is now feasible, in the medical arena this is often an ad hoc process, not founded on proven database technology or formal methods. In this paper we illustrate the use of a high-level object- oriented semantic association method to model information found in different databases into an integrated conceptual global model that integrates the databases. We provide examples from the medical domain to illustrate an integration approach resulting in a consistent global view, without attacking the autonomy of the underlying databases.

Heterogeneous distributed databases: A case study

NASA Technical Reports Server (NTRS)

Stewart, Tracy R.; Mukkamala, Ravi

1991-01-01

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

DITOP: drug-induced toxicity related protein database.

PubMed

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

2007-07-01

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

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.

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

PubMed Central

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

1998-01-01

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

Monitoring outcomes with relational databases: does it improve quality of care?

PubMed

Clemmer, Terry P

2004-12-01

There are 3 key ingredients in improving quality of medial care: 1) using a scientific process of improvement, 2) executing the process at the lowest possible level in the organization, and 3) measuring the results of any change reliably. Relational databases when used within these guidelines are of great value in these efforts if they contain reliable information that is pertinent to the project and used in a scientific process of quality improvement by a front line team. Unfortunately, the data are frequently unreliable and/or not pertinent to the local process and is used by persons at very high levels in the organization without a scientific process and without reliable measurement of the outcome. Under these circumstances the effectiveness of relational databases in improving care is marginal at best, frequently wasteful and has the potential to be harmful. This article explores examples of these concepts.

Grant-Funded Research in Environmental Economics

EPA Pesticide Factsheets

This database contains summaries of these awards, as well as project reports and publications, developed under environmental economics-related grants made by EPA's Office of Research and Development, NCEE and their partners since 1990.

SchizConnect: Mediating Neuroimaging Databases on Schizophrenia and Related Disorders for Large-Scale Integration

PubMed Central

Wang, Lei; Alpert, Kathryn I.; Calhoun, Vince D.; Cobia, Derin J.; Keator, David B.; King, Margaret D.; Kogan, Alexandr; Landis, Drew; Tallis, Marcelo; Turner, Matthew D.; Potkin, Steven G.; Turner, Jessica A.; Ambite, Jose Luis

2015-01-01

SchizConnect (www.schizconnect.org) is built to address the issues of multiple data repositories in schizophrenia neuroimaging studies. It includes a level of mediation—translating across data sources—so that the user can place one query, e.g. for diffusion images from male individuals with schizophrenia, and find out from across participating data sources how many datasets there are, as well as downloading the imaging and related data. The current version handles the Data Usage Agreements across different studies, as well as interpreting database-specific terminologies into a common framework. New data repositories can also be mediated to bring immediate access to existing datasets. Compared with centralized, upload data sharing models, SchizConnect is a unique, virtual database with a focus on schizophrenia and related disorders that can mediate live data as information are being updated at each data source. It is our hope that SchizConnect can facilitate testing new hypotheses through aggregated datasets, promoting discovery related to the mechanisms underlying schizophrenic dysfunction. PMID:26142271

Maximizing the use of Special Olympics International's Healthy Athletes database: A call to action.

PubMed

Lloyd, Meghann; Foley, John T; Temple, Viviene A

2018-02-01

There is a critical need for high-quality population-level data related to the health of individuals with intellectual disabilities. For more than 15 years Special Olympics International has been conducting free Healthy Athletes screenings at local, national and international events. The Healthy Athletes database is the largest known international database specifically on the health of people with intellectual disabilities; however, it is relatively under-utilized by the research community. A consensus meeting with two dozen North American researchers, stakeholders, clinicians and policymakers took place in Toronto, Canada. The purpose of the meeting was to: 1) establish the perceived utility of the database, and 2) to identify and prioritize 3-5 specific priorities related to using the Healthy Athletes database to promote the health of individuals with intellectual disabilities. There was unanimous agreement from the meeting participants that this database represents an immense opportunity both from the data already collected, and data that will be collected in the future. The 3 top priorities for the database were deemed to be: 1) establish the representativeness of data collected on Special Olympics athletes compared to the general population with intellectual disabilities, 2) create a scientific advisory group for Special Olympics International, and 3) use the data to improve Special Olympics programs around the world. The Special Olympics Healthy Athletes database includes data not found in any other source and should be used, in partnership with Special Olympics International, by researchers to significantly increase our knowledge and understanding of the health of individuals with intellectual disabilities. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Query by forms: User-oriented relational database retrieving system and its application in analysis of experiment data

NASA Astrophysics Data System (ADS)

Skotniczny, Zbigniew

1989-12-01

The Query by Forms (QbF) system is a user-oriented interactive tool for querying large relational database with minimal queries difinition cost. The system was worked out under the assumption that user's time and effort for defining needed queries is the most severe bottleneck. The system may be applied in any Rdb/VMS databases system and is recommended for specific information systems of any project where end-user queries cannot be foreseen. The tool is dedicated to specialist of an application domain who have to analyze data maintained in database from any needed point of view, who do not need to know commercial databases languages. The paper presents the system developed as a compromise between its functionality and usability. User-system communication via a menu-driven "tree-like" structure of screen-forms which produces a query difinition and execution is discussed in detail. Output of query results (printed reports and graphics) is also discussed. Finally the paper shows one application of QbF to a HERA-project.

Ontological interpretation of biomedical database content.

PubMed

Santana da Silva, Filipe; Jansen, Ludger; Freitas, Fred; Schulz, Stefan

2017-06-26

Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology. The first three models interpret database entries as individuals (IND), defined classes (SUBC), and classes with dispositions (DISP), respectively; the fourth model (HYBR) is a combination of SUBC and DISP. For the evaluation of these four models, we consider (i) database content retrieval, using ontologies as query vocabulary; (ii) information completeness; and, (iii) DL complexity and decidability. The models were tested under these criteria against four competency questions (CQs). IND does not raise any ontological claim, besides asserting the existence of sample individuals and relations among them. Modelling patterns have to be created for each type of annotation referent. SUBC is interpreted regarding maximally fine-grained defined subclasses under the classes referred to by the data. DISP attempts to extract truly ontological statements from the database records, claiming the existence of dispositions. HYBR is a hybrid of SUBC and DISP and is more parsimonious regarding expressiveness and query answering complexity. For each of the four models, the four CQs were submitted as DL queries. This shows the ability to retrieve individuals with IND, and classes in SUBC and HYBR. DISP does not retrieve anything because the axioms with disposition are embedded in General Class Inclusion (GCI) statements. Ambiguity of biological database content is addressed by a method that identifies implicit knowledge behind semantic annotations in biological databases and grounds it in an expressive upper-level ontology. The result is a seamless representation of database structure, content and annotations as OWL models.

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

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

Ball, G.; Kuznetsov, V.; Evans, D.

We present the Data Aggregation System, a system for information retrieval and aggregation from heterogenous sources of relational and non-relational data for the Compact Muon Solenoid experiment on the CERN Large Hadron Collider. The experiment currently has a number of organically-developed data sources, including front-ends to a number of different relational databases and non-database data services which do not share common data structures or APIs (Application Programming Interfaces), and cannot at this stage be readily converged. DAS provides a single interface for querying all these services, a caching layer to speed up access to expensive underlying calls and the abilitymore » to merge records from different data services pertaining to a single primary key.« less

Analysis of Patent Databases Using VxInsight

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

BOYACK,KEVIN W.; WYLIE,BRIAN N.; DAVIDSON,GEORGE S.

2000-12-12

We present the application of a new knowledge visualization tool, VxInsight, to the mapping and analysis of patent databases. Patent data are mined and placed in a database, relationships between the patents are identified, primarily using the citation and classification structures, then the patents are clustered using a proprietary force-directed placement algorithm. Related patents cluster together to produce a 3-D landscape view of the tens of thousands of patents. The user can navigate the landscape by zooming into or out of regions of interest. Querying the underlying database places a colored marker on each patent matching the query. Automatically generatedmore » labels, showing landscape content, update continually upon zooming. Optionally, citation links between patents may be shown on the landscape. The combination of these features enables powerful analyses of patent databases.« less

A mapping review of the literature on UK-focused health and social care databases.

PubMed

Cooper, Chris; Rogers, Morwenna; Bethel, Alison; Briscoe, Simon; Lowe, Jenny

2015-03-01

Bibliographic databases are a day-to-day tool of the researcher: they offer the researcher easy and organised access to knowledge, but how much is actually known about the databases on offer? The focus of this paper is UK health and social care databases. These databases are often small, specialised by topic, and provide a complementary literature to the large, international databases. There is, however, good evidence that these databases are overlooked in systematic reviews, perhaps because little is known about what they can offer. To systematically locate and map, published and unpublished literature on the key UK health and social care bibliographic databases. Systematic searching and mapping. Two hundred and forty-two items were identified which specifically related to the 24 of the 34 databases under review. There is little published or unpublished literature specifically analysing the key UK health and social care databases. Since several UK databases have closed, others are at risk, and some are overlooked in reviews, better information is required to enhance our knowledge. Further research on UK health and social care databases is required. This paper suggests the need to develop the evidence base through a series of case studies on each of the databases. © 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Journal.

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1996

1996-01-01

This annotated list includes media-related resources classified under the following headings: artificial intelligence and robotics, CD-ROM, computer-assisted instruction, databases and online searching, distance education, educational research, educational technology, electronic publishing, information science and technology, instructional design…

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1997

1997-01-01

This annotated list includes media-related resources classified under the following headings: artificial intelligence and robotics, CD-ROM, computer-assisted instruction, databases and online searching, distance education, educational research, educational technology, electronic publishing, information science and technology, instructional design…

A Foot-Mounted Inertial Measurement Unit (IMU) Positioning Algorithm Based on Magnetic Constraint

PubMed Central

Zou, Jiaheng

2018-01-01

With the development of related applications, indoor positioning techniques have been more and more widely developed. Based on Wi-Fi, Bluetooth low energy (BLE) and geomagnetism, indoor positioning techniques often rely on the physical location of fingerprint information. The focus and difficulty of establishing the fingerprint database are in obtaining a relatively accurate physical location with as little given information as possible. This paper presents a foot-mounted inertial measurement unit (IMU) positioning algorithm under the loop closure constraint based on magnetic information. It can provide relatively reliable position information without maps and geomagnetic information and provides a relatively accurate coordinate for the collection of a fingerprint database. In the experiment, the features extracted by the multi-level Fourier transform method proposed in this paper are validated and the validity of loop closure matching is tested with a RANSAC-based method. Moreover, the loop closure detection results show that the cumulative error of the trajectory processed by the graph optimization algorithm is significantly suppressed, presenting a good accuracy. The average error of the trajectory under loop closure constraint is controlled below 2.15 m. PMID:29494542

A Foot-Mounted Inertial Measurement Unit (IMU) Positioning Algorithm Based on Magnetic Constraint.

PubMed

Wang, Yan; Li, Xin; Zou, Jiaheng

2018-03-01

With the development of related applications, indoor positioning techniques have been more and more widely developed. Based on Wi-Fi, Bluetooth low energy (BLE) and geomagnetism, indoor positioning techniques often rely on the physical location of fingerprint information. The focus and difficulty of establishing the fingerprint database are in obtaining a relatively accurate physical location with as little given information as possible. This paper presents a foot-mounted inertial measurement unit (IMU) positioning algorithm under the loop closure constraint based on magnetic information. It can provide relatively reliable position information without maps and geomagnetic information and provides a relatively accurate coordinate for the collection of a fingerprint database. In the experiment, the features extracted by the multi-level Fourier transform method proposed in this paper are validated and the validity of loop closure matching is tested with a RANSAC-based method. Moreover, the loop closure detection results show that the cumulative error of the trajectory processed by the graph optimization algorithm is significantly suppressed, presenting a good accuracy. The average error of the trajectory under loop closure constraint is controlled below 2.15 m.

Risk factors for manipulation after total knee arthroplasty: a pooled electronic health record database study.

PubMed

Pfefferle, Kiel J; Shemory, Scott T; Dilisio, Matthew F; Fening, Stephen D; Gradisar, Ian M

2014-10-01

A commercially available software platform, Explorys (Explorys, Inc., Cleveland, OH), was used to mine a pooled electronic healthcare database consisting of the medical records of more than 27 million patients. A total of 229,420 patients had undergone a total knee arthroplasty; 3470 (1.51%) patients were identified to have undergone manipulation under anesthesia. Individual risk factors of being female, African American race, age less than 60, BMI >30 and nicotine dependence were determined to have relative risk of 1.25, 2.20, 3.46, 1.33 and 1.32 respectively. Depressive disorder, diabetes mellitus, opioid abuse/dependence and rheumatoid arthritis were not significant risk factors. African Americans under the age of 60 at time of TKA had the greatest incidence of MUA (5.17%) and relative risk of 3.73 (CI: 3.36, 4.13). Copyright © 2014 Elsevier Inc. All rights reserved.

How Do You Like Your Science, Wet or Dry? How Two Lab Experiences Influence Student Understanding of Science Concepts and Perceptions of Authentic Scientific Practice.

PubMed

Munn, Maureen; Knuth, Randy; Van Horne, Katie; Shouse, Andrew W; Levias, Sheldon

2017-01-01

This study examines how two kinds of authentic research experiences related to smoking behavior-genotyping human DNA (wet lab) and using a database to test hypotheses about factors that affect smoking behavior (dry lab)-influence students' perceptions and understanding of scientific research and related science concepts. The study used pre and post surveys and a focus group protocol to compare students who conducted the research experiences in one of two sequences: genotyping before database and database before genotyping. Students rated the genotyping experiment to be more like real science than the database experiment, in spite of the fact that they associated more scientific tasks with the database experience than genotyping. Independent of the order of completing the labs, students showed gains in their understanding of science concepts after completion of the two experiences. There was little change in students' attitudes toward science pre to post, as measured by the Scientific Attitude Inventory II. However, on the basis of their responses during focus groups, students developed more sophisticated views about the practices and nature of science after they had completed both research experiences, independent of the order in which they experienced them. © 2017 M. Munn et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

Behavioral ecology of captive species: using behavioral adaptations to assess and enhance welfare of nonhuman zoo animals.

PubMed

Koene, Paul

2013-01-01

This project aimed to estimate a species' adaptations in nature and in captivity, assess welfare, suggest environmental changes, and find species characteristics that underlie welfare problems in nonhuman animals in the zoo. First, the current status of zoo animal welfare assessment was reviewed, and the behavioral ecology approach was outlined. In this approach, databases of species characteristics were developed using (a) literature of natural behavior and (b) captive behavior. Species characteristics were grouped in 8 functional behavioral ecological fitness-related categories: space, time, metabolic, safety, reproductive, comfort, social, and information adaptations. Assessments of the strength of behavioral adaptations in relation to environmental demands were made based on the results available from the literature. The databases with literature at the species level were coupled with databases of (c) behavioral observations and (d) welfare assessments under captive conditions. Observation and welfare assessment methods were adapted from the animal on the farm realm and applied to zoo species. It was expected that the comparison of the repertoire of behaviors in natural and captive environments would highlight welfare problems, provide solutions to welfare problems by environmental changes, and identify species characteristics underlying zoo animal welfare problems.

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.

SchizConnect: Mediating neuroimaging databases on schizophrenia and related disorders for large-scale integration.

PubMed

Wang, Lei; Alpert, Kathryn I; Calhoun, Vince D; Cobia, Derin J; Keator, David B; King, Margaret D; Kogan, Alexandr; Landis, Drew; Tallis, Marcelo; Turner, Matthew D; Potkin, Steven G; Turner, Jessica A; Ambite, Jose Luis

2016-01-01

SchizConnect (www.schizconnect.org) is built to address the issues of multiple data repositories in schizophrenia neuroimaging studies. It includes a level of mediation--translating across data sources--so that the user can place one query, e.g. for diffusion images from male individuals with schizophrenia, and find out from across participating data sources how many datasets there are, as well as downloading the imaging and related data. The current version handles the Data Usage Agreements across different studies, as well as interpreting database-specific terminologies into a common framework. New data repositories can also be mediated to bring immediate access to existing datasets. Compared with centralized, upload data sharing models, SchizConnect is a unique, virtual database with a focus on schizophrenia and related disorders that can mediate live data as information is being updated at each data source. It is our hope that SchizConnect can facilitate testing new hypotheses through aggregated datasets, promoting discovery related to the mechanisms underlying schizophrenic dysfunction. Copyright © 2015 Elsevier Inc. All rights reserved.

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity

PubMed Central

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping). PMID:29065644

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity.

PubMed

Zhang, Yinsheng; Zhang, Guoming; Shang, Qian

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping).

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.

ELSI Bibliography: Ethical legal and social implications of the Human Genome Project

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

Yesley, M.S.

This second edition of the ELSI Bibliography provides a current and comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. Since the first edition of the ELSI Bibliography was printed last year, new publications and earlier ones identified by additional searching have doubled our computer database of ELSI publications to over 5600 entries. The second edition of the ELSI Bibliography reflects this growth of the underlying computer database. Researchers should note that an extensive collection of publications in the database is available for public use atmore » the General Law Library of Los Alamos National Laboratory (LANL).« less

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.

NRLMSISE-00 Empirical Model of the Atmosphere: Statistical Comparisons and Scientific Issues

NASA Technical Reports Server (NTRS)

Aikin, A. C.; Picone, J. M.; Hedin, A. E.; Drob, D. P.

2001-01-01

The new NRLMSISE-00 model and the associated NRLMSIS database now include the following data: (1) total mass density from satellite accelerometers and from orbit determination, including the Jacchia and Barlier data; (2) temperature from incoherent scatter radar, and; (3) molecular oxygen number density, [O2], from solar ultraviolet occultation aboard the Solar Maximum Mission (SMM). A new component, 'anomalous oxygen,' allows for appreciable O(+) and hot atomic oxygen contributions to the total mass density at high altitudes and applies primarily to drag estimation above 500 km. Extensive tables compare our entire database to the NRLMSISE-00, MSISE-90, and Jacchia-70 models for different altitude bands and levels of geomagnetic activity. We also investigate scientific issues related to the new data sets in the NRLMSIS database. Especially noteworthy is the solar activity dependence of the Jacchia data, with which we investigate a large O(+) contribution to the total mass density under the combination of summer, low solar activity, high latitudes, and high altitudes. Under these conditions, except at very low solar activity, the Jacchia data and the Jacchia-70 model indeed show a significantly higher total mass density than does MSISE-90. However, under the corresponding winter conditions, the MSIS-class models represent a noticeable improvement relative to Jacchia-70 over a wide range of F(sub 10.7). Considering the two regimes together, NRLMSISE-00 achieves an improvement over both MSISE-90 and Jacchia-70 by incorporating advantages of each.

Current Readings on the Iran-Iraq Conflict and Its Effects on U.S. Foreign Relations and Policy.

ERIC Educational Resources Information Center

El-Sherbini, Magda

1989-01-01

Provides background on the Iran-Iraq conflict and suggests readings dating from 1980 to 1988 in both English and Arabic which are classified under seven broad categories: the roots of the conflict; Iran-United States relations; the American hostage crisis; the Iran-Contra affair; periodicals and indexes; online databases; and bibliographies. (105…

Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension

USDA-ARS?s Scientific Manuscript database

The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, bovine WGS databases comprised of related influential sires from relatively few breeds tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our ...

On the Future of Thermochemical Databases, the Development of Solution Models and the Practical Use of Computational Thermodynamics in Volcanology, Geochemistry and Petrology: Can Innovations of Modern Data Science Democratize an Oligarchy?

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2014-12-01

Computational thermodynamics (CT) has now become an essential tool of petrologic and geochemical research. CT is the basis for the construction of phase diagrams, the application of geothermometers and geobarometers, the equilibrium speciation of solutions, the construction of pseudosections, calculations of mass transfer between minerals, melts and fluids, and, it provides a means of estimating materials properties for the evaluation of constitutive relations in fluid dynamical simulations. The practical application of CT to Earth science problems requires data. Data on the thermochemical properties and the equation of state of relevant materials, and data on the relative stability and partitioning of chemical elements between phases as a function of temperature and pressure. These data must be evaluated and synthesized into a self consistent collection of theoretical models and model parameters that is colloquially known as a thermodynamic database. Quantitative outcomes derived from CT reply on the existence, maintenance and integrity of thermodynamic databases. Unfortunately, the community is reliant on too few such databases, developed by a small number of research groups, and mostly under circumstances where refinement and updates to the database lag behind or are unresponsive to need. Given the increasing level of reliance on CT calculations, what is required is a paradigm shift in the way thermodynamic databases are developed, maintained and disseminated. They must become community resources, with flexible and assessable software interfaces that permit easy modification, while at the same time maintaining theoretical integrity and fidelity to the underlying experimental observations. Advances in computational and data science give us the tools and resources to address this problem, allowing CT results to be obtained at the speed of thought, and permitting geochemical and petrological intuition to play a key role in model development and calibration.

Application of new type of distributed multimedia databases to networked electronic museum

NASA Astrophysics Data System (ADS)

Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

1999-01-01

Recently, various kinds of multimedia application systems have actively been developed based on the achievement of advanced high sped communication networks, computer processing technologies, and digital contents-handling technologies. Under this background, this paper proposed a new distributed multimedia database system which can effectively perform a new function of cooperative retrieval among distributed databases. The proposed system introduces a new concept of 'Retrieval manager' which functions as an intelligent controller so that the user can recognize a set of distributed databases as one logical database. The logical database dynamically generates and performs a preferred combination of retrieving parameters on the basis of both directory data and the system environment. Moreover, a concept of 'domain' is defined in the system as a managing unit of retrieval. The retrieval can effectively be performed by cooperation of processing among multiple domains. Communication language and protocols are also defined in the system. These are used in every action for communications in the system. A language interpreter in each machine translates a communication language into an internal language used in each machine. Using the language interpreter, internal processing, such internal modules as DBMS and user interface modules can freely be selected. A concept of 'content-set' is also introduced. A content-set is defined as a package of contents. Contents in the content-set are related to each other. The system handles a content-set as one object. The user terminal can effectively control the displaying of retrieved contents, referring to data indicating the relation of the contents in the content- set. In order to verify the function of the proposed system, a networked electronic museum was experimentally built. The results of this experiment indicate that the proposed system can effectively retrieve the objective contents under the control to a number of distributed domains. The result also indicate that the system can effectively work even if the system becomes large.

Soil Organic Carbon for Global Benefits - assessing potential SOC increase under SLM technologies worldwide and evaluating tradeoffs and gains of upscaling SLM technologies

NASA Astrophysics Data System (ADS)

Wolfgramm, Bettina; Hurni, Hans; Liniger, Hanspeter; Ruppen, Sebastian; Milne, Eleanor; Bader, Hans-Peter; Scheidegger, Ruth; Amare, Tadele; Yitaferu, Birru; Nazarmavloev, Farrukh; Conder, Malgorzata; Ebneter, Laura; Qadamov, Aslam; Shokirov, Qobiljon; Hergarten, Christian; Schwilch, Gudrun

2013-04-01

There is a fundamental mutual interest between enhancing soil organic carbon (SOC) in the world's soils and the objectives of the major global environmental conventions (UNFCCC, UNCBD, UNCCD). While there is evidence at the case study level that sustainable land management (SLM) technologies increase SOC stocks and SOC related benefits, there is no quantitative data available on the potential for increasing SOC benefits from different SLM technologies and especially from case studies in the developing countries, and a clear understanding of the trade-offs related to SLM up-scaling is missing. This study aims at assessing the potential increase of SOC under SLM technologies worldwide, evaluating tradeoffs and gains in up-scaling SLM for case studies in Tajikistan, Ethiopia and Switzerland. It makes use of the SLM technologies documented in the online database of the World Overview of Conservation Approaches and Technologies (WOCAT). The study consists of three components: 1) Identifying SOC benefits contributing to the major global environmental issues for SLM technologies worldwide as documented in the WOCAT global database 2) Validation of SOC storage potentials and SOC benefit predictions for SLM technologies from the WOCAT database using results from existing comparative case studies at the plot level, using soil spectral libraries and standardized documentations of ecosystem service from the WOCAT database. 3) Understanding trade-offs and win-win scenarios of up-scaling SLM technologies from the plot to the household and landscape level using material flow analysis. This study builds on the premise that the most promising way to increase benefits from land management is to consider already existing sustainable strategies. Such SLM technologies from all over the world documented are accessible in a standardized way in the WOCAT online database. The study thus evaluates SLM technologies from the WOCAT database by calculating the potential SOC storage increase and related benefits by comparing SOC estimates before-and-after establishment of the SLM technology. These results are validated using comparative case studies of plots with-and-without SLM technologies (existing SLM systems versus surrounding, degrading systems). In view of upscaling SLM technologies, it is crucial to understand tradeoffs and gains supporting or hindering the further spread. Systemic biomass management analysis using material flow analysis allows quantifying organic carbon flows and storages for different land management options at the household, but also at landscape level. The study shows results relevant for science, policy and practice for accounting, monitoring and evaluating SOC related ecosystem services: - A comprehensive methodology for SLM impact assessments allowing quantification of SOC storage and SOC related benefits under different SLM technologies, and - Improved understanding of upscaling options for SLM technologies and tradeoffs as well as win-win opportunities for biomass management, SOC content increase, and ecosystem services improvement at the plot and household level.

Global Distribution of Outbreaks of Water-Associated Infectious Diseases

PubMed Central

Yang, Kun; LeJeune, Jeffrey; Alsdorf, Doug; Lu, Bo; Shum, C. K.; Liang, Song

2012-01-01

Background Water plays an important role in the transmission of many infectious diseases, which pose a great burden on global public health. However, the global distribution of these water-associated infectious diseases and underlying factors remain largely unexplored. Methods and Findings Based on the Global Infectious Disease and Epidemiology Network (GIDEON), a global database including water-associated pathogens and diseases was developed. In this study, reported outbreak events associated with corresponding water-associated infectious diseases from 1991 to 2008 were extracted from the database. The location of each reported outbreak event was identified and geocoded into a GIS database. Also collected in the GIS database included geo-referenced socio-environmental information including population density (2000), annual accumulated temperature, surface water area, and average annual precipitation. Poisson models with Bayesian inference were developed to explore the association between these socio-environmental factors and distribution of the reported outbreak events. Based on model predictions a global relative risk map was generated. A total of 1,428 reported outbreak events were retrieved from the database. The analysis suggested that outbreaks of water-associated diseases are significantly correlated with socio-environmental factors. Population density is a significant risk factor for all categories of reported outbreaks of water-associated diseases; water-related diseases (e.g., vector-borne diseases) are associated with accumulated temperature; water-washed diseases (e.g., conjunctivitis) are inversely related to surface water area; both water-borne and water-related diseases are inversely related to average annual rainfall. Based on the model predictions, “hotspots” of risks for all categories of water-associated diseases were explored. Conclusions At the global scale, water-associated infectious diseases are significantly correlated with socio-environmental factors, impacting all regions which are affected disproportionately by different categories of water-associated infectious diseases. PMID:22348158

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

PubMed

Carver, Tim; Berriman, Matthew; Tivey, Adrian; Patel, Chinmay; Böhme, Ulrike; Barrell, Barclay G; Parkhill, Julian; Rajandream, Marie-Adèle

2008-12-01

Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/

PHASE I MATERIALS PROPERTY DATABASE DEVELOPMENT FOR ASME CODES AND STANDARDS

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

Ren, Weiju; Lin, Lianshan

2013-01-01

To support the ASME Boiler and Pressure Vessel Codes and Standard (BPVC) in modern information era, development of a web-based materials property database is initiated under the supervision of ASME Committee on Materials. To achieve efficiency, the project heavily draws upon experience from development of the Gen IV Materials Handbook and the Nuclear System Materials Handbook. The effort is divided into two phases. Phase I is planned to deliver a materials data file warehouse that offers a depository for various files containing raw data and background information, and Phase II will provide a relational digital database that provides advanced featuresmore » facilitating digital data processing and management. Population of the database will start with materials property data for nuclear applications and expand to data covering the entire ASME Code and Standards including the piping codes as the database structure is continuously optimized. The ultimate goal of the effort is to establish a sound cyber infrastructure that support ASME Codes and Standards development and maintenance.« less

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

Background qualitative analysis of the European Reference Life Cycle Database (ELCD) energy datasets - part I: fuel datasets.

PubMed

Garraín, Daniel; Fazio, Simone; de la Rúa, Cristina; Recchioni, Marco; Lechón, Yolanda; Mathieux, Fabrice

2015-01-01

The aim of this study is to identify areas of potential improvement of the European Reference Life Cycle Database (ELCD) fuel datasets. The revision is based on the data quality indicators described by the ILCD Handbook, applied on sectorial basis. These indicators evaluate the technological, geographical and time-related representativeness of the dataset and the appropriateness in terms of completeness, precision and methodology. Results show that ELCD fuel datasets have a very good quality in general terms, nevertheless some findings and recommendations in order to improve the quality of Life-Cycle Inventories have been derived. Moreover, these results ensure the quality of the fuel-related datasets to any LCA practitioner, and provide insights related to the limitations and assumptions underlying in the datasets modelling. Giving this information, the LCA practitioner will be able to decide whether the use of the ELCD fuel datasets is appropriate based on the goal and scope of the analysis to be conducted. The methodological approach would be also useful for dataset developers and reviewers, in order to improve the overall DQR of databases.

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.

PubMed

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. © The Author(s) 2014. Published by Oxford University Press.

Methods for structuring scientific knowledge from many areas related to aging research.

PubMed

Zhavoronkov, Alex; Cantor, Charles R

2011-01-01

Aging and age-related disease represents a substantial quantity of current natural, social and behavioral science research efforts. Presently, no centralized system exists for tracking aging research projects across numerous research disciplines. The multidisciplinary nature of this research complicates the understanding of underlying project categories, the establishment of project relations, and the development of a unified project classification scheme. We have developed a highly visual database, the International Aging Research Portfolio (IARP), available at AgingPortfolio.org to address this issue. The database integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research. Grant applications often precede publications and some grants do not result in publications, thus, this system provides utility to investigate an earlier and broader view on research activity in many research disciplines. This project is a first attempt to provide a centralized database system for research grants and to categorize aging research projects into multiple subcategories utilizing both advanced machine algorithms and a hierarchical environment for scientific collaboration.

Study of an External Neutron Source for an Accelerator-Driven System using the PHITS Code

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

Sugawara, Takanori; Iwasaki, Tomohiko; Chiba, Takashi

A code system for the Accelerator Driven System (ADS) has been under development for analyzing dynamic behaviors of a subcritical core coupled with an accelerator. This code system named DSE (Dynamics calculation code system for a Subcritical system with an External neutron source) consists of an accelerator part and a reactor part. The accelerator part employs a database, which is calculated by using PHITS, for investigating the effect related to the accelerator such as the changes of beam energy, beam diameter, void generation, and target level. This analysis method using the database may introduce some errors into dynamics calculations sincemore » the neutron source data derived from the database has some errors in fitting or interpolating procedures. In this study, the effects of various events are investigated to confirm that the method based on the database is appropriate.« less

Information, intelligence, and interface: the pillars of a successful medical information system.

PubMed

Hadzikadic, M; Harrington, A L; Bohren, B F

1995-01-01

This paper addresses three key issues facing developers of clinical and/or research medical information systems. 1. INFORMATION. The basic function of every database is to store information about the phenomenon under investigation. There are many ways to organize information in a computer; however only a few will prove optimal for any real life situation. Computer Science theory has developed several approaches to database structure, with relational theory leading in popularity among end users [8]. Strict conformance to the rules of relational database design rewards the user with consistent data and flexible access to that data. A properly defined database structure minimizes redundancy i.e.,multiple storage of the same information. Redundancy introduces problems when updating a database, since the repeated value has to be updated in all locations--missing even a single value corrupts the whole database, and incorrect reports are produced [8]. To avoid such problems, relational theory offers a formal mechanism for determining the number and content of data files. These files not only preserve the conceptual schema of the application domain, but allow a virtually unlimited number of reports to be efficiently generated. 2. INTELLIGENCE. Flexible access enables the user to harvest additional value from collected data. This value is usually gained via reports defined at the time of database design. Although these reports are indispensable, with proper tools more information can be extracted from the database. For example, machine learning, a sub-discipline of artificial intelligence, has been successfully used to extract knowledge from databases of varying size by uncovering a correlation among fields and records[1-6, 9]. This knowledge, represented in the form of decision trees, production rules, and probabilistic networks, clearly adds a flavor of intelligence to the data collection and manipulation system. 3. INTERFACE. Despite the obvious importance of collecting data and extracting knowledge, current systems often impede these processes. Problems stem from the lack of user friendliness and functionality. To overcome these problems, several features of a successful human-computer interface have been identified [7], including the following "golden" rules of dialog design [7]: consistency, use of shortcuts for frequent users, informative feedback, organized sequence of actions, simple error handling, easy reversal of actions, user-oriented focus of control, and reduced short-term memory load. To this list of rules, we added visual representation of both data and query results, since our experience has demonstrated that users react much more positively to visual rather than textual information. In our design of the Orthopaedic Trauma Registry--under development at the Carolinas Medical Center--we have made every effort to follow the above rules. The results were rewarding--the end users actually not only want to use the product, but also to participate in its development.

Sugeno Fuzzy Integral as a Basis for the Interpretation of Flexible Queries Involving Monotonic Aggregates.

ERIC Educational Resources Information Center

Bosc, P.; Lietard, L.; Pivert, O.

2003-01-01

Considers flexible querying of relational databases. Highlights include SQL languages and basic aggregate operators; Sugeno's fuzzy integral; evaluation examples; and how and under what conditions other aggregate functions could be applied to fuzzy sets in a flexible query. (Author/LRW)

FJET Database Project: Extract, Transform, and Load

NASA Technical Reports Server (NTRS)

Samms, Kevin O.

2015-01-01

The Data Mining & Knowledge Management team at Kennedy Space Center is providing data management services to the Frangible Joint Empirical Test (FJET) project at Langley Research Center (LARC). FJET is a project under the NASA Engineering and Safety Center (NESC). The purpose of FJET is to conduct an assessment of mild detonating fuse (MDF) frangible joints (FJs) for human spacecraft separation tasks in support of the NASA Commercial Crew Program. The Data Mining & Knowledge Management team has been tasked with creating and managing a database for the efficient storage and retrieval of FJET test data. This paper details the Extract, Transform, and Load (ETL) process as it is related to gathering FJET test data into a Microsoft SQL relational database, and making that data available to the data users. Lessons learned, procedures implemented, and programming code samples are discussed to help detail the learning experienced as the Data Mining & Knowledge Management team adapted to changing requirements and new technology while maintaining flexibility of design in various aspects of the data management project.

[Relational database for urinary stone ambulatory consultation. Assessment of initial outcomes].

PubMed

Sáenz Medina, J; Páez Borda, A; Crespo Martinez, L; Gómez Dos Santos, V; Barrado, C; Durán Poveda, M

2010-05-01

To create a relational database for monitoring lithiasic patients. We describe the architectural details and the initial results of the statistical analysis. Microsoft Access 2002 was used as template. Four different tables were constructed to gather demographic data (table 1), clinical and laboratory findings (table 2), stone features (table 3) and therapeutic approach (table 4). For a reliability analysis of the database the number of correctly stored data was gathered. To evaluate the performance of the database, a prospective analysis was conducted, from May 2004 to August 2009, on 171 stone free patients after treatment (EWSL, surgery or medical) from a total of 511 patients stored in the database. Lithiasic status (stone free or stone relapse) was used as primary end point, while demographic factors (age, gender), lithiasic history, upper urinary tract alterations and characteristics of the stone (side, location, composition and size) were considered as predictive factors. An univariate analysis was conducted initially by chi square test and supplemented by Kaplan Meier estimates for time to stone recurrence. A multiple Cox proportional hazards regression model was generated to jointly assess the prognostic value of the demographic factors and the predictive value of stones characteristics. For the reliability analysis 22,084 data were available corresponding to 702 consultations on 511 patients. Analysis of data showed a recurrence rate of 85.4% (146/171, median time to recurrence 608 days, range 70-1758). In the univariate and multivariate analysis, none of the factors under consideration had a significant effect on recurrence rate (p=ns). The relational database is useful for monitoring patients with urolithiasis. It allows easy control and update, as well as data storage for later use. The analysis conducted for its evaluation showed no influence of demographic factors and stone features on stone recurrence.

Joint Battlespace Infosphere: Information Management Within a C2 Enterprise

DTIC Science & Technology

2005-06-01

using. In version 1.2, we support both MySQL and Oracle as underlying implementations where the XML metadata schema is mapped into relational tables in...Identity Servers, Role-Based Access Control, and Policy Representation – Databases: Oracle , MySQL , TigerLogic, Berkeley XML DB 15 Instrumentation Services...converted to SQL for execution. Invocations are then forwarded to the appropriate underlying IOR core components that have the responsibility of issuing

SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

PubMed

Baran, Michael C; Moseley, Hunter N B; Sahota, Gurmukh; Montelione, Gaetano T

2002-10-01

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. Additional facilities include a data mining query tool, graphical database administration tools, and a NMRStar v2. 1.1 file generator. SPINS also includes a user-friendly internet-based graphical user interface, which is optionally integrated with Varian VNMR NMR data collection software. This paper provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and an outline of future plans for the SPINS project.

Examining database persistence of ISO/EN 13606 standardized electronic health record extracts: relational vs. NoSQL approaches.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Lozano-Rubí, Raimundo; Serrano-Balazote, Pablo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2017-08-18

The objective of this research is to compare the relational and non-relational (NoSQL) database systems approaches in order to store, recover, query and persist standardized medical information in the form of ISO/EN 13606 normalized Electronic Health Record XML extracts, both in isolation and concurrently. NoSQL database systems have recently attracted much attention, but few studies in the literature address their direct comparison with relational databases when applied to build the persistence layer of a standardized medical information system. One relational and two NoSQL databases (one document-based and one native XML database) of three different sizes have been created in order to evaluate and compare the response times (algorithmic complexity) of six different complexity growing queries, which have been performed on them. Similar appropriate results available in the literature have also been considered. Relational and non-relational NoSQL database systems show almost linear algorithmic complexity query execution. However, they show very different linear slopes, the former being much steeper than the two latter. Document-based NoSQL databases perform better in concurrency than in isolation, and also better than relational databases in concurrency. Non-relational NoSQL databases seem to be more appropriate than standard relational SQL databases when database size is extremely high (secondary use, research applications). Document-based NoSQL databases perform in general better than native XML NoSQL databases. EHR extracts visualization and edition are also document-based tasks more appropriate to NoSQL database systems. However, the appropriate database solution much depends on each particular situation and specific problem.

Enhancing navigation in biomedical databases by community voting and database-driven text classification

PubMed Central

Duchrow, Timo; Shtatland, Timur; Guettler, Daniel; Pivovarov, Misha; Kramer, Stefan; Weissleder, Ralph

2009-01-01

Background The breadth of biological databases and their information content continues to increase exponentially. Unfortunately, our ability to query such sources is still often suboptimal. Here, we introduce and apply community voting, database-driven text classification, and visual aids as a means to incorporate distributed expert knowledge, to automatically classify database entries and to efficiently retrieve them. Results Using a previously developed peptide database as an example, we compared several machine learning algorithms in their ability to classify abstracts of published literature results into categories relevant to peptide research, such as related or not related to cancer, angiogenesis, molecular imaging, etc. Ensembles of bagged decision trees met the requirements of our application best. No other algorithm consistently performed better in comparative testing. Moreover, we show that the algorithm produces meaningful class probability estimates, which can be used to visualize the confidence of automatic classification during the retrieval process. To allow viewing long lists of search results enriched by automatic classifications, we added a dynamic heat map to the web interface. We take advantage of community knowledge by enabling users to cast votes in Web 2.0 style in order to correct automated classification errors, which triggers reclassification of all entries. We used a novel framework in which the database "drives" the entire vote aggregation and reclassification process to increase speed while conserving computational resources and keeping the method scalable. In our experiments, we simulate community voting by adding various levels of noise to nearly perfectly labelled instances, and show that, under such conditions, classification can be improved significantly. Conclusion Using PepBank as a model database, we show how to build a classification-aided retrieval system that gathers training data from the community, is completely controlled by the database, scales well with concurrent change events, and can be adapted to add text classification capability to other biomedical databases. The system can be accessed at . PMID:19799796

Solving Relational Database Problems with ORDBMS in an Advanced Database Course

ERIC Educational Resources Information Center

Wang, Ming

2011-01-01

This paper introduces how to use the object-relational database management system (ORDBMS) to solve relational database (RDB) problems in an advanced database course. The purpose of the paper is to provide a guideline for database instructors who desire to incorporate the ORDB technology in their traditional database courses. The paper presents…

Consistent Query Answering of Conjunctive Queries under Primary Key Constraints

ERIC Educational Resources Information Center

Pema, Enela

2014-01-01

An inconsistent database is a database that violates one or more of its integrity constraints. In reality, violations of integrity constraints arise frequently under several different circumstances. Inconsistent databases have long posed the challenge to develop suitable tools for meaningful query answering. A principled approach for querying…

2016 update of the PRIDE database and its related tools

PubMed Central

Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi; Dianes, José A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez-Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qing-Wei; Wang, Rui; Hermjakob, Henning

2016-01-01

The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive. PMID:26527722

Identifying work-related motor vehicle crashes in multiple databases.

PubMed

Thomas, Andrea M; Thygerson, Steven M; Merrill, Ray M; Cook, Lawrence J

2012-01-01

To compare and estimate the magnitude of work-related motor vehicle crashes in Utah using 2 probabilistically linked statewide databases. Data from 2006 and 2007 motor vehicle crash and hospital databases were joined through probabilistic linkage. Summary statistics and capture-recapture were used to describe occupants injured in work-related motor vehicle crashes and estimate the size of this population. There were 1597 occupants in the motor vehicle crash database and 1673 patients in the hospital database identified as being in a work-related motor vehicle crash. We identified 1443 occupants with at least one record from either the motor vehicle crash or hospital database indicating work-relatedness that linked to any record in the opposing database. We found that 38.7 percent of occupants injured in work-related motor vehicle crashes identified in the motor vehicle crash database did not have a primary payer code of workers' compensation in the hospital database and 40.0 percent of patients injured in work-related motor vehicle crashes identified in the hospital database did not meet our definition of a work-related motor vehicle crash in the motor vehicle crash database. Depending on how occupants injured in work-related motor crashes are identified, we estimate the population to be between 1852 and 8492 in Utah for the years 2006 and 2007. Research on single databases may lead to biased interpretations of work-related motor vehicle crashes. Combining 2 population based databases may still result in an underestimate of the magnitude of work-related motor vehicle crashes. Improved coding of work-related incidents is needed in current databases.

Information system of mineral deposits in Slovenia

NASA Astrophysics Data System (ADS)

Hribernik, K.; Rokavec, D.; Šinigioj, J.; Šolar, S.

2010-03-01

At the Geologic Survey of Slovenia the need for complex overview and control of the deposits of available non-metallic mineral raw materials and of their exploitations became urgent. In the framework of the Geologic Information System we established the Database of non-metallic mineral deposits comprising all important data of deposits and concessionars. Relational database is built with program package MS Access, but in year 2008 we plan to transfer it on SQL server. In the evidence there is 272 deposits and 200 concessionars. The mineral resources information system of Slovenia, which was started back in 2002, consists of two integrated parts, mentioned relational database of mineral deposits, which relates information in tabular way so that rules of relational algebra can be applied, and geographic information system (GIS), which relates spatial information of deposits. . The complex relationships between objects and the concepts of normalized data structures, lead to the practical informative and useful data model, transparent to the user and to better decision-making by allowing future scenarios to be developed and inspected. Computerized storage, and display system is as already said, developed and managed under the support of Geological Survey of Slovenia, which conducts research on the occurrence, quality, quantity, and availability of mineral resources in order to help the Nation make informed decisions using earth-science information. Information about deposit is stored in records in approximately hundred data fields. A numeric record number uniquely identifies each site. The data fields are grouped under principal categories. Each record comprise elementary data of deposit (name, type, location, prospect, rock), administrative data (concessionar, number of decree in official paper, object of decree, number of contract and its duration) and data of mineral resource produced amount and size of exploration area). The data can also be searched, sorted and printed using any of these fields. New records are being added annually, and existing records updated or upgraded. Relational database is connected with scanned exploration/exploitation areas of deposits, defined on the base of digital ortofoto. Register of those areas is indispensable because of spatial planning and spatial municipal and regional strategy development. Database is also part of internet application for quick search and review of data and part of web page of mineral resources of Slovenia. The technology chosen for internet application is ESRI's ArcIMS Internet Map Server. ArcIMS allows users to readily and easily display, analyze, and interpret spatial data from desktop using a Web browser connected to the Internet. We believe that there is an opportunity for cooperation within this activity. We can offer a single location where users can come to browse relatively simply for geoscience-related digital data sets.

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

PubMed

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

2012-08-01

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

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

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

PubMed

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

2012-01-01

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

Development of the method and U.S. normalization database for Life Cycle Impact Assessment and sustainability metrics.

PubMed

Bare, Jane; Gloria, Thomas; Norris, Gregory

2006-08-15

Normalization is an optional step within Life Cycle Impact Assessment (LCIA) that may be used to assist in the interpretation of life cycle inventory data as well as life cycle impact assessment results. Normalization transforms the magnitude of LCI and LCIA results into relative contribution by substance and life cycle impact category. Normalization thus can significantly influence LCA-based decisions when tradeoffs exist. The U. S. Environmental Protection Agency (EPA) has developed a normalization database based on the spatial scale of the 48 continental U.S. states, Hawaii, Alaska, the District of Columbia, and Puerto Rico with a one-year reference time frame. Data within the normalization database were compiled based on the impact methodologies and lists of stressors used in TRACI-the EPA's Tool for the Reduction and Assessment of Chemical and other environmental Impacts. The new normalization database published within this article may be used for LCIA case studies within the United States, and can be used to assist in the further development of a global normalization database. The underlying data analyzed for the development of this database are included to allow the development of normalization data consistent with other impact assessment methodologies as well.

Risks associated with clinical databases.

PubMed

Eleazar, P Y

1991-11-01

Providers will succeed who are evaluating themselves, and who are continuously striving to examine who they are and where they are going. Conscientious providers know that countless other agencies have them under the microscope and that they have to work to stay ahead in assessing their actions through their clinical database. "Medical care value purchasing" is what every employer and payor is looking for, and providers need to find ways to illustrate cost in relation to quality. The basics of data security and protection should be in place in order to concentrate on the bigger picture. The knowledge of the risk associated with individual hospital databases as well as the risk associated with comparative databases is critical. The hospital-level clinical database is the hub of the wheel. If the risk there can be minimized, the data headed for various investigative sites will have less inherent risk. When it is really recognized and accepted that all financial decisions are made based upon the clinical data generated at the site of care, then data integrity will become a strategic advantage for the industry. Clinical database goals will, over time, cause minimization of risk at all levels. As this occurs, variation in treatment will be explained artfully.

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

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

PubMed

Machado, Helena; Silva, Susana

2015-10-01

The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of 'solidarity', traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Update of the Diatom EST Database: a new tool for digital transcriptomics

PubMed Central

Maheswari, Uma; Mock, Thomas; Armbrust, E. Virginia; Bowler, Chris

2009-01-01

The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3. PMID:19029140

Chemical hazards database and detection system for Microgravity and Materials Processing Facility (MMPF)

NASA Technical Reports Server (NTRS)

Steele, Jimmy; Smith, Robert E.

1991-01-01

The ability to identify contaminants associated with experiments and facilities is directly related to the safety of the Space Station. A means of identifying these contaminants has been developed through this contracting effort. The delivered system provides a listing of the materials and/or chemicals associated with each facility, information as to the contaminant's physical state, a list of the quantity and/or volume of each suspected contaminant, a database of the toxicological hazards associated with each contaminant, a recommended means of rapid identification of the contaminants under operational conditions, a method of identifying possible failure modes and effects analysis associated with each facility, and a fault tree-type analysis that will provide a means of identifying potential hazardous conditions related to future planned missions.

Background qualitative analysis of the European reference life cycle database (ELCD) energy datasets - part II: electricity datasets.

PubMed

Garraín, Daniel; Fazio, Simone; de la Rúa, Cristina; Recchioni, Marco; Lechón, Yolanda; Mathieux, Fabrice

2015-01-01

The aim of this paper is to identify areas of potential improvement of the European Reference Life Cycle Database (ELCD) electricity datasets. The revision is based on the data quality indicators described by the International Life Cycle Data system (ILCD) Handbook, applied on sectorial basis. These indicators evaluate the technological, geographical and time-related representativeness of the dataset and the appropriateness in terms of completeness, precision and methodology. Results show that ELCD electricity datasets have a very good quality in general terms, nevertheless some findings and recommendations in order to improve the quality of Life-Cycle Inventories have been derived. Moreover, these results ensure the quality of the electricity-related datasets to any LCA practitioner, and provide insights related to the limitations and assumptions underlying in the datasets modelling. Giving this information, the LCA practitioner will be able to decide whether the use of the ELCD electricity datasets is appropriate based on the goal and scope of the analysis to be conducted. The methodological approach would be also useful for dataset developers and reviewers, in order to improve the overall Data Quality Requirements of databases.

Nutritional Awareness of Mothers in Relation to Nutritional Status of the Preschool Children

ERIC Educational Resources Information Center

Halder, Santoshi; Kejriwal, Sunita

2016-01-01

Background: In the developing world, nearly one-third (35%) of under-five children are stunted and rural children are twice likely to be underweight as those in urban areas (United Nations, Children education Fund, UNICEF Global Database (2006-2010). United Nations Development Assistance Framework of Uganda. Retrieved from…

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2013 CFR

2013-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2012 CFR

2012-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...

22 CFR 41.62 - Exchange visitors.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Relations DEPARTMENT OF STATE VISAS VISAS: DOCUMENTATION OF NONIMMIGRANTS UNDER THE IMMIGRATION AND... to SEVIS or ISEAS prior to the issuance of a J-1 or J-2 visa. Evidence of the payment of any... Consular Database or direct access to SEVIS. Upon issuance of a J-1 or J-2 visa, notification of such...

47 CFR 54.416 - Annual certifications by eligible telecommunications carriers.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Administrator the following annual certifications, under penalty of perjury, relating to the Lifeline program... Administrator as part of the carrier's submission of annual re-certification data pursuant to this section. In... eligibility databases, as defined in § 54.410(b)(1)(i)(A) or (c)(1)(i)(A), the representative must attest...

47 CFR 54.416 - Annual certifications by eligible telecommunications carriers.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Administrator the following annual certifications, under penalty of perjury, relating to the Lifeline program... Administrator as part of the carrier's submission of annual re-certification data pursuant to this section. In... eligibility databases, as defined in § 54.410(b)(1)(i)(A) or (c)(1)(i)(A), the representative must attest...

47 CFR 54.416 - Annual certifications by eligible telecommunications carriers.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Administrator the following annual certifications, under penalty of perjury, relating to the Lifeline program... Administrator as part of the carrier's submission of annual re-certification data pursuant to this section. In... eligibility databases, as defined in § 54.410(b)(1)(i)(A) or (c)(1)(i)(A), the representative must attest...

A New Paradigm to Analyze Data Completeness of Patient Data.

PubMed

Nasir, Ayan; Gurupur, Varadraj; Liu, Xinliang

2016-08-03

There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data.

A New Paradigm to Analyze Data Completeness of Patient Data

PubMed Central

Nasir, Ayan; Liu, Xinliang

2016-01-01

Summary Background There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Objectives Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. Methods The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. Results The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. Conclusion DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data. PMID:27484918

Genome databases

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

Courteau, J.

1991-10-11

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

Spatial cyberinfrastructures, ontologies, and the humanities.

PubMed

Sieber, Renee E; Wellen, Christopher C; Jin, Yuan

2011-04-05

We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success.

Synopsis of discussion session on physicochemical factors affecting toxicity

USGS Publications Warehouse

Erickson, R.J.; Bills, T.D.; Clark, J.R.; Hansen, D.J.; Knezovich, J.; Hamelink, J.L.; Landrum, P.F.; Bergman, H.L.; Benson, W.H.

1994-01-01

The paper documents the workshop discussion regarding the role of these factors in altering toxicity. For each factor, the nature, magnitude, and uncertainty of its empirical relation to the toxicity of various chemicals or chemical classes is discussed. Limitations in the empirical database regarding the variety of species and endpoints tested were addressed. Possible mechanisms underlying the empirical relations are identified. Finally, research needed to better understand these effects is identified.

Short Fiction on Film: A Relational DataBase.

ERIC Educational Resources Information Center

May, Charles

Short Fiction on Film is a database that was created and will run on DataRelator, a relational database manager created by Bill Finzer for the California State Department of Education in 1986. DataRelator was designed for use in teaching students database management skills and to provide teachers with examples of how a database manager might be…

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

Class dependency of fuzzy relational database using relational calculus and conditional probability

NASA Astrophysics Data System (ADS)

Deni Akbar, Mohammad; Mizoguchi, Yoshihiro; Adiwijaya

2018-03-01

In this paper, we propose a design of fuzzy relational database to deal with a conditional probability relation using fuzzy relational calculus. In the previous, there are several researches about equivalence class in fuzzy database using similarity or approximate relation. It is an interesting topic to investigate the fuzzy dependency using equivalence classes. Our goal is to introduce a formulation of a fuzzy relational database model using the relational calculus on the category of fuzzy relations. We also introduce general formulas of the relational calculus for the notion of database operations such as ’projection’, ’selection’, ’injection’ and ’natural join’. Using the fuzzy relational calculus and conditional probabilities, we introduce notions of equivalence class, redundant, and dependency in the theory fuzzy relational database.

Supporting user-defined granularities in a spatiotemporal conceptual model

USGS Publications Warehouse

Khatri, V.; Ram, S.; Snodgrass, R.T.; O'Brien, G. M.

2002-01-01

Granularities are integral to spatial and temporal data. A large number of applications require storage of facts along with their temporal and spatial context, which needs to be expressed in terms of appropriate granularities. For many real-world applications, a single granularity in the database is insufficient. In order to support any type of spatial or temporal reasoning, the semantics related to granularities needs to be embedded in the database. Specifying granularities related to facts is an important part of conceptual database design because under-specifying the granularity can restrict an application, affect the relative ordering of events and impact the topological relationships. Closely related to granularities is indeterminacy, i.e., an occurrence time or location associated with a fact that is not known exactly. In this paper, we present an ontology for spatial granularities that is a natural analog of temporal granularities. We propose an upward-compatible, annotation-based spatiotemporal conceptual model that can comprehensively capture the semantics related to spatial and temporal granularities, and indeterminacy without requiring new spatiotemporal constructs. We specify the formal semantics of this spatiotemporal conceptual model via translation to a conventional conceptual model. To underscore the practical focus of our approach, we describe an on-going case study. We apply our approach to a hydrogeologic application at the United States Geologic Survey and demonstrate that our proposed granularity-based spatiotemporal conceptual model is straightforward to use and is comprehensive.

Final report for DOE Award # DE- SC0010039*: Carbon dynamics of forest recovery under a changing climate: Forcings, feedbacks, and implications for earth system modeling

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

Anderson-Teixeira, Kristina J.; DeLucia, Evan H.; Duval, Benjamin D.

2015-10-29

To advance understanding of C dynamics of forests globally, we compiled a new database, the Forest C database (ForC-db), which contains data on ground-based measurements of ecosystem-level C stocks and annual fluxes along with disturbance history. This database currently contains 18,791 records from 2009 sites, making it the largest and most comprehensive database of C stocks and flows in forest ecosystems globally. The tropical component of the database will be published in conjunction with a manuscript that is currently under review (Anderson-Teixeira et al., in review). Database development continues, and we hope to maintain a dynamic instance of the entiremore » (global) database.« less

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites.

PubMed

Li, Li; Crabtree, Jonathan; Fischer, Steve; Pinney, Deborah; Stoeckert, Christian J; Sibley, L David; Roos, David S

2004-01-01

ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently incorporates a total of nearly 100,000 ESTs from several parasite species of clinical and/or veterinary interest, including Eimeria tenella, Neospora caninum, Plasmodium falciparum, Sarcocystis neurona and Toxoplasma gondii. To facilitate analysis of these data, EST sequences were clustered and assembled to form consensus sequences for each organism, and these assemblies were then subjected to automated annotation via similarity searches against protein and domain databases. The underlying relational database infrastructure, Genomics Unified Schema (GUS), enables complex biologically based queries, facilitating validation of gene models, identification of alternative splicing, detection of single nucleotide polymorphisms, identification of stage-specific genes and recognition of phylogenetically conserved and phylogenetically restricted sequences.

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

PubMed

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

2005-04-01

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

LARCRIM user's guide, version 1.0

NASA Technical Reports Server (NTRS)

Davis, John S.; Heaphy, William J.

1993-01-01

LARCRIM is a relational database management system (RDBMS) which performs the conventional duties of an RDBMS with the added feature that it can store attributes which consist of arrays or matrices. This makes it particularly valuable for scientific data management. It is accessible as a stand-alone system and through an application program interface. The stand-alone system may be executed in two modes: menu or command. The menu mode prompts the user for the input required to create, update, and/or query the database. The command mode requires the direct input of LARCRIM commands. Although LARCRIM is an update of an old database family, its performance on modern computers is quite satisfactory. LARCRIM is written in FORTRAN 77 and runs under the UNIX operating system. Versions have been released for the following computers: SUN (3 & 4), Convex, IRIS, Hewlett-Packard, CRAY 2 & Y-MP.

The Innate Immune Database (IIDB)

PubMed Central

Korb, Martin; Rust, Aistair G; Thorsson, Vesteinn; Battail, Christophe; Li, Bin; Hwang, Daehee; Kennedy, Kathleen A; Roach, Jared C; Rosenberger, Carrie M; Gilchrist, Mark; Zak, Daniel; Johnson, Carrie; Marzolf, Bruz; Aderem, Alan; Shmulevich, Ilya; Bolouri, Hamid

2008-01-01

Background As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site . Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens. Description We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser. Conclusion We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at . PMID:18321385

Ventilator-Related Adverse Events: A Taxonomy and Findings From 3 Incident Reporting Systems.

PubMed

Pham, Julius Cuong; Williams, Tamara L; Sparnon, Erin M; Cillie, Tam K; Scharen, Hilda F; Marella, William M

2016-05-01

In 2009, researchers from Johns Hopkins University's Armstrong Institute for Patient Safety and Quality; public agencies, including the FDA; and private partners, including the Emergency Care Research Institute and the University HealthSystem Consortium (UHC) Safety Intelligence Patient Safety Organization, sought to form a public-private partnership for the promotion of patient safety (P5S) to advance patient safety through voluntary partnerships. The study objective was to test the concept of the P5S to advance our understanding of safety issues related to ventilator events, to develop a common classification system for categorizing adverse events related to mechanical ventilators, and to perform a comparison of adverse events across different adverse event reporting systems. We performed a cross-sectional analysis of ventilator-related adverse events reported in 2012 from the following incident reporting systems: the Pennsylvania Patient Safety Authority's Patient Safety Reporting System, UHC's Safety Intelligence Patient Safety Organization database, and the FDA's Manufacturer and User Facility Device Experience database. Once each organization had its dataset of ventilator-related adverse events, reviewers read the narrative descriptions of each event and classified it according to the developed common taxonomy. A Pennsylvania Patient Safety Authority, FDA, and UHC search provided 252, 274, and 700 relevant reports, respectively. The 3 event types most commonly reported to the UHC and the Pennsylvania Patient Safety Authority's Patient Safety Reporting System databases were airway/breathing circuit issue, human factor issues, and ventilator malfunction events. The top 3 event types reported to the FDA were ventilator malfunction, power source issue, and alarm failure. Overall, we found that (1) through the development of a common taxonomy, adverse events from 3 reporting systems can be evaluated, (2) the types of events reported in each database were related to the purpose of the database and the source of the reports, resulting in significant differences in reported event categories across the 3 systems, and (3) a public-private collaboration for investigating ventilator-related adverse events under the P5S model is feasible. Copyright © 2016 by Daedalus Enterprises.

FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster

PubMed Central

Robinson, Scott W.; Herzyk, Pawel; Dow, Julian A. T.; Leader, David P.

2013-01-01

The FlyAtlas resource contains data on the expression of the genes of Drosophila melanogaster in different tissues (currently 25—17 adult and 8 larval) obtained by hybridization of messenger RNA to Affymetrix Drosophila Genome 2 microarrays. The microarray probe sets cover 13 250 Drosophila genes, detecting 12 533 in an unambiguous manner. The data underlying the original web application (http://flyatlas.org) have been restructured into a relational database and a Java servlet written to provide a new web interface, FlyAtlas 2 (http://flyatlas.gla.ac.uk/), which allows several additional queries. Users can retrieve data for individual genes or for groups of genes belonging to the same or related ontological categories. Assistance in selecting valid search terms is provided by an Ajax ‘autosuggest’ facility that polls the database as the user types. Searches can also focus on particular tissues, and data can be retrieved for the most highly expressed genes, for genes of a particular category with above-average expression or for genes with the greatest difference in expression between the larval and adult stages. A novel facility allows the database to be queried with a specific gene to find other genes with a similar pattern of expression across the different tissues. PMID:23203866

FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster.

PubMed

Robinson, Scott W; Herzyk, Pawel; Dow, Julian A T; Leader, David P

2013-01-01

The FlyAtlas resource contains data on the expression of the genes of Drosophila melanogaster in different tissues (currently 25-17 adult and 8 larval) obtained by hybridization of messenger RNA to Affymetrix Drosophila Genome 2 microarrays. The microarray probe sets cover 13,250 Drosophila genes, detecting 12,533 in an unambiguous manner. The data underlying the original web application (http://flyatlas.org) have been restructured into a relational database and a Java servlet written to provide a new web interface, FlyAtlas 2 (http://flyatlas.gla.ac.uk/), which allows several additional queries. Users can retrieve data for individual genes or for groups of genes belonging to the same or related ontological categories. Assistance in selecting valid search terms is provided by an Ajax 'autosuggest' facility that polls the database as the user types. Searches can also focus on particular tissues, and data can be retrieved for the most highly expressed genes, for genes of a particular category with above-average expression or for genes with the greatest difference in expression between the larval and adult stages. A novel facility allows the database to be queried with a specific gene to find other genes with a similar pattern of expression across the different tissues.

The Hierarchical Database Decomposition Approach to Database Concurrency Control.

DTIC Science & Technology

1984-12-01

approach, we postulate a model of transaction behavior under two phase locking as shown in Figure 39(a) and a model of that under multiversion ...transaction put in the block queue until it is reactivated. Under multiversion timestamping, however, the request is always granted. Once the request

SAMMD: Staphylococcus aureus microarray meta-database.

PubMed

Nagarajan, Vijayaraj; Elasri, Mohamed O

2007-10-02

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

SAMMD: Staphylococcus aureus Microarray Meta-Database

PubMed Central

Nagarajan, Vijayaraj; Elasri, Mohamed O

2007-01-01

Background Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). Conclusion SAMMD is hosted and available at . Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes. PMID:17910768

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

USGS Publications Warehouse

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

2008-01-01

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

[Home care to the elderly who had stroke].

PubMed

Pedreira, Larissa Chaves; Lopes, Regina Lúcia Mendonça

2010-01-01

The purpose was to Identify the knowledge production about the stroke in elderly under home care. Bibliographic research whose data were collected though the abstracts from 1997 to 2007, contained in LILACS and SciELO databases. The following key words were used: home assistance, aged people and cerebrovascular accident. Fifty-two references were found in the LILACS database, nine in the SciELO Brazil, and three in the SciELO Cuba. Most of the researches were carried out in 2000. Regarding the method, qualitative method predominance were observed, and central theme is related to the care giver, as well as to the clinical and epidemiologic aspects of the disease. It was observed that this knowledge is still established in Brazil, and the themes related to the person submitted to home care and violence to the aged are still little explored.

Migration from relational to NoSQL database

NASA Astrophysics Data System (ADS)

Ghotiya, Sunita; Mandal, Juhi; Kandasamy, Saravanakumar

2017-11-01

Data generated by various real time applications, social networking sites and sensor devices is of very huge amount and unstructured, which makes it difficult for Relational database management systems to handle the data. Data is very precious component of any application and needs to be analysed after arranging it in some structure. Relational databases are only able to deal with structured data, so there is need of NoSQL Database management System which can deal with semi -structured data also. Relational database provides the easiest way to manage the data but as the use of NoSQL is increasing it is becoming necessary to migrate the data from Relational to NoSQL databases. Various frameworks has been proposed previously which provides mechanisms for migration of data stored at warehouses in SQL, middle layer solutions which can provide facility of data to be stored in NoSQL databases to handle data which is not structured. This paper provides a literature review of some of the recent approaches proposed by various researchers to migrate data from relational to NoSQL databases. Some researchers proposed mechanisms for the co-existence of NoSQL and Relational databases together. This paper provides a summary of mechanisms which can be used for mapping data stored in Relational databases to NoSQL databases. Various techniques for data transformation and middle layer solutions are summarised in the paper.

Automating Relational Database Design for Microcomputer Users.

ERIC Educational Resources Information Center

Pu, Hao-Che

1991-01-01

Discusses issues involved in automating the relational database design process for microcomputer users and presents a prototype of a microcomputer-based system (RA, Relation Assistant) that is based on expert systems technology and helps avoid database maintenance problems. Relational database design is explained and the importance of easy input…

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus).

PubMed

Ribas, Laia; Pardo, Belén G; Fernández, Carlos; Alvarez-Diós, José Antonio; Gómez-Tato, Antonio; Quiroga, María Isabel; Planas, Josep V; Sitjà-Bobadilla, Ariadna; Martínez, Paulino; Piferrer, Francesc

2013-03-15

Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database ("Turbot 2 database") was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences ("Turbot 3 database"), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50-90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.

Economic evaluation of manual therapy for musculoskeletal diseases: a protocol for a systematic review and narrative synthesis of evidence.

PubMed

Kim, Chang-Gon; Mun, Su-Jeong; Kim, Ka-Na; Shin, Byung-Cheul; Kim, Nam-Kwen; Lee, Dong-Hyo; Lee, Jung-Han

2016-05-13

Manual therapy is the non-surgical conservative management of musculoskeletal disorders using the practitioner's hands on the patient's body for diagnosing and treating disease. The aim of this study is to systematically review trial-based economic evaluations of manual therapy relative to other interventions used for the management of musculoskeletal diseases. Randomised clinical trials (RCTs) on the economic evaluation of manual therapy for musculoskeletal diseases will be included in the review. The following databases will be searched from their inception: Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Econlit, Mantis, Index to Chiropractic Literature, Science Citation Index, Social Science Citation Index, Allied and Complementary Medicine Database (AMED), Cochrane Database of Systematic Reviews (CDSR), National Health Service Database of Abstracts of Reviews of Effects (NHS DARE), National Health Service Health Technology Assessment Database (NHS HTA), National Health Service Economic Evaluation Database (NHS EED), CENTRAL, five Korean medical databases (Oriental Medicine Advanced Searching Integrated System (OASIS), Research Information Service System (RISS), DBPIA, Korean Traditional Knowledge Portal (KTKP) and KoreaMed) and three Chinese databases (China National Knowledge Infrastructure (CNKI), VIP and Wanfang). The evidence for the cost-effectiveness, cost-utility and cost-benefit of manual therapy for musculoskeletal diseases will be assessed as the primary outcome. Health-related quality of life and adverse effects will be assessed as secondary outcomes. We will critically appraise the included studies using the Cochrane risk of bias tool and the Drummond checklist. Results will be summarised using Slavin's qualitative best-evidence synthesis approach. The results of the study will be disseminated via a peer-reviewed journal and/or conference presentations. PROSPERO CRD42015026757. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Alignment of systematic reviews published in the Cochrane Database of Systematic Reviews and the Database of Abstracts and Reviews of Effectiveness with global burden-of-disease data: a bibliographic analysis.

PubMed

Yoong, Sze Lin; Hall, Alix; Williams, Christopher M; Skelton, Eliza; Oldmeadow, Christopher; Wiggers, John; Karimkhani, Chante; Boyers, Lindsay N; Dellavalle, Robert P; Hilton, John; Wolfenden, Luke

2015-07-01

Systematic reviews of high-quality evidence are used to inform policy and practice. To improve community health, the production of such reviews should align with burden of disease. This study aims to assess if the volume of research output from systematic reviews proportionally aligns with burden of disease assessed using percentages of mortality and disability-adjusted life years (DALYs). A cross-sectional audit of reviews published between January 2012 and August 2013 in the Cochrane Database of Systematic Reviews (CDSR) and Database of Abstracts of Reviews of Effects (DARE) was undertaken. Percentages of mortality and DALYs were obtained from the 2010 Global Burden of Disease study. Standardised residual differences (SRD) based on percentages of mortality and DALYs were calculated, where conditions with SRD of more than or less than three were considered overstudied or understudied, respectively. 1029 reviews from CDSR and 1928 reviews from DARE were examined. There was a significant correlation between percentage DALYs and systematic reviews published in CDSR and DARE databases (CDSR: r=0.68, p=0.001; DARE: r=0.60, p<0.001). There was no significant correlation between percentage mortality and number of systematic reviews published in either database (CDSR: r=0.34, p=0.14; DARE: r=0.22, p=0.34). Relative to percentage of mortality, mental and behavioural disorders, musculoskeletal conditions and other non-communicable diseases were overstudied. Maternal disorders were overstudied relative to percentages of mortality and DALYs in CDSR. The focus of systematic reviews is moderately correlated with DALYs. A number of conditions may be overstudied relative to percentage of mortality particularly in the context of health and medical reviews. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

Multi-Sensor Scene Synthesis and Analysis

DTIC Science & Technology

1981-09-01

Quad Trees for Image Representation and Processing ...... ... 126 2.6.2 Databases ..... ..... ... ..... ... ..... ..... 138 2.6.2.1 Definitions and...Basic Concepts ....... 138 2.6.3 Use of Databases in Hierarchical Scene Analysis ...... ... ..................... 147 2.6.4 Use of Relational Tables...Multisensor Image Database Systems (MIDAS) . 161 2.7.2 Relational Database System for Pictures .... ..... 168 2.7.3 Relational Pictorial Database

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.

The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S. A.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.

2006-12-01

The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all measurements and the derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. The query result set is displayed in a digestible tabular format allowing the user to descend through hierarchical levels such as from locations to sites, samples, specimens, and measurements. At each stage, the result set can be saved and, if supported by the data, can be visualized by plotting global location maps, equal area plots, or typical Zijderveld, hysteresis, and various magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (Version 2.1) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload and takes only a few minutes to process several thousand data records. The standardized MagIC template files are stored in the digital archives of EarthRef.org where they remain available for download by the public (in both text and Excel format). Finally, the contents of these template files are automatically parsed into the online relational database, making the data available for online searches in the paleomagnetic and rock magnetic search nodes. The MagIC database contains all data transferred from the IAGA paleomagnetic poles database (GPMDB), the lava flow paleosecular variation database (PSVRL), lake sediment database (SECVR) and the PINT database. Additionally, a substantial number of data compiled under the Time Averaged Field Investigations project is now included plus a significant fraction of the data collected at SIO and the IRM. Ongoing additions of legacy data include over 40 papers from studies on the Hawaiian Islands and Mexico, data compilations from archeomagnetic studies and updates to the lake sediment dataset.

Spatial cyberinfrastructures, ontologies, and the humanities

PubMed Central

Sieber, Renee E.; Wellen, Christopher C.; Jin, Yuan

2011-01-01

We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success. PMID:21444819

Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

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

Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.

2004-05-12

An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view,more » create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.« less

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

Design and implementation of a distributed large-scale spatial database system based on J2EE

NASA Astrophysics Data System (ADS)

Gong, Jianya; Chen, Nengcheng; Zhu, Xinyan; Zhang, Xia

2003-03-01

With the increasing maturity of distributed object technology, CORBA, .NET and EJB are universally used in traditional IT field. However, theories and practices of distributed spatial database need farther improvement in virtue of contradictions between large scale spatial data and limited network bandwidth or between transitory session and long transaction processing. Differences and trends among of CORBA, .NET and EJB are discussed in details, afterwards the concept, architecture and characteristic of distributed large-scale seamless spatial database system based on J2EE is provided, which contains GIS client application, web server, GIS application server and spatial data server. Moreover the design and implementation of components of GIS client application based on JavaBeans, the GIS engine based on servlet, the GIS Application server based on GIS enterprise JavaBeans(contains session bean and entity bean) are explained.Besides, the experiments of relation of spatial data and response time under different conditions are conducted, which proves that distributed spatial database system based on J2EE can be used to manage, distribute and share large scale spatial data on Internet. Lastly, a distributed large-scale seamless image database based on Internet is presented.

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.

AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.

PubMed

Major, Sylvia M; Nishizuka, Satoshi; Morita, Daisaku; Rowland, Rick; Sunshine, Margot; Shankavaram, Uma; Washburn, Frank; Asin, Daniel; Kouros-Mehr, Hosein; Kane, David; Weinstein, John N

2006-04-06

Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different tissues of origin. AbMiner is a relational database that provides extensive information from our own laboratory and other sources on more than 600 available antibodies and the genes that encode the antibodies' antigens. The data will be made freely available at http://discover.nci.nih.gov/abminer.

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

Catalogue of HI PArameters (CHIPA)

NASA Astrophysics Data System (ADS)

Saponara, J.; Benaglia, P.; Koribalski, B.; Andruchow, I.

2015-08-01

The catalogue of HI parameters of galaxies HI (CHIPA) is the natural continuation of the compilation by M.C. Martin in 1998. CHIPA provides the most important parameters of nearby galaxies derived from observations of the neutral Hydrogen line. The catalogue contains information of 1400 galaxies across the sky and different morphological types. Parameters like the optical diameter of the galaxy, the blue magnitude, the distance, morphological type, HI extension are listed among others. Maps of the HI distribution, velocity and velocity dispersion can also be display for some cases. The main objective of this catalogue is to facilitate the bibliographic queries, through searching in a database accessible from the internet that will be available in 2015 (the website is under construction). The database was built using the open source `` mysql (SQL, Structured Query Language, management system relational database) '', while the website was built with ''HTML (Hypertext Markup Language)'' and ''PHP (Hypertext Preprocessor)''.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.

PubMed

Schorn, Michelle A; Alanjary, Mohammad M; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R; Ziemert, Nadine; Moore, Bradley S

2016-12-01

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters

PubMed Central

Schorn, Michelle A.; Alanjary, Mohammad M.; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R.; Ziemert, Nadine

2016-01-01

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites. PMID:27902408

Technical Aspects of Interfacing MUMPS to an External SQL Relational Database Management System

PubMed Central

Kuzmak, Peter M.; Walters, Richard F.; Penrod, Gail

1988-01-01

This paper describes an interface connecting InterSystems MUMPS (M/VX) to an external relational DBMS, the SYBASE Database Management System. The interface enables MUMPS to operate in a relational environment and gives the MUMPS language full access to a complete set of SQL commands. MUMPS generates SQL statements as ASCII text and sends them to the RDBMS. The RDBMS executes the statements and returns ASCII results to MUMPS. The interface suggests that the language features of MUMPS make it an attractive tool for use in the relational database environment. The approach described in this paper separates MUMPS from the relational database. Positioning the relational database outside of MUMPS promotes data sharing and permits a number of different options to be used for working with the data. Other languages like C, FORTRAN, and COBOL can access the RDBMS database. Advanced tools provided by the relational database vendor can also be used. SYBASE is an advanced high-performance transaction-oriented relational database management system for the VAX/VMS and UNIX operating systems. SYBASE is designed using a distributed open-systems architecture, and is relatively easy to interface with MUMPS.

Empirical performance of the self-controlled case series design: lessons for developing a risk identification and analysis system.

PubMed

Suchard, Marc A; Zorych, Ivan; Simpson, Shawn E; Schuemie, Martijn J; Ryan, Patrick B; Madigan, David

2013-10-01

The self-controlled case series (SCCS) offers potential as an statistical method for risk identification involving medical products from large-scale observational healthcare data. However, analytic design choices remain in encoding the longitudinal health records into the SCCS framework and its risk identification performance across real-world databases is unknown. To evaluate the performance of SCCS and its design choices as a tool for risk identification in observational healthcare data. We examined the risk identification performance of SCCS across five design choices using 399 drug-health outcome pairs in five real observational databases (four administrative claims and one electronic health records). In these databases, the pairs involve 165 positive controls and 234 negative controls. We also consider several synthetic databases with known relative risks between drug-outcome pairs. We evaluate risk identification performance through estimating the area under the receiver-operator characteristics curve (AUC) and bias and coverage probability in the synthetic examples. The SCCS achieves strong predictive performance. Twelve of the twenty health outcome-database scenarios return AUCs >0.75 across all drugs. Including all adverse events instead of just the first per patient and applying a multivariate adjustment for concomitant drug use are the most important design choices. However, the SCCS as applied here returns relative risk point-estimates biased towards the null value of 1 with low coverage probability. The SCCS recently extended to apply a multivariate adjustment for concomitant drug use offers promise as a statistical tool for risk identification in large-scale observational healthcare databases. Poor estimator calibration dampens enthusiasm, but on-going work should correct this short-coming.

System for face recognition under expression variations of neutral-sampled individuals using recognized expression warping and a virtual expression-face database

NASA Astrophysics Data System (ADS)

Petpairote, Chayanut; Madarasmi, Suthep; Chamnongthai, Kosin

2018-01-01

The practical identification of individuals using facial recognition techniques requires the matching of faces with specific expressions to faces from a neutral face database. A method for facial recognition under varied expressions against neutral face samples of individuals via recognition of expression warping and the use of a virtual expression-face database is proposed. In this method, facial expressions are recognized and the input expression faces are classified into facial expression groups. To aid facial recognition, the virtual expression-face database is sorted into average facial-expression shapes and by coarse- and fine-featured facial textures. Wrinkle information is also employed in classification by using a process of masking to adjust input faces to match the expression-face database. We evaluate the performance of the proposed method using the CMU multi-PIE, Cohn-Kanade, and AR expression-face databases, and we find that it provides significantly improved results in terms of face recognition accuracy compared to conventional methods and is acceptable for facial recognition under expression variation.

The Magnetics Information Consortium (MagIC)

NASA Astrophysics Data System (ADS)

Johnson, C.; Constable, C.; Tauxe, L.; Koppers, A.; Banerjee, S.; Jackson, M.; Solheid, P.

2003-12-01

The Magnetics Information Consortium (MagIC) is a multi-user facility to establish and maintain a state-of-the-art relational database and digital archive for rock and paleomagnetic data. The goal of MagIC is to make such data generally available and to provide an information technology infrastructure for these and other research-oriented databases run by the international community. As its name implies, MagIC will not be restricted to paleomagnetic or rock magnetic data only, although MagIC will focus on these kinds of information during its setup phase. MagIC will be hosted under EarthRef.org at http://earthref.org/MAGIC/ where two "integrated" web portals will be developed, one for paleomagnetism (currently functional as a prototype that can be explored via the http://earthref.org/databases/PMAG/ link) and one for rock magnetism. The MagIC database will store all measurements and their derived properties for studies of paleomagnetic directions (inclination, declination) and their intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Ultimately, this database will allow researchers to study "on the internet" and to download important data sets that display paleo-secular variations in the intensity of the Earth's magnetic field over geological time, or that display magnetic data in typical Zijderveld, hysteresis/FORC and various magnetization/remanence diagrams. The MagIC database is completely integrated in the EarthRef.org relational database structure and thus benefits significantly from already-existing common database components, such as the EarthRef Reference Database (ERR) and Address Book (ERAB). The ERR allows researchers to find complete sets of literature resources as used in GERM (Geochemical Earth Reference Model), REM (Reference Earth Model) and MagIC. The ERAB contains addresses for all contributors to the EarthRef.org databases, and also for those who participated in data collection, archiving and analysis in the magnetic studies. Integration with these existing components will guarantee direct traceability to the original sources of the MagIC data and metadata. The MagIC database design focuses around the general workflow that results in the determination of typical paleomagnetic and rock magnetic analyses. This ensures that individual data points can be traced between the actual measurements and their associated specimen, sample, site, rock formation and locality. This permits a distinction between original and derived data, where the actual measurements are performed at the specimen level, and data at the sample level and higher are then derived products in the database. These relations will also allow recalculation of derived properties, such as site means, when new data becomes available for a specific locality. Data contribution to the MagIC database is critical in achieving a useful research tool. We have developed a standard data and metadata template that can be used to provide all data at the same time as publication. Software tools are provided to facilitate easy population of these templates. The tools allow for the import/export of data files in a delimited text format, and they provide some advanced functionality to validate data and to check internal coherence of the data in the template. During and after publication these standardized MagIC templates will be stored in the ERR database of EarthRef.org from where they can be downloaded at all times. Finally, the contents of these template files will be automatically parsed into the online relational database.

Under-coding of secondary conditions in coded hospital health data: Impact of co-existing conditions, death status and number of codes in a record.

PubMed

Peng, Mingkai; Southern, Danielle A; Williamson, Tyler; Quan, Hude

2017-12-01

This study examined the coding validity of hypertension, diabetes, obesity and depression related to the presence of their co-existing conditions, death status and the number of diagnosis codes in hospital discharge abstract database. We randomly selected 4007 discharge abstract database records from four teaching hospitals in Alberta, Canada and reviewed their charts to extract 31 conditions listed in Charlson and Elixhauser comorbidity indices. Conditions associated with the four study conditions were identified through multivariable logistic regression. Coding validity (i.e. sensitivity, positive predictive value) of the four conditions was related to the presence of their associated conditions. Sensitivity increased with increasing number of diagnosis code. Impact of death on coding validity is minimal. Coding validity of conditions is closely related to its clinical importance and complexity of patients' case mix. We recommend mandatory coding of certain secondary diagnosis to meet the need of health research based on administrative health data.

Relating polarizability to volume, ionization energy, electronegativity, hardness, moments of momentum, and other molecular properties

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

Blair, Shamus A.; Thakkar, Ajit J., E-mail: ajit@unb.ca

2014-08-21

Semiquantitative relationships between the mean static dipole polarizability and other molecular properties such as the volume, ionization energy, electronegativity, hardness, and moments of momentum are explored. The relationships are tested using density functional theory computations on the 1641 neutral, ground-state, organic molecules in the TABS database. The best polarizability approximations have median errors under 5%.

Relating polarizability to volume, ionization energy, electronegativity, hardness, moments of momentum, and other molecular properties.

PubMed

Blair, Shamus A; Thakkar, Ajit J

2014-08-21

Semiquantitative relationships between the mean static dipole polarizability and other molecular properties such as the volume, ionization energy, electronegativity, hardness, and moments of momentum are explored. The relationships are tested using density functional theory computations on the 1641 neutral, ground-state, organic molecules in the TABS database. The best polarizability approximations have median errors under 5%.

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.

Global Aerodynamic Modeling for Stall/Upset Recovery Training Using Efficient Piloted Flight Test Techniques

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.; Cunningham, Kevin; Hill, Melissa A.

2013-01-01

Flight test and modeling techniques were developed for efficiently identifying global aerodynamic models that can be used to accurately simulate stall, upset, and recovery on large transport airplanes. The techniques were developed and validated in a high-fidelity fixed-base flight simulator using a wind-tunnel aerodynamic database, realistic sensor characteristics, and a realistic flight deck representative of a large transport aircraft. Results demonstrated that aerodynamic models for stall, upset, and recovery can be identified rapidly and accurately using relatively simple piloted flight test maneuvers. Stall maneuver predictions and comparisons of identified aerodynamic models with data from the underlying simulation aerodynamic database were used to validate the techniques.

The Reach Address Database (RAD)

EPA Pesticide Factsheets

The Reach Address Database (RAD) stores reach address information for each Water Program feature that has been linked to the underlying surface water features (streams, lakes, etc) in the National Hydrology Database (NHD) Plus dataset.

MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.

PubMed

Kalyanaraman, Ananth; Cannon, William R; Latt, Benjamin; Baxter, Douglas J

2011-11-01

A MapReduce-based implementation called MR-MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs. The source code along with user documentation are available on http://compbio.eecs.wsu.edu/MR-MSPolygraph. ananth@eecs.wsu.edu; william.cannon@pnnl.gov. Supplementary data are available at Bioinformatics online.

PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine

PubMed Central

Lee, Ji-Hyun; Park, Kyoung Mii; Han, Dong-Jin; Bang, Nam Young; Kim, Do-Hee; Na, Hyeongjin; Lim, Semi; Kim, Tae Bum; Kim, Dae Gyu; Kim, Hyun-Jung; Chung, Yeonseok; Sung, Sang Hyun; Surh, Young-Joon; Kim, Sunghoon; Han, Byung Woo

2015-01-01

Despite the growing attention given to Traditional Medicine (TM) worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM) database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound), disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software) and BioMart (a data federation framework) for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org. PMID:26555441

Distributed data collection for a database of radiological image interpretations

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Ostchega, Yechiam; Goh, Gin-Hua; Thoma, George R.

1997-01-01

The National Library of Medicine, in collaboration with the National Center for Health Statistics and the National Institute for Arthritis and Musculoskeletal and Skin Diseases, has built a system for collecting radiological interpretations for a large set of x-ray images acquired as part of the data gathered in the second National Health and Nutrition Examination Survey. This system is capable of delivering across the Internet 5- and 10-megabyte x-ray images to Sun workstations equipped with X Window based 2048 X 2560 image displays, for the purpose of having these images interpreted for the degree of presence of particular osteoarthritic conditions in the cervical and lumbar spines. The collected interpretations can then be stored in a database at the National Library of Medicine, under control of the Illustra DBMS. This system is a client/server database application which integrates (1) distributed server processing of client requests, (2) a customized image transmission method for faster Internet data delivery, (3) distributed client workstations with high resolution displays, image processing functions and an on-line digital atlas, and (4) relational database management of the collected data.

The HARPS-N archive through a Cassandra, NoSQL database suite?

NASA Astrophysics Data System (ADS)

Molinari, Emilio; Guerra, Jose; Harutyunyan, Avet; Lodi, Marcello; Martin, Adrian

2016-07-01

The TNG-INAF is developing the science archive for the WEAVE instrument. The underlying architecture of the archive is based on a non relational database, more precisely, on Apache Cassandra cluster, which uses a NoSQL technology. In order to test and validate the use of this architecture, we created a local archive which we populated with all the HARPSN spectra collected at the TNG since the instrument's start of operations in mid-2012, as well as developed tools for the analysis of this data set. The HARPS-N data set is two orders of magnitude smaller than WEAVE, but we want to demonstrate the ability to walk through a complete data set and produce scientific output, as valuable as that produced by an ordinary pipeline, though without accessing directly the FITS files. The analytics is done by Apache Solr and Spark and on a relational PostgreSQL database. As an example, we produce observables like metallicity indexes for the targets in the archive and compare the results with the ones coming from the HARPS-N regular data reduction software. The aim of this experiment is to explore the viability of a high availability cluster and distributed NoSQL database as a platform for complex scientific analytics on a large data set, which will then be ported to the WEAVE Archive System (WAS) which we are developing for the WEAVE multi object, fiber spectrograph.

An expression database for roots of the model legume Medicago truncatula under salt stress

PubMed Central

2009-01-01

Background Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. Description The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. Conclusion MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/. PMID:19906315

An expression database for roots of the model legume Medicago truncatula under salt stress.

PubMed

Li, Daofeng; Su, Zhen; Dong, Jiangli; Wang, Tao

2009-11-11

Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.

The mini mental state examination at the time of Alzheimer's disease and related disorders diagnosis, according to age, education, gender and place of residence: a cross-sectional study among the French National Alzheimer database.

PubMed

Pradier, Christian; Sakarovitch, Charlotte; Le Duff, Franck; Layese, Richard; Metelkina, Asya; Anthony, Sabine; Tifratene, Karim; Robert, Philippe

2014-01-01

was firstly to describe the MMSE (Mini-Mental State Examination) score upon initial diagnosis of Alzheimer's disease and related disorders among the French population, according to age. Secondly, education, gender and place of residence were studied as factors potentially associated with delayed Alzheimer's disease diagnosis. we conducted a cross sectional analysis of the French National Alzheimer database (BNA). Data from 2008 to 2012 were extracted. Patients were selected at the moment of their first diagnosis of AD (n = 39,451). The MMSE score at initial diagnosis dropped significantly with increasing age. The test score increased with the degree of educational background regardless of age. Gender and place of residence were significantly related to the MMSE score, women and persons living in medical institutions having lower MMSE scores under the age of 90 years and at all educational levels. Health care professionals should be aware of these risk factors in order to maximize chances of earliest possible diagnosis of Alzheimer's disease and related disorders.

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

PubMed

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

2015-09-01

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

24 CFR 990.200 - Determination of formula amount.

Code of Federal Regulations, 2010 CFR

2010-04-01

... part) and its formula income (as calculated under subpart D of this part). (b) Use of HUD databases to calculate formula amount. HUD shall utilize its databases to make the formula calculations. HUD's databases... units in HUD's databases. (c) PHA responsibility to submit timely data. PHAs shall submit data used in...

24 CFR 990.200 - Determination of formula amount.

Code of Federal Regulations, 2012 CFR

2012-04-01

... part) and its formula income (as calculated under subpart D of this part). (b) Use of HUD databases to calculate formula amount. HUD shall utilize its databases to make the formula calculations. HUD's databases... units in HUD's databases. (c) PHA responsibility to submit timely data. PHAs shall submit data used in...

24 CFR 990.200 - Determination of formula amount.

Code of Federal Regulations, 2013 CFR

2013-04-01

... part) and its formula income (as calculated under subpart D of this part). (b) Use of HUD databases to calculate formula amount. HUD shall utilize its databases to make the formula calculations. HUD's databases... units in HUD's databases. (c) PHA responsibility to submit timely data. PHAs shall submit data used in...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

24 CFR 990.200 - Determination of formula amount.

Code of Federal Regulations, 2014 CFR

2014-04-01

... part) and its formula income (as calculated under subpart D of this part). (b) Use of HUD databases to calculate formula amount. HUD shall utilize its databases to make the formula calculations. HUD's databases... units in HUD's databases. (c) PHA responsibility to submit timely data. PHAs shall submit data used in...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

24 CFR 990.200 - Determination of formula amount.

Code of Federal Regulations, 2011 CFR

2011-04-01

... part) and its formula income (as calculated under subpart D of this part). (b) Use of HUD databases to calculate formula amount. HUD shall utilize its databases to make the formula calculations. HUD's databases... units in HUD's databases. (c) PHA responsibility to submit timely data. PHAs shall submit data used in...

75 FR 4827 - Submission for OMB Review; Comment Request Clinical Trials Reporting Program (CTRP) Database (NCI)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

...; Comment Request Clinical Trials Reporting Program (CTRP) Database (NCI) Summary: Under the provisions of... Collection: Title: Clinical Trials Reporting Program (CTRP) Database. Type of Information Collection Request... Program (CTRP) Database, to serve as a single, definitive source of information about all NCI-supported...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

A Relational Database System for Student Use.

ERIC Educational Resources Information Center

Fertuck, Len

1982-01-01

Describes an APL implementation of a relational database system suitable for use in a teaching environment in which database development and database administration are studied, and discusses the functions of the user and the database administrator. An appendix illustrating system operation and an eight-item reference list are attached. (Author/JL)

Relational-database model for improving quality assurance and process control in a composite manufacturing environment

NASA Astrophysics Data System (ADS)

Gentry, Jeffery D.

2000-05-01

A relational database is a powerful tool for collecting and analyzing the vast amounts of inner-related data associated with the manufacture of composite materials. A relational database contains many individual database tables that store data that are related in some fashion. Manufacturing process variables as well as quality assurance measurements can be collected and stored in database tables indexed according to lot numbers, part type or individual serial numbers. Relationships between manufacturing process and product quality can then be correlated over a wide range of product types and process variations. This paper presents details on how relational databases are used to collect, store, and analyze process variables and quality assurance data associated with the manufacture of advanced composite materials. Important considerations are covered including how the various types of data are organized and how relationships between the data are defined. Employing relational database techniques to establish correlative relationships between process variables and quality assurance measurements is then explored. Finally, the benefits of database techniques such as data warehousing, data mining and web based client/server architectures are discussed in the context of composite material manufacturing.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Searching the ASRS Database Using QUORUM Keyword Search, Phrase Search, Phrase Generation, and Phrase Discovery

NASA Technical Reports Server (NTRS)

McGreevy, Michael W.; Connors, Mary M. (Technical Monitor)

2001-01-01

To support Search Requests and Quick Responses at the Aviation Safety Reporting System (ASRS), four new QUORUM methods have been developed: keyword search, phrase search, phrase generation, and phrase discovery. These methods build upon the core QUORUM methods of text analysis, modeling, and relevance-ranking. QUORUM keyword search retrieves ASRS incident narratives that contain one or more user-specified keywords in typical or selected contexts, and ranks the narratives on their relevance to the keywords in context. QUORUM phrase search retrieves narratives that contain one or more user-specified phrases, and ranks the narratives on their relevance to the phrases. QUORUM phrase generation produces a list of phrases from the ASRS database that contain a user-specified word or phrase. QUORUM phrase discovery finds phrases that are related to topics of interest. Phrase generation and phrase discovery are particularly useful for finding query phrases for input to QUORUM phrase search. The presentation of the new QUORUM methods includes: a brief review of the underlying core QUORUM methods; an overview of the new methods; numerous, concrete examples of ASRS database searches using the new methods; discussion of related methods; and, in the appendices, detailed descriptions of the new methods.

Relational Databases and Biomedical Big Data.

PubMed

de Silva, N H Nisansa D

2017-01-01

In various biomedical applications that collect, handle, and manipulate data, the amounts of data tend to build up and venture into the range identified as bigdata. In such occurrences, a design decision has to be taken as to what type of database would be used to handle this data. More often than not, the default and classical solution to this in the biomedical domain according to past research is relational databases. While this used to be the norm for a long while, it is evident that there is a trend to move away from relational databases in favor of other types and paradigms of databases. However, it still has paramount importance to understand the interrelation that exists between biomedical big data and relational databases. This chapter will review the pros and cons of using relational databases to store biomedical big data that previous researches have discussed and used.

PropBase Query Layer: a single portal to UK subsurface physical property databases

NASA Astrophysics Data System (ADS)

Kingdon, Andrew; Nayembil, Martin L.; Richardson, Anne E.; Smith, A. Graham

2013-04-01

Until recently, the delivery of geological information for industry and public was achieved by geological mapping. Now pervasively available computers mean that 3D geological models can deliver realistic representations of the geometric location of geological units, represented as shells or volumes. The next phase of this process is to populate these with physical properties data that describe subsurface heterogeneity and its associated uncertainty. Achieving this requires capture and serving of physical, hydrological and other property information from diverse sources to populate these models. The British Geological Survey (BGS) holds large volumes of subsurface property data, derived both from their own research data collection and also other, often commercially derived data sources. This can be voxelated to incorporate this data into the models to demonstrate property variation within the subsurface geometry. All property data held by BGS has for many years been stored in relational databases to ensure their long-term continuity. However these have, by necessity, complex structures; each database contains positional reference data and model information, and also metadata such as sample identification information and attributes that define the source and processing. Whilst this is critical to assessing these analyses, it also hugely complicates the understanding of variability of the property under assessment and requires multiple queries to study related datasets making extracting physical properties from these databases difficult. Therefore the PropBase Query Layer has been created to allow simplified aggregation and extraction of all related data and its presentation of complex data in simple, mostly denormalized, tables which combine information from multiple databases into a single system. The structure from each relational database is denormalized in a generalised structure, so that each dataset can be viewed together in a common format using a simple interface. Data are re-engineered to facilitate easy loading. The query layer structure comprises tables, procedures, functions, triggers, views and materialised views. The structure contains a main table PRB_DATA which contains all of the data with the following attribution: • a unique identifier • the data source • the unique identifier from the parent database for traceability • the 3D location • the property type • the property value • the units • necessary qualifiers • precision information and an audit trail Data sources, property type and units are constrained by dictionaries, a key component of the structure which defines what properties and inheritance hierarchies are to be coded and also guides the process as to what and how these are extracted from the structure. Data types served by the Query Layer include site investigation derived geotechnical data, hydrogeology datasets, regional geochemistry, geophysical logs as well as lithological and borehole metadata. The size and complexity of the data sets with multiple parent structures requires a technically robust approach to keep the layer synchronised. This is achieved through Oracle procedures written in PL/SQL containing the logic required to carry out the data manipulation (inserts, updates, deletes) to keep the layer synchronised with the underlying databases either as regular scheduled jobs (weekly, monthly etc) or invoked on demand. The PropBase Query Layer's implementation has enabled rapid data discovery, visualisation and interpretation of geological data with greater ease, simplifying the parametrisation of 3D model volumes and facilitating the study of intra-unit heterogeneity.

Universal Index System

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

1993-01-01

The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

PubMed

Mishima, Hiroyuki; Aerts, Jan; Katayama, Toshiaki; Bonnal, Raoul J P; Yoshiura, Koh-ichiro

2012-09-21

The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

The Ruby UCSC API: accessing the UCSC genome database using Ruby

PubMed Central

2012-01-01

Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/. PMID:22994508

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.

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

PubMed

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

2007-01-01

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

A Relational Algebra Query Language for Programming Relational Databases

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Anderson, Nicole

2011-01-01

In this paper, we describe a Relational Algebra Query Language (RAQL) and Relational Algebra Query (RAQ) software product we have developed that allows database instructors to teach relational algebra through programming. Instead of defining query operations using mathematical notation (the approach commonly taken in database textbooks), students…

Identification of contaminant trends and data gaps for terrestrial vertebrates residing in northeastern estuaries of the United States

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Golden, N.H.; Erwin, R.M.; Ottinger, M.A.

1998-01-01

The Biomonitoring of Environmental Status and Trends (BEST) program of the Department of the Interior is focused to identify and understand effects of contaminant stressors on biological resources under their stewardship. One BEST program activity involves evaluation of retrospective data to assess and predict the condition of biota in Atlantic coast estuaries. A 'Contaminant Exposure and Effects--Terrestrial Vertebrates' database (CEE-TV) has been compiled through computerized literature searches of Fish and Wildlife Reviews, BIOSIS, AGRICOLA, and TOXLINE, review of existing databases (e.g., US EPA Ecological Incident Information System, USGS Diagnostic and Epizootic Databases), and solicitation of unpublished reports from conservation agencies, private groups, and universities. Summary information has been entered into the CEE-TV database, including species, collection date (1965-present), site coordinates, sample matrix, contaminant concentrations, biomarker and bioindicator responses, and reference source, utilizing a 96-field dBase format. Currently, the CEE-TV database contains 3500 georeferenced records representing >200 vertebrate species and > 100,000 individuals residing in estuaries from Maine through Florida. This relational database can be directly queried, imported into the ARC/INFO geographic information system (GIS) to examine spatial tendencies, and used to identify 'hot-spots', generate hypotheses, and focus ecotoxicological assessments. An overview of temporal, phylogenetic, and geographic contaminant exposure and effects information, trends, and data gaps will be presented for terrestrial vertebrates residing in estuaries in the northeast United States.

Disruption Warning Database Development and Exploratory Machine Learning Studies on Alcator C-Mod

NASA Astrophysics Data System (ADS)

Montes, Kevin; Rea, Cristina; Granetz, Robert

2017-10-01

A database of about 1800 shots from the 2015 campaign on the Alcator C-Mod tokamak is assembled, including disruptive and non-disruptive discharges. The database consists of 40 relevant plasma parameters with data taken from 160k time slices. In order to investigate the possibility of developing a robust disruption prediction algorithm that is tokamak-independent, we focused machine learning studies on a subset of dimensionless parameters such as βp, n /nG , etc. The Random Forests machine learning algorithm provides insight on the available data set by ranking the relative importance of the input features. Its application on the C-Mod database, however, reveals that virtually no one parameter has more importance than any other, and that its classification algorithm has a low rate of successfully predicted samples, as well as poor false positive and false negative rates. Comparing the analysis of this algorithm on the C-Mod database with its application to a similar database on DIII-D, we conclude that disruption prediction may not be feasible on C-Mod. This conclusion is supported by empirical observations that most C-Mod disruptions are caused by radiative collapse due to molybdenum from the first wall, which happens on just a 1-2ms timescale. Supported by the US Dept. of Energy under DE-FC02-99ER54512 and DE-FC02-04ER54698.

The NASA ASTP Combined-Cycle Propulsion Database Project

NASA Technical Reports Server (NTRS)

Hyde, Eric H.; Escher, Daric W.; Heck, Mary T.; Roddy, Jordan E.; Lyles, Garry (Technical Monitor)

2000-01-01

The National Aeronautics and Space Administration (NASA) communicated its long-term R&D goals for aeronautics and space transportation technologies in its 1997-98 annual progress report (Reference 1). Under "Pillar 3, Goal 9" a 25-year-horizon set of objectives has been stated for the Generation 3 Reusable Launch Vehicle ("Gen 3 RLV") class of space transportation systems. An initiative referred to as "Spaceliner 100" is being conducted to identify technology roadmaps in support of these objectives. Responsibility for running "Spaceliner 100" technology development and demonstration activities have been assigned to NASA's agency-wide Advanced Space Transportation Program (ASTP) office located at the Marshall Space Flight Center. A key technology area in which advances will be required in order to meet these objectives is propulsion. In 1996, in order to expand their focus beyond "allrocket" propulsion systems and technologies (see Appendix A for further discussion), ASTP initiated technology development and demonstration work on combined-cycle airbreathing/rocket propulsion systems (ARTT Contracts NAS8-40890 through 40894). Combined-cycle propulsion (CCP) activities (see Appendix B for definitions) have been pursued in the U.S. for over four decades, resulting in a large documented knowledge base on this subject (see Reference 2). In the fall of 1999 the Combined-Cycle Propulsion Database (CCPD) project was established with the primary purpose of collecting and consolidating CCP related technical information in support of the ASTP's ongoing technology development and demonstration program. Science Applications International Corporation (SAIC) was selected to perform the initial development of the Database under its existing support contract with MSFC (Contract NAS8-99060) because of the company's unique combination of capabilities in database development, information technology (IT) and CCP knowledge. The CCPD is summarized in the descriptive 2-page flyer appended to this paper as Appendix C. The purpose of this paper is to provide the reader with an understanding of the objectives of the CCPD and relate the progress that has been made toward meeting those objectives.

A dynamic clinical dental relational database.

PubMed

Taylor, D; Naguib, R N G; Boulton, S

2004-09-01

The traditional approach to relational database design is based on the logical organization of data into a number of related normalized tables. One assumption is that the nature and structure of the data is known at the design stage. In the case of designing a relational database to store historical dental epidemiological data from individual clinical surveys, the structure of the data is not known until the data is presented for inclusion into the database. This paper addresses the issues concerned with the theoretical design of a clinical dynamic database capable of adapting the internal table structure to accommodate clinical survey data, and presents a prototype database application capable of processing, displaying, and querying the dental data.

Exploring performance issues for a clinical database organized using an entity-attribute-value representation.

PubMed

Chen, R S; Nadkarni, P; Marenco, L; Levin, F; Erdos, J; Miller, P L

2000-01-01

The entity-attribute-value representation with classes and relationships (EAV/CR) provides a flexible and simple database schema to store heterogeneous biomedical data. In certain circumstances, however, the EAV/CR model is known to retrieve data less efficiently than conventionally based database schemas. To perform a pilot study that systematically quantifies performance differences for database queries directed at real-world microbiology data modeled with EAV/CR and conventional representations, and to explore the relative merits of different EAV/CR query implementation strategies. Clinical microbiology data obtained over a ten-year period were stored using both database models. Query execution times were compared for four clinically oriented attribute-centered and entity-centered queries operating under varying conditions of database size and system memory. The performance characteristics of three different EAV/CR query strategies were also examined. Performance was similar for entity-centered queries in the two database models. Performance in the EAV/CR model was approximately three to five times less efficient than its conventional counterpart for attribute-centered queries. The differences in query efficiency became slightly greater as database size increased, although they were reduced with the addition of system memory. The authors found that EAV/CR queries formulated using multiple, simple SQL statements executed in batch were more efficient than single, large SQL statements. This paper describes a pilot project to explore issues in and compare query performance for EAV/CR and conventional database representations. Although attribute-centered queries were less efficient in the EAV/CR model, these inefficiencies may be addressable, at least in part, by the use of more powerful hardware or more memory, or both.

Measuring Educators' Perceptions of Their Skills Relative to Response to Intervention: A Psychometric Study of a Survey Tool

ERIC Educational Resources Information Center

Castillo, Jose M.; March, Amanda L.; Stockslager, Kevin M.; Hines, Constance V.

2016-01-01

The "Perceptions of RtI Skills Survey" is a self-report measure that assesses educators' perceptions of their data-based problem-solving skills--a critical element of many Response-to-Intervention (RtI) models. Confirmatory factor analysis (CFA) was used to evaluate the underlying factor structure of this tool. Educators from 68 (n =…

A Quantum Private Query Protocol for Enhancing both User and Database Privacy

NASA Astrophysics Data System (ADS)

Zhou, Yi-Hua; Bai, Xue-Wei; Li, Lei-Lei; Shi, Wei-Min; Yang, Yu-Guang

2018-01-01

In order to protect the privacy of query user and database, some QKD-based quantum private query (QPQ) protocols were proposed. Unfortunately some of them cannot resist internal attack from database perfectly; some others can ensure better user privacy but require a reduction of database privacy. In this paper, a novel two-way QPQ protocol is proposed to ensure the privacy of both sides of communication. In our protocol, user makes initial quantum states and derives the key bit by comparing initial quantum state and outcome state returned from database by ctrl or shift mode instead of announcing two non-orthogonal qubits as others which may leak part secret information. In this way, not only the privacy of database be ensured but also user privacy is strengthened. Furthermore, our protocol can also realize the security of loss-tolerance, cheat-sensitive, and resisting JM attack etc. Supported by National Natural Science Foundation of China under Grant Nos. U1636106, 61572053, 61472048, 61602019, 61502016; Beijing Natural Science Foundation under Grant Nos. 4152038, 4162005; Basic Research Fund of Beijing University of Technology (No. X4007999201501); The Scientific Research Common Program of Beijing Municipal Commission of Education under Grant No. KM201510005016

Scaffolding across the lifespan in history-dependent decision-making.

PubMed

Cooper, Jessica A; Worthy, Darrell A; Gorlick, Marissa A; Maddox, W Todd

2013-06-01

We examined the relationship between pressure and age-related changes in decision-making using a task for which currently available rewards depend on the participant's previous history of choices. Optimal responding in this task requires the participant to learn how his or her current choices affect changes in the future rewards given for each option. Building on the scaffolding theory of aging and cognition, we predicted that when additional frontal resources are available, compensatory recruitment leads to increased monitoring and increased use of heuristic-based strategies, ultimately leading to better performance. Specifically, we predicted that scaffolding would result in an age-related performance advantage under no pressure conditions. We also predicted that, although younger adults would engage in scaffolding under pressure, older adults would not have additional resources available for increased scaffolding under pressure-packed conditions, leading to an age-related performance deficit. Both predictions were supported by the data. In addition, computational models were used to evaluate decision-making strategies employed by each participant group. As expected, older adults under no pressure conditions and younger adults under pressure conditions showed increased use of heuristic-based strategies relative to older adults under pressure and younger adults under no pressure, respectively. These results are consistent with the notion that scaffolding can occur across the life span in the face of an environmental challenge. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Covariance analysis for evaluating head trackers

NASA Astrophysics Data System (ADS)

Kang, Donghoon

2017-10-01

Existing methods for evaluating the performance of head trackers usually rely on publicly available face databases, which contain facial images and the ground truths of their corresponding head orientations. However, most of the existing publicly available face databases are constructed by assuming that a frontal head orientation can be determined by compelling the person under examination to look straight ahead at the camera on the first video frame. Since nobody can accurately direct one's head toward the camera, this assumption may be unrealistic. Rather than obtaining estimation errors, we present a method for computing the covariance of estimation error rotations to evaluate the reliability of head trackers. As an uncertainty measure of estimators, the Schatten 2-norm of a square root of error covariance (or the algebraic average of relative error angles) can be used. The merit of the proposed method is that it does not disturb the person under examination by asking him to direct his head toward certain directions. Experimental results using real data validate the usefulness of our method.

Autocommander: A Supervisory Controller for Integrated Guidance and Control for the 2nd Generation Reusable Launch Vehicle

NASA Technical Reports Server (NTRS)

Fisher, J. E.; Lawrence, D. A.; Zhu, J. J.; Jackson, Scott (Technical Monitor)

2002-01-01

This paper presents a hierarchical architecture for integrated guidance and control that achieves risk and cost reduction for NASA's 2d generation reusable launch vehicle (RLV). Guidance, attitude control, and control allocation subsystems that heretofore operated independently will now work cooperatively under the coordination of a top-level autocommander. In addition to delivering improved performance from a flight mechanics perspective, the autocommander is intended to provide an autonomous supervisory control capability for traditional mission management under nominal conditions, G&C reconfiguration in response to effector saturation, and abort mode decision-making upon vehicle malfunction. This high-level functionality is to be implemented through the development of a relational database that is populated with the broad range of vehicle and mission specific data and translated into a discrete event system model for analysis, simulation, and onboard implementation. A Stateflow Autocoder software tool that translates the database into the Stateflow component of a Matlab/Simulink simulation is also presented.

A proposed model for the flowering signaling pathway of sugarcane under photoperiodic control.

PubMed

Coelho, C P; Costa Netto, A P; Colasanti, J; Chalfun-Júnior, A

2013-04-25

Molecular analysis of floral induction in Arabidopsis has identified several flowering time genes related to 4 response networks defined by the autonomous, gibberellin, photoperiod, and vernalization pathways. Although grass flowering processes include ancestral functions shared by both mono- and dicots, they have developed their own mechanisms to transmit floral induction signals. Despite its high production capacity and its important role in biofuel production, almost no information is available about the flowering process in sugarcane. We searched the Sugarcane Expressed Sequence Tags database to look for elements of the flowering signaling pathway under photoperiodic control. Sequences showing significant similarity to flowering time genes of other species were clustered, annotated, and analyzed for conserved domains. Multiple alignments comparing the sequences found in the sugarcane database and those from other species were performed and their phylogenetic relationship assessed using the MEGA 4.0 software. Electronic Northerns were run with Cluster and TreeView programs, allowing us to identify putative members of the photoperiod-controlled flowering pathway of sugarcane.

Risk of pneumococcal diseases in adults with underlying medical conditions: a retrospective, cohort study using two Japanese healthcare databases.

PubMed

Imai, Kentaro; Petigara, Tanaz; Kohn, Melvin A; Nakashima, Kei; Aoshima, Masahiro; Shito, Akihito; Kanazu, Shinichi

2018-03-02

To quantify the risk of pneumococcal pneumonia (PP) and invasive pneumococcal disease (IPD) in adults aged ≥19 years with underlying medical conditions compared with healthy adults of the same age in Japan. An observational, retrospective, cohort study using two healthcare claims databases in Japan: Japan Medical Data Center (JMDC) and Medical Data Vision (MDV) databases. A total of 10.4 million individuals, representing 9.3 million person-years of follow-up, were included in the analysis. Eleven medical conditions as well as PP and IPD were identified by the International Statistical Classification of Diseases and Related Health Problems version 10 diagnostic codes and/or local disease codes used in Japan. Adjusted rate ratios (RRs) for PP and IPD in adults with a medical condition versus adults without any medical condition were calculated using multivariate Poisson regression models with age and/or sex as covariates. In the JMDC and MDV databases, respectively, adults ≥19 years with a medical condition (RRs for PP: 3.3 to 13.4, 1.7 to 5.2; RRs for IPD: 12.6 to 43.3, 4.4 to 7.1), adults with two or more medical conditions (PP: 11.6, 2.8; IPD: 18.7, 5.8) and high-risk adults (PP: 12.9, 1.8; IPD: 29.7, 4.0) were at greater risk of PP and IPD compared with their healthy counterparts. Adults aged 50-64 years with an underlying medical condition (PP rate: 38.6 to 212.1 per 100 000 person-years) had a higher rate of PP than those aged ≥65 years without any condition (PP rate: 13.2 to 93.0 per 100 000 person-years). Adults of all ages with an underlying medical condition are at greater risk of PP and IPD compared with adults without any medical condition. This risk increases with the number of underlying medical conditions. Our results support extending pneumococcal vaccination to younger adults with an underlying medical condition, especially those aged 50-64 years. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The Danish Testicular Cancer database.

PubMed

Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel; Mortensen, Mette Saksø; Larsson, Heidi; Søgaard, Mette; Toft, Birgitte Groenkaer; Engvad, Birte; Agerbæk, Mads; Holm, Niels Vilstrup; Lauritsen, Jakob

2016-01-01

The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients.

Alternatives to relational database: comparison of NoSQL and XML approaches for clinical data storage.

PubMed

Lee, Ken Ka-Yin; Tang, Wai-Choi; Choi, Kup-Sze

2013-04-01

Clinical data are dynamic in nature, often arranged hierarchically and stored as free text and numbers. Effective management of clinical data and the transformation of the data into structured format for data analysis are therefore challenging issues in electronic health records development. Despite the popularity of relational databases, the scalability of the NoSQL database model and the document-centric data structure of XML databases appear to be promising features for effective clinical data management. In this paper, three database approaches--NoSQL, XML-enabled and native XML--are investigated to evaluate their suitability for structured clinical data. The database query performance is reported, together with our experience in the databases development. The results show that NoSQL database is the best choice for query speed, whereas XML databases are advantageous in terms of scalability, flexibility and extensibility, which are essential to cope with the characteristics of clinical data. While NoSQL and XML technologies are relatively new compared to the conventional relational database, both of them demonstrate potential to become a key database technology for clinical data management as the technology further advances. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

PubMed

Hancock, David; Wilson, Michael; Velarde, Giles; Morrison, Norman; Hayes, Andrew; Hulme, Helen; Wood, A Joseph; Nashar, Karim; Kell, Douglas B; Brass, Andy

2005-11-03

maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

NASA Astrophysics Data System (ADS)

Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.; Genevey, A.; Delaney, R.; Baker, P.; Sbarbori, E.

2005-12-01

The Magnetics Information Consortium (MagIC) operates an online relational database including both rock and paleomagnetic data. The goal of MagIC is to store all measurements and their derived properties for studies of paleomagnetic directions (inclination, declination) and their intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. These nodes provide basic search capabilities based on location, reference, methods applied, material type and geological age, while allowing the user to drill down from sites all the way to the measurements. At each stage, the data can be saved and, if the available data supports it, the data can be visualized by plotting equal area plots, VGP location maps or typical Zijderveld, hysteresis, FORC, and various magnetization and remanence diagrams. All plots are made in SVG (scalable vector graphics) and thus can be saved and easily read into the user's favorite graphics programs without loss of resolution. User contributions to the MagIC database are critical to achieve a useful research tool. We have developed a standard data and metadata template (version 1.6) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate easy population of these templates within Microsoft Excel. These tools allow for the import/export of text files and they provide advanced functionality to manage/edit the data, and to perform various internal checks to high grade the data and to make them ready for uploading. The uploading is all done online by using the MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm that takes only a few minutes to process a contribution of approximately 5,000 data records. After uploading these standardized MagIC template files will be stored in the digital archives of EarthRef.org from where they can be downloaded at all times. Finally, the contents of these template files will be automatically parsed into the online relational database, making the data available for online searches in the paleomagnetic and rock magnetic search nodes. The MagIC database contains all data transferred from the IAGA paleomagnetic poles database (GPMDB), the lava flow paleosecular variation database (PSVRL), lake sediment database (SECVR) and the PINT database. In addition to that a substantial number of data compiled under the Time Averaged Field Investigations project is now included plus a significant fraction of the data collected at SIO and the IRM. Ongoing additions of legacy data include ~40 papers from studies on the Hawaiian Islands, data compilations from archeomagnetic studies and updates to the lake sediment dataset.

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.

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.

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. ...

Using SQL Databases for Sequence Similarity Searching and Analysis.

PubMed

Pearson, William R; Mackey, Aaron J

2017-09-13

Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Towards linked open gene mutations data

PubMed Central

2012-01-01

Background With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. Methods A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. Results We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. Conclusions This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development. The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine. PMID:22536974

Towards linked open gene mutations data.

PubMed

Zappa, Achille; Splendiani, Andrea; Romano, Paolo

2012-03-28

With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.

HypoxiaDB: a database of hypoxia-regulated proteins

PubMed Central

Khurana, Pankaj; Sugadev, Ragumani; Jain, Jaspreet; Singh, Shashi Bala

2013-01-01

There has been intense interest in the cellular response to hypoxia, and a large number of differentially expressed proteins have been identified through various high-throughput experiments. These valuable data are scattered, and there have been no systematic attempts to document the various proteins regulated by hypoxia. Compilation, curation and annotation of these data are important in deciphering their role in hypoxia and hypoxia-related disorders. Therefore, we have compiled HypoxiaDB, a database of hypoxia-regulated proteins. It is a comprehensive, manually-curated, non-redundant catalog of proteins whose expressions are shown experimentally to be altered at different levels and durations of hypoxia. The database currently contains 72 000 manually curated entries taken on 3500 proteins extracted from 73 peer-reviewed publications selected from PubMed. HypoxiaDB is distinctive from other generalized databases: (i) it compiles tissue-specific protein expression changes under different levels and duration of hypoxia. Also, it provides manually curated literature references to support the inclusion of the protein in the database and establish its association with hypoxia. (ii) For each protein, HypoxiaDB integrates data on gene ontology, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, protein–protein interactions, protein family (Pfam), OMIM (Online Mendelian Inheritance in Man), PDB (Protein Data Bank) structures and homology to other sequenced genomes. (iii) It also provides pre-compiled information on hypoxia-proteins, which otherwise requires tedious computational analysis. This includes information like chromosomal location, identifiers like Entrez, HGNC, Unigene, Uniprot, Ensembl, Vega, GI numbers and Genbank accession numbers associated with the protein. These are further cross-linked to respective public databases augmenting HypoxiaDB to the external repositories. (iv) In addition, HypoxiaDB provides an online sequence-similarity search tool for users to compare their protein sequences with HypoxiaDB protein database. We hope that HypoxiaDB will enrich our knowledge about hypoxia-related biology and eventually will lead to the development of novel hypothesis and advancements in diagnostic and therapeutic activities. HypoxiaDB is freely accessible for academic and non-profit users via http://www.hypoxiadb.com. Database URL: http://www.hypoxiadb.com PMID:24178989

System, method and apparatus for generating phrases from a database

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A phrase generation is a method of generating sequences of terms, such as phrases, that may occur within a database of subsets containing sequences of terms, such as text. A database is provided and a relational model of the database is created. A query is then input. The query includes a term or a sequence of terms or multiple individual terms or multiple sequences of terms or combinations thereof. Next, several sequences of terms that are contextually related to the query are assembled from contextual relations in the model of the database. The sequences of terms are then sorted and output. Phrase generation can also be an iterative process used to produce sequences of terms from a relational model of a database.

Interactive entity resolution in relational data: a visual analytic tool and its evaluation.

PubMed

Kang, Hyunmo; Getoor, Lise; Shneiderman, Ben; Bilgic, Mustafa; Licamele, Louis

2008-01-01

Databases often contain uncertain and imprecise references to real-world entities. Entity resolution, the process of reconciling multiple references to underlying real-world entities, is an important data cleaning process required before accurate visualization or analysis of the data is possible. In many cases, in addition to noisy data describing entities, there is data describing the relationships among the entities. This relational data is important during the entity resolution process; it is useful both for the algorithms which determine likely database references to be resolved and for visual analytic tools which support the entity resolution process. In this paper, we introduce a novel user interface, D-Dupe, for interactive entity resolution in relational data. D-Dupe effectively combines relational entity resolution algorithms with a novel network visualization that enables users to make use of an entity's relational context for making resolution decisions. Since resolution decisions often are interdependent, D-Dupe facilitates understanding this complex process through animations which highlight combined inferences and a history mechanism which allows users to inspect chains of resolution decisions. An empirical study with 12 users confirmed the benefits of the relational context visualization on the performance of entity resolution tasks in relational data in terms of time as well as users' confidence and satisfaction.

MySQL/PHP web database applications for IPAC proposal submission

NASA Astrophysics Data System (ADS)

Crane, Megan K.; Storrie-Lombardi, Lisa J.; Silbermann, Nancy A.; Rebull, Luisa M.

2008-07-01

The Infrared Processing and Analysis Center (IPAC) is NASA's multi-mission center of expertise for long-wavelength astrophysics. Proposals for various IPAC missions and programs are ingested via MySQL/PHP web database applications. Proposers use web forms to enter coversheet information and upload PDF files related to the proposal. Upon proposal submission, a unique directory is created on the webserver into which all of the uploaded files are placed. The coversheet information is converted into a PDF file using a PHP extension called FPDF. The files are concatenated into one PDF file using the command-line tool pdftk and then forwarded to the review committee. This work was performed at the California Institute of Technology under contract to the National Aeronautics and Space Administration.

OOMM--Object-Oriented Matrix Modelling: an instrument for the integration of the Brasilia Regional Health Information System.

PubMed

Cammarota, M; Huppes, V; Gaia, S; Degoulet, P

1998-01-01

The development of Health Information Systems is widely determined by the establishment of the underlying information models. An Object-Oriented Matrix Model (OOMM) is described which target is to facilitate the integration of the overall health system. The model is based on information modules named micro-databases that are structured in a three-dimensional network: planning, health structures and information systems. The modelling tool has been developed as a layer on top of a relational database system. A visual browser facilitates the development and maintenance of the information model. The modelling approach has been applied to the Brasilia University Hospital since 1991. The extension of the modelling approach to the Brasilia regional health system is considered.

A fragile zero watermarking scheme to detect and characterize malicious modifications in database relations.

PubMed

Khan, Aihab; Husain, Syed Afaq

2013-01-01

We put forward a fragile zero watermarking scheme to detect and characterize malicious modifications made to a database relation. Most of the existing watermarking schemes for relational databases introduce intentional errors or permanent distortions as marks into the database original content. These distortions inevitably degrade the data quality and data usability as the integrity of a relational database is violated. Moreover, these fragile schemes can detect malicious data modifications but do not characterize the tempering attack, that is, the nature of tempering. The proposed fragile scheme is based on zero watermarking approach to detect malicious modifications made to a database relation. In zero watermarking, the watermark is generated (constructed) from the contents of the original data rather than introduction of permanent distortions as marks into the data. As a result, the proposed scheme is distortion-free; thus, it also resolves the inherent conflict between security and imperceptibility. The proposed scheme also characterizes the malicious data modifications to quantify the nature of tempering attacks. Experimental results show that even minor malicious modifications made to a database relation can be detected and characterized successfully.

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

Statistical EMC: A new dimension electromagnetic compatibility of digital electronic systems

NASA Astrophysics Data System (ADS)

Tsaliovich, Anatoly

Electromagnetic compatibility compliance test results are used as a database for addressing three classes of electromagnetic-compatibility (EMC) related problems: statistical EMC profiles of digital electronic systems, the effect of equipment-under-test (EUT) parameters on the electromagnetic emission characteristics, and EMC measurement specifics. Open area test site (OATS) and absorber line shielded room (AR) results are compared for equipment-under-test highest radiated emissions. The suggested statistical evaluation methodology can be utilized to correlate the results of different EMC test techniques, characterize the EMC performance of electronic systems and components, and develop recommendations for electronic product optimal EMC design.

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

PubMed

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

2005-01-01

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

A Tool for Conditions Tag Management in ATLAS

NASA Astrophysics Data System (ADS)

Sharmazanashvili, A.; Batiashvili, G.; Gvaberidze, G.; Shekriladze, L.; Formica, A.; Atlas Collaboration

2014-06-01

ATLAS Conditions data include about 2 TB in a relational database and 400 GB of files referenced from the database. Conditions data is entered and retrieved using COOL, the API for accessing data in the LCG Conditions Database infrastructure. It is managed using an ATLAS-customized python based tool set. Conditions data are required for every reconstruction and simulation job, so access to them is crucial for all aspects of ATLAS data taking and analysis, as well as by preceding tasks to derive optimal corrections to reconstruction. Optimized sets of conditions for processing are accomplished using strict version control on those conditions: a process which assigns COOL Tags to sets of conditions, and then unifies those conditions over data-taking intervals into a COOL Global Tag. This Global Tag identifies the set of conditions used to process data so that the underlying conditions can be uniquely identified with 100% reproducibility should the processing be executed again. Understanding shifts in the underlying conditions from one tag to another and ensuring interval completeness for all detectors for a set of runs to be processed is a complex task, requiring tools beyond the above mentioned python utilities. Therefore, a JavaScript /PHP based utility called the Conditions Tag Browser (CTB) has been developed. CTB gives detector and conditions experts the possibility to navigate through the different databases and COOL folders; explore the content of given tags and the differences between them, as well as their extent in time; visualize the content of channels associated with leaf tags. This report describes the structure and PHP/ JavaScript classes of functions of the CTB.

A natural language interface plug-in for cooperative query answering in biological databases.

PubMed

Jamil, Hasan M

2012-06-11

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed using sophisticated tools. In such highly interpretive environments, rigidly structured databases do not always perform well. In this paper, our goal is to propose a semantic correspondence plug-in to aid natural language query processing over arbitrary biological database schema with an aim to providing cooperative responses to queries tailored to users' interpretations. Natural language interfaces for databases are generally effective when they are tuned to the underlying database schema and its semantics. Therefore, changes in database schema become impossible to support, or a substantial reorganization cost must be absorbed to reflect any change. We leverage developments in natural language parsing, rule languages and ontologies, and data integration technologies to assemble a prototype query processor that is able to transform a natural language query into a semantically equivalent structured query over the database. We allow knowledge rules and their frequent modifications as part of the underlying database schema. The approach we adopt in our plug-in overcomes some of the serious limitations of many contemporary natural language interfaces, including support for schema modifications and independence from underlying database schema. The plug-in introduced in this paper is generic and facilitates connecting user selected natural language interfaces to arbitrary databases using a semantic description of the intended application. We demonstrate the feasibility of our approach with a practical example.

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

PubMed

Wickens, C D; Seidler, K S

1997-09-01

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

Estrogen alters the profile of the transcriptome in river snail Bellamya aeruginosa.

PubMed

Lei, Kun; Liu, Ruizhi; An, Li-Hui; Luo, Ying-Feng; LeBlanc, Gerald A

2015-03-01

We evaluated the transcriptome dynamics of the freshwater river snail Bellamya aeruginosa exposed to 17β-estradiol (E2) using the Roche/454 GS-FLX platform. In total, 41,869 unigenes, with an average length of 586 bp, representing 36,181 contigs and 5,688 singlets were obtained. Among them, 18.08, 36.85, and 25.47 % matched sequences in the GenBank non-redundant nucleic acid database, non-redundant protein database, and Swiss protein database, respectively. Annotation of the unigenes with gene ontology, and then mapping them to biological pathways, revealed large groups of genes related to growth, development, reproduction, signal transduction, and defense mechanisms. Significant differences were found in gene expression in both liver and testicular tissues between control and E2-exposed organisms. These changes in gene expression will help in understanding the molecular mechanisms of the response to physiological stress in the river snail exposed to estrogen, and will facilitate research into biological processes and underlying physiological adaptations to xenoestrogen exposure in gastropods.

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

Integrative neuroscience: the role of a standardized database.

PubMed

Gordon, E; Cooper, N; Rennie, C; Hermens, D; Williams, L M

2005-04-01

Most brain related databases bring together specialized information, with a growing number that include neuroimaging measures. This article outlines the potential use and insights from the first entirely standardized and centralized database, which integrates information from neuroimaging measures (EEG, event related potential (ERP), structural/functional MRI), arousal (skin conductance responses (SCR)s, heart rate, respiration), neuropsychological and personality tests, genomics and demographics: The Brain Resource International Database. It comprises data from over 2000 "normative" subjects and a growing number of patients with neurological and psychiatric illnesses, acquired from over 50 laboratories (in the U.S.A, United Kingdom, Holland, South Africa, Israel and Australia), all with identical equipment and experimental procedures. Three primary goals of this database are to quantify individual differences in normative brain function, to compare an individual's performance to their database peers, and to provide a robust normative framework for clinical assessment and treatment prediction. We present three example demonstrations in relation to these goals. First, we show how consistent age differences may be quantified when large subject numbers are available, using EEG and ERP data from nearly 2000 stringently screened. normative subjects. Second, the use of a normalization technique provides a means to compare clinical subjects (50 ADHD subjects in this study) to the normative database with the effects of age and gender taken into account. Third, we show how a profile of EEG/ERP and autonomic measures potentially provides a means to predict treatment response in ADHD subjects. The example data consists of EEG under eyes open and eyes closed and ERP data for auditory oddball, working memory and Go-NoGo paradigms. Autonomic measures of skin conductance (tonic skin conductance level, SCL, and phasic skin conductance responses, SCRs) were acquired simultaneously with central EEG/ERP measures. The findings show that the power of large samples, tested using standardized protocols, allows for the quantification of individual differences that can subsequently be used to control such variation and to enhance the sensitivity and specificity of comparisons between normative and clinical groups. In terms of broader significance, the combination of size and multidimensional measures tapping the brain's core cognitive competencies, may provide a normative and evidence-based framework for individually-based assessments in "Personalized Medicine."

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

ToxReporter: viewing the genome through the eyes of a toxicologist.

PubMed

Gosink, Mark

2016-01-01

One of the many roles of a toxicologist is to determine if an observed adverse event (AE) is related to a previously unrecognized function of a given gene/protein. Towards that end, he or she will search a variety of public and propriety databases for information linking that protein to the observed AE. However, these databases tend to present all available information about a protein, which can be overwhelming, limiting the ability to find information about the specific toxicity being investigated. ToxReporter compiles information from a broad selection of resources and limits display of the information to user-selected areas of interest. ToxReporter is a PERL-based web-application which utilizes a MySQL database to streamline this process by categorizing public and proprietary domain-derived information into predefined safety categories according to a customizable lexicon. Users can view gene information that is 'red-flagged' according to the safety issue under investigation. ToxReporter also uses a scoring system based on relative counts of the red-flags to rank all genes for the amount of information pertaining to each safety issue and to display their scored ranking as an easily interpretable 'Tox-At-A-Glance' chart. Although ToxReporter was originally developed to display safety information, its flexible design could easily be adapted to display disease information as well.Database URL: ToxReporter is freely available at https://github.com/mgosink/ToxReporter. © The Author(s) 2016. Published by Oxford University Press.

Missouri River Flood 2011 Vulnerabilities Assessment Report. Volume 2 - Technical Report

DTIC Science & Technology

2012-10-01

202 Figure 98. Dams damage/erosion: Gavins Point - Excess debris led to clogging of water intake at Hydropower Plant (under...and a description of the economic vulnerabilities related to Missouri River flooding, even beyond the impacts from 2011. 2.4.1.1 Geographic Extent...Database, 2011. Two nuclear power plants are located within the floodplain, which poses potential risks to health and safety of nearby populations as a

Mechanical Properties of Plasma-Sprayed ZrO2-8 wt% Y2O3 Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Choi, Sung R.; Zhu, Dongming; Miller, Robert A.

2004-01-01

Mechanical behavior of free standing, plasma-sprayed ZrO2-8 wt% Y2O3 thermal barrier coatings, including strength, fracture toughness, fatigue, constitutive relation, elastic modulus, and directionality, has been determined under various loading-specimen configurations. This report presents and describes a summary of mechanical properties of the plasma-sprayed coating material to provide them as a design database.

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

PubMed

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

2000-01-01

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

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

PubMed Central

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

2000-01-01

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

Aviation Trends Related to Atmospheric Environment Safety Technologies Project Technical Challenges

NASA Technical Reports Server (NTRS)

Reveley, Mary S.; Withrow, Colleen A.; Barr, Lawrence C.; Evans, Joni K.; Leone, Karen M.; Jones, Sharon M.

2014-01-01

Current and future aviation safety trends related to the National Aeronautics and Space Administration's Atmospheric Environment Safety Technologies Project's three technical challenges (engine icing characterization and simulation capability; airframe icing simulation and engineering tool capability; and atmospheric hazard sensing and mitigation technology capability) were assessed by examining the National Transportation Safety Board (NTSB) accident database (1989 to 2008), incidents from the Federal Aviation Administration (FAA) accident/incident database (1989 to 2006), and literature from various industry and government sources. The accident and incident data were examined for events involving fixed-wing airplanes operating under Federal Aviation Regulation (FAR) Parts 121, 135, and 91 for atmospheric conditions related to airframe icing, ice-crystal engine icing, turbulence, clear air turbulence, wake vortex, lightning, and low visibility (fog, low ceiling, clouds, precipitation, and low lighting). Five future aviation safety risk areas associated with the three AEST technical challenges were identified after an exhaustive survey of a variety of sources and include: approach and landing accident reduction, icing/ice detection, loss of control in flight, super density operations, and runway safety.

Why Save Your Course as a Relational Database?

ERIC Educational Resources Information Center

Hamilton, Gregory C.; Katz, David L.; Davis, James E.

2000-01-01

Describes a system that stores course materials for computer-based training programs in a relational database called Of Course! Outlines the basic structure of the databases; explains distinctions between Of Course! and other authoring languages; and describes how data is retrieved from the database and presented to the student. (Author/LRW)

Simple Logic for Big Problems: An Inside Look at Relational Databases.

ERIC Educational Resources Information Center

Seba, Douglas B.; Smith, Pat

1982-01-01

Discusses database design concept termed "normalization" (process replacing associations between data with associations in two-dimensional tabular form) which results in formation of relational databases (they are to computers what dictionaries are to spoken languages). Applications of the database in serials control and complex systems…

Relational Database Design in Information Science Education.

ERIC Educational Resources Information Center

Brooks, Terrence A.

1985-01-01

Reports on database management system (dbms) applications designed by library school students for university community at University of Iowa. Three dbms design issues are examined: synthesis of relations, analysis of relations (normalization procedure), and data dictionary usage. Database planning prior to automation using data dictionary approach…

Overview of Nuclear Physics Data: Databases, Web Applications and Teaching Tools

NASA Astrophysics Data System (ADS)

McCutchan, Elizabeth

2017-01-01

The mission of the United States Nuclear Data Program (USNDP) is to provide current, accurate, and authoritative data for use in pure and applied areas of nuclear science and engineering. This is accomplished by compiling, evaluating, and disseminating extensive datasets. Our main products include the Evaluated Nuclear Structure File (ENSDF) containing information on nuclear structure and decay properties and the Evaluated Nuclear Data File (ENDF) containing information on neutron-induced reactions. The National Nuclear Data Center (NNDC), through the website www.nndc.bnl.gov, provides web-based retrieval systems for these and many other databases. In addition, the NNDC hosts several on-line physics tools, useful for calculating various quantities relating to basic nuclear physics. In this talk, I will first introduce the quantities which are evaluated and recommended in our databases. I will then outline the searching capabilities which allow one to quickly and efficiently retrieve data. Finally, I will demonstrate how the database searches and web applications can provide effective teaching tools concerning the structure of nuclei and how they interact. Work supported by the Office of Nuclear Physics, Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-98CH10886.

Herpes zoster surveillance using electronic databases in the Valencian Community (Spain)

PubMed Central

2013-01-01

Background Epidemiologic data of Herpes Zoster (HZ) disease in Spain are scarce. The objective of this study was to assess the epidemiology of HZ in the Valencian Community (Spain), using outpatient and hospital electronic health databases. Methods Data from 2007 to 2010 was collected from computerized health databases of a population of around 5 million inhabitants. Diagnoses were recorded by physicians using the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). A sample of medical records under different criteria was reviewed by a general practitioner, to assess the reliability of codification. Results The average annual incidence of HZ was 4.60 per 1000 persons-year (PY) for all ages (95% CI: 4.57-4.63), is more frequent in women [5.32/1000PY (95% CI: 5.28-5.37)] and is strongly age-related, with a peak incidence at 70-79 years. A total of 7.16/1000 cases of HZ required hospitalization. Conclusions Electronic health database used in the Valencian Community is a reliable electronic surveillance tool for HZ disease and will be useful to define trends in disease burden before and after HZ vaccine introduction. PMID:24094135

Military, Charter, Unreported Domestic Traffic and General Aviation 1976, 1984, 1992, and 2015 Emission Scenarios

NASA Technical Reports Server (NTRS)

Mortlock, Alan; VanAlstyne, Richard

1998-01-01

The report describes development of databases estimating aircraft engine exhaust emissions for the years 1976 and 1984 from global operations of Military, Charter, historic Soviet and Chinese, Unreported Domestic traffic, and General Aviation (GA). These databases were developed under the National Aeronautics and Space Administration's (NASA) Advanced Subsonic Assessment (AST). McDonnell Douglas Corporation's (MDC), now part of the Boeing Company has previously estimated engine exhaust emissions' databases for the baseline year of 1992 and a 2015 forecast year scenario. Since their original creation, (Ward, 1994 and Metwally, 1995) revised technology algorithms have been developed. Additionally, GA databases have been created and all past NIDC emission inventories have been updated to reflect the new technology algorithms. Revised data (Baughcum, 1996 and Baughcum, 1997) for the scheduled inventories have been used in this report to provide a comparison of the total aviation emission forecasts from various components. Global results of two historic years (1976 and 1984), a baseline year (1992) and a forecast year (2015) are presented. Since engine emissions are directly related to fuel usage, an overview of individual aviation annual global fuel use for each inventory component is also given in this report.

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

PubMed Central

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

2000-01-01

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

Population-based drug-related anaphylaxis in children and adolescents captured by South Carolina Emergency Room Hospital Discharge Database (SCERHDD) (2000-2002).

PubMed

West, Suzanne L; D'Aloisio, Aimee A; Ringel-Kulka, Tamar; Waller, Anna E; Clayton Bordley, W

2007-12-01

Anaphylaxis is a life-threatening condition; drug-related anaphylaxis represents approximately 10% of all cases. We assessed the utility of a statewide emergency department (ED) database for identifying drug-related anaphylaxis in children by developing and validating an algorithm composed of ICD-9-CM codes. There were 1 314,760 visits to South Carolina (SC) emergency departments (EDs) for patients <19 years in 2000-2002. We used ICD-9-CM disease or external cause of injury codes (E-codes) that suggested drug-related anaphylaxis or a severe drug-related allergic reaction. We found 50 cases classifiable as probable or possible drug-related anaphylaxis and 13 as drug-related allergic reactions. We used clinical evaluation by two pediatricians as the 'alloyed gold standard'1 for estimating sensitivity, specificity, and positive predictive value (PPV) of our algorithm. ED-treated drug-related anaphylaxis in the SC pediatric population was 1.56/100,000 person-years based on the algorithm and 0.50/100,000 person-years based on clinical evaluation. Assuming the disease codes we used identified all potential anaphylaxis cases in the database, the sensitivity was 1.00 (95%CI: 0.79, 1.00), specificity was 0.28 (95%CI: 0.16, 0.43), and the PPV was 0.32 (0.20, 0.47) for the algorithm. Sensitivity analyses improved the measurement properties of the algorithm. E-codes were invaluable for developing an anaphylaxis algorithm although the frequently used code of E947.9 was often incorrectly applied. We believe that our algorithm may have over-ascertained drug-related anaphylaxis patients seen in an ED, but the clinical evaluation may have under-represented this diagnosis due to limited information on the offending agent in the abstracted ED records. Post-marketing drug surveillance using ED records may be viable if clinicians were to document drug-related anaphylaxis in the charts so that billing codes could be assigned properly. Copyright 2007 John Wiley & Sons, Ltd.

Validation of chronic obstructive pulmonary disease (COPD) diagnoses in healthcare databases: a systematic review protocol.

PubMed

Rimland, Joseph M; Abraha, Iosief; Luchetta, Maria Laura; Cozzolino, Francesco; Orso, Massimiliano; Cherubini, Antonio; Dell'Aquila, Giuseppina; Chiatti, Carlos; Ambrosio, Giuseppe; Montedori, Alessandro

2016-06-01

Healthcare databases are useful sources to investigate the epidemiology of chronic obstructive pulmonary disease (COPD), to assess longitudinal outcomes in patients with COPD, and to develop disease management strategies. However, in order to constitute a reliable source for research, healthcare databases need to be validated. The aim of this protocol is to perform the first systematic review of studies reporting the validation of codes related to COPD diagnoses in healthcare databases. MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched using appropriate search strategies. Studies that evaluated the validity of COPD codes (such as the International Classification of Diseases 9th Revision and 10th Revision system; the Real codes system or the International Classification of Primary Care) in healthcare databases will be included. Inclusion criteria will be: (1) the presence of a reference standard case definition for COPD; (2) the presence of at least one test measure (eg, sensitivity, positive predictive values, etc); and (3) the use of a healthcare database (including administrative claims databases, electronic healthcare databases or COPD registries) as a data source. Pairs of reviewers will independently abstract data using standardised forms and will assess quality using a checklist based on the Standards for Reporting of Diagnostic accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 statement. Ethics approval is not required. Results of this study will be submitted to a peer-reviewed journal for publication. The results from this systematic review will be used for outcome research on COPD and will serve as a guide to identify appropriate case definitions of COPD, and reference standards, for researchers involved in validating healthcare databases. CRD42015029204. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

BIOSPIDA: A Relational Database Translator for NCBI.

PubMed

Hagen, Matthew S; Lee, Eva K

2010-11-13

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.

Congenital Etiology is an Independent Risk Factor for Complications in Adolescents Undergoing Corrective Scoliosis Surgery: Comparison of In-hospital Comorbidities Using Nationwide KID's Inpatient Database.

PubMed

Poorman, Gregory W; Jalai, Cyrus M; Diebo, Bassel; Vira, Shaleen; Buza, John; Baker, Joe; Tishelman, Jared; Horn, Samantha; Bono, Olivia; Shenoy, Kartik; Hasan, Saqib; Paul, Justin; Isaacs, Evan; Kaye, Ian; Atanda, Abiola; Buckland, Aaron J; LaFage, Virginie; Errico, Thomas; Passias, Peter G

2017-04-24

Congenital scoliosis (CS) is associated with more rigid, complex deformities relative to adolescent idiopathic scoliosis (AIS) which theoretically increases surgical complications. Despite extensive literature studying AIS patients, few studies have been performed on CS patients. The purpose of this study was to evaluate complications associated with spinal fusions for CS and AIS. A retrospective review of the Kid's Inpatient Database (KID) years 2000 to 2009 was performed. Inclusion: patients under 20 years with ICD-9 diagnosis codes for idiopathic scoliosis (IS-without concomitant congenital anomalies) and CS, undergoing spinal fusion from the KID years 2000 to 2009. Two analyses were performed according to age below 10 years and 10 years and above. Univariate analysis described differences in demographics, comorbidities, intraoperative complications, and clinical values between groups. Binary logistic regression controlling for age, sex, race, and invasiveness predicted complications risk in CS (odds ratios; 95% confidence interval). In total, 25,131 patients included (IS, n=22443; CS, n=2688). For patients under age 10, CS patients underwent 1 level shorter fusions (P<0.001), had fewer comorbidities (P<0.001), and sustained similar complication incidence. In the 10 and over age analysis, CS patients similarly had shorter fusions, but greater comorbidities, and significantly more complications (odds ratio, 1.6; confidence interval, 1.4-1.8). CS patients have higher in-hospital complication rates. With more comorbidities, these patients have increased risk of sustaining procedure-related complications such as shock, infection, and Adult Respiratory Distress Syndrome. These data help to counsel patients and their families before spinal fusion. Level III-retrospective review of a prospectively collected database.

NADM Conceptual Model 1.0 -- A Conceptual Model for Geologic Map Information

USGS Publications Warehouse

,

2004-01-01

Executive Summary -- The NADM Data Model Design Team was established in 1999 by the North American Geologic Map Data Model Steering Committee (NADMSC) with the purpose of drafting a geologic map data model for consideration as a standard for developing interoperable geologic map-centered databases by state, provincial, and federal geological surveys. The model is designed to be a technology-neutral conceptual model that can form the basis for a web-based interchange format using evolving information technology (e.g., XML, RDF, OWL), and guide implementation of geoscience databases in a common conceptual framework. The intended purpose is to allow geologic information sharing between geologic map data providers and users, independent of local information system implementation. The model emphasizes geoscience concepts and relationships related to information presented on geologic maps. Design has been guided by an informal requirements analysis, documentation of existing databases, technology developments, and other standardization efforts in the geoscience and computer-science communities. A key aspect of the model is the notion that representation of the conceptual framework (ontology) that underlies geologic map data must be part of the model, because this framework changes with time and understanding, and varies between information providers. The top level of the model distinguishes geologic concepts, geologic representation concepts, and metadata. The geologic representation part of the model provides a framework for representing the ontology that underlies geologic map data through a controlled vocabulary, and for establishing the relationships between this vocabulary and a geologic map visualization or portrayal. Top-level geologic classes in the model are Earth material (substance), geologic unit (parts of the Earth), geologic age, geologic structure, fossil, geologic process, geologic relation, and geologic event.

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.

PubMed

Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin; Senger, Philipp

2015-01-01

Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html. © The Author(s) 2015. Published by Oxford University Press.

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

PubMed Central

Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin

2015-01-01

Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article’s supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer’s disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html PMID:26475471

A Look Under the Hood: How the JPL Tropical Cyclone Information System Uses Database Technologies to Present Big Data to Users

NASA Astrophysics Data System (ADS)

Knosp, B.; Gangl, M.; Hristova-Veleva, S. M.; Kim, R. M.; Li, P.; Turk, J.; Vu, Q. A.

2015-12-01

The JPL Tropical Cyclone Information System (TCIS) brings together satellite, aircraft, and model forecast data from several NASA, NOAA, and other data centers to assist researchers in comparing and analyzing data and model forecast related to tropical cyclones. The TCIS has been running a near-real time (NRT) data portal during North Atlantic hurricane season that typically runs from June through October each year, since 2010. Data collected by the TCIS varies by type, format, contents, and frequency and is served to the user in two ways: (1) as image overlays on a virtual globe and (2) as derived output from a suite of analysis tools. In order to support these two functions, the data must be collected and then made searchable by criteria such as date, mission, product, pressure level, and geospatial region. Creating a database architecture that is flexible enough to manage, intelligently interrogate, and ultimately present this disparate data to the user in a meaningful way has been the primary challenge. The database solution for the TCIS has been to use a hybrid MySQL + Solr implementation. After testing other relational database and NoSQL solutions, such as PostgreSQL and MongoDB respectively, this solution has given the TCIS the best offerings in terms of query speed and result reliability. This database solution also supports the challenging (and memory overwhelming) geospatial queries that are necessary to support analysis tools requested by users. Though hardly new technologies on their own, our implementation of MySQL + Solr had to be customized and tuned to be able to accurately store, index, and search the TCIS data holdings. In this presentation, we will discuss how we arrived on our MySQL + Solr database architecture, why it offers us the most consistent fast and reliable results, and how it supports our front end so that we can offer users a look into our "big data" holdings.

A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

PubMed

Mungall, Christopher J; Emmert, David B

2007-07-01

A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).

Electrosurgical injuries during robot assisted surgery: insights from the FDA MAUDE database

NASA Astrophysics Data System (ADS)

Fuller, Andrew; Vilos, George A.; Pautler, Stephen E.

2012-02-01

Introduction: The da Vinci surgical system requires the use of electrosurgical instruments. The re-use of such instruments creates the potential for stray electrical currents from capacitive coupling and/or insulation failure with subsequent injury. The morbidity of such injuries may negate many of the benefits of minimally invasive surgery. We sought to evaluate the rate and nature of electrosurgical injury (ESI) associated with this device. Methods: The Manufacturer and User Facility Device Experience (MAUDE) database is administered by the US Food and Drug Administration (FDA) and reports adverse events related to medical devices in the United States. We analyzed all incidents in the context of robotic surgery between January 2001 and June 2011 to identify those related to the use of electrosurgery. Results: In the past decade, a total of 605 reports have been submitted to the FDA with regard to adverse events related to the da Vinci robotic surgical platform. Of these, 24 (3.9%) were related to potential or actual ESI. Nine out of the 24 cases (37.5%) resulted in additional surgical intervention for repair. There were 6 bowel injuries of which only one was recognized and managed intra-operatively. The remainder required laparotomy between 5 and 8 days after the initial robotic procedure. Additionally, there were 3 skin burns. The remaining cases required conservative management or resulted in no harm. Conclusion: ESI in the context of robotic surgery is uncommon but remains under-recognized and under-reported. Surgeons performing robot assisted surgery should be aware that ESI can occur with robotic instruments and vigilance for intra- and post-operative complications is paramount.

49 CFR 630.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.3 Definitions. (a) Except as otherwise provided, terms defined in... current editions of the National Transit Database Reporting Manuals and the NTD Uniform System of Accounts... benefits from assistance under 49 U.S.C. 5307 or 5311. Current edition of the National Transit Database...

49 CFR 630.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.3 Definitions. (a) Except as otherwise provided, terms defined in... current editions of the National Transit Database Reporting Manuals and the NTD Uniform System of Accounts... benefits from assistance under 49 U.S.C. 5307 or 5311. Current edition of the National Transit Database...

49 CFR 630.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.3 Definitions. (a) Except as otherwise provided, terms defined in... current editions of the National Transit Database Reporting Manuals and the NTD Uniform System of Accounts... benefits from assistance under 49 U.S.C. 5307 or 5311. Current edition of the National Transit Database...

49 CFR 630.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.3 Definitions. (a) Except as otherwise provided, terms defined in... current editions of the National Transit Database Reporting Manuals and the NTD Uniform System of Accounts... benefits from assistance under 49 U.S.C. 5307 or 5311. Current edition of the National Transit Database...

49 CFR 630.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.3 Definitions. (a) Except as otherwise provided, terms defined in... current editions of the National Transit Database Reporting Manuals and the NTD Uniform System of Accounts... benefits from assistance under 49 U.S.C. 5307 or 5311. Current edition of the National Transit Database...

[Stepwise occupational reintegration under the German pension insurance scheme--results of comprehensive routine data analyses and participants surveys].

PubMed

Bürger, W; Glaser-Möller, N; Kulick, B; Pallenberg, C; Stapel, M

2011-04-01

This paper presents for the first time research results of a comprehensive analysis on stepwise occupational reintegration (SOR) provided under the German pension insurance scheme. SORs under the German pension insurance scheme directly after medical rehabilitation have recently become possible as legal changes came into force in April 2004; until then, they had been provided by the health insurance funds independent of earlier medical rehabilitation. Against the background of this amendment of the law, the present study was commissioned by Deutsche Rentenversicherung Bund to get information relative to indication, introduction, implementation and results of the new SOR procedure. Analysis of routine data from the German pension insurance scheme pertaining to more than 140 000 insured persons treated in more than 1 083 medical rehabilitation centres, as well as of more than 6 500 participant surveys, resulted in a so far unique database for investigating SOR. This database offers a comprehensive collection of data and experiences relative to the amount of SOR prescribed and realized, to participants, procedure and results of SOR under the pension insurance scheme. This amount of data has never before been available when SOR was provided by the health insurance funds. The data collected suggest pinpoint indication of SOR, a positive rating of participants and an effective contribution to reintegration into working life and prevention of premature retirement. According to the present data, medical rehabilitation centres and their recommendations have an important influence on SOR utilization. Findings suggest major differences in the recommendation behaviours of rehabilitation centres, the possibilities offered by SOR not made use of to the same degree everywhere. © Georg Thieme Verlag KG Stuttgart · New York.

System, method and apparatus for conducting a phrase search

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A phrase search is a method of searching a database for subsets of the database that are relevant to an input query. First, a number of relational models of subsets of a database are provided. A query is then input. The query can include one or more sequences of terms. Next, a relational model of the query is created. The relational model of the query is then compared to each one of the relational models of subsets of the database. The identifiers of the relevant subsets are then output.

Quantitative evaluation of Iranian radiology papers and its comparison with selected countries.

PubMed

Ghafoori, Mahyar; Emami, Hasan; Sedaghat, Abdolrasoul; Ghiasi, Mohammad; Shakiba, Madjid; Alavi, Manijeh

2014-01-01

Recent technological developments in medicine, including modern radiology have promoted the impact of scientific researches on social life. The scientific outputs such as article and patents are products that show the scientists' attempt to access these achievements. In the current study, we evaluate the current situation of Iranian scientists in the field of radiology and compare it with the selected countries in terms of scientific papers. For this purpose, we used scientometric tools to quantitatively assess the scientific papers in the field of radiology. Radiology papers were evaluated in the context of medical field audit using retrospective model. We used the related databases of biomedical sciences for extraction of articles related to radiology. In the next step, the situation of radiology scientific products of the country were determined with respect to the under study regional countries. Results of the current study showed a ratio of 0.19% for Iranian papers in PubMed database published in 2009. In addition, in 2009, Iranian papers constituted 0.29% of the Scopus scientific database. The proportion of Iranian papers in the understudy region was 7.6%. To diminish the gap between Iranian scientific radiology papers and other competitor countries in the region and achievement of document 2025 goals, multifold effort of the society of radiology is necessary.

Identification of Functionally Related Enzymes by Learning-to-Rank Methods.

PubMed

Stock, Michiel; Fober, Thomas; Hüllermeier, Eyke; Glinca, Serghei; Klebe, Gerhard; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

2014-01-01

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work, we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes.

Evaluation of DNA mixtures from database search.

PubMed

Chung, Yuk-Ka; Hu, Yue-Qing; Fung, Wing K

2010-03-01

With the aim of bridging the gap between DNA mixture analysis and DNA database search, a novel approach is proposed to evaluate the forensic evidence of DNA mixtures when the suspect is identified by the search of a database of DNA profiles. General formulae are developed for the calculation of the likelihood ratio for a two-person mixture under general situations including multiple matches and imperfect evidence. The influence of the prior probabilities on the weight of evidence under the scenario of multiple matches is demonstrated by a numerical example based on Hong Kong data. Our approach is shown to be capable of presenting the forensic evidence of DNA mixtures in a comprehensive way when the suspect is identified through database search.

A clear human footprint in the coral reefs of the Caribbean.

PubMed

Mora, Camilo

2008-04-07

The recent degradation of coral reefs worldwide is increasingly well documented, yet the underlying causes remain debated. In this study, we used a large-scale database on the status of coral reef communities in the Caribbean and analysed it in combination with a comprehensive set of socioeconomic and environmental databases to decouple confounding factors and identify the drivers of change in coral reef communities. Our results indicated that human activities related to agricultural land use, coastal development, overfishing and climate change had created independent and overwhelming responses in fishes, corals and macroalgae. While the effective implementation of marine protected areas (MPAs) increased the biomass of fish populations, coral reef builders and macroalgae followed patterns of change independent of MPAs. However, we also found significant ecological links among all these groups of organisms suggesting that the long-term stability of coral reefs as a whole requires a holistic and regional approach to the control of human-related stressors in addition to the improvement and establishment of new MPAs.

A clear human footprint in the coral reefs of the Caribbean

PubMed Central

Mora, Camilo

2008-01-01

The recent degradation of coral reefs worldwide is increasingly well documented, yet the underlying causes remain debated. In this study, we used a large-scale database on the status of coral reef communities in the Caribbean and analysed it in combination with a comprehensive set of socioeconomic and environmental databases to decouple confounding factors and identify the drivers of change in coral reef communities. Our results indicated that human activities related to agricultural land use, coastal development, overfishing and climate change had created independent and overwhelming responses in fishes, corals and macroalgae. While the effective implementation of marine protected areas (MPAs) increased the biomass of fish populations, coral reef builders and macroalgae followed patterns of change independent of MPAs. However, we also found significant ecological links among all these groups of organisms suggesting that the long-term stability of coral reefs as a whole requires a holistic and regional approach to the control of human-related stressors in addition to the improvement and establishment of new MPAs. PMID:18182370

Telemedicine information analysis center.

PubMed

Zajtchuk, Joan T; Zajtchuk, Russ; Petrovic, Joseph J; Gutz, Ryan P; Walrath, Benjamin D

2004-01-01

Congress mandated a pilot project to demonstrate the feasibility of establishing a Department of Defense (DoD) telemedicine information analysis center (TIAC). The project developed a medical information support system to show the core capabilities of a TIAC. The productivity and effectiveness of telemedicine researchers and clinical practitioners can be enhanced by the existence of an information analysis center (IACs) devoted to the collection, analysis, synthesis, and dissemination of worldwide scientific and technical information related to the field of telemedicine. The work conducted under the TIAC pilot project establishes the basic IAC functions and assesses the utility of the TIAC to the military medical departments. The pilot project capabilities are Web-based and include: (1) applying the science of classification (taxonomy) to telemedicine to identify key words; (2) creating a relational database of this taxonomy to a bibliographic database using these key words; (3) developing and disseminating information via a public TIAC Web site; (4) performing a specific baseline technical area task for the U.S. Army Medical Command; and (5) providing analyses by subject matter experts.

An automated system for terrain database construction

NASA Technical Reports Server (NTRS)

Johnson, L. F.; Fretz, R. K.; Logan, T. L.; Bryant, N. A.

1987-01-01

An automated Terrain Database Preparation System (TDPS) for the construction and editing of terrain databases used in computerized wargaming simulation exercises has been developed. The TDPS system operates under the TAE executive, and it integrates VICAR/IBIS image processing and Geographic Information System software with CAD/CAM data capture and editing capabilities. The terrain database includes such features as roads, rivers, vegetation, and terrain roughness.

The Danish Fracture Database can monitor quality of fracture-related surgery, surgeons' experience level and extent of supervision.

PubMed

Andersen, Morten Jon; Gromov, Kiril; Brix, Michael; Troelsen, Anders

2014-06-01

The importance of supervision and of surgeons' level of experience in relation to patient outcome have been demonstrated in both hip fracture and arthroplasty surgery. The aim of this study was to describe the surgeons' experience level and the extent of supervision for: 1) fracture-related surgery in general; 2) the three most frequent primary operations and reoperations; and 3) primary operations during and outside regular working hours. A total of 9,767 surgical procedures were identified from the Danish Fracture Database (DFDB). Procedures were grouped based on the surgeons' level of experience, extent of supervision, type (primary, planned secondary or reoperation), classification (AO Müller), and whether they were performed during or outside regular hours. Interns and junior residents combined performed 46% of all procedures. A total of 90% of surgeries by interns were performed under supervision, whereas 32% of operations by junior residents were unsupervised. Supervision was absent in 14-16% and 22-33% of the three most frequent primary procedures and reoperations when performed by interns and junior residents, respectively. The proportion of unsupervised procedures by junior residents grew from 30% during to 40% (p < 0.001) outside regular hours. Interns and junior residents together performed almost half of all fracture-related surgery. The extent of supervision was generally high; however, a third of the primary procedures performed by junior residents were unsupervised. The extent of unsupervised surgery performed by junior residents was significantly higher outside regular hours. not relevant. The Danish Fracture Database ("Dansk Frakturdatabase") was approved by the Danish Data Protection Agency ID: 01321.

Component, Context and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2013-03-01

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

47 CFR 15.713 - TV bands database.

Code of Federal Regulations, 2011 CFR

2011-10-01

... authorized services operating in the TV bands. In addition, a TV bands database must also verify that the FCC identifier (FCC ID) of a device seeking access to its services is valid; under this requirement the TV bands... information will come from the official Commission database. These services include: (i) Digital television...

77 FR 66622 - Submission for OMB Review; Comment Request: National Database for Autism Research (NDAR) Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-06

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Submission for OMB Review; Comment Request: National Database for Autism Research (NDAR) Data Access Request SUMMARY: Under the... currently valid OMB control number. Proposed Collection: Title: National Database for Autism Research (NDAR...

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

PubMed

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

2012-10-01

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

BIOSPIDA: A Relational Database Translator for NCBI

PubMed Central

Hagen, Matthew S.; Lee, Eva K.

2010-01-01

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time. PMID:21347013

MeDReaders: a database for transcription factors that bind to methylated DNA.

PubMed

Wang, Guohua; Luo, Ximei; Wang, Jianan; Wan, Jun; Xia, Shuli; Zhu, Heng; Qian, Jiang; Wang, Yadong

2018-01-04

Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development. Hence, we constructed a database, named as MeDReaders, to collect information about methylated DNA binding activities. A total of 731 TFs, which could bind to methylated DNA sequences, were manually curated in human and mouse studies reported in the literature. In silico approaches were applied to predict methylated and unmethylated motifs of 292 TFs by integrating whole genome bisulfite sequencing (WGBS) and ChIP-Seq datasets in six human cell lines and one mouse cell line extracted from ENCODE and GEO database. MeDReaders database will provide a comprehensive resource for further studies and aid related experiment designs. The database implemented unified access for users to most TFs involved in such methylation-associated binding actives. The website is available at http://medreader.org/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of Vision Based Multiview Gait Recognition System with MMUGait Database

PubMed Central

Ng, Hu; Tan, Wooi-Haw; Tong, Hau-Lee

2014-01-01

This paper describes the acquisition setup and development of a new gait database, MMUGait. This database consists of 82 subjects walking under normal condition and 19 subjects walking with 11 covariate factors, which were captured under two views. This paper also proposes a multiview model-based gait recognition system with joint detection approach that performs well under different walking trajectories and covariate factors, which include self-occluded or external occluded silhouettes. In the proposed system, the process begins by enhancing the human silhouette to remove the artifacts. Next, the width and height of the body are obtained. Subsequently, the joint angular trajectories are determined once the body joints are automatically detected. Lastly, crotch height and step-size of the walking subject are determined. The extracted features are smoothened by Gaussian filter to eliminate the effect of outliers. The extracted features are normalized with linear scaling, which is followed by feature selection prior to the classification process. The classification experiments carried out on MMUGait database were benchmarked against the SOTON Small DB from University of Southampton. Results showed correct classification rate above 90% for all the databases. The proposed approach is found to outperform other approaches on SOTON Small DB in most cases. PMID:25143972

Method applied to the background analysis of energy data to be considered for the European Reference Life Cycle Database (ELCD).

PubMed

Fazio, Simone; Garraín, Daniel; Mathieux, Fabrice; De la Rúa, Cristina; Recchioni, Marco; Lechón, Yolanda

2015-01-01

Under the framework of the European Platform on Life Cycle Assessment, the European Reference Life-Cycle Database (ELCD - developed by the Joint Research Centre of the European Commission), provides core Life Cycle Inventory (LCI) data from front-running EU-level business associations and other sources. The ELCD contains energy-related data on power and fuels. This study describes the methods to be used for the quality analysis of energy data for European markets (available in third-party LC databases and from authoritative sources) that are, or could be, used in the context of the ELCD. The methodology was developed and tested on the energy datasets most relevant for the EU context, derived from GaBi (the reference database used to derive datasets for the ELCD), Ecoinvent, E3 and Gemis. The criteria for the database selection were based on the availability of EU-related data, the inclusion of comprehensive datasets on energy products and services, and the general approval of the LCA community. The proposed approach was based on the quality indicators developed within the International Reference Life Cycle Data System (ILCD) Handbook, further refined to facilitate their use in the analysis of energy systems. The overall Data Quality Rating (DQR) of the energy datasets can be calculated by summing up the quality rating (ranging from 1 to 5, where 1 represents very good, and 5 very poor quality) of each of the quality criteria indicators, divided by the total number of indicators considered. The quality of each dataset can be estimated for each indicator, and then compared with the different databases/sources. The results can be used to highlight the weaknesses of each dataset and can be used to guide further improvements to enhance the data quality with regard to the established criteria. This paper describes the application of the methodology to two exemplary datasets, in order to show the potential of the methodological approach. The analysis helps LCA practitioners to evaluate the usefulness of the ELCD datasets for their purposes, and dataset developers and reviewers to derive information that will help improve the overall DQR of databases.

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

PubMed

Mackey, Aaron J; Pearson, William R

2004-10-01

Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

Relational Databases: A Transparent Framework for Encouraging Biology Students to Think Informatically

ERIC Educational Resources Information Center

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a…

SQL is Dead; Long-live SQL: Relational Database Technology in Science Contexts

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

Relational databases are often perceived as a poor fit in science contexts: Rigid schemas, poor support for complex analytics, unpredictable performance, significant maintenance and tuning requirements --- these idiosyncrasies often make databases unattractive in science contexts characterized by heterogeneous data sources, complex analysis tasks, rapidly changing requirements, and limited IT budgets. In this talk, I'll argue that although the value proposition of typical relational database systems are weak in science, the core ideas that power relational databases have become incredibly prolific in open source science software, and are emerging as a universal abstraction for both big data and small data. In addition, I'll talk about two open source systems we are building to "jailbreak" the core technology of relational databases and adapt them for use in science. The first is SQLShare, a Database-as-a-Service system supporting collaborative data analysis and exchange by reducing database use to an Upload-Query-Share workflow with no installation, schema design, or configuration required. The second is Myria, a service that supports much larger scale data, complex analytics, and supports multiple back end systems. Finally, I'll describe some of the ways our collaborators in oceanography, astronomy, biology, fisheries science, and more are using these systems to replace script-based workflows for reasons of performance, flexibility, and convenience.

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI.

PubMed

Wang, Weijing; Jiang, Wenjie; Hou, Lin; Duan, Haiping; Wu, Yili; Xu, Chunsheng; Tan, Qihua; Li, Shuxia; Zhang, Dongfeng

2017-11-13

The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed. We identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired.

EasyKSORD: A Platform of Keyword Search Over Relational Databases

NASA Astrophysics Data System (ADS)

Peng, Zhaohui; Li, Jing; Wang, Shan

Keyword Search Over Relational Databases (KSORD) enables casual users to use keyword queries (a set of keywords) to search relational databases just like searching the Web, without any knowledge of the database schema or any need of writing SQL queries. Based on our previous work, we design and implement a novel KSORD platform named EasyKSORD for users and system administrators to use and manage different KSORD systems in a novel and simple manner. EasyKSORD supports advanced queries, efficient data-graph-based search engines, multiform result presentations, and system logging and analysis. Through EasyKSORD, users can search relational databases easily and read search results conveniently, and system administrators can easily monitor and analyze the operations of KSORD and manage KSORD systems much better.

“NaKnowBase”: A Nanomaterials Relational Database

EPA Science Inventory

NaKnowBase is an internal relational database populated with data from peer-reviewed ORD nanomaterials research publications. The database focuses on papers describing the actions of nanomaterials in environmental or biological media including their interactions, transformations...

A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals

ERIC Educational Resources Information Center

Takusi, Gabriel Samuto

2010-01-01

This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA…

Biodiversity's big wet secret: the global distribution of marine biological records reveals chronic under-exploration of the deep pelagic ocean.

PubMed

Webb, Thomas J; Vanden Berghe, Edward; O'Dor, Ron

2010-08-02

Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean--the largest biome on Earth--is chronically under-represented in global databases of marine biodiversity. We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented. The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity's big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth's largest ecosystem.

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…

Coding accuracy for Parkinson's disease hospital admissions: implications for healthcare planning in the UK.

PubMed

Muzerengi, S; Rick, C; Begaj, I; Ives, N; Evison, F; Woolley, R L; Clarke, C E

2017-05-01

Hospital Episode Statistics data are used for healthcare planning and hospital reimbursements. Reliability of these data is dependent on the accuracy of individual hospitals reporting Secondary Uses Service (SUS) which includes hospitalisation. The number and coding accuracy for Parkinson's disease hospital admissions at a tertiary centre in Birmingham was assessed. Retrospective, routine-data-based study. A retrospective electronic database search for all Parkinson's disease patients admitted to the tertiary hospital over a 4-year period (2009-2013) was performed on the SUS database using International Classification of Disease codes, and on the local inpatient electronic prescription database, Prescription and Information Communications System, using medication prescriptions. Capture-recapture methods were used to estimate the number of patients and admissions missed by both databases. From the two databases, between July 2009 and June 2013, 1068 patients with Parkinson's disease accounted for 1999 admissions. During these admissions, the Parkinson's disease was coded as a primary or secondary diagnosis. Ninety-one percent of these admissions were recorded on the SUS database. Capture-recapture methods estimated that the number of Parkinson's disease patients admitted during this period was 1127 patients (95% confidence interval: 1107-1146). A supplementary search of both SUS and Prescription and Information Communications System was undertaken using the hospital numbers of these 1068 patients. This identified another 479 admissions. SUS database under-estimated Parkinson's disease admissions by 27% during the study period. The accuracy of disease coding is critical for healthcare policy planning and must be improved. If the under-reporting of Parkinson's disease admissions on the SUS database is repeated nationally, expenditure on Parkinson's disease admissions in England is under-estimated by approximately £61 million per year. Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

DWARF – a data warehouse system for analyzing protein families

PubMed Central

Fischer, Markus; Thai, Quan K; Grieb, Melanie; Pleiss, Jürgen

2006-01-01

Background The emerging field of integrative bioinformatics provides the tools to organize and systematically analyze vast amounts of highly diverse biological data and thus allows to gain a novel understanding of complex biological systems. The data warehouse DWARF applies integrative bioinformatics approaches to the analysis of large protein families. Description The data warehouse system DWARF integrates data on sequence, structure, and functional annotation for protein fold families. The underlying relational data model consists of three major sections representing entities related to the protein (biochemical function, source organism, classification to homologous families and superfamilies), the protein sequence (position-specific annotation, mutant information), and the protein structure (secondary structure information, superimposed tertiary structure). Tools for extracting, transforming and loading data from public available resources (ExPDB, GenBank, DSSP) are provided to populate the database. The data can be accessed by an interface for searching and browsing, and by analysis tools that operate on annotation, sequence, or structure. We applied DWARF to the family of α/β-hydrolases to host the Lipase Engineering database. Release 2.3 contains 6138 sequences and 167 experimentally determined protein structures, which are assigned to 37 superfamilies 103 homologous families. Conclusion DWARF has been designed for constructing databases of large structurally related protein families and for evaluating their sequence-structure-function relationships by a systematic analysis of sequence, structure and functional annotation. It has been applied to predict biochemical properties from sequence, and serves as a valuable tool for protein engineering. PMID:17094801

Effectiveness of influenza vaccination for preventing influenza-related complications in people with asthma: a systematic review protocol.

PubMed

Vasileiou, Eleftheria; Sheikh, Aziz; Butler, Chris; von Wissmann, Beatrix; McMenamin, Jim; Ritchie, Lewis; Tian, Lilly; Simpson, Colin

2016-03-29

Influenza vaccination is administered annually as a preventive measure against influenza infection and influenza-related complications in high-risk individuals, such as those with asthma. However, the effectiveness of influenza vaccination in people with asthma against influenza-related complications is still not well established. We will search the following databases: MEDLINE (Ovid), EMBASE (Ovid), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Cochrane Central Register of Controlled Trials (CENTRAL), Scopus, Cochrane Database of Systematic Reviews (CDSR), Web of Science Core Collection, Science direct, WHO Library Information System (WHOLIS), Global Health Library and Chinese databases (CNKI, Wanfang and ChongQing VIP) from Jan 1970 to Jan 2016 for observational and experimental studies on effectiveness of influenza vaccine in people with asthma. The identification of studies will be complemented with the searching of the reference lists and citations, and contacting influenza vaccine manufacturers to identify unpublished or ongoing studies. Two reviewers will extract data and appraise the quality of each study independently. Separate meta-analyses will be undertaken for observational and experimental evidence using fixed-effect or random-effects models, as appropriate. Formal ethical approval is not required, as primary data will not be collected. The review will be disseminated in peer-reviewed publications and conference presentations. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Resident database interfaces to the DAVID system, a heterogeneous distributed database management system

NASA Technical Reports Server (NTRS)

Moroh, Marsha

1988-01-01

A methodology for building interfaces of resident database management systems to a heterogeneous distributed database management system under development at NASA, the DAVID system, was developed. The feasibility of that methodology was demonstrated by construction of the software necessary to perform the interface task. The interface terminology developed in the course of this research is presented. The work performed and the results are summarized.

ARTI Refrigerant Database

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

Calm, J.M.

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

Effects of the gay publishing boom on classes of titles retrieved under the subject headings "Homosexuality," "Gay Men," and "Gays" in the OCLC WorldCat database.

PubMed

Carmichael, James V

2002-01-01

What do searchers find when they look for literature on homosexuality? This question has profound implications for older as well as younger gays in their coming out, as well as in their subsequent identity development. Library records provide credible data to answer the question, since they represent relatively free sources of information, unlike data from bookstores, publishers, and some World Wide Web sites. The records of WorldCat, the world's largest union database of library records, comprise over 30 million records listed in the Online Computer Library Center. For the purposes of the study, 18,757 records listed under "Homosexuality," "Gay Men," and "Gays" were downloaded; records for "Lesbian" and "Lesbians" were not examined. Findings of the study suggest that while there has indeed been considerable growth in terms of the quantity of gay literature produced since 1969, such gains may be offset by the deteriorating quality of cataloging copy, which makes the experience of browsing records a discouraging and confusing one.

“NaKnowBase”: A Nanomaterials Relational Database

EPA Science Inventory

NaKnowBase is a relational database populated with data from peer-reviewed ORD nanomaterials research publications. The database focuses on papers describing the actions of nanomaterials in environmental or biological media including their interactions, transformations and poten...

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.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2014-03-01

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

Fuzzy queries above relational database

NASA Astrophysics Data System (ADS)

Smolka, Pavel; Bradac, Vladimir

2017-11-01

The aim of the theme is to introduce a possibility of fuzzy queries implemented in relational databases. The issue is described on a model which identifies the appropriate part of the problem domain for fuzzy approach. The model is demonstrated on a database of wines focused on searching in it. The construction of the database complies with the Law of the Czech Republic.

Sensitivity of spring phenology to warming across temporal and spatial climate gradients in two independent databases

USGS Publications Warehouse

Cook, Benjamin I.; Wolkovich, Elizabeth M.; Davies, T. Jonathan; Ault, Toby R.; Betancourt, Julio L.; Allen, Jenica M.; Bolmgren, Kjell; Cleland, Elsa E.; Crimmins, Theresa M.; Kraft, Nathan J.B.; Lancaster, Lesley T.; Mazer, Susan J.; McCabe, Gregory J.; McGill, Brian J.; Parmesan, Camille; Pau, Stephanie; Regetz, James; Salamin, Nicolas; Schwartz, Mark D.; Travers, Steven E.

2012-01-01

Disparate ecological datasets are often organized into databases post hoc and then analyzed and interpreted in ways that may diverge from the purposes of the original data collections. Few studies, however, have attempted to quantify how biases inherent in these data (for example, species richness, replication, climate) affect their suitability for addressing broad scientific questions, especially in under-represented systems (for example, deserts, tropical forests) and wild communities. Here, we quantitatively compare the sensitivity of species first flowering and leafing dates to spring warmth in two phenological databases from the Northern Hemisphere. One—PEP725—has high replication within and across sites, but has low species diversity and spans a limited climate gradient. The other—NECTAR—includes many more species and a wider range of climates, but has fewer sites and low replication of species across sites. PEP725, despite low species diversity and relatively low seasonality, accurately captures the magnitude and seasonality of warming responses at climatically similar NECTAR sites, with most species showing earlier phenological events in response to warming. In NECTAR, the prevalence of temperature responders significantly declines with increasing mean annual temperature, a pattern that cannot be detected across the limited climate gradient spanned by the PEP725 flowering and leafing data. Our results showcase broad areas of agreement between the two databases, despite significant differences in species richness and geographic coverage, while also noting areas where including data across broader climate gradients may provide added value. Such comparisons help to identify gaps in our observations and knowledge base that can be addressed by ongoing monitoring and research efforts. Resolving these issues will be critical for improving predictions in understudied and under-sampled systems outside of the temperature seasonal mid-latitudes.

Methodological challenges when evaluating potential off-label prescribing of drugs using electronic health care databases: A case study of dabigatran etexilate in Europe.

PubMed

Cainzos-Achirica, Miguel; Varas-Lorenzo, Cristina; Pottegård, Anton; Asmar, Joelle; Plana, Estel; Rasmussen, Lotte; Bizouard, Geoffray; Forns, Joan; Hellfritzsch, Maja; Zint, Kristina; Perez-Gutthann, Susana; Pladevall-Vila, Manel

2018-03-23

To report and discuss estimated prevalence of potential off-label use and associated methodological challenges using a case study of dabigatran. Observational, cross-sectional study using 3 databases with different types of clinical information available: Cegedim Strategic Data Longitudinal Patient Database (CSD-LPD), France (cardiologist panel, n = 1706; general practitioner panel, n = 2813; primary care data); National Health Databases, Denmark (n = 28 619; hospital episodes and dispensed ambulatory medications); and Clinical Practice Research Datalink (CPRD), UK (linkable to Hospital Episode Statistics [HES], n = 2150; not linkable, n = 1285; primary care data plus hospital data for HES-linkable patients). August 2011 to August 2015. Two definitions were used to estimate potential off-label use: a broad definition of on-label prescribing using codes for disease indication (eg, atrial fibrillation [AF]), and a restrictive definition excluding patients with conditions for which dabigatran is not indicated (eg, valvular AF). Prevalence estimates under the broad definition ranged from 5.7% (CPRD-HES) to 34.0% (CSD-LPD) and, under the restrictive definition, from 17.4% (CPRD-HES) to 44.1% (CSD-LPD). For the majority of potential off-label users, no diagnosis potentially related to anticoagulant use was identified. Key methodological challenges were the limited availability of detailed clinical information, likely leading to overestimation of off-label use, and differences in the information available, which may explain the disparate prevalence estimates across data sources. Estimates of potential off-label use should be interpreted cautiously due to limitations in available information. In this context, CPRD HES-linkable estimates are likely to be the most accurate. Copyright © 2018 John Wiley & Sons, Ltd.

Livestock Anaerobic Digester Database

EPA Pesticide Factsheets

The Anaerobic Digester Database provides basic information about anaerobic digesters on livestock farms in the United States, organized in Excel spreadsheets. It includes projects that are under construction, operating, or shut down.

Age-related differences in associative memory: the role of sensory decline.

PubMed

Naveh-Benjamin, Moshe; Kilb, Angela

2014-09-01

Numerous studies show age-related decline in episodic memory. One of the explanations for this decline points to older adults' deficit in associative memory, reflecting the difficulties they have in binding features of episodes into cohesive entities and retrieving these bindings. Here, we evaluate the degree to which this deficit may be mediated by sensory loss associated with increased age. In 2 experiments, young adults studied word pairs that were degraded at encoding either visually (Experiment 1) or auditorily (Experiment 2). We then tested their memory for both the component words and the associations with recognition tests. For both experiments, young adults under nondegraded conditions showed an advantage in associative over item memory, relative to a group of older adults. In contrast, under perceptually degraded conditions younger adults performed similarly to the older adults who were tested under nondegraded conditions. More specifically, under perceptual degradation, young adults' associative memory declined and their component memory improved somewhat, resulting in an associative deficit, similar to that shown by older adults. This evidence is consistent with a sensory acuity decline in old age being one mediator in the associative deficit of older adults. These results broaden our understanding of age-related memory changes and how sensory and cognitive processes interact to shape these changes. The theoretical implications of these results are discussed with respect to mechanisms underlying age-related changes in episodic memory and resource tradeoffs in the encoding of component and associative memory. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Reach Address Database (RAD)

EPA Pesticide Factsheets

The Reach Address Database (RAD) stores the reach address of each Water Program feature that has been linked to the underlying surface water features (streams, lakes, etc) in the National Hydrology Database (NHD). (A reach is the portion of a stream between two points of confluence. A confluence is the location where two or more streams flow together.)

Comparison Study of Overlap among 21 Scientific Databases in Searching Pesticide Information.

ERIC Educational Resources Information Center

Meyer, Daniel E.; And Others

1983-01-01

Evaluates overlapping coverage of 21 scientific databases used in 10 online pesticide searches in an attempt to identify minimum number of databases needed to generate 90 percent of unique, relevant citations for given search. Comparison of searches combined under given pesticide usage (herbicide, fungicide, insecticide) is discussed. Nine…

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

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

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

47 CFR 52.32 - Allocation of the shared costs of long-term number portability.

Code of Federal Regulations, 2012 CFR

2012-10-01

....21(h), of each regional database, as defined in § 52.21(1), shall recover the shared costs of long-term number portability attributable to that regional database from all telecommunications carriers providing telecommunications service in areas that regional database serves. Pursuant to its duties under...

8 CFR 338.11 - Execution and issuance of certificate of naturalization by clerk of court.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the petitioner. If the court maintains naturalization records on an electronic database then only the... and maintained in the court's electronic database. (b) The certificate shall show under “former..., or if using automation equipment, ensure it is part of the electronic database record. The clerk of...

47 CFR 52.32 - Allocation of the shared costs of long-term number portability.

Code of Federal Regulations, 2010 CFR

2010-10-01

....21(h), of each regional database, as defined in § 52.21(1), shall recover the shared costs of long-term number portability attributable to that regional database from all telecommunications carriers providing telecommunications service in areas that regional database serves. Pursuant to its duties under...

8 CFR 338.11 - Execution and issuance of certificate of naturalization by clerk of court.

Code of Federal Regulations, 2011 CFR

2011-01-01

... the petitioner. If the court maintains naturalization records on an electronic database then only the... and maintained in the court's electronic database. (b) The certificate shall show under “former..., or if using automation equipment, ensure it is part of the electronic database record. The clerk of...

47 CFR 52.32 - Allocation of the shared costs of long-term number portability.

Code of Federal Regulations, 2011 CFR

2011-10-01

....21(h), of each regional database, as defined in § 52.21(1), shall recover the shared costs of long-term number portability attributable to that regional database from all telecommunications carriers providing telecommunications service in areas that regional database serves. Pursuant to its duties under...

47 CFR 52.32 - Allocation of the shared costs of long-term number portability.

Code of Federal Regulations, 2014 CFR

2014-10-01

....21(h), of each regional database, as defined in § 52.21(1), shall recover the shared costs of long-term number portability attributable to that regional database from all telecommunications carriers providing telecommunications service in areas that regional database serves. Pursuant to its duties under...

47 CFR 52.32 - Allocation of the shared costs of long-term number portability.

Code of Federal Regulations, 2013 CFR

2013-10-01

....21(h), of each regional database, as defined in § 52.21(1), shall recover the shared costs of long-term number portability attributable to that regional database from all telecommunications carriers providing telecommunications service in areas that regional database serves. Pursuant to its duties under...

Limitations and obstacles of the spontaneous adverse drugs reactions reporting: Two “challenging” case reports

PubMed Central

Palleria, Caterina; Leporini, Christian; Chimirri, Serafina; Marrazzo, Giuseppina; Sacchetta, Sabrina; Bruno, Lucrezia; Lista, Rosaria M.; Staltari, Orietta; Scuteri, Antonio; Scicchitano, Francesca; Russo, Emilio

2013-01-01

Introduction: Nowadays, based on several epidemiological data, iatrogenic disease is an emerging public health problem, especially in industrialized countries. Adverse drugs reactions (ADRs) are extremely common and, therefore, clinically, socially, and economically worthy of attention. Spontaneous reporting system for suspected ADRs represents the cornerstone of the pharmacovigilance, because it allows rapid detection of potential alarm signals related to drugs use. However, spontaneous reporting system shows several limitations, which are mainly related to under-reporting. In this paper, we describe two particular case reports, which emphasize some reasons of under-reporting and other common criticisms of spontaneous reporting systems. Materials and Methods: We performed a computer-aided search of Medline, PubMed, Embase, Cochrane library databases, national and international databases of suspected ADRs reports in order to identify previous published case reports and spontaneous reports about the ADRs reviewed in this paper, and to examine the role of suspected drugs in the pathogenesis of the described adverse reactions. Results: First, we reported a case of tizanidine-induced hemorrhagic cystitis. In the second case report, we presented an episode of asthma exacerbation after taking bimatoprost. Through the review of these two cases, we highlighted some common criticisms of spontaneous reporting systems: under-reporting and false causality attribution. Discussion and Conclusion: Healthcare workers sometimes do not report ADRs because it is challenging to establish with certainty the causal relationship between drug and adverse reaction; however, according to a key principle of pharmacovigilance, it is always better to report even a suspicion to generate an alarm in the interest of protecting public health. PMID:24347986

Limitations and obstacles of the spontaneous adverse drugs reactions reporting: Two "challenging" case reports.

PubMed

Palleria, Caterina; Leporini, Christian; Chimirri, Serafina; Marrazzo, Giuseppina; Sacchetta, Sabrina; Bruno, Lucrezia; Lista, Rosaria M; Staltari, Orietta; Scuteri, Antonio; Scicchitano, Francesca; Russo, Emilio

2013-12-01

Nowadays, based on several epidemiological data, iatrogenic disease is an emerging public health problem, especially in industrialized countries. Adverse drugs reactions (ADRs) are extremely common and, therefore, clinically, socially, and economically worthy of attention. Spontaneous reporting system for suspected ADRs represents the cornerstone of the pharmacovigilance, because it allows rapid detection of potential alarm signals related to drugs use. However, spontaneous reporting system shows several limitations, which are mainly related to under-reporting. In this paper, we describe two particular case reports, which emphasize some reasons of under-reporting and other common criticisms of spontaneous reporting systems. We performed a computer-aided search of Medline, PubMed, Embase, Cochrane library databases, national and international databases of suspected ADRs reports in order to identify previous published case reports and spontaneous reports about the ADRs reviewed in this paper, and to examine the role of suspected drugs in the pathogenesis of the described adverse reactions. First, we reported a case of tizanidine-induced hemorrhagic cystitis. In the second case report, we presented an episode of asthma exacerbation after taking bimatoprost. Through the review of these two cases, we highlighted some common criticisms of spontaneous reporting systems: under-reporting and false causality attribution. Healthcare workers sometimes do not report ADRs because it is challenging to establish with certainty the causal relationship between drug and adverse reaction; however, according to a key principle of pharmacovigilance, it is always better to report even a suspicion to generate an alarm in the interest of protecting public health.

Food Composition Database Format and Structure: A User Focused Approach

PubMed Central

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

2015-01-01

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

The Network Configuration of an Object Relational Database Management System

NASA Technical Reports Server (NTRS)

Diaz, Philip; Harris, W. C.

2000-01-01

The networking and implementation of the Oracle Database Management System (ODBMS) requires developers to have knowledge of the UNIX operating system as well as all the features of the Oracle Server. The server is an object relational database management system (DBMS). By using distributed processing, processes are split up between the database server and client application programs. The DBMS handles all the responsibilities of the server. The workstations running the database application concentrate on the interpretation and display of data.

Spanish personal name variations in national and international biomedical databases: implications for information retrieval and bibliometric studies

PubMed Central

Ruiz-Pérez, R.; López-Cózar, E. Delgado; Jiménez-Contreras, E.

2002-01-01

Objectives: The study sought to investigate how Spanish names are handled by national and international databases and to identify mistakes that can undermine the usefulness of these databases for locating and retrieving works by Spanish authors. Methods: The authors sampled 172 articles published by authors from the University of Granada Medical School between 1987 and 1996 and analyzed the variations in how each of their names was indexed in Science Citation Index (SCI), MEDLINE, and Índice Médico Español (IME). The number and types of variants that appeared for each author's name were recorded and compared across databases to identify inconsistencies in indexing practices. We analyzed the relationship between variability (number of variants of an author's name) and productivity (number of items the name was associated with as an author), the consequences for retrieval of information, and the most frequent indexing structures used for Spanish names. Results: The proportion of authors who appeared under more then one name was 48.1% in SCI, 50.7% in MEDLINE, and 69.0% in IME. Productivity correlated directly with variability: more than 50% of the authors listed on five to ten items appeared under more than one name in any given database, and close to 100% of the authors listed on more than ten items appeared under two or more variants. Productivity correlated inversely with retrievability: as the number of variants for a name increased, the number of items retrieved under each variant decreased. For the most highly productive authors, the number of items retrieved under each variant tended toward one. The most frequent indexing methods varied between databases. In MEDLINE and IME, names were indexed correctly as “first surname second surname, first name initial middle name initial” (if present) in 41.7% and 49.5% of the records, respectively. However, in SCI, the most frequent method was “first surname, first name initial second name initial” (48.0% of the records) and first surname and second surname run together, first name initial (18.3%). Conclusions: Retrievability on the basis of author's name was poor in all three databases. Each database uses accurate indexing methods, but these methods fail to result in consistency or coherence for specific entries. The likely causes of inconsistency are: (1) use by authors of variants of their names during their publication careers, (2) lack of authority control in all three databases, (3) the use of an inappropriate indexing method for Spanish names in SCI, (4) authors' inconsistent behaviors, and (5) possible editorial interventions by some journals. We offer some suggestions as to how to avert the proliferation of author name variants in the databases. PMID:12398248

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)

PubMed Central

2013-01-01

Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. Conclusions The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs. PMID:23497389

Reliability of intensive care unit admitting and comorbid diagnoses, race, elements of Acute Physiology and Chronic Health Evaluation II score, and predicted probability of mortality in an electronic intensive care unit database.

PubMed

Wenner, Joshua B; Norena, Monica; Khan, Nadia; Palepu, Anita; Ayas, Najib T; Wong, Hubert; Dodek, Peter M

2009-09-01

Although reliability of severity of illness and predicted probability of hospital mortality have been assessed, interrater reliability of the abstraction of primary and other intensive care unit (ICU) admitting diagnoses and underlying comorbidities has not been studied. Patient data from one ICU were originally abstracted and entered into an electronic database by an ICU nurse. A research assistant reabstracted patient demographics, ICU admitting diagnoses and underlying comorbidities, and elements of Acute Physiology and Chronic Health Evaluation II (APACHE II) score from 100 random patients of 474 admitted during 2005 using an identical electronic database. Chamberlain's percent positive agreement was used to compare diagnoses and comorbidities between the 2 data abstractors. A kappa statistic was calculated for demographic variables, Glasgow Coma Score, APACHE II chronic health points, and HIV status. Intraclass correlation was calculated for acute physiology points and predicted probability of hospital mortality. Percent positive agreement for ICU primary and other admitting diagnoses ranged from 0% (primary brain injury) to 71% (sepsis), and for underlying comorbidities, from 40% (coronary artery bypass graft) to 100% (HIV). Agreement as measured by kappa statistic was strong for race (0.81) and age points (0.95), moderate for chronic health points (0.50) and HIV (0.66), and poor for Glasgow Coma Score (0.36). Intraclass correlation showed a moderate-high agreement for acute physiology points (0.88) and predicted probability of hospital mortality (0.71). Reliability for ICU diagnoses and elements of the APACHE II score is related to the objectivity of primary data in the medical charts.

An approach to combining heuristic and qualitative reasoning in an expert system

NASA Technical Reports Server (NTRS)

Jiang, Wei-Si; Han, Chia Yung; Tsai, Lian Cheng; Wee, William G.

1988-01-01

An approach to combining the heuristic reasoning from shallow knowledge and the qualitative reasoning from deep knowledge is described. The shallow knowledge is represented in production rules and under the direct control of the inference engine. The deep knowledge is represented in frames, which may be put in a relational DataBase Management System. This approach takes advantage of both reasoning schemes and results in improved efficiency as well as expanded problem solving ability.

Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data.

PubMed

Turcan, Sevin; Vetter, Douglas E; Maron, Jill L; Wei, Xintao; Slonim, Donna K

2011-01-01

Gene set analyses have become a standard approach for increasing the sensitivity of transcriptomic studies. However, analytical methods incorporating gene sets require the availability of pre-defined gene sets relevant to the underlying physiology being studied. For novel physiological problems, relevant gene sets may be unavailable or existing gene set databases may bias the results towards only the best-studied of the relevant biological processes. We describe a successful attempt to mine novel functional gene sets for translational projects where the underlying physiology is not necessarily well characterized in existing annotation databases. We choose targeted training data from public expression data repositories and define new criteria for selecting biclusters to serve as candidate gene sets. Many of the discovered gene sets show little or no enrichment for informative Gene Ontology terms or other functional annotation. However, we observe that such gene sets show coherent differential expression in new clinical test data sets, even if derived from different species, tissues, and disease states. We demonstrate the efficacy of this method on a human metabolic data set, where we discover novel, uncharacterized gene sets that are diagnostic of diabetes, and on additional data sets related to neuronal processes and human development. Our results suggest that our approach may be an efficient way to generate a collection of gene sets relevant to the analysis of data for novel clinical applications where existing functional annotation is relatively incomplete.

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Bibliometrics of NIHR HTA monographs and their related journal articles.

PubMed

Royle, Pamela; Waugh, Norman

2015-02-18

A bibliometric analysis of the UK National Institute for Health Research (NIHR) Health Technology Assessment (HTA) monographs and their related journal articles by: (1) exploring the differences in citations to the HTA monographs in Google Scholar (GS), Scopus and Web of Science (WoS), and (2) comparing Scopus citations to the monographs with their related journal articles. A study of 111 HTA monographs published in 2010 and 2011, and their external journal articles. Citations to the monographs in GS, Scopus and WoS, and to their external journal articles in Scopus. The number of citations varied among the three databases, with GS having the highest and WoS the lowest; however, the citation-based rankings among the databases were highly correlated. Overall, 56% of monographs had a related publication, with the highest proportion for primary research (76%) and lowest for evidence syntheses (43%). There was a large variation in how the monographs were cited, compared to journal articles, resulting in more frequent problems, with unlinked citations in Scopus and WoS. When comparing differences in the number of citations between monograph publications with their related journal articles from the same project, we found that monographs received more citations than their journal articles for evidence syntheses and methodology projects; by contrast, journal articles related to primary research monographs were more highly cited than their monograph. The numbers of citations to the HTA monographs differed considerably between the databases, but were highly correlated. When a HTA monograph had a journal article from the same study, there were more citations to the journal article for primary research, but more to the monographs for evidence syntheses. Citations to the related journal articles were more reliably recorded than citations to the HTA monographs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Cost convergence between public and for-profit hospitals under prospective payment and high competition in Taiwan.

PubMed

Xirasagar, Sudha; Lin, Herng-Ching

2004-12-01

To test the hypotheses that: (1) average adjusted costs per discharge are higher in high-competition relative to low-competition markets, and (2) increased competition is associated with cost convergence between public and for-profit (FP) hospitals for case payment diagnoses, but not for cost-plus reimbursed diagnoses. Taiwan's National Health Insurance database; 325,851 inpatient claims for cesarean section, vaginal delivery, prostatectomy, and thyroidectomy (all case payment), and bronchial asthma and cholelithiasis (both cost-based payment). Retrospective population-based, cross-sectional study. Diagnosis-wise regression analyses were done to explore associations between cost per discharge and hospital ownership under high and low competition, adjusted for clinical severity and institutional characteristics. Adjusted costs per discharge are higher for all diagnoses in high-competition markets. For case payment diagnoses, the magnitudes of adjusted cost differences between public and FP hospitals are lower under high competition relative to low competition. This is not so for the cost-based diagnoses. We find that the empirical evidence supports both our hypotheses.

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

PubMed

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

2008-01-01

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

StarView: The object oriented design of the ST DADS user interface

NASA Technical Reports Server (NTRS)

Williams, J. D.; Pollizzi, J. A.

1992-01-01

StarView is the user interface being developed for the Hubble Space Telescope Data Archive and Distribution Service (ST DADS). ST DADS is the data archive for HST observations and a relational database catalog describing the archived data. Users will use StarView to query the catalog and select appropriate datasets for study. StarView sends requests for archived datasets to ST DADS which processes the requests and returns the database to the user. StarView is designed to be a powerful and extensible user interface. Unique features include an internal relational database to navigate query results, a form definition language that will work with both CRT and X interfaces, a data definition language that will allow StarView to work with any relational database, and the ability to generate adhoc queries without requiring the user to understand the structure of the ST DADS catalog. Ultimately, StarView will allow the user to refine queries in the local database for improved performance and merge in data from external sources for correlation with other query results. The user will be able to create a query from single or multiple forms, merging the selected attributes into a single query. Arbitrary selection of attributes for querying is supported. The user will be able to select how query results are viewed. A standard form or table-row format may be used. Navigation capabilities are provided to aid the user in viewing query results. Object oriented analysis and design techniques were used in the design of StarView to support the mechanisms and concepts required to implement these features. One such mechanism is the Model-View-Controller (MVC) paradigm. The MVC allows the user to have multiple views of the underlying database, while providing a consistent mechanism for interaction regardless of the view. This approach supports both CRT and X interfaces while providing a common mode of user interaction. Another powerful abstraction is the concept of a Query Model. This concept allows a single query to be built form a single or multiple forms before it is submitted to ST DADS. Supporting this concept is the adhoc query generator which allows the user to select and qualify an indeterminate number attributes from the database. The user does not need any knowledge of how the joins across various tables are to be resolved. The adhoc generator calculates the joins automatically and generates the correct SQL query.

NHD Event Data Dictionary

EPA Pesticide Factsheets

The Reach Address Database (RAD) stores reach address information for each Water Program feature that has been linked to the underlying surface water features (streams, lakes, etc) in the National Hydrology Database (NHD) Plus dataset.

Technology for organization of the onboard system for processing and storage of ERS data for ultrasmall spacecraft

NASA Astrophysics Data System (ADS)

Strotov, Valery V.; Taganov, Alexander I.; Konkin, Yuriy V.; Kolesenkov, Aleksandr N.

2017-10-01

Task of processing and analysis of obtained Earth remote sensing data on ultra-small spacecraft board is actual taking into consideration significant expenditures of energy for data transfer and low productivity of computers. Thereby, there is an issue of effective and reliable storage of the general information flow obtained from onboard systems of information collection, including Earth remote sensing data, into a specialized data base. The paper has considered peculiarities of database management system operation with the multilevel memory structure. For storage of data in data base the format has been developed that describes a data base physical structure which contains required parameters for information loading. Such structure allows reducing a memory size occupied by data base because it is not necessary to store values of keys separately. The paper has shown architecture of the relational database management system oriented into embedment into the onboard ultra-small spacecraft software. Data base for storage of different information, including Earth remote sensing data, can be developed by means of such database management system for its following processing. Suggested database management system architecture has low requirements to power of the computer systems and memory resources on the ultra-small spacecraft board. Data integrity is ensured under input and change of the structured information.

An Initial Design of ISO 19152:2012 LADM Based Valuation and Taxation Data Model

NASA Astrophysics Data System (ADS)

Çağdaş, V.; Kara, A.; van Oosterom, P.; Lemmen, C.; Işıkdağ, Ü.; Kathmann, R.; Stubkjær, E.

2016-10-01

A fiscal registry or database is supposed to record geometric, legal, physical, economic, and environmental characteristics in relation to property units, which are subject to immovable property valuation and taxation. Apart from procedural standards, there is no internationally accepted data standard that defines the semantics of fiscal databases. The ISO 19152:2012 Land Administration Domain Model (LADM), as an international land administration standard focuses on legal requirements, but considers out of scope specifications of external information systems including valuation and taxation databases. However, it provides a formalism which allows for an extension that responds to the fiscal requirements. This paper introduces an initial version of a LADM - Fiscal Extension Module for the specification of databases used in immovable property valuation and taxation. The extension module is designed to facilitate all stages of immovable property taxation, namely the identification of properties and taxpayers, assessment of properties through single or mass appraisal procedures, automatic generation of sales statistics, and the management of tax collection, dealing with arrears and appeals. It is expected that the initial version will be refined through further activities held by a possible joint working group under FIG Commission 7 (Cadastre and Land Management) and FIG Commission 9 (Valuation and the Management of Real Estate) in collaboration with other relevant international bodies.

Global Thermal Power Plants Database: Unit-Based CO2, SO2, NOX and PM2.5 Emissions in 2010

NASA Astrophysics Data System (ADS)

Tong, D.; Qiang, Z.; Davis, S. J.

2016-12-01

There are more than 30,000 thermal power plants now operating worldwide, reflecting a tremendously diverse infrastructure that includes units burning oil, natural gas, coal and biomass and ranging in capacity from <1MW to >1GW. Although the electricity generated by this infrastructure is vital to economic activities across the world, it also produces more CO2 and air pollution emissions than any other industry sector. Here we present a new database of global thermal power-generating units and their emissions as of 2010, GPED (Global Power Emissions Database), including the detailed unit information of installed capacity, operation year, geographic location, fuel type and control measures for more than 70000 units. In this study, we have compiled, combined, and harmonized the available underlying data related to thermal power-generating units (e.g. eGRID of USA, CPED of China and published Indian power plants database), and then analyzed the generating capacity, capacity factor, fuel type, age, location, and installed pollution-control technology in order to determine those units with disproportionately high levels of emissions. In total, this work is of great importance for improving spatial distribution of global thermal power plants emissions and exploring their environmental impacts at global scale.

Constructing a Geology Ontology Using a Relational Database

NASA Astrophysics Data System (ADS)

Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

2013-12-01

In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances relationship. Based on a Quaternary database of downtown of Foshan city, Guangdong Province, in Southern China, a geological ontology was constructed using the proposed method. To measure the maintenance of semantics in the conversation process and the results, an inverse mapping from the ontology to a relational database was tested based on a proposed conversation rule. The comparison of schema and entities and the reduction of tables between the inverse database and the original database illustrated that the proposed method retains the semantic information well during the conversation process. An application for abstracting sandstone information showed that semantic relationships among concepts in the geological database were successfully reorganized in the constructed ontology. Key words: geological ontology; geological spatial database; multiple inheritance; OWL Acknowledgement: This research is jointly funded by the Specialized Research Fund for the Doctoral Program of Higher Education of China (RFDP) (20100171120001), NSFC (41102207) and the Fundamental Research Funds for the Central Universities (12lgpy19).

Case Study Analyses of the Success DC-8 Scanning Lidar Database

NASA Technical Reports Server (NTRS)

Uthe, Edward E.

2000-01-01

Under project SUCCESS (Subsonic Aircraft Contrail and Cloud Effects Special Study) funded by the Atmospheric Effects of Aviation Program, SRI International (SRI) developed an angular scanning back'scatter lidar for operation on the NASA DC-8 research aircraft and deployed the scanning lidar during the SUCCESS field campaign. The primary purpose of the lidar was to generate real-time video displays of clouds and contrails above, ahead of, and below the DC-8 as a means to help position the aircraft for optimum cloud and contrail sampling by onboard in situ sensors, and to help extend the geometrical domain of the in situ sampling records. A large, relatively complex lidar database was collected and several data examples were processed to illustrate the value of the lidar data for interpreting the other data records collected during SUCCESS. These data examples were used to develop a journal publication for the special SUCCESS Geophysical Research Letters issue (reprint presented as Appendix A). The data examples justified data analyses of a larger part of the DC-8 lidar database and is the objective of the current study.

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

PubMed

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

2007-01-01

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

WHOLE-BODY VIBRATION EXERCISE IMPROVES FUNCTIONAL PARAMETERS IN PATIENTS WITH OSTEOGENESIS IMPERFECTA: A SYSTEMATIC REVIEW WITH A SUITABLE APPROACH.

PubMed

Sá-Caputo, Danubia C; Dionello, Carla da F; Frederico, Éric Heleno F F; Paineiras-Domingos, Laisa L; Sousa-Gonçalves, Cintia Renata; Morel, Danielle S; Moreira-Marconi, Eloá; Unger, Marianne; Bernardo-Filho, Mario

2017-01-01

Patients with osteogenesis imperfecta (OI) have abnormal bone modelling and resorption. The bone tissue adaptation and responsivity to dynamic and mechanical loading may be of therapeutic use under controlled circumstances. Improvements due to the wholebody vibration (WBV) exercises have been reported in strength, motion, gait, balance, posture and bone density in several osteopenic individuals, as in post-menopausal women or children with disabling conditions, as patients with OI. The aim of this investigation was to systematically analyse the current available literature to determine the effect of WBV exercises on functional parameters of OI patients. Three reviewers independently accessed bibliographical databases. Searches were performed in the PubMed, Scopus, Science Direct and PEDro databases using keywords related to possible interventions (including WBV) used in the management of patients with osteogenesis imperfecta . Three eligible studies were identified by searches in the analysed databases. It was concluded that WBV exercises could be an important option in the management of OI patients improving the mobility and functional parameters. However, further studies are necessary for establishing suitable protocols for these patients.

Molecular Oxygen in the Thermosphere: Issues and Measurement Strategies

NASA Astrophysics Data System (ADS)

Picone, J. M.; Hedin, A. E.; Drob, D. P.; Meier, R. R.; Bishop, J.; Budzien, S. A.

2002-05-01

We review the state of empirical knowledge regarding the distribution of molecular oxygen in the lower thermosphere (100-200 km), as embodied by the new NRLMSISE-00 empirical atmospheric model, its predecessors, and the underlying databases. For altitudes above 120 km, the two major classes of data (mass spectrometer and solar ultraviolet [UV] absorption) disagree significantly regarding the magnitude of the O2 density and the dependence on solar activity. As a result, the addition of the Solar Maximum Mission (SMM) data set (based on solar UV absorption) to the NRLMSIS database has directly impacted the new model, increasing the complexity of the model's formulation and generally reducing the thermospheric O2 density relative to MSISE-90. Beyond interest in the thermosphere itself, this issue materially affects detailed models of ionospheric chemistry and dynamics as well as modeling of the upper atmospheric airglow. Because these are key elements of both experimental and operational systems which measure and forecast the near-Earth space environment, we present strategies for augmenting the database through analysis of existing data and through future measurements in order to resolve this issue.

49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

Code of Federal Regulations, 2011 CFR

2011-10-01

..., national security, or of terrorism: (i) Relevant criminal history databases; (ii) In the case of an alien... databases to determine the status of the alien under the immigration laws of the United States; and (iii) Other relevant information or databases, as determined by the Secretary of Homeland Security. (c...

49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

Code of Federal Regulations, 2010 CFR

2010-10-01

..., national security, or of terrorism: (i) Relevant criminal history databases; (ii) In the case of an alien... databases to determine the status of the alien under the immigration laws of the United States; and (iii) Other relevant information or databases, as determined by the Secretary of Homeland Security. (c...

49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

Code of Federal Regulations, 2012 CFR

2012-10-01

..., national security, or of terrorism: (i) Relevant criminal history databases; (ii) In the case of an alien... databases to determine the status of the alien under the immigration laws of the United States; and (iii) Other relevant information or databases, as determined by the Secretary of Homeland Security. (c...

49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

Code of Federal Regulations, 2013 CFR

2013-10-01

..., national security, or of terrorism: (i) Relevant criminal history databases; (ii) In the case of an alien... databases to determine the status of the alien under the immigration laws of the United States; and (iii) Other relevant information or databases, as determined by the Secretary of Homeland Security. (c...

National Transportation Atlas Databases : 2001

DOT National Transportation Integrated Search

2001-01-01

The National Transportation Atlas Databases-2001 (NTAD-2001) is a set of national geographic databases of transportation facilities. These databases include geospatial information for transportation modal networks and intermodal terminals and related...

National Transportation Atlas Databases : 2000

DOT National Transportation Integrated Search

2000-01-01

The National Transportation Atlas Databases-2000 (NTAD-2000) is a set of national geographic databases of transportation facilities. These databases include geospatial information for transportation modal networks and intermodal terminals and related...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2011 CFR

2011-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2014 CFR

2014-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2012 CFR

2012-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2013 CFR

2013-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

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

PubMed

Hühne, Rolf; Thalheim, Torsten; Sühnel, Jürgen

2014-01-01

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

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

USGS Publications Warehouse

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

2014-01-01

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

WATERS Terms of Use and Disclaimer

EPA Pesticide Factsheets

The Reach Address Database (RAD) stores reach address information for each Water Program feature that has been linked to the underlying surface water features (streams, lakes, etc) in the National Hydrology Database (NHD) Plus dataset.

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

PubMed

Arita, Masanori; Suwa, Kazuhiro

2008-09-17

In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

PubMed Central

Arita, Masanori; Suwa, Kazuhiro

2008-01-01

Background In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. Conclusion This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated. PMID:18822113

An integrated biomedical telemetry system for sleep monitoring employing a portable body area network of sensors (SENSATION).

PubMed

Astaras, Alexander; Arvanitidou, Marina; Chouvarda, Ioanna; Kilintzis, Vassilis; Koutkias, Vassilis; Sanchez, Eduardo Monton; Stalidis, George; Triantafyllidis, Andreas; Maglaveras, Nicos

2008-01-01

A flexible, scaleable and cost-effective medical telemetry system is described for monitoring sleep-related disorders in the home environment. The system was designed and built for real-time data acquisition and processing, allowing for additional use in intensive care unit scenarios where rapid medical response is required in case of emergency. It comprises a wearable body area network of Zigbee-compatible wireless sensors worn by the subject, a central database repository residing in the medical centre and thin client workstations located at the subject's home and in the clinician's office. The system supports heterogeneous setup configurations, involving a variety of data acquisition sensors to suit several medical applications. All telemetry data is securely transferred and stored in the central database under the clinicians' ownership and control.

Archetype relational mapping - a practical openEHR persistence solution.

PubMed

Wang, Li; Min, Lingtong; Wang, Rui; Lu, Xudong; Duan, Huilong

2015-11-05

One of the primary obstacles to the widespread adoption of openEHR methodology is the lack of practical persistence solutions for future-proof electronic health record (EHR) systems as described by the openEHR specifications. This paper presents an archetype relational mapping (ARM) persistence solution for the archetype-based EHR systems to support healthcare delivery in the clinical environment. First, the data requirements of the EHR systems are analysed and organized into archetype-friendly concepts. The Clinical Knowledge Manager (CKM) is queried for matching archetypes; when necessary, new archetypes are developed to reflect concepts that are not encompassed by existing archetypes. Next, a template is designed for each archetype to apply constraints related to the local EHR context. Finally, a set of rules is designed to map the archetypes to data tables and provide data persistence based on the relational database. A comparison study was conducted to investigate the differences among the conventional database of an EHR system from a tertiary Class A hospital in China, the generated ARM database, and the Node + Path database. Five data-retrieving tests were designed based on clinical workflow to retrieve exams and laboratory tests. Additionally, two patient-searching tests were designed to identify patients who satisfy certain criteria. The ARM database achieved better performance than the conventional database in three of the five data-retrieving tests, but was less efficient in the remaining two tests. The time difference of query executions conducted by the ARM database and the conventional database is less than 130 %. The ARM database was approximately 6-50 times more efficient than the conventional database in the patient-searching tests, while the Node + Path database requires far more time than the other two databases to execute both the data-retrieving and the patient-searching tests. The ARM approach is capable of generating relational databases using archetypes and templates for archetype-based EHR systems, thus successfully adapting to changes in data requirements. ARM performance is similar to that of conventionally-designed EHR systems, and can be applied in a practical clinical environment. System components such as ARM can greatly facilitate the adoption of openEHR architecture within EHR systems.

Relational databases for rare disease study: application to vascular anomalies.

PubMed

Perkins, Jonathan A; Coltrera, Marc D

2008-01-01

To design a relational database integrating clinical and basic science data needed for multidisciplinary treatment and research in the field of vascular anomalies. Based on data points agreed on by the American Society of Pediatric Otolaryngology (ASPO) Vascular Anomalies Task Force. The database design enables sharing of data subsets in a Health Insurance Portability and Accountability Act (HIPAA)-compliant manner for multisite collaborative trials. Vascular anomalies pose diagnostic and therapeutic challenges. Our understanding of these lesions and treatment improvement is limited by nonstandard terminology, severity assessment, and measures of treatment efficacy. The rarity of these lesions places a premium on coordinated studies among multiple participant sites. The relational database design is conceptually centered on subjects having 1 or more lesions. Each anomaly can be tracked individually along with their treatment outcomes. This design allows for differentiation between treatment responses and untreated lesions' natural course. The relational database design eliminates data entry redundancy and results in extremely flexible search and data export functionality. Vascular anomaly programs in the United States. A relational database correlating clinical findings and photographic, radiologic, histologic, and treatment data for vascular anomalies was created for stand-alone and multiuser networked systems. Proof of concept for independent site data gathering and HIPAA-compliant sharing of data subsets was demonstrated. The collaborative effort by the ASPO Vascular Anomalies Task Force to create the database helped define a common vascular anomaly data set. The resulting relational database software is a powerful tool to further the study of vascular anomalies and the development of evidence-based treatment innovation.

Keeping Track of Our Treasures: Managing Historical Data with Relational Database Software.

ERIC Educational Resources Information Center

Gutmann, Myron P.; And Others

1989-01-01

Describes the way a relational database management system manages a large historical data collection project. Shows that such databases are practical to construct. States that the programing tasks involved are not for beginners, but the rewards of having data organized are worthwhile. (GG)

The Polish Genetic Database of Victims of Totalitarianisms.

PubMed

Ossowski, A; Kuś, M; Kupiec, T; Bykowska, M; Zielińska, G; Jasiński, M E; March, A L

2016-01-01

This paper describes the creation of the Polish Genetic Database of Victims of Totalitarianism and the first research conducted under this project. On September 28th 2012, the Pomeranian Medical University in Szczecin and the Institute of National Remembrance-Commission for Prosecution of Crimes against the Polish Nation agreed to support the creation of the Polish Genetic Database of Victims of Totalitarianism (PBGOT, www.pbgot.pl). The purpose was to employ state-of-the-art methods of forensic genetics to identify the remains of unidentified victims of Communist and Nazi totalitarian regimes. The database was designed to serve as a central repository of genetic information of the victim's DNA and that of the victim's nearest living relatives, with the goal of making a positive identification of the victim. Along the way, PGBOT encountered several challenges. First, extracting useable DNA samples from the remains of individuals who had been buried for over half a century required forensic geneticists to create special procedures and protocols. Second, obtaining genetic reference material and historical information from the victim's closest relatives was both problematic and urgent. The victim's nearest living relatives were part of a dying generation, and the opportunity to obtain the best genetic and historical information about the victims would soon die with them. For this undertaking, PGBOT assembled a team of historians, archaeologists, forensic anthropologists, and forensic geneticists from several European research institutions. The field work was divided into five broad categories: (1) exhumation of victim remains and storing their biological material for later genetic testing; (2) researching archives and historical data for a more complete profile of those killed or missing and the families that lost them; (3) locating the victim's nearest relatives to obtain genetic reference samples (swabs), (4) entering the genetic data from both victims and family members into a common database; (5) making a conclusive, final identification of the victim. PGBOT's first project was to identify victims of the Communist regime buried in hidden mass graves in the Powązki Military Cemetery in Warsaw. Throughout 2012 and 2013, PGBOT carried out archaeological exhumations in the Powązki Military Cemetery that resulted in the recovery of the skeletal remains of 194 victims in several mass graves. Of the 194 sets of remains, more than 50 victims have been successfully matched and identified through genetic evidence. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Trends in death associated with pediatric dental sedation and general anesthesia.

PubMed

Lee, Helen H; Milgrom, Peter; Starks, Helene; Burke, Wylie

2013-08-01

Inadequate access to oral health care places children at risk of caries. Disease severity and inability to cooperate often result in treatment with general anesthesia (GA). Sedation is increasingly popular and viewed as lower risk than GA in community settings. Currently, few data are available to quantify pediatric morbidity and mortality related to dental anesthesia. Summarize dental anesthesia-related pediatric deaths described in media reports. Review of media reports in the Lexis-Nexis Academic database and a private foundation website. Dental offices, ambulatory surgery centers, and hospitals. Patients :US-based children (≤21 years old) who died subsequently receiving anesthesia for a dental procedure between 1980-2011. Most deaths occurred among 2-5 year-olds (n = 21/44), in an office setting (n = 21/44), and with a general/pediatric dentist (n = 25/44) as the anesthesia provider. In this latter group, 17 of 25 deaths were linked with a sedation anesthetic. This series of media reports likely represent only a fraction of the overall morbidity and mortality related to dental anesthesia. These data may indicate an association between mortality and pediatric dental procedures under sedation, particularly in office settings. However, these relationships are difficult to test in the absence of a database that could provide an estimate of incidence and prevalence of morbidity and mortality. With growing numbers of children receiving anesthesia for dental procedures from providers with variable training, it is imperative to be able to track anesthesia-related adverse outcomes. Creating a national database of adverse outcomes will enable future research to advance patient safety and quality. © 2013 John Wiley & Sons Ltd.

Retrospective Mining of Toxicology Data to Discover ...

EPA Pesticide Factsheets

In vivo toxicology data is subject to multiple sources of uncertainty: observer severity bias (a pathologist may record only more severe effects and ignore less severe ones); dose spacing issues (this can lead to missing data, e.g. if a severe effect has a less severe precursor, but both occur at the same tested dose); imperfect control of key independent variables (in databases, one can rarely control key input variables such as animal strain or dosing schedules); effect description heterogeneity (terminology changes over time which can lead to information loss); statistical issues (too few chemicals with a given phenotype, or too few animals in dose groups). These issues directly contribute to uncertainties in models built from the data. We are investigating the use of collections of endpoints (toxicity syndromes) to address these issues. These are identical in concept to medical syndromes which allow a physician to diagnose an underlying disease more accurately than can be done when relying on examination of one symptom at a time. Our test case is anemia, for several reasons: most of the phenotypes (e.g. cell counts) are quantitative; related effects are measured in an automated way; anemia is relatively common, at least at high doses (~30% of chemicals in our database show significant drops in red cell count); the causes of anemia are well understood; and, there is a standard clinical decision tree to classify anemia. Using a database of 658 chemicals, we ha

gPhoton: The GALEX Photon Data Archive

NASA Astrophysics Data System (ADS)

Million, Chase; Fleming, Scott W.; Shiao, Bernie; Seibert, Mark; Loyd, Parke; Tucker, Michael; Smith, Myron; Thompson, Randy; White, Richard L.

2016-12-01

gPhoton is a new database product and software package that enables analysis of GALEX ultraviolet data at the photon level. The project’s stand-alone, pure-Python calibration pipeline reproduces the functionality of the original mission pipeline to reduce raw spacecraft data to lists of time-tagged, sky-projected photons, which are then hosted in a publicly available database by the Mikulski Archive at Space Telescope. This database contains approximately 130 terabytes of data describing approximately 1.1 trillion sky-projected events with a timestamp resolution of five milliseconds. A handful of Python and command-line modules serve as a front end to interact with the database and to generate calibrated light curves and images from the photon-level data at user-defined temporal and spatial scales. The gPhoton software and source code are in active development and publicly available under a permissive license. We describe the motivation, design, and implementation of the calibration pipeline, database, and tools, with emphasis on divergence from prior work, as well as challenges created by the large data volume. We summarize the astrometric and photometric performance of gPhoton relative to the original mission pipeline. For a brief example of short time-domain science capabilities enabled by gPhoton, we show new flares from the known M-dwarf flare star CR Draconis. The gPhoton software has permanent object identifiers with the ASCL (ascl:1603.004) and DOI (doi:10.17909/T9CC7G). This paper describes the software as of version v1.27.2.

Validity of breast, lung and colorectal cancer diagnoses in administrative databases: a systematic review protocol.

PubMed

Abraha, Iosief; Giovannini, Gianni; Serraino, Diego; Fusco, Mario; Montedori, Alessandro

2016-03-18

Breast, lung and colorectal cancers constitute the most common cancers worldwide and their epidemiology, related health outcomes and quality indicators can be studied using administrative healthcare databases. To constitute a reliable source for research, administrative healthcare databases need to be validated. The aim of this protocol is to perform the first systematic review of studies reporting the validation of International Classification of Diseases 9th and 10th revision codes to identify breast, lung and colorectal cancer diagnoses in administrative healthcare databases. This review protocol has been developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 statement. We will search the following databases: MEDLINE, EMBASE, Web of Science and the Cochrane Library, using appropriate search strategies. We will include validation studies that used administrative data to identify breast, lung and colorectal cancer diagnoses or studies that evaluated the validity of breast, lung and colorectal cancer codes in administrative data. The following inclusion criteria will be used: (1) the presence of a reference standard case definition for the disease of interest; (2) the presence of at least one test measure (eg, sensitivity, positive predictive values, etc) and (3) the use of data source from an administrative database. Pairs of reviewers will independently abstract data using standardised forms and will assess quality using a checklist based on the Standards for Reporting of Diagnostic accuracy (STARD) criteria. Ethics approval is not required. We will submit results of this study to a peer-reviewed journal for publication. The results will serve as a guide to identify appropriate case definitions and algorithms of breast, lung and colorectal cancers for researchers involved in validating administrative healthcare databases as well as for outcome research on these conditions that used administrative healthcare databases. CRD42015026881. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

An Animated Introduction to Relational Databases for Many Majors

ERIC Educational Resources Information Center

Dietrich, Suzanne W.; Goelman, Don; Borror, Connie M.; Crook, Sharon M.

2015-01-01

Database technology affects many disciplines beyond computer science and business. This paper describes two animations developed with images and color that visually and dynamically introduce fundamental relational database concepts and querying to students of many majors. The goal is for educators in diverse academic disciplines to incorporate the…

A Parallel Relational Database Management System Approach to Relevance Feedback in Information Retrieval.

ERIC Educational Resources Information Center

Lundquist, Carol; Frieder, Ophir; Holmes, David O.; Grossman, David

1999-01-01

Describes a scalable, parallel, relational database-drive information retrieval engine. To support portability across a wide range of execution environments, all algorithms adhere to the SQL-92 standard. By incorporating relevance feedback algorithms, accuracy is enhanced over prior database-driven information retrieval efforts. Presents…

Historical return on investment and improved quality resulting from development and mining of a hospital laboratory relational database.

PubMed

Brimhall, Bradley B; Hall, Timothy E; Walczak, Steven

2006-01-01

A hospital laboratory relational database, developed over eight years, has demonstrated significant cost savings and a substantial financial return on investment (ROI). In addition, the database has been used to measurably improve laboratory operations and the quality of patient care.

BioImaging Database

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

David Nix, Lisa Simirenko

2006-10-25

The Biolmaging Database (BID) is a relational database developed to store the data and meta-data for the 3D gene expression in early Drosophila embryo development on a cellular level. The schema was written to be used with the MySQL DBMS but with minor modifications can be used on any SQL compliant relational DBMS.

The relational clinical database: a possible solution to the star wars in registry systems.

PubMed

Michels, D K; Zamieroski, M

1990-12-01

In summary, having data from other service areas available in a relational clinical database could resolve many of the problems existing in today's registry systems. Uniting sophisticated information systems into a centralized database system could definitely be a corporate asset in managing the bottom line.

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.

Creating Your Own Database.

ERIC Educational Resources Information Center

Blair, John C., Jr.

1982-01-01

Outlines the important factors to be considered in selecting a database management system for use with a microcomputer and presents a series of guidelines for developing a database. General procedures, report generation, data manipulation, information storage, word processing, data entry, database indexes, and relational databases are among the…

Biological Databases for Human Research

PubMed Central

Zou, Dong; Ma, Lina; Yu, Jun; Zhang, Zhang

2015-01-01

The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation. PMID:25712261

Spatiotemporal conceptual platform for querying archaeological information systems

NASA Astrophysics Data System (ADS)

Partsinevelos, Panagiotis; Sartzetaki, Mary; Sarris, Apostolos

2015-04-01

Spatial and temporal distribution of archaeological sites has been shown to associate with several attributes including marine, water, mineral and food resources, climate conditions, geomorphological features, etc. In this study, archeological settlement attributes are evaluated under various associations in order to provide a specialized query platform in a geographic information system (GIS). Towards this end, a spatial database is designed to include a series of archaeological findings for a secluded geographic area of Crete in Greece. The key categories of the geodatabase include the archaeological type (palace, burial site, village, etc.), temporal information of the habitation/usage period (pre Minoan, Minoan, Byzantine, etc.), and the extracted geographical attributes of the sites (distance to sea, altitude, resources, etc.). Most of the related spatial attributes are extracted with readily available GIS tools. Additionally, a series of conceptual data attributes are estimated, including: Temporal relation of an era to a future one in terms of alteration of the archaeological type, topologic relations of various types and attributes, spatial proximity relations between various types. These complex spatiotemporal relational measures reveal new attributes towards better understanding of site selection for prehistoric and/or historic cultures, yet their potential combinations can become numerous. Therefore, after the quantification of the above mentioned attributes, they are classified as of their importance for archaeological site location modeling. Under this new classification scheme, the user may select a geographic area of interest and extract only the important attributes for a specific archaeological type. These extracted attributes may then be queried against the entire spatial database and provide a location map of possible new archaeological sites. This novel type of querying is robust since the user does not have to type a standard SQL query but graphically select an area of interest. In addition, according to the application at hand, novel spatiotemporal attributes and relations can be supported, towards the understanding of historical settlement patterns.

Atlas - a data warehouse for integrative bioinformatics.

PubMed

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

2005-02-21

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

[Critical analysis of French DRG based information system (PMSI) databases for the epidemiology of cancer: a longitudinal approach becomes possible].

PubMed

Olive, F; Gomez, F; Schott, A-M; Remontet, L; Bossard, N; Mitton, N; Polazzi, S; Colonna, M; Trombert-Paviot, B

2011-02-01

Use of French Diagnosis Related Groups (DRGs) program databases, apart from financial purposes, has recently been improved since a unique anonymous patient identification number has been created for each inpatient in administrative case mix database. Based on the work of the group for cancer epidemiological observation in the Rhône-Alpes area, (ONC-EPI group), we review the remaining difficulties in the use of DRG data for epidemiological purposes and we consider a longitudinal approach based on analysis of database over several years. We also discuss limitations of this approach. The main problems are related to a lack of quality of administrative data, especially coding of diagnoses. These errors come from missing or inappropriate codes, or not being in accordance with prioritization rules (causing an over- or under-reporting or inconsistencies in coding over time). One difficulty, partly due to the hierarchy of coding and the type of cancer, is the choice of an extraction algorithm. In two studies designed to estimate the incidence of cancer cared in hospitals (breast, colon-rectum, kidney, ovaries), a first algorithm, including a code of cancer as principal diagnosis with a selection of surgical procedures less performed than the second one including a code of cancer as principal diagnosis only, for which the number of hospitalizations per patient ratio was stable across time and space. The chaining over several years allows, by tracing the trajectory of the patient, to detect and correct inaccuracies, errors and missing values, and for incidence studies, to correct incident cases by removing prevalent cases. However, linkage, complete only since 2007, does not correct data in all cases. Ways of future improvement certainly pass through improved algorithms for case identification and especially by linking DRG data with other databases. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Atlas – a data warehouse for integrative bioinformatics

PubMed Central

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

2005-01-01

Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

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.

SQL/NF Translator for the Triton Nested Relational Database System

DTIC Science & Technology

1990-12-01

18as., Ohio .. 9~~ ~~ 1 4- AFIT/GCE/ENG/90D-05 SQL/Nk1 TRANSLATOR FOR THE TRITON NESTED RELATIONAL DATABASE SYSTEM THESIS Craig William Schnepf Captain...FOR THE TRITON NESTED RELATIONAL DATABASE SYSTEM THESIS Presented to the Faculty of the School of Engineering of the Air Force Institute of Technnlogy... systems . The SQL/NF query language used for the nested relationil model is an extension of the popular relational model query language SQL. The query

Biodiversity's Big Wet Secret: The Global Distribution of Marine Biological Records Reveals Chronic Under-Exploration of the Deep Pelagic Ocean

PubMed Central

Webb, Thomas J.; Vanden Berghe, Edward; O'Dor, Ron

2010-01-01

Background Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean – the largest biome on Earth – is chronically under-represented in global databases of marine biodiversity. Methodology/Principal Findings We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented. Conclusions/Significance The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity's big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth's largest ecosystem. PMID:20689845

The end is (not) near: Aging, essentialism, and future time perspective.

PubMed

Weiss, David; Job, Veronika; Mathias, Maya; Grah, Stephanie; Freund, Alexandra M

2016-06-01

Beliefs about aging influence how we interpret and respond to changes within and around us. Essentialist beliefs about aging are defined as views that link chronological age with inherent and immutable properties underlying aging-related changes. These beliefs may influence the experience of aging-related changes and shape people's outlook of the future. We hypothesized that people who endorse essentialist beliefs about aging report a more limited future time perspective. Two studies provided correlational (Study 1, N = 250; 18-77 years) and experimental (Study 2, N = 103; 20-77 years) evidence that essentialist beliefs about aging affect people's future time perspective. In addition, Study 2 and Study 3 (N = 174; 34-67 years) tested the underlying mechanism and provided evidence that perception of aging-related threat explains the effect of essentialist beliefs on a reduced future time perspective. These findings highlight the fundamental role of essentialist beliefs about aging for the perception of time horizons in the context of aging. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Using a Semi-Realistic Database to Support a Database Course

ERIC Educational Resources Information Center

Yue, Kwok-Bun

2013-01-01

A common problem for university relational database courses is to construct effective databases for instructions and assignments. Highly simplified "toy" databases are easily available for teaching, learning, and practicing. However, they do not reflect the complexity and practical considerations that students encounter in real-world…

Task III: Development of an Effective Computational Methodology for Body Force Representation of High-speed Rotor 37

NASA Technical Reports Server (NTRS)

Tan, Choon-Sooi; Suder, Kenneth (Technical Monitor)

2003-01-01

A framework for an effective computational methodology for characterizing the stability and the impact of distortion in high-speed multi-stage compressor is being developed. The methodology consists of using a few isolated-blade row Navier-Stokes solutions for each blade row to construct a body force database. The purpose of the body force database is to replace each blade row in a multi-stage compressor by a body force distribution to produce same pressure rise and flow turning. To do this, each body force database is generated in such a way that it can respond to the changes in local flow conditions. Once the database is generated, no hrther Navier-Stokes computations are necessary. The process is repeated for every blade row in the multi-stage compressor. The body forces are then embedded as source terms in an Euler solver. The method is developed to have the capability to compute the performance in a flow that has radial as well as circumferential non-uniformity with a length scale larger than a blade pitch; thus it can potentially be used to characterize the stability of a compressor under design. It is these two latter features as well as the accompanying procedure to obtain the body force representation that distinguish the present methodology from the streamline curvature method. The overall computational procedures have been developed. A dimensional analysis was carried out to determine the local flow conditions for parameterizing the magnitudes of the local body force representation of blade rows. An Euler solver was modified to embed the body forces as source terms. The results from the dimensional analysis show that the body forces can be parameterized in terms of the two relative flow angles, the relative Mach number, and the Reynolds number. For flow in a high-speed transonic blade row, they can be parameterized in terms of the local relative Mach number alone.

Improving the understanding of sleep apnea characterization using Recurrence Quantification Analysis by defining overall acceptable values for the dimensionality of the system, the delay, and the distance threshold.

PubMed

Martín-González, Sofía; Navarro-Mesa, Juan L; Juliá-Serdá, Gabriel; Ramírez-Ávila, G Marcelo; Ravelo-García, Antonio G

2018-01-01

Our contribution focuses on the characterization of sleep apnea from a cardiac rate point of view, using Recurrence Quantification Analysis (RQA), based on a Heart Rate Variability (HRV) feature selection process. Three parameters are crucial in RQA: those related to the embedding process (dimension and delay) and the threshold distance. There are no overall accepted parameters for the study of HRV using RQA in sleep apnea. We focus on finding an overall acceptable combination, sweeping a range of values for each of them simultaneously. Together with the commonly used RQA measures, we include features related to recurrence times, and features originating in the complex network theory. To the best of our knowledge, no author has used them all for sleep apnea previously. The best performing feature subset is entered into a Linear Discriminant classifier. The best results in the "Apnea-ECG Physionet database" and the "HuGCDN2014 database" are, according to the area under the receiver operating characteristic curve, 0.93 (Accuracy: 86.33%) and 0.86 (Accuracy: 84.18%), respectively. Our system outperforms, using a relatively small set of features, previously existing studies in the context of sleep apnea. We conclude that working with dimensions around 7-8 and delays about 4-5, and using for the threshold distance the Fixed Amount of Nearest Neighbours (FAN) method with 5% of neighbours, yield the best results. Therefore, we would recommend these reference values for future work when applying RQA to the analysis of HRV in sleep apnea. We also conclude that, together with the commonly used vertical and diagonal RQA measures, there are newly used features that contribute valuable information for apnea minutes discrimination. Therefore, they are especially interesting for characterization purposes. Using two different databases supports that the conclusions reached are potentially generalizable, and are not limited by database variability.

DFACS - DATABASE, FORMS AND APPLICATIONS FOR CABLING AND SYSTEMS, VERSION 3.30

NASA Technical Reports Server (NTRS)

Billitti, J. W.

1994-01-01

DFACS is an interactive multi-user computer-aided engineering tool for system level electrical integration and cabling engineering. The purpose of the program is to provide the engineering community with a centralized database for entering and accessing system functional definitions, subsystem and instrument-end circuit pinout details, and harnessing data. The primary objective is to provide an instantaneous single point of information interchange, thus avoiding error-prone, time-consuming, and costly multiple-path data shuttling. The DFACS program, which is centered around a single database, has built-in menus that provide easy data input and access for all involved system, subsystem, and cabling personnel. The DFACS program allows parallel design of circuit data sheets and harness drawings. It also recombines raw information to automatically generate various project documents and drawings including the Circuit Data Sheet Index, the Electrical Interface Circuits List, Assembly and Equipment Lists, Electrical Ground Tree, Connector List, Cable Tree, Cabling Electrical Interface and Harness Drawings, Circuit Data Sheets, and ECR List of Affected Interfaces/Assemblies. Real time automatic production of harness drawings and circuit data sheets from the same data reservoir ensures instant system and cabling engineering design harmony. DFACS also contains automatic wire routing procedures and extensive error checking routines designed to minimize the possibility of engineering error. DFACS is designed to run on DEC VAX series computers under VMS using Version 6.3/01 of INGRES QUEL/OSL, a relational database system which is available through Relational Technology, Inc. The program is available in VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard media) or a TK50 tape cartridge. DFACS was developed in 1987 and last updated in 1990. DFACS is a copyrighted work with all copyright vested in NASA. DEC, VAX and VMS are trademarks of Digital Equipment Corporation. INGRES QUEL/OSL is a trademark of Relational Technology, Inc.

PedNavigator: a pedigree drawing servlet for large and inbred populations.

PubMed

Mancosu, Gianmaria; Ledda, Giuseppe; Melis, Paola M

2003-03-22

PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to 'walk' through family ties by point-and-clicking on person's symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.

Data-Base Software For Tracking Technological Developments

NASA Technical Reports Server (NTRS)

Aliberti, James A.; Wright, Simon; Monteith, Steve K.

1996-01-01

Technology Tracking System (TechTracS) computer program developed for use in storing and retrieving information on technology and related patent information developed under auspices of NASA Headquarters and NASA's field centers. Contents of data base include multiple scanned still images and quick-time movies as well as text. TechTracS includes word-processing, report-editing, chart-and-graph-editing, and search-editing subprograms. Extensive keyword searching capabilities enable rapid location of technologies, innovators, and companies. System performs routine functions automatically and serves multiple users.

epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens.

PubMed

Amadoz, Alicia; González-Candelas, Fernando

2007-04-20

Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their needs. The database schema, tool scripts and web-based interface are free software but data stored in our database server are not publicly available. epiPATH is distributed under the terms of GNU General Public License. More details about epiPATH can be found at http://genevo.uv.es/epipath.

International Shock-Wave Database: Current Status

NASA Astrophysics Data System (ADS)

Levashov, Pavel

2013-06-01

Shock-wave and related dynamic material response data serve for calibrating, validating, and improving material models over very broad regions of the pressure-temperature-density phase space. Since the middle of the 20th century vast amount of shock-wave experimental information has been obtained. To systemize it a number of compendiums of shock-wave data has been issued by LLNL, LANL (USA), CEA (France), IPCP and VNIIEF (Russia). In mid-90th the drawbacks of the paper handbooks became obvious, so the first version of the online shock-wave database appeared in 1997 (http://www.ficp.ac.ru/rusbank). It includes approximately 20000 experimental points on shock compression, adiabatic expansion, measurements of sound velocity behind the shock front and free-surface-velocity for more than 650 substances. This is still a useful tool for the shock-wave community, but it has a number of serious disadvantages which can't be easily eliminated: (i) very simple data format for points and references; (ii) minimalistic user interface for data addition; (iii) absence of history of changes; (iv) bad feedback from users. The new International Shock-Wave database (ISWdb) is intended to solve these and some other problems. The ISWdb project objectives are: (i) to develop a database on thermodynamic and mechanical properties of materials under conditions of shock-wave and other dynamic loadings, selected related quantities of interest, and the meta-data that describes the provenance of the measurements and material models; and (ii) to make this database available internationally through the Internet, in an interactive form. The development and operation of the ISWdb is guided by an advisory committee. The database will be installed on two mirrored web-servers, one in Russia and the other in USA (currently only one server is available). The database provides access to original experimental data on shock compression, non-shock dynamic loadings, isentropic expansion, measurements of sound speed in the Hugoniot state, and time-dependent free-surface or window-interface velocity profiles. Users are able to search the information in the database and obtain the experimental points in tabular or plain text formats directly via the Internet using common browsers. It is also possible to plot the experimental points for comparison with different approximations and results of equation-of-state calculations. The user can present the results of calculations in text or graphical forms and compare them with any experimental data available in the database. A short history of the shock-wave database will be presented and current possibilities of ISWdb will be demonstrated. Web-site of the project: http://iswdb.info. This work is supported by SNL contracts # 1143875, 1196352.

9 CFR 81.2 - Identification of deer, elk, and moose in interstate commerce.

Code of Federal Regulations, 2011 CFR

2011-01-01

... is linked to that animal in the CWD National Database. The second animal identification must be... CWD National Database. (Approved by the Office of Management and Budget under control number 0579-0237) ...

9 CFR 81.2 - Identification of deer, elk, and moose in interstate commerce.

Code of Federal Regulations, 2010 CFR

2010-01-01

... is linked to that animal in the CWD National Database. The second animal identification must be... CWD National Database. (Approved by the Office of Management and Budget under control number 0579-0237) ...

78 FR 6732 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-31

... Boating Accident Report Database AGENCY: Coast Guard, DHS. ACTION: Rule; information collection approval... Identification System, and Boating Accident Report Database rule became effective on April 27, 2012. Under the...

9 CFR 81.2 - Identification of deer, elk, and moose in interstate commerce.

Code of Federal Regulations, 2012 CFR

2012-01-01

... is linked to that animal in the CWD National Database. The second animal identification must be... CWD National Database. (Approved by the Office of Management and Budget under control number 0579-0237) ...

PrimateLit Database

Science.gov Websites

Primate Info Net Related Databases NCRR PrimateLit: A bibliographic database for primatology Top of any problems with this service. We welcome your feedback. The PrimateLit database is no longer being Resources, National Institutes of Health. The database is a collaborative project of the Wisconsin Primate

DBGC: A Database of Human Gastric Cancer

PubMed Central

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

2015-01-01

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

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

ERIC Educational Resources Information Center

Friedman, Debra; Hoffman, Phillip

2001-01-01

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

77 FR 36034 - Notice of Funding Availability for the Small Business Transportation Resource Center Program

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... construct a database of regional small businesses that currently or may in the future participate in DOT direct and DOT funded transportation related contracts, and make this database available to OSDBU, upon request. 2. Utilize the database of regional transportation-related small businesses to match...

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

PubMed

Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

2016-10-01

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.

Database Management: Building, Changing and Using Databases. Collected Papers and Abstracts of the Mid-Year Meeting of the American Society for Information Science (15th, Portland, Oregon, May 1986).

ERIC Educational Resources Information Center

American Society for Information Science, Washington, DC.

This document contains abstracts of papers on database design and management which were presented at the 1986 mid-year meeting of the American Society for Information Science (ASIS). Topics considered include: knowledge representation in a bilingual art history database; proprietary database design; relational database design; in-house databases;…

Nonmaterialized Relations and the Support of Information Retrieval Applications by Relational Database Systems.

ERIC Educational Resources Information Center

Lynch, Clifford A.

1991-01-01

Describes several aspects of the problem of supporting information retrieval system query requirements in the relational database management system (RDBMS) environment and proposes an extension to query processing called nonmaterialized relations. User interactions with information retrieval systems are discussed, and nonmaterialized relations are…

Persistent dysphagia after head and neck radiotherapy: a common and under-reported complication with significant effect on non-cancer-related mortality.

PubMed

Szczesniak, M M; Maclean, J; Zhang, T; Graham, P H; Cook, I J

2014-11-01

Dysphagia is a well-recognised acute complication after radiotherapy. However, knowledge about the long-term prevalence and effect remains limited. The aims of this study were to determine the prevalence, severity, morbidity, time course and reporting patterns of dysphagia symptoms after head and neck radiotherapy. An observational cross-sectional study was conducted in a large consecutive series of head and neck cancer patients. All patients in the St George Hospital Cancer Care database who had received head and neck radiotherapy with curative intent 0.5-8 years previously and recorded as being alive were surveyed using the Sydney Swallow Questionnaire (SSQ). Case notes were reviewed to determine the level of awareness of swallowing dysfunction in all patients, as well as the causes of mortality in the 83 deceased patients. The mean follow-up at the time of survey was 3 years after radiotherapy (range 0.5-8 years). Of the 116 patients surveyed by questionnaire, the response rate was 72% (83). Impaired swallowing (SSQ score > 234) was reported by 59% of patients. Dysphagia severity was not predicted by tumour site or stage, nor by the time since therapy, age, gender or adjuvant chemotherapy. Review of the hospital medical records and cancer database revealed that cancer accounted for 55% of deaths and aspiration pneumonia was responsible for 19% of non-cancer-related deaths. Of those with abnormal SSQ scores, only 47% reported dysphagia during follow-up clinic visits. Persistent dysphagia is a prevalent, under-recognised and under-reported long-term complication of head and neck radiotherapy which currently cannot be predicted on the basis of patient, tumour or treatment characteristics. Aspiration pneumonia is an important contributor to non-cancer-related mortality in these patients. These data highlight the need for closer monitoring of swallow dysfunction and its sequelae in this population. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

CHERNOLITTM. Chernobyl Bibliographic Search System

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

Caff, F., Jr.; Kennedy, R.A.; Mahaffey, J.A.

1992-03-02

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world`s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Chernobyl Bibliographic Search System

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

Carr, Jr, F.; Kennedy, R. A.; Mahaffey, J. A.

1992-05-11

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world''s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

Querying clinical data in HL7 RIM based relational model with morph-RDB.

PubMed

Priyatna, Freddy; Alonso-Calvo, Raul; Paraiso-Medina, Sergio; Corcho, Oscar

2017-10-05

Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources. Our previous efforts involved materialized RDF datasets, hence losing data freshness. In this paper we present a solution that uses an ontology based on the HL7 v3 Reference Information Model and a set of R2RML mappings that relate this ontology to an underlying relational database implementation, and where morph-RDB is used to expose a virtual, non-materialized SPARQL endpoint over the data. By applying a set of optimization techniques on the SPARQL-to-SQL query translation algorithm, we can now issue SPARQL queries to the underlying relational data with generally acceptable performance.

Small Business Innovations (Integrated Database)

NASA Technical Reports Server (NTRS)

1992-01-01

Because of the diversity of NASA's information systems, it was necessary to develop DAVID as a central database management system. Under a Small Business Innovation Research (SBIR) grant, Ken Wanderman and Associates, Inc. designed software tools enabling scientists to interface with DAVID and commercial database management systems, as well as artificial intelligence programs. The software has been installed at a number of data centers and is commercially available.

Database interfaces on NASA's heterogeneous distributed database system

NASA Technical Reports Server (NTRS)

Huang, S. H. S.

1986-01-01

The purpose of the ORACLE interface is to enable the DAVID program to submit queries and transactions to databases running under the ORACLE DBMS. The interface package is made up of several modules. The progress of these modules is described below. The two approaches used in implementing the interface are also discussed. Detailed discussion of the design of the templates is shown and concluding remarks are presented.

Hierarchical Control of Semi-Autonomous Teams Under Uncertainty (HICST)

DTIC Science & Technology

2004-05-01

17 2.4 Module 4: Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 2.5... Database SoW 1 2 34 5 Txt file: paths Figure 3: Integration of modules 1-5. The modules make provision for human intervention, not indicated in the...figure. SoW is ‘state of the world’. 3. Task execution; 4. Database for state estimation; 5. Java interface to OEP; 6. Robust dynamic programming for

Microbial properties database editor tutorial

USDA-ARS?s Scientific Manuscript database

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbialrelevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pathogens. Physical prop...

NATIVE HEALTH DATABASES: NATIVE HEALTH RESEARCH DATABASE (NHRD)

EPA Science Inventory

The Native Health Databases contain bibliographic information and abstracts of health-related articles, reports, surveys, and other resource documents pertaining to the health and health care of American Indians, Alaska Natives, and Canadian First Nations. The databases provide i...

Microbial Properties Database Editor Tutorial

EPA Science Inventory

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbial-relevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pat...

Lessons Learned From Developing Reactor Pressure Vessel Steel Embrittlement Database

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

Wang, Jy-An John

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

Building a database on geological hazards in karst: some considerations about certainty, accuracy and reliability in the collection of data

NASA Astrophysics Data System (ADS)

Parise, Mario; Vennari, Carmela

2015-04-01

Sinkholes are definitely the most typical geohazard affecting karst territories. Even though typically their formation is related to an underground cave, and the related subterranean drainage, sinkholes can also be observed on non-soluble deposits such as alluvial and/or colluvial materials. Further, the presence of cavities excavated by man (for different purposes, and in different ages) may be at the origin of other phenomena of sinkholes, the so-called anthropogenic sinkholes, that characterize many historical centres of built-up areas. In Italy, due to the long history of the country, these latter, too, are of great importance, being those that typically involve human buildings and infrastructures, and cause damage and losses to society. As for any other geohazard, building a database through collection of information on the past events is a mandatory step to start the analyses aimed at the evaluation of susceptibility, hazard, and risk. The Institute of Research for the Hydrological Protection (IRPI) of the National Research Council of Italy (CNR) has been working in the last years at the construction of a specific chronological database on sinkholes in the whole country. In the database, the natural and anthropogenic sinkholes are treated in two different subsets, given the strong differences existing as regards both the causal and triggering factors, and the stabilization works as well. A particular care was given in the database to the precise site and date of occurrence of the events, as crucial information for assessing, respectively, the susceptibility and the hazard related to the particular phenomenon under study. As a requirement to be included in the database, a temporal reference of the sinkhole occurrence must be therefore known. Certainty in the geographical position of the event is a fundamental information to correctly locate the sinkhole, and to develop geological and morphological considerations aimed at performing a susceptibility analysis. This factor does not have to be disregarded since, especially for the most ancient events, the data from the sources may be not of high precision for a correct positioning of the sinkhole site. As a consequence, each sinkhole in the database was ranked according to the degree of certainty in the location, subdivided into three different levels. Accuracy of the date of occurrence of the sinkhole was then evaluated, and the highest accuracy was assigned when all the information required (hour, day, month and year of occurrence) were available. The temporal reference is of crucial importance in the IRPI database, since the final goal of the research project is the definition of the sinkhole hazard in Italy. In order to reach such goal, given the definition of hazard, the time of occurrence, and the most likely return time of the events have to be assessed. Overall, the aforementioned elements of the database allow to make some considerations about the reliability of the information presented, their precision, and to give the correct weight to the outcomes deriving from its analyses. Such issues are discussed in the present contribution, as crucial elements that need to be clearly defined in a scientifically-sound database. The database has reached so far about 900 events (31% natural sinkholes and 48% anthropogenic sinkholes, whilst 21% of sinkholes have an uncertain origin). It is continuously updated, and represents a good starting point for analysis of the sinkhole hazard at the national scale, aimed at increasing the level of attention by scientists, practitioners and authorities on this subtle hazard.

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

NASA Astrophysics Data System (ADS)

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

2013-11-01

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

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

PubMed

Ravagli, Carlo; Pognan, Francois; Marc, Philippe

2017-01-01

The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com This software is designed to run on a Java EE application server and store data in a relational database. philippe.marc@novartis.com. © The Author 2016. Published by Oxford University Press.

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts

PubMed Central

Ravagli, Carlo; Pognan, Francois

2017-01-01

Summary: The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. Availability and implementation: The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com. This software is designed to run on a Java EE application server and store data in a relational database. Contact: philippe.marc@novartis.com PMID:27605099

The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data.

PubMed

O'Neill, M A; Hilgetag, C C

2001-08-29

Many problems in analytical biology, such as the classification of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow efficient computational representation and analysis of such data. The system can also be used as a general development tool for database and classification applications. As the complexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a flexible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in different analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-defined cost functions, thus providing flexible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal effectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identification system (DAISY), a system for the automated classification of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture- and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed (http://www.pups.org.uk) as open-source software under the GNU license agreement.

The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data.

PubMed Central

O'Neill, M A; Hilgetag, C C

2001-01-01

Many problems in analytical biology, such as the classification of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow efficient computational representation and analysis of such data. The system can also be used as a general development tool for database and classification applications. As the complexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a flexible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in different analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-defined cost functions, thus providing flexible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal effectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identification system (DAISY), a system for the automated classification of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture- and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed (http://www.pups.org.uk) as open-source software under the GNU license agreement. PMID:11545702

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

PubMed Central

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

2011-01-01

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

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

PubMed Central

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

2006-01-01

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

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

PubMed

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

2006-01-01

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

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

NASA Astrophysics Data System (ADS)

Brown, Christa L.

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

[Privacy and public benefit in using large scale health databases].

PubMed

Yamamoto, Ryuichi

2014-01-01

In Japan, large scale heath databases were constructed in a few years, such as National Claim insurance and health checkup database (NDB) and Japanese Sentinel project. But there are some legal issues for making adequate balance between privacy and public benefit by using such databases. NDB is carried based on the act for elderly person's health care but in this act, nothing is mentioned for using this database for general public benefit. Therefore researchers who use this database are forced to pay much concern about anonymization and information security that may disturb the research work itself. Japanese Sentinel project is a national project to detecting drug adverse reaction using large scale distributed clinical databases of large hospitals. Although patients give the future consent for general such purpose for public good, it is still under discussion using insufficiently anonymized data. Generally speaking, researchers of study for public benefit will not infringe patient's privacy, but vague and complex requirements of legislation about personal data protection may disturb the researches. Medical science does not progress without using clinical information, therefore the adequate legislation that is simple and clear for both researchers and patients is strongly required. In Japan, the specific act for balancing privacy and public benefit is now under discussion. The author recommended the researchers including the field of pharmacology should pay attention to, participate in the discussion of, and make suggestion to such act or regulations.

Using a Relational Database to Index Infectious Disease Information

PubMed Central

Brown, Jay A.

2010-01-01

Mapping medical knowledge into a relational database became possible with the availability of personal computers and user-friendly database software in the early 1990s. To create a database of medical knowledge, the domain expert works like a mapmaker to first outline the domain and then add the details, starting with the most prominent features. The resulting “intelligent database” can support the decisions of healthcare professionals. The intelligent database described in this article contains profiles of 275 infectious diseases. Users can query the database for all diseases matching one or more specific criteria (symptom, endemic region of the world, or epidemiological factor). Epidemiological factors include sources (patients, water, soil, or animals), routes of entry, and insect vectors. Medical and public health professionals could use such a database as a decision-support software tool. PMID:20623018

The Use of a Relational Database in Qualitative Research on Educational Computing.

ERIC Educational Resources Information Center

Winer, Laura R.; Carriere, Mario

1990-01-01

Discusses the use of a relational database as a data management and analysis tool for nonexperimental qualitative research, and describes the use of the Reflex Plus database in the Vitrine 2001 project in Quebec to study computer-based learning environments. Information systems are also discussed, and the use of a conceptual model is explained.…

Towards a collaborative, global infrastructure for biodiversity assessment

PubMed Central

Guralnick, Robert P; Hill, Andrew W; Lane, Meredith

2007-01-01

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge. PMID:17594421

Benchmarking Using Basic DBMS Operations

NASA Astrophysics Data System (ADS)

Crolotte, Alain; Ghazal, Ahmad

The TPC-H benchmark proved to be successful in the decision support area. Many commercial database vendors and their related hardware vendors used these benchmarks to show the superiority and competitive edge of their products. However, over time, the TPC-H became less representative of industry trends as vendors keep tuning their database to this benchmark-specific workload. In this paper, we present XMarq, a simple benchmark framework that can be used to compare various software/hardware combinations. Our benchmark model is currently composed of 25 queries that measure the performance of basic operations such as scans, aggregations, joins and index access. This benchmark model is based on the TPC-H data model due to its maturity and well-understood data generation capability. We also propose metrics to evaluate single-system performance and compare two systems. Finally we illustrate the effectiveness of this model by showing experimental results comparing two systems under different conditions.

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

PubMed Central

Li, Jing; Su, Zengliu; Ma, Ze-Qiang; Slebos, Robbert J. C.; Halvey, Patrick; Tabb, David L.; Liebler, Daniel C.; Pao, William; Zhang, Bing

2011-01-01

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics. PMID:21389108

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

PubMed Central

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2018-01-01

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form. PMID:29608174

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2018-03-19

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form.

ADA Implementation Issues as Discovered through a Literature Survey of Applications Outside the United States

DTIC Science & Technology

1992-03-01

compile time, ensuring that operations conducted are appropriate for the object type. Each implementation requires a database known as the program...Finnish bank being developed by Nokia • Oil drilling control system managed by Sedco- Forex * Vigile - an industrial installation supervisor project by...user interface and Oracle database backend control. The software is being developed in Ada under DOD-STD-2167 under OS/2. BELGIUM BATS S.A. Project title

Organizing, exploring, and analyzing antibody sequence data: the case for relational-database managers.

PubMed

Owens, John

2009-01-01

Technological advances in the acquisition of DNA and protein sequence information and the resulting onrush of data can quickly overwhelm the scientist unprepared for the volume of information that must be evaluated and carefully dissected to discover its significance. Few laboratories have the luxury of dedicated personnel to organize, analyze, or consistently record a mix of arriving sequence data. A methodology based on a modern relational-database manager is presented that is both a natural storage vessel for antibody sequence information and a conduit for organizing and exploring sequence data and accompanying annotation text. The expertise necessary to implement such a plan is equal to that required by electronic word processors or spreadsheet applications. Antibody sequence projects maintained as independent databases are selectively unified by the relational-database manager into larger database families that contribute to local analyses, reports, interactive HTML pages, or exported to facilities dedicated to sophisticated sequence analysis techniques. Database files are transposable among current versions of Microsoft, Macintosh, and UNIX operating systems.

The effect of marital status on breast cancer-related outcomes in women under 65: A SEER database analysis.

PubMed

Hinyard, Leslie; Wirth, Lorinette Saphire; Clancy, Jennifer M; Schwartz, Theresa

2017-04-01

Marital status is strongly associated with improved health and longevity. Being married has been shown to be positively associated with survival in patients with multiple different types of malignancy; however, little is known about the relationship between marital status and breast cancer in younger women. The purpose of this study is to investigate the effect of marital status on diagnosis, and survival of women under the age of 65 with breast cancer. The SEER 18 regions database was used to identify women between the ages of 25-64 diagnosed with invasive breast cancer in the years 2004-2009. Logistic regression was used to predict later stage diagnosis by marital status and Cox proportional hazards models were used to compare breast cancer-related and all-cause survival by marital status classification. Models were stratified by AJCC stage. After adjusting for age, race, and ER status, unmarried women were 1.18 times more likely to be diagnosed at a later stage than married women (95% CI 1.15, 1.20). In adjusted analysis unmarried women were more likely to die of breast cancer and more likely to die of all causes than married women across all AJCC stages. Younger unmarried women with breast cancer may benefit from additional counseling, psychosocial support and case management at the time of diagnosis to ensure their overall outcomes are optimized. Copyright © 2016 Elsevier Ltd. All rights reserved.

Online research databases and journals of Chinese medicine.

PubMed

Fan, Ka Wai

2004-12-01

This paper introduces journals and other research resources about Chinese medicine available online. Web sites are categorized under four headings: databases, comprehensive journals, acupuncture journals, and history and philosophy of Chinese medicine. It may assist interested people in furthering their studies.

TMDL TRACKING SYSTEM

EPA Science Inventory

Resource Purpose:The TMDL Tracking System database contains information on the waters listed under section 303(d) of the Clean Water Act and to track those listed waters through TMDL development. The purpose of the database is to allow EPA, the States/Territories/Tribes, ...

Overview of a compre­hensive resource database for the assessment of recoverable hydrocarbons produced by carbon dioxide enhanced oil recovery

USGS Publications Warehouse

Carolus, Marshall; Biglarbigi, Khosrow; Warwick, Peter D.; Attanasi, Emil D.; Freeman, Philip A.; Lohr, Celeste D.

2017-10-24

A database called the “Comprehensive Resource Database” (CRD) was prepared to support U.S. Geological Survey (USGS) assessments of technically recoverable hydrocarbons that might result from the injection of miscible or immiscible carbon dioxide (CO2) for enhanced oil recovery (EOR). The CRD was designed by INTEK Inc., a consulting company under contract to the USGS. The CRD contains data on the location, key petrophysical properties, production, and well counts (number of wells) for the major oil and gas reservoirs in onshore areas and State waters of the conterminous United States and Alaska. The CRD includes proprietary data on petrophysical properties of fields and reservoirs from the “Significant Oil and Gas Fields of the United States Database,” prepared by Nehring Associates in 2012, and proprietary production and drilling data from the “Petroleum Information Data Model Relational U.S. Well Data,” prepared by IHS Inc. in 2012. This report describes the CRD and the computer algorithms used to (1) estimate missing reservoir property values in the Nehring Associates (2012) database, and to (2) generate values of additional properties used to characterize reservoirs suitable for miscible or immiscible CO2 flooding for EOR. Because of the proprietary nature of the data and contractual obligations, the CRD and actual data from Nehring Associates (2012) and IHS Inc. (2012) cannot be presented in this report.

Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database.

PubMed

Härtig, Claus

2008-01-04

A multidimensional approach for the identification of fatty acid methyl esters (FAME) based on GC/MS analysis is described. Mass spectra and retention data of more than 130 FAME from various sources (chain lengths in the range from 4 to 24 carbon atoms) were collected in a database. Hints for the interpretation of FAME mass spectra are given and relevant diagnostic marker ions are deduced indicating specific groups of fatty acids. To verify the identity of single species and to ensure an optimized chromatographic resolution, the database was compiled with retention data libraries acquired on columns of different polarity (HP-5, DB-23, and HP-88). For a combined use of mass spectra and retention data standardized methods of measurement for each of these columns are required. Such master methods were developed and always applied under the conditions of retention time locking (RTL) which allowed an excellent reproducibility and comparability of absolute retention times. Moreover, as a relative retention index system, equivalent chain lengths (ECL) of FAME were determined by linear interpolation. To compare and to predict ECL values by means of structural features, fractional chain lengths (FCL) were calculated and fitted as well. As shown in an example, the use of retention data and mass spectral information together in a database search leads to an improved and reliable identification of FAME (including positional and geometrical isomers) without further derivatizations.

Searching Across the International Space Station Databases

NASA Technical Reports Server (NTRS)

Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

2007-01-01

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

New Powder Diffraction File (PDF-4) in relational database format: advantages and data-mining capabilities.

PubMed

Kabekkodu, Soorya N; Faber, John; Fawcett, Tim

2002-06-01

The International Centre for Diffraction Data (ICDD) is responding to the changing needs in powder diffraction and materials analysis by developing the Powder Diffraction File (PDF) in a very flexible relational database (RDB) format. The PDF now contains 136,895 powder diffraction patterns. In this paper, an attempt is made to give an overview of the PDF-4, search/match methods and the advantages of having the PDF-4 in RDB format. Some case studies have been carried out to search for crystallization trends, properties, frequencies of space groups and prototype structures. These studies give a good understanding of the basic structural aspects of classes of compounds present in the database. The present paper also reports data-mining techniques and demonstrates the power of a relational database over the traditional (flat-file) database structures.

An Extensible "SCHEMA-LESS" Database Framework for Managing High-Throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semistructured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

An Extensible Schema-less Database Framework for Managing High-throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.; La, Tracy; Clancy, Daniel (Technical Monitor)

2002-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword searches of records for both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high throughput open database framework for managing, storing, and searching unstructured or semi structured arbitrary hierarchal models, XML and HTML.

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.

Relational Data Bases--Are You Ready?

ERIC Educational Resources Information Center

Marshall, Dorothy M.

1989-01-01

Migrating from a traditional to a relational database technology requires more than traditional project management techniques. An overview of what to consider before migrating to relational database technology is presented. Leadership, staffing, vendor support, hardware, software, and application development are discussed. (MLW)

Constructing a Graph Database for Semantic Literature-Based Discovery.

PubMed

Hristovski, Dimitar; Kastrin, Andrej; Dinevski, Dejan; Rindflesch, Thomas C

2015-01-01

Literature-based discovery (LBD) generates discoveries, or hypotheses, by combining what is already known in the literature. Potential discoveries have the form of relations between biomedical concepts; for example, a drug may be determined to treat a disease other than the one for which it was intended. LBD views the knowledge in a domain as a network; a set of concepts along with the relations between them. As a starting point, we used SemMedDB, a database of semantic relations between biomedical concepts extracted with SemRep from Medline. SemMedDB is distributed as a MySQL relational database, which has some problems when dealing with network data. We transformed and uploaded SemMedDB into the Neo4j graph database, and implemented the basic LBD discovery algorithms with the Cypher query language. We conclude that storing the data needed for semantic LBD is more natural in a graph database. Also, implementing LBD discovery algorithms is conceptually simpler with a graph query language when compared with standard SQL.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

[Chickenpox-related mortality trends in the state of São Paulo, Brazil, 1985-2004: a multiple cause approach].

PubMed

Santo, Augusto Hasiak

2007-08-01

To study mortality trends related to chickenpox, as either the underlying or associated cause-of-death (recorded in any field of the medical section of the death certificate), in São Paulo, Brazil. Mortality data for 1985-2004 were obtained from the multiple cause-of-death database maintained by the São Paulo State Data Analysis System (SEADE). Causes-of-death were processed using the Multiple-Causes-of-Death Tabulator. During this 20-year period, chickenpox was identified as the underlying cause-of-death in 1 037 deaths and an associated cause in 150. The mortality coefficients were higher for chickenpox as the underlying, as opposed to the associated cause, and these declined in the analyzed period; whereas a slight increase was observed in mortality due to chickenpox as an associated cause. Seventy-six percent of the deaths were of children under 10 years of age, with the highest incidence among those under 1 year. Most deaths occurred from July to January (86.8% of 1 187 deaths), with a peak in October. In the state's capital city, the mortality coefficients for chickenpox as underlying cause and as associated cause were 47% and 50% higher, respectively, than in the rest of the state. Where chickenpox was identified as the underlying cause, pneumonias and septicemias were the major associated causes; where it was the associated cause, AIDS or neoplasia were most often the underlying cause. Although chickenpox as the underlying cause-of-death has declined, the present study indicates that certain groups are at risk of chickenpox-related mortality, namely children 1-4 years of age and individuals with AIDS or neoplasia.

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

PubMed

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

2007-01-01

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

A Novel Approach: Chemical Relational Databases, and the ...

EPA Pesticide Factsheets

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as

Aging Will Amplify the Heat-related Mortality Risk under a Changing Climate: Projection for the Elderly in Beijing, China

NASA Astrophysics Data System (ADS)

Li, Tiantian; Horton, Radley M.; Bader, Daniel A.; Zhou, Maigeng; Liang, Xudong; Ban, Jie; Sun, Qinghua; Kinney, Patrick L.

2016-06-01

An aging population could substantially enhance the burden of heat-related health risks in a warming climate because of their higher susceptibility to extreme heat health effects. Here, we project heat-related mortality for adults 65 years and older in Beijing China across 31 downscaled climate models and 2 representative concentration pathways (RCPs) in the 2020s, 2050s, and 2080s. Under a scenario of medium population and RCP8.5, by the 2080s, Beijing is projected to experience 14,401 heat-related deaths per year for elderly individuals, which is a 264.9% increase compared with the 1980s. These impacts could be moderated through adaptation. In the 2080s, even with the 30% and 50% adaptation rate assumed in our study, the increase in heat-related death is approximately 7.4 times and 1.3 times larger than in the 1980s respectively under a scenario of high population and RCP8.5. These findings could assist countries in establishing public health intervention policies for the dual problems of climate change and aging population. Examples could include ensuring facilities with large elderly populations are protected from extreme heat (for example through back-up power supplies and/or passive cooling) and using databases and community networks to ensure the home-bound elderly are safe during extreme heat events.

A general temporal data model and the structured population event history register

PubMed Central

Clark, Samuel J.

2010-01-01

At this time there are 37 demographic surveillance system sites active in sub-Saharan Africa, Asia and Central America, and this number is growing continuously. These sites and other longitudinal population and health research projects generate large quantities of complex temporal data in order to describe, explain and investigate the event histories of individuals and the populations they constitute. This article presents possible solutions to some of the key data management challenges associated with those data. The fundamental components of a temporal system are identified and both they and their relationships to each other are given simple, standardized definitions. Further, a metadata framework is proposed to endow this abstract generalization with specific meaning and to bind the definitions of the data to the data themselves. The result is a temporal data model that is generalized, conceptually tractable, and inherently contains a full description of the primary data it organizes. Individual databases utilizing this temporal data model can be customized to suit the needs of their operators without modifying the underlying design of the database or sacrificing the potential to transparently share compatible subsets of their data with other similar databases. A practical working relational database design based on this general temporal data model is presented and demonstrated. This work has arisen out of experience with demographic surveillance in the developing world, and although the challenges and their solutions are more general, the discussion is organized around applications in demographic surveillance. An appendix contains detailed examples and working prototype databases that implement the examples discussed in the text. PMID:20396614

gPhoton: THE GALEX PHOTON DATA ARCHIVE

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

Million, Chase; Fleming, Scott W.; Shiao, Bernie

gPhoton is a new database product and software package that enables analysis of GALEX ultraviolet data at the photon level. The project’s stand-alone, pure-Python calibration pipeline reproduces the functionality of the original mission pipeline to reduce raw spacecraft data to lists of time-tagged, sky-projected photons, which are then hosted in a publicly available database by the Mikulski Archive at Space Telescope. This database contains approximately 130 terabytes of data describing approximately 1.1 trillion sky-projected events with a timestamp resolution of five milliseconds. A handful of Python and command-line modules serve as a front end to interact with the database andmore » to generate calibrated light curves and images from the photon-level data at user-defined temporal and spatial scales. The gPhoton software and source code are in active development and publicly available under a permissive license. We describe the motivation, design, and implementation of the calibration pipeline, database, and tools, with emphasis on divergence from prior work, as well as challenges created by the large data volume. We summarize the astrometric and photometric performance of gPhoton relative to the original mission pipeline. For a brief example of short time-domain science capabilities enabled by gPhoton, we show new flares from the known M-dwarf flare star CR Draconis. The gPhoton software has permanent object identifiers with the ASCL (ascl:1603.004) and DOI (doi:10.17909/T9CC7G). This paper describes the software as of version v1.27.2.« less

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.

Databases in the Central Government : State-of-the-art and the Future

NASA Astrophysics Data System (ADS)

Ohashi, Tomohiro

Management and Coordination Agency, Prime Minister’s Office, conducted a survey by questionnaire against all Japanese Ministries and Agencies, in November 1985, on a subject of the present status of databases produced or planned to be produced by the central government. According to the results, the number of the produced databases has been 132 in 19 Ministries and Agencies. Many of such databases have been possessed by Defence Agency, Ministry of Construction, Ministry of Agriculture, Forestry & Fisheries, and Ministry of International Trade & Industries and have been in the fields of architecture & civil engineering, science & technology, R & D, agriculture, forestry and fishery. However the ratio of the databases available for other Ministries and Agencies has amounted to only 39 percent of all produced databases and the ratio of the databases unavailable for them has amounted to 60 percent of all of such databases, because of in-house databases and so forth. The outline of such results of the survey is reported and the databases produced by the central government are introduced under the items of (1) databases commonly used by all Ministries and Agencies, (2) integrated databases, (3) statistical databases and (4) bibliographic databases. The future problems are also described from the viewpoints of technology developments and mutual uses of databases.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

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.

Dynamic tables: an architecture for managing evolving, heterogeneous biomedical data in relational database management systems.

PubMed

Corwin, John; Silberschatz, Avi; Miller, Perry L; Marenco, Luis

2007-01-01

Data sparsity and schema evolution issues affecting clinical informatics and bioinformatics communities have led to the adoption of vertical or object-attribute-value-based database schemas to overcome limitations posed when using conventional relational database technology. This paper explores these issues and discusses why biomedical data are difficult to model using conventional relational techniques. The authors propose a solution to these obstacles based on a relational database engine using a sparse, column-store architecture. The authors provide benchmarks comparing the performance of queries and schema-modification operations using three different strategies: (1) the standard conventional relational design; (2) past approaches used by biomedical informatics researchers; and (3) their sparse, column-store architecture. The performance results show that their architecture is a promising technique for storing and processing many types of data that are not handled well by the other two semantic data models.

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

PubMed

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

2013-11-15

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

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

NASA Astrophysics Data System (ADS)

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

2010-04-01

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

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

NASA Astrophysics Data System (ADS)

Dziedzic, Adam; Mulawka, Jan

2014-11-01

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

IPD—the Immuno Polymorphism Database

PubMed Central

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

2013-01-01

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

Generic Entity Resolution in Relational Databases

NASA Astrophysics Data System (ADS)

Sidló, Csaba István

Entity Resolution (ER) covers the problem of identifying distinct representations of real-world entities in heterogeneous databases. We consider the generic formulation of ER problems (GER) with exact outcome. In practice, input data usually resides in relational databases and can grow to huge volumes. Yet, typical solutions described in the literature employ standalone memory resident algorithms. In this paper we utilize facilities of standard, unmodified relational database management systems (RDBMS) to enhance the efficiency of GER algorithms. We study and revise the problem formulation, and propose practical and efficient algorithms optimized for RDBMS external memory processing. We outline a real-world scenario and demonstrate the advantage of algorithms by performing experiments on insurance customer data.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

The Data Base and Decision Making in Public Schools.

ERIC Educational Resources Information Center

Hedges, William D.

1984-01-01

Describes generic types of databases--file management systems, relational database management systems, and network/hierarchical database management systems--with their respective strengths and weaknesses; discusses factors to be considered in determining whether a database is desirable; and provides evaluative criteria for use in choosing…

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.

RREL TREATABILITY DATABASE - VERSION 5.0

EPA Science Inventory

There is no abstract available for this product. If further information is requested, please refer to the bibliographic citation and contact the person listed under Contact field. This database can be obtained by contacting Tom Holdsworth, U.S. EPA, 26 West Martin Luther King D...

AN EPA SPONSORED LITERATURE REVIEW DATABASE TO SUPPORT STRESSOR IDENTIFICATION

EPA Science Inventory

The Causal Analysis/Diagnosis Decision Information System (CADDIS) is an EPA decision-support system currently under development for evaluating the biological impact of stressors on water bodies. In support of CADDIS, EPA is developing CADLIT, a searchable database of the scient...

Necessity and feasibility of improving mental health services in China: A systematic qualitative review.

PubMed

Zhao, Xudong; Liu, Liang; Hu, Chengping; Chen, Fazhan; Sun, Xirong

2017-07-01

It has been nearly 40 years since the reform and opening up of Mainland China. The mental health services system has developed rapidly as a part of the profound socioeconomic changes that ensued. However, its development has not been as substantial as other areas of medical care. For the current qualitative systematic review, we searched databases, including China Biology Medicine disc, Weipu, China National Knowledge Infrastructure, Wanfang digital periodical full text data, China's important newspaper full text database, China Statistical Yearbook database, etc. The content of primary research, literature, and policy papers about the evolution and development of Chinese mental health services was systemically reviewed and analysed by using thematic analysis. Two main themes relative to the necessity and feasibility of reforming the current mental health services system emerged. We discuss 5 corresponding subthemes under the umbrella of the necessity of improving the current treatment, rehabilitation, prevention, and service systems and 7 requirements for the feasibility of reforming the current system. We conclude that as the development of the Chinese economy and the spirit of humanistic care continue, the improvement and reformation of the mental health services system are both necessary and feasible. Copyright © 2017 John Wiley & Sons, Ltd.

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

STOPGAP: a database for systematic target opportunity assessment by genetic association predictions.

PubMed

Shen, Judong; Song, Kijoung; Slater, Andrew J; Ferrero, Enrico; Nelson, Matthew R

2017-09-01

We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes. This database can be used for a multitude of investigations into the genes and genetic mechanisms underlying inter-individual variation in human traits, as well as supporting drug discovery applications. Shell, R, Perl and Python scripts and STOPGAP R data files (version 2.5.1 at publication) are available at https://github.com/StatGenPRD/STOPGAP . Some of the most useful STOPGAP fields can be queried through an R Shiny web application at http://stopgapwebapp.com . matthew.r.nelson@gsk.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

WHOLE-BODY VIBRATION EXERCISE IMPROVES FUNCTIONAL PARAMETERS IN PATIENTS WITH OSTEOGENESIS IMPERFECTA: A SYSTEMATIC REVIEW WITH A SUITABLE APPROACH

PubMed Central

Sá-Caputo, Danubia C; Dionello, Carla da F; Frederico, Éric Heleno F. F; Paineiras-Domingos, Laisa L; Sousa-Gonçalves, Cintia Renata; Morel, Danielle S; Moreira-Marconi, Eloá; Unger, Marianne; Bernardo-Filho, Mario

2017-01-01

Background: Patients with osteogenesis imperfecta (OI) have abnormal bone modelling and resorption. The bone tissue adaptation and responsivity to dynamic and mechanical loading may be of therapeutic use under controlled circumstances. Improvements due to the wholebody vibration (WBV) exercises have been reported in strength, motion, gait, balance, posture and bone density in several osteopenic individuals, as in post-menopausal women or children with disabling conditions, as patients with OI. The aim of this investigation was to systematically analyse the current available literature to determine the effect of WBV exercises on functional parameters of OI patients. Materials and methods: Three reviewers independently accessed bibliographical databases. Searches were performed in the PubMed, Scopus, Science Direct and PEDro databases using keywords related to possible interventions (including WBV) used in the management of patients with osteogenesis imperfecta. Results: Three eligible studies were identified by searches in the analysed databases. Conclusion: It was concluded that WBV exercises could be an important option in the management of OI patients improving the mobility and functional parameters. However, further studies are necessary for establishing suitable protocols for these patients. PMID:28480432

An evaluation of case completeness for New Zealand Coronial case files held on the Australasian National Coronial Information System (NCIS).

PubMed

Lilley, Rebbecca; Davie, Gabrielle; Wilson, Suzanne

2016-10-01

Large administrative databases provide powerful opportunities for examining the epidemiology of injury. The National Coronial Information System (NCIS) contains Coronial data from Australia and New Zealand (NZ); however, only closed cases are stored for NZ. This paper examines the completeness of NZ data within the NCIS and its impact upon the validity and utility of this database. A retrospective review of the capture of NZ cases of quad-related fatalities held in the NCIS was undertaken by identifying outstanding Coronial cases held on the NZ Coronial Management System (primary source of NZ Coronial data). NZ data held on the NCIS database were incomplete due to the non-capture of closed cases and the unavailability of open cases. Improvements to the information provided on the NCIS about the completeness of NZ data are needed to improve the validity of NCIS-derived findings and the overall utility of the NCIS for research. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Studies of the DIII-D disruption database using Machine Learning algorithms

NASA Astrophysics Data System (ADS)

Rea, Cristina; Granetz, Robert; Meneghini, Orso

2017-10-01

A Random Forests Machine Learning algorithm, trained on a large database of both disruptive and non-disruptive DIII-D discharges, predicts disruptive behavior in DIII-D with about 90% of accuracy. Several algorithms have been tested and Random Forests was found superior in performances for this particular task. Over 40 plasma parameters are included in the database, with data for each of the parameters taken from 500k time slices. We focused on a subset of non-dimensional plasma parameters, deemed to be good predictors based on physics considerations. Both binary (disruptive/non-disruptive) and multi-label (label based on the elapsed time before disruption) classification problems are investigated. The Random Forests algorithm provides insight on the available dataset by ranking the relative importance of the input features. It is found that q95 and Greenwald density fraction (n/nG) are the most relevant parameters for discriminating between DIII-D disruptive and non-disruptive discharges. A comparison with the Gradient Boosted Trees algorithm is shown and the first results coming from the application of regression algorithms are presented. Work supported by the US Department of Energy under DE-FC02-04ER54698, DE-SC0014264 and DE-FG02-95ER54309.

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

PubMed

Nadkarni, P M; Cheung, K H

1995-12-01

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

New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models.

PubMed

Schofield, Paul N; Sundberg, John P; Hoehndorf, Robert; Gkoutos, Georgios V

2011-09-01

The systematic investigation of the phenotypes associated with genotypes in model organisms holds the promise of revealing genotype-phenotype relations directly and without additional, intermediate inferences. Large-scale projects are now underway to catalog the complete phenome of a species, notably the mouse. With the increasing amount of phenotype information becoming available, a major challenge that biology faces today is the systematic analysis of this information and the translation of research results across species and into an improved understanding of human disease. The challenge is to integrate and combine phenotype descriptions within a species and to systematically relate them to phenotype descriptions in other species, in order to form a comprehensive understanding of the relations between those phenotypes and the genotypes involved in human disease. We distinguish between two major approaches for comparative phenotype analyses: the first relies on evolutionary relations to bridge the species gap, while the other approach compares phenotypes directly. In particular, the direct comparison of phenotypes relies heavily on the quality and coherence of phenotype and disease databases. We discuss major achievements and future challenges for these databases in light of their potential to contribute to the understanding of the molecular mechanisms underlying human disease. In particular, we discuss how the use of ontologies and automated reasoning can significantly contribute to the analysis of phenotypes and demonstrate their potential for enabling translational research.

Cost Convergence between Public and For-Profit Hospitals under Prospective Payment and High Competition in Taiwan

PubMed Central

Xirasagar, Sudha; Lin, Herng-Ching

2004-01-01

Objective To test the hypotheses that: (1) average adjusted costs per discharge are higher in high-competition relative to low-competition markets, and (2) increased competition is associated with cost convergence between public and for-profit (FP) hospitals for case payment diagnoses, but not for cost-plus reimbursed diagnoses. Data Sources Taiwan's National Health Insurance database; 325,851 inpatient claims for cesarean section, vaginal delivery, prostatectomy, and thyroidectomy (all case payment), and bronchial asthma and cholelithiasis (both cost-based payment). Study Design Retrospective population-based, cross-sectional study. Data Analysis Diagnosis-wise regression analyses were done to explore associations between cost per discharge and hospital ownership under high and low competition, adjusted for clinical severity and institutional characteristics. Principal Findings Adjusted costs per discharge are higher for all diagnoses in high-competition markets. For case payment diagnoses, the magnitudes of adjusted cost differences between public and FP hospitals are lower under high competition relative to low competition. This is not so for the cost-based diagnoses. Conclusions We find that the empirical evidence supports both our hypotheses. PMID:15544646

Radiation Embrittlement Archive Project

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

Klasky, Hilda B; Bass, Bennett Richard; Williams, Paul T

2013-01-01

The Radiation Embrittlement Archive Project (REAP), which is being conducted by the Probabilistic Integrity Safety Assessment (PISA) Program at Oak Ridge National Laboratory under funding from the U.S. Nuclear Regulatory Commission s (NRC) Office of Nuclear Regulatory Research, aims to provide an archival source of information about the effect of neutron radiation on the properties of reactor pressure vessel (RPV) steels. Specifically, this project is an effort to create an Internet-accessible RPV steel embrittlement database. The project s website, https://reap.ornl.gov, provides information in two forms: (1) a document archive with surveillance capsule(s) reports and related technical reports, in PDF format,more » for the 104 commercial nuclear power plants (NPPs) in the United States, with similar reports from other countries; and (2) a relational database archive with detailed information extracted from the reports. The REAP project focuses on data collected from surveillance capsule programs for light-water moderated, nuclear power reactor vessels operated in the United States, including data on Charpy V-notch energy testing results, tensile properties, composition, exposure temperatures, neutron flux (rate of irradiation damage), and fluence, (Fast Neutron Fluence a cumulative measure of irradiation for E>1 MeV). Additionally, REAP contains data from surveillance programs conducted in other countries. REAP is presently being extended to focus on embrittlement data analysis, as well. This paper summarizes the current status of the REAP database and highlights opportunities to access the data and to participate in the project.« less

Infrared target simulation environment for pattern recognition applications

NASA Astrophysics Data System (ADS)

Savakis, Andreas E.; George, Nicholas

1994-07-01

The generation of complete databases of IR data is extremely useful for training human observers and testing automatic pattern recognition algorithms. Field data may be used for realism, but require expensive and time-consuming procedures. IR scene simulation methods have emerged as a more economical and efficient alternative for the generation of IR databases. A novel approach to IR target simulation is presented in this paper. Model vehicles at 1:24 scale are used for the simulation of real targets. The temperature profile of the model vehicles is controlled using resistive circuits which are embedded inside the models. The IR target is recorded using an Inframetrics dual channel IR camera system. Using computer processing we place the recorded IR target in a prerecorded background. The advantages of this approach are: (1) the range and 3D target aspect can be controlled by the relative position between the camera and model vehicle; (2) the temperature profile can be controlled by adjusting the power delivered to the resistive circuit; (3) the IR sensor effects are directly incorporated in the recording process, because the real sensor is used; (4) the recorded target can embedded in various types of backgrounds recorded under different weather conditions, times of day etc. The effectiveness of this approach is demonstrated by generating an IR database of three vehicles which is used to train a back propagation neural network. The neural network is capable of classifying vehicle type, vehicle aspect, and relative temperature with a high degree of accuracy.

Quantum Search in Hilbert Space

NASA Technical Reports Server (NTRS)

Zak, Michail

2003-01-01

A proposed quantum-computing algorithm would perform a search for an item of information in a database stored in a Hilbert-space memory structure. The algorithm is intended to make it possible to search relatively quickly through a large database under conditions in which available computing resources would otherwise be considered inadequate to perform such a task. The algorithm would apply, more specifically, to a relational database in which information would be stored in a set of N complex orthonormal vectors, each of N dimensions (where N can be exponentially large). Each vector would constitute one row of a unitary matrix, from which one would derive the Hamiltonian operator (and hence the evolutionary operator) of a quantum system. In other words, all the stored information would be mapped onto a unitary operator acting on a quantum state that would represent the item of information to be retrieved. Then one could exploit quantum parallelism: one could pose all search queries simultaneously by performing a quantum measurement on the system. In so doing, one would effectively solve the search problem in one computational step. One could exploit the direct- and inner-product decomposability of the unitary matrix to make the dimensionality of the memory space exponentially large by use of only linear resources. However, inasmuch as the necessary preprocessing (the mapping of the stored information into a Hilbert space) could be exponentially expensive, the proposed algorithm would likely be most beneficial in applications in which the resources available for preprocessing were much greater than those available for searching.

Structural Mechanics Predictions Relating to Clinical Coronary Stent Fracture in a 5 Year Period in FDA MAUDE Database

PubMed Central

Everett, Kay D.; Conway, Claire; Desany, Gerard J.; Baker, Brian L.; Choi, Gilwoo; Taylor, Charles A.; Edelman, Elazer R.

2016-01-01

Endovascular stents are the mainstay of interventional cardiovascular medicine. Technological advances have reduced biological and clinical complications but not mechanical failure. Stent strut fracture is increasingly recognized as of paramount clinical importance. Though consensus reigns that fractures can result from material fatigue, how fracture is induced and the mechanisms underlying its clinical sequelae remain ill-defined. In this study, strut fractures were identified in the prospectively maintained Food and Drug Administration's (FDA) Manufacturer and User Facility Device Experience Database (MAUDE), covering years 2006–2011, and differentiated based on specific coronary artery implantation site and device configuration. These data, and knowledge of the extent of dynamic arterial deformations obtained from patient CT images and published data, were used to define boundary conditions for 3D finite element models incorporating multimodal, multi-cycle deformation. The structural response for a range of stent designs and configurations was predicted by computational models and included estimation of maximum principal, minimum principal and equivalent plastic strains. Fatigue assessment was performed with Goodman diagrams and safe/unsafe regions defined for different stent designs. Von Mises stress and maximum principal strain increased with multimodal, fully reversed deformation. Spatial maps of unsafe locations corresponded to the identified locations of fracture in different coronary arteries in the clinical database. These findings, for the first time, provide insight into a potential link between patient adverse events and computational modeling of stent deformation. Understanding of the mechanical forces imposed under different implantation conditions may assist in rational design and optimal placement of these devices. PMID:26467552

Structural Mechanics Predictions Relating to Clinical Coronary Stent Fracture in a 5 Year Period in FDA MAUDE Database.

PubMed

Everett, Kay D; Conway, Claire; Desany, Gerard J; Baker, Brian L; Choi, Gilwoo; Taylor, Charles A; Edelman, Elazer R

2016-02-01

Endovascular stents are the mainstay of interventional cardiovascular medicine. Technological advances have reduced biological and clinical complications but not mechanical failure. Stent strut fracture is increasingly recognized as of paramount clinical importance. Though consensus reigns that fractures can result from material fatigue, how fracture is induced and the mechanisms underlying its clinical sequelae remain ill-defined. In this study, strut fractures were identified in the prospectively maintained Food and Drug Administration's (FDA) Manufacturer and User Facility Device Experience Database (MAUDE), covering years 2006-2011, and differentiated based on specific coronary artery implantation site and device configuration. These data, and knowledge of the extent of dynamic arterial deformations obtained from patient CT images and published data, were used to define boundary conditions for 3D finite element models incorporating multimodal, multi-cycle deformation. The structural response for a range of stent designs and configurations was predicted by computational models and included estimation of maximum principal, minimum principal and equivalent plastic strains. Fatigue assessment was performed with Goodman diagrams and safe/unsafe regions defined for different stent designs. Von Mises stress and maximum principal strain increased with multimodal, fully reversed deformation. Spatial maps of unsafe locations corresponded to the identified locations of fracture in different coronary arteries in the clinical database. These findings, for the first time, provide insight into a potential link between patient adverse events and computational modeling of stent deformation. Understanding of the mechanical forces imposed under different implantation conditions may assist in rational design and optimal placement of these devices.

BDVC (Bimodal Database of Violent Content): A database of violent audio and video

NASA Astrophysics Data System (ADS)

Rivera Martínez, Jose Luis; Mijes Cruz, Mario Humberto; Rodríguez Vázqu, Manuel Antonio; Rodríguez Espejo, Luis; Montoya Obeso, Abraham; García Vázquez, Mireya Saraí; Ramírez Acosta, Alejandro Álvaro

2017-09-01

Nowadays there is a trend towards the use of unimodal databases for multimedia content description, organization and retrieval applications of a single type of content like text, voice and images, instead bimodal databases allow to associate semantically two different types of content like audio-video, image-text, among others. The generation of a bimodal database of audio-video implies the creation of a connection between the multimedia content through the semantic relation that associates the actions of both types of information. This paper describes in detail the used characteristics and methodology for the creation of the bimodal database of violent content; the semantic relationship is stablished by the proposed concepts that describe the audiovisual information. The use of bimodal databases in applications related to the audiovisual content processing allows an increase in the semantic performance only and only if these applications process both type of content. This bimodal database counts with 580 audiovisual annotated segments, with a duration of 28 minutes, divided in 41 classes. Bimodal databases are a tool in the generation of applications for the semantic web.

Toward unification of taxonomy databases in a distributed computer environment

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

Kitakami, Hajime; Tateno, Yoshio; Gojobori, Takashi

1994-12-31

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomymore » databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.« less

Silent slips, trips and broken hips in the under 60s: A review of the literature.

PubMed

Janes, Gillian; Serrant, Laura; Sque, Magi

2018-02-24

This critical review of the literature regarding the recovery experiences and healthcare needs of people under 60 following a fragility hip fracture seeks to identify the associated implications for nursing practice and inform care delivery. Forty papers were included following a structured database, citation and grey literature search and filtering of results in line with specified inclusion criteria. Hip fracture is a common, serious and complex injury and an important cause of morbidity, mortality and rising healthcare costs worldwide. This review indicates that although commonly associated with the elderly, incidence and impact in the under 60s has been under-explored. Current health policy, professional and social norms almost exclusively focus on the elderly, surgical interventions and short-term outcomes, rendering the under 60s an inadvertently marginalised, relatively 'silent' sub-set of the hip fracture population. Nurses must be aware, however, of the different recovery needs of this younger group. The limited evidence available indicates these include work related needs and long term physical and psychosocial limitations in this socially and economically active group. Priorities are identified for research to inform policy and practice. Meanwhile, nurses can address the needs of this group by listening to and involving them and their families as healthcare partners. Copyright © 2018. Published by Elsevier Ltd.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

System, method and apparatus for conducting a keyterm search

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A keyterm search is a method of searching a database for subsets of the database that are relevant to an input query. First, a number of relational models of subsets of a database are provided. A query is then input. The query can include one or more keyterms. Next, a gleaning model of the query is created. The gleaning model of the query is then compared to each one of the relational models of subsets of the database. The identifiers of the relevant subsets are then output.

Case 3693 Cryptodacus Hendel, 1914 (Insecta: Diptera: Tephritidae): Proposed suppression of Cryptodacus Gundlach, 1862 (Reptilia, Serpentes, Colubridae)

USGS Publications Warehouse

Norrbom, Allen L.; McDiarmid, Roy W.; Chen, Xiao-Lin; David, King J.; De Meyer, Marc; Freidberg, Amnon; Han, Ho-Yeon; Steck, Gary J.; Thompson, F. Christian; White, Ian M.; Zucchi, Roberto A.

2015-01-01

The purpose of this application, under Article 23.9.3, is to conserve current usage of the well-established genus-group name Cryptodacus Hendel, 1914 for a genus of Neotropical fruit flies by suppression of the earlier, unused name Crypto- dacus Gundlach, 1862, currently a junior synonym of Arrhyton Günther, 1858, a genus of snakes, under the plenary power of the Commission, in the interest of nomenclatural stability. Cryptodacus Gundlach has not been used as a valid name since 1883, whereas Cryptodacus Hendel has been used in a significant body of literature relating to fruit fly systematics, morphology and phylogeny and is the currently used name in various name and molecular databases. 

Databases for rRNA gene profiling of microbial communities

DOEpatents

Ashby, Matthew

2013-07-02

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

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

EPA Science Inventory

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

Network pharmacology-based prediction of active compounds and molecular targets in Yijin-Tang acting on hyperlipidaemia and atherosclerosis.

PubMed

Lee, A Yeong; Park, Won; Kang, Tae-Wook; Cha, Min Ho; Chun, Jin Mi

2018-07-15

Yijin-Tang (YJT) is a traditional prescription for the treatment of hyperlipidaemia, atherosclerosis and other ailments related to dampness phlegm, a typical pathological symptom of abnormal body fluid metabolism in Traditional Korean Medicine. However, a holistic network pharmacology approach to understanding the therapeutic mechanisms underlying hyperlipidaemia and atherosclerosis has not been pursued. To examine the network pharmacological potential effects of YJT on hyperlipidaemia and atherosclerosis, we analysed components, performed target prediction and network analysis, and investigated interacting pathways using a network pharmacology approach. Information on compounds in herbal medicines was obtained from public databases, and oral bioavailability and drug-likeness was screened using absorption, distribution, metabolism, and excretion (ADME) criteria. Correlations between compounds and genes were linked using the STITCH database, and genes related to hyperlipidaemia and atherosclerosis were gathered using the GeneCards database. Human genes were identified and subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Network analysis identified 447 compounds in five herbal medicines that were subjected to ADME screening, and 21 compounds and 57 genes formed the main pathways linked to hyperlipidaemia and atherosclerosis. Among them, 10 compounds (naringenin, nobiletin, hesperidin, galangin, glycyrrhizin, homogentisic acid, stigmasterol, 6-gingerol, quercetin and glabridin) were linked to more than four genes, and are bioactive compounds and key chemicals. Core genes in this network were CASP3, CYP1A1, CYP1A2, MMP2 and MMP9. The compound-target gene network revealed close interactions between multiple components and multiple targets, and facilitates a better understanding of the potential therapeutic effects of YJT. Pharmacological network analysis can help to explain the potential effects of YJT for treating dampness phlegm-related diseases such as hyperlipidaemia and atherosclerosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Equipment Management for Sensor Networks: Linking Physical Infrastructure and Actions to Observational Data

NASA Astrophysics Data System (ADS)

Jones, A. S.; Horsburgh, J. S.; Matos, M.; Caraballo, J.

2015-12-01

Networks conducting long term monitoring using in situ sensors need the functionality to track physical equipment as well as deployments, calibrations, and other actions related to site and equipment maintenance. The observational data being generated by sensors are enhanced if direct linkages to equipment details and actions can be made. This type of information is typically recorded in field notebooks or in static files, which are rarely linked to observations in a way that could be used to interpret results. However, the record of field activities is often relevant to analysis or post-processing of the observational data. We have developed an underlying database schema and deployed a web interface for recording and retrieving information on physical infrastructure and related actions for observational networks. The database schema for equipment was designed as an extension to the Observations Data Model 2 (ODM2), a community-developed information model for spatially discrete, feature based earth observations. The core entities of ODM2 describe location, observed variable, and timing of observations, and the equipment extension contains entities to provide additional metadata specific to the inventory of physical infrastructure and associated actions. The schema is implemented in a relational database system for storage and management with an associated web interface. We designed the web-based tools for technicians to enter and query information on the physical equipment and actions such as site visits, equipment deployments, maintenance, and calibrations. These tools were implemented for the iUTAH (innovative Urban Transitions and Aridregion Hydrosustainability) ecohydrologic observatory, and we anticipate that they will be useful for similar large-scale monitoring networks desiring to link observing infrastructure to observational data to increase the quality of sensor-based data products.

Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by High Light with Acetate and Fe2.

PubMed

He, Bangxiang; Hou, Lulu; Dong, Manman; Shi, Jiawei; Huang, Xiaoyun; Ding, Yating; Cong, Xiaomei; Zhang, Feng; Zhang, Xuecheng; Zang, Xiaonan

2018-01-07

Haematococcus pluvialis is a commercial microalga, that produces abundant levels of astaxanthin under stress conditions. Acetate and Fe 2+ are reported to be important for astaxanthin accumulation in H. pluvialis . In order to study the synergistic effects of high light stress and these two factors, we obtained transcriptomes for four groups: high light irradiation (HL), addition of 25 mM acetate under high light (HA), addition of 20 μM Fe 2+ under high light (HF) and normal green growing cells (HG). Among the total clean reads of the four groups, 156,992 unigenes were found, of which 48.88% were annotated in at least one database (Nr, Nt, Pfam, KOG/COG, SwissProt, KEGG, GO). The statistics for DEGs (differentially expressed genes) showed that there were more than 10 thousand DEGs caused by high light and 1800-1900 DEGs caused by acetate or Fe 2+ . The results of DEG analysis by GO and KEGG enrichments showed that, under the high light condition, the expression of genes related to many pathways had changed, such as the pathway for carotenoid biosynthesis, fatty acid elongation, photosynthesis-antenna proteins, carbon fixation in photosynthetic organisms and so on. Addition of acetate under high light significantly promoted the expression of key genes related to the pathways for carotenoid biosynthesis and fatty acid elongation. Furthermore, acetate could obviously inhibit the expression of genes related to the pathway for photosynthesis-antenna proteins. For addition of Fe 2+ , the genes related to photosynthesis-antenna proteins were promoted significantly and there was no obvious change in the gene expressions related to carotenoid and fatty acid synthesis.

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

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

2004-01-01

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

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

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

2004-01-01

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

RefPrimeCouch—a reference gene primer CouchApp

PubMed Central

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html PMID:24368831

RefPrimeCouch--a reference gene primer CouchApp.

PubMed

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html.

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.

[The future of clinical laboratory database management system].

PubMed

Kambe, M; Imidy, D; Matsubara, A; Sugimoto, Y

1999-09-01

To assess the present status of the clinical laboratory database management system, the difference between the Clinical Laboratory Information System and Clinical Laboratory System was explained in this study. Although three kinds of database management systems (DBMS) were shown including the relational model, tree model and network model, the relational model was found to be the best DBMS for the clinical laboratory database based on our experience and developments of some clinical laboratory expert systems. As a future clinical laboratory database management system, the IC card system connected to an automatic chemical analyzer was proposed for personal health data management and a microscope/video system was proposed for dynamic data management of leukocytes or bacteria.

A web based relational database management system for filariasis control

PubMed Central

Murty, Upadhyayula Suryanarayana; Kumar, Duvvuri Venkata Rama Satya; Sriram, Kumaraswamy; Rao, Kadiri Madhusudhan; Bhattacharyulu, Chakravarthula Hayageeva Narasimha Venakata; Praveen, Bhoopathi; Krishna, Amirapu Radha

2005-01-01

The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface. Availability http://www.webfil.org (login and password can be obtained from the authors) PMID:17597846

Resources | Division of Cancer Prevention

Cancer.gov

Manual of Operations Version 3, 12/13/2012 (PDF, 162KB) Database Sources Consortium for Functional Glycomics databases Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases (EUROCarbDB) |

Projecting Future Heat-Related Mortality under Climate Change Scenarios: A Systematic Review

PubMed Central

Barnett, Adrian Gerard; Wang, Xiaoming; Vaneckova, Pavla; FitzGerald, Gerard; Tong, Shilu

2011-01-01

Background: Heat-related mortality is a matter of great public health concern, especially in the light of climate change. Although many studies have found associations between high temperatures and mortality, more research is needed to project the future impacts of climate change on heat-related mortality. Objectives: We conducted a systematic review of research and methods for projecting future heat-related mortality under climate change scenarios. Data sources and extraction: A literature search was conducted in August 2010, using the electronic databases PubMed, Scopus, ScienceDirect, ProQuest, and Web of Science. The search was limited to peer-reviewed journal articles published in English from January 1980 through July 2010. Data synthesis: Fourteen studies fulfilled the inclusion criteria. Most projections showed that climate change would result in a substantial increase in heat-related mortality. Projecting heat-related mortality requires understanding historical temperature–mortality relationships and considering the future changes in climate, population, and acclimatization. Further research is needed to provide a stronger theoretical framework for projections, including a better understanding of socioeconomic development, adaptation strategies, land-use patterns, air pollution, and mortality displacement. Conclusions: Scenario-based projection research will meaningfully contribute to assessing and managing the potential impacts of climate change on heat-related mortality. PMID:21816703

The "Prediflood" database of historical floods in Catalonia (NE Iberian Peninsula) AD 1035-2013, and its potential applications in flood analysis

NASA Astrophysics Data System (ADS)

Barriendos, M.; Ruiz-Bellet, J. L.; Tuset, J.; Mazón, J.; Balasch, J. C.; Pino, D.; Ayala, J. L.

2014-07-01

"Prediflood" is a database of historical floods occurred in Catalonia (NE Iberian Peninsula), between 10th Century and 21th Century. More than 2700 flood cases are catalogued, and more than 1100 flood events. This database contains information acquired under modern historiographical criteria and it is, therefore, apt to be used in multidisciplinary flood analysis techniques, as meteorological or hydraullic reconstructions.

PERFORMANCE AUDITING OF A HUMAN AIR POLLUTION EXPOSURE CHAMBER FOR PM2.5

EPA Science Inventory

Databases derived from human health effects research play a vital role in setting environmental standards. An underlying assumption in using these databases for standard setting purposes is that they are of adequate quality. The performance auditing program described provides n...

76 FR 15953 - Agency Information Collection Activities; Announcement of Office of Management and Budget...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-22

... CONSUMER PRODUCT SAFETY COMMISSION Agency Information Collection Activities; Announcement of Office of Management and Budget Approval; Publicly Available Consumer Product Safety Information Database... Product Safety Information Database has been approved by the Office of Management and Budget (OMB) under...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Read-only database. 1400.13 Section 1400.13 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY AND DEPARTMENT OF JUSTICE ACCIDENTAL RELEASE PREVENTION REQUIREMENTS; RISK MANAGEMENT PROGRAMS UNDER THE CLEAN AIR ACT SECTION 112(r)(7...

Relational Multimodal Freight Database Webinar

DOT National Transportation Integrated Search

2012-02-01

The relational Multimodal Freight Database (MFD) was developed as part of Texas Department : of Transportation (TxDOT) Research Project 0-6297 entitled Freight Planning Factors Impacting : Texas Commodity Flows, conducted by the Center for Transporta...

Effective components of exercise and physical activity-related behaviour-change interventions for chronic non-communicable diseases in Africa: protocol for a systematic mixed studies review with meta-analysis.

PubMed

Igwesi-Chidobe, Chinonso N; Godfrey, Emma L; Kengne, Andre P

2015-08-12

Chronic non-communicable diseases (NCDs) account for a high burden of mortality and morbidity in Africa. Evidence-based clinical guidelines recommend exercise training and promotion of physical activity behaviour changes to control NCDs. Developing such interventions in Africa requires an understanding of the essential components that make them effective in this context. This is a protocol for a systematic mixed studies review that aims to determine the effective components of exercise and physical activity-related behaviour-change interventions for chronic diseases in Africa, by combining quantitative and qualitative research evidence from studies published until July 2015. We will conduct a detailed search to identify all published and unpublished studies that assessed the effects of exercise and physical activity-related interventions or the experiences/perspectives of patients to these interventions for NCDs from bibliographic databases and the grey literature. Bibliographic databases include MEDLINE, EMBASE, CENTRAL (Cochrane Central Register of Controlled Trials), PsycINFO, CINAHL and Web of Science. We will include the following African regional databases: African Index Medicus (AIM) and AFROLIB, which is the WHO's regional office database for Africa. The databases will be searched from inception until 18 July 2015. Appraisal of study quality will be performed after results synthesis. Data synthesis will be performed independently for quantitative and qualitative data using a mixed methods sequential explanatory synthesis for systematic mixed studies reviews. Meta-analysis will be conducted for the quantitative studies, and thematic synthesis for qualitative studies and qualitative results from the non-controlled observational studies. The primary outcome will include exercise adherence and physical activity behaviour changes. This review protocol is reported according to Preferred Reporting Items for Systematic reviews and Meta-Analysis protocols (PRISMA-P) 2015 guidelines. There is no ethical requirement for this study, as it utilises published data. This review is expected to inform the development of exercise and physical activity-related behaviour-change interventions in Africa, and will be presented at conferences, and published in peer reviewed journals and a PhD thesis at King's College London. This study was registered with the International Prospective Register of Systematic Reviews (PROSPERO) on 22 January 2015 (registration number: PROSPERO 2015: CRD42015016084). Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Human Ageing Genomic Resources: new and updated databases

PubMed Central

Tacutu, Robi; Thornton, Daniel; Johnson, Emily; Budovsky, Arie; Barardo, Diogo; Craig, Thomas; Diana, Eugene; Lehmann, Gilad; Toren, Dmitri; Wang, Jingwei; Fraifeld, Vadim E

2018-01-01

Abstract In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/). PMID:29121237

An Improved Database System for Program Assessment

ERIC Educational Resources Information Center

Haga, Wayne; Morris, Gerard; Morrell, Joseph S.

2011-01-01

This research paper presents a database management system for tracking course assessment data and reporting related outcomes for program assessment. It improves on a database system previously presented by the authors and in use for two years. The database system presented is specific to assessment for ABET (Accreditation Board for Engineering and…

Database Management Systems: New Homes for Migrating Bibliographic Records.

ERIC Educational Resources Information Center

Brooks, Terrence A.; Bierbaum, Esther G.

1987-01-01

Assesses bibliographic databases as part of visionary text systems such as hypertext and scholars' workstations. Downloading is discussed in terms of the capability to search records and to maintain unique bibliographic descriptions, and relational database management systems, file managers, and text databases are reviewed as possible hosts for…

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...

Citation parameters of contact lens-related articles published in the ophthalmic literature.

PubMed

Cardona, Genís; Sanz, Joan P

2014-09-01

This study aimed at exploring the citation parameters of contact lenses articles published in the Ophthalmology thematic category of the Journal Citation Reports (JCR). The Thompson Reuters Web of Science database was accessed to record bibliometric information and citation parameters of all journals listed under the Ophthalmology area of the 2011 JCR edition, including the journals with main publication interests in the contact lens field. In addition, the same database was used to unveil all contact lens-related articles published in 2011 in the same thematic area, whereupon differences in citation parameters between those articles published in contact lens and non-contact lens-related journals were explored. Significant differences in some bibliometric indicators such as half-life and overall citation count were found between contact lens-related journals (shorter half-life and fewer citations) and the median values for the Ophthalmology thematic area of the JCR. Visual examination of all Ophthalmology journals uncovered a total of 156 contact lens-related articles, published in 28 different journals, with 27 articles each for Contact Lens & Anterior Eye, Eye & Contact Lens, and Optometry and Vision Science. Significant differences in citation parameters were encountered between those articles published in contact lens and non-contact lens source journals. These findings, which disclosed contact lenses to be a fertile area of research, may be of interest to researchers and institutions. Differences in bibliometric indicators are of relevance to avoid unwanted bias when conducting between- and within-discipline comparisons of articles, journals, and researchers.