Standardization of XML Database Exchanges and the James Webb Space Telescope Experience

NASA Technical Reports Server (NTRS)

Gal-Edd, Jonathan; Detter, Ryan; Jones, Ron; Fatig, Curtis C.

2007-01-01

Personnel from the National Aeronautics and Space Administration (NASA) James Webb Space Telescope (JWST) Project have been working with various standard communities such the Object Management Group (OMG) and the Consultative Committee for Space Data Systems (CCSDS) to assist in the definition of a common extensible Markup Language (XML) for database exchange format. The CCSDS and OMG standards are intended for the exchange of core command and telemetry information, not for all database information needed to exercise a NASA space mission. The mission-specific database, containing all the information needed for a space mission, is translated from/to the standard using a translator. The standard is meant to provide a system that encompasses 90% of the information needed for command and telemetry processing. This paper will discuss standardization of the XML database exchange format, tools used, and the JWST experience, as well as future work with XML standard groups both commercial and government.

15 CFR 995.4 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... database resulting from the transformation of the ENC by ECDIS for appropriate use, updates to the ENC by... of the 1974 SOLAS Convention. Electronic Navigational Chart (ENC) means a database, standardized as to content, structure, and format, issued for use with ECDIS on the authority of government...

Design and implementation of the NPOI database and website

NASA Astrophysics Data System (ADS)

Newman, K.; Jorgensen, A. M.; Landavazo, M.; Sun, B.; Hutter, D. J.; Armstrong, J. T.; Mozurkewich, David; Elias, N.; van Belle, G. T.; Schmitt, H. R.; Baines, E. K.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) has been recording astronomical observations for nearly two decades, at this point with hundreds of thousands of individual observations recorded to date for a total data volume of many terabytes. To make maximum use of the NPOI data it is necessary to organize them in an easily searchable manner and be able to extract essential diagnostic information from the data to allow users to quickly gauge data quality and suitability for a specific science investigation. This sets the motivation for creating a comprehensive database of observation metadata as well as, at least, reduced data products. The NPOI database is implemented in MySQL using standard database tools and interfaces. The use of standard database tools allows us to focus on top-level database and interface implementation and take advantage of standard features such as backup, remote access, mirroring, and complex queries which would otherwise be time-consuming to implement. A website was created in order to give scientists a user friendly interface for searching the database. It allows the user to select various metadata to search for and also allows them to decide how and what results are displayed. This streamlines the searches, making it easier and quicker for scientists to find the information they are looking for. The website has multiple browser and device support. In this paper we present the design of the NPOI database and website, and give examples of its use.

Normal values and standardization of parameters in nuclear cardiology: Japanese Society of Nuclear Medicine working group database.

PubMed

Nakajima, Kenichi; Matsumoto, Naoya; Kasai, Tokuo; Matsuo, Shinro; Kiso, Keisuke; Okuda, Koichi

2016-04-01

As a 2-year project of the Japanese Society of Nuclear Medicine working group activity, normal myocardial imaging databases were accumulated and summarized. Stress-rest with gated and non-gated image sets were accumulated for myocardial perfusion imaging and could be used for perfusion defect scoring and normal left ventricular (LV) function analysis. For single-photon emission computed tomography (SPECT) with multi-focal collimator design, databases of supine and prone positions and computed tomography (CT)-based attenuation correction were created. The CT-based correction provided similar perfusion patterns between genders. In phase analysis of gated myocardial perfusion SPECT, a new approach for analyzing dyssynchrony, normal ranges of parameters for phase bandwidth, standard deviation and entropy were determined in four software programs. Although the results were not interchangeable, dependency on gender, ejection fraction and volumes were common characteristics of these parameters. Standardization of (123)I-MIBG sympathetic imaging was performed regarding heart-to-mediastinum ratio (HMR) using a calibration phantom method. The HMRs from any collimator types could be converted to the value with medium-energy comparable collimators. Appropriate quantification based on common normal databases and standard technology could play a pivotal role for clinical practice and researches.

The ChEMBL database as linked open data

PubMed Central

2013-01-01

Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

Key comparison BIPM.RI(I)-K9 of the absorbed dose to water standards of the PTB, Germany and the BIPM in medium-energy x-rays

NASA Astrophysics Data System (ADS)

Burns, D. T.; Kessler, C.; Büermann, L.; Ketelhut, S.

2018-01-01

A key comparison has been made between the absorbed dose to water standards of the PTB, Germany and the BIPM in the medium-energy x-ray range. The results show the standards to be in general agreement at the level of the standard uncertainty of the comparison of 9 to 11 parts in 103. The results are combined with those of a EURAMET comparison and presented in terms of degrees of equivalence for entry in the BIPM key comparison database. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Solving the Problem: Genome Annotation Standards before the Data Deluge.

PubMed

Klimke, William; O'Donovan, Claire; White, Owen; Brister, J Rodney; Clark, Karen; Fedorov, Boris; Mizrachi, Ilene; Pruitt, Kim D; Tatusova, Tatiana

2011-10-15

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.

Solving the Problem: Genome Annotation Standards before the Data Deluge

PubMed Central

Klimke, William; O'Donovan, Claire; White, Owen; Brister, J. Rodney; Clark, Karen; Fedorov, Boris; Mizrachi, Ilene; Pruitt, Kim D.; Tatusova, Tatiana

2011-01-01

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries. PMID:22180819

Mass measurement errors of Fourier-transform mass spectrometry (FTMS): distribution, recalibration, and application.

PubMed

Zhang, Jiyang; Ma, Jie; Dou, Lei; Wu, Songfeng; Qian, Xiaohong; Xie, Hongwei; Zhu, Yunping; He, Fuchu

2009-02-01

The hybrid linear trap quadrupole Fourier-transform (LTQ-FT) ion cyclotron resonance mass spectrometer, an instrument with high accuracy and resolution, is widely used in the identification and quantification of peptides and proteins. However, time-dependent errors in the system may lead to deterioration of the accuracy of these instruments, negatively influencing the determination of the mass error tolerance (MET) in database searches. Here, a comprehensive discussion of LTQ/FT precursor ion mass error is provided. On the basis of an investigation of the mass error distribution, we propose an improved recalibration formula and introduce a new tool, FTDR (Fourier-transform data recalibration), that employs a graphic user interface (GUI) for automatic calibration. It was found that the calibration could adjust the mass error distribution to more closely approximate a normal distribution and reduce the standard deviation (SD). Consequently, we present a new strategy, LDSF (Large MET database search and small MET filtration), for database search MET specification and validation of database search results. As the name implies, a large-MET database search is conducted and the search results are then filtered using the statistical MET estimated from high-confidence results. By applying this strategy to a standard protein data set and a complex data set, we demonstrate the LDSF can significantly improve the sensitivity of the result validation procedure.

Clinical decision support tools: personal digital assistant versus online dietary supplement databases.

PubMed

Clauson, Kevin A; Polen, Hyla H; Peak, Amy S; Marsh, Wallace A; DiScala, Sandra L

2008-11-01

Clinical decision support tools (CDSTs) on personal digital assistants (PDAs) and online databases assist healthcare practitioners who make decisions about dietary supplements. To assess and compare the content of PDA dietary supplement databases and their online counterparts used as CDSTs. A total of 102 question-and-answer pairs were developed within 10 weighted categories of the most clinically relevant aspects of dietary supplement therapy. PDA versions of AltMedDex, Lexi-Natural, Natural Medicines Comprehensive Database, and Natural Standard and their online counterparts were assessed by scope (percent of correct answers present), completeness (3-point scale), ease of use, and a composite score integrating all 3 criteria. Descriptive statistics and inferential statistics, including a chi(2) test, Scheffé's multiple comparison test, McNemar's test, and the Wilcoxon signed rank test were used to analyze data. The scope scores for PDA databases were: Natural Medicines Comprehensive Database 84.3%, Natural Standard 58.8%, Lexi-Natural 50.0%, and AltMedDex 36.3%, with Natural Medicines Comprehensive Database statistically superior (p < 0.01). Completeness scores were: Natural Medicines Comprehensive Database 78.4%, Natural Standard 51.0%, Lexi-Natural 43.5%, and AltMedDex 29.7%. Lexi-Natural was superior in ease of use (p < 0.01). Composite scores for PDA databases were: Natural Medicines Comprehensive Database 79.3, Natural Standard 53.0, Lexi-Natural 48.0, and AltMedDex 32.5, with Natural Medicines Comprehensive Database superior (p < 0.01). There was no difference between the scope for PDA and online database pairs with Lexi-Natural (50.0% and 53.9%, respectively) or Natural Medicines Comprehensive Database (84.3% and 84.3%, respectively) (p > 0.05), whereas differences existed for AltMedDex (36.3% vs 74.5%, respectively) and Natural Standard (58.8% vs 80.4%, respectively) (p < 0.01). For composite scores, AltMedDex and Natural Standard online were better than their PDA counterparts (p < 0.01). Natural Medicines Comprehensive Database achieved significantly higher scope, completeness, and composite scores compared with other dietary supplement PDA CDSTs in this study. There was no difference between the PDA and online databases for Lexi-Natural and Natural Medicines Comprehensive Database, whereas online versions of AltMedDex and Natural Standard were significantly better than their PDA counterparts.

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

PubMed Central

2009-01-01

Background DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases. Results We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses. Conclusion Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org. PMID:19958506

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

Wohlgemuth, John; Silverman, Timothy; Miller, David C.

This paper describes an effort to inspect and evaluate PV modules in order to determine what failure or degradation modes are occurring in field installations. This paper will report on the results of six site visits, including the Sacramento Municipal Utility District (SMUD) Hedge Array, Tucson Electric Power (TEP) Springerville, Central Florida Utility, Florida Solar Energy Center (FSEC), the TEP Solar Test Yard, and University of Toledo installations. The effort here makes use of a recently developed field inspection data collection protocol, and the results were input into a corresponding database. The results of this work have also been usedmore » to develop a draft of the IEC standard for climate and application specific accelerated stress testing beyond module qualification. TEP Solar Test Yard, and University of Toledo installations. The effort here makes use of a recently developed field inspection data collection protocol, and the results were input into a corresponding database. The results of this work have also been used to develop a draft of the IEC standard for climate and application specific accelerated stress testing beyond module qualification. TEP Solar Test Yard, and University of Toledo installations. The effort here makes use of a recently developed field inspection data collection protocol, and the results were input into a corresponding database. The results of this work have also been used to develop a draft of the IEC standard for climate and application specific accelerated stress testing beyond module qualification.« less

Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm.

PubMed

Harju, Inka; Lange, Christoph; Kostrzewa, Markus; Maier, Thomas; Rantakokko-Jalava, Kaisu; Haanperä, Marjo

2017-03-01

Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcus mitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae , whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper. Copyright © 2017 American Society for Microbiology.

Pathology Imagebase-a reference image database for standardization of pathology.

PubMed

Egevad, Lars; Cheville, John; Evans, Andrew J; Hörnblad, Jonas; Kench, James G; Kristiansen, Glen; Leite, Katia R M; Magi-Galluzzi, Cristina; Pan, Chin-Chen; Samaratunga, Hemamali; Srigley, John R; True, Lawrence; Zhou, Ming; Clements, Mark; Delahunt, Brett

2017-11-01

Despite efforts to standardize histopathology practice through the development of guidelines, the interpretation of morphology is still hampered by subjectivity. We here describe Pathology Imagebase, a novel mechanism for establishing an international standard for the interpretation of pathology specimens. The International Society of Urological Pathology (ISUP) established a reference image database through the input of experts in the field. Three panels were formed, one each for prostate, urinary bladder and renal pathology, consisting of 24 international experts. Each of the panel members uploaded microphotographs of cases into a non-public database. The remaining 23 experts were asked to vote from a multiple-choice menu. Prior to and while voting, panel members were unable to access the results of voting by the other experts. When a consensus level of at least two-thirds or 16 votes was reached, cases were automatically transferred to the main database. Consensus was reached in a total of 287 cases across five projects on the grading of prostate, bladder and renal cancer and the classification of renal tumours and flat lesions of the bladder. The full database is available to all ISUP members at www.isupweb.org. Non-members may access a selected number of cases. It is anticipated that the database will assist pathologists in calibrating their grading, and will also promote consistency in the diagnosis of difficult cases. © 2017 John Wiley & Sons Ltd.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR DEFINING WORKING DATABASES AND DATA ENTRY FORMS (HAND ENTRY) (UA-D-3.0)

EPA Science Inventory

The purpose of this SOP is to outline a standard approach to naming and defining variables, data types, and data entry forms. This procedure applies to all working databases created during the NHEXAS project and the "Border" study. Keywords: databases; standards.

The National...

Integrating Scientific Array Processing into Standard SQL

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Bachhuber, Johannes; Baumann, Peter

2014-05-01

We live in a time that is dominated by data. Data storage is cheap and more applications than ever accrue vast amounts of data. Storing the emerging multidimensional data sets efficiently, however, and allowing them to be queried by their inherent structure, is a challenge many databases have to face today. Despite the fact that multidimensional array data is almost always linked to additional, non-array information, array databases have mostly developed separately from relational systems, resulting in a disparity between the two database categories. The current SQL standard and SQL DBMS supports arrays - and in an extension also multidimensional arrays - but does so in a very rudimentary and inefficient way. This poster demonstrates the practicality of an SQL extension for array processing, implemented in a proof-of-concept multi-faceted system that manages a federation of array and relational database systems, providing transparent, efficient and scalable access to the heterogeneous data in them.

Development of an Integrated Biospecimen Database among the Regional Biobanks in Korea.

PubMed

Park, Hyun Sang; Cho, Hune; Kim, Hwa Sun

2016-04-01

This study developed an integrated database for 15 regional biobanks that provides large quantities of high-quality bio-data to researchers to be used for the prevention of disease, for the development of personalized medicines, and in genetics studies. We collected raw data, managed independently by 15 regional biobanks, for database modeling and analyzed and defined the metadata of the items. We also built a three-step (high, middle, and low) classification system for classifying the item concepts based on the metadata. To generate clear meanings of the items, clinical items were defined using the Systematized Nomenclature of Medicine Clinical Terms, and specimen items were defined using the Logical Observation Identifiers Names and Codes. To optimize database performance, we set up a multi-column index based on the classification system and the international standard code. As a result of subdividing 7,197,252 raw data items collected, we refined the metadata into 1,796 clinical items and 1,792 specimen items. The classification system consists of 15 high, 163 middle, and 3,588 low class items. International standard codes were linked to 69.9% of the clinical items and 71.7% of the specimen items. The database consists of 18 tables based on a table from MySQL Server 5.6. As a result of the performance evaluation, the multi-column index shortened query time by as much as nine times. The database developed was based on an international standard terminology system, providing an infrastructure that can integrate the 7,197,252 raw data items managed by the 15 regional biobanks. In particular, it resolved the inevitable interoperability issues in the exchange of information among the biobanks, and provided a solution to the synonym problem, which arises when the same concept is expressed in a variety of ways.

Standards for Clinical Grade Genomic Databases.

PubMed

Yohe, Sophia L; Carter, Alexis B; Pfeifer, John D; Crawford, James M; Cushman-Vokoun, Allison; Caughron, Samuel; Leonard, Debra G B

2015-11-01

Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

[Establishment of database with standard 3D tooth crowns based on 3DS MAX].

PubMed

Cheng, Xiaosheng; An, Tao; Liao, Wenhe; Dai, Ning; Yu, Qing; Lu, Peijun

2009-08-01

The database with standard 3D tooth crowns has laid the groundwork for dental CAD/CAM system. In this paper, we design the standard tooth crowns in 3DS MAX 9.0 and create a database with these models successfully. Firstly, some key lines are collected from standard tooth pictures. Then we use 3DS MAX 9.0 to design the digital tooth model based on these lines. During the design process, it is important to refer to the standard plaster tooth model. After some tests, the standard tooth models designed with this method are accurate and adaptable; furthermore, it is very easy to perform some operations on the models such as deforming and translating. This method provides a new idea to build the database with standard 3D tooth crowns and a basis for dental CAD/CAM system.

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

PubMed

Zhao, Li-Mei; Tan, Ning-Hua

2015-01-01

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

Automated database-guided expert-supervised orientation for immunophenotypic diagnosis and classification of acute leukemia

PubMed Central

Lhermitte, L; Mejstrikova, E; van der Sluijs-Gelling, A J; Grigore, G E; Sedek, L; Bras, A E; Gaipa, G; Sobral da Costa, E; Novakova, M; Sonneveld, E; Buracchi, C; de Sá Bacelar, T; te Marvelde, J G; Trinquand, A; Asnafi, V; Szczepanski, T; Matarraz, S; Lopez, A; Vidriales, B; Bulsa, J; Hrusak, O; Kalina, T; Lecrevisse, Q; Martin Ayuso, M; Brüggemann, M; Verde, J; Fernandez, P; Burgos, L; Paiva, B; Pedreira, C E; van Dongen, J J M; Orfao, A; van der Velden, V H J

2018-01-01

Precise classification of acute leukemia (AL) is crucial for adequate treatment. EuroFlow has previously designed an AL orientation tube (ALOT) to guide towards the relevant classification panel (T-cell acute lymphoblastic leukemia (T-ALL), B-cell precursor (BCP)-ALL and/or acute myeloid leukemia (AML)) and final diagnosis. Now we built a reference database with 656 typical AL samples (145 T-ALL, 377 BCP-ALL, 134 AML), processed and analyzed via standardized protocols. Using principal component analysis (PCA)-based plots and automated classification algorithms for direct comparison of single-cells from individual patients against the database, another 783 cases were subsequently evaluated. Depending on the database-guided results, patients were categorized as: (i) typical T, B or Myeloid without or; (ii) with a transitional component to another lineage; (iii) atypical; or (iv) mixed-lineage. Using this automated algorithm, in 781/783 cases (99.7%) the right panel was selected, and data comparable to the final WHO-diagnosis was already provided in >93% of cases (85% T-ALL, 97% BCP-ALL, 95% AML and 87% mixed-phenotype AL patients), even without data on the full-characterization panels. Our results show that database-guided analysis facilitates standardized interpretation of ALOT results and allows accurate selection of the relevant classification panels, hence providing a solid basis for designing future WHO AL classifications. PMID:29089646

[The importance of data].

PubMed

Planas, M; Rodríguez, T; Lecha, M

2004-01-01

Decisions have to be made about what data on patient characteristics and processes and outcome need to be collected, and standard definitions of these data items need to be developed to identify data quality concerns as promptly as possible and to establish ways to improve data quality. The usefulness of any clinical database depends strongly on the quality of the collected data. If the data quality is poor, the results of studies using the database might be biased and unreliable. Furthermore, if the quality of the database has not been verified, the results might be given little credence, especially if they are unwelcome or unexpected. To assure the quality of clinical database is essential the clear definition of the uses to which the database is going to be put; the database should to be developed that is comprehensive in terms of its usefulness but limited in its size.

Key comparison BIPM.RI(I)-K5 of the air kerma standards of the ININ, Mexico and the BIPM in 137Cs gamma radiation

NASA Astrophysics Data System (ADS)

Kessler, C.; Burns, D. T.; Alvarez Romero, J. T.; De la Cruz Hernández, D.; Cabrera Vertti, M. R.; Tovar-Muñoz, V. M.

2015-01-01

A direct comparison of the standards for air kerma of the Instituto Nacional de Investigaciones Nucleares (ININ), Mexico, and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 137Cs radiation beam of the BIPM in February 2015. The comparison result, evaluated as a ratio of the ININ and the BIPM standards for air kerma, is 1.0048 with a combined standard uncertainty of 2.0 × 10-3. The results are analysed and presented in terms of degrees of equivalence for entry in the BIPM key comparison database. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

[Technical improvement of cohort constitution in administrative health databases: Providing a tool for integration and standardization of data applicable in the French National Health Insurance Database (SNIIRAM)].

PubMed

Ferdynus, C; Huiart, L

2016-09-01

Administrative health databases such as the French National Heath Insurance Database - SNIIRAM - are a major tool to answer numerous public health research questions. However the use of such data requires complex and time-consuming data management. Our objective was to develop and make available a tool to optimize cohort constitution within administrative health databases. We developed a process to extract, transform and load (ETL) data from various heterogeneous sources in a standardized data warehouse. This data warehouse is architected as a star schema corresponding to an i2b2 star schema model. We then evaluated the performance of this ETL using data from a pharmacoepidemiology research project conducted in the SNIIRAM database. The ETL we developed comprises a set of functionalities for creating SAS scripts. Data can be integrated into a standardized data warehouse. As part of the performance assessment of this ETL, we achieved integration of a dataset from the SNIIRAM comprising more than 900 million lines in less than three hours using a desktop computer. This enables patient selection from the standardized data warehouse within seconds of the request. The ETL described in this paper provides a tool which is effective and compatible with all administrative health databases, without requiring complex database servers. This tool should simplify cohort constitution in health databases; the standardization of warehouse data facilitates collaborative work between research teams. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Preliminary Integrated Geologic Map Databases for the United States: Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, Rhode Island and Vermont

USGS Publications Warehouse

Nicholson, Suzanne W.; Dicken, Connie L.; Horton, John D.; Foose, Michael P.; Mueller, Julia A.L.; Hon, Rudi

2006-01-01

The rapid growth in the use of Geographic Information Systems (GIS) has highlighted the need for regional and national scale digital geologic maps that have standardized information about geologic age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. Although two digital geologic maps (Schruben and others, 1994; Reed and Bush, 2004) of the United States currently exist, their scales (1:2,500,000 and 1:5,000,000) are too general for many regional applications. Most states have digital geologic maps at scales of about 1:500,000, but the databases are not comparably structured and, thus, it is difficult to use the digital database for more than one state at a time. This report describes the result for a seven state region of an effort by the U.S. Geological Survey to produce a series of integrated and standardized state geologic map databases that cover the entire United States. In 1997, the United States Geological Survey's Mineral Resources Program initiated the National Surveys and Analysis (NSA) Project to develop national digital databases. One primary activity of this project was to compile a national digital geologic map database, utilizing state geologic maps, to support studies in the range of 1:250,000- to 1:1,000,000-scale. To accomplish this, state databases were prepared using a common standard for the database structure, fields, attribution, and data dictionaries. For Alaska and Hawaii new state maps are being prepared and the preliminary work for Alaska is being released as a series of 1:250,000 scale quadrangle reports. This document provides background information and documentation for the integrated geologic map databases of this report. This report is one of a series of such reports releasing preliminary standardized geologic map databases for the United States. The data products of the project consist of two main parts, the spatial databases and a set of supplemental tables relating to geologic map units. The datasets serve as a data resource to generate a variety of stratigraphic, age, and lithologic maps. This documentation is divided into four main sections: (1) description of the set of data files provided in this report, (2) specifications of the spatial databases, (3) specifications of the supplemental tables, and (4) an appendix containing the data dictionaries used to populate some fields of the spatial database and supplemental tables.

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.

Landscape features, standards, and semantics in U.S. national topographic mapping databases

USGS Publications Warehouse

Varanka, Dalia

2009-01-01

The objective of this paper is to examine the contrast between local, field-surveyed topographical representation and feature representation in digital, centralized databases and to clarify their ontological implications. The semantics of these two approaches are contrasted by examining the categorization of features by subject domains inherent to national topographic mapping. When comparing five USGS topographic mapping domain and feature lists, results indicate that multiple semantic meanings and ontology rules were applied to the initial digital database, but were lost as databases became more centralized at national scales, and common semantics were replaced by technological terms.

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

National Water Quality Standards Database (NWQSD)

EPA Pesticide Factsheets

The National Water Quality Standards Database (WQSDB) provides access to EPA and state water quality standards (WQS) information in text, tables, and maps. This data source was last updated in December 2007 and will no longer be updated.

CSE database: extended annotations and new recommendations for ECG software testing.

PubMed

Smíšek, Radovan; Maršánová, Lucie; Němcová, Andrea; Vítek, Martin; Kozumplík, Jiří; Nováková, Marie

2017-08-01

Nowadays, cardiovascular diseases represent the most common cause of death in western countries. Among various examination techniques, electrocardiography (ECG) is still a highly valuable tool used for the diagnosis of many cardiovascular disorders. In order to diagnose a person based on ECG, cardiologists can use automatic diagnostic algorithms. Research in this area is still necessary. In order to compare various algorithms correctly, it is necessary to test them on standard annotated databases, such as the Common Standards for Quantitative Electrocardiography (CSE) database. According to Scopus, the CSE database is the second most cited standard database. There were two main objectives in this work. First, new diagnoses were added to the CSE database, which extended its original annotations. Second, new recommendations for diagnostic software quality estimation were established. The ECG recordings were diagnosed by five new cardiologists independently, and in total, 59 different diagnoses were found. Such a large number of diagnoses is unique, even in terms of standard databases. Based on the cardiologists' diagnoses, a four-round consensus (4R consensus) was established. Such a 4R consensus means a correct final diagnosis, which should ideally be the output of any tested classification software. The accuracy of the cardiologists' diagnoses compared with the 4R consensus was the basis for the establishment of accuracy recommendations. The accuracy was determined in terms of sensitivity = 79.20-86.81%, positive predictive value = 79.10-87.11%, and the Jaccard coefficient = 72.21-81.14%, respectively. Within these ranges, the accuracy of the software is comparable with the accuracy of cardiologists. The accuracy quantification of the correct classification is unique. Diagnostic software developers can objectively evaluate the success of their algorithm and promote its further development. The annotations and recommendations proposed in this work will allow for faster development and testing of classification software. As a result, this might facilitate cardiologists' work and lead to faster diagnoses and earlier treatment.

Key comparison BIPM.RI(I)-K5 of the air-kerma standards of the SMU, Slovakia and the BIPM in 137Cs gamma radiation

NASA Astrophysics Data System (ADS)

Kessler, C.; Burns, D.; Durný, N.

2018-01-01

The first direct comparison of the standards for air kerma of the Slovak Institute of Metrology (SMU), Slovakia and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 137Cs radiation beam of the BIPM in June 2017. The comparison result, evaluated as a ratio of the SMU and the BIPM standards for air kerma, is 1.0051 with a combined standard uncertainty of 2.7 × 10-3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 2 parts in 104. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the SMU, Slovakia and the BIPM in 60Co gamma radiation

NASA Astrophysics Data System (ADS)

Kessler, C.; Burns, D.; Durný, N.

2018-01-01

A key comparison of the standards for air kerma of the Slovak Institute of Metrology (SMU), Slovakia and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in June 2017. The comparison result, evaluated as a ratio of the SMU and the BIPM standards for air kerma, is 1.0042 with a combined standard uncertainty of 2.7 × 10-3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 2 parts in 104. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the MKEH, Hungary and the BIPM in 60Co gamma radiation

NASA Astrophysics Data System (ADS)

Kessler, C.; Burns, D.; Machula, G.

2018-01-01

A comparison of the standards for air kerma of the Hungarian Trade Licensing Office (MKEH), Hungary and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in March 2016. The comparison result, evaluated as a ratio of the MKEH and the BIPM standards for air kerma, is 1.0047 with a combined standard uncertainty of 1.9 × 10-3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 2.6 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Key comparison BIPM.RI(I)-K3 of the air-kerma standards of the NIST, USA and the BIPM in medium-energy x-rays.

PubMed

Burns, D T; Kessler, C; O'Brien, M; Minniti, R

2012-01-01

A key comparison has been made between the air-kerma standards of the NIST, USA and the BIPM in the medium-energy x-ray range. The results show the standards to be in agreement at the level of the standard uncertainty of the comparison of 3.8 parts in 10 3 , except at 250 kV where the difference is 1.5 times the standard uncertainty. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

Standardization of the Food Composition Database Used in the Latin American Nutrition and Health Study (ELANS).

PubMed

Kovalskys, Irina; Fisberg, Mauro; Gómez, Georgina; Rigotti, Attilio; Cortés, Lilia Yadira; Yépez, Martha Cecilia; Pareja, Rossina G; Herrera-Cuenca, Marianella; Zimberg, Ioná Z; Tucker, Katherine L; Koletzko, Berthold; Pratt, Michael

2015-09-16

Between-country comparisons of estimated dietary intake are particularly prone to error when different food composition tables are used. The objective of this study was to describe our procedures and rationale for the selection and adaptation of available food composition to a single database to enable cross-country nutritional intake comparisons. Latin American Study of Nutrition and Health (ELANS) is a multicenter cross-sectional study of representative samples from eight Latin American countries. A standard study protocol was designed to investigate dietary intake of 9000 participants enrolled. Two 24-h recalls using the Multiple Pass Method were applied among the individuals of all countries. Data from 24-h dietary recalls were entered into the Nutrition Data System for Research (NDS-R) program after a harmonization process between countries to include local foods and appropriately adapt the NDS-R database. A food matching standardized procedure involving nutritional equivalency of local food reported by the study participants with foods available in the NDS-R database was strictly conducted by each country. Standardization of food and nutrient assessments has the potential to minimize systematic and random errors in nutrient intake estimations in the ELANS project. This study is expected to result in a unique dataset for Latin America, enabling cross-country comparisons of energy, macro- and micro-nutrient intake within this region.

Standardization of the Food Composition Database Used in the Latin American Nutrition and Health Study (ELANS)

PubMed Central

Kovalskys, Irina; Fisberg, Mauro; Gómez, Georgina; Rigotti, Attilio; Cortés, Lilia Yadira; Yépez, Martha Cecilia; Pareja, Rossina G.; Herrera-Cuenca, Marianella; Zimberg, Ioná Z.; Tucker, Katherine L.; Koletzko, Berthold; Pratt, Michael

2015-01-01

Between-country comparisons of estimated dietary intake are particularly prone to error when different food composition tables are used. The objective of this study was to describe our procedures and rationale for the selection and adaptation of available food composition to a single database to enable cross-country nutritional intake comparisons. Latin American Study of Nutrition and Health (ELANS) is a multicenter cross-sectional study of representative samples from eight Latin American countries. A standard study protocol was designed to investigate dietary intake of 9000 participants enrolled. Two 24-h recalls using the Multiple Pass Method were applied among the individuals of all countries. Data from 24-h dietary recalls were entered into the Nutrition Data System for Research (NDS-R) program after a harmonization process between countries to include local foods and appropriately adapt the NDS-R database. A food matching standardized procedure involving nutritional equivalency of local food reported by the study participants with foods available in the NDS-R database was strictly conducted by each country. Standardization of food and nutrient assessments has the potential to minimize systematic and random errors in nutrient intake estimations in the ELANS project. This study is expected to result in a unique dataset for Latin America, enabling cross-country comparisons of energy, macro- and micro-nutrient intake within this region. PMID:26389952

Standard Electronic Format Specification for Tank Characterization Data Loader Version 3.5

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

ADAMS, M.R.

2001-01-31

The purpose of this document is to describe the standard electronic format for data files that will be sent for entry into the Tank Characterization Database (TCD). There are 2 different file types needed for each data load: (1) Analytical Results and (2) Sample Descriptions.

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

PubMed Central

Gilliland, Gary L.; Tung, Michael; Ladner, Jane

1996-01-01

The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge.

PubMed

Ningthoujam, Sanjoy Singh; Talukdar, Anupam Das; Potsangbam, Kumar Singh; Choudhury, Manabendra Dutta

2012-05-07

Major research contributions in ethnopharmacology have generated vast amount of data associated with medicinal plants. Computerized databases facilitate data management and analysis making coherent information available to researchers, planners and other users. Web-based databases also facilitate knowledge transmission and feed the circle of information exchange between the ethnopharmacological studies and public audience. However, despite the development of many medicinal plant databases, a lack of uniformity is still discernible. Therefore, it calls for defining a common standard to achieve the common objectives of ethnopharmacology. The aim of the study is to review the diversity of approaches in storing ethnopharmacological information in databases and to provide some minimal standards for these databases. Survey for articles on medicinal plant databases was done on the Internet by using selective keywords. Grey literatures and printed materials were also searched for information. Listed resources were critically analyzed for their approaches in content type, focus area and software technology. Necessity for rapid incorporation of traditional knowledge by compiling primary data has been felt. While citation collection is common approach for information compilation, it could not fully assimilate local literatures which reflect traditional knowledge. Need for defining standards for systematic evaluation, checking quality and authenticity of the data is felt. Databases focussing on thematic areas, viz., traditional medicine system, regional aspect, disease and phytochemical information are analyzed. Issues pertaining to data standard, data linking and unique identification need to be addressed in addition to general issues like lack of update and sustainability. In the background of the present study, suggestions have been made on some minimum standards for development of medicinal plant database. In spite of variations in approaches, existence of many overlapping features indicates redundancy of resources and efforts. As the development of global data in a single database may not be possible in view of the culture-specific differences, efforts can be given to specific regional areas. Existing scenario calls for collaborative approach for defining a common standard in medicinal plant database for knowledge sharing and scientific advancement. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Applications of Automation Methods for Nonlinear Fracture Test Analysis

NASA Technical Reports Server (NTRS)

Allen, Phillip A.; Wells, Douglas N.

2013-01-01

As fracture mechanics material testing evolves, the governing test standards continue to be refined to better reflect the latest understanding of the physics of the fracture processes involved. The traditional format of ASTM fracture testing standards, utilizing equations expressed directly in the text of the standard to assess the experimental result, is self-limiting in the complexity that can be reasonably captured. The use of automated analysis techniques to draw upon a rich, detailed solution database for assessing fracture mechanics tests provides a foundation for a new approach to testing standards that enables routine users to obtain highly reliable assessments of tests involving complex, non-linear fracture behavior. Herein, the case for automating the analysis of tests of surface cracks in tension in the elastic-plastic regime is utilized as an example of how such a database can be generated and implemented for use in the ASTM standards framework. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

LSE-Sign: A lexical database for Spanish Sign Language.

PubMed

Gutierrez-Sigut, Eva; Costello, Brendan; Baus, Cristina; Carreiras, Manuel

2016-03-01

The LSE-Sign database is a free online tool for selecting Spanish Sign Language stimulus materials to be used in experiments. It contains 2,400 individual signs taken from a recent standardized LSE dictionary, and a further 2,700 related nonsigns. Each entry is coded for a wide range of grammatical, phonological, and articulatory information, including handshape, location, movement, and non-manual elements. The database is accessible via a graphically based search facility which is highly flexible both in terms of the search options available and the way the results are displayed. LSE-Sign is available at the following website: http://www.bcbl.eu/databases/lse/.

Redefining the Practice of Peer Review Through Intelligent Automation Part 1: Creation of a Standardized Methodology and Referenceable Database.

PubMed

Reiner, Bruce I

2017-10-01

Conventional peer review practice is compromised by a number of well-documented biases, which in turn limit standard of care analysis, which is fundamental to determination of medical malpractice. In addition to these intrinsic biases, other existing deficiencies exist in current peer review including the lack of standardization, objectivity, retrospective practice, and automation. An alternative model to address these deficiencies would be one which is completely blinded to the peer reviewer, requires independent reporting from both parties, utilizes automated data mining techniques for neutral and objective report analysis, and provides data reconciliation for resolution of finding-specific report differences. If properly implemented, this peer review model could result in creation of a standardized referenceable peer review database which could further assist in customizable education, technology refinement, and implementation of real-time context and user-specific decision support.

Data Mining the Ogle-II I-band Database for Eclipsing Binary Stars

NASA Astrophysics Data System (ADS)

Ciocca, M.

2013-08-01

The OGLE I-band database is a searchable database of quality photometric data available to the public. During Phase 2 of the experiment, known as "OGLE-II", I-band observations were made over a period of approximately 1,000 days, resulting in over 1010 measurements of more than 40 million stars. This was accomplished by using a filter with a passband near the standard Cousins Ic. The database of these observations is fully searchable using the mysql database engine, and provides the magnitude measurements and their uncertainties. In this work, a program of data mining the OGLE I-band database was performed, resulting in the discovery of 42 previously unreported eclipsing binaries. Using the software package Peranso (Vanmuster 2011) to analyze the light curves obtained from OGLE-II, the eclipsing types, the epochs and the periods of these eclipsing variables were determined, to one part in 106. A preliminary attempt to model the physical parameters of these binaries was also performed, using the Binary Maker 3 software (Bradstreet and Steelman 2004).

Prototype of web-based database of surface wave investigation results for site classification

NASA Astrophysics Data System (ADS)

Hayashi, K.; Cakir, R.; Martin, A. J.; Craig, M. S.; Lorenzo, J. M.

2016-12-01

As active and passive surface wave methods are getting popular for evaluating site response of earthquake ground motion, demand on the development of database for investigation results is also increasing. Seismic ground motion not only depends on 1D velocity structure but also on 2D and 3D structures so that spatial information of S-wave velocity must be considered in ground motion prediction. The database can support to construct 2D and 3D underground models. Inversion of surface wave processing is essentially non-unique so that other information must be combined into the processing. The database of existed geophysical, geological and geotechnical investigation results can provide indispensable information to improve the accuracy and reliability of investigations. Most investigations, however, are carried out by individual organizations and investigation results are rarely stored in the unified and organized database. To study and discuss appropriate database and digital standard format for the surface wave investigations, we developed a prototype of web-based database to store observed data and processing results of surface wave investigations that we have performed at more than 400 sites in U.S. and Japan. The database was constructed on a web server using MySQL and PHP so that users can access to the database through the internet from anywhere with any device. All data is registered in the database with location and users can search geophysical data through Google Map. The database stores dispersion curves, horizontal to vertical spectral ratio and S-wave velocity profiles at each site that was saved in XML files as digital data so that user can review and reuse them. The database also stores a published 3D deep basin and crustal structure and user can refer it during the processing of surface wave data.

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

NASA Technical Reports Server (NTRS)

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

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

James Webb Space Telescope XML Database: From the Beginning to Today

NASA Technical Reports Server (NTRS)

Gal-Edd, Jonathan; Fatig, Curtis C.

2005-01-01

The James Webb Space Telescope (JWST) Project has been defining, developing, and exercising the use of a common eXtensible Markup Language (XML) for the command and telemetry (C&T) database structure. JWST is the first large NASA space mission to use XML for databases. The JWST project started developing the concepts for the C&T database in 2002. The database will need to last at least 20 years since it will be used beginning with flight software development, continuing through Observatory integration and test (I&T) and through operations. Also, a database tool kit has been provided to the 18 various flight software development laboratories located in the United States, Europe, and Canada that allows the local users to create their own databases. Recently the JWST Project has been working with the Jet Propulsion Laboratory (JPL) and Object Management Group (OMG) XML Telemetry and Command Exchange (XTCE) personnel to provide all the information needed by JWST and JPL for exchanging database information using a XML standard structure. The lack of standardization requires custom ingest scripts for each ground system segment, increasing the cost of the total system. Providing a non-proprietary standard of the telemetry and command database definition formation will allow dissimilar systems to communicate without the need for expensive mission specific database tools and testing of the systems after the database translation. The various ground system components that would benefit from a standardized database are the telemetry and command systems, archives, simulators, and trending tools. JWST has exchanged the XML database with the Eclipse, EPOCH, ASIST ground systems, Portable spacecraft simulator (PSS), a front-end system, and Integrated Trending and Plotting System (ITPS) successfully. This paper will discuss how JWST decided to use XML, the barriers to a new concept, experiences utilizing the XML structure, exchanging databases with other users, and issues that have been experienced in creating databases for the C&T system.

Sodium content of foods contributing to sodium intake: A comparison between selected foods from the CDC Packaged Food Database and the USDA National Nutrient Database for Standard Reference

USDA-ARS?s Scientific Manuscript database

The sodium concentration (mg/100g) for 23 of 125 Sentinel Foods were identified in the 2009 CDC Packaged Food Database (PFD) and compared with data in the USDA’s 2013 Standard Reference 26 (SR 26) database. Sentinel Foods are foods and beverages identified by USDA to be monitored as primary indicat...

Informatics in radiology: use of CouchDB for document-based storage of DICOM objects.

PubMed

Rascovsky, Simón J; Delgado, Jorge A; Sanz, Alexander; Calvo, Víctor D; Castrillón, Gabriel

2012-01-01

Picture archiving and communication systems traditionally have depended on schema-based Structured Query Language (SQL) databases for imaging data management. To optimize database size and performance, many such systems store a reduced set of Digital Imaging and Communications in Medicine (DICOM) metadata, discarding informational content that might be needed in the future. As an alternative to traditional database systems, document-based key-value stores recently have gained popularity. These systems store documents containing key-value pairs that facilitate data searches without predefined schemas. Document-based key-value stores are especially suited to archive DICOM objects because DICOM metadata are highly heterogeneous collections of tag-value pairs conveying specific information about imaging modalities, acquisition protocols, and vendor-supported postprocessing options. The authors used an open-source document-based database management system (Apache CouchDB) to create and test two such databases; CouchDB was selected for its overall ease of use, capability for managing attachments, and reliance on HTTP and Representational State Transfer standards for accessing and retrieving data. A large database was created first in which the DICOM metadata from 5880 anonymized magnetic resonance imaging studies (1,949,753 images) were loaded by using a Ruby script. To provide the usual DICOM query functionality, several predefined "views" (standard queries) were created by using JavaScript. For performance comparison, the same queries were executed in both the CouchDB database and a SQL-based DICOM archive. The capabilities of CouchDB for attachment management and database replication were separately assessed in tests of a similar, smaller database. Results showed that CouchDB allowed efficient storage and interrogation of all DICOM objects; with the use of information retrieval algorithms such as map-reduce, all the DICOM metadata stored in the large database were searchable with only a minimal increase in retrieval time over that with the traditional database management system. Results also indicated possible uses for document-based databases in data mining applications such as dose monitoring, quality assurance, and protocol optimization. RSNA, 2012

Key comparison BIPM.RI(I)-K3 of the air-kerma standards of the NIST, USA and the BIPM in medium-energy x-rays

PubMed Central

Burns, D T; Kessler, C; O’Brien, M; Minniti, R

2017-01-01

A key comparison has been made between the air-kerma standards of the NIST, USA and the BIPM in the medium-energy x–ray range. The results show the standards to be in agreement at the level of the standard uncertainty of the comparison of 3.8 parts in 103, except at 250 kV where the difference is 1.5 times the standard uncertainty. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database. PMID:28966399

Database of Standardized Questionnaires About Walking & Bicycling

Cancer.gov

This database contains questionnaire items and a list of validation studies for standardized items related to walking and biking. The items come from multiple national and international physical activity questionnaires.

The EPIC nutrient database project (ENDB): a first attempt to standardize nutrient databases across the 10 European countries participating in the EPIC study.

PubMed

Slimani, N; Deharveng, G; Unwin, I; Southgate, D A T; Vignat, J; Skeie, G; Salvini, S; Parpinel, M; Møller, A; Ireland, J; Becker, W; Farran, A; Westenbrink, S; Vasilopoulou, E; Unwin, J; Borgejordet, A; Rohrmann, S; Church, S; Gnagnarella, P; Casagrande, C; van Bakel, M; Niravong, M; Boutron-Ruault, M C; Stripp, C; Tjønneland, A; Trichopoulou, A; Georga, K; Nilsson, S; Mattisson, I; Ray, J; Boeing, H; Ocké, M; Peeters, P H M; Jakszyn, P; Amiano, P; Engeset, D; Lund, E; de Magistris, M Santucci; Sacerdote, C; Welch, A; Bingham, S; Subar, A F; Riboli, E

2007-09-01

This paper describes the ad hoc methodological concepts and procedures developed to improve the comparability of Nutrient databases (NDBs) across the 10 European countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC). This was required because there is currently no European reference NDB available. A large network involving national compilers, nutritionists and experts on food chemistry and computer science was set up for the 'EPIC Nutrient DataBase' (ENDB) project. A total of 550-1500 foods derived from about 37,000 standardized EPIC 24-h dietary recalls (24-HDRS) were matched as closely as possible to foods available in the 10 national NDBs. The resulting national data sets (NDS) were then successively documented, standardized and evaluated according to common guidelines and using a DataBase Management System specifically designed for this project. The nutrient values of foods unavailable or not readily available in NDSs were approximated by recipe calculation, weighted averaging or adjustment for weight changes and vitamin/mineral losses, using common algorithms. The final ENDB contains about 550-1500 foods depending on the country and 26 common components. Each component value was documented and standardized for unit, mode of expression, definition and chemical method of analysis, as far as possible. Furthermore, the overall completeness of NDSs was improved (>or=99%), particularly for beta-carotene and vitamin E. The ENDB constitutes a first real attempt to improve the comparability of NDBs across European countries. This methodological work will provide a useful tool for nutritional research as well as end-user recommendations to improve NDBs in the future.

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

Geographical Information Science (GIS) is now graduated from traditional desktop system to Internet system. Internet GIS is emerging as one of the most promising technologies for addressing Emergency Management. Web services with different privileges are playing an important role in dissemination of the emergency services to the decision makers. Spatial database is one of the most important components in the successful implementation of Emergency Management. It contains spatial data in the form of raster, vector, linked with non-spatial information. Comprehensive data is required to handle emergency situation in different phases. These database elements comprise core data, hazard specific data, corresponding attribute data, and live data coming from the remote locations. Core data sets are minimum required data including base, thematic, infrastructure layers to handle disasters. Disaster specific information is required to handle a particular disaster situation like flood, cyclone, forest fire, earth quake, land slide, drought. In addition to this Emergency Management require many types of data with spatial and temporal attributes that should be made available to the key players in the right format at right time. The vector database needs to be complemented with required resolution satellite imagery for visualisation and analysis in disaster management. Therefore, the database is interconnected and comprehensive to meet the requirement of an Emergency Management. This kind of integrated, comprehensive and structured database with appropriate information is required to obtain right information at right time for the right people. However, building spatial database for Emergency Management is a challenging task because of the key issues such as availability of data, sharing policies, compatible geospatial standards, data interoperability etc. Therefore, to facilitate using, sharing, and integrating the spatial data, there is a need to define standards to build emergency database systems. These include aspects such as i) data integration procedures namely standard coding scheme, schema, meta data format, spatial format ii) database organisation mechanism covering data management, catalogues, data models iii) database dissemination through a suitable environment, as a standard service for effective service dissemination. National Database for Emergency Management (NDEM) is such a comprehensive database for addressing disasters in India at the national level. This paper explains standards for integrating, organising the multi-scale and multi-source data with effective emergency response using customized user interfaces for NDEM. It presents standard procedure for building comprehensive emergency information systems for enabling emergency specific functions through geospatial technologies.

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

Use of dual-energy X-ray absorptiometry (DXA) for diagnosis and fracture risk assessment; WHO-criteria, T- and Z-score, and reference databases.

PubMed

Dimai, Hans P

2017-11-01

Dual-energy X-ray absorptiometry (DXA) is a two-dimensional imaging technology developed to assess bone mineral density (BMD) of the entire human skeleton and also specifically of skeletal sites known to be most vulnerable to fracture. In order to simplify interpretation of BMD measurement results and allow comparability among different DXA-devices, the T-score concept was introduced. This concept involves an individual's BMD which is then compared with the mean value of a young healthy reference population, with the difference expressed as a standard deviation (SD). Since the early nineties of the past century, the diagnostic categories "normal, osteopenia, and osteoporosis", as recommended by a WHO working Group, are based on this concept. Thus, DXA is still the globally accepted "gold-standard" method for the noninvasive diagnosis of osteoporosis. Another score obtained from DXA measurement, termed Z-score, describes the number of SDs by which the BMD in an individual differs from the mean value expected for age and sex. Although not intended for diagnosis of osteoporosis in adults, it nevertheless provides information about an individual's fracture risk compared to peers. DXA measurement can either be used as a "stand-alone" means in the assessment of an individual's fracture risk, or incorporated into one of the available fracture risk assessment tools such as FRAX® or Garvan, thus improving the predictive power of such tools. The issue which reference databases should be used by DXA-device manufacturers for T-score reference standards has been recently addressed by an expert group, who recommended use National Health and Nutrition Examination Survey III (NHANES III) databases for the hip reference standard but own databases for the lumbar spine. Furthermore, in men it is recommended use female reference databases for calculation of the T-score and use male reference databases for calculation of Z-score. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution of a Patient Information Management System in a Local Area Network Environment at Loyola University of Chicago Medical Center

PubMed Central

Price, Ronald N; Chandrasekhar, Arcot J; Tamirisa, Balaji

1990-01-01

The Department of Medicine at Loyola University Medical Center (LUMC) of Chicago has implemented a local area network (LAN) based Patient Information Management System (PIMS) as part of its integrated departmental database management system. PIMS consists of related database applications encompassing demographic information, current medications, problem lists, clinical data, prior events, and on-line procedure results. Integration into the existing departmental database system permits PIMS to capture and manipulate data in other departmental applications. Standardization of clinical data is accomplished through three data tables that verify diagnosis codes, procedures codes and a standardized set of clinical data elements. The modularity of the system, coupled with standardized data formats, allowed the development of a Patient Information Protocol System (PIPS). PIPS, a userdefinable protocol processor, provides physicians with individualized data entry or review screens customized for their specific research protocols or practice habits. Physician feedback indicates that the PIMS/PIPS combination enhances their ability to collect and review specific patient information by filtering large amount of clinical data.

Ground truth and benchmarks for performance evaluation

NASA Astrophysics Data System (ADS)

Takeuchi, Ayako; Shneier, Michael; Hong, Tsai Hong; Chang, Tommy; Scrapper, Christopher; Cheok, Geraldine S.

2003-09-01

Progress in algorithm development and transfer of results to practical applications such as military robotics requires the setup of standard tasks, of standard qualitative and quantitative measurements for performance evaluation and validation. Although the evaluation and validation of algorithms have been discussed for over a decade, the research community still faces a lack of well-defined and standardized methodology. The range of fundamental problems include a lack of quantifiable measures of performance, a lack of data from state-of-the-art sensors in calibrated real-world environments, and a lack of facilities for conducting realistic experiments. In this research, we propose three methods for creating ground truth databases and benchmarks using multiple sensors. The databases and benchmarks will provide researchers with high quality data from suites of sensors operating in complex environments representing real problems of great relevance to the development of autonomous driving systems. At NIST, we have prototyped a High Mobility Multi-purpose Wheeled Vehicle (HMMWV) system with a suite of sensors including a Riegl ladar, GDRS ladar, stereo CCD, several color cameras, Global Position System (GPS), Inertial Navigation System (INS), pan/tilt encoders, and odometry . All sensors are calibrated with respect to each other in space and time. This allows a database of features and terrain elevation to be built. Ground truth for each sensor can then be extracted from the database. The main goal of this research is to provide ground truth databases for researchers and engineers to evaluate algorithms for effectiveness, efficiency, reliability, and robustness, thus advancing the development of algorithms.

Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the IST-LPSR, Portugal and the BIPM in 60Co gamma radiation

NASA Astrophysics Data System (ADS)

Kessler, C.; Burns, D.; Cardoso, J.

2018-01-01

A comparison of the standards for air kerma of the Instituto Superior Técnico, Laboratório de Proteção e Segurança Radiológica (IST-LPSR), Portugal and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in December 2015. The comparison result, evaluated as a ratio of the IST-LPSR and the BIPM standards for air kerma, is 1.0026 with a combined standard uncertainty of 1.7 × 10-3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 1.1 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

KEY COMPARISON: Comparison of the standards for absorbed dose to water of the VNIIFTRI, Russia and the BIPM in 60Co γ rays

NASA Astrophysics Data System (ADS)

Allisy-Roberts, P. J.; Kessler, C.; Burns, D. T.; Berlyand, V.; Berlyand, A.

2010-01-01

A new comparison of the standards for absorbed dose to water of the All-Russian Scientific Research Institute for Physical-Technical and Radiotechnical Measurements (VNIIFTRI), Russia and of the Bureau International des Poids et Mesures (BIPM) has been made in 60Co gamma radiation in 2009. The results show that the VNIIFTRI and the BIPM standards for absorbed dose to water are in agreement, yielding a mean ratio of 0.9976 for the calibration coefficients of the transfer chambers, the difference from unity being within the combined standard uncertainty (0.0043) for this result. This result is consistent with the earlier 2001 comparison result of 0.9967 (43). The updated degrees of equivalence for the VNIIFTRI are compared with those of the other national metrology institutes as presented in the BIPM key comparison database. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI Section I, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

Cold Climate Foundation Retrofit Experimental Hygrothermal Performance. Cloquet Residential Research Facility Laboratory Results

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

Goldberg, Louise F.; Harmon, Anna C.

2015-04-09

This project was funded jointly by the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL). ORNL focused on developing a full basement wall system experimental database to enable others to validate hygrothermal simulation codes. NREL focused on testing the moisture durability of practical basement wall interior insulation retrofit solutions for cold climates. The project has produced a physically credible and reliable long-term hygrothermal performance database for retrofit foundation wall insulation systems in zone 6 and 7 climates that are fully compliant with the performance criteria in the 2009 Minnesota Energy Code. These data currently span the periodmore » from November 10, 2012 through May 31, 2014 and are anticipated to be extended through November 2014. The experimental data were configured into a standard format that can be published online and that is compatible with standard commercially available spreadsheet and database software.« 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

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Establishment of a Universal Size Standard Strain for Use with the PulseNet Standardized Pulsed-Field Gel Electrophoresis Protocols: Converting the National Databases to the New Size Standard

PubMed Central

Hunter, Susan B.; Vauterin, Paul; Lambert-Fair, Mary Ann; Van Duyne, M. Susan; Kubota, Kristy; Graves, Lewis; Wrigley, Donna; Barrett, Timothy; Ribot, Efrain

2005-01-01

The PulseNet National Database, established by the Centers for Disease Control and Prevention in 1996, consists of pulsed-field gel electrophoresis (PFGE) patterns obtained from isolates of food-borne pathogens (currently Escherichia coli O157:H7, Salmonella, Shigella, and Listeria) and textual information about the isolates. Electronic images and accompanying text are submitted from over 60 U.S. public health and food regulatory agency laboratories. The PFGE patterns are generated according to highly standardized PFGE protocols. Normalization and accurate comparison of gel images require the use of a well-characterized size standard in at least three lanes of each gel. Originally, a well-characterized strain of each organism was chosen as the reference standard for that particular database. The increasing number of databases, difficulty in identifying an organism-specific standard for each database, the increased range of band sizes generated by the use of additional restriction endonucleases, and the maintenance of many different organism-specific strains encouraged us to search for a more versatile and universal DNA size marker. A Salmonella serotype Braenderup strain (H9812) was chosen as the universal size standard. This strain was subjected to rigorous testing in our laboratories to ensure that it met the desired criteria, including coverage of a wide range of DNA fragment sizes, even distribution of bands, and stability of the PFGE pattern. The strategy used to convert and compare data generated by the new and old reference standards is described. PMID:15750058

[Occupational exposure to silica dust by selected sectors of national economy in Poland based on electronic database].

PubMed

Bujak-Pietrek, Stella; Mikołajczyk, Urszula; Szadkowska-Stańczyk, Irena; Stroszejn-Mrowca, Grazyna

2008-01-01

To evaluate occupational exposure to dusts, the Nofer Institute of Occupational Medicine in Łódź, in collaboration with the Chief Sanitary Inspectorate, has developed the national database to store the results of routine dust exposure measurements performed by occupational hygiene and environmental protection laboratories in Poland in the years 2001-2005. It was assumed that the collected information will be useful in analyzing workers' exposure to free crystalline silica (WKK)-containing dusts in Poland, identyfing exceeded hygiene standards and showing relevant trends, which illustrate the dynamics of exposure in the years under study. Inhalable and respirable dust measurement using personal dosimetry were done according to polish standard PN-91/Z-04030/05 and PN-91/Z-04030/06. In total, 148 638 measurement records, provided by sanitary inspection services from all over Poland, were entered into the database. The database enables the estimation of occupational exposure to dust by the sectors of national economy, according to the Polish Classification of Activity (PKD) and by kinds of dust. The highest exposure level of inhalable and respirable dusts was found in coal mining. Also in this sector, almost 60% of surveys demonstrated exceeded current hygiene standards. High concentrations of both dust fractions (inhalable and respirable) and a considerable percentage of measurements exceeding hygiene standards were found in the manufacture of transport equipment (except for cars), as well as in the chemical, mining (rock, sand, gravel, clay mines) and construction industries. The highest percentage of surveys (inhalable and respirable dust) showing exceeded hygiene standards were observed for coal dust with different content of crystalline silica, organic dust containing more than 10% of SiO2, and highly fibrosis dust containing more than 50% of SiO2.

GlycoRDF: an ontology to standardize glycomics data in RDF.

PubMed

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-03-15

Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Oak Ridge Reservation Environmental Protection Rad Neshaps Radionuclide Inventory Web Database and Rad Neshaps Source and Dose Database

DOE PAGES

Scofield, Patricia A.; Smith, Linda Lenell; Johnson, David N.

2017-07-01

The U.S. Environmental Protection Agency promulgated national emission standards for emissions of radionuclides other than radon from US Department of Energy facilities in Chapter 40 of the Code of Federal Regulations (CFR) 61, Subpart H. This regulatory standard limits the annual effective dose that any member of the public can receive from Department of Energy facilities to 0.1 mSv. As defined in the preamble of the final rule, all of the facilities on the Oak Ridge Reservation, i.e., the Y–12 National Security Complex, Oak Ridge National Laboratory, East Tennessee Technology Park, and any other U.S. Department of Energy operations onmore » Oak Ridge Reservation, combined, must meet the annual dose limit of 0.1 mSv. At Oak Ridge National Laboratory, there are monitored sources and numerous unmonitored sources. To maintain radiological source and inventory information for these unmonitored sources, e.g., laboratory hoods, equipment exhausts, and room exhausts not currently venting to monitored stacks on the Oak Ridge National Laboratory campus, the Environmental Protection Rad NESHAPs Inventory Web Database was developed. This database is updated annually and is used to compile emissions data for the annual Radionuclide National Emission Standards for Hazardous Air Pollutants (Rad NESHAPs) report required by 40 CFR 61.94. It also provides supporting documentation for facility compliance audits. In addition, a Rad NESHAPs source and dose database was developed to import the source and dose summary data from Clean Air Act Assessment Package—1988 computer model files. As a result, this database provides Oak Ridge Reservation and facility-specific source inventory; doses associated with each source and facility; and total doses for the Oak Ridge Reservation dose.« less

Oak Ridge Reservation Environmental Protection Rad Neshaps Radionuclide Inventory Web Database and Rad Neshaps Source and Dose Database

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

Scofield, Patricia A.; Smith, Linda Lenell; Johnson, David N.

The U.S. Environmental Protection Agency promulgated national emission standards for emissions of radionuclides other than radon from US Department of Energy facilities in Chapter 40 of the Code of Federal Regulations (CFR) 61, Subpart H. This regulatory standard limits the annual effective dose that any member of the public can receive from Department of Energy facilities to 0.1 mSv. As defined in the preamble of the final rule, all of the facilities on the Oak Ridge Reservation, i.e., the Y–12 National Security Complex, Oak Ridge National Laboratory, East Tennessee Technology Park, and any other U.S. Department of Energy operations onmore » Oak Ridge Reservation, combined, must meet the annual dose limit of 0.1 mSv. At Oak Ridge National Laboratory, there are monitored sources and numerous unmonitored sources. To maintain radiological source and inventory information for these unmonitored sources, e.g., laboratory hoods, equipment exhausts, and room exhausts not currently venting to monitored stacks on the Oak Ridge National Laboratory campus, the Environmental Protection Rad NESHAPs Inventory Web Database was developed. This database is updated annually and is used to compile emissions data for the annual Radionuclide National Emission Standards for Hazardous Air Pollutants (Rad NESHAPs) report required by 40 CFR 61.94. It also provides supporting documentation for facility compliance audits. In addition, a Rad NESHAPs source and dose database was developed to import the source and dose summary data from Clean Air Act Assessment Package—1988 computer model files. As a result, this database provides Oak Ridge Reservation and facility-specific source inventory; doses associated with each source and facility; and total doses for the Oak Ridge Reservation dose.« less

Standardizing clinical laboratory data for secondary use.

PubMed

Abhyankar, Swapna; Demner-Fushman, Dina; McDonald, Clement J

2012-08-01

Clinical databases provide a rich source of data for answering clinical research questions. However, the variables recorded in clinical data systems are often identified by local, idiosyncratic, and sometimes redundant and/or ambiguous names (or codes) rather than unique, well-organized codes from standard code systems. This reality discourages research use of such databases, because researchers must invest considerable time in cleaning up the data before they can ask their first research question. Researchers at MIT developed MIMIC-II, a nearly complete collection of clinical data about intensive care patients. Because its data are drawn from existing clinical systems, it has many of the problems described above. In collaboration with the MIT researchers, we have begun a process of cleaning up the data and mapping the variable names and codes to LOINC codes. Our first step, which we describe here, was to map all of the laboratory test observations to LOINC codes. We were able to map 87% of the unique laboratory tests that cover 94% of the total number of laboratory tests results. Of the 13% of tests that we could not map, nearly 60% were due to test names whose real meaning could not be discerned and 29% represented tests that were not yet included in the LOINC table. These results suggest that LOINC codes cover most of laboratory tests used in critical care. We have delivered this work to the MIMIC-II researchers, who have included it in their standard MIMIC-II database release so that researchers who use this database in the future will not have to do this work. Published by Elsevier Inc.

A New Standardized Emotional Film Database for Asian Culture

PubMed Central

Deng, Yaling; Yang, Meng; Zhou, Renlai

2017-01-01

Researchers interested in emotions have endeavored to elicit emotional responses in the laboratory and have determined that films were one of the most effective ways to elicit emotions. The present study presented the development of a new standardized emotional film database for Asian culture. There were eight kinds of emotion: fear, disgust, anger, sadness, neutrality, surprise, amusement, and pleasure. Each kind included eight film clips, and a total of 64 emotional films were viewed by 110 participants. We analyzed both the subjective experience (valence, arousal, motivation, and dominance) and physiological response (heart rate and respiration rate) to the presentation of each film. The results of the subjective ratings indicated that our set of 64 films successfully elicited the target emotions. Heart rate declined while watching high-arousal films compared to neutral ones. Films that expressed amusement elicited the lowest respiration rate, whereas fear elicited the highest. The amount and category of emotional films in this database were considerable. This database may help researchers choose applicable emotional films for study according to their own purposes and help in studies of cultural differences in emotion. PMID:29163312

The OAuth 2.0 Web Authorization Protocol for the Internet Addiction Bioinformatics (IABio) Database.

PubMed

Choi, Jeongseok; Kim, Jaekwon; Lee, Dong Kyun; Jang, Kwang Soo; Kim, Dai-Jin; Choi, In Young

2016-03-01

Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA.

A data model and database for high-resolution pathology analytical image informatics.

PubMed

Wang, Fusheng; Kong, Jun; Cooper, Lee; Pan, Tony; Kurc, Tahsin; Chen, Wenjin; Sharma, Ashish; Niedermayr, Cristobal; Oh, Tae W; Brat, Daniel; Farris, Alton B; Foran, David J; Saltz, Joel

2011-01-01

The systematic analysis of imaged pathology specimens often results in a vast amount of morphological information at both the cellular and sub-cellular scales. While microscopy scanners and computerized analysis are capable of capturing and analyzing data rapidly, microscopy image data remain underutilized in research and clinical settings. One major obstacle which tends to reduce wider adoption of these new technologies throughout the clinical and scientific communities is the challenge of managing, querying, and integrating the vast amounts of data resulting from the analysis of large digital pathology datasets. This paper presents a data model, which addresses these challenges, and demonstrates its implementation in a relational database system. This paper describes a data model, referred to as Pathology Analytic Imaging Standards (PAIS), and a database implementation, which are designed to support the data management and query requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines on whole-slide images and tissue microarrays (TMAs). (1) Development of a data model capable of efficiently representing and storing virtual slide related image, annotation, markup, and feature information. (2) Development of a database, based on the data model, capable of supporting queries for data retrieval based on analysis and image metadata, queries for comparison of results from different analyses, and spatial queries on segmented regions, features, and classified objects. The work described in this paper is motivated by the challenges associated with characterization of micro-scale features for comparative and correlative analyses involving whole-slides tissue images and TMAs. Technologies for digitizing tissues have advanced significantly in the past decade. Slide scanners are capable of producing high-magnification, high-resolution images from whole slides and TMAs within several minutes. Hence, it is becoming increasingly feasible for basic, clinical, and translational research studies to produce thousands of whole-slide images. Systematic analysis of these large datasets requires efficient data management support for representing and indexing results from hundreds of interrelated analyses generating very large volumes of quantifications such as shape and texture and of classifications of the quantified features. We have designed a data model and a database to address the data management requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines. The data model represents virtual slide related image, annotation, markup and feature information. The database supports a wide range of metadata and spatial queries on images, annotations, markups, and features. We currently have three databases running on a Dell PowerEdge T410 server with CentOS 5.5 Linux operating system. The database server is IBM DB2 Enterprise Edition 9.7.2. The set of databases consists of 1) a TMA database containing image analysis results from 4740 cases of breast cancer, with 641 MB storage size; 2) an algorithm validation database, which stores markups and annotations from two segmentation algorithms and two parameter sets on 18 selected slides, with 66 GB storage size; and 3) an in silico brain tumor study database comprising results from 307 TCGA slides, with 365 GB storage size. The latter two databases also contain human-generated annotations and markups for regions and nuclei. Modeling and managing pathology image analysis results in a database provide immediate benefits on the value and usability of data in a research study. The database provides powerful query capabilities, which are otherwise difficult or cumbersome to support by other approaches such as programming languages. Standardized, semantic annotated data representation and interfaces also make it possible to more efficiently share image data and analysis results.

The quest for the perfect gravity anomaly: Part 1 - New calculation standards

USGS Publications Warehouse

Li, X.; Hildenbrand, T.G.; Hinze, W. J.; Keller, Gordon R.; Ravat, D.; Webring, M.

2006-01-01

The North American gravity database together with databases from Canada, Mexico, and the United States are being revised to improve their coverage, versatility, and accuracy. An important part of this effort is revision of procedures and standards for calculating gravity anomalies taking into account our enhanced computational power, modern satellite-based positioning technology, improved terrain databases, and increased interest in more accurately defining different anomaly components. The most striking revision is the use of one single internationally accepted reference ellipsoid for the horizontal and vertical datums of gravity stations as well as for the computation of the theoretical gravity. The new standards hardly impact the interpretation of local anomalies, but do improve regional anomalies. Most importantly, such new standards can be consistently applied to gravity database compilations of nations, continents, and even the entire world. ?? 2005 Society of Exploration Geophysicists.

Introducing glycomics data into the Semantic Web

PubMed Central

2013-01-01

Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. Results In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as “proofs-of-concept” to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. Conclusions We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains. PMID:24280648

New standards for reducing gravity data: The North American gravity database

USGS Publications Warehouse

Hinze, W. J.; Aiken, C.; Brozena, J.; Coakley, B.; Dater, D.; Flanagan, G.; Forsberg, R.; Hildenbrand, T.; Keller, Gordon R.; Kellogg, J.; Kucks, R.; Li, X.; Mainville, A.; Morin, R.; Pilkington, M.; Plouff, D.; Ravat, D.; Roman, D.; Urrutia-Fucugauchi, J.; Veronneau, M.; Webring, M.; Winester, D.

2005-01-01

The North American gravity database as well as databases from Canada, Mexico, and the United States are being revised to improve their coverage, versatility, and accuracy. An important part of this effort is revising procedures for calculating gravity anomalies, taking into account our enhanced computational power, improved terrain databases and datums, and increased interest in more accurately defining long-wavelength anomaly components. Users of the databases may note minor differences between previous and revised database values as a result of these procedures. Generally, the differences do not impact the interpretation of local anomalies but do improve regional anomaly studies. The most striking revision is the use of the internationally accepted terrestrial ellipsoid for the height datum of gravity stations rather than the conventionally used geoid or sea level. Principal facts of gravity observations and anomalies based on both revised and previous procedures together with germane metadata will be available on an interactive Web-based data system as well as from national agencies and data centers. The use of the revised procedures is encouraged for gravity data reduction because of the widespread use of the global positioning system in gravity fieldwork and the need for increased accuracy and precision of anomalies and consistency with North American and national databases. Anomalies based on the revised standards should be preceded by the adjective "ellipsoidal" to differentiate anomalies calculated using heights with respect to the ellipsoid from those based on conventional elevations referenced to the geoid. ?? 2005 Society of Exploration Geophysicists. All rights reserved.

A Molecular Framework for Understanding DCIS

DTIC Science & Technology

2016-10-01

well. Pathologic and Clinical Annotation Database A clinical annotation database titled the Breast Oncology Database has been established to...complement the procured SPORE sample characteristics and annotated pathology data. This Breast Oncology Database is an offsite clinical annotation...database adheres to CSMC Enterprise Information Services (EIS) research database security standards. The Breast Oncology Database consists of: 9 Baseline

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

Challenges to the Standardization of Burn Data Collection: A Call for Common Data Elements for Burn Care.

PubMed

Schneider, Jeffrey C; Chen, Liang; Simko, Laura C; Warren, Katherine N; Nguyen, Brian Phu; Thorpe, Catherine R; Jeng, James C; Hickerson, William L; Kazis, Lewis E; Ryan, Colleen M

2018-02-20

The use of common data elements (CDEs) is growing in medical research; CDEs have demonstrated benefit in maximizing the impact of existing research infrastructure and funding. However, the field of burn care does not have a standard set of CDEs. The objective of this study is to examine the extent of common data collected in current burn databases.This study examines the data dictionaries of six U.S. burn databases to ascertain the extent of common data. This was assessed from a quantitative and qualitative perspective. Thirty-two demographic and clinical data elements were examined. The number of databases that collect each data element was calculated. The data values for each data element were compared across the six databases for common terminology. Finally, the data prompts of the data elements were examined for common language and structure.Five (16%) of the 32 data elements are collected by all six burn databases; additionally, five data elements (16%) are present in only one database. Furthermore, there are considerable variations in data values and prompts used among the burn databases. Only one of the 32 data elements (age) contains the same data values across all databases.The burn databases examined show minimal evidence of common data. There is a need to develop CDEs and standardized coding to enhance interoperability of burn databases.

Building a QC Database of Meteorological Data from NASA KSC and the United States Air Force's Eastern Range

NASA Technical Reports Server (NTRS)

Brenton, J. C.; Barbre, R. E.; Decker, R. K.; Orcutt, J. M.

2018-01-01

The National Aeronautics and Space Administration's (NASA) Marshall Space Flight Center (MSFC) Natural Environments Branch (EV44) provides atmospheric databases and analysis in support of space vehicle design and day-of-launch operations for NASA and commercial launch vehicle programs launching from the NASA Kennedy Space Center (KSC), co-located on the United States Air Force's Eastern Range (ER) at the Cape Canaveral Air Force Station. The ER complex is one of the most heavily instrumented sites in the United States with over 31 towers measuring various atmospheric parameters on a continuous basis. An inherent challenge with large datasets consists of ensuring erroneous data are removed from databases, and thus excluded from launch vehicle design analyses. EV44 has put forth great effort in developing quality control (QC) procedures for individual meteorological instruments, however no standard QC procedures for all databases currently exists resulting in QC databases that have inconsistencies in variables, development methodologies, and periods of record. The goal of this activity is to use the previous efforts to develop a standardized set of QC procedures from which to build meteorological databases from KSC and the ER, while maintaining open communication with end users from the launch community to develop ways to improve, adapt and grow the QC database. Details of the QC procedures will be described. As the rate of launches increases with additional launch vehicle programs, It is becoming more important that weather databases are continually updated and checked for data quality before use in launch vehicle design and certification analyses.

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/

Toward a standard reference database for computer-aided mammography

NASA Astrophysics Data System (ADS)

Oliveira, Júlia E. E.; Gueld, Mark O.; de A. Araújo, Arnaldo; Ott, Bastian; Deserno, Thomas M.

2008-03-01

Because of the lack of mammography databases with a large amount of codified images and identified characteristics like pathology, type of breast tissue, and abnormality, there is a problem for the development of robust systems for computer-aided diagnosis. Integrated to the Image Retrieval in Medical Applications (IRMA) project, we present an available mammography database developed from the union of: The Mammographic Image Analysis Society Digital Mammogram Database (MIAS), The Digital Database for Screening Mammography (DDSM), the Lawrence Livermore National Laboratory (LLNL), and routine images from the Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen. Using the IRMA code, standardized coding of tissue type, tumor staging, and lesion description was developed according to the American College of Radiology (ACR) tissue codes and the ACR breast imaging reporting and data system (BI-RADS). The import was done automatically using scripts for image download, file format conversion, file name, web page and information file browsing. Disregarding the resolution, this resulted in a total of 10,509 reference images, and 6,767 images are associated with an IRMA contour information feature file. In accordance to the respective license agreements, the database will be made freely available for research purposes, and may be used for image based evaluation campaigns such as the Cross Language Evaluation Forum (CLEF). We have also shown that it can be extended easily with further cases imported from a picture archiving and communication system (PACS).

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. PMID:24564380

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

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

PubMed

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

2015-01-01

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

XML technology planning database : lessons learned

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Neff, Jon M.

2005-01-01

A hierarchical Extensible Markup Language(XML) database called XCALIBR (XML Analysis LIBRary) has been developed by Millennium Program to assist in technology investment (ROI) analysis and technology Language Capability the New return on portfolio optimization. The database contains mission requirements and technology capabilities, which are related by use of an XML dictionary. The XML dictionary codifies a standardized taxonomy for space missions, systems, subsystems and technologies. In addition to being used for ROI analysis, the database is being examined for use in project planning, tracking and documentation. During the past year, the database has moved from development into alpha testing. This paper describes the lessons learned during construction and testing of the prototype database and the motivation for moving from an XML taxonomy to a standard XML-based ontology.

DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing.

PubMed

Parson, W; Gusmão, L; Hares, D R; Irwin, J A; Mayr, W R; Morling, N; Pokorak, E; Prinz, M; Salas, A; Schneider, P M; Parsons, T J

2014-11-01

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the question of human identification. Previous recommendations published in 2000 addressed the analysis and interpretation of mitochondrial DNA (mtDNA) in forensic casework. While the foundations set forth in the earlier recommendations still apply, new approaches to the quality control, alignment and nomenclature of mitochondrial sequences, as well as the establishment of mtDNA reference population databases, have been developed. Here, we describe these developments and discuss their application to both mtDNA casework and mtDNA reference population databasing applications. While the generation of mtDNA for forensic casework has always been guided by specific standards, it is now well-established that data of the same quality are required for the mtDNA reference population data used to assess the statistical weight of the evidence. As a result, we introduce guidelines regarding sequence generation, as well as quality control measures based on the known worldwide mtDNA phylogeny, that can be applied to ensure the highest quality population data possible. For both casework and reference population databasing applications, the alignment and nomenclature of haplotypes is revised here and the phylogenetic alignment proffered as acceptable standard. In addition, the interpretation of heteroplasmy in the forensic context is updated, and the utility of alignment-free database searches for unbiased probability estimates is highlighted. Finally, we discuss statistical issues and define minimal standards for mtDNA database searches. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Biomedical informatics as support to individual healthcare in hereditary colon cancer: the Danish HNPCC system.

PubMed

Bernstein, Inge T; Lindorff-Larsen, Karen; Timshel, Susanne; Brandt, Carsten A; Dinesen, Birger; Fenger, Mogens; Gerdes, Anne-Marie; Iversen, Lene H; Madsen, Mogens R; Okkels, Henrik; Sunde, Lone; Rahr, Hans B; Wikman, Friedrick P; Rossing, Niels

2011-05-01

The Danish HNPCC register is a publically financed national database. The register gathers epidemiological and genomic data in HNPCC families to improve prognosis by screening and identifying family members at risk. Diagnostic data are generated throughout the country and collected over several decades. Until recently, paper-based reports were sent to the register and typed into the database. In the EC cofunded-INFOBIOMED network of excellence, the register was a model for electronic exchange of epidemiological and genomic data between diagnosing/treating departments and the central database. The aim of digitization was to optimize the organization of screening by facilitating combination of genotype-phenotype information, and to generate IT-tools sufficiently usable and generic to be implemented in other countries and for other oncogenetic diseases. The focus was on integration of heterogeneous data, elaboration, and dissemination of classification systems and development of communication standards. At the conclusion of the EU project in 2007 the system was implemented in 12 pilot departments. In the surgical departments this resulted in a 192% increase of reports to the database. Several gaps were identified: lack of standards for data to be exchanged, lack of local databases suitable for direct communication, reporting being time-consuming and dependent on interest and feedback. © 2011 Wiley-Liss, Inc.

Worldwide Report, Telecommunications Policy, Research and Development

DTIC Science & Technology

1985-12-31

3 Hong Kong Database Signs Contract With PRC (K. Gopinath; Hong Kong HONGKONG STANDARD, 18 Oct 85) .... 5 Briefs Hong Kong-London Data Link...KONG HONG KONG DATABASE SIGNS CONTRACT WITH PRC Hong Kong HONGKONG STANDARD in English Supplement 18 Oct 85 p 1 [Article by K. Gopinath] [Text...information group. The agreement between state-owned China Hua Yang Technology and Trade Corporation and DataBase Asia of Hong- kong, authorises

Development and application of basis database for materials life cycle assessment in china

NASA Astrophysics Data System (ADS)

Li, Xiaoqing; Gong, Xianzheng; Liu, Yu

2017-03-01

As the data intensive method, high quality environmental burden data is an important premise of carrying out materials life cycle assessment (MLCA), and the reliability of data directly influences the reliability of the assessment results and its application performance. Therefore, building Chinese MLCA database is the basic data needs and technical supports for carrying out and improving LCA practice. Firstly, some new progress on database which related to materials life cycle assessment research and development are introduced. Secondly, according to requirement of ISO 14040 series standards, the database framework and main datasets of the materials life cycle assessment are studied. Thirdly, MLCA data platform based on big data is developed. Finally, the future research works were proposed and discussed.

Seismic Search Engine: A distributed database for mining large scale seismic data

NASA Astrophysics Data System (ADS)

Liu, Y.; Vaidya, S.; Kuzma, H. A.

2009-12-01

The International Monitoring System (IMS) of the CTBTO collects terabytes worth of seismic measurements from many receiver stations situated around the earth with the goal of detecting underground nuclear testing events and distinguishing them from other benign, but more common events such as earthquakes and mine blasts. The International Data Center (IDC) processes and analyzes these measurements, as they are collected by the IMS, to summarize event detections in daily bulletins. Thereafter, the data measurements are archived into a large format database. Our proposed Seismic Search Engine (SSE) will facilitate a framework for data exploration of the seismic database as well as the development of seismic data mining algorithms. Analogous to GenBank, the annotated genetic sequence database maintained by NIH, through SSE, we intend to provide public access to seismic data and a set of processing and analysis tools, along with community-generated annotations and statistical models to help interpret the data. SSE will implement queries as user-defined functions composed from standard tools and models. Each query is compiled and executed over the database internally before reporting results back to the user. Since queries are expressed with standard tools and models, users can easily reproduce published results within this framework for peer-review and making metric comparisons. As an illustration, an example query is “what are the best receiver stations in East Asia for detecting events in the Middle East?” Evaluating this query involves listing all receiver stations in East Asia, characterizing known seismic events in that region, and constructing a profile for each receiver station to determine how effective its measurements are at predicting each event. The results of this query can be used to help prioritize how data is collected, identify defective instruments, and guide future sensor placements.

[Review of digital ground object spectral library].

PubMed

Zhou, Xiao-Hu; Zhou, Ding-Wu

2009-06-01

A higher spectral resolution is the main direction of developing remote sensing technology, and it is quite important to set up the digital ground object reflectance spectral database library, one of fundamental research fields in remote sensing application. Remote sensing application has been increasingly relying on ground object spectral characteristics, and quantitative analysis has been developed to a new stage. The present article summarized and systematically introduced the research status quo and development trend of digital ground object reflectance spectral libraries at home and in the world in recent years. Introducing the spectral libraries has been established, including desertification spectral database library, plants spectral database library, geological spectral database library, soil spectral database library, minerals spectral database library, cloud spectral database library, snow spectral database library, the atmosphere spectral database library, rocks spectral database library, water spectral database library, meteorites spectral database library, moon rock spectral database library, and man-made materials spectral database library, mixture spectral database library, volatile compounds spectral database library, and liquids spectral database library. In the process of establishing spectral database libraries, there have been some problems, such as the lack of uniform national spectral database standard and uniform standards for the ground object features as well as the comparability between different databases. In addition, data sharing mechanism can not be carried out, etc. This article also put forward some suggestions on those problems.

Semi-Automated Annotation of Biobank Data Using Standard Medical Terminologies in a Graph Database.

PubMed

Hofer, Philipp; Neururer, Sabrina; Goebel, Georg

2016-01-01

Data describing biobank resources frequently contains unstructured free-text information or insufficient coding standards. (Bio-) medical ontologies like Orphanet Rare Diseases Ontology (ORDO) or the Human Disease Ontology (DOID) provide a high number of concepts, synonyms and entity relationship properties. Such standard terminologies increase quality and granularity of input data by adding comprehensive semantic background knowledge from validated entity relationships. Moreover, cross-references between terminology concepts facilitate data integration across databases using different coding standards. In order to encourage the use of standard terminologies, our aim is to identify and link relevant concepts with free-text diagnosis inputs within a biobank registry. Relevant concepts are selected automatically by lexical matching and SPARQL queries against a RDF triplestore. To ensure correctness of annotations, proposed concepts have to be confirmed by medical data administration experts before they are entered into the registry database. Relevant (bio-) medical terminologies describing diseases and phenotypes were identified and stored in a graph database which was tied to a local biobank registry. Concept recommendations during data input trigger a structured description of medical data and facilitate data linkage between heterogeneous systems.

Grid-enabled measures: using Science 2.0 to standardize measures and share data.

PubMed

Moser, Richard P; Hesse, Bradford W; Shaikh, Abdul R; Courtney, Paul; Morgan, Glen; Augustson, Erik; Kobrin, Sarah; Levin, Kerry Y; Helba, Cynthia; Garner, David; Dunn, Marsha; Coa, Kisha

2011-05-01

Scientists are taking advantage of the Internet and collaborative web technology to accelerate discovery in a massively connected, participative environment--a phenomenon referred to by some as Science 2.0. As a new way of doing science, this phenomenon has the potential to push science forward in a more efficient manner than was previously possible. The Grid-Enabled Measures (GEM) database has been conceptualized as an instantiation of Science 2.0 principles by the National Cancer Institute (NCI) with two overarching goals: (1) promote the use of standardized measures, which are tied to theoretically based constructs; and (2) facilitate the ability to share harmonized data resulting from the use of standardized measures. The first is accomplished by creating an online venue where a virtual community of researchers can collaborate together and come to consensus on measures by rating, commenting on, and viewing meta-data about the measures and associated constructs. The second is accomplished by connecting the constructs and measures to an ontological framework with data standards and common data elements such as the NCI Enterprise Vocabulary System (EVS) and the cancer Data Standards Repository (caDSR). This paper will describe the web 2.0 principles on which the GEM database is based, describe its functionality, and discuss some of the important issues involved with creating the GEM database such as the role of mutually agreed-on ontologies (i.e., knowledge categories and the relationships among these categories--for data sharing). Published by Elsevier Inc.

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2013 CFR

2013-10-01

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2014 CFR

2014-10-01

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2012 CFR

2012-10-01

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

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

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

Correction to storm, Tressoldi, and di Risio (2010).

PubMed

2015-03-01

Reports an error in "Meta-analysis of free-response studies, 1992-2008: Assessing the noise reduction model in parapsychology" by Lance Storm, Patrizio E. Tressoldi and Lorenzo Di Risio (Psychological Bulletin, 2010[Jul], Vol 136[4], 471-485). In the article, the sentence giving the formula in the second paragraph on p. 479 was stated incorrectly. The corrected sentence is included. (The following abstract of the original article appeared in record 2010-12718-001.) [Correction Notice: An erratum for this article was reported in Vol 136(5) of Psychological Bulletin (see record 2010-17510-009). In the article, the second to last sentence of the abstract (p. 471) was stated incorrectly. The sentence should read as follows: "The mean effect size value of the ganzfeld database was significantly higher than the mean effect size of the standard free-response database but was not higher than the effect size of the nonganzfeld noise reduction database."] We report the results of meta-analyses on 3 types of free-response study: (a) ganzfeld (a technique that enhances a communication anomaly referred to as "psi"); (b) nonganzfeld noise reduction using alleged psi-enhancing techniques such as dream psi, meditation, relaxation, or hypnosis; and (c) standard free response (nonganzfeld, no noise reduction). For the period 1997-2008, a homogeneous data set of 29 ganzfeld studies yielded a mean effect size of 0.142 (Stouffer Z = 5.48, p = 2.13 × 10-8). A homogeneous nonganzfeld noise reduction data set of 16 studies yielded a mean effect size of 0.110 (Stouffer Z = 3.35, p = 2.08 × 10-4), and a homogeneous data set of 14 standard free-response studies produced a weak negative mean effect size of -0.029 (Stouffer Z = -2.29, p = .989). The mean effect size value of the ganzfeld database were significantly higher than the mean effect size of the nonganzfeld noise reduction and the standard free-response databases. We also found that selected participants (believers in the paranormal, meditators, etc.) had a performance advantage over unselected participants, but only if they were in the ganzfeld condition. PsycINFO Database Record (c) 2015 APA, all rights reserved.

An Information System for European culture collections: the way forward.

PubMed

Casaregola, Serge; Vasilenko, Alexander; Romano, Paolo; Robert, Vincent; Ozerskaya, Svetlana; Kopf, Anna; Glöckner, Frank O; Smith, David

2016-01-01

Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible to their users. Clearly, the needs of culture collection curators coincide with those of users on the crucial point of database interoperability. In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.

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...

A Database of Woody Vegetation Responses to Elevated Atmospheric CO2 (NDP-072)

DOE Data Explorer

Curtis, Peter S [The Ohio State Univ., Columbus, OH (United States); Cushman, Robert M [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brenkert, Antoinette L [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

1999-01-01

To perform a statistically rigorous meta-analysis of research results on the response by woody vegetation to increased atmospheric CO2 levels, a multiparameter database of responses was compiled. Eighty-four independent CO2-enrichment studies, covering 65 species and 35 response parameters, met the necessary criteria for inclusion in the database: reporting mean response, sample size, and variance of the response (either as standard deviation or standard error). Data were retrieved from the published literature and unpublished reports. This numeric data package contains a 29-field data set of CO2-exposure experiment responses by woody plants (as both a flat ASCII file and a spreadsheet file), files listing the references to the CO2-exposure experiments and specific comments relevant to the data in the data set, and this documentation file (which includes SAS and Fortran codes to read the ASCII data file; SAS is a registered trademark of the SAS Institute, Inc., Cary, North Carolina 27511).

The quest for the perfect gravity anomaly: Part 2 - Mass effects and anomaly inversion

USGS Publications Warehouse

Keller, Gordon R.; Hildenbrand, T.G.; Hinze, W. J.; Li, X.; Ravat, D.; Webring, M.

2006-01-01

Gravity anomalies have become an important tool for geologic studies since the widespread use of high-precision gravimeters after the Second World War. More recently the development of instrumentation for airborne gravity observations, procedures for acquiring data from satellite platforms, the readily available Global Positioning System for precise vertical and horizontal control, improved global data bases, and enhancement of computational hardware and software have accelerated the use of the gravity method. As a result, efforts are being made to improve the gravity databases that are made available to the geoscience community by broadening their observational holdings and increasing the accuracy and precision of the included data. Currently the North American Gravity Database as well as the individual databases of Canada, Mexico, and the United States of America are being revised using new formats and standards. The objective of this paper is to describe the use of the revised standards for gravity data processing and modeling and there impact on geological interpretations. ?? 2005 Society of Exploration Geophysicists.

Study on distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database

NASA Astrophysics Data System (ADS)

WANG, Qingrong; ZHU, Changfeng

2017-06-01

Integration of distributed heterogeneous data sources is the key issues under the big data applications. In this paper the strategy of variable precision is introduced to the concept lattice, and the one-to-one mapping mode of variable precision concept lattice and ontology concept lattice is constructed to produce the local ontology by constructing the variable precision concept lattice for each subsystem, and the distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database is proposed to draw support from the special relationship between concept lattice and ontology construction. Finally, based on the standard of main concept lattice of the existing heterogeneous database generated, a case study has been carried out in order to testify the feasibility and validity of this algorithm, and the differences between the main concept lattice and the standard concept lattice are compared. Analysis results show that this algorithm above-mentioned can automatically process the construction process of distributed concept lattice under the heterogeneous data sources.

Building a Quality Controlled Database of Meteorological Data from NASA Kennedy Space Center and the United States Air Force's Eastern Range

NASA Technical Reports Server (NTRS)

Brenton, James C.; Barbre. Robert E., Jr.; Decker, Ryan K.; Orcutt, John M.

2018-01-01

The National Aeronautics and Space Administration's (NASA) Marshall Space Flight Center (MSFC) Natural Environments Branch (EV44) has provided atmospheric databases and analysis in support of space vehicle design and day-of-launch operations for NASA and commercial launch vehicle programs launching from the NASA Kennedy Space Center (KSC), co-located on the United States Air Force's Eastern Range (ER) at the Cape Canaveral Air Force Station. The ER complex is one of the most heavily instrumented sites in the United States with over 31 towers measuring various atmospheric parameters on a continuous basis. An inherent challenge with large sets of data consists of ensuring erroneous data is removed from databases, and thus excluded from launch vehicle design analyses. EV44 has put forth great effort in developing quality control (QC) procedures for individual meteorological instruments, however no standard QC procedures for all databases currently exists resulting in QC databases that have inconsistencies in variables, methodologies, and periods of record. The goal of this activity is to use the previous efforts by EV44 to develop a standardized set of QC procedures from which to build meteorological databases from KSC and the ER, while maintaining open communication with end users from the launch community to develop ways to improve, adapt and grow the QC database. Details of the QC procedures will be described. As the rate of launches increases with additional launch vehicle programs, it is becoming more important that weather databases are continually updated and checked for data quality before use in launch vehicle design and certification analyses.

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...-compatible format. All databases must be supported with adequate documentation on data attributes, SQL...

Results from a new 193nm die-to-database reticle inspection platform

NASA Astrophysics Data System (ADS)

Broadbent, William H.; Alles, David S.; Giusti, Michael T.; Kvamme, Damon F.; Shi, Rui-fang; Sousa, Weston L.; Walsh, Robert; Xiong, Yalin

2010-05-01

A new 193nm wavelength high resolution reticle defect inspection platform has been developed for both die-to-database and die-to-die inspection modes. In its initial configuration, this innovative platform has been designed to meet the reticle qualification requirements of the IC industry for the 22nm logic and 3xhp memory generations (and shrinks) with planned extensions to the next generation. The 22nm/3xhp IC generation includes advanced 193nm optical lithography using conventional RET, advanced computational lithography, and double patterning. Further, EUV pilot line lithography is beginning. This advanced 193nm inspection platform has world-class performance and the capability to meet these diverse needs in optical and EUV lithography. The architecture of the new 193nm inspection platform is described. Die-to-database inspection results are shown on a variety of reticles from industry sources; these reticles include standard programmed defect test reticles, as well as advanced optical and EUV product and product-like reticles. Results show high sensitivity and low false and nuisance detections on complex optical reticle designs and small feature size EUV reticles. A direct comparison with the existing industry standard 257nm wavelength inspection system shows measurable sensitivity improvement for small feature sizes

Firefighters' hearing: a comparison with population databases from the International Standards Organization.

PubMed

Kales, S N; Freyman, R L; Hill, J M; Polyhronopoulos, G N; Aldrich, J M; Christiani, D C

2001-07-01

We investigated firefighters' hearing relative to general population data to adjust for age-expected hearing loss. For five groups of male firefighters with increasing mean ages, we compared their hearing thresholds at the 50th and 90th percentiles with normative and age- and sex-matched hearing data from the International Standards Organization (databases A and B). At the 50th percentile, from a mean age of 28 to a mean age of 53 years, relative to databases A and B, the firefighters lost an excess of 19 to 23 dB, 20 to 23 dB, and 16 to 19 dB at 3000, 4000, and 6000 Hz, respectively. At the 90th percentile, from a mean age of 28 to a mean age of 53 years, relative to databases A and B, the firefighters lost an excess of 12 to 20 dB, 38 to 44 dB, 41 to 45 dB, and 22 to 28 dB at 2000, 3000, 4000, and 6000 Hz, respectively. The results are consistent with accelerated hearing loss in excess of age-expected loss among the firefighters, especially at or above the 90th percentile.

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.

Revisiting the Canadian English vowel space

NASA Astrophysics Data System (ADS)

Hagiwara, Robert

2005-04-01

In order to fill a need for experimental-acoustic baseline measurements of Canadian English vowels, a database is currently being constructed in Winnipeg, Manitoba. The database derives from multiple repetitions of fifteen English vowels (eleven standard monophthongs, syllabic /r/ and three standard diphthongs) in /hVd/ and /hVt/ contexts, as spoken by multiple speakers. Frequencies of the first four formants are taken from three timepoints in every vowel token (25, 50, and 75% of vowel duration). Preliminary results (from five men and five women) confirm some features characteristic of Canadian English, but call others into question. For instance the merger of low back vowels appears to be complete for these speakers, but the result is a lower-mid and probably rounded vowel rather than the low back unround vowel often described. With these data Canadian Raising can be quantified as an average 200 Hz or 1.5 Bark downward shift in the frequency of F1 before voiceless /t/. Analysis of the database will lead to a more accurate picture of the Canadian English vowel system, as well as provide a practical and up-to-date point of reference for further phonetic and sociophonetic comparisons.

PERFORMANCE AUDITING OF A HUMAN AIR POLLUTION EXPOSURE SYSTEM 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 in this ma...

77 FR 66617 - HIT Policy and Standards Committees; Workgroup Application Database

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-06

... Database AGENCY: Office of the National Coordinator for Health Information Technology, HHS. ACTION: Notice of New ONC HIT FACA Workgroup Application Database. The Office of the National Coordinator (ONC) has launched a new Health Information Technology Federal Advisory Committee Workgroup Application Database...

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

PubMed

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

2013-01-01

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

Mobile Source Observation Database (MSOD)

EPA Pesticide Factsheets

The Mobile Source Observation Database (MSOD) is a relational database developed by the Assessment and Standards Division (ASD) of the U.S. EPA Office of Transportation and Air Quality (formerly the Office of Mobile Sources).

A literature search tool for intelligent extraction of disease-associated genes.

PubMed

Jung, Jae-Yoon; DeLuca, Todd F; Nelson, Tristan H; Wall, Dennis P

2014-01-01

To extract disorder-associated genes from the scientific literature in PubMed with greater sensitivity for literature-based support than existing methods. We developed a PubMed query to retrieve disorder-related, original research articles. Then we applied a rule-based text-mining algorithm with keyword matching to extract target disorders, genes with significant results, and the type of study described by the article. We compared our resulting candidate disorder genes and supporting references with existing databases. We demonstrated that our candidate gene set covers nearly all genes in manually curated databases, and that the references supporting the disorder-gene link are more extensive and accurate than other general purpose gene-to-disorder association databases. We implemented a novel publication search tool to find target articles, specifically focused on links between disorders and genotypes. Through comparison against gold-standard manually updated gene-disorder databases and comparison with automated databases of similar functionality we show that our tool can search through the entirety of PubMed to extract the main gene findings for human diseases rapidly and accurately.

PERFORMANCE AUDITING OF A HUMAN AIR POLLUTION EXPOSURE SYSTEM FOR COARSE PARTICULATE MATTER (PM2.5-10)

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 in this ma...

USDA National Nutrient Database for Standard Reference, release 28

USDA-ARS?s Scientific Manuscript database

The USDA National Nutrient Database for Standard Reference, Release 28 contains data for nearly 8,800 food items for up to 150 food components. SR28 replaces the previous release, SR27, originally issued in August 2014. Data in SR28 supersede values in the printed handbooks and previous electronic...

Exposure to benzodiazepines (anxiolytics, hypnotics and related drugs) in seven European electronic healthcare databases: a cross-national descriptive study from the PROTECT-EU Project.

PubMed

Huerta, Consuelo; Abbing-Karahagopian, Victoria; Requena, Gema; Oliva, Belén; Alvarez, Yolanda; Gardarsdottir, Helga; Miret, Montserrat; Schneider, Cornelia; Gil, Miguel; Souverein, Patrick C; De Bruin, Marie L; Slattery, Jim; De Groot, Mark C H; Hesse, Ulrik; Rottenkolber, Marietta; Schmiedl, Sven; Montero, Dolores; Bate, Andrew; Ruigomez, Ana; García-Rodríguez, Luis Alberto; Johansson, Saga; de Vries, Frank; Schlienger, Raymond G; Reynolds, Robert F; Klungel, Olaf H; de Abajo, Francisco José

2016-03-01

Studies on drug utilization usually do not allow direct cross-national comparisons because of differences in the respective applied methods. This study aimed to compare time trends in BZDs prescribing by applying a common protocol and analyses plan in seven European electronic healthcare databases. Crude and standardized prevalence rates of drug prescribing from 2001-2009 were calculated in databases from Spain, United Kingdon (UK), The Netherlands, Germany and Denmark. Prevalence was stratified by age, sex, BZD type [(using ATC codes), i.e. BZD-anxiolytics BZD-hypnotics, BZD-related drugs and clomethiazole], indication and number of prescription. Crude prevalence rates of BZDs prescribing ranged from 570 to 1700 per 10,000 person-years over the study period. Standardization by age and sex did not substantially change the differences. Standardized prevalence rates increased in the Spanish (+13%) and UK databases (+2% and +8%) over the study period, while they decreased in the Dutch databases (-4% and -22%), the German (-12%) and Danish (-26%) database. Prevalence of anxiolytics outweighed that of hypnotics in the Spanish, Dutch and Bavarian databases, but the reverse was shown in the UK and Danish databases. Prevalence rates consistently increased with age and were two-fold higher in women than in men in all databases. A median of 18% of users received 10 or more prescriptions in 2008. Although similar methods were applied, the prevalence of BZD prescribing varied considerably across different populations. Clinical factors related to BZDs and characteristics of the databases may explain these differences. Copyright © 2015 John Wiley & Sons, Ltd.

A Partnership for Public Health: USDA Branded Food Products Database

USDA-ARS?s Scientific Manuscript database

The importance of comprehensive food composition databases is more critical than ever in helping to address global food security. The USDA National Nutrient Database for Standard Reference is the “gold standard” for food composition databases. The presentation will include new developments in stren...

Lessons Learned and Technical Standards: A Logical Marriage

NASA Technical Reports Server (NTRS)

Gill, Paul; Vaughan, William W.; Garcia, Danny; Gill, Maninderpal S. (Technical Monitor)

2001-01-01

A comprehensive database of lessons learned that corresponds with relevant technical standards would be a boon to technical personnel and standards developers. The authors discuss the emergence of one such database within NASA, and show how and why the incorporation of lessons learned into technical standards databases can be an indispensable tool for government and industry. Passed down from parent to child, teacher to pupil, and from senior to junior employees, lessons learned have been the basis for our accomplishments throughout the ages. Government and industry, too, have long recognized the need to systematically document And utilize the knowledge gained from past experiences in order to avoid the repetition of failures and mishaps. The use of lessons learned is a principle component of any organizational culture committed to continuous improvement. They have formed the foundation for discoveries, inventions, improvements, textbooks, and technical standards. Technical standards are a very logical way to communicate these lessons. Using the time-honored tradition of passing on lessons learned while utilizing the newest in information technology, the National Aeronautics and Space Administration (NASA) has launched an intensive effort to link lessons learned with specific technical standards through various Internet databases. This article will discuss the importance of lessons learned to engineers, the difficulty in finding relevant lessons learned while engaged in an engineering project, and the new NASA project that can help alleviate this difficulty. The article will conclude with recommendations for more expanded cross-sectoral uses of lessons learned with reference to technical standards.

Development, Use, and Impact of a Global Laboratory Database During the 2014 Ebola Outbreak in West Africa.

PubMed

Durski, Kara N; Singaravelu, Shalini; Teo, Junxiong; Naidoo, Dhamari; Bawo, Luke; Jambai, Amara; Keita, Sakoba; Yahaya, Ali Ahmed; Muraguri, Beatrice; Ahounou, Brice; Katawera, Victoria; Kuti-George, Fredson; Nebie, Yacouba; Kohar, T Henry; Hardy, Patrick Jowlehpah; Djingarey, Mamoudou Harouna; Kargbo, David; Mahmoud, Nuha; Assefa, Yewondwossen; Condell, Orla; N'Faly, Magassouba; Van Gurp, Leon; Lamanu, Margaret; Ryan, Julia; Diallo, Boubacar; Daffae, Foday; Jackson, Dikena; Malik, Fayyaz Ahmed; Raftery, Philomena; Formenty, Pierre

2017-06-15

The international impact, rapid widespread transmission, and reporting delays during the 2014 Ebola outbreak in West Africa highlighted the need for a global, centralized database to inform outbreak response. The World Health Organization and Emerging and Dangerous Pathogens Laboratory Network addressed this need by supporting the development of a global laboratory database. Specimens were collected in the affected countries from patients and dead bodies meeting the case definitions for Ebola virus disease. Test results were entered in nationally standardized spreadsheets and consolidated onto a central server. From March 2014 through August 2016, 256343 specimens tested for Ebola virus disease were captured in the database. Thirty-one specimen types were collected, and a variety of diagnostic tests were performed. Regular analysis of data described the functionality of laboratory and response systems, positivity rates, and the geographic distribution of specimens. With data standardization and end user buy-in, the collection and analysis of large amounts of data with multiple stakeholders and collaborators across various user-access levels was made possible and contributed to outbreak response needs. The usefulness and value of a multifunctional global laboratory database is far reaching, with uses including virtual biobanking, disease forecasting, and adaption to other disease outbreaks. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Cross-Border Use of Food Databases: Equivalence of US and Australian Databases for Macronutrients

PubMed Central

Summer, Suzanne S.; Ollberding, Nicholas J.; Guy, Trish; Setchell, Kenneth D. R.; Brown, Nadine; Kalkwarf, Heidi J.

2013-01-01

When estimating dietary intake across multiple countries, the lack of a single comprehensive dietary database may lead researchers to modify one database to analyze intakes for all participants. This approach may yield results different from those using the country-specific database and introduce measurement error. We examined whether nutrient intakes of Australians calculated with a modified US database would be similar to those calculated with an Australian database. We analyzed 3-day food records of 68 Australian adults using the US-based Nutrition Data System for Research, modified to reflect food items consumed in Australia. Modification entailed identifying a substitute food whose energy and macronutrient content were within 10% of the Australian food or by adding a new food to the database. Paired Wilcoxon signed rank tests were used to compare differences in nutrient intakes estimated by both databases, and Pearson and intraclass correlation coefficients measured degree of association and agreement between intake estimates for individuals. Median intakes of energy, carbohydrate, protein, and fiber differed by <5% at the group level. Larger discrepancies were seen for fat (11%; P<0.0001) and most micronutrients. Despite strong correlations, nutrient intakes differed by >10% for an appreciable percentage of participants (35% for energy to 69% for total fat). Adding country-specific food items to an existing database resulted in similar overall macronutrient intake estimates but was insufficient for estimating individual intakes. When analyzing nutrient intakes in multinational studies, greater standardization and modification of databases may be required to more accurately estimate intake of individuals. PMID:23871108

Probiotics in Helicobacter pylori eradication therapy: A systematic review and meta-analysis

PubMed Central

Zhang, Min-Min; Qian, Wei; Qin, Ying-Yi; He, Jia; Zhou, Yu-Hao

2015-01-01

AIM: To summarize the evidence from randomized controlled trials (RCTs) regarding the effect of probiotics by using a meta-analytic approach. METHODS: In July 2013, we searched PubMed, EMBASE, Ovid, the Cochrane Library, and three Chinese databases (Chinese Biomedical Literature Database, Chinese Medical Current Content, and Chinese Scientific Journals database) to identify relevant RCTs. We included RCTs investigating the effect of a combination of probiotics and standard therapy (probiotics group) with standard therapy alone (control group). Risk ratios (RRs) were used to measure the effect of probiotics plus standard therapy on Helicobacter pylori (H. pylori) eradication rates, adverse events, and patient compliance using a random-effect model. RESULTS: We included data on 6997 participants from 45 RCTs, the overall eradication rates of the probiotic group and the control group were 82.31% and 72.08%, respectively. We noted that the use of probiotics plus standard therapy was associated with an increased eradication rate by per-protocol set analysis (RR = 1.11; 95%CI: 1.08-1.15; P < 0.001) or intention-to-treat analysis (RR = 1.13; 95%CI: 1.10-1.16; P < 0.001). Furthermore, the incidence of adverse events was 21.44% in the probiotics group and 36.27% in the control group, and it was found that the probiotics plus standard therapy significantly reduced the risk of adverse events (RR = 0.59; 95%CI: 0.48-0.71; P < 0.001), which demonstrated a favorable effect of probiotics in reducing adverse events associated with H. pylori eradication therapy. The specific reduction in adverse events ranged from 30% to 59%, and this reduction was statistically significant. Finally, probiotics plus standard therapy had little or no effect on patient compliance (RR = 0.98; 95%CI: 0.68-1.39; P = 0.889). CONCLUSION: The use of probiotics plus standard therapy was associated with an increase in the H. pylori eradication rate, and a reduction in adverse events resulting from treatment in the general population. However, this therapy did not improve patient compliance. PMID:25892886

Database Systems. Course Three. Information Systems Curriculum.

ERIC Educational Resources Information Center

O'Neil, Sharon Lund; Everett, Donna R.

This course is the third of seven in the Information Systems curriculum. The purpose of the course is to familiarize students with database management concepts and standard database management software. Databases and their roles, advantages, and limitations are explained. An overview of the course sets forth the condition and performance standard…

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

NASA Astrophysics Data System (ADS)

Jin, Peiquan; Wan, Shouhong; Yue, Lihua

2009-12-01

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

The database of the Nikolaev Astronomical Observatory as a unit of an international virtual observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Yu.; Pinigin, G.; Shulga, A.

2005-06-01

Results of the development and organization of the digital database of the Nikolaev Astronomical Observatory (NAO) are presented. At present, three telescopes are connected to the local area network of NAO. All the data obtained, and results of data processing are entered into the common database of NAO. The daily average volume of new astronomical information obtained from the CCD instruments ranges from 300 MB up to 2 GB, depending on the purposes and conditions of observations. The overwhelming majority of the data are stored in the FITS format. Development and further improvement of storage standards, procedures of data handling and data processing are being carried out. It is planned to create an astronomical web portal with the possibility to have interactive access to databases and telescopes. In the future, this resource may become a part of an international virtual observatory. There are the prototypes of search tools with the use of PHP and MySQL. Efforts for getting more links to the Internet are being made.

The future application of GML database in GIS

NASA Astrophysics Data System (ADS)

Deng, Yuejin; Cheng, Yushu; Jing, Lianwen

2006-10-01

In 2004, the Geography Markup Language (GML) Implementation Specification (version 3.1.1) was published by Open Geospatial Consortium, Inc. Now more and more applications in geospatial data sharing and interoperability depend on GML. The primary purpose of designing GML is for exchange and transportation of geo-information by standard modeling and encoding of geography phenomena. However, the problems of how to organize and access lots of GML data effectively arise in applications. The research on GML database focuses on these problems. The effective storage of GML data is a hot topic in GIS communities today. GML Database Management System (GDBMS) mainly deals with the problem of storage and management of GML data. Now two types of XML database, namely Native XML Database, and XML-Enabled Database are classified. Since GML is an application of the XML standard to geographic data, the XML database system can also be used for the management of GML. In this paper, we review the status of the art of XML database, including storage, index and query languages, management systems and so on, then move on to the GML database. At the end, the future prospect of GML database in GIS application is presented.

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

PubMed

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

2008-03-01

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

Meta-analysis of free-response studies, 1992-2008: assessing the noise reduction model in parapsychology.

PubMed

Storm, Lance; Tressoldi, Patrizio E; Di Risio, Lorenzo

2010-07-01

We report the results of meta-analyses on 3 types of free-response study: (a) ganzfeld (a technique that enhances a communication anomaly referred to as "psi"); (b) nonganzfeld noise reduction using alleged psi-enhancing techniques such as dream psi, meditation, relaxation, or hypnosis; and (c) standard free response (nonganzfeld, no noise reduction). For the period 1997-2008, a homogeneous data set of 29 ganzfeld studies yielded a mean effect size of 0.142 (Stouffer Z = 5.48, p = 2.13 x 10(-8)). A homogeneous nonganzfeld noise reduction data set of 16 studies yielded a mean effect size of 0.110 (Stouffer Z = 3.35, p = 2.08 x 10(-4)), and a homogeneous data set of 14 standard free-response studies produced a weak negative mean effect size of -0.029 (Stouffer Z = -2.29, p = .989). The mean effect size value of the ganzfeld database was significantly higher than the mean effect size of the standard free-response database but was not higher than the effect size of the nonganzfeld noise reduction database [corrected].We also found that selected participants (believers in the paranormal, meditators, etc.) had a performance advantage over unselected participants, but only if they were in the ganzfeld condition.

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

PubMed

Gacesa, Ranko; Zucko, Jurica; Petursdottir, Solveig K; Gudmundsdottir, Elisabet Eik; Fridjonsson, Olafur H; Diminic, Janko; Long, Paul F; Cullum, John; Hranueli, Daslav; Hreggvidsson, Gudmundur O; Starcevic, Antonio

2017-06-01

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya . The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

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

EPA Science Inventory

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

USDA National Nutrient Database for Standard Reference, Release 25

USDA-ARS?s Scientific Manuscript database

The USDA National Nutrient Database for Standard Reference, Release 25(SR25)contains data for over 8,100 food items for up to 146 food components. It replaces the previous release, SR24, issued in September 2011. Data in SR25 supersede values in the printed handbooks and previous electronic releas...

USDA National Nutrient Database for Standard Reference, Release 24

USDA-ARS?s Scientific Manuscript database

The USDA Nutrient Database for Standard Reference, Release 24 contains data for over 7,900 food items for up to 146 food components. It replaces the previous release, SR23, issued in September 2010. Data in SR24 supersede values in the printed Handbooks and previous electronic releases of the databa...

A Comprehensive Strategy to Construct In-house Database for Accurate and Batch Identification of Small Molecular Metabolites.

PubMed

Zhao, Xinjie; Zeng, Zhongda; Chen, Aiming; Lu, Xin; Zhao, Chunxia; Hu, Chunxiu; Zhou, Lina; Liu, Xinyu; Wang, Xiaolin; Hou, Xiaoli; Ye, Yaorui; Xu, Guowang

2018-05-29

Identification of the metabolites is an essential step in metabolomics study to interpret regulatory mechanism of pathological and physiological processes. However, it is still a big headache in LC-MSn-based studies because of the complexity of mass spectrometry, chemical diversity of metabolites, and deficiency of standards database. In this work, a comprehensive strategy is developed for accurate and batch metabolite identification in non-targeted metabolomics studies. First, a well defined procedure was applied to generate reliable and standard LC-MS2 data including tR, MS1 and MS2 information at a standard operational procedure (SOP). An in-house database including about 2000 metabolites was constructed and used to identify the metabolites in non-targeted metabolic profiling by retention time calibration using internal standards, precursor ion alignment and ion fusion, auto-MS2 information extraction and selection, and database batch searching and scoring. As an application example, a pooled serum sample was analyzed to deliver the strategy, 202 metabolites were identified in the positive ion mode. It shows our strategy is useful for LC-MSn-based non-targeted metabolomics study.

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.

Building a QC Database of Meteorological Data From NASA KSC and the United States Air Force's Eastern Range

NASA Technical Reports Server (NTRS)

Brenton, James C.; Barbre, Robert E.; Orcutt, John M.; Decker, Ryan K.

2018-01-01

The National Aeronautics and Space Administration's (NASA) Marshall Space Flight Center (MSFC) Natural Environments Branch (EV44) has provided atmospheric databases and analysis in support of space vehicle design and day-of-launch operations for NASA and commercial launch vehicle programs launching from the NASA Kennedy Space Center (KSC), co-located on the United States Air Force's Eastern Range (ER) at the Cape Canaveral Air Force Station. The ER is one of the most heavily instrumented sites in the United States measuring various atmospheric parameters on a continuous basis. An inherent challenge with the large databases that EV44 receives from the ER consists of ensuring erroneous data are removed from the databases, and thus excluded from launch vehicle design analyses. EV44 has put forth great effort in developing quality control (QC) procedures for individual meteorological instruments; however, no standard QC procedures for all databases currently exist resulting in QC databases that have inconsistencies in variables, methodologies, and periods of record. The goal of this activity is to use the previous efforts by EV44 to develop a standardized set of QC procedures from which to build flags within the meteorological databases from KSC and the ER, while maintaining open communication with end users from the launch community to develop ways to improve, adapt and grow the QC database. Details of the QC checks are described. The flagged data points will be plotted in a graphical user interface (GUI) as part of a manual confirmation that the flagged data do indeed need to be removed from the archive. As the rate of launches increases with additional launch vehicle programs, more emphasis is being placed to continually update and check weather databases for data quality before use in launch vehicle design and certification analyses.

An SQL query generator for CLIPS

NASA Technical Reports Server (NTRS)

Snyder, James; Chirica, Laurian

1990-01-01

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

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources.

PubMed

Lim, Jeongheui; Kim, Sang-Yoon; Kim, Sungmin; Eo, Hae-Seok; Kim, Chang-Bae; Paek, Woon Kee; Kim, Won; Bhak, Jong

2009-12-03

DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases. We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses. Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org.

Occupational exposure to silica in construction workers: a literature-based exposure database.

PubMed

Beaudry, Charles; Lavoué, Jérôme; Sauvé, Jean-François; Bégin, Denis; Senhaji Rhazi, Mounia; Perrault, Guy; Dion, Chantal; Gérin, Michel

2013-01-01

We created an exposure database of respirable crystalline silica levels in the construction industry from the literature. We extracted silica and dust exposure levels in publications reporting silica exposure levels or quantitative evaluations of control effectiveness published in or after 1990. The database contains 6118 records (2858 of respirable crystalline silica) extracted from 115 sources, summarizing 11,845 measurements. Four hundred and eighty-eight records represent summarized exposure levels instead of individual values. For these records, the reported summary parameters were standardized into a geometric mean and a geometric standard deviation. Each record is associated with 80 characteristics, including information on trade, task, materials, tools, sampling strategy, analytical methods, and control measures. Although the database was constructed in French, 38 essential variables were standardized and translated into English. The data span the period 1974-2009, with 92% of the records corresponding to personal measurements. Thirteen standardized trades and 25 different standardized tasks are associated with at least five individual silica measurements. Trade-specific respirable crystalline silica geometric means vary from 0.01 (plumber) to 0.30 mg/m³ (tunnel construction skilled labor), while tasks vary from 0.01 (six categories, including sanding and electrical maintenance) to 1.59 mg/m³ (abrasive blasting). Despite limitations associated with the use of literature data, this database can be analyzed using meta-analytical and multivariate techniques and currently represents the most important source of exposure information about silica exposure in the construction industry. It is available on request to the research community.

Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

PubMed

Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

2017-11-01

Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Compiling Holocene RSL databases from near- to far-field regions: proxies, difficulties and possible solutions

NASA Astrophysics Data System (ADS)

Vacchi, M.; Horton, B.; Mann, T.; Engelhart, S. E.; Rovere, A.; Nikitina, D.; Bender, M.; Roy, K.; Peltier, W. R.

2017-12-01

Reconstructions of relative sea level (RSL) have implications for investigation of crustal movements, calibration of earth rheology models and the reconstruction of ice sheets. In recent years, efforts were made to create RSL databases following a standardized methodology. These regional databases provide a framework for developing our understanding of the primary mechanisms of RSL change since the Last Glacial Maximum and a long-term baseline against which to gauge changes in sea level during the 20th century and forecasts for the 21st. We report here the results of recently compiled databases in very different climatic and geographic contexts that are the northeastern Canadian coast, the Mediterranean Sea as well as the southeastern Asiatic region. Our re-evaluation of sea-level indicators from geological and archaeological investigations have yielded more than 3000 RSL data-points mainly from salt and freshwater wetlands or adjacent estuarine sediment, isolation basins, beach ridges, fixed biological indicators, beachrocks as well as coastal archaeological structures. We outline some of the inherent difficulties, and potential solutions to analyse sea-level data in such different depositional environments. In particular, we discuss problems related with the definition of standardized indicative meaning, and with the re-evaluation of old radiocarbon samples. We further address complex tectonics influences and the framework to compare such large variability of RSL data-points. Finally we discuss the implications of our results for the patterns of glacio-isostatic adjustment in these regions.

Standard-Chinese Lexical Neighborhood Test in normal-hearing young children.

PubMed

Liu, Chang; Liu, Sha; Zhang, Ning; Yang, Yilin; Kong, Ying; Zhang, Luo

2011-06-01

The purposes of the present study were to establish the Standard-Chinese version of Lexical Neighborhood Test (LNT) and to examine the lexical and age effects on spoken-word recognition in normal-hearing children. Six lists of monosyllabic and six lists of disyllabic words (20 words/list) were selected from the database of daily speech materials for normal-hearing (NH) children of ages 3-5 years. The lists were further divided into "easy" and "hard" halves according to the word frequency and neighborhood density in the database based on the theory of Neighborhood Activation Model (NAM). Ninety-six NH children (age ranged between 4.0 and 7.0 years) were divided into three different age groups of 1-year intervals. Speech-perception tests were conducted using the Standard-Chinese monosyllabic and disyllabic LNT. The inter-list performance was found to be equivalent and inter-rater reliability was high with 92.5-95% consistency. Results of word-recognition scores showed that the lexical effects were all significant. Children scored higher with disyllabic words than with monosyllabic words. "Easy" words scored higher than "hard" words. The word-recognition performance also increased with age in each lexical category. A multiple linear regression analysis showed that neighborhood density, age, and word frequency appeared to have increasingly more contributions to Chinese word recognition. The results of the present study indicated that performances of Chinese word recognition were influenced by word frequency, age, and neighborhood density, with word frequency playing a major role. These results were consistent with those in other languages, supporting the application of NAM in the Chinese language. The development of Standard-Chinese version of LNT and the establishment of a database of children of 4-6 years old can provide a reliable means for spoken-word recognition test in children with hearing impairment. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

PubMed Central

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. PMID:25202745

Database for propagation models

NASA Astrophysics Data System (ADS)

Kantak, Anil V.

1991-07-01

A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR DATABASE TREE AND DATA SOURCES (UA-D-41.0)

EPA Science Inventory

The purpose of this SOP is to describe the database storage organization, as well as describe the sources of data for each database used during the Arizona NHEXAS project and the "Border" study. Keywords: data; database; organization.

The National Human Exposure Assessment Sur...

Design and Establishment of Quality Model of Fundamental Geographic Information Database

NASA Astrophysics Data System (ADS)

Ma, W.; Zhang, J.; Zhao, Y.; Zhang, P.; Dang, Y.; Zhao, T.

2018-04-01

In order to make the quality evaluation for the Fundamental Geographic Information Databases(FGIDB) more comprehensive, objective and accurate, this paper studies and establishes a quality model of FGIDB, which formed by the standardization of database construction and quality control, the conformity of data set quality and the functionality of database management system, and also designs the overall principles, contents and methods of the quality evaluation for FGIDB, providing the basis and reference for carry out quality control and quality evaluation for FGIDB. This paper designs the quality elements, evaluation items and properties of the Fundamental Geographic Information Database gradually based on the quality model framework. Connected organically, these quality elements and evaluation items constitute the quality model of the Fundamental Geographic Information Database. This model is the foundation for the quality demand stipulation and quality evaluation of the Fundamental Geographic Information Database, and is of great significance on the quality assurance in the design and development stage, the demand formulation in the testing evaluation stage, and the standard system construction for quality evaluation technology of the Fundamental Geographic Information Database.

Geospatial Database for Strata Objects Based on Land Administration Domain Model (ladm)

NASA Astrophysics Data System (ADS)

Nasorudin, N. N.; Hassan, M. I.; Zulkifli, N. A.; Rahman, A. Abdul

2016-09-01

Recently in our country, the construction of buildings become more complex and it seems that strata objects database becomes more important in registering the real world as people now own and use multilevel of spaces. Furthermore, strata title was increasingly important and need to be well-managed. LADM is a standard model for land administration and it allows integrated 2D and 3D representation of spatial units. LADM also known as ISO 19152. The aim of this paper is to develop a strata objects database using LADM. This paper discusses the current 2D geospatial database and needs for 3D geospatial database in future. This paper also attempts to develop a strata objects database using a standard data model (LADM) and to analyze the developed strata objects database using LADM data model. The current cadastre system in Malaysia includes the strata title is discussed in this paper. The problems in the 2D geospatial database were listed and the needs for 3D geospatial database in future also is discussed. The processes to design a strata objects database are conceptual, logical and physical database design. The strata objects database will allow us to find the information on both non-spatial and spatial strata title information thus shows the location of the strata unit. This development of strata objects database may help to handle the strata title and information.

Is the coverage of google scholar enough to be used alone for systematic reviews

PubMed Central

2013-01-01

Background In searches for clinical trials and systematic reviews, it is said that Google Scholar (GS) should never be used in isolation, but in addition to PubMed, Cochrane, and other trusted sources of information. We therefore performed a study to assess the coverage of GS specifically for the studies included in systematic reviews and evaluate if GS was sensitive enough to be used alone for systematic reviews. Methods All the original studies included in 29 systematic reviews published in the Cochrane Database Syst Rev or in the JAMA in 2009 were gathered in a gold standard database. GS was searched for all these studies one by one to assess the percentage of studies which could have been identified by searching only GS. Results All the 738 original studies included in the gold standard database were retrieved in GS (100%). Conclusion The coverage of GS for the studies included in the systematic reviews is 100%. If the authors of the 29 systematic reviews had used only GS, no reference would have been missed. With some improvement in the research options, to increase its precision, GS could become the leading bibliographic database in medicine and could be used alone for systematic reviews. PMID:23302542

USDA National Nutrient Database for Standard Reference Dataset for What We Eat in America, NHANES (Survey-SR) 2013-2014

USDA-ARS?s Scientific Manuscript database

USDA National Nutrient Database for Standard Reference Dataset for What We Eat In America, NHANES (Survey-SR) provides the nutrient data for assessing dietary intakes from the national survey What We Eat In America, National Health and Nutrition Examination Survey (WWEIA, NHANES). The current versi...

Guide on Data Models in the Selection and Use of Database Management Systems. Final Report.

ERIC Educational Resources Information Center

Gallagher, Leonard J.; Draper, Jesse M.

A tutorial introduction to data models in general is provided, with particular emphasis on the relational and network models defined by the two proposed ANSI (American National Standards Institute) database language standards. Examples based on the network and relational models include specific syntax and semantics, while examples from the other…

National Vulnerability Database (NVD)

National Institute of Standards and Technology Data Gateway

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

Dictionary as Database.

ERIC Educational Resources Information Center

Painter, Derrick

1996-01-01

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

Diet History Questionnaire: Database Utility Program

Cancer.gov

If you need to modify the standard nutrient database, a single nutrient value must be provided by gender and portion size. If you have modified the database to have fewer or greater demographic groups, nutrient values must be included for each group.

Standardized classification unsuitable for spontaneous reporting: the example of osteonecrosis of the jaw.

PubMed

de Boissieu, Paul; Trenque, Thierry

2015-07-01

This study assessed the impact of using a standardized definition of bisphosphonate-related osteonecrosis of the jaw (BRONJ) in the analysis of a spontaneous reporting database. All notifications of osteonecrosis of the jaw (ONJ) in the French National Pharmacovigilance Database as of 31 December 2013 were analyzed. First, we considered all reports of ONJ with bisphosphonates as BRONJ. Second, we applied the 2014 definition of BRONJ from the American Association of Oral and Maxillofacial Surgeons (AAOMS), retaining only bisphosphonates as antiresorptive medication. In the absence of any one of these criteria, or missing data, cases were not considered as BRONJ. The first analysis found 158 cases of ONJ, among which 153 were associated with bisphosphonate use. The second analysis identified only 43 cases of BRONJ (28.1%). The definition of BRONJ as laid down by the AAOMS is not suitable for use in spontaneous reporting database. The use of the AAOMS definition alone should be avoided, as it leads to the exclusion of over 70% of cases. When cases of ONJ are identified, all results should be presented including confirmed and excluded cases.

Designing Reliable Cohorts of Cardiac Patients across MIMIC and eICU

PubMed Central

Chronaki, Catherine; Shahin, Abdullah; Mark, Roger

2016-01-01

The design of the patient cohort is an essential and fundamental part of any clinical patient study. Knowledge of the Electronic Health Records, underlying Database Management System, and the relevant clinical workflows are central to an effective cohort design. However, with technical, semantic, and organizational interoperability limitations, the database queries associated with a patient cohort may need to be reconfigured in every participating site. i2b2 and SHRINE advance the notion of patient cohorts as first class objects to be shared, aggregated, and recruited for research purposes across clinical sites. This paper reports on initial efforts to assess the integration of Medical Information Mart for Intensive Care (MIMIC) and Philips eICU, two large-scale anonymized intensive care unit (ICU) databases, using standard terminologies, i.e. LOINC, ICD9-CM and SNOMED-CT. Focus of this work is lab and microbiology observations and key demographics for patients with a primary cardiovascular ICD9-CM diagnosis. Results and discussion reflecting on reference core terminology standards, offer insights on efforts to combine detailed intensive care data from multiple ICUs worldwide. PMID:27774488

Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW).

PubMed

Gálvez, Sergio; Ferusic, Adis; Esteban, Francisco J; Hernández, Pilar; Caballero, Juan A; Dorado, Gabriel

2016-10-01

The Smith-Waterman algorithm has a great sensitivity when used for biological sequence-database searches, but at the expense of high computing-power requirements. To overcome this problem, there are implementations in literature that exploit the different hardware-architectures available in a standard PC, such as GPU, CPU, and coprocessors. We introduce an application that splits the original database-search problem into smaller parts, resolves each of them by executing the most efficient implementations of the Smith-Waterman algorithms in different hardware architectures, and finally unifies the generated results. Using non-overlapping hardware allows simultaneous execution, and up to 2.58-fold performance gain, when compared with any other algorithm to search sequence databases. Even the performance of the popular BLAST heuristic is exceeded in 78% of the tests. The application has been tested with standard hardware: Intel i7-4820K CPU, Intel Xeon Phi 31S1P coprocessors, and nVidia GeForce GTX 960 graphics cards. An important increase in performance has been obtained in a wide range of situations, effectively exploiting the available hardware.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

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

2013-01-01

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

Taichi exercise for self-rated sleep quality in older people: a systematic review and meta-analysis.

PubMed

Du, Shizheng; Dong, Jianshu; Zhang, Heng; Jin, Shengji; Xu, Guihua; Liu, Zengxia; Chen, Lixia; Yin, Haiyan; Sun, Zhiling

2015-01-01

Self-reported sleep disorders are common in older adults, resulting in serious consequences. Non-pharmacological measures are important complementary interventions, among which Taichi exercise is a popular alternative. Some experiments have been performed; however, the effect of Taichi exercise in improving sleep quality in older people has yet to be validated by systematic review. Using systematic review and meta-analysis, this study aimed to examine the efficacy of Taichi exercise in promoting self-reported sleep quality in older adults. Systematic review and meta-analysis of randomized controlled studies. 4 English databases: Pubmed, Cochrane Library, Web of Science and CINAHL, and 4 Chinese databases: CBMdisc, CNKI, VIP, and Wanfang database were searched through December 2013. Two reviewers independently selected eligible trials, conducted critical appraisal of the methodological quality by using the quality appraisal criteria for randomized controlled studies recommended by Cochrane Handbook. A standardized data form was used to extract information. Meta-analysis was performed. Five randomized controlled studies met inclusion criteria. All suffered from some methodological flaws. The results of this study showed that Taichi has large beneficial effect on sleep quality in older people, as indicated by decreases in the global Pittsburgh Sleep Quality Index score [standardized mean difference=-0.87, 95% confidence intervals (95% confidence interval) (-1.25, -0.49)], as well as its sub-domains of subjective sleep quality [standardized mean difference=-0.83, 95% confidence interval (-1.08, -0.57)], sleep latency [standardized mean difference=-0.75, 95% confidence interval (-1.42, -0.07)], sleep duration [standardized mean difference=-0.55, 95% confidence interval (-0.90, -0.21)], habitual sleep efficiency [standardized mean difference=-0.49, 95% confidence interval (-0.74, -0.23)], sleep disturbance [standardized mean difference=-0.44, 95% confidence interval (-0.69, -0.19)], and daytime dysfunction [standardized mean difference=-0.34, 95% confidence interval (-0.59, -0.09)]. Daytime sleepiness improvement was also observed. Weak evidence shows that Taichi exercise has a beneficial effect in improving self-rated sleep quality for older adults, suggesting that Taichi could be an effective alternative and complementary approach to existing therapies for older people with sleep problems. More rigorous experimental studies are required. Copyright © 2014 Elsevier Ltd. All rights reserved.

Computer-Assisted Classification Patterns in Autoimmune Diagnostics: The AIDA Project

PubMed Central

Benammar Elgaaied, Amel; Cascio, Donato; Bruno, Salvatore; Ciaccio, Maria Cristina; Cipolla, Marco; Fauci, Alessandro; Morgante, Rossella; Taormina, Vincenzo; Gorgi, Yousr; Marrakchi Triki, Raja; Ben Ahmed, Melika; Louzir, Hechmi; Yalaoui, Sadok; Imene, Sfar; Issaoui, Yassine; Abidi, Ahmed; Ammar, Myriam; Bedhiafi, Walid; Ben Fraj, Oussama; Bouhaha, Rym; Hamdi, Khouloud; Soumaya, Koudhi; Neili, Bilel; Asma, Gati; Lucchese, Mariano; Catanzaro, Maria; Barbara, Vincenza; Brusca, Ignazio; Fregapane, Maria; Amato, Gaetano; Friscia, Giuseppe; Neila, Trai; Turkia, Souayeh; Youssra, Haouami; Rekik, Raja; Bouokez, Hayet; Vasile Simone, Maria; Fauci, Francesco; Raso, Giuseppe

2016-01-01

Antinuclear antibodies (ANAs) are significant biomarkers in the diagnosis of autoimmune diseases in humans, done by mean of Indirect ImmunoFluorescence (IIF) method, and performed by analyzing patterns and fluorescence intensity. This paper introduces the AIDA Project (autoimmunity: diagnosis assisted by computer) developed in the framework of an Italy-Tunisia cross-border cooperation and its preliminary results. A database of interpreted IIF images is being collected through the exchange of images and double reporting and a Gold Standard database, containing around 1000 double reported images, has been settled. The Gold Standard database is used for optimization of a CAD (Computer Aided Detection) solution and for the assessment of its added value, in order to be applied along with an Immunologist as a second Reader in detection of autoantibodies. This CAD system is able to identify on IIF images the fluorescence intensity and the fluorescence pattern. Preliminary results show that CAD, used as second Reader, appeared to perform better than Junior Immunologists and hence may significantly improve their efficacy; compared with two Junior Immunologists, the CAD system showed higher Intensity Accuracy (85,5% versus 66,0% and 66,0%), higher Patterns Accuracy (79,3% versus 48,0% and 66,2%), and higher Mean Class Accuracy (79,4% versus 56,7% and 64.2%). PMID:27042658

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

PubMed

Hermjakob, Henning; Montecchi-Palazzi, Luisa; Bader, Gary; Wojcik, Jérôme; Salwinski, Lukasz; Ceol, Arnaud; Moore, Susan; Orchard, Sandra; Sarkans, Ugis; von Mering, Christian; Roechert, Bernd; Poux, Sylvain; Jung, Eva; Mersch, Henning; Kersey, Paul; Lappe, Michael; Li, Yixue; Zeng, Rong; Rana, Debashis; Nikolski, Macha; Husi, Holger; Brun, Christine; Shanker, K; Grant, Seth G N; Sander, Chris; Bork, Peer; Zhu, Weimin; Pandey, Akhilesh; Brazma, Alvis; Jacq, Bernard; Vidal, Marc; Sherman, David; Legrain, Pierre; Cesareni, Gianni; Xenarios, Ioannis; Eisenberg, David; Steipe, Boris; Hogue, Chris; Apweiler, Rolf

2004-02-01

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

Development of a standardized Intranet database of formulation records for nonsterile compounding, Part 2.

PubMed

Haile, Michael; Anderson, Kim; Evans, Alex; Crawford, Angela

2012-01-01

In part 1 of this series, we outlined the rationale behind the development of a centralized electronic database used to maintain nonsterile compounding formulation records in the Mission Health System, which is a union of several independent hospitals and satellite and regional pharmacies that form the cornerstone of advanced medical care in several areas of western North Carolina. Hospital providers in many healthcare systems require compounded formulations to meet the needs of their patients (in particular, pediatric patients). Before a centralized electronic compounding database was implemented in the Mission Health System, each satellite or regional pharmacy affiliated with that system had a specific set of formulation records, but no standardized format for those records existed. In this article, we describe the quality control, database platform selection, description, implementation, and execution of our intranet database system, which is designed to maintain, manage, and disseminate nonsterile compounding formulation records in the hospitals and affiliated pharmacies of the Mission Health System. The objectives of that project were to standardize nonsterile compounding formulation records, create a centralized computerized database that would increase healthcare staff members' access to formulation records, establish beyond-use dates based on published stability studies, improve quality control, reduce the potential for medication errors related to compounding medications, and (ultimately) improve patient safety.

The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.

PubMed

Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

2015-01-01

There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set. CVSP web site is located at http://cvsp.chemspider.com/. A platform for the validation and standardization of chemical structure representations of various formats has been developed and made available to the community to assist and encourage the processing of chemical structure files to produce more homogeneous compound representations for exchange and interchange between online databases. While the CVSP platform is designed with flexibility inherent to the rules that can be used for processing the data we have produced a recommended rule set based on our own experiences with the large data sets such as DrugBank, ChEMBL, and data sets from ChemSpider.

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.

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

PubMed

Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

2017-04-07

Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

The Global Genome Biodiversity Network (GGBN) Data Standard specification

PubMed Central

Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

An Automated Technique to Construct a Knowledge Base of Traditional Chinese Herbal Medicine for Cancers: An Exploratory Study for Breast Cancer.

PubMed

Nguyen, Phung Anh; Yang, Hsuan-Chia; Xu, Rong; Li, Yu-Chuan Jack

2018-01-01

Traditional Chinese Medicine utilization has rapidly increased worldwide. However, there is limited database provides the information of TCM herbs and diseases. The study aims to identify and evaluate the meaningful associations between TCM herbs and breast cancer by using the association rule mining (ARM) techniques. We employed the ARM techniques for 19.9 million TCM prescriptions by using Taiwan National Health Insurance claim database from 1999 to 2013. 364 TCM herbs-breast cancer associations were derived from those prescriptions and were then filtered by their support of 20. Resulting of 296 associations were evaluated by comparing to a gold-standard that was curated information from Chinese-Wikipedia with the following terms, cancer, tumor, malignant. All 14 TCM herbs-breast cancer associations with their confidence of 1% were valid when compared to gold-standard. For other confidences, the statistical results showed consistently with high precisions. We thus succeed to identify the TCM herbs-breast cancer associations with useful techniques.

NHEXAS PHASE I MARYLAND STUDY--STANDARD OPERATING PROCEDURE FOR LAB RESULTS DATA ENTRY AND PREPARATION (D03)

EPA Science Inventory

The purpose of this SOP is to describe how lab results are organized and processed into the official database known as the Complete Dataset (CDS); to describe the structure and creation of the Analysis-ready Dataset (ADS); and to describe the structure and process of creating the...

Introducing glycomics data into the Semantic Web.

PubMed

Aoki-Kinoshita, Kiyoko F; Bolleman, Jerven; Campbell, Matthew P; Kawano, Shin; Kim, Jin-Dong; Lütteke, Thomas; Matsubara, Masaaki; Okuda, Shujiro; Ranzinger, Rene; Sawaki, Hiromichi; Shikanai, Toshihide; Shinmachi, Daisuke; Suzuki, Yoshinori; Toukach, Philip; Yamada, Issaku; Packer, Nicolle H; Narimatsu, Hisashi

2013-11-26

Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.

LOINC, a universal standard for identifying laboratory observations: a 5-year update.

PubMed

McDonald, Clement J; Huff, Stanley M; Suico, Jeffrey G; Hill, Gilbert; Leavelle, Dennis; Aller, Raymond; Forrey, Arden; Mercer, Kathy; DeMoor, Georges; Hook, John; Williams, Warren; Case, James; Maloney, Pat

2003-04-01

The Logical Observation Identifier Names and Codes (LOINC) database provides a universal code system for reporting laboratory and other clinical observations. Its purpose is to identify observations in electronic messages such as Health Level Seven (HL7) observation messages, so that when hospitals, health maintenance organizations, pharmaceutical manufacturers, researchers, and public health departments receive such messages from multiple sources, they can automatically file the results in the right slots of their medical records, research, and/or public health systems. For each observation, the database includes a code (of which 25 000 are laboratory test observations), a long formal name, a "short" 30-character name, and synonyms. The database comes with a mapping program called Regenstrief LOINC Mapping Assistant (RELMA(TM)) to assist the mapping of local test codes to LOINC codes and to facilitate browsing of the LOINC results. Both LOINC and RELMA are available at no cost from http://www.regenstrief.org/loinc/. The LOINC medical database carries records for >30 000 different observations. LOINC codes are being used by large reference laboratories and federal agencies, e.g., the CDC and the Department of Veterans Affairs, and are part of the Health Insurance Portability and Accountability Act (HIPAA) attachment proposal. Internationally, they have been adopted in Switzerland, Hong Kong, Australia, and Canada, and by the German national standards organization, the Deutsches Instituts für Normung. Laboratories should include LOINC codes in their outbound HL7 messages so that clinical and research clients can easily integrate these results into their clinical and research repositories. Laboratories should also encourage instrument vendors to deliver LOINC codes in their instrument outputs and demand LOINC codes in HL7 messages they get from reference laboratories to avoid the need to lump so many referral tests under the "send out lab" code.

Observational intensity bias associated with illness adjustment: cross sectional analysis of insurance claims

PubMed Central

Staiger, Douglas O; Sharp, Sandra M; Gottlieb, Daniel J; Bevan, Gwyn; McPherson, Klim; Welch, H Gilbert

2013-01-01

Objective To determine the bias associated with frequency of visits by physicians in adjusting for illness, using diagnoses recorded in administrative databases. Setting Claims data from the US Medicare program for services provided in 2007 among 306 US hospital referral regions. Design Cross sectional analysis. Participants 20% sample of fee for service Medicare beneficiaries residing in the United States in 2007 (n=5 153 877). Main outcome measures The effect of illness adjustment on regional mortality and spending rates using standard and visit corrected illness methods for adjustment. The standard method adjusts using comorbidity measures based on diagnoses listed in administrative databases; the modified method corrects these measures for the frequency of visits by physicians. Three conventions for measuring comorbidity are used: the Charlson comorbidity index, Iezzoni chronic conditions, and hierarchical condition categories risk scores. Results The visit corrected Charlson comorbidity index explained more of the variation in age, sex, and race mortality across the 306 hospital referral regions than did the standard index (R2=0.21 v 0.11, P<0.001) and, compared with sex and race adjusted mortality, reduced regional variation, whereas adjustment using the standard Charlson comorbidity index increased it. Although visit corrected and age, sex, and race adjusted mortality rates were similar in hospital referral regions with the highest and lowest fifths of visits, adjustment using the standard index resulted in a rate that was 18% lower in the highest fifth (46.4 v 56.3 deaths per 1000, P<0.001). Age, sex, and race adjusted spending as well as visit corrected spending was more than 30% greater in the highest fifth of visits than in the lowest fifth, but only 12% greater after adjustment using the standard index. Similar results were obtained using the Iezzoni and the hierarchical condition categories conventions for measuring comorbidity. Conclusion The rates of visits by physicians introduce substantial bias when regional mortality and spending rates are adjusted for illness using comorbidity measures based on the observed number of diagnoses recorded in Medicare’s administrative database. Adjusting without correction for regional variation in visit rates tends to make regions with high rates of visits seem to have lower mortality and lower costs, and vice versa. Visit corrected comorbidity measures better explain variation in age, sex, and race mortality than observed measures, and reduce observational intensity bias. PMID:23430282

Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.

Improving Database Simulations for Bayesian Precipitation Retrieval using Non-Spherical Ice Particles

NASA Astrophysics Data System (ADS)

Ringerud, S.; Skofronick Jackson, G.; Kulie, M.; Randel, D.

2016-12-01

NASA's Global Precipitation Measurement Mission (GPM) provides a wealth of both active and passive microwave observations aimed at furthering understanding of global precipitation and the hydrologic cycle. Employing a constellation of passive microwave radiometers increases global coverage and sampling, while the core satellite acts as a transfer standard, enabling consistent retrievals across individual constellation members. The transfer standard is applied in the form of a physically based a priori database constructed for use in Bayesian retrieval algorithms for each radiometer. The database is constructed using hydrometeor profiles optimized for the best fit to simultaneous active/passive core satellite measurements via the GPM Combined Algorithm. Initial validation of GPM rainfall products using the combined database suggests high retrieval errors for convective precipitation over land and at high latitudes. In such regimes, the signal from ice scattering observed at the higher microwave frequencies becomes particularly important for detecting and retrieving precipitation. For cross-track sounders such as MHS and SAPHIR, this signal is crucial. It is therefore important that the scattering signals associated with precipitation are accurately represented and modeled in the retrieval database. In the current GPM combined retrieval and constellation databases, ice hydrometeors are represented as "fluffy spheres", with assumed density and scattering parameters calculated using Mie theory. Resulting simulated Tb agree reasonably well at frequencies up to 89 GHz, but show significant biases at higher frequencies. In this work the database is recreated using an ensemble of non-spherical ice particles with single scattering properties calculated using discrete dipole approximation. Simulated Tb agreement is significantly improved across the high frequencies, decreasing biases by an order of magnitude in several of the channels. The new database is applied for a sample of GPM constellation retrievals and the retrieved precipitation rates compared, to demonstrate areas where the use of more complex ice particles will have the greatest effect upon the final retrievals.

15 years of monitoring occupational exposure to respirable dust and quartz within the European industrial minerals sector.

PubMed

Zilaout, Hicham; Vlaanderen, Jelle; Houba, Remko; Kromhout, Hans

2017-07-01

In 2000, a prospective Dust Monitoring Program (DMP) was started in which measurements of worker's exposure to respirable dust and quartz are collected in member companies from the European Industrial Minerals Association (IMA-Europe). After 15 years, the resulting IMA-DMP database allows a detailed overview of exposure levels of respirable dust and quartz over time within this industrial sector. Our aim is to describe the IMA-DMP and the current state of the corresponding database which due to continuation of the IMA-DMP is still growing. The future use of the database will also be highlighted including its utility for the industrial minerals producing sector. Exposure data are being obtained following a common protocol including a standardized sampling strategy, standardized sampling and analytical methods and a data management system. Following strict quality control procedures, exposure data are consequently added to a central database. The data comprises personal exposure measurements including auxiliary information on work and other conditions during sampling. Currently, the IMA-DMP database consists of almost 28,000 personal measurements which have been performed from 2000 until 2015 representing 29 half-yearly sampling campaigns. The exposure data have been collected from 160 different worksites owned by 35 industrial mineral companies and comes from 23 European countries and approximately 5000 workers. The IMA-DMP database provides the European minerals sector with reliable data regarding worker personal exposures to respirable dust and quartz. The database can be used as a powerful tool to address outstanding scientific issues on long-term exposure trends and exposure variability, and importantly, as a surveillance tool to evaluate exposure control measures. The database will be valuable for future epidemiological studies on respiratory health effects and will allow for estimation of quantitative exposure response relationships. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Validation of asthma recording in electronic health records: a systematic review

PubMed Central

Nissen, Francis; Quint, Jennifer K; Wilkinson, Samantha; Mullerova, Hana; Smeeth, Liam; Douglas, Ian J

2017-01-01

Objective To describe the methods used to validate asthma diagnoses in electronic health records and summarize the results of the validation studies. Background Electronic health records are increasingly being used for research on asthma to inform health services and health policy. Validation of the recording of asthma diagnoses in electronic health records is essential to use these databases for credible epidemiological asthma research. Methods We searched EMBASE and MEDLINE databases for studies that validated asthma diagnoses detected in electronic health records up to October 2016. Two reviewers independently assessed the full text against the predetermined inclusion criteria. Key data including author, year, data source, case definitions, reference standard, and validation statistics (including sensitivity, specificity, positive predictive value [PPV], and negative predictive value [NPV]) were summarized in two tables. Results Thirteen studies met the inclusion criteria. Most studies demonstrated a high validity using at least one case definition (PPV >80%). Ten studies used a manual validation as the reference standard; each had at least one case definition with a PPV of at least 63%, up to 100%. We also found two studies using a second independent database to validate asthma diagnoses. The PPVs of the best performing case definitions ranged from 46% to 58%. We found one study which used a questionnaire as the reference standard to validate a database case definition; the PPV of the case definition algorithm in this study was 89%. Conclusion Attaining high PPVs (>80%) is possible using each of the discussed validation methods. Identifying asthma cases in electronic health records is possible with high sensitivity, specificity or PPV, by combining multiple data sources, or by focusing on specific test measures. Studies testing a range of case definitions show wide variation in the validity of each definition, suggesting this may be important for obtaining asthma definitions with optimal validity. PMID:29238227

Compressing DNA sequence databases with coil

PubMed Central

White, W Timothy J; Hendy, Michael D

2008-01-01

Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work. PMID:18489794

The Chicago Thoracic Oncology Database Consortium: A Multisite Database Initiative

PubMed Central

Carey, George B; Tan, Yi-Hung Carol; Bokhary, Ujala; Itkonen, Michelle; Szeto, Kyle; Wallace, James; Campbell, Nicholas; Hensing, Thomas; Salgia, Ravi

2016-01-01

Objective: An increasing amount of clinical data is available to biomedical researchers, but specifically designed database and informatics infrastructures are needed to handle this data effectively. Multiple research groups should be able to pool and share this data in an efficient manner. The Chicago Thoracic Oncology Database Consortium (CTODC) was created to standardize data collection and facilitate the pooling and sharing of data at institutions throughout Chicago and across the world. We assessed the CTODC by conducting a proof of principle investigation on lung cancer patients who took erlotinib. This study does not look into epidermal growth factor receptor (EGFR) mutations and tyrosine kinase inhibitors, but rather it discusses the development and utilization of the database involved. Methods:  We have implemented the Thoracic Oncology Program Database Project (TOPDP) Microsoft Access, the Thoracic Oncology Research Program (TORP) Velos, and the TORP REDCap databases for translational research efforts. Standard operating procedures (SOPs) were created to document the construction and proper utilization of these databases. These SOPs have been made available freely to other institutions that have implemented their own databases patterned on these SOPs. Results: A cohort of 373 lung cancer patients who took erlotinib was identified. The EGFR mutation statuses of patients were analyzed. Out of the 70 patients that were tested, 55 had mutations while 15 did not. In terms of overall survival and duration of treatment, the cohort demonstrated that EGFR-mutated patients had a longer duration of erlotinib treatment and longer overall survival compared to their EGFR wild-type counterparts who received erlotinib. Discussion: The investigation successfully yielded data from all institutions of the CTODC. While the investigation identified challenges, such as the difficulty of data transfer and potential duplication of patient data, these issues can be resolved with greater cross-communication between institutions of the consortium. Conclusion: The investigation described herein demonstrates the successful data collection from multiple institutions in the context of a collaborative effort. The data presented here can be utilized as the basis for further collaborative efforts and/or development of larger and more streamlined databases within the consortium. PMID:27092293

Upgrade Summer Severe Weather Tool

NASA Technical Reports Server (NTRS)

Watson, Leela

2011-01-01

The goal of this task was to upgrade to the existing severe weather database by adding observations from the 2010 warm season, update the verification dataset with results from the 2010 warm season, use statistical logistic regression analysis on the database and develop a new forecast tool. The AMU analyzed 7 stability parameters that showed the possibility of providing guidance in forecasting severe weather, calculated verification statistics for the Total Threat Score (TTS), and calculated warm season verification statistics for the 2010 season. The AMU also performed statistical logistic regression analysis on the 22-year severe weather database. The results indicated that the logistic regression equation did not show an increase in skill over the previously developed TTS. The equation showed less accuracy than TTS at predicting severe weather, little ability to distinguish between severe and non-severe weather days, and worse standard categorical accuracy measures and skill scores over TTS.

Validity of peptic ulcer disease and upper gastrointestinal bleeding diagnoses in administrative databases: a systematic review protocol.

PubMed

Montedori, Alessandro; Abraha, Iosief; Chiatti, Carlos; Cozzolino, Francesco; Orso, Massimiliano; Luchetta, Maria Laura; Rimland, Joseph M; Ambrosio, Giuseppe

2016-09-15

Administrative healthcare databases are useful to investigate the epidemiology, health outcomes, quality indicators and healthcare utilisation concerning peptic ulcers and gastrointestinal bleeding, but the databases need to be validated in order to be a reliable source for research. The aim of this protocol is to perform the first systematic review of studies reporting the validation of International Classification of Diseases, 9th Revision and 10th version (ICD-9 and ICD-10) codes for peptic ulcer and upper gastrointestinal bleeding diagnoses. MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched, using appropriate search strategies. We will include validation studies that used administrative data to identify peptic ulcer disease and upper gastrointestinal bleeding diagnoses or studies that evaluated the validity of peptic ulcer and upper gastrointestinal bleeding codes in administrative data. The following inclusion criteria will be used: (a) the presence of a reference standard case definition for the diseases of interest; (b) the presence of at least one test measure (eg, sensitivity, etc) and (c) the use of an administrative database as a source of data. Pairs of reviewers will independently abstract data using standardised forms and will evaluate quality using the checklist of 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-Analysis Protocol (PRISMA-P) 2015 statement. Ethics approval is not required given that this is a protocol for a systematic review. We will submit results of this study to a peer-reviewed journal for publication. The results will serve as a guide for researchers validating administrative healthcare databases to determine appropriate case definitions for peptic ulcer disease and upper gastrointestinal bleeding, as well as to perform outcome research using administrative healthcare databases of these conditions. CRD42015029216. 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/

Nominal ISOMERs (Incorrect Spellings Of Medicines Eluding Researchers)—variants in the spellings of drug names in PubMed: a database review

PubMed Central

Aronson, Jeffrey K

2016-01-01

Objective To examine how misspellings of drug names could impede searches for published literature. Design Database review. Data source PubMed. Review methods The study included 30 drug names that are commonly misspelt on prescription charts in hospitals in Birmingham, UK (test set), and 30 control names randomly chosen from a hospital formulary (control set). The following definitions were used: standard names—the international non-proprietary names, variant names—deviations in spelling from standard names that are not themselves standard names in English language nomenclature, and hidden reference variants—variant spellings that identified publications in textword (tw) searches of PubMed or other databases, and which were not identified by textword searches for the standard names. Variant names were generated from standard names by applying letter substitutions, omissions, additions, transpositions, duplications, deduplications, and combinations of these. Searches were carried out in PubMed (30 June 2016) for “standard name[tw]” and “variant name[tw] NOT standard name[tw].” Results The 30 standard names of drugs in the test set gave 325 979 hits in total, and 160 hidden reference variants gave 3872 hits (1.17%). The standard names of the control set gave 470 064 hits, and 79 hidden reference variants gave 766 hits (0.16%). Letter substitutions (particularly i to y and vice versa) and omissions together accounted for 2924 (74%) of the variants. Amitriptyline (8530 hits) yielded 18 hidden reference variants (179 (2.1%) hits). Names ending in “in,” “ine,” or “micin” were commonly misspelt. Failing to search for hidden reference variants of “gentamicin,” “amitriptyline,” “mirtazapine,” and “trazodone” would miss at least 19 systematic reviews. A hidden reference variant related to Christmas, “No-el”, was rare; variants of “X-miss” were rarer. Conclusion When performing searches, researchers should include misspellings of drug names among their search terms. PMID:27974346

DSSTOX: NEW ON-LINE RESOURCE FOR PUBLISHING AND INTEGRATING STANDARDIZED STRUCTURE-INCLUSIVE TOXICITY DATABASES

EPA Science Inventory

DSSTox: New On-line Resource for Publishing Structure-Standardized Toxicity Databases

Ann M Richard1, Jamie Burch2, ClarLynda Williams3
1Nat. Health and Environ. Effects Res. Lb, US EP& Ret Triangle Park, NC 27711; 2EPA-NC
Central Univ Student COOP, US EPA, lies. Tri...

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

EPA Science Inventory

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

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

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.

Producing approximate answers to database queries

NASA Technical Reports Server (NTRS)

Vrbsky, Susan V.; Liu, Jane W. S.

1993-01-01

We have designed and implemented a query processor, called APPROXIMATE, that makes approximate answers available if part of the database is unavailable or if there is not enough time to produce an exact answer. The accuracy of the approximate answers produced improves monotonically with the amount of data retrieved to produce the result. The exact answer is produced if all of the needed data are available and query processing is allowed to continue until completion. The monotone query processing algorithm of APPROXIMATE works within the standard relational algebra framework and can be implemented on a relational database system with little change to the relational architecture. We describe here the approximation semantics of APPROXIMATE that serves as the basis for meaningful approximations of both set-valued and single-valued queries. We show how APPROXIMATE is implemented to make effective use of semantic information, provided by an object-oriented view of the database, and describe the additional overhead required by APPROXIMATE.

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.

Disbiome database: linking the microbiome to disease.

PubMed

Janssens, Yorick; Nielandt, Joachim; Bronselaer, Antoon; Debunne, Nathan; Verbeke, Frederick; Wynendaele, Evelien; Van Immerseel, Filip; Vandewynckel, Yves-Paul; De Tré, Guy; De Spiegeleer, Bart

2018-06-04

Recent research has provided fascinating indications and evidence that the host health is linked to its microbial inhabitants. Due to the development of high-throughput sequencing technologies, more and more data covering microbial composition changes in different disease types are emerging. However, this information is dispersed over a wide variety of medical and biomedical disciplines. Disbiome is a database which collects and presents published microbiota-disease information in a standardized way. The diseases are classified using the MedDRA classification system and the micro-organisms are linked to their NCBI and SILVA taxonomy. Finally, each study included in the Disbiome database is assessed for its reporting quality using a standardized questionnaire. Disbiome is the first database giving a clear, concise and up-to-date overview of microbial composition differences in diseases, together with the relevant information of the studies published. The strength of this database lies within the combination of the presence of references to other databases, which enables both specific and diverse search strategies within the Disbiome database, and the human annotation which ensures a simple and structured presentation of the available data.

Report on the Project for Establishment of the Standardized Korean Laboratory Terminology Database, 2015.

PubMed

Jung, Bo Kyeung; Kim, Jeeyong; Cho, Chi Hyun; Kim, Ju Yeon; Nam, Myung Hyun; Shin, Bong Kyung; Rho, Eun Youn; Kim, Sollip; Sung, Heungsup; Kim, Shinyoung; Ki, Chang Seok; Park, Min Jung; Lee, Kap No; Yoon, Soo Young

2017-04-01

The National Health Information Standards Committee was established in 2004 in Korea. The practical subcommittee for laboratory test terminology was placed in charge of standardizing laboratory medicine terminology in Korean. We aimed to establish a standardized Korean laboratory terminology database, Korea-Logical Observation Identifier Names and Codes (K-LOINC) based on former products sponsored by this committee. The primary product was revised based on the opinions of specialists. Next, we mapped the electronic data interchange (EDI) codes that were revised in 2014, to the corresponding K-LOINC. We established a database of synonyms, including the laboratory codes of three reference laboratories and four tertiary hospitals in Korea. Furthermore, we supplemented the clinical microbiology section of K-LOINC using an alternative mapping strategy. We investigated other systems that utilize laboratory codes in order to investigate the compatibility of K-LOINC with statistical standards for a number of tests. A total of 48,990 laboratory codes were adopted (21,539 new and 16,330 revised). All of the LOINC synonyms were translated into Korean, and 39,347 Korean synonyms were added. Moreover, 21,773 synonyms were added from reference laboratories and tertiary hospitals. Alternative strategies were established for mapping within the microbiology domain. When we applied these to a smaller hospital, the mapping rate was successfully increased. Finally, we confirmed K-LOINC compatibility with other statistical standards, including a newly proposed EDI code system. This project successfully established an up-to-date standardized Korean laboratory terminology database, as well as an updated EDI mapping to facilitate the introduction of standard terminology into institutions. © 2017 The Korean Academy of Medical Sciences.

Architecture Knowledge for Evaluating Scalable Databases

DTIC Science & Technology

2015-01-16

problems, arising from the proliferation of new data models and distributed technologies for building scalable, available data stores . Architects must...longer are relational databases the de facto standard for building data repositories. Highly distributed, scalable “ NoSQL ” databases [11] have emerged...This is especially challenging at the data storage layer. The multitude of competing NoSQL database technologies creates a complex and rapidly

The Forest Inventory and Analysis Database: Database description and users manual version 4.0 for Phase 2

Treesearch

Sharon W. Woudenberg; Barbara L. Conkling; Barbara M. O' Connell; Elizabeth B. LaPoint; Jeffery A. Turner; Karen L. Waddell

2010-01-01

This document is based on previous documentation of the nationally standardized Forest Inventory and Analysis database (Hansen and others 1992; Woudenberg and Farrenkopf 1995; Miles and others 2001). Documentation of the structure of the Forest Inventory and Analysis database (FIADB) for Phase 2 data, as well as codes and definitions, is provided. Examples for...

Inorganic Crystal Structure Database (ICSD)

National Institute of Standards and Technology Data Gateway

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

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR DATABASE TREE AND DATA SOURCES (UA-D-41.0)

EPA Science Inventory

The purpose of this SOP is to describe the database storage organization, and to describe the sources of data for each database used during the Arizona NHEXAS project and the Border study. Keywords: data; database; organization.

The U.S.-Mexico Border Program is sponsored by t...

Projections for fast protein structure retrieval

PubMed Central

Bhattacharya, Sourangshu; Bhattacharyya, Chiranjib; Chandra, Nagasuma R

2006-01-01

Background In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniques, for retrieving protein structures similar to a query structure from a large protein structure database. Each protein structure is specified by the 3D coordinates of residues of the protein. The algorithm is based on a novel characterization of the residues, called projections, leading to a similarity measure between the residues of the two proteins. This measure is exploited to efficiently compute the optimal equivalences. Results Experimental results show that, the current algorithm outperforms the state of the art on benchmark datasets in terms of speed without losing accuracy. Search results on SCOP 95% nonredundant database, for fold similarity with 5 proteins from different SCOP classes show that the current method performs competitively with the standard algorithm CE. The algorithm is also capable of detecting non-topological similarities between two proteins which is not possible with most of the state of the art tools like Dali. PMID:17254310

Development and Feasibility Testing of a Critical Care EEG Monitoring Database for Standardized Clinical Reporting and Multicenter Collaborative Research.

PubMed

Lee, Jong Woo; LaRoche, Suzette; Choi, Hyunmi; Rodriguez Ruiz, Andres A; Fertig, Evan; Politsky, Jeffrey M; Herman, Susan T; Loddenkemper, Tobias; Sansevere, Arnold J; Korb, Pearce J; Abend, Nicholas S; Goldstein, Joshua L; Sinha, Saurabh R; Dombrowski, Keith E; Ritzl, Eva K; Westover, Michael B; Gavvala, Jay R; Gerard, Elizabeth E; Schmitt, Sarah E; Szaflarski, Jerzy P; Ding, Kan; Haas, Kevin F; Buchsbaum, Richard; Hirsch, Lawrence J; Wusthoff, Courtney J; Hopp, Jennifer L; Hahn, Cecil D

2016-04-01

The rapid expansion of the use of continuous critical care electroencephalogram (cEEG) monitoring and resulting multicenter research studies through the Critical Care EEG Monitoring Research Consortium has created the need for a collaborative data sharing mechanism and repository. The authors describe the development of a research database incorporating the American Clinical Neurophysiology Society standardized terminology for critical care EEG monitoring. The database includes flexible report generation tools that allow for daily clinical use. Key clinical and research variables were incorporated into a Microsoft Access database. To assess its utility for multicenter research data collection, the authors performed a 21-center feasibility study in which each center entered data from 12 consecutive intensive care unit monitoring patients. To assess its utility as a clinical report generating tool, three large volume centers used it to generate daily clinical critical care EEG reports. A total of 280 subjects were enrolled in the multicenter feasibility study. The duration of recording (median, 25.5 hours) varied significantly between the centers. The incidence of seizure (17.6%), periodic/rhythmic discharges (35.7%), and interictal epileptiform discharges (11.8%) was similar to previous studies. The database was used as a clinical reporting tool by 3 centers that entered a total of 3,144 unique patients covering 6,665 recording days. The Critical Care EEG Monitoring Research Consortium database has been successfully developed and implemented with a dual role as a collaborative research platform and a clinical reporting tool. It is now available for public download to be used as a clinical data repository and report generating tool.

A taxonomy has been developed for outcomes in medical research to help improve knowledge discovery.

PubMed

Dodd, Susanna; Clarke, Mike; Becker, Lorne; Mavergames, Chris; Fish, Rebecca; Williamson, Paula R

2018-04-01

There is increasing recognition that insufficient attention has been paid to the choice of outcomes measured in clinical trials. The lack of a standardized outcome classification system results in inconsistencies due to ambiguity and variation in how outcomes are described across different studies. Being able to classify by outcome would increase efficiency in searching sources such as clinical trial registries, patient registries, the Cochrane Database of Systematic Reviews, and the Core Outcome Measures in Effectiveness Trials (COMET) database of core outcome sets (COS), thus aiding knowledge discovery. A literature review was carried out to determine existing outcome classification systems, none of which were sufficiently comprehensive or granular for classification of all potential outcomes from clinical trials. A new taxonomy for outcome classification was developed, and as proof of principle, outcomes extracted from all published COS in the COMET database, selected Cochrane reviews, and clinical trial registry entries were classified using this new system. Application of this new taxonomy to COS in the COMET database revealed that 274/299 (92%) COS include at least one physiological outcome, whereas only 177 (59%) include at least one measure of impact (global quality of life or some measure of functioning) and only 105 (35%) made reference to adverse events. This outcome taxonomy will be used to annotate outcomes included in COS within the COMET database and is currently being piloted for use in Cochrane Reviews within the Cochrane Linked Data Project. Wider implementation of this standard taxonomy in trial and systematic review databases and registries will further promote efficient searching, reporting, and classification of trial outcomes. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

A Practical Standardized Composite Nutrition Score Based on Lean Tissue Index: Application in Nutrition Screening and Prediction of Outcome in Hemodialysis Population.

PubMed

Chen, Huan-Sheng; Cheng, Chun-Ting; Hou, Chun-Cheng; Liou, Hung-Hsiang; Chang, Cheng-Tsung; Lin, Chun-Ju; Wu, Tsai-Kun; Chen, Chang-Hsu; Lim, Paik-Seong

2017-07-01

Rapid screening and monitoring of nutritional status is mandatory in hemodialysis population because of the increasingly encountered nutritional problems. Considering the limitations of previous composite nutrition scores applied in this population, we tried to develop a standardized composite nutrition score (SCNS) using low lean tissue index as a marker of protein wasting to facilitate clinical screening and monitoring and to predict outcome. This retrospective cohort used 2 databases of dialysis populations from Taiwan between 2011 and 2014. First database consisting of data from 629 maintenance hemodialysis patients was used to develop the SCNS and the second database containing data from 297 maintenance hemodialysis patients was used to validate this developed score. SCNS containing albumin, creatinine, potassium, and body mass index was developed from the first database using low lean tissue index as a marker of protein wasting. When applying this score in the original database, significantly higher risk of developing protein wasting was found for patients with lower SCNS (odds ratio 1.38 [middle tertile vs highest tertile, P < .0001] and 2.40 [lowest tertile vs middle tertile, P < .0001]). The risk of death was also shown to be higher for patients with lower SCNS (hazard ratio 4.45 [below median level vs above median level, P < .0001]). These results were validated in the second database. We developed an SCNS consisting of 4 easily available biochemical parameters. This kind of scoring system can be easily applied in different dialysis facilities for screening and monitoring of protein wasting. The wide application of body composition monitor in dialysis population will also facilitate the development of specific nutrition scoring model for individual facility. Copyright © 2017 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

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.

Truth in Reporting: How Data Capture Methods Obfuscate Actual Surgical Site Infection Rates within a Health Care Network System.

PubMed

Bordeianou, Liliana; Cauley, Christy E; Antonelli, Donna; Bird, Sarah; Rattner, David; Hutter, Matthew; Mahmood, Sadiqa; Schnipper, Deborah; Rubin, Marc; Bleday, Ronald; Kenney, Pardon; Berger, David

2017-01-01

Two systems measure surgical site infection rates following colorectal surgeries: the American College of Surgeons National Surgical Quality Improvement Program and the Centers for Disease Control and Prevention National Healthcare Safety Network. The Centers for Medicare & Medicaid Services pay-for-performance initiatives use National Healthcare Safety Network data for hospital comparisons. This study aimed to compare database concordance. This is a multi-institution cohort study of systemwide Colorectal Surgery Collaborative. The National Surgical Quality Improvement Program requires rigorous, standardized data capture techniques; National Healthcare Safety Network allows 5 data capture techniques. Standardized surgical site infection rates were compared between databases. The Cohen κ-coefficient was calculated. This study was conducted at Boston-area hospitals. National Healthcare Safety Network or National Surgical Quality Improvement Program patients undergoing colorectal surgery were included. Standardized surgical site infection rates were the primary outcomes of interest. Thirty-day surgical site infection rates of 3547 (National Surgical Quality Improvement Program) vs 5179 (National Healthcare Safety Network) colorectal procedures (2012-2014). Discrepancies appeared: National Surgical Quality Improvement Program database of hospital 1 (N = 1480 patients) routinely found surgical site infection rates of approximately 10%, routinely deemed rate "exemplary" or "as expected" (100%). National Healthcare Safety Network data from the same hospital and time period (N = 1881) revealed a similar overall surgical site infection rate (10%), but standardized rates were deemed "worse than national average" 80% of the time. Overall, hospitals using less rigorous capture methods had improved surgical site infection rates for National Healthcare Safety Network compared with standardized National Surgical Quality Improvement Program reports. The correlation coefficient between standardized infection rates was 0.03 (p = 0.88). During 25 site-time period observations, National Surgical Quality Improvement Program and National Healthcare Safety Network data matched for 52% of observations (13/25). κ = 0.10 (95% CI, -0.1366 to 0.3402; p = 0.403), indicating poor agreement. This study investigated hospitals located in the Northeastern United States only. Variation in Centers for Medicare & Medicaid Services-mandated National Healthcare Safety Network infection surveillance methodology leads to unreliable results, which is apparent when these results are compared with standardized data. High-quality data would improve care quality and compare outcomes among institutions.

Addressing information gaps in wild-caught foods in the US: Brook trout nutritional analysis for inclusion into the USDA national nutrient database for standard reference

USDA-ARS?s Scientific Manuscript database

Many species of wild game and fish that are legal to hunt or catch do not have nutrition information in the USDA National Nutrient Database for Standard Reference (SR). Among those species that lack nutrition information are brook trout. The research team worked with the Nutrient Data Laboratory wit...

User's guide to FBASE: Relational database software for managing R1/R4 (Northern/Intermountain Regions) fish habitat inventory data

Treesearch

Sherry P. Wollrab

1999-01-01

FBASE is a microcomputer relational database package that handles data collected using the R1/R4 Fish and Fish Habitat Standard Inventory Procedures (Overton and others 1997). FBASE contains standard data entry screens, data validations for quality control, data maintenance features, and summary report options. This program also prepares data for importation into an...

Profiling Chemicals Based on Chronic Toxicity Results from the U.S. EPA ToxRef Database

EPA Science Inventory

Thirty years of pesticide registration toxicity data have been historically stored as hardcopy and scanned documents by the U.S. Environmental Protection Agency (EPA) . A significant portion of these data have now been processed into standardized and structured toxicity data with...

Applying transpose matrix on advanced encryption standard (AES) for database content

NASA Astrophysics Data System (ADS)

Manurung, E. B. P.; Sitompul, O. S.; Suherman

2018-03-01

Advanced Encryption Standard (AES) is a specification for the encryption of electronic data established by the U.S. National Institute of Standards and Technology (NIST) and has been adopted by the U.S. government and is now used worldwide. This paper reports the impact of transpose matrix integration to AES. Transpose matrix implementation on AES is aimed at first stage of chypertext modifications for text based database security so that the confidentiality improves. The matrix is also able to increase the avalanche effect of the cryptography algorithm 4% in average.

Compliance with minimum information guidelines in public metabolomics repositories

PubMed Central

Spicer, Rachel A.; Salek, Reza; Steinbeck, Christoph

2017-01-01

The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards. PMID:28949328

Compliance with minimum information guidelines in public metabolomics repositories.

PubMed

Spicer, Rachel A; Salek, Reza; Steinbeck, Christoph

2017-09-26

The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards.

Impact of database quality in knowledge-based treatment planning for prostate cancer.

PubMed

Wall, Phillip D H; Carver, Robert L; Fontenot, Jonas D

2018-03-13

This article investigates dose-volume prediction improvements in a common knowledge-based planning (KBP) method using a Pareto plan database compared with using a conventional, clinical plan database. Two plan databases were created using retrospective, anonymized data of 124 volumetric modulated arc therapy (VMAT) prostate cancer patients. The clinical plan database (CPD) contained planning data from each patient's clinically treated VMAT plan, which were manually optimized by various planners. The multicriteria optimization database (MCOD) contained Pareto-optimal plan data from VMAT plans created using a standardized multicriteria optimization protocol. Overlap volume histograms, incorporating fractional organ at risk volumes only within the treatment fields, were computed for each patient and used to match new patient anatomy to similar database patients. For each database patient, CPD and MCOD KBP predictions were generated for D 10 , D 30 , D 50 , D 65 , and D 80 of the bladder and rectum in a leave-one-out manner. Prediction achievability was evaluated through a replanning study on a subset of 31 randomly selected database patients using the best KBP predictions, regardless of plan database origin, as planning goals. MCOD predictions were significantly lower than CPD predictions for all 5 bladder dose-volumes and rectum D 50 (P = .004) and D 65 (P < .001), whereas CPD predictions for rectum D 10 (P = .005) and D 30 (P < .001) were significantly less than MCOD predictions. KBP predictions were statistically achievable in the replans for all predicted dose-volumes, excluding D 10 of bladder (P = .03) and rectum (P = .04). Compared with clinical plans, replans showed significant average reductions in D mean for bladder (7.8 Gy; P < .001) and rectum (9.4 Gy; P < .001), while maintaining statistically similar planning target volume, femoral head, and penile bulb dose. KBP dose-volume predictions derived from Pareto plans were more optimal overall than those resulting from manually optimized clinical plans, which significantly improved KBP-assisted plan quality. This work investigates how the plan quality of knowledge databases affects the performance and achievability of dose-volume predictions from a common knowledge-based planning approach for prostate cancer. Bladder and rectum dose-volume predictions derived from a database of standardized Pareto-optimal plans were compared with those derived from clinical plans manually designed by various planners. Dose-volume predictions from the Pareto plan database were significantly lower overall than those from the clinical plan database, without compromising achievability. Copyright © 2018 Elsevier Inc. All rights reserved.

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…

Integrating Borrowed Records into a Database: Impact on Thesaurus Development and Retrieval.

ERIC Educational Resources Information Center

And Others; Kirtland, Monika

1980-01-01

Discusses three approaches to thesaurus and indexing/retrieval language maintenance for combined databases: reindexing, merging, and initial standardization. Two thesauri for a combined database are evaluated in terms of their compatibility, and indexing practices are compared. Tables and figures help illustrate aspects of the comparison. (SW)

DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES

EPA Science Inventory

The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

75 FR 49869 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-16

... Boating Accident Report Database AGENCY: Coast Guard, DHS. ACTION: Reopening of public comment period... Boating Accident Report Database. DATES: Comments and related material must either be submitted to our... Database that, collectively, are intended to improve recreational boating safety efforts, enhance law...

The Global Genome Biodiversity Network (GGBN) Data Standard specification.

PubMed

Droege, G; Barker, K; Seberg, O; Coddington, J; Benson, E; Berendsohn, W G; Bunk, B; Butler, C; Cawsey, E M; Deck, J; Döring, M; Flemons, P; Gemeinholzer, B; Güntsch, A; Hollowell, T; Kelbert, P; Kostadinov, I; Kottmann, R; Lawlor, R T; Lyal, C; Mackenzie-Dodds, J; Meyer, C; Mulcahy, D; Nussbeck, S Y; O'Tuama, É; Orrell, T; Petersen, G; Robertson, T; Söhngen, C; Whitacre, J; Wieczorek, J; Yilmaz, P; Zetzsche, H; Zhang, Y; Zhou, X

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard. © The Author(s) 2016. Published by Oxford University Press.

Results from a new die-to-database reticle inspection platform

NASA Astrophysics Data System (ADS)

Broadbent, William; Xiong, Yalin; Giusti, Michael; Walsh, Robert; Dayal, Aditya

2007-03-01

A new die-to-database high-resolution reticle defect inspection system has been developed for the 45nm logic node and extendable to the 32nm node (also the comparable memory nodes). These nodes will use predominantly 193nm immersion lithography although EUV may also be used. According to recent surveys, the predominant reticle types for the 45nm node are 6% simple tri-tone and COG. Other advanced reticle types may also be used for these nodes including: dark field alternating, Mask Enhancer, complex tri-tone, high transmission, CPL, EUV, etc. Finally, aggressive model based OPC will typically be used which will include many small structures such as jogs, serifs, and SRAF (sub-resolution assist features) with accompanying very small gaps between adjacent structures. The current generation of inspection systems is inadequate to meet these requirements. The architecture and performance of a new die-to-database inspection system is described. This new system is designed to inspect the aforementioned reticle types in die-to-database and die-to-die modes. Recent results from internal testing of the prototype systems are shown. The results include standard programmed defect test reticles and advanced 45nm and 32nm node reticles from industry sources. The results show high sensitivity and low false detections being achieved.

Development of a North American paleoclimate pollen-based reconstruction database application

NASA Astrophysics Data System (ADS)

Ladd, Matthew; Mosher, Steven; Viau, Andre

2013-04-01

Recent efforts in synthesizing paleoclimate records across the globe has warranted an effort to standardize the different paleoclimate archives currently available in order to facilitate data-model comparisons and hence improve our estimates of future climate change. It is often the case that the methodology and programs make it challenging for other researchers to reproduce the results for a reconstruction, therefore there is a need for to standardize paleoclimate reconstruction databases in an application specific to proxy data. Here we present a methodology using the open source R language using North American pollen databases (e.g. NAPD, NEOTOMA) where this application can easily be used to perform new reconstructions and quickly analyze and output/plot the data. The application was developed to easily test methodological and spatial/temporal issues that might affect the reconstruction results. The application allows users to spend more time analyzing and interpreting results instead of on data management and processing. Some of the unique features of this R program are the two modules each with a menu making the user feel at ease with the program, the ability to use different pollen sums, select one of 70 climate variables available, substitute an appropriate modern climate dataset, a user-friendly regional target domain, temporal resolution criteria, linear interpolation and many other features for a thorough exploratory data analysis. The application program will be available for North American pollen-based reconstructions and eventually be made available as a package through the CRAN repository by late 2013.

Large Scale Landslide Database System Established for the Reservoirs in Southern Taiwan

NASA Astrophysics Data System (ADS)

Tsai, Tsai-Tsung; Tsai, Kuang-Jung; Shieh, Chjeng-Lun

2017-04-01

Typhoon Morakot seriously attack southern Taiwan awaken the public awareness of large scale landslide disasters. Large scale landslide disasters produce large quantity of sediment due to negative effects on the operating functions of reservoirs. In order to reduce the risk of these disasters within the study area, the establishment of a database for hazard mitigation / disaster prevention is necessary. Real time data and numerous archives of engineering data, environment information, photo, and video, will not only help people make appropriate decisions, but also bring the biggest concern for people to process and value added. The study tried to define some basic data formats / standards from collected various types of data about these reservoirs and then provide a management platform based on these formats / standards. Meanwhile, in order to satisfy the practicality and convenience, the large scale landslide disasters database system is built both provide and receive information abilities, which user can use this large scale landslide disasters database system on different type of devices. IT technology progressed extreme quick, the most modern system might be out of date anytime. In order to provide long term service, the system reserved the possibility of user define data format /standard and user define system structure. The system established by this study was based on HTML5 standard language, and use the responsive web design technology. This will make user can easily handle and develop this large scale landslide disasters database system.

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.

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

Sodium Content of Foods Contributing to Sodium Intake: Comparison between Selected Foods from the CDC Packaged Food Database and the USDA National Nutrient Database for Standard Reference

PubMed Central

Maalouf, Joyce; Cogswell, Mary E.; Yuan, Keming; Martin, Carrie; Gillespie, Cathleen; Ahuja, Jaspreet KC; Pehrsson, Pamela; Merritt, Robert

2015-01-01

The sodium concentration (mg/100g) for 23 of 125 Sentinel Foods (e.g. white bread) were identified in the 2009 CDC Packaged Food Database (PFD) and compared with data in the USDA’s 2013 National Nutrient Database for Standard Reference(SR 26). Sentinel Foods are foods identified by USDA to be monitored as primary indicators to assess the changes in the sodium content of commercially processed foods from stores and restaurants. Overall, 937 products were evaluated in the CDC PFD, and between 3 (one brand of ready-to-eat cereal) and 126 products (white bread) were evaluated per selected food. The mean sodium concentrations of 17 of the 23 (74%) selected foods in the CDC PFD were 90%–110% of the mean sodium concentrations in SR 26 and differences in sodium concentration were statistically significant for 6 Sentinel Foods. The sodium concentration of most of the Sentinel Foods, as selected in the PFD, appeared to represent the sodium concentrations of the corresponding food category. The results of our study help improve the understanding of how nutrition information compares between national analytic values and the label and whether the selected Sentinel Foods represent their corresponding food category as indicators for assessment of change of the sodium content in the food supply. PMID:26484010

The Development of a Korean Drug Dosing Database

PubMed Central

Kim, Sun Ah; Kim, Jung Hoon; Jang, Yoo Jin; Jeon, Man Ho; Hwang, Joong Un; Jeong, Young Mi; Choi, Kyung Suk; Lee, Iyn Hyang; Jeon, Jin Ok; Lee, Eun Sook; Lee, Eun Kyung; Kim, Hong Bin; Chin, Ho Jun; Ha, Ji Hye; Kim, Young Hoon

2011-01-01

Objectives This report describes the development process of a drug dosing database for ethical drugs approved by the Korea Food & Drug Administration (KFDA). The goal of this study was to develop a computerized system that supports physicians' prescribing decisions, particularly in regards to medication dosing. Methods The advisory committee, comprised of doctors, pharmacists, and nurses from the Seoul National University Bundang Hospital, pharmacists familiar with drug databases, KFDA officials, and software developers from the BIT Computer Co. Ltd. analyzed approved KFDA drug dosing information, defined the fields and properties of the information structure, and designed a management program used to enter dosing information. The management program was developed using a web based system that allows multiple researchers to input drug dosing information in an organized manner. The whole process was improved by adding additional input fields and eliminating the unnecessary existing fields used when the dosing information was entered, resulting in an improved field structure. Results A total of 16,994 drugs sold in the Korean market in July 2009, excluding the exclusion criteria (e.g., radioactivity drugs, X-ray contrast medium), usage and dosing information were made into a database. Conclusions The drug dosing database was successfully developed and the dosing information for new drugs can be continually maintained through the management mode. This database will be used to develop the drug utilization review standards and to provide appropriate dosing information. PMID:22259729

Functional integration of automated system databases by means of artificial intelligence

NASA Astrophysics Data System (ADS)

Dubovoi, Volodymyr M.; Nikitenko, Olena D.; Kalimoldayev, Maksat; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

2017-08-01

The paper presents approaches for functional integration of automated system databases by means of artificial intelligence. The peculiarities of turning to account the database in the systems with the usage of a fuzzy implementation of functions were analyzed. Requirements for the normalization of such databases were defined. The question of data equivalence in conditions of uncertainty and collisions in the presence of the databases functional integration is considered and the model to reveal their possible occurrence is devised. The paper also presents evaluation method of standardization of integrated database normalization.

Space debris mitigation - engineering strategies

NASA Astrophysics Data System (ADS)

Taylor, E.; Hammond, M.

The problem of space debris pollution is acknowledged to be of growing concern by space agencies, leading to recent activities in the field of space debris mitigation. A review of the current (and near-future) mitigation guidelines, handbooks, standards and licensing procedures has identified a number of areas where further work is required. In order for space debris mitigation to be implemented in spacecraft manufacture and operation, the authors suggest that debris-related criteria need to become design parameters (following the same process as applied to reliability and radiation). To meet these parameters, spacecraft manufacturers and operators will need processes (supported by design tools and databases and implementation standards). A particular aspect of debris mitigation, as compared with conventional requirements (e.g. radiation and reliability) is the current and near-future national and international regulatory framework and associated liability aspects. A framework for these implementation standards is presented, in addition to results of in-house research and development on design tools and databases (including collision avoidance in GTO and SSTO and evaluation of failure criteria on composite and aluminium structures).

Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding.

PubMed

Normand, A C; Packeu, A; Cassagne, C; Hendrickx, M; Ranque, S; Piarroux, R

2018-05-01

Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton , mainly T. rubrum complex ( n = 184), T. interdigitale ( n = 40), T. tonsurans ( n = 26), and T. benhamiae ( n = 5). Other genera included Microsporum (e.g., M. canis [ n = 21], M. audouinii [ n = 10], Nannizzia gypsea [ n = 3], and Epidermophyton [ n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified. Copyright © 2018 American Society for Microbiology.

Why are we prolonging QT interval monitoring?

PubMed

Barrett, Trina

2015-01-01

At present, monitoring of the QT interval (QTI) is not a standard practice in the medical intensive care unit setting, where many drugs that prolong the QTI are administered. This literature review looked at the current research for evidence-based standards to support QTI monitoring of patients with risk factors for QTI prolongation, which can result in life-threatening arrhythmias such as torsade de pointes. The objective of this article is to establish the existence of evidence-based standards for monitoring of the QTI and to raise awareness in the nursing profession of the need for such monitoring among patients who are at high risk for prolonged QTI. To determine whether published standards for QTI monitoring exist, a search was conducted of the bibliographic databases CINAHL, EBSCOhost, Medline, PubMed, Google Scholar, and the Cochrane Library for the years 2013 and 2014. Also, a survey was conducted to determine whether practice standards for QTI monitoring are being implemented at 4 major hospitals in the Memphis area, including a level 1 trauma center. The database search established the existence of published guidelines that support the need for QTI monitoring. Results of the hospital survey indicated that direct care nurses were not aware of the need to identify high-risk patients, drugs with the potential to prolong QTI that were being administered to their patients, or evidence-based standards for QTI monitoring. Review of the research literature underscored the need for QTI monitoring among high-risk patients, that is, those with genetic conditions that predispose them to QTI prolongation, those with existing cardiac conditions being treated with antiarrhythmic medications, or those who are prescribed any new medication classified as high risk on the basis of clinical research. This need is especially crucial in intensive care unit settings, where many antiarrhythmic medications are administered.

Peptide reranking with protein-peptide correspondence and precursor peak intensity information.

PubMed

Yang, Chao; He, Zengyou; Yang, Can; Yu, Weichuan

2012-01-01

Searching tandem mass spectra against a protein database has been a mainstream method for peptide identification. Improving peptide identification results by ranking true Peptide-Spectrum Matches (PSMs) over their false counterparts leads to the development of various reranking algorithms. In peptide reranking, discriminative information is essential to distinguish true PSMs from false PSMs. Generally, most peptide reranking methods obtain discriminative information directly from database search scores or by training machine learning models. Information in the protein database and MS1 spectra (i.e., single stage MS spectra) is ignored. In this paper, we propose to use information in the protein database and MS1 spectra to rerank peptide identification results. To quantitatively analyze their effects to peptide reranking results, three peptide reranking methods are proposed: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information. According to our experiments on a standard protein mixture data set, a human data set and a mouse data set, PPMRanker and MIRanker achieve better peptide reranking results than PetideProphet, PeptideProphet+NSP (number of sibling peptides) and a score regularization method SRPI. The source codes of PPMRanker, PPIRanker, and MIRanker, and all supplementary documents are available at our website: http://bioinformatics.ust.hk/pepreranking/. Alternatively, these documents can also be downloaded from: http://sourceforge.net/projects/pepreranking/.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

PubMed Central

2010-01-01

Background Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft® Excel® spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data. PMID:20591175

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

Variability in Standard Outcomes of Posterior Lumbar Fusion Determined by National Databases.

PubMed

Joseph, Jacob R; Smith, Brandon W; Park, Paul

2017-01-01

National databases are used with increasing frequency in spine surgery literature to evaluate patient outcomes. The differences between individual databases in relationship to outcomes of lumbar fusion are not known. We evaluated the variability in standard outcomes of posterior lumbar fusion between the University HealthSystem Consortium (UHC) database and the Healthcare Cost and Utilization Project National Inpatient Sample (NIS). NIS and UHC databases were queried for all posterior lumbar fusions (International Classification of Diseases, Ninth Revision code 81.07) performed in 2012. Patient demographics, comorbidities (including obesity), length of stay (LOS), in-hospital mortality, and complications such as urinary tract infection, deep venous thrombosis, pulmonary embolism, myocardial infarction, durotomy, and surgical site infection were collected using specific International Classification of Diseases, Ninth Revision codes. Analysis included 21,470 patients from the NIS database and 14,898 patients from the UHC database. Demographic data were not significantly different between databases. Obesity was more prevalent in UHC (P = 0.001). Mean LOS was 3.8 days in NIS and 4.55 in UHC (P < 0.0001). Complications were significantly higher in UHC, including urinary tract infection, deep venous thrombosis, pulmonary embolism, myocardial infarction, surgical site infection, and durotomy. In-hospital mortality was similar between databases. NIS and UHC databases had similar demographic patient populations undergoing posterior lumbar fusion. However, the UHC database reported significantly higher complication rate and longer LOS. This difference may reflect academic institutions treating higher-risk patients; however, a definitive reason for the variability between databases is unknown. The inability to precisely determine the basis of the variability between databases highlights the limitations of using administrative databases for spinal outcome analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Cold Climate Foundation Retrofit Experimental Hygrothermal Performance: Cloquet Residential Research Facility Laboratory Results

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

Goldberg, Louise F.; Harmon, Anna C.

2015-04-01

Thermal and moisture problems in existing basements create a unique challenge because the exterior face of the wall is not easily or inexpensively accessible. This approach addresses thermal and moisture management from the interior face of the wall without disturbing the exterior soil and landscaping. the interior and exterior environments. This approach has the potential for improving durability, comfort, and indoor air quality. This project was funded jointly by the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL). ORNL focused on developing a full basement wall system experimental database to enable others to validate hygrothermal simulation codes.more » NREL focused on testing the moisture durability of practical basement wall interior insulation retrofit solutions for cold climates. The project has produced a physically credible and reliable long-term hygrothermal performance database for retrofit foundation wall insulation systems in zone 6 and 7 climates that are fully compliant with the performance criteria in the 2009 Minnesota Energy Code. The experimental data were configured into a standard format that can be published online and that is compatible with standard commercially available spreadsheet and database software.« less

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

PubMed Central

2012-01-01

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

[A basic research to share Fourier transform near-infrared spectrum information resource].

PubMed

Zhang, Lu-Da; Li, Jun-Hui; Zhao, Long-Lian; Zhao, Li-Li; Qin, Fang-Li; Yan, Yan-Lu

2004-08-01

A method to share the information resource in the database of Fourier transform near-infrared(FTNIR) spectrum information of agricultural products and utilize the spectrum information sufficiently is explored in this paper. Mapping spectrum information from one instrument to another is studied to express the spectrum information accurately between the instruments. Then mapping spectrum information is used to establish a mathematical model of quantitative analysis without including standard samples. The analysis result is that the relative coefficient r is 0.941 and the relative error is 3.28% between the model estimate values and the Kjeldahl's value for the protein content of twenty-two wheat samples, while the relative coefficient r is 0.963 and the relative error is 2.4% for the other model, which is established by using standard samples. It is shown that the spectrum information can be shared by using the mapping spectrum information. So it can be concluded that the spectrum information in one FTNIR spectrum information database can be transformed to another instrument's mapping spectrum information, which makes full use of the information resource in the database of FTNIR spectrum information to realize the resource sharing between different instruments.

Sequence tagging reveals unexpected modifications in toxicoproteomics

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

2010-01-01

Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

Web application and database modeling of traffic impact analysis using Google Maps

NASA Astrophysics Data System (ADS)

Yulianto, Budi; Setiono

2017-06-01

Traffic impact analysis (TIA) is a traffic study that aims at identifying the impact of traffic generated by development or change in land use. In addition to identifying the traffic impact, TIA is also equipped with mitigation measurement to minimize the arising traffic impact. TIA has been increasingly important since it was defined in the act as one of the requirements in the proposal of Building Permit. The act encourages a number of TIA studies in various cities in Indonesia, including Surakarta. For that reason, it is necessary to study the development of TIA by adopting the concept Transportation Impact Control (TIC) in the implementation of the TIA standard document and multimodal modeling. It includes TIA's standardization for technical guidelines, database and inspection by providing TIA checklists, monitoring and evaluation. The research was undertaken by collecting the historical data of junctions, modeling of the data in the form of relational database, building a user interface for CRUD (Create, Read, Update and Delete) the TIA data in the form of web programming with Google Maps libraries. The result research is a system that provides information that helps the improvement and repairment of TIA documents that exist today which is more transparent, reliable and credible.

WE-D-9A-06: Open Source Monitor Calibration and Quality Control Software for Enterprise Display Management

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

Bevins, N; Vanderhoek, M; Lang, S

2014-06-15

Purpose: Medical display monitor calibration and quality control present challenges to medical physicists. The purpose of this work is to demonstrate and share experiences with an open source package that allows for both initial monitor setup and routine performance evaluation. Methods: A software package, pacsDisplay, has been developed over the last decade to aid in the calibration of all monitors within the radiology group in our health system. The software is used to calibrate monitors to follow the DICOM Grayscale Standard Display Function (GSDF) via lookup tables installed on the workstation. Additional functionality facilitates periodic evaluations of both primary andmore » secondary medical monitors to ensure satisfactory performance. This software is installed on all radiology workstations, and can also be run as a stand-alone tool from a USB disk. Recently, a database has been developed to store and centralize the monitor performance data and to provide long-term trends for compliance with internal standards and various accrediting organizations. Results: Implementation and utilization of pacsDisplay has resulted in improved monitor performance across the health system. Monitor testing is now performed at regular intervals and the software is being used across multiple imaging modalities. Monitor performance characteristics such as maximum and minimum luminance, ambient luminance and illuminance, color tracking, and GSDF conformity are loaded into a centralized database for system performance comparisons. Compliance reports for organizations such as MQSA, ACR, and TJC are generated automatically and stored in the same database. Conclusion: An open source software solution has simplified and improved the standardization of displays within our health system. This work serves as an example method for calibrating and testing monitors within an enterprise health system.« less

Database for Safety-Oriented Tracking of Chemicals

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

[Trauma and accident documentation in Germany compared with elsewhere in Europe].

PubMed

Probst, C; Richter, M; Haasper, C; Lefering, R; Otte, D; Oestern, H J; Krettek, C; Hüfner, T

2008-07-01

The role of trauma documentation has grown continuously since the 1970s. Prevention and management of injuries were adapted according to the results of many analyses. Since 1993 there have been two different trauma databases in Germany: the German trauma registry (TR) and the database of the Accident Research Unit (UFO). Modern computer applications improved the data processing. Our study analysed the pros and cons of each system and compared them with those of our European neighbours. We compared the TR and the UFO databases with respect to aims and goals, advantages and disadvantages, and current status. Results were reported as means +/- standard errors of the mean. The level of significance was set at P<0.05. There were differences between the two databases concerning number and types of items, aims and goals, and demographics. The TR documents care for severely injured patients and the clinical course of different types of accidents. The UFO describes traffic accidents, accident conditions, and interrelations. The German and British systems are similar, and the French system shows interesting differences. The German trauma documentation systems focus on different points. Therefore both can be used for substantiated analyses of different hypotheses. Certain intersections of both databases may help to answer very special questions in the future.

Quality standards for real-world research. Focus on observational database studies of comparative effectiveness.

PubMed

Roche, Nicolas; Reddel, Helen; Martin, Richard; Brusselle, Guy; Papi, Alberto; Thomas, Mike; Postma, Dirjke; Thomas, Vicky; Rand, Cynthia; Chisholm, Alison; Price, David

2014-02-01

Real-world research can use observational or clinical trial designs, in both cases putting emphasis on high external validity, to complement the classical efficacy randomized controlled trials (RCTs) with high internal validity. Real-world research is made necessary by the variety of factors that can play an important a role in modulating effectiveness in real life but are often tightly controlled in RCTs, such as comorbidities and concomitant treatments, adherence, inhalation technique, access to care, strength of doctor-caregiver communication, and socio-economic and other organizational factors. Real-world studies belong to two main categories: pragmatic trials and observational studies, which can be prospective or retrospective. Focusing on comparative database observational studies, the process aimed at ensuring high-quality research can be divided into three parts: preparation of research, analyses and reporting, and discussion of results. Key points include a priori planning of data collection and analyses, identification of appropriate database(s), proper outcomes definition, study registration with commitment to publish, bias minimization through matching and adjustment processes accounting for potential confounders, and sensitivity analyses testing the robustness of results. When these conditions are met, observational database studies can reach a sufficient level of evidence to help create guidelines (i.e., clinical and regulatory decision-making).

Standardizing terminology and definitions of medication adherence and persistence in research employing electronic databases.

PubMed

Raebel, Marsha A; Schmittdiel, Julie; Karter, Andrew J; Konieczny, Jennifer L; Steiner, John F

2013-08-01

To propose a unifying set of definitions for prescription adherence research utilizing electronic health record prescribing databases, prescription dispensing databases, and pharmacy claims databases and to provide a conceptual framework to operationalize these definitions consistently across studies. We reviewed recent literature to identify definitions in electronic database studies of prescription-filling patterns for chronic oral medications. We then develop a conceptual model and propose standardized terminology and definitions to describe prescription-filling behavior from electronic databases. The conceptual model we propose defines 2 separate constructs: medication adherence and persistence. We define primary and secondary adherence as distinct subtypes of adherence. Metrics for estimating secondary adherence are discussed and critiqued, including a newer metric (New Prescription Medication Gap measure) that enables estimation of both primary and secondary adherence. Terminology currently used in prescription adherence research employing electronic databases lacks consistency. We propose a clear, consistent, broadly applicable conceptual model and terminology for such studies. The model and definitions facilitate research utilizing electronic medication prescribing, dispensing, and/or claims databases and encompasses the entire continuum of prescription-filling behavior. Employing conceptually clear and consistent terminology to define medication adherence and persistence will facilitate future comparative effectiveness research and meta-analytic studies that utilize electronic prescription and dispensing records.

Re-thinking organisms: The impact of databases on model organism biology.

PubMed

Leonelli, Sabina; Ankeny, Rachel A

2012-03-01

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. Copyright © 2011 Elsevier Ltd. All rights reserved.

An Experimental Investigation of Complexity in Database Query Formulation Tasks

ERIC Educational Resources Information Center

Casterella, Gretchen Irwin; Vijayasarathy, Leo

2013-01-01

Information Technology professionals and other knowledge workers rely on their ability to extract data from organizational databases to respond to business questions and support decision making. Structured query language (SQL) is the standard programming language for querying data in relational databases, and SQL skills are in high demand and are…

Nuclear data made easily accessible through the Notre Dame Nuclear Database

NASA Astrophysics Data System (ADS)

Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

GANESH: software for customized annotation of genome regions.

PubMed

Huntley, Derek; Hummerich, Holger; Smedley, Damian; Kittivoravitkul, Sasivimol; McCarthy, Mark; Little, Peter; Sergot, Marek

2003-09-01

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2

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

Wolery, Thomas J.; Jove Colon, Carlos F.

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data.more » Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2, water, and aqueous species such as Na + and Cl -. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.« less

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data

NASA Astrophysics Data System (ADS)

Wolery, Thomas J.; Jové Colón, Carlos F.

2017-09-01

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data. Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO2, water, and aqueous species such as Na+ and Cl-. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15 K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of "links" to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare "key" or "reference" datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2

DOE PAGES

Wolery, Thomas J.; Jove Colon, Carlos F.

2016-09-26

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data.more » Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2, water, and aqueous species such as Na + and Cl -. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.« less

New Data Bases and Standards for Gravity Anomalies

NASA Astrophysics Data System (ADS)

Keller, G. R.; Hildenbrand, T. G.; Webring, M. W.; Hinze, W. J.; Ravat, D.; Li, X.

2008-12-01

Ever since the use of high-precision gravimeters emerged in the 1950's, gravity surveys have been an important tool for geologic studies. Recent developments that make geologically useful measurements from airborne and satellite platforms, the ready availability of the Global Positioning System that provides precise vertical and horizontal control, improved global data bases, and the increased availability of processing and modeling software have accelerated the use of the gravity method. As a result, efforts are being made to improve the gravity databases publicly available to the geoscience community by expanding their holdings and increasing the accuracy and precision of the data in them. Specifically the North American Gravity Database as well as the individual databases of Canada, Mexico, and the United States are being revised using new formats and standards to improve their coverage, standardization, and accuracy. An important part of this effort is revision of procedures and standards for calculating gravity anomalies taking into account the enhanced computational power available, modern satellite-based positioning technology, improved terrain databases, and increased interest in more accurately defining the different components of gravity anomalies. The most striking revision is the use of one single internationally accepted reference ellipsoid for the horizontal and vertical datums of gravity stations as well as for the computation of the calculated value of theoretical gravity. The new standards hardly impact the interpretation of local anomalies, but do improve regional anomalies in that long wavelength artifacts are removed. Most importantly, such new standards can be consistently applied to gravity database compilations of nations, continents, and even the entire world. Although many types of gravity anomalies have been described, they fall into three main classes. The primary class incorporates planetary effects, which are analytically prescribed, to derive the predicted or modeled gravity, and thus, anomalies of this class are termed planetary. The most primitive version of a gravity anomaly is simply the difference between the value of gravity predicted by the effect of the reference ellipsoid and the observed gravity anomaly. When the height of the gravity station increases, the ellipsoidal gravity anomaly decreases because of the increased distance of measurement from the anomaly- producing masses. The two primary anomalies in geophysics, which are appropriately classified as planetary anomalies, are the Free-air and Bouguer gravity anomalies. They employ models that account for planetary effects on gravity including the topography of the earth. A second class of anomaly, geological anomalies, includes the modeled gravity effect of known or assumed masses leading to the predicted gravity by using geological data such as densities and crustal thickness. The third class of anomaly, filtered anomalies, removes arbitrary gravity effects of largely unknown sources that are empirically or analytically determined from the nature of the gravity anomalies by filtering.

Second chronological supplement to the Carcinogenic Potency Database: standardized results of animal bioassays published through December 1984 and by the National Toxicology Program through May 1986.

PubMed Central

Gold, L S; Slone, T H; Backman, G M; Magaw, R; Da Costa, M; Lopipero, P; Blumenthal, M; Ames, B N

1987-01-01

This paper is the second chronological supplement to the Carcinogenic Potency Database, published earlier in this journal (1,2,4). We report here results of carcinogenesis bioassays published in the general literature between January 1983 and December 1984, and in Technical Reports of the National Cancer Institute/National Toxicology Program between January 1983 and May 1986. This supplement includes results of 525 long-term, chronic experiments of 199 test compounds, and reports the same information about each experiment in the same plot format as the earlier papers: e.g., the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications for a description of the numerical index of carcinogenic potency (TD50), a guide to the plot of the database, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The three plots of the database are to be used together, since results of experiments published in earlier plots are not repeated. Taken together, the three plots include results for more than 3500 experiments on 975 chemicals. Appendix 14 is an index to all chemicals in the database and indicates which plot(s) each chemical appears in. PMID:3691431

Expert searching in public health

PubMed Central

Alpi, Kristine M.

2005-01-01

Objective: The article explores the characteristics of public health information needs and the resources available to address those needs that distinguish it as an area of searching requiring particular expertise. Methods: Public health searching activities from reference questions and literature search requests at a large, urban health department library were reviewed to identify the challenges in finding relevant public health information. Results: The terminology of the information request frequently differed from the vocabularies available in the databases. Searches required the use of multiple databases and/or Web resources with diverse interfaces. Issues of the scope and features of the databases relevant to the search questions were considered. Conclusion: Expert searching in public health differs from other types of expert searching in the subject breadth and technical demands of the databases to be searched, the fluidity and lack of standardization of the vocabulary, and the relative scarcity of high-quality investigations at the appropriate level of geographic specificity. Health sciences librarians require a broad exposure to databases, gray literature, and public health terminology to perform as expert searchers in public health. PMID:15685281

Metrics and Science Monograph Collections at the Marston Science Library, University of Florida

ERIC Educational Resources Information Center

Leonard, Michelle F.; Haas, Stephanie C.; Kisling, Vernon N.

2010-01-01

As academic libraries are increasingly supported by a matrix of database functions, the use of data mining and visualization techniques offer significant potential for future collection development and service initiatives based on quantifiable data. While data collection techniques are still not standardized and results may be skewed because of…

Proposal for Standardized Tabular Reporting of Observational Surgical Studies Illustrated in a Study on Primary Repair of Bile Duct Injuries.

PubMed

Cho, Jai Young; Jaeger, Allison R; Sanford, Dominic E; Fields, Ryan C; Strasberg, Steven M

2015-09-01

A standard format for reporting observational surgical studies does not exist. This creates difficulties in comparing studies and in performing synthesis through systematic reviews and meta-analyses. This article proposes a method called "standard tabular reporting" and illustrates its use in a case series of bile duct reconstructions for biliary injuries occurring during cholecystectomy. A database dealing with biliary injuries was constructed in sections. Each section was designed to be turned into a table covering one element of the subject. Whenever possible, American College of Surgeons NSQIP "Classic Variables and Definitions" were used for forming sections and tables. However, most tables are original and specific to biliary injury. The database was populated from clinical records of patients who sustained a biliary injury during cholecystectomy. Tables were created dealing with the following subjects: demographics, index operation, presentation, classification of injury, preoperative risk assessment, preoperative laboratory values, operative repair technique, postoperative complications, and long-term outcomes. Between 1997 and 2013, 122 primary bile duct reconstructions were performed, with 1 mortality and 47 complications. Good long-term results were obtained in 113 (92.6%) patients. No secondary surgical reconstructions have been needed. Presentation of data in a standard format would facilitate comparison and synthesis of observational studies on the same subject. The biliary reconstructive methods used resulted in very satisfactory outcomes. Copyright © 2015 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Survey of standards applicable to a database management system

NASA Technical Reports Server (NTRS)

Urena, J. L.

1981-01-01

Industry, government, and NASA standards, and the status of standardization activities of standards setting organizations applicable to the design, implementation and operation of a data base management system for space related applications are identified. The applicability of the standards to a general purpose, multimission data base management system is addressed.

Developing an A Priori Database for Passive Microwave Snow Water Retrievals Over Ocean

NASA Astrophysics Data System (ADS)

Yin, Mengtao; Liu, Guosheng

2017-12-01

A physically optimized a priori database is developed for Global Precipitation Measurement Microwave Imager (GMI) snow water retrievals over ocean. The initial snow water content profiles are derived from CloudSat Cloud Profiling Radar (CPR) measurements. A radiative transfer model in which the single-scattering properties of nonspherical snowflakes are based on the discrete dipole approximate results is employed to simulate brightness temperatures and their gradients. Snow water content profiles are then optimized through a one-dimensional variational (1D-Var) method. The standard deviations of the difference between observed and simulated brightness temperatures are in a similar magnitude to the observation errors defined for observation error covariance matrix after the 1D-Var optimization, indicating that this variational method is successful. This optimized database is applied in a Bayesian retrieval snow water algorithm. The retrieval results indicated that the 1D-Var approach has a positive impact on the GMI retrieved snow water content profiles by improving the physical consistency between snow water content profiles and observed brightness temperatures. Global distribution of snow water contents retrieved from the a priori database is compared with CloudSat CPR estimates. Results showed that the two estimates have a similar pattern of global distribution, and the difference of their global means is small. In addition, we investigate the impact of using physical parameters to subset the database on snow water retrievals. It is shown that using total precipitable water to subset the database with 1D-Var optimization is beneficial for snow water retrievals.

ADAM-M Data and Information

Atmospheric Science Data Center

2017-05-11

... Information Creating a Unified Airborne Database for Assessment and Validation of Global Models of Atmospheric ...  (3)  To generate a standardized in-situ observational database with best possible matching temporal and spatial scales to model ...

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

PubMed Central

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

Building-up a database of spectro-photometric standards from the UV to the NIR

NASA Astrophysics Data System (ADS)

Vernet, J.; Kerber, F.; Mainieri, V.; Rauch, T.; Saitta, F.; D'Odorico, S.; Bohlin, R.; Ivanov, V.; Lidman, C.; Mason, E.; Smette, A.; Walsh, J.; Fosbury, R.; Goldoni, P.; Groot, P.; Hammer, F.; Kaper, L.; Horrobin, M.; Kjaergaard-Rasmussen, P.; Royer, F.

2010-11-01

We present results of a project aimed at establishing a set of 12 spectro-photometric standards over a wide wavelength range from 320 to 2500 nm. Currently no such set of standard stars covering the near-IR is available. Our strategy is to extend the useful range of existing well-established optical flux standards (Oke 1990, Hamuy et al. 1992, 1994) into the near-IR by means of integral field spectroscopy with SINFONI at the VLT combined with state-of-the-art white dwarf stellar atmospheric models (TMAP, Holberg et al. 2008). As a solid reference, we use two primary HST standard white dwarfs GD71 and GD153 and one HST secondary standard BD+17 4708. The data were collected through an ESO “Observatory Programme” over ~40 nights between February 2007 and September 2008.

Certification of elements in and use of standard reference material 3280 multivitamin/multielement tablets.

PubMed

Turk, Gregory C; Sharpless, Katherine E; Cleveland, Danielle; Jongsma, Candice; Mackey, Elizabeth A; Marlow, Anthony F; Oflaz, Rabia; Paul, Rick L; Sieber, John R; Thompson, Robert Q; Wood, Laura J; Yu, Lee L; Zeisler, Rolf; Wise, Stephen A; Yen, James H; Christopher, Steven J; Day, Russell D; Long, Stephen E; Greene, Ella; Harnly, James; Ho, I-Pin; Betz, Joseph M

2013-01-01

Standard Reference Material 3280 Multivitamin/ Multielement Tablets was issued by the National Institute of Standards and Technology in 2009, and has certified and reference mass fraction values for 13 vitamins, 26 elements, and two carotenoids. Elements were measured using two or more analytical methods at NIST with additional data contributed by collaborating laboratories. This reference material is expected to serve a dual purpose: to provide quality assurance in support of a database of dietary supplement products and to provide a means for analysts, dietary supplement manufacturers, and researchers to assess the appropriateness and validity of their analytical methods and the accuracy of their results.

Geospatial Data Management Platform for Urban Groundwater

NASA Astrophysics Data System (ADS)

Gaitanaru, D.; Priceputu, A.; Gogu, C. R.

2012-04-01

Due to the large amount of civil work projects and research studies, large quantities of geo-data are produced for the urban environments. These data are usually redundant as well as they are spread in different institutions or private companies. Time consuming operations like data processing and information harmonisation represents the main reason to systematically avoid the re-use of data. The urban groundwater data shows the same complex situation. The underground structures (subway lines, deep foundations, underground parkings, and others), the urban facility networks (sewer systems, water supply networks, heating conduits, etc), the drainage systems, the surface water works and many others modify continuously. As consequence, their influence on groundwater changes systematically. However, these activities provide a large quantity of data, aquifers modelling and then behaviour prediction can be done using monitored quantitative and qualitative parameters. Due to the rapid evolution of technology in the past few years, transferring large amounts of information through internet has now become a feasible solution for sharing geoscience data. Furthermore, standard platform-independent means to do this have been developed (specific mark-up languages like: GML, GeoSciML, WaterML, GWML, CityML). They allow easily large geospatial databases updating and sharing through internet, even between different companies or between research centres that do not necessarily use the same database structures. For Bucharest City (Romania) an integrated platform for groundwater geospatial data management is developed under the framework of a national research project - "Sedimentary media modeling platform for groundwater management in urban areas" (SIMPA) financed by the National Authority for Scientific Research of Romania. The platform architecture is based on three components: a geospatial database, a desktop application (a complex set of hydrogeological and geological analysis tools) and a front-end geoportal service. The SIMPA platform makes use of mark-up transfer standards to provide a user-friendly application that can be accessed through internet to query, analyse, and visualise geospatial data related to urban groundwater. The platform holds the information within the local groundwater geospatial databases and the user is able to access this data through a geoportal service. The database architecture allows storing accurate and very detailed geological, hydrogeological, and infrastructure information that can be straightforwardly generalized and further upscaled. The geoportal service offers the possibility of querying a dataset from the spatial database. The query is coded in a standard mark-up language, and sent to the server through a standard Hyper Text Transfer Protocol (http) to be processed by the local application. After the validation of the query, the results are sent back to the user to be displayed by the geoportal application. The main advantage of the SIMPA platform is that it offers to the user the possibility to make a primary multi-criteria query, which results in a smaller set of data to be analysed afterwards. This improves both the transfer process parameters and the user's means of creating the desired query.

Estimating a Service-Life Distribution Based on Production Counts and a Failure Database

DOE PAGES

Ryan, Kenneth J.; Hamada, Michael Scott; Vardeman, Stephen B.

2017-04-01

A manufacturer wanted to compare the service-life distributions of two similar products. These concern product lifetimes after installation (not manufacture). For each product, there were available production counts and an imperfect database providing information on failing units. In the real case, these units were expensive repairable units warrantied against repairs. Failure (of interest here) was relatively rare and driven by a different mode/mechanism than ordinary repair events (not of interest here). Approach: Data models for the service life based on a standard parametric lifetime distribution and a related limited failure population were developed. These models were used to develop expressionsmore » for the likelihood of the available data that properly accounts for information missing in the failure database. Results: A Bayesian approach was employed to obtain estimates of model parameters (with associated uncertainty) in order to investigate characteristics of the service-life distribution. Custom software was developed and is included as Supplemental Material to this case study. One part of a responsible approach to the original case was a simulation experiment used to validate the correctness of the software and the behavior of the statistical methodology before using its results in the application, and an example of such an experiment is included here. Because of confidentiality issues that prevent use of the original data, simulated data with characteristics like the manufacturer’s proprietary data are used to illustrate some aspects of our real analyses. Lastly, we also note that, although this case focuses on rare and complete product failure, the statistical methodology provided is directly applicable to more standard warranty data problems involving typically much larger warranty databases where entries are warranty claims (often for repairs) rather than reports of complete failures.« less

XTCE (XML Telemetric and Command Exchange) Standard Making It Work at NASA. Can It Work For You?

NASA Technical Reports Server (NTRS)

Munoz-Fernandez, Michela; Smith, Danford S.; Rice, James K.; Jones, Ronald A.

2017-01-01

The XML Telemetric and Command Exchange (XTCE) standard is intended as a way to describe telemetry and command databases to be exchanged across centers and space agencies. XTCE usage has the potential to lead to consolidation of the Mission Operations Center (MOC) Monitor and Control displays for mission cross-support, reducing equipment and configuration costs, as well as a decrease in the turnaround time for telemetry and command modifications during all the mission phases. The adoption of XTCE will reduce software maintenance costs by reducing the variation between our existing mission dictionaries. The main objective of this poster is to show how powerful XTCE is in terms of interoperability across centers and missions. We will provide results for a use case where two centers can use their local tools to process and display the same mission telemetry in their MOC independently of one another. In our use case we have first quantified the ability for XTCE to capture the telemetry definitions of the mission by use of our suite of support tools (Conversion, Validation, and Compliance measurement). The next step was to show processing and monitoring of the same telemetry in two mission centers. Once the database was converted to XTCE using our tool, the XTCE file became our primary database and was shared among the various tool chains through their XTCE importers and ultimately configured to ingest the telemetry stream and display or capture the telemetered information in similar ways.Summary results include the ability to take a real mission database and real mission telemetry and display them on various tools from two centers, as well as using commercially free COTS.

Estimating a Service-Life Distribution Based on Production Counts and a Failure Database

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

Ryan, Kenneth J.; Hamada, Michael Scott; Vardeman, Stephen B.

A manufacturer wanted to compare the service-life distributions of two similar products. These concern product lifetimes after installation (not manufacture). For each product, there were available production counts and an imperfect database providing information on failing units. In the real case, these units were expensive repairable units warrantied against repairs. Failure (of interest here) was relatively rare and driven by a different mode/mechanism than ordinary repair events (not of interest here). Approach: Data models for the service life based on a standard parametric lifetime distribution and a related limited failure population were developed. These models were used to develop expressionsmore » for the likelihood of the available data that properly accounts for information missing in the failure database. Results: A Bayesian approach was employed to obtain estimates of model parameters (with associated uncertainty) in order to investigate characteristics of the service-life distribution. Custom software was developed and is included as Supplemental Material to this case study. One part of a responsible approach to the original case was a simulation experiment used to validate the correctness of the software and the behavior of the statistical methodology before using its results in the application, and an example of such an experiment is included here. Because of confidentiality issues that prevent use of the original data, simulated data with characteristics like the manufacturer’s proprietary data are used to illustrate some aspects of our real analyses. Lastly, we also note that, although this case focuses on rare and complete product failure, the statistical methodology provided is directly applicable to more standard warranty data problems involving typically much larger warranty databases where entries are warranty claims (often for repairs) rather than reports of complete failures.« less

The Virtual Observatory Service TheoSSA: Establishing a Database of Synthetic Stellar Flux Standards II. NLTE Spectral Analysis of the OB-Type Subdwarf Feige 110

NASA Technical Reports Server (NTRS)

Rauch, T.; Rudkowski, A.; Kampka, D.; Werner, K.; Kruk, J. W.; Moehler, S.

2014-01-01

Context. In the framework of the Virtual Observatory (VO), the German Astrophysical VO (GAVO) developed the registered service TheoSSA (Theoretical Stellar Spectra Access). It provides easy access to stellar spectral energy distributions (SEDs) and is intended to ingest SEDs calculated by any model-atmosphere code, generally for all effective temperatures, surface gravities, and elemental compositions. We will establish a database of SEDs of flux standards that are easily accessible via TheoSSA's web interface. Aims. The OB-type subdwarf Feige 110 is a standard star for flux calibration. State-of-the-art non-local thermodynamic equilibrium stellar-atmosphere models that consider opacities of species up to trans-iron elements will be used to provide a reliable synthetic spectrum to compare with observations. Methods. In case of Feige 110, we demonstrate that the model reproduces not only its overall continuum shape from the far-ultraviolet (FUV) to the optical wavelength range but also the numerous metal lines exhibited in its FUV spectrum. Results. We present a state-of-the-art spectral analysis of Feige 110. We determined Teff =47 250 +/- 2000 K, log g=6.00 +/- 0.20, and the abundances of He, N, P, S, Ti, V, Cr, Mn, Fe, Co, Ni, Zn, and Ge. Ti, V, Mn, Co, Zn, and Ge were identified for the first time in this star. Upper abundance limits were derived for C, O, Si, Ca, and Sc. Conclusions. The TheoSSA database of theoretical SEDs of stellar flux standards guarantees that the flux calibration of astronomical data and cross-calibration between different instruments can be based on models and SEDs calculated with state-of-the-art model atmosphere codes.

VarioML framework for comprehensive variation data representation and exchange

PubMed Central

2012-01-01

Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity. PMID:23031277

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

PubMed

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

2017-11-21

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

New orthopaedic implant management tool for computer-assisted planning, navigation, and simulation: from implant CAD files to a standardized XML-based implant database.

PubMed

Sagbo, S; Blochaou, F; Langlotz, F; Vangenot, C; Nolte, L-P; Zheng, G

2005-01-01

Computer-Assisted Orthopaedic Surgery (CAOS) has made much progress over the last 10 years. Navigation systems have been recognized as important tools that help surgeons, and various such systems have been developed. A disadvantage of these systems is that they use non-standard formalisms and techniques. As a result, there are no standard concepts for implant and tool management or data formats to store information for use in 3D planning and navigation. We addressed these limitations and developed a practical and generic solution that offers benefits for surgeons, implant manufacturers, and CAS application developers. We developed a virtual implant database containing geometrical as well as calibration information for orthopedic implants and instruments, with a focus on trauma. This database has been successfully tested for various applications in the client/server mode. The implant information is not static, however, because manufacturers periodically revise their implants, resulting in the deletion of some implants and the introduction of new ones. Tracking these continuous changes and keeping CAS systems up to date is a tedious task if done manually. This leads to additional costs for system development, and some errors are inevitably generated due to the huge amount of information that has to be processed. To ease management with respect to implant life cycle, we developed a tool to assist end-users (surgeons, hospitals, CAS system providers, and implant manufacturers) in managing their implants. Our system can be used for pre-operative planning and intra-operative navigation, and also for any surgical simulation involving orthopedic implants. Currently, this tool allows addition of new implants, modification of existing ones, deletion of obsolete implants, export of a given implant, and also creation of backups. Our implant management system has been successfully tested in the laboratory with very promising results. It makes it possible to fill the current gap that exists between the CAS system and implant manufacturers, hospitals, and surgeons.

The Icelandic 16-electrode electrohysterogram database

PubMed Central

Alexandersson, Asgeir; Steingrimsdottir, Thora; Terrien, Jeremy; Marque, Catherine; Karlsson, Brynjar

2015-01-01

External recordings of the electrohysterogram (EHG) can provide new knowledge on uterine electrical activity associated with contractions. Better understanding of the mechanisms underlying labor can contribute to preventing preterm birth which is the main cause of mortality and morbidity in newborns. Promising results using the EHG for labor prediction and other uses in obstetric care are the drivers of this work. This paper presents a database of 122 4-by-4 electrode EHG recordings performed on 45 pregnant women using a standardized recording protocol and a placement guide system. The recordings were performed in Iceland between 2008 and 2010. Of the 45 participants, 32 were measured repeatedly during the same pregnancy and participated in two to seven recordings. Recordings were performed in the third trimester (112 recordings) and during labor (10 recordings). The database includes simultaneously recorded tocographs, annotations of events and obstetric information on participants. The publication of this database enables independent and novel analysis of multi-electrode EHG by the researchers in the field and hopefully development towards new life-saving technology. PMID:25984349

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species

PubMed Central

Kumar, Sujai; Stevens, Lewis; Blaxter, Mark

2017-01-01

Abstract As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive application programming interface. Here we introduce GenomeHubs, which provide a containerized environment to facilitate the setup and hosting of custom Ensembl genome browsers. This simplifies mirroring of existing content and import of new genomic data into the Ensembl database schema. GenomeHubs also provide a set of analysis containers to decorate imported genomes with results of standard analyses and functional annotations and support export to flat files, including EMBL format for submission of assemblies and annotations to International Nucleotide Sequence Database Collaboration. Database URL: http://GenomeHubs.org PMID:28605774

Hydroacoustic propagation grids for the CTBT knowledge databaes BBN technical memorandum W1303

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

J. Angell

1998-05-01

The Hydroacoustic Coverage Assessment Model (HydroCAM) has been used to develop components of the hydroacoustic knowledge database required by operational monitoring systems, particularly the US National Data Center (NDC). The database, which consists of travel time, amplitude correction and travel time standard deviation grids, is planned to support source location, discrimination and estimation functions of the monitoring network. The grids will also be used under the current BBN subcontract to support an analysis of the performance of the International Monitoring System (IMS) and national sensor systems. This report describes the format and contents of the hydroacoustic knowledgebase grids, and themore » procedures and model parameters used to generate these grids. Comparisons between the knowledge grids, measured data and other modeled results are presented to illustrate the strengths and weaknesses of the current approach. A recommended approach for augmenting the knowledge database with a database of expected spectral/waveform characteristics is provided in the final section of the report.« less

The Icelandic 16-electrode electrohysterogram database

NASA Astrophysics Data System (ADS)

Alexandersson, Asgeir; Steingrimsdottir, Thora; Terrien, Jeremy; Marque, Catherine; Karlsson, Brynjar

2015-04-01

External recordings of the electrohysterogram (EHG) can provide new knowledge on uterine electrical activity associated with contractions. Better understanding of the mechanisms underlying labor can contribute to preventing preterm birth which is the main cause of mortality and morbidity in newborns. Promising results using the EHG for labor prediction and other uses in obstetric care are the drivers of this work. This paper presents a database of 122 4-by-4 electrode EHG recordings performed on 45 pregnant women using a standardized recording protocol and a placement guide system. The recordings were performed in Iceland between 2008 and 2010. Of the 45 participants, 32 were measured repeatedly during the same pregnancy and participated in two to seven recordings. Recordings were performed in the third trimester (112 recordings) and during labor (10 recordings). The database includes simultaneously recorded tocographs, annotations of events and obstetric information on participants. The publication of this database enables independent and novel analysis of multi-electrode EHG by the researchers in the field and hopefully development towards new life-saving technology.

A carcinogenic potency database of the standardized results of animal bioassays

PubMed Central

Gold, Lois Swirsky; Sawyer, Charles B.; Magaw, Renae; Backman, Georganne M.; De Veciana, Margarita; Levinson, Robert; Hooper, N. Kim; Havender, William R.; Bernstein, Leslie; Peto, Richard; Pike, Malcolm C.; Ames, Bruce N.

1984-01-01

The preceding paper described our numerical index of carcinogenic potency, the TD50 and the statistical procedures adopted for estimating it from experimental data. This paper presents the Carcinogenic Potency Database, which includes results of about 3000 long-term, chronic experiments of 770 test compounds. Part II is a discussion of the sources of our data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. Part III is a guide to the plot of results presented in Part IV. A number of appendices are provided to facilitate use of the database. The plot includes information about chronic cancer tests in mammals, such as dose and other aspects of experimental protocol, histopathology and tumor incidence, TD50 and its statistical significance, dose response, author's opinion and literature reference. The plot readily permits comparisons of carcinogenic potency and many other aspects of cancer tests; it also provides quantitative information about negative tests. The range of carcinogenic potency is over 10 million-fold. PMID:6525996

Development of a database of health insurance claims: standardization of disease classifications and anonymous record linkage.

PubMed

Kimura, Shinya; Sato, Toshihiko; Ikeda, Shunya; Noda, Mitsuhiko; Nakayama, Takeo

2010-01-01

Health insurance claims (ie, receipts) record patient health care treatments and expenses and, although created for the health care payment system, are potentially useful for research. Combining different types of receipts generated for the same patient would dramatically increase the utility of these receipts. However, technical problems, including standardization of disease names and classifications, and anonymous linkage of individual receipts, must be addressed. In collaboration with health insurance societies, all information from receipts (inpatient, outpatient, and pharmacy) was collected. To standardize disease names and classifications, we developed a computer-aided post-entry standardization method using a disease name dictionary based on International Classification of Diseases (ICD)-10 classifications. We also developed an anonymous linkage system by using an encryption code generated from a combination of hash values and stream ciphers. Using different sets of the original data (data set 1: insurance certificate number, name, and sex; data set 2: insurance certificate number, date of birth, and relationship status), we compared the percentage of successful record matches obtained by using data set 1 to generate key codes with the percentage obtained when both data sets were used. The dictionary's automatic conversion of disease names successfully standardized 98.1% of approximately 2 million new receipts entered into the database. The percentage of anonymous matches was higher for the combined data sets (98.0%) than for data set 1 (88.5%). The use of standardized disease classifications and anonymous record linkage substantially contributed to the construction of a large, chronologically organized database of receipts. This database is expected to aid in epidemiologic and health services research using receipt information.

Third chronological supplement to the carcinogenic potency database: standardized results of animal bioassays published through December 1986 and by the National Toxicology Program through June 1987.

PubMed Central

Gold, L S; Slone, T H; Backman, G M; Eisenberg, S; Da Costa, M; Wong, M; Manley, N B; Rohrbach, L; Ames, B N

1990-01-01

This paper is the third chronological supplement to the Carcinogenic Potency Database that first appeared in this journal in 1984. We report here results of carcinogenesis bioassays published in the general literature between January 1985 and December 1986, and in Technical Reports of the National Toxicology Program between June 1986 and June 1987. This supplement includes results of 337 long-term, chronic experiments of 121 compounds, and reports the same information about each experiment in the same plot format as the earlier papers, e.g., the species and strain of animal, the route and duration of compound administration, dose level, and other aspects of experimental protocol, histopathology, and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, opinion of the author about carcinogenicity, and literature citation. The reader needs to refer to the 1984 publication for a guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The four plots of the database are to be used together as results published earlier are not repeated. In all, the four plots include results for approximately 4000 experiments on 1050 chemicals. Appendix 14 of this paper is an alphabetical index to all chemicals in the database and indicates which plot(s) each chemical appears in. A combined plot of all results from the four separate papers, that is ordered alphabetically by chemical, is available from the first author, in printed form or on computer tape or diskette. PMID:2351123

Data structures and organisation: Special problems in scientific applications

NASA Astrophysics Data System (ADS)

Read, Brian J.

1989-12-01

In this paper we discuss and offer answers to the following questions: What, really, are the benifits of databases in physics? Are scientific databases essentially different from conventional ones? What are the drawbacks of a commercial database management system for use with scientific data? Do they outweigh the advantages? Do databases systems have adequate graphics facilities, or is a separate graphics package necessary? SQL as a standard language has deficiencies, but what are they for scientific data in particular? Indeed, is the relational model appropriate anyway? Or, should we turn to object oriented databases?

A national database for essential drugs in South Africa.

PubMed

Zweygarth, M; Summers, R S

2000-06-01

In the process of drafting standard treatment guidelines for adults and children at hospital level, the Secretariat of the National Essential Drugs List Committee made use of a database designed with technical support from the School of Pharmacy, MEDUNSA. The database links the current 697 drugs on the Essential Drugs List with Standard Treatment Guidelines for over 400 conditions. It served to streamline the inclusion of different drugs and dosage forms in the various guidelines, and provided concise, updated information to other departments involved in drug procurement. From information on drug prices and morbidity, it can also be used to calculate drug consumption and cost estimates and compare them with actual figures.

An evaluation of matching unknown writing inks with the United States International Ink Library.

PubMed

Laporte, Gerald M; Arredondo, Marlo D; McConnell, Tyra S; Stephens, Joseph C; Cantu, Antonio A; Shaffer, Douglas K

2006-05-01

Utilizing a database of standards for forensic casework is a valuable resource. Undoubtedly, as more standards (and corresponding information about the specimens) are collected, there is a greater certainty of identification when a questioned and a known item cannot be distinguished after a series of analyses. The United States Secret Service and the Internal Revenue Service National Forensic Laboratory jointly maintain the largest known forensic collection of writing inks in the world, which is comprised of over 8500 ink standards collected worldwide, dating back to the 1920s. This study was conducted to evaluate the reliability of matching arbitrarily purchased pens with known inks from a database. One hundred pens were randomly obtained from a variety of sources and their respective ink compositions were compared with standards. Eighty-five of the inks were determined to be suitable for comparison utilizing optical examinations and thin-layer chromatography. Three of the inks did not match any of the specimens on record; one of these inks was similar to an ink from an identical brand of pen that was in the database, but had a modified formulation.

Mock jurors' use of error rates in DNA database trawls.

PubMed

Scurich, Nicholas; John, Richard S

2013-12-01

Forensic science is not infallible, as data collected by the Innocence Project have revealed. The rate at which errors occur in forensic DNA testing-the so-called "gold standard" of forensic science-is not currently known. This article presents a Bayesian analysis to demonstrate the profound impact that error rates have on the probative value of a DNA match. Empirical evidence on whether jurors are sensitive to this effect is equivocal: Studies have typically found they are not, while a recent, methodologically rigorous study found that they can be. This article presents the results of an experiment that examined this issue within the context of a database trawl case in which one DNA profile was tested against a multitude of profiles. The description of the database was manipulated (i.e., "medical" or "offender" database, or not specified) as was the rate of error (i.e., one-in-10 or one-in-1,000). Jury-eligible participants were nearly twice as likely to convict in the offender database condition compared to the condition not specified. The error rates did not affect verdicts. Both factors, however, affected the perception of the defendant's guilt, in the expected direction, although the size of the effect was meager compared to Bayesian prescriptions. The results suggest that the disclosure of an offender database to jurors might constitute prejudicial evidence, and calls for proficiency testing in forensic science as well as training of jurors are echoed. (c) 2013 APA, all rights reserved

Generation of signature databases with fast codes

NASA Astrophysics Data System (ADS)

Bradford, Robert A.; Woodling, Arthur E.; Brazzell, James S.

1990-09-01

Using the FASTSIG signature code to generate optical signature databases for the Ground-based Surveillance and Traking System (GSTS) Program has improved the efficiency of the database generation process. The goal of the current GSTS database is to provide standardized, threat representative target signatures that can easily be used for acquisition and trk studies, discrimination algorithm development, and system simulations. Large databases, with as many as eight interpolalion parameters, are required to maintain the fidelity demands of discrimination and to generalize their application to other strateg systems. As the need increases for quick availability of long wave infrared (LWIR) target signatures for an evolving design4o-threat, FASTSIG has become a database generation alternative to using the industry standard OptiCal Signatures Code (OSC). FASTSIG, developed in 1985 to meet the unique strategic systems demands imposed by the discrimination function, has the significant advantage of being a faster running signature code than the OSC, typically requiring two percent of the cpu time. It uses analytical approximations to model axisymmetric targets, with the fidelity required for discrimination analysis. Access of the signature database is accomplished through use of the waveband integration and interpolation software, INTEG and SIGNAT. This paper gives details of this procedure as well as sample interpolated signatures and also covers sample verification by comparison to the OSC, in order to establish the fidelity of the FASTSIG generated database.

TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan.

PubMed

Lin, Ying-Chi; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng; Tung, Chun-Wei

2013-01-01

The unique geographic features of Taiwan are attributed to the rich indigenous and endemic plant species in Taiwan. These plants serve as resourceful bank for biologically active phytochemicals. Given that these plant-derived chemicals are prototypes of potential drugs for diseases, databases connecting the chemical structures and pharmacological activities may facilitate drug development. To enhance the utility of the data, it is desirable to develop a database of chemical compounds and corresponding activities from indigenous plants in Taiwan. A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan was constructed. The database, TIPdb, is composed of a standardized format of published anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. A browse function was implemented for users to browse the database in a taxonomy-based manner. Search functions can be utilized to filter records of interest by botanical name, part, chemical class, or compound name. The structured and searchable database TIPdb was constructed to serve as a comprehensive and standardized resource for anticancer, antiplatelet, and antituberculosis compounds search. The manually curated chemical structures and activities provide a great opportunity to develop quantitative structure-activity relationship models for the high-throughput screening of potential anticancer, antiplatelet, and antituberculosis drugs.

TIPdb: A Database of Anticancer, Antiplatelet, and Antituberculosis Phytochemicals from Indigenous Plants in Taiwan

PubMed Central

Lin, Ying-Chi; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng; Tung, Chun-Wei

2013-01-01

The unique geographic features of Taiwan are attributed to the rich indigenous and endemic plant species in Taiwan. These plants serve as resourceful bank for biologically active phytochemicals. Given that these plant-derived chemicals are prototypes of potential drugs for diseases, databases connecting the chemical structures and pharmacological activities may facilitate drug development. To enhance the utility of the data, it is desirable to develop a database of chemical compounds and corresponding activities from indigenous plants in Taiwan. A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan was constructed. The database, TIPdb, is composed of a standardized format of published anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. A browse function was implemented for users to browse the database in a taxonomy-based manner. Search functions can be utilized to filter records of interest by botanical name, part, chemical class, or compound name. The structured and searchable database TIPdb was constructed to serve as a comprehensive and standardized resource for anticancer, antiplatelet, and antituberculosis compounds search. The manually curated chemical structures and activities provide a great opportunity to develop quantitative structure-activity relationship models for the high-throughput screening of potential anticancer, antiplatelet, and antituberculosis drugs. PMID:23766708

Cost-effectiveness of ceftolozane/tazobactam plus metronidazole versus piperacillin/tazobactam as initial empiric therapy for the treatment of complicated intra-abdominal infections based on pathogen distributions drawn from national surveillance data in the United States.

PubMed

Prabhu, Vimalanand S; Solomkin, Joseph S; Medic, Goran; Foo, Jason; Borse, Rebekah H; Kauf, Teresa; Miller, Benjamin; Sen, Shuvayu S; Basu, Anirban

2017-01-01

The prevalence of antimicrobial resistance among gram-negative pathogens in complicated intra-abdominal infections (cIAIs) has increased. In the absence of timely information on the infecting pathogens and their susceptibilities, local or regional epidemiology may guide initial empirical therapy and reduce treatment failure, length of stay and mortality. The objective of this study was to assess the cost-effectiveness of ceftolozane/tazobactam + metronidazole compared with piperacillin/tazobactam in the treatment of hospitalized US patients with cIAI at risk of infection with resistant pathogens. We used a decision-analytic Monte Carlo simulation model to compare the costs and quality-adjusted life years (QALYs) of persons infected with nosocomial gram-negative cIAI treated empirically with either ceftolozane/tazobactam + metronidazole or piperacillin/tazobactam. Pathogen isolates were randomly drawn from the Program to Assess Ceftolozane/Tazobactam Susceptibility (PACTS) database, a surveillance database of non-duplicate bacterial isolates collected from patients with cIAIs in medical centers in the USA from 2011 to 2013. Susceptibility to initial therapy was based on the measured susceptibilities reported in the PACTS database determined using standard broth micro-dilution methods as described by the Clinical and Laboratory Standards Institute (CLSI). Our model results, with baseline resistance levels from the PACTS database, indicated that ceftolozane/tazobactam + metronidazole dominated piperacillin/tazobactam, with lower costs ($44,226/patient vs. $44,811/patient respectively) and higher QALYs (12.85/patient vs. 12.70/patient, respectively). Ceftolozane/tazobactam + metronidazole remained the dominant choice in one-way and probabilistic sensitivity analyses. Based on surveillance data, ceftolozane/tazobactam is more likely to be an appropriate empiric therapy for cIAI in the US. Results from a decision-analytic simulation model indicate that use of ceftolozane/tazobactam + metronidazole would result in cost savings and improves QALYs, compared with piperacillin/tazobactam.

Scoring Package

National Institute of Standards and Technology Data Gateway

NIST Scoring Package (PC database for purchase)   The NIST Scoring Package (Special Database 1) is a reference implementation of the draft Standard Method for Evaluating the Performance of Systems Intended to Recognize Hand-printed Characters from Image Data Scanned from Forms.

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...

Multi-window detection for P-wave in electrocardiograms based on bilateral accumulative area.

PubMed

Chen, Riqing; Huang, Yingsong; Wu, Jian

2016-11-01

P-wave detection is one of the most challenging aspects in electrocardiograms (ECGs) due to its low amplitude, low frequency, and variable waveforms. This work introduces a novel multi-window detection method for P-wave delineation based on the bilateral accumulative area. The bilateral accumulative area is calculated by summing the areas covered by the P-wave curve with left and right sliding windows. The onset and offset of a positive P-wave correspond to the local maxima of the area detector. The position drift and difference in area variation of local extreme points with different windows are used to systematically combine multi-window and 12-lead synchronous detection methods, which are used to screen the optimization boundary points from all extreme points of different window widths and adaptively match the P-wave location. The proposed method was validated with ECG signals from various databases, including the Standard CSE Database, T-Wave Alternans Challenge Database, PTB Diagnostic ECG Database, and the St. Petersburg Institute of Cardiological Technics 12-Lead Arrhythmia Database. The average sensitivity Se was 99.44% with a positive predictivity P+ of 99.37% for P-wave detection. Standard deviations of 3.7 and 4.3ms were achieved for the onset and offset of P-waves, respectively, which is in agreement with the accepted tolerances required by the CSE committee. Compared with well-known delineation methods, this method can achieve high sensitivity and positive predictability using a simple calculation process. The experiment results suggest that the bilateral accumulative area could be an effective detection tool for ECG signal analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

ANZSoilML: An Australian - New Zealand standard for exchange of soil data

NASA Astrophysics Data System (ADS)

Simons, Bruce; Wilson, Peter; Ritchie, Alistair; Cox, Simon

2013-04-01

The Australian-New Zealand soil information exchange standard (ANZSoilML) is a GML-based standard designed to allow the discovery, query and delivery of soil and landscape data via standard Open Geospatial Consortium (OGC) Web Feature Services. ANZSoilML modifies the Australian soil exchange standard (OzSoilML), which is based on the Australian Soil Information Transfer and Evaluation System (SITES) database design and exchange protocols, to meet the New Zealand National Soils Database requirements. The most significant change was the removal of the lists of CodeList terms in OzSoilML, which were based on the field methods specified in the 'Australian Soil and Land Survey Field Handbook'. These were replaced with empty CodeLists as placeholders to external vocabularies to allow the use of New Zealand vocabularies without violating the data model. Testing of the use of these separately governed Australian and New Zealand vocabularies has commenced. ANZSoilML attempts to accommodate the proposed International Organization for Standardization ISO/DIS 28258 standard for soil quality. For the most part, ANZSoilML is consistent with the ISO model, although major differences arise as a result of: • The need to specify the properties appropriate for each feature type; • The inclusion of soil-related 'Landscape' features; • Allowing the mapping of soil surfaces, bodies, layers and horizons, independent of the soil profile; • Allowing specifying the relationships between the various soil features; • Specifying soil horizons as specialisations of soil layers; • Removing duplication of features provided by the ISO Observation & Measurements standard. The International Union of Soil Sciences (IUSS) Working Group on Soil Information Standards (WG-SIS) aims to develop, promote and maintain a standard to facilitate the exchange of soils data and information. Developing an international exchange standard that is compatible with existing and emerging national and regional standards is a considerable challenge. ANZSoilML is proposed as a profile of the more generalised SoilML model being progressed through the IUSS Working Group.

International energy: Research organizations, 1988--1992. Revision 1

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

Hendricks, P.; Jordan, S.

This publication contains the standardized names of energy research organizations used in energy information databases. Involved in this cooperative task are (1) the technical staff of the US DOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the Energy Technology Data Exchange (ETDE) and (2) the International Nuclear Information System (INIS). ETDE member countries are also members of the International Nuclear Information System (INIS). Nuclear organization names recorded for INIS by these ETDE member countries are also included in the ETDE Energy Database. Therefore, these organization names are cooperatively standardized for use in bothmore » information systems. This publication identifies current organizations doing research in all energy fields, standardizes the format for recording these organization names in bibliographic citations, assigns a numeric code to facilitate data entry, and identifies report number prefixes assigned by these organizations. These research organization names may be used in searching the databases ``Energy Science & Technology`` on DIALOG and ``Energy`` on STN International. These organization names are also used in USDOE databases on the Integrated Technical Information System. Research organizations active in the past five years, as indicated by database records, were identified to form this publication. This directory includes approximately 31,000 organizations that reported energy-related literature from 1988 to 1992 and updates the DOE Energy Data Base: Corporate Author Entries.« less

Initiative for standardization of reporting genetics of male infertility.

PubMed

Traven, Eva; Ogrinc, Ana; Kunej, Tanja

2017-02-01

The number of publications on research of male infertility is increasing. Technologies used in research of male infertility generate complex results and various types of data that need to be appropriately managed, arranged, and made available to other researchers for further use. In our previous study, we collected over 800 candidate loci for male fertility in seven mammalian species. However, the continuation of the work towards a comprehensive database of candidate genes associated with different types of idiopathic human male infertility is challenging due to fragmented information, obtained from a variety of technologies and various omics approaches. Results are published in different forms and usually need to be excavated from the text, which hinders the gathering of information. Standardized reporting of genetic anomalies as well as causative and risk factors of male infertility therefore presents an important issue. The aim of the study was to collect examples of diverse genomic loci published in association with human male infertility and to propose a standardized format for reporting genetic causes of male infertility. From the currently available data we have selected 75 studies reporting 186 representative genomic loci which have been proposed as genetic risk factors for male infertility. Based on collected and formatted data, we suggested a first step towards unification of reporting the genetics of male infertility in original and review studies. The proposed initiative consists of five relevant data types: 1) genetic locus, 2) race/ethnicity, number of participants (infertile/controls), 3) methodology, 4) phenotype (clinical data, disease ontology, and disease comorbidity), and 5) reference. The proposed form for standardized reporting presents a baseline for further optimization with additional genetic and clinical information. This data standardization initiative will enable faster multi-omics data integration, database development and sharing, establishing more targeted hypotheses, and facilitating biomarker discovery.

Passive ozone network of Dallas: a modeling opportunity with community involvement. 2.

PubMed

Sather, M E; Varns, J L; Mulik, J D; Glen, G; Smith, L; Stallings, C

2001-11-15

Attaining the current lower tropospheric U.S. ozone standards continues to be a difficult task for many areas in the U.S. Concentrations of ozone above the standards negatively affects human health, agricultural crops, forests, and other ecosystem elements. This paper describes year two (1999) of a regional networking of passive and continuous ozone monitoring sites in the Dallas-Fort Worth (DFW) Metroplex region. The objectives of the second year of study were to (1) validate conclusions of the 1998 Passive Ozone Network of Dallas (POND) I study, (2) define the value of taking 12-h diurnal samples in addition to 24-h samples, and (3) add to the scientific knowledge base of rural/urban ozone comparison studies. Results of the POND II (1999) study demonstrated that ozone concentrations exceeding the new 8-h ozone standard could be recorded at least 130 km, or 80 miles, from the DFW Metroplex core in more rural areas. In addition, results of the POND II study indicated that ozone concentrations exceeding the 8-h standard probably occurred in areas recording a 12-h daytime ozone concentration above 60 parts per billion (ppb). The 12-h passive ozone data from POND II also suggests the relative magnitude of anthropogenic pollution influence could be assessed for rural passive ozone sites. The data from the POND II study provide modelers a rich database for future photochemical subgrid development for the DFW ozone nonattainment area. Indeed, the POND database provides a great amount of additional ozone ambient data covering 26 8-h and 13 1-h ozone standard exceedance days over an approximate 25000 km2 region. These data should help decrease uncertainties derived from future DFW ozone model exercises.

New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

PubMed

Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

2013-07-01

Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR GLOBAL CODING USED BY NHEXAS ARIZONA (HAND ENTRY) (UA-D-5.0)

EPA Science Inventory

The purpose of this SOP is to define the global coding scheme to used in the working and master databases. This procedure applies to all of the databases used during the Arizona NHEXAS project and the "Border" study. Keywords: data; coding; databases.

The National Human Exposu...

NIST/ASME Steam Properties Database

National Institute of Standards and Technology Data Gateway

SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

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

PubMed

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

2010-10-01

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

The Database Management Module of the Splice System.

DTIC Science & Technology

1983-06-01

standardization is the only wise chocs . E. FUNCTIONS OF THE EATABASE MkNAGEMENT MODULE As a result of onqoing research in thmc impl1msntaticn of SPLICE, thns...u an e-v Offset by one or mc--l orders of ma#-inuIs inorcvesnnt --L tue execution time cf user transacdrioas. Purthermore, ’is s-toraqe requlrement

Towards G2G: Systems of Technology Database Systems

NASA Technical Reports Server (NTRS)

Maluf, David A.; Bell, David

2005-01-01

We present an approach and methodology for developing Government-to-Government (G2G) Systems of Technology Database Systems. G2G will deliver technologies for distributed and remote integration of technology data for internal use in analysis and planning as well as for external communications. G2G enables NASA managers, engineers, operational teams and information systems to "compose" technology roadmaps and plans by selecting, combining, extending, specializing and modifying components of technology database systems. G2G will interoperate information and knowledge that is distributed across organizational entities involved that is ideal for NASA future Exploration Enterprise. Key contributions of the G2G system will include the creation of an integrated approach to sustain effective management of technology investments that supports the ability of various technology database systems to be independently managed. The integration technology will comply with emerging open standards. Applications can thus be customized for local needs while enabling an integrated management of technology approach that serves the global needs of NASA. The G2G capabilities will use NASA s breakthrough in database "composition" and integration technology, will use and advance emerging open standards, and will use commercial information technologies to enable effective System of Technology Database systems.

The TERRA-PNW Dataset: A New Source for Standardized Plant Trait, Forest Carbon Cycling, and Soil Properties Measurements from the Pacific Northwest US, 2000-2014.

NASA Astrophysics Data System (ADS)

Berner, L. T.; Law, B. E.

2015-12-01

Plant traits include physiological, morphological, and biogeochemical characteristics that in combination determine a species sensitivity to environmental conditions. Standardized, co-located, and geo-referenced species- and plot-level measurements are needed to address variation in species sensitivity to climate change impacts and for ecosystem process model development, parameterization and testing. We present a new database of plant trait, forest carbon cycling, and soil property measurements derived from multiple TERRA-PNW projects in the Pacific Northwest US, spanning 2000-2014. The database includes measurements from over 200 forest plots across Oregon and northern California, where the data were explicitly collected for scaling and modeling regional terrestrial carbon processes with models such as Biome-BGC and the Community Land Model. Some of the data are co-located at AmeriFlux sites in the region. The database currently contains leaf trait measurements (specific leaf area, leaf longevity, leaf carbon and nitrogen) from over 1,200 branch samples and 30 species, as well as plot-level biomass and productivity components, and soil carbon and nitrogen. Standardized protocols were used across projects, as summarized in an FAO protocols document. The database continues to expand and will include agricultural crops. The database will be hosted by the Oak Ridge National Laboratory (ORLN) Distributed Active Archive Center (DAAC). We hope that other regional databases will become publicly available to help enable Earth System Modeling to simulate species-level sensitivity to climate at regional to global scales.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

PubMed Central

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-01-01

Background Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired. PMID:17877794

Numerical Model Sensitivity to Heterogeneous Satellite Derived Vegetation Roughness

NASA Technical Reports Server (NTRS)

Jasinski, Michael; Eastman, Joseph; Borak, Jordan

2011-01-01

The sensitivity of a mesoscale weather prediction model to a 1 km satellite-based vegetation roughness initialization is investigated for a domain within the south central United States. Three different roughness databases are employed: i) a control or standard lookup table roughness that is a function only of land cover type, ii) a spatially heterogeneous roughness database, specific to the domain, that was previously derived using a physically based procedure and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, and iii) a MODIS climatologic roughness database that like (i) is a function only of land cover type, but possesses domain specific mean values from (ii). The model used is the Weather Research and Forecast Model (WRF) coupled to the Community Land Model within the Land Information System (LIS). For each simulation, a statistical comparison is made between modeled results and ground observations within a domain including Oklahoma, Eastern Arkansas, and Northwest Louisiana during a 4-day period within IHOP 2002. Sensitivity analysis compares the impact the three roughness initializations on time-series temperature, precipitation probability of detection (POD), average wind speed, boundary layer height, and turbulent kinetic energy (TKE). Overall, the results indicate that, for the current investigation, replacement of the standard look-up table values with the satellite-derived values statistically improves model performance for most observed variables. Such natural roughness heterogeneity enhances the surface wind speed, PBL height and TKE production up to 10 percent, with a lesser effect over grassland, and greater effect over mixed land cover domains.

Developmental validation of the PowerPlex(®) Fusion System for analysis of casework and reference samples: A 24-locus multiplex for new database standards.

PubMed

Oostdik, Kathryn; Lenz, Kristy; Nye, Jeffrey; Schelling, Kristin; Yet, Donald; Bruski, Scott; Strong, Joshua; Buchanan, Clint; Sutton, Joel; Linner, Jessica; Frazier, Nicole; Young, Hays; Matthies, Learden; Sage, Amber; Hahn, Jeff; Wells, Regina; Williams, Natasha; Price, Monica; Koehler, Jody; Staples, Melisa; Swango, Katie L; Hill, Carolyn; Oyerly, Karen; Duke, Wendy; Katzilierakis, Lesley; Ensenberger, Martin G; Bourdeau, Jeanne M; Sprecher, Cynthia J; Krenke, Benjamin; Storts, Douglas R

2014-09-01

The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. Yet there remain situations that argue for inclusion of more loci and increased discrimination. The PowerPlex(®) Fusion System allows simultaneous amplification of the following loci: Amelogenin, D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, DYS391, D8S1179, D12S391, D19S433, FGA, and D22S1045. The comprehensive list of loci amplified by the system generates a profile compatible with databases based on either the expanded CODIS or European Standard Set (ESS) requirements. Developmental validation testing followed SWGDAM guidelines and demonstrated the quality and robustness of the PowerPlex(®) Fusion System across a number of variables. Consistent and high-quality results were compiled using data from 12 separate forensic and research laboratories. The results verify that the PowerPlex(®) Fusion System is a robust and reliable STR-typing multiplex suitable for human identification. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Latest developments for the IAGOS database: Interoperability and metadata

NASA Astrophysics Data System (ADS)

Boulanger, Damien; Gautron, Benoit; Thouret, Valérie; Schultz, Martin; van Velthoven, Peter; Broetz, Bjoern; Rauthe-Schöch, Armin; Brissebrat, Guillaume

2014-05-01

In-service Aircraft for a Global Observing System (IAGOS, http://www.iagos.org) aims at the provision of long-term, frequent, regular, accurate, and spatially resolved in situ observations of the atmospheric composition. IAGOS observation systems are deployed on a fleet of commercial aircraft. The IAGOS database is an essential part of the global atmospheric monitoring network. Data access is handled by open access policy based on the submission of research requests which are reviewed by the PIs. Users can access the data through the following web sites: http://www.iagos.fr or http://www.pole-ether.fr as the IAGOS database is part of the French atmospheric chemistry data centre ETHER (CNES and CNRS). The database is in continuous development and improvement. In the framework of the IGAS project (IAGOS for GMES/COPERNICUS Atmospheric Service), major achievements will be reached, such as metadata and format standardisation in order to interoperate with international portals and other databases, QA/QC procedures and traceability, CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) data integration within the central database, and the real-time data transmission. IGAS work package 2 aims at providing the IAGOS data to users in a standardized format including the necessary metadata and information on data processing, data quality and uncertainties. We are currently redefining and standardizing the IAGOS metadata for interoperable use within GMES/Copernicus. The metadata are compliant with the ISO 19115, INSPIRE and NetCDF-CF conventions. IAGOS data will be provided to users in NetCDF or NASA Ames format. We also are implementing interoperability between all the involved IAGOS data services, including the central IAGOS database, the former MOZAIC and CARIBIC databases, Aircraft Research DLR database and the Jülich WCS web application JOIN (Jülich OWS Interface) which combines model outputs with in situ data for intercomparison. The optimal data transfer protocol is being investigated to insure the interoperability. To facilitate satellite and model validation, tools will be made available for co-location and comparison with IAGOS. We will enhance the JOIN application in order to properly display aircraft data as vertical profiles and along individual flight tracks and to allow for graphical comparison to model results that are accessible through interoperable web services, such as the daily products from the GMES/Copernicus atmospheric service.

De-MA: a web Database for electron Microprobe Analyses to assist EMP lab manager and users

NASA Astrophysics Data System (ADS)

Allaz, J. M.

2012-12-01

Lab managers and users of electron microprobe (EMP) facilities require comprehensive, yet flexible documentation structures, as well as an efficient scheduling mechanism. A single on-line database system for managing reservations, and providing information on standards, quantitative and qualitative setups (element mapping, etc.), and X-ray data has been developed for this purpose. This system is particularly useful in multi-user facilities where experience ranges from beginners to the highly experienced. New users and occasional facility users will find these tools extremely useful in developing and maintaining high quality, reproducible, and efficient analyses. This user-friendly database is available through the web, and uses MySQL as a database and PHP/HTML as script language (dynamic website). The database includes several tables for standards information, X-ray lines, X-ray element mapping, PHA, element setups, and agenda. It is configurable for up to five different EMPs in a single lab, each of them having up to five spectrometers and as many diffraction crystals as required. The installation should be done on a web server supporting PHP/MySQL, although installation on a personal computer is possible using third-party freeware to create a local Apache server, and to enable PHP/MySQL. Since it is web-based, any user outside the EMP lab can access this database anytime through any web browser and on any operating system. The access can be secured using a general password protection (e.g. htaccess). The web interface consists of 6 main menus. (1) "Standards" lists standards defined in the database, and displays detailed information on each (e.g. material type, name, reference, comments, and analyses). Images such as EDS spectra or BSE can be associated with a standard. (2) "Analyses" lists typical setups to use for quantitative analyses, allows calculation of mineral composition based on a mineral formula, or calculation of mineral formula based on a fixed amount of oxygen, or of cation (using an analysis in element or oxide weight-%); this latter includes re-calculation of H2O/CO2 based on stoichiometry, and oxygen correction for F and Cl. Another option offers a list of any available standards and possible peak or background interferences for a series of elements. (3) "X-ray maps" lists the different setups recommended for element mapping using WDS, and a map calculator to facilitate maps setups and to estimate the total mapping time. (4) "X-ray data" lists all x-ray lines for a specific element (K, L, M, absorption edges, and satellite peaks) in term of energy, wavelength and peak position. A check for possible interferences on peak or background is also possible. Theoretical x-ray peak positions for each crystal are calculated based on the 2d spacing of each crystal and the wavelength of each line. (5) "Agenda" menu displays the reservation dates for each month and for each EMP lab defined. It also offers a reservation request option, this request being sent by email to the EMP manager for approval. (6) Finally, "Admin" is password restricted, and contains all necessary options to manage the database through user-friendly forms. The installation of this database is made easy and knowledge of HTML, PHP, or MySQL is unnecessary to install, configure, manage, or use it. A working database is accessible at http://cub.geoloweb.ch.

Comparison of published and unpublished phase I clinical cancer trials: an analysis of the CliniclTrials.gov database.

PubMed

Shepshelovich, D; Goldvaser, H; Wang, L; Abdul Razak, A R

2017-12-13

Introduction The role of phase I cancer trials is constantly evolving and they are increasingly being used in 'go/no' decisions in drug development. As a result, there is a growing need to ensure trials are published when completed. There are limited data on the publication rate and the factors associated with publication in phase I trials. Methods The ClinicalTrials.gov database was searched for completed adult phase I cancer trials with reported results. PubMed was searched for matching publications published prior to April 1, 2017. Logistic regression was used to identify factors associated with unpublished trials. Linear regression was used to explore factors associated with time lag from study database lock to publication for published trials. Results The study cohort included 319 trials. 95 (30%) trials had no matching publication. Thirty (9%) trials were not published in abstract form as well. On multivariable analysis, the most significant factor associated with unpublished trials was industry funding (odds ratio 3.3, 95% confidence interval 1.7-6.6, p=0.019). For published trials, time lag between database lock and publication was longer by 10.9 months (standard error 3.6, p<0.001) for industry funded trials compared with medical center funded trials. Conclusions Timely publishing of early cancer clinical trials results remains unsatisfactory. Industry funded phase I cancer trials were more likely to remain unpublished, and were associated with a longer time lag from database lock to publication. Policies that promote transparency and data sharing in clinical trial research might improve accountability among industry and investigators and improve timely results publication.

Establishment of reliable mass spectra and retention indices library: identification of fatty acids in human plasma without authentic standards.

PubMed

Zhang, Liangxiao; Tan, Binbin; Zeng, Maomao; Lu, Hongmei; Liang, Yizeng

2012-01-15

Gas chromatography mass spectrometry (GC-MS) is routinely employed to analyze small molecules in various samples. The more challenge of GC-MS data processing is to identify the unknown compounds in samples. Mass spectra and retention indices library searching are commonly used method. However, the current libraries are often built through collecting data from different groups. To unknown compounds with similar mass spectra and retention indices (e.g. geometric (cis/trans) isomers), the inaccurate results sometime are supplied. In this case, the costly standard compounds have to be used in every analysis. In this report, taking identification of fatty acids as an example, we proposed a strategy of establishment of special database constructed by equivalent chain length (ECL) values in uniform conditions and mass spectra of fatty acid methyl esters (FAMEs). The mass spectral characteristics were firstly used to identify all expected straight saturated fatty acids, and subsequently calculate the ECL for fatty acids in the sample. Finally, the ECL values of fatty acids in the sample were compared with those of fatty acids in the customized database to identify their structures. The results showed that the method developed in this report could effectively identify similar unknown compounds (FAMEs in the human plasma) after validated by the authentic standards. Copyright © 2011 Elsevier B.V. All rights reserved.

A Priori Subgrid Analysis of Temporal Mixing Layers with Evaporating Droplets

NASA Technical Reports Server (NTRS)

Okongo, Nora; Bellan, Josette

1999-01-01

Subgrid analysis of a transitional temporal mixing layer with evaporating droplets has been performed using three sets of results from a Direct Numerical Simulation (DNS) database, with Reynolds numbers (based on initial vorticity thickness) as large as 600 and with droplet mass loadings as large as 0.5. In the DNS, the gas phase is computed using a Eulerian formulation, with Lagrangian droplet tracking. The Large Eddy Simulation (LES) equations corresponding to the DNS are first derived, and key assumptions in deriving them are first confirmed by computing the terms using the DNS database. Since LES of this flow requires the computation of unfiltered gas-phase variables at droplet locations from filtered gas-phase variables at the grid points, it is proposed to model these by assuming the gas-phase variables to be the sum of the filtered variables and a correction based on the filtered standard deviation; this correction is then computed from the Subgrid Scale (SGS) standard deviation. This model predicts the unfiltered variables at droplet locations considerably better than simply interpolating the filtered variables. Three methods are investigated for modeling the SGS standard deviation: the Smagorinsky approach, the Gradient model and the Scale-Similarity formulation. When the proportionality constant inherent in the SGS models is properly calculated, the Gradient and Scale-Similarity methods give results in excellent agreement with the DNS.

Molecular Identification and Databases in Fusarium

USDA-ARS?s Scientific Manuscript database

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

DSSTox and Chemical Information Technologies in Support of PredictiveToxicology

EPA Science Inventory

The EPA NCCT Distributed Structure-Searchable Toxicity (DSSTox) Database project initially focused on the curation and publication of high-quality, standardized, chemical structure-annotated toxicity databases for use in structure-activity relationship (SAR) modeling. In recent y...

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.

PubMed

McQuilton, Peter; Gonzalez-Beltran, Alejandra; Rocca-Serra, Philippe; Thurston, Milo; Lister, Allyson; Maguire, Eamonn; Sansone, Susanna-Assunta

2016-01-01

BioSharing (http://www.biosharing.org) is a manually curated, searchable portal of three linked registries. These resources cover standards (terminologies, formats and models, and reporting guidelines), databases, and data policies in the life sciences, broadly encompassing the biological, environmental and biomedical sciences. Launched in 2011 and built by the same core team as the successful MIBBI portal, BioSharing harnesses community curation to collate and cross-reference resources across the life sciences from around the world. BioSharing makes these resources findable and accessible (the core of the FAIR principle). Every record is designed to be interlinked, providing a detailed description not only on the resource itself, but also on its relations with other life science infrastructures. Serving a variety of stakeholders, BioSharing cultivates a growing community, to which it offers diverse benefits. It is a resource for funding bodies and journal publishers to navigate the metadata landscape of the biological sciences; an educational resource for librarians and information advisors; a publicising platform for standard and database developers/curators; and a research tool for bench and computer scientists to plan their work. BioSharing is working with an increasing number of journals and other registries, for example linking standards and databases to training material and tools. Driven by an international Advisory Board, the BioSharing user-base has grown by over 40% (by unique IP address), in the last year thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint RDA/Force11 working group and a collaboration with the International Society for Biocuration. In this article, we describe BioSharing, with a particular focus on community-led curation.Database URL: https://www.biosharing.org. © The Author(s) 2016. Published by Oxford University Press.

Mobile Source Observation Database (MSOD)

EPA Pesticide Factsheets

The Mobile Source Observation Database (MSOD) is a relational database being developed by the Assessment and Standards Division (ASD) of the US Environmental Protection Agency Office of Transportation and Air Quality (formerly the Office of Mobile Sources). The MSOD contains emission test data from in-use mobile air- pollution sources such as cars, trucks, and engines from trucks and nonroad vehicles. Data in the database was collected from 1982 to the present. The data is intended to be representative of in-use vehicle emissions in the United States.

Comprehensive Routing Security Development and Deployment for the Internet

DTIC Science & Technology

2015-02-01

feature enhancement and bug fixes. • MySQL : MySQL is a widely used and popular open source database package. It was chosen for database support in the...RPSTIR depends on several other open source packages. • MySQL : MySQL is used for the the local RPKI database cache. • OpenSSL: OpenSSL is used for...cryptographic libraries for X.509 certificates. • ODBC mySql Connector: ODBC (Open Database Connectivity) is a standard programming interface (API) for

Analysis and preliminary design of Kunming land use and planning management information system

NASA Astrophysics Data System (ADS)

Li, Li; Chen, Zhenjie

2007-06-01

This article analyzes Kunming land use planning and management information system from the system building objectives and system building requirements aspects, nails down the system's users, functional requirements and construction requirements. On these bases, the three-tier system architecture based on C/S and B/S is defined: the user interface layer, the business logic layer and the data services layer. According to requirements for the construction of land use planning and management information database derived from standards of the Ministry of Land and Resources and the construction program of the Golden Land Project, this paper divides system databases into planning document database, planning implementation database, working map database and system maintenance database. In the design of the system interface, this paper uses various methods and data formats for data transmission and sharing between upper and lower levels. According to the system analysis results, main modules of the system are designed as follows: planning data management, the planning and annual plan preparation and control function, day-to-day planning management, planning revision management, decision-making support, thematic inquiry statistics, planning public participation and so on; besides that, the system realization technologies are discussed from the system operation mode, development platform and other aspects.

GMDD: a database of GMO detection methods

PubMed Central

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

2008-01-01

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

The Mouse Heart Attack Research Tool (mHART) 1.0 Database.

PubMed

DeLeon-Pennell, Kristine Y; Iyer, Rugmani Padmanabhan; Ma, Yonggang; Yabluchanskiy, Andriy; Zamilpa, Rogelio; Chiao, Ying Ann; Cannon, Presley; Cates, Courtney; Flynn, Elizabeth R; Halade, Ganesh V; de Castro Bras, Lisandra E; Lindsey, Merry L

2018-05-18

The generation of Big Data has enabled systems-level dissections into the mechanisms of cardiovascular pathology. Integration of genetic, proteomic, and pathophysiological variables across platforms and laboratories fosters discoveries through multidisciplinary investigations and minimizes unnecessary redundancy in research efforts. The Mouse Heart Attack Research Tool (mHART) consolidates a large dataset of over 10 years of experiments from a single laboratory for cardiovascular investigators to generate novel hypotheses and identify new predictive markers of progressive left ventricular remodeling following myocardial infarction (MI) in mice. We designed the mHART REDCap database using our own data to integrate cardiovascular community participation. We generated physiological, biochemical, cellular, and proteomic outputs from plasma and left ventricles obtained from post-MI and no MI (naïve) control groups. We included both male and female mice ranging in age from 3 to 36 months old. After variable collection, data underwent quality assessment for data curation (e.g. eliminate technical errors, check for completeness, remove duplicates, and define terms). Currently, mHART 1.0 contains >888,000 data points and includes results from >2,100 unique mice. Database performance was tested and an example provided to illustrate database utility. This report explains how the first version of the mHART database was established and provides researchers with a standard framework to aid in the integration of their data into our database or in the development of a similar database.

SU-E-T-255: Development of a Michigan Quality Assurance (MQA) Database for Clinical Machine Operations

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

Roberts, D

Purpose: A unified database system was developed to allow accumulation, review and analysis of quality assurance (QA) data for measurement, treatment, imaging and simulation equipment in our department. Recording these data in a database allows a unified and structured approach to review and analysis of data gathered using commercial database tools. Methods: A clinical database was developed to track records of quality assurance operations on linear accelerators, a computed tomography (CT) scanner, high dose rate (HDR) afterloader and imaging systems such as on-board imaging (OBI) and Calypso in our department. The database was developed using Microsoft Access database and visualmore » basic for applications (VBA) programming interface. Separate modules were written for accumulation, review and analysis of daily, monthly and annual QA data. All modules were designed to use structured query language (SQL) as the basis of data accumulation and review. The SQL strings are dynamically re-written at run time. The database also features embedded documentation, storage of documents produced during QA activities and the ability to annotate all data within the database. Tests are defined in a set of tables that define test type, specific value, and schedule. Results: Daily, Monthly and Annual QA data has been taken in parallel with established procedures to test MQA. The database has been used to aggregate data across machines to examine the consistency of machine parameters and operations within the clinic for several months. Conclusion: The MQA application has been developed as an interface to a commercially available SQL engine (JET 5.0) and a standard database back-end. The MQA system has been used for several months for routine data collection.. The system is robust, relatively simple to extend and can be migrated to a commercial SQL server.« less

Grid-Enabled Measures

PubMed Central

Moser, Richard P.; Hesse, Bradford W.; Shaikh, Abdul R.; Courtney, Paul; Morgan, Glen; Augustson, Erik; Kobrin, Sarah; Levin, Kerry; Helba, Cynthia; Garner, David; Dunn, Marsha; Coa, Kisha

2011-01-01

Scientists are taking advantage of the Internet and collaborative web technology to accelerate discovery in a massively connected, participative environment —a phenomenon referred to by some as Science 2.0. As a new way of doing science, this phenomenon has the potential to push science forward in a more efficient manner than was previously possible. The Grid-Enabled Measures (GEM) database has been conceptualized as an instantiation of Science 2.0 principles by the National Cancer Institute with two overarching goals: (1) Promote the use of standardized measures, which are tied to theoretically based constructs; and (2) Facilitate the ability to share harmonized data resulting from the use of standardized measures. This is done by creating an online venue connected to the Cancer Biomedical Informatics Grid (caBIG®) where a virtual community of researchers can collaborate together and come to consensus on measures by rating, commenting and viewing meta-data about the measures and associated constructs. This paper will describe the web 2.0 principles on which the GEM database is based, describe its functionality, and discuss some of the important issues involved with creating the GEM database, such as the role of mutually agreed-on ontologies (i.e., knowledge categories and the relationships among these categories— for data sharing). PMID:21521586

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.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

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

Reddy, Tatiparthi B. K.; Thomas, Alex D.; Stamatis, Dimitri

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencingmore » projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.« less

Second Line of Defense Master Spares Catalog

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

Henderson, Dale L.; Muller, George; Mercier, Theresa M.

This catalog is intended to be a comprehensive listing of repair parts, components, kits, and consumable items used on the equipment deployed at SLD sites worldwide. The catalog covers detection, CAS, network, ancillary equipment, and tools. The catalog is backed by a Master Parts Database which is used to generate the standard report views of the catalog. The master parts database is a relational database containing a record for every part in the master parts catalog along with supporting tables for normalizing fields in the records. The database also includes supporting queries, database maintenance forms, and reports.

Development of Database for Accident Analysis in Indian Mines

NASA Astrophysics Data System (ADS)

Tripathy, Debi Prasad; Guru Raghavendra Reddy, K.

2016-10-01

Mining is a hazardous industry and high accident rates associated with underground mining is a cause of deep concern. Technological developments notwithstanding, rate of fatal accidents and reportable incidents have not shown corresponding levels of decline. This paper argues that adoption of appropriate safety standards by both mine management and the government may result in appreciable reduction in accident frequency. This can be achieved by using the technology in improving the working conditions, sensitising workers and managers about causes and prevention of accidents. Inputs required for a detailed analysis of an accident include information on location, time, type, cost of accident, victim, nature of injury, personal and environmental factors etc. Such information can be generated from data available in the standard coded accident report form. This paper presents a web based application for accident analysis in Indian mines during 2001-2013. An accident database (SafeStat) prototype based on Intranet of the TCP/IP agreement, as developed by the authors, is also discussed.

Current projects in Pre-analytics: where to go?

PubMed

Sapino, Anna; Annaratone, Laura; Marchiò, Caterina

2015-01-01

The current clinical practice of tissue handling and sample preparation is multifaceted and lacks strict standardisation: this scenario leads to significant variability in the quality of clinical samples. Poor tissue preservation has a detrimental effect thus leading to morphological artefacts, hampering the reproducibility of immunocytochemical and molecular diagnostic results (protein expression, DNA gene mutations, RNA gene expression) and affecting the research outcomes with irreproducible gene expression and post-transcriptional data. Altogether, this limits the opportunity to share and pool national databases into European common databases. At the European level, standardization of pre-analytical steps is just at the beginning and issues regarding bio-specimen collection and management are still debated. A joint (public-private) project entitled on standardization of tissue handling in pre-analytical procedures has been recently funded in Italy with the aim of proposing novel approaches to the neglected issue of pre-analytical procedures. In this chapter, we will show how investing in pre-analytics may impact both public health problems and practical innovation in solid tumour processing.

The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer.

PubMed

Krupke, Debra M; Begley, Dale A; Sundberg, John P; Richardson, Joel E; Neuhauser, Steven B; Bult, Carol J

2017-11-01

Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. The Mouse Tumor Biology (MTB) database is an expertly curated, comprehensive compendium of mouse models of human cancer. Through the enforcement of nomenclature and related annotation standards, MTB supports aggregation of data about a cancer model from diverse sources and assessment of how genetic background of a mouse strain influences the biological properties of a specific tumor type and model utility. Cancer Res; 77(21); e67-70. ©2017 AACR . ©2017 American Association for Cancer Research.

Predictive biological markers of systemic lupus erythematosus flares: a systematic literature review.

PubMed

Gensous, Noémie; Marti, Aurélie; Barnetche, Thomas; Blanco, Patrick; Lazaro, Estibaliz; Seneschal, Julien; Truchetet, Marie-Elise; Duffau, Pierre; Richez, Christophe

2017-10-24

The aim of this study was to identify the most reliable biomarkers in the literature that could be used as flare predictors in systemic lupus erythematosus (SLE). A systematic review of the literature was performed using two databases (MEDLINE and EMBASE) through April 2015 and congress abstracts from the American College of Rheumatology and the European League Against Rheumatism were reviewed from 2010 to 2014. Two independent reviewers screened titles and abstracts and analysed selected papers in detail, using a specific questionnaire. Reports addressing the relationships between one or more defined biological test(s) and the occurrence of disease exacerbation were included in the systematic review. From all of the databases, 4668 records were retrieved, of which 69 studies or congress abstracts were selected for the systematic review. The performance of seven types of biomarkers performed routinely in clinical practice and nine types of novel biological markers was evaluated. Despite some encouraging results for anti-double-stranded DNA antibodies, anti-C1q antibodies, B-lymphocyte stimulator and tumour necrosis factor-like weak inducer of apoptosis, none of the biomarkers stood out from the others as a potential gold standard for flare prediction. The results were heterogeneous, and a lack of standardized data prevented us from identifying a powerful biomarker. No powerful conclusions could be drawn from this systematic review due to a lack of standardized data. Efforts should be undertaken to optimize future research on potential SLE biomarkers to develop validated candidates. Thus, we propose a standardized pattern for future studies.

48 CFR 211.204 - Solicitation provisions and contract clauses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... performance requires use of specifications, standards, and data item descriptions that are not listed in the Acquisition Streamlining and Standardization Information System database, use provisions, as appropriate...

48 CFR 211.204 - Solicitation provisions and contract clauses.

Code of Federal Regulations, 2011 CFR

2011-10-01

... performance requires use of specifications, standards, and data item descriptions that are not listed in the Acquisition Streamlining and Standardization Information System database, use provisions, as appropriate...

Proteomics data exchange and storage: the need for common standards and public repositories.

PubMed

Jiménez, Rafael C; Vizcaíno, Juan Antonio

2013-01-01

Both the existence of data standards and public databases or repositories have been key factors behind the development of the existing "omics" approaches. In this book chapter we first review the main existing mass spectrometry (MS)-based proteomics resources: PRIDE, PeptideAtlas, GPMDB, and Tranche. Second, we report on the current status of the different proteomics data standards developed by the Proteomics Standards Initiative (PSI): the formats mzML, mzIdentML, mzQuantML, TraML, and PSI-MI XML are then reviewed. Finally, we present an easy way to query and access MS proteomics data in the PRIDE database, as a representative of the existing repositories, using the workflow management system (WMS) tool Taverna. Two different publicly available workflows are explained and described.

Online Databases. Ingenta Grows in the U.S. Market.

ERIC Educational Resources Information Center

Tenopir, Carol

2002-01-01

Focuses on the growth of the United Kingdom company Ingenta in the United States. Highlights include a new partnership with Gale Group related to their InfoTrac databases; indexing and full text coverage; standards; and other Ingenta acquisitions. (LRW)

EUnetHTA information management system: development and lessons learned.

PubMed

Chalon, Patrice X; Kraemer, Peter

2014-11-01

The aim of this study was to describe the techniques used in achieving consensus on common standards to be implemented in the EUnetHTA Information Management System (IMS); and to describe how interoperability between tools was explored. Three face to face meetings were organized to identify and agree on common standards to the development of online tools. Two tools were created to demonstrate the added value of implementing interoperability standards at local levels. Developers of tools outside EUnetHTA were identified and contacted. Four common standards have been agreed on by consensus; and consequently all EUnetHTA tools have been modified or designed accordingly. RDF Site Summary (RSS) has demonstrated a good potential to support rapid dissemination of HTA information. Contacts outside EUnetHTA resulted in direct collaboration (HTA glossary, HTAi Vortal), evaluation of options for interoperability between tools (CRD HTA database) or a formal framework to prepare cooperation on concrete projects (INAHTA projects database). While being entitled a project on IT infrastructure, the work program was also about people. When having to agree on complex topics, fostering a cohesive group dynamic and hosting face to face meetings brings added value and enhances understanding between partners. The adoption of widespread standards enhanced the homogeneity of the EUnetHTA tools and should thus contribute to their wider use, therefore, to the general objective of EUnetHTA. The initiatives on interoperability of systems need to be developed further to support a general interoperable information system that could benefit the whole HTA community.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

PubMed Central

2011-01-01

Background Multiple pathway databases are available that describe the human metabolic network and have proven their usefulness in many applications, ranging from the analysis and interpretation of high-throughput data to their use as a reference repository. However, so far the various human metabolic networks described by these databases have not been systematically compared and contrasted, nor has the extent to which they differ been quantified. For a researcher using these databases for particular analyses of human metabolism, it is crucial to know the extent of the differences in content and their underlying causes. Moreover, the outcomes of such a comparison are important for ongoing integration efforts. Results We compared the genes, EC numbers and reactions of five frequently used human metabolic pathway databases. The overlap is surprisingly low, especially on reaction level, where the databases agree on 3% of the 6968 reactions they have combined. Even for the well-established tricarboxylic acid cycle the databases agree on only 5 out of the 30 reactions in total. We identified the main causes for the lack of overlap. Importantly, the databases are partly complementary. Other explanations include the number of steps a conversion is described in and the number of possible alternative substrates listed. Missing metabolite identifiers and ambiguous names for metabolites also affect the comparison. Conclusions Our results show that each of the five networks compared provides us with a valuable piece of the puzzle of the complete reconstruction of the human metabolic network. To enable integration of the networks, next to a need for standardizing the metabolite names and identifiers, the conceptual differences between the databases should be resolved. Considerable manual intervention is required to reach the ultimate goal of a unified and biologically accurate model for studying the systems biology of human metabolism. Our comparison provides a stepping stone for such an endeavor. PMID:21999653

Inside a VAMDC data node—putting standards into practical software

NASA Astrophysics Data System (ADS)

Regandell, Samuel; Marquart, Thomas; Piskunov, Nikolai

2018-03-01

Access to molecular and atomic data is critical for many forms of remote sensing analysis across different fields. Many atomic and molecular databases are however highly specialised for their intended application, complicating querying and combination data between sources. The Virtual Atomic and Molecular Data Centre, VAMDC, is an electronic infrastructure that allows each database to register as a ‘node’. Through services such as VAMDC’s portal website, users can then access and query all nodes in a homogenised way. Today all major Atomic and Molecular databases are attached to VAMDC This article describes the software tools we developed to help data providers create and manage a VAMDC node. It gives an overview of the VAMDC infrastructure and of the various standards it uses. The article then discusses the development choices made and how the standards are implemented in practice. It concludes with a full example of implementing a VAMDC node using a real-life case as well as future plans for the node software.

TCOF1 mutation database: novel mutation in the alternatively spliced exon 6A and update in mutation nomenclature.

PubMed

Splendore, Alessandra; Fanganiello, Roberto D; Masotti, Cibele; Morganti, Lucas S C; Passos-Bueno, M Rita

2005-05-01

Recently, a novel exon was described in TCOF1 that, although alternatively spliced, is included in the major protein isoform. In addition, most published mutations in this gene do not conform to current mutation nomenclature guidelines. Given these observations, we developed an online database of TCOF1 mutations in which all the reported mutations are renamed according to standard recommendations and in reference to the genomic and novel cDNA reference sequences (www.genoma.ib.usp.br/TCOF1_database). We also report in this work: 1) results of the first screening for large deletions in TCOF1 by Southern blot in patients without mutation detected by direct sequencing; 2) the identification of the first pathogenic mutation in the newly described exon 6A; and 3) statistical analysis of pathogenic mutations and polymorphism distribution throughout the gene.

[Experience and present situation of Western China Gastric Cancer Collaboration].

PubMed

Hu, Jiankun; Zhang, Weihan; Western China Gastric Cancer Collaboration, China

2017-03-25

The Western China Gastric Cancer Collaboration (WCGCC) was founded in Chongqing, China in 2011. At the early stage of the collaboration, there were only about 20 centers. While now, there are 36 centers from western area of China, including Sichuan, Chongqing, Yunnan, Shanxi, Guizhou, Gansu, Qinghai, Xinjiang, Ningxia and Tibet. During the past few years, the WCGCC organized routinely gastric cancer standardized treatment tours, training courses of mini-invasive surgical treatment of gastric cancer and the clinical research methodology for members of the collaboration. Meanwhile, the WCGCC built a multicenter database of gastric cancer since 2011 and the entering and management refer to national gastric cancer registration entering system of Japan Gastric Cancer Association. During the entering and collection of data, 190 items of data have unified definition and entering standard from Japan Gastric Cancer Guidelines. Nowadays, this database included about 11 872 gastric cancer cases, and in this paper we will introduce the initial results of these cases. Next, the collaboration will conduct some retrospective studies based on this database to analyze the clinicopathological characteristics of patients in the western area of China. Besides, the WCGCC performed a prospective study, also. The first randomized clinical trial of the collaboration aims to compare the postoperative quality of life between different reconstruction methods for total gastrectomy(WCGCC-1202, ClinicalTrials.gov Identifier: NCT02110628), which began in 2015, and now this study is in the recruitment period. In the next steps, we will improve the quality of the database, optimize the management processes. Meanwhile, we will engage in more exchanges and cooperation with the Chinese Cochrane Center, reinforce the foundation of the clinical trials research methodology. In aspect of standardized surgical treatment of gastric cancer, we will further strengthen communication with other international centers in order to improve both the treatment and research levels of gastric cancer in Western China.

Creating a standardized watersheds database for the Lower Rio Grande/Río Bravo, Texas

USGS Publications Warehouse

Brown, J.R.; Ulery, Randy L.; Parcher, Jean W.

2000-01-01

This report describes the creation of a large-scale watershed database for the lower Rio Grande/Río Bravo Basin in Texas. The watershed database includes watersheds delineated to all 1:24,000-scale mapped stream confluences and other hydrologically significant points, selected watershed characteristics, and hydrologic derivative datasets.Computer technology allows generation of preliminary watershed boundaries in a fraction of the time needed for manual methods. This automated process reduces development time and results in quality improvements in watershed boundaries and characteristics. These data can then be compiled in a permanent database, eliminating the time-consuming step of data creation at the beginning of a project and providing a stable base dataset that can give users greater confidence when further subdividing watersheds.A standardized dataset of watershed characteristics is a valuable contribution to the understanding and management of natural resources. Vertical integration of the input datasets used to automatically generate watershed boundaries is crucial to the success of such an effort. The optimum situation would be to use the digital orthophoto quadrangles as the source of all the input datasets. While the hydrographic data from the digital line graphs can be revised to match the digital orthophoto quadrangles, hypsography data cannot be revised to match the digital orthophoto quadrangles. Revised hydrography from the digital orthophoto quadrangle should be used to create an updated digital elevation model that incorporates the stream channels as revised from the digital orthophoto quadrangle. Computer-generated, standardized watersheds that are vertically integrated with existing digital line graph hydrographic data will continue to be difficult to create until revisions can be made to existing source datasets. Until such time, manual editing will be necessary to make adjustments for man-made features and changes in the natural landscape that are not reflected in the digital elevation model data.

Creating a standardized watersheds database for the lower Rio Grande/Rio Bravo, Texas

USGS Publications Warehouse

Brown, Julie R.; Ulery, Randy L.; Parcher, Jean W.

2000-01-01

This report describes the creation of a large-scale watershed database for the lower Rio Grande/Rio Bravo Basin in Texas. The watershed database includes watersheds delineated to all 1:24,000-scale mapped stream confluences and other hydrologically significant points, selected watershed characteristics, and hydrologic derivative datasets. Computer technology allows generation of preliminary watershed boundaries in a fraction of the time needed for manual methods. This automated process reduces development time and results in quality improvements in watershed boundaries and characteristics. These data can then be compiled in a permanent database, eliminating the time-consuming step of data creation at the beginning of a project and providing a stable base dataset that can give users greater confidence when further subdividing watersheds. A standardized dataset of watershed characteristics is a valuable contribution to the understanding and management of natural resources. Vertical integration of the input datasets used to automatically generate watershed boundaries is crucial to the success of such an effort. The optimum situation would be to use the digital orthophoto quadrangles as the source of all the input datasets. While the hydrographic data from the digital line graphs can be revised to match the digital orthophoto quadrangles, hypsography data cannot be revised to match the digital orthophoto quadrangles. Revised hydrography from the digital orthophoto quadrangle should be used to create an updated digital elevation model that incorporates the stream channels as revised from the digital orthophoto quadrangle. Computer-generated, standardized watersheds that are vertically integrated with existing digital line graph hydrographic data will continue to be difficult to create until revisions can be made to existing source datasets. Until such time, manual editing will be necessary to make adjustments for man-made features and changes in the natural landscape that are not reflected in the digital elevation model data.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

The challenges of measuring quality-of-care indicators in rural emergency departments: a cross-sectional descriptive study

PubMed Central

Layani, Géraldine; Fleet, Richard; Dallaire, Renée; Tounkara, Fatoumata K.; Poitras, Julien; Archambault, Patrick; Chauny, Jean-Marc; Ouimet, Mathieu; Gauthier, Josée; Dupuis, Gilles; Tanguay, Alain; Lévesque, Jean-Frédéric; Simard-Racine, Geneviève; Haggerty, Jeannie; Légaré, France

2016-01-01

Background: Evidence-based indicators of quality of care have been developed to improve care and performance in Canadian emergency departments. The feasibility of measuring these indicators has been assessed mainly in urban and academic emergency departments. We sought to assess the feasibility of measuring quality-of-care indicators in rural emergency departments in Quebec. Methods: We previously identified rural emergency departments in Quebec that offered medical coverage with hospital beds 24 hours a day, 7 days a week and were located in rural areas or small towns as defined by Statistics Canada. A standardized protocol was sent to each emergency department to collect data on 27 validated quality-of-care indicators in 8 categories: duration of stay, patient safety, pain management, pediatrics, cardiology, respiratory care, stroke and sepsis/infection. Data were collected by local professional medical archivists between June and December 2013. Results: Fifteen (58%) of the 26 emergency departments invited to participate completed data collection. The ability to measure the 27 quality-of-care indicators with the use of databases varied across departments. Centres 2, 5, 6 and 13 used databases for at least 21 of the indicators (78%-92%), whereas centres 3, 8, 9, 11, 12 and 15 used databases for 5 (18%) or fewer of the indicators. On average, the centres were able to measure only 41% of the indicators using heterogeneous databases and manual extraction. The 15 centres collected data from 15 different databases or combinations of databases. The average data collection time for each quality-of-care indicator varied from 5 to 88.5 minutes. The median data collection time was 15 minutes or less for most indicators. Interpretation: Quality-of-care indicators were not easily captured with the use of existing databases in rural emergency departments in Quebec. Further work is warranted to improve standardized measurement of these indicators in rural emergency departments in the province and to generalize the information gathered in this study to other health care environments. PMID:27730103

Compressing DNA sequence databases with coil.

PubMed

White, W Timothy J; Hendy, Michael D

2008-05-20

Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression - the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

“Gone are the days of mass-media marketing plans and short term customer relationships”: tobacco industry direct mail and database marketing strategies

PubMed Central

Lewis, M Jane; Ling, Pamela M

2015-01-01

Background As limitations on traditional marketing tactics and scrutiny by tobacco control have increased, the tobacco industry has benefited from direct mail marketing which transmits marketing messages directly to carefully targeted consumers utilising extensive custom consumer databases. However, research in these areas has been limited. This is the first study to examine the development, purposes and extent of direct mail and customer databases. Methods We examined direct mail and database marketing by RJ Reynolds and Philip Morris utilising internal tobacco industry documents from the Legacy Tobacco Document Library employing standard document research techniques. Results Direct mail marketing utilising industry databases began in the 1970s and grew from the need for a promotional strategy to deal with declining smoking rates, growing numbers of products and a cluttered media landscape. Both RJ Reynolds and Philip Morris started with existing commercial consumer mailing lists, but subsequently decided to build their own databases of smokers’ names, addresses, brand preferences, purchase patterns, interests and activities. By the mid-1990s both RJ Reynolds and Philip Morris databases contained at least 30 million smokers’ names each. These companies valued direct mail/database marketing’s flexibility, efficiency and unique ability to deliver specific messages to particular groups as well as direct mail’s limited visibility to tobacco control, public health and regulators. Conclusions Database marketing is an important and increasingly sophisticated tobacco marketing strategy. Additional research is needed on the prevalence of receipt and exposure to direct mail items and their influence on receivers’ perceptions and smoking behaviours. PMID:26243810

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

A Community Database of Quartz Microstructures: Can we make measurements that constrain rheology?

NASA Astrophysics Data System (ADS)

Toy, Virginia; Peternell, Mark; Morales, Luiz; Kilian, Ruediger

2014-05-01

Rheology can be explored by performing deformation experiments, and by examining resultant microstructures and textures as links to naturally deformed rocks. Certain deformation processes are assumed to result in certain microstructures or textures, of which some might be uniquely indicative, while most cannot be unequivocally used to interpret the deformation mechanism and hence rheology. Despite our lack of a sufficient understanding of microstructure and texture forming processes, huge advances in texture measurements and quantification of microstructural parameters have been made. Unfortunately, there are neither standard procedures nor a common consensus on interpretation of many parameters (e.g. texture, grain size, shape preferred orientation). Textures (crystallographic preferred orientations) have been extensively correlated to the interpretation of deformation mechanisms. For example the strength of textures can be measured either from the orientation distribution function (e.g. the J-index (Bunge, 1983) or texture entropy (Hielscher et al., 2007) or via the intensity of polefigures. However, there are various ways to identify a representative volume, to measure, to process the data and to calculate an odf and texture descriptors, which restricts their use as a comparative and diagnostic measurement. Microstructural parameters such as grain size, grain shape descriptors and fabric descriptors are similarly used to deduce and quantify deformation mechanisms. However there is very little consensus on how to measure and calculate some of these very important parameters, e.g. grain size which makes comparison of a vast amount of precious data in the literature very difficult. We propose establishing a community database of a standard set of such measurements, made using typical samples of different types of quartz rocks through standard methods of microstructural and texture quantification. We invite suggestions and discussion from the community about the worth of proposed parameters, methodology and usefulness and willingness to contribute to a database with free access of the community. We further invite institutions to participate on a benchmark analysis of a set of 'standard' thin sections. Bunge, H.J. 1983, Texture Analysis in Materials Science: mathematical methods. Butterworth-Heinemann, 593pp. Hielscher, R., Schaeben, H., Chateigner, D., 2007, On the entropy to texture index relationship in quantitative texture analysis: Journal of Applied Crystallography 40, 371-375.

Databases applicable to quantitative hazard/risk assessment-Towards a predictive systems toxicology

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

Waters, Michael; Jackson, Marcus

2008-11-15

The Workshop on The Power of Aggregated Toxicity Data addressed the requirement for distributed databases to support quantitative hazard and risk assessment. The authors have conceived and constructed with federal support several databases that have been used in hazard identification and risk assessment. The first of these databases, the EPA Gene-Tox Database was developed for the EPA Office of Toxic Substances by the Oak Ridge National Laboratory, and is currently hosted by the National Library of Medicine. This public resource is based on the collaborative evaluation, by government, academia, and industry, of short-term tests for the detection of mutagens andmore » presumptive carcinogens. The two-phased evaluation process resulted in more than 50 peer-reviewed publications on test system performance and a qualitative database on thousands of chemicals. Subsequently, the graphic and quantitative EPA/IARC Genetic Activity Profile (GAP) Database was developed in collaboration with the International Agency for Research on Cancer (IARC). A chemical database driven by consideration of the lowest effective dose, GAP has served IARC for many years in support of hazard classification of potential human carcinogens. The Toxicological Activity Profile (TAP) prototype database was patterned after GAP and utilized acute, subchronic, and chronic data from the Office of Air Quality Planning and Standards. TAP demonstrated the flexibility of the GAP format for air toxics, water pollutants and other environmental agents. The GAP format was also applied to developmental toxicants and was modified to represent quantitative results from the rodent carcinogen bioassay. More recently, the authors have constructed: 1) the NIEHS Genetic Alterations in Cancer (GAC) Database which quantifies specific mutations found in cancers induced by environmental agents, and 2) the NIEHS Chemical Effects in Biological Systems (CEBS) Knowledgebase that integrates genomic and other biological data including dose-response studies in toxicology and pathology. Each of the public databases has been discussed in prior publications. They will be briefly described in the present report from the perspective of aggregating datasets to augment the data and information contained within them.« less

Full value documentation in the Czech Food Composition Database.

PubMed

Machackova, M; Holasova, M; Maskova, E

2010-11-01

The aim of this project was to launch a new Food Composition Database (FCDB) Programme in the Czech Republic; to implement a methodology for food description and value documentation according to the standards designed by the European Food Information Resource (EuroFIR) Network of Excellence; and to start the compilation of a pilot FCDB. Foods for the initial data set were selected from the list of foods included in the Czech Food Consumption Basket. Selection of 24 priority components was based on the range of components used in former Czech tables. The priority list was extended with components for which original Czech analytical data or calculated data were available. Values that were input into the compiled database were documented according to the EuroFIR standards within the entities FOOD, COMPONENT, VALUE and REFERENCE using Excel sheets. Foods were described using the LanguaL Thesaurus. A template for documentation of data according to the EuroFIR standards was designed. The initial data set comprised documented data for 162 foods. Values were based on original Czech analytical data (available for traditional and fast foods, milk and milk products, wheat flour types), data derived from literature (for example, fruits, vegetables, nuts, legumes, eggs) and calculated data. The Czech FCDB programme has been successfully relaunched. Inclusion of the Czech data set into the EuroFIR eSearch facility confirmed compliance of the database format with the EuroFIR standards. Excel spreadsheets are applicable for full value documentation in the FCDB.

Building a Database for the Historical Analysis of the General Chemistry Curriculum Using ACS General Chemistry Exams as Artifacts

ERIC Educational Resources Information Center

Luxford, Cynthia J.; Linenberger, Kimberly J.; Raker, Jeffrey R.; Baluyut, John Y.; Reed, Jessica J.; De Silva, Chamila; Holme, Thomas A.

2015-01-01

As a discipline, chemistry enjoys a unique position. While many academic areas prepared "cooperative examinations" in the 1930s, only chemistry maintained the activity within what has become the ACS Examinations Institute. As a result, the long-term existence of community-built, norm-referenced, standardized exams provides a historical…

Assembling proteomics data as a prerequisite for the analysis of large scale experiments

PubMed Central

Schmidt, Frank; Schmid, Monika; Thiede, Bernd; Pleißner, Klaus-Peter; Böhme, Martina; Jungblut, Peter R

2009-01-01

Background Despite the complete determination of the genome sequence of a huge number of bacteria, their proteomes remain relatively poorly defined. Beside new methods to increase the number of identified proteins new database applications are necessary to store and present results of large- scale proteomics experiments. Results In the present study, a database concept has been developed to address these issues and to offer complete information via a web interface. In our concept, the Oracle based data repository system SQL-LIMS plays the central role in the proteomics workflow and was applied to the proteomes of Mycobacterium tuberculosis, Helicobacter pylori, Salmonella typhimurium and protein complexes such as 20S proteasome. Technical operations of our proteomics labs were used as the standard for SQL-LIMS template creation. By means of a Java based data parser, post-processed data of different approaches, such as LC/ESI-MS, MALDI-MS and 2-D gel electrophoresis (2-DE), were stored in SQL-LIMS. A minimum set of the proteomics data were transferred in our public 2D-PAGE database using a Java based interface (Data Transfer Tool) with the requirements of the PEDRo standardization. Furthermore, the stored proteomics data were extractable out of SQL-LIMS via XML. Conclusion The Oracle based data repository system SQL-LIMS played the central role in the proteomics workflow concept. Technical operations of our proteomics labs were used as standards for SQL-LIMS templates. Using a Java based parser, post-processed data of different approaches such as LC/ESI-MS, MALDI-MS and 1-DE and 2-DE were stored in SQL-LIMS. Thus, unique data formats of different instruments were unified and stored in SQL-LIMS tables. Moreover, a unique submission identifier allowed fast access to all experimental data. This was the main advantage compared to multi software solutions, especially if personnel fluctuations are high. Moreover, large scale and high-throughput experiments must be managed in a comprehensive repository system such as SQL-LIMS, to query results in a systematic manner. On the other hand, these database systems are expensive and require at least one full time administrator and specialized lab manager. Moreover, the high technical dynamics in proteomics may cause problems to adjust new data formats. To summarize, SQL-LIMS met the requirements of proteomics data handling especially in skilled processes such as gel-electrophoresis or mass spectrometry and fulfilled the PSI standardization criteria. The data transfer into a public domain via DTT facilitated validation of proteomics data. Additionally, evaluation of mass spectra by post-processing using MS-Screener improved the reliability of mass analysis and prevented storage of data junk. PMID:19166578

MATD Operational Phase: Experiences and Lessons Learned

NASA Astrophysics Data System (ADS)

Messidoro, P.; Bader, M.; Brunner, O.; Cerrato, A.; Sembenini, G.

2004-08-01

The Model And Test Effectiveness Database (MATD) initiative is ending the first year of its operational phase. MATD represents a common repository of project data, Assembly Integration and Verification (AIV) data, on ground and flight anomalies data, of recent space projects, and offers, with the application of specific methodologies, the possibility to analyze the collected data in order to improve the test philosophies and the related standards. Basically the following type of results can be derived from the database: - Statistics on ground failures and flight anomalies - Feed-back from the flight anomalies to the Test Philosophies - Test Effectiveness evaluation at system and lower levels - Estimate of the index of effectiveness of a specific Model and Test Philosophy in comparison with the applicable standards - Simulation of different Test philosophies and related balancing of Risk/cost/schedule on the basis of MATD data The paper after a short presentation of the status of the MATD initiative, summarises the most recent lessons learned which are resulting from the data analysis and highlights how MATD is being utilized for the actual risk/cost/schedule/Test effectiveness evaluations of the past programmes so as for the prediction of the new space projects.

Sample and data processing considerations for the NIST quantitative infrared database

NASA Astrophysics Data System (ADS)

Chu, Pamela M.; Guenther, Franklin R.; Rhoderick, George C.; Lafferty, Walter J.; Phillips, William

1999-02-01

Fourier-transform infrared (FT-IR) spectrometry has become a useful real-time in situ analytical technique for quantitative gas phase measurements. In fact, the U.S. Environmental Protection Agency (EPA) has recently approved open-path FT-IR monitoring for the determination of hazardous air pollutants (HAP) identified in EPA's Clean Air Act of 1990. To support infrared based sensing technologies, the National Institute of Standards and Technology (NIST) is currently developing a standard quantitative spectral database of the HAPs based on gravimetrically prepared standard samples. The procedures developed to ensure the quantitative accuracy of the reference data are discussed, including sample preparation, residual sample contaminants, data processing considerations, and estimates of error.

MARC and Relational Databases.

ERIC Educational Resources Information Center

Llorens, Jose; Trenor, Asuncion

1993-01-01

Discusses the use of MARC format in relational databases and addresses problems of incompatibilities. A solution is presented that is in accordance with Open Systems Interconnection (OSI) standards and is based on experiences at the library of the Universidad Politecnica de Valencia (Spain). (four references) (EA)

Illinois Occupational Skill Standards: Information Technology Design/Build Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document contains Illinois Occupational Skill Standards for occupations in the Information Technology Design and Build Cluster (technical writer, programmer, system analyst, network architect, application product architect, network engineer, and database administrator). The skill standards define what an individual should know and the…

A Novel Database to Rank and Display Archeomagnetic Intensity Data

NASA Astrophysics Data System (ADS)

Donadini, F.; Korhonen, K.; Riisager, P.; Pesonen, L. J.; Kahma, K.

2005-12-01

To understand the content and the causes of the changes in the Earth's magnetic field beyond the observatory records one has to rely on archeomagnetic and lake sediment paleomagnetic data. The regional archeointensity curves are often of different quality and temporally variable which hampers the global analysis of the data in terms of dipole vs non-dipole field. We have developed a novel archeointensity database application utilizing MySQL, PHP (PHP Hypertext Preprocessor), and the Generic Mapping Tools (GMT) for ranking and displaying geomagnetic intensity data from the last 12000 years. Our application has the advantage that no specific software is required to query the database and view the results. Querying the database is performed using any Web browser; a fill-out form is used to enter the site location and a minimum ranking value to select the data points to be displayed. The form also features the possibility to select plotting of the data as an archeointensity curve with error bars, and a Virtual Axial Dipole Moment (VADM) or ancient field value (Ba) curve calculated using the CALS7K model (Continuous Archaeomagnetic and Lake Sediment geomagnetic model) of (Korte and Constable, 2005). The results of a query are displayed on a Web page containing a table summarizing the query parameters, a table showing the archeointensity values satisfying the query parameters, and a plot of VADM or Ba as a function of sample age. The database consists of eight related tables. The main one, INTENSITIES, stores the 3704 archeointensity measurements collected from 159 publications as VADM (and VDM when available) and Ba values, including their standard deviations and sampling locations. It also contains the number of samples and specimens measured from each site. The REFS table stores the references to a particular study. The names, latitudes, and longitudes of the regions where the samples were collected are stored in the SITES table. The MATERIALS, METHODS, SPECIMEN_TYPES and DATING_METHODS tables store information about the sample materials, intensity determination methods, specimen types and age determination methods. The SIGMA_COUNT table is used indirectly for ranking data according to the number of samples measured and their standard deviations. Each intensity measurement is assigned a score (0--2) depending on the number of specimens measured and their standard deviations, the intensity determination method, the type of specimens measured and materials. The ranking of each data point is calculated as the sum of the four scores and varies between 0 and 8. Additionally, users can select the parameters that will be included in the ranking.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

PubMed

Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord Hendrix; Bonnal, Raoul Jp; Bruskiewich, Richard; Bryne, Jan C; Fernández, José M; Funahashi, Akira; Gordon, Paul Mk; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, René; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A; Wilkinson, Mark D; York, William; Zmasek, Christian M; Asai, Kiyoshi; Takagi, Toshihisa

2010-08-21

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

PubMed Central

2010-01-01

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies. PMID:20727200

Oak Ridge Reservation Environmental Protection Rad Neshaps Radionuclide Inventory Web Database and Rad Neshaps Source and Dose Database.

PubMed

Scofield, Patricia A; Smith, Linda L; Johnson, David N

2017-07-01

The U.S. Environmental Protection Agency promulgated national emission standards for emissions of radionuclides other than radon from US Department of Energy facilities in Chapter 40 of the Code of Federal Regulations (CFR) 61, Subpart H. This regulatory standard limits the annual effective dose that any member of the public can receive from Department of Energy facilities to 0.1 mSv. As defined in the preamble of the final rule, all of the facilities on the Oak Ridge Reservation, i.e., the Y-12 National Security Complex, Oak Ridge National Laboratory, East Tennessee Technology Park, and any other U.S. Department of Energy operations on Oak Ridge Reservation, combined, must meet the annual dose limit of 0.1 mSv. At Oak Ridge National Laboratory, there are monitored sources and numerous unmonitored sources. To maintain radiological source and inventory information for these unmonitored sources, e.g., laboratory hoods, equipment exhausts, and room exhausts not currently venting to monitored stacks on the Oak Ridge National Laboratory campus, the Environmental Protection Rad NESHAPs Inventory Web Database was developed. This database is updated annually and is used to compile emissions data for the annual Radionuclide National Emission Standards for Hazardous Air Pollutants (Rad NESHAPs) report required by 40 CFR 61.94. It also provides supporting documentation for facility compliance audits. In addition, a Rad NESHAPs source and dose database was developed to import the source and dose summary data from Clean Air Act Assessment Package-1988 computer model files. This database provides Oak Ridge Reservation and facility-specific source inventory; doses associated with each source and facility; and total doses for the Oak Ridge Reservation dose.

Research Directions in Database Security IV

DTIC Science & Technology

1993-07-01

second algorithm, which is based on multiversion timestamp ordering, is that high level transactions can be forced to read arbitrarily old data values...system. The first, the single ver- sion model, stores only the latest veision of each data item, while the second, the 88 multiversion model, stores... Multiversion Database Model In the standard database model, where there is only one version of each data item, all transactions compete for the most recent

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR INSTRUCTIONS FOR THE ADDITION OF INDIVIDUAL CLEANED NON SCANNED DATA BATCHES TO MASTER DATABASES (UA-D-27.0)

EPA Science Inventory

The purpose of this SOP is to define the procedures involved in appending cleaned individual data batches to the master databases. This procedure applies to the Arizona NHEXAS project and the Border study. Keywords: data; database.

The U.S.-Mexico Border Program is sponsored b...

The Binding Database: data management and interface design.

PubMed

Chen, Xi; Lin, Yuhmei; Liu, Ming; Gilson, Michael K

2002-01-01

The large and growing body of experimental data on biomolecular binding is of enormous value in developing a deeper understanding of molecular biology, in developing new therapeutics, and in various molecular design applications. However, most of these data are found only in the published literature and are therefore difficult to access and use. No existing public database has focused on measured binding affinities and has provided query capabilities that include chemical structure and sequence homology searches. We have created Binding DataBase (BindingDB), a public, web-accessible database of measured binding affinities. BindingDB is based upon a relational data specification for describing binding measurements via Isothermal Titration Calorimetry (ITC) and enzyme inhibition. A corresponding XML Document Type Definition (DTD) is used to create and parse intermediate files during the on-line deposition process and will also be used for data interchange, including collection of data from other sources. The on-line query interface, which is constructed with Java Servlet technology, supports standard SQL queries as well as searches for molecules by chemical structure and sequence homology. The on-line deposition interface uses Java Server Pages and JavaBean objects to generate dynamic HTML and to store intermediate results. The resulting data resource provides a range of functionality with brisk response-times, and lends itself well to continued development and enhancement.

A manual for a laboratory information management system (LIMS) for light stable isotopes

USGS Publications Warehouse

Coplen, Tyler B.

1997-01-01

The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program is presented herein. Major benefits of this system include (i) an increase in laboratory efficiency, (ii) reduction in the use of paper, (iii) reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) decreased errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for stable isotope laboratories. Since the original publication of the manual for LIMS for Light Stable Isotopes, the isotopes 3 H, 3 He, and 14 C, and the chlorofluorocarbons (CFCs), CFC-11, CFC-12, and CFC-113, have been added to this program.

A manual for a Laboratory Information Management System (LIMS) for light stable isotopes

USGS Publications Warehouse

Coplen, Tyler B.

1998-01-01

The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program is presented herein. Major benefits of this system include (i) an increase in laboratory efficiency, (ii) reduction in the use of paper, (iii) reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) decreased errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for stable isotope laboratories. Since the original publication of the manual for LIMS for Light Stable Isotopes, the isotopes 3 H, 3 He, and 14 C, and the chlorofluorocarbons (CFCs), CFC-11, CFC-12, and CFC-113, have been added to this program.

A Web-based tool for UV irradiance data: predictions for European and Southeast Asian sites.

PubMed

Kift, Richard; Webb, Ann R; Page, John; Rimmer, John; Janjai, Serm

2006-01-01

There are a range of UV models available, but one needs significant pre-existing knowledge and experience in order to be able to use them. In this article a comparatively simple Web-based model developed for the SoDa (Integration and Exploitation of Networked Solar Radiation Databases for Environment Monitoring) project is presented. This is a clear-sky model with modifications for cloud effects. To determine if the model produces realistic UV data the output is compared with 1 year sets of hourly measurements at sites in the United Kingdom and Thailand. The accuracy of the output depends on the input, but reasonable results were obtained with the use of the default database inputs and improved when pyranometer instead of modeled data provided the global radiation input needed to estimate the UV. The average modeled values of UV for the UK site were found to be within 10% of measurements. For the tropical sites in Thailand the average modeled values were within 1120% of measurements for the four sites with the use of the default SoDa database values. These results improved when pyranometer data and TOMS ozone data from 2002 replaced the standard SoDa database values, reducing the error range for all four sites to less than 15%.

Damming the genomic data flood using a comprehensive analysis and storage data structure

PubMed Central

Bouffard, Marc; Phillips, Michael S.; Brown, Andrew M.K.; Marsh, Sharon; Tardif, Jean-Claude; van Rooij, Tibor

2010-01-01

Data generation, driven by rapid advances in genomic technologies, is fast outpacing our analysis capabilities. Faced with this flood of data, more hardware and software resources are added to accommodate data sets whose structure has not specifically been designed for analysis. This leads to unnecessarily lengthy processing times and excessive data handling and storage costs. Current efforts to address this have centered on developing new indexing schemas and analysis algorithms, whereas the root of the problem lies in the format of the data itself. We have developed a new data structure for storing and analyzing genotype and phenotype data. By leveraging data normalization techniques, database management system capabilities and the use of a novel multi-table, multidimensional database structure we have eliminated the following: (i) unnecessarily large data set size due to high levels of redundancy, (ii) sequential access to these data sets and (iii) common bottlenecks in analysis times. The resulting novel data structure horizontally divides the data to circumvent traditional problems associated with the use of databases for very large genomic data sets. The resulting data set required 86% less disk space and performed analytical calculations 6248 times faster compared to a standard approach without any loss of information. Database URL: http://castor.pharmacogenomics.ca PMID:21159730

The SUPERFAMILY database in 2004: additions and improvements.

PubMed

Madera, Martin; Vogel, Christine; Kummerfeld, Sarah K; Chothia, Cyrus; Gough, Julian

2004-01-01

The SUPERFAMILY database provides structural assignments to protein sequences and a framework for analysis of the results. At the core of the database is a library of profile Hidden Markov Models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent an entire superfamily. We have applied the library to predicted proteins from all completely sequenced genomes (currently 154), the Swiss-Prot and TrEMBL databases and other sequence collections. Close to 60% of all proteins have at least one match, and one half of all residues are covered by assignments. All models and full results are available for download and online browsing at http://supfam.org. Users can study the distribution of their superfamily of interest across all completely sequenced genomes, investigate with which other superfamilies it combines and retrieve proteins in which it occurs. Alternatively, concentrating on a particular genome as a whole, it is possible first, to find out its superfamily composition, and secondly, to compare it with that of other genomes to detect superfamilies that are over- or under-represented. In addition, the webserver provides the following standard services: sequence search; keyword search for genomes, superfamilies and sequence identifiers; and multiple alignment of genomic, PDB and custom sequences.

USGS national surveys and analysis projects: Preliminary compilation of integrated geological datasets for the United States

USGS Publications Warehouse

Nicholson, Suzanne W.; Stoeser, Douglas B.; Wilson, Frederic H.; Dicken, Connie L.; Ludington, Steve

2007-01-01

The growth in the use of Geographic nformation Systems (GS) has highlighted the need for regional and national digital geologic maps attributed with age and rock type information. Such spatial data can be conveniently used to generate derivative maps for purposes that include mineral-resource assessment, metallogenic studies, tectonic studies, human health and environmental research. n 1997, the United States Geological Survey’s Mineral Resources Program initiated an effort to develop national digital databases for use in mineral resource and environmental assessments. One primary activity of this effort was to compile a national digital geologic map database, utilizing state geologic maps, to support mineral resource studies in the range of 1:250,000- to 1:1,000,000-scale. Over the course of the past decade, state databases were prepared using a common standard for the database structure, fields, attributes, and data dictionaries. As of late 2006, standardized geological map databases for all conterminous (CONUS) states have been available on-line as USGS Open-File Reports. For Alaska and Hawaii, new state maps are being prepared, and the preliminary work for Alaska is being released as a series of 1:500,000-scale regional compilations. See below for a list of all published databases.

Wavelet/scalar quantization compression standard for fingerprint images

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

Brislawn, C.M.

1996-06-12

US Federal Bureau of Investigation (FBI) has recently formulated a national standard for digitization and compression of gray-scale fingerprint images. Fingerprints are scanned at a spatial resolution of 500 dots per inch, with 8 bits of gray-scale resolution. The compression algorithm for the resulting digital images is based on adaptive uniform scalar quantization of a discrete wavelet transform subband decomposition (wavelet/scalar quantization method). The FBI standard produces archival-quality images at compression ratios of around 15 to 1 and will allow the current database of paper fingerprint cards to be replaced by digital imagery. The compression standard specifies a class ofmore » potential encoders and a universal decoder with sufficient generality to reconstruct compressed images produced by any compliant encoder, allowing flexibility for future improvements in encoder technology. A compliance testing program is also being implemented to ensure high standards of image quality and interchangeability of data between different implementations.« less

The Results of Development of the Project ZOOINT and its Future Perspectives

NASA Astrophysics Data System (ADS)

Smirnov, I. S.; Lobanov, A. L.; Alimov, A. F.; Medvedev, S. G.; Golikov, A. A.

The work on a computerization of main processes of accumulation and analysis of the collection, expert and literary data on a systematics and faunistics of various taxa of animal (a basis of studying of a biological diversity) was started in the Zoological Institute in 1987. In 1991 the idea of creating of the software package, ZOOlogical INTegrated system (ZOOINT) was born. ZOOINT could provide a loading operation about collections and simultaneously would allow to analyze the accumulated data with the help of various queries. During execution, the project ZOOINT was transformed slightly and has given results a little bit distinguished from planned earlier, but even more valuable. In the Internet the site about the information retrieval system (IRS) ZOOINT was built also ( ZOOINT ). The implementation of remote access to the taxonomic information, with possibility to work with databases (DB) of the IRS ZOOINT in the on-line mode was scheduled. It has required not only innovation of computer park of the developers and users, but also mastering of new software: language HTML, operating system of Windows NT, and technology of Active Server Pages (ASP). One of the serious problems of creating of databases and the IRS on zoology is the problem of representation of hierarchical classification. Building the classifiers, specialized standard taxonomic databases, which have obtained the name ZOOCOD solved this problem. The lately magnified number of attempts of creating of taxonomic electronic lists, tables and DB has required development of some primary rules of unification of zoological systematic databases. These rules assume their application in institutes of the biological profile, in which the processes of a computerization are very slowly, and the building of databases is in the most rudimentary state. These some positions and the standards of construction of biological (taxonomic) databases should facilitate dialogue of the biologists, application in the near future of most advanced technologies of development of the DB (for example, usage of the XML platform) and, eventually, building of the modern information systems. The work on the project is carried out at support of the RFBR grant N 02-07-90217; programs "The Information system on a biodiversity of Russia" and Project N 15 "Antarctic Regions".

Nutrient estimation from an FFQ developed for a black Zimbabwean population

PubMed Central

Merchant, Anwar T; Dehghan, Mahshid; Chifamba, Jephat; Terera, Getrude; Yusuf, Salim

2005-01-01

Background There is little information in the literature on methods of food composition database development to calculate nutrient intake from food frequency questionnaire (FFQ) data. The aim of this study is to describe the development of an FFQ and a food composition table to calculate nutrient intake in a Black Zimbabwean population. Methods Trained interviewers collected 24-hour dietary recalls (24 hr DR) from high and low income families in urban and rural Zimbabwe. Based on these data and input from local experts we developed an FFQ, containing a list of frequently consumed foods, standard portion sizes, and categories of consumption frequency. We created a food composition table of the foods found in the FFQ so that we could compute nutrient intake. We used the USDA nutrient database as the main resource because it is relatively complete, updated, and easily accessible. To choose the food item in the USDA nutrient database that most closely matched the nutrient content of the local food we referred to a local food composition table. Results Almost all the participants ate sadza (maize porridge) at least 5 times a week, and about half had matemba (fish) and caterpillar more than once a month. Nutrient estimates obtained from the FFQ data by using the USDA and Zimbabwean food composition tables were similar for total energy intake intra class correlation (ICC) = 0.99, and carbohydrate (ICC = 0.99), but different for vitamin A (ICC = 0.53), and total folate (ICC = 0.68). Conclusion We have described a standardized process of FFQ and food composition database development for a Black Zimbabwean population. PMID:16351722

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.

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

Webb-Robertson, Bobbie-Jo M.

Accurate identification of peptides is a current challenge in mass spectrometry (MS) based proteomics. The standard approach uses a search routine to compare tandem mass spectra to a database of peptides associated with the target organism. These database search routines yield multiple metrics associated with the quality of the mapping of the experimental spectrum to the theoretical spectrum of a peptide. The structure of these results make separating correct from false identifications difficult and has created a false identification problem. Statistical confidence scores are an approach to battle this false positive problem that has led to significant improvements in peptidemore » identification. We have shown that machine learning, specifically support vector machine (SVM), is an effective approach to separating true peptide identifications from false ones. The SVM-based peptide statistical scoring method transforms a peptide into a vector representation based on database search metrics to train and validate the SVM. In practice, following the database search routine, a peptides is denoted in its vector representation and the SVM generates a single statistical score that is then used to classify presence or absence in the sample« less

Long-term cycles in the history of life: periodic biodiversity in the paleobiology database.

PubMed

Melott, Adrian L

2008-01-01

Time series analysis of fossil biodiversity of marine invertebrates in the Paleobiology Database (PBDB) shows a significant periodicity at approximately 63 My, in agreement with previous analyses based on the Sepkoski database. I discuss how this result did not appear in a previous analysis of the PBDB. The existence of the 63 My periodicity, despite very different treatment of systematic error in both PBDB and Sepkoski databases strongly argues for consideration of its reality in the fossil record. Cross-spectral analysis of the two datasets finds that a 62 My periodicity coincides in phase by 1.6 My, equivalent to better than the errors in either measurement. Consequently, the two data sets not only contain the same strong periodicity, but its peaks and valleys closely correspond in time. Two other spectral peaks appear in the PBDB analysis, but appear to be artifacts associated with detrending and with the increased interval length. Sampling-standardization procedures implemented by the PBDB collaboration suggest that the signal is not an artifact of sampling bias. Further work should focus on finding the cause of the 62 My periodicity.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

PubMed

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-09-18

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

Results from prototype die-to-database reticle inspection system

NASA Astrophysics Data System (ADS)

Mu, Bo; Dayal, Aditya; Broadbent, Bill; Lim, Phillip; Goonesekera, Arosha; Chen, Chunlin; Yeung, Kevin; Pinto, Becky

2009-03-01

A prototype die-to-database high-resolution reticle defect inspection system has been developed for 32nm and below logic reticles, and 4X Half Pitch (HP) production and 3X HP development memory reticles. These nodes will use predominantly 193nm immersion lithography (with some layers double patterned), although EUV may also be used. Many different reticle types may be used for these generations including: binary (COG, EAPSM), simple tritone, complex tritone, high transmission, dark field alternating (APSM), mask enhancer, CPL, and EUV. Finally, aggressive model based OPC is typically used, which includes many small structures such as jogs, serifs, and SRAF (sub-resolution assist features), accompanied by very small gaps between adjacent structures. The architecture and performance of the prototype inspection system is described. This system is designed to inspect the aforementioned reticle types in die-todatabase mode. Die-to-database inspection results are shown on standard programmed defect test reticles, as well as advanced 32nm logic, and 4X HP and 3X HP memory reticles from industry sources. Direct comparisons with currentgeneration inspection systems show measurable sensitivity improvement and a reduction in false detections.

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

Solutions for medical databases optimal exploitation.

PubMed

Branescu, I; Purcarea, V L; Dobrescu, R

2014-03-15

The paper discusses the methods to apply OLAP techniques for multidimensional databases that leverage the existing, performance-enhancing technique, known as practical pre-aggregation, by making this technique relevant to a much wider range of medical applications, as a logistic support to the data warehousing techniques. The transformations have practically low computational complexity and they may be implemented using standard relational database technology. The paper also describes how to integrate the transformed hierarchies in current OLAP systems, transparently to the user and proposes a flexible, "multimodel" federated system for extending OLAP querying to external object databases.

Uniform standards for genome databases in forest and fruit trees

USDA-ARS?s Scientific Manuscript database

TreeGenes and tfGDR serve the international forestry and fruit tree genomics research communities, respectively. These databases hold similar sequence data and provide resources for the submission and recovery of this information in order to enable comparative genomics research. Large-scale genotype...

CTEPP STANDARD OPERATING PROCEDURE FOR ENTERING OR IMPORTING ELECTRONIC DATA INTO THE CTEPP DATABASE (SOP-4.12)

EPA Science Inventory

This SOP described the method used to automatically parse analytical data generated from gas chromatography/mass spectrometry (GC/MS) analyses into CTEPP summary spreadsheets and electronically import the summary spreadsheets into the CTEPP study database.

National Nutrient Database for Standard Reference - Find Nutrient Value of Common Foods by Nutrient

MedlinePlus

... grams Household * required field ​ USDA Food Composition Databases Software developed by the National Agricultural Library v.3.9.4.1 2018-06-11 NAL Home | USDA.gov | Agricultural Research Service | Plain Language | FOIA | Accessibility Statement | Information Quality | Privacy ...

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.

Technologies and standards in the information systems of the soil-geographic database of Russia

NASA Astrophysics Data System (ADS)

Golozubov, O. M.; Rozhkov, V. A.; Alyabina, I. O.; Ivanov, A. V.; Kolesnikova, V. M.; Shoba, S. A.

2015-01-01

The achievements, problems, and challenges of the modern stage of the development of the Soil-Geographic Database of Russia (SGDBR) and the history of this project are outlined. The structure of the information system of the SGDBR as an internet-based resource to collect data on soil profiles and to integrate the geographic and attribute databases on the same platform is described. The pilot project in Rostov oblast illustrates the inclusion of regional information in the SGDBR and its application for solving practical problems. For the first time in Russia, the GeoRSS standard based on the structured hypertext representation of the geographic and attribute information has been applied in the state system for the agromonitoring of agricultural lands in Rostov oblast and information exchange through the internet.

Evaluation and validity of a LORETA normative EEG database.

PubMed

Thatcher, R W; North, D; Biver, C

2005-04-01

To evaluate the reliability and validity of a Z-score normative EEG database for Low Resolution Electromagnetic Tomography (LORETA), EEG digital samples (2 second intervals sampled 128 Hz, 1 to 2 minutes eyes closed) were acquired from 106 normal subjects, and the cross-spectrum was computed and multiplied by the Key Institute's LORETA 2,394 gray matter pixel T Matrix. After a log10 transform or a Box-Cox transform the mean and standard deviation of the *.lor files were computed for each of the 2394 gray matter pixels, from 1 to 30 Hz, for each of the subjects. Tests of Gaussianity were computed in order to best approximate a normal distribution for each frequency and gray matter pixel. The relative sensitivity of a Z-score database was computed by measuring the approximation to a Gaussian distribution. The validity of the LORETA normative database was evaluated by the degree to which confirmed brain pathologies were localized using the LORETA normative database. Log10 and Box-Cox transforms approximated Gaussian distribution in the range of 95.64% to 99.75% accuracy. The percentage of normative Z-score values at 2 standard deviations ranged from 1.21% to 3.54%, and the percentage of Z-scores at 3 standard deviations ranged from 0% to 0.83%. Left temporal lobe epilepsy, right sensory motor hematoma and a right hemisphere stroke exhibited maximum Z-score deviations in the same locations as the pathologies. We conclude: (1) Adequate approximation to a Gaussian distribution can be achieved using LORETA by using a log10 transform or a Box-Cox transform and parametric statistics, (2) a Z-Score normative database is valid with adequate sensitivity when using LORETA, and (3) the Z-score LORETA normative database also consistently localized known pathologies to the expected Brodmann areas as an hypothesis test based on the surface EEG before computing LORETA.

32 CFR 2001.42 - Standards for security equipment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... publish uniform standards, specifications, qualified product lists or databases, and supply schedules for... use prior to January 1, 2011, and not found on an EPL, may be utilized for the destruction of...

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure

PubMed Central

Boué, Stéphanie; Exner, Thomas; Ghosh, Samik; Belcastro, Vincenzo; Dokler, Joh; Page, David; Boda, Akash; Bonjour, Filipe; Hardy, Barry; Vanscheeuwijck, Patrick; Hoeng, Julia; Peitsch, Manuel

2017-01-01

The US FDA defines modified risk tobacco products (MRTPs) as products that aim to reduce harm or the risk of tobacco-related disease associated with commercially marketed tobacco products.  Establishing a product’s potential as an MRTP requires scientific substantiation including toxicity studies and measures of disease risk relative to those of cigarette smoking.  Best practices encourage verification of the data from such studies through sharing and open standards. Building on the experience gained from the OpenTox project, a proof-of-concept database and website ( INTERVALS) has been developed to share results from both in vivo inhalation studies and in vitro studies conducted by Philip Morris International R&D to assess candidate MRTPs. As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and tools. The data-management framework described here accounts for the latest standards of data sharing and research reproducibility. Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website. The portal allows users to browse the data by study or mechanism (e.g., inflammation, oxidative stress) and obtain information relevant to study design, methods, and the most important results. Given the successful development of the initial infrastructure, the goal is to grow this initiative and establish a public repository for 21 st-century preclinical systems toxicology MRTP assessment data and results that supports open data principles. PMID:29123642

Modernized Techniques for Dealing with Quality Data and Derived Products

NASA Astrophysics Data System (ADS)

Neiswender, C.; Miller, S. P.; Clark, D.

2008-12-01

"I just want a picture of the ocean floor in this area" is expressed all too often by researchers, educators, and students in the marine geosciences. As more sophisticated systems are developed to handle data collection and processing, the demand for quality data, and standardized products continues to grow. Data management is an invisible bridge between science and researchers/educators. The SIOExplorer digital library presents more than 50 years of ocean-going research. Prior to publication, all data is checked for quality using standardized criterion developed for each data stream. Despite the evolution of data formats and processing systems, SIOExplorer continues to present derived products in well- established formats. Standardized products are published for each cruise, and include a cruise report, MGD77 merged data, multi-beam flipbook, and underway profiles. Creation of these products is made possible by processing scripts, which continue to change with ever-evolving data formats. We continue to explore the potential of database-enabled creation of standardized products, such as the metadata-rich MGD77 header file. Database-enabled, automated processing produces standards-compliant metadata for each data and derived product. Metadata facilitates discovery and interpretation of published products. This descriptive information is stored both in an ASCII file, and a searchable digital library database. SIOExplorer's underlying technology allows focused search and retrieval of data and products. For example, users can initiate a search of only multi-beam data, which includes data-specific parameters. This customization is made possible with a synthesis of database, XML, and PHP technology. The combination of standardized products and digital library technology puts quality data and derived products in the hands of scientists. Interoperable systems enable distribution these published resources using technology such as web services. By developing modernized strategies to deal with data, Scripps Institution of Oceanography is able to produce and distribute well-formed, and quality-tested derived products, which aid research, understanding, and education.

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

PubMed

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

2016-06-01

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

Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data.

PubMed

Santos, Eduardo Jose Melos Dos; McCabe, Antony; Gonzalez-Galarza, Faviel F; Jones, Andrew R; Middleton, Derek

2016-03-01

The Allele Frequencies Net Database (AFND) is a freely accessible database which stores population frequencies for alleles or genes of the immune system in worldwide populations. Herein we introduce two new tools. We have defined new classifications of data (gold, silver and bronze) to assist users in identifying the most suitable populations for their tasks. The gold standard datasets are defined by allele frequencies summing to 1, sample sizes >50 and high resolution genotyping, while silver standard datasets do not meet gold standard genotyping resolution and/or sample size criteria. The bronze standard datasets are those that could not be classified under the silver or gold standards. The gold standard includes >500 datasets covering over 3 million individuals from >100 countries at one or more of the following loci: HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1 and -DRB1 - with all loci except DPA1 present in more than 220 datasets. Three out of 12 geographic regions have low representation (the majority of their countries having less than five datasets) and the Central Asia region has no representation. There are 18 countries that are not represented by any gold standard datasets but are represented by at least one dataset that is either silver or bronze standard. We also briefly summarize the data held by AFND for KIR genes, alleles and their ligands. Our second new component is a data submission tool to assist users in the collection of the genotypes of the individuals (raw data), facilitating submission of short population reports to Human Immunology, as well as simplifying the submission of population demographics and frequency data. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Bilateral key comparison SIM.T-K6.1 on humidity standards in the dew/frost-point temperature range from -25 °C to +20 °C

NASA Astrophysics Data System (ADS)

Meyer, C. W.; Hill, K. D.

2015-01-01

A Regional Metrology Organization (RMO) Key Comparison of dew/frost point temperatures was carried out by the National Institute of Standards and Technology (NIST, USA) and the National Research Council (NRC, Canada) between December 2014 and April 2015. The results of this comparison are reported here, along with descriptions of the humidity laboratory standards for NIST and NRC and the uncertainty budget for these standards. This report also describes the protocol for the comparison and presents the data acquired. The results are analyzed, determining degree of equivalence between the dew/frost-point standards of NIST and NRC. This paper is the final report of the comparison including analysis of the uncertainty of measurement results. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT WG-KC, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

High-resolution global grids of revised Priestley-Taylor and Hargreaves-Samani coefficients for assessing ASCE-standardized reference crop evapotranspiration and solar radiation

NASA Astrophysics Data System (ADS)

Aschonitis, Vassilis G.; Papamichail, Dimitris; Demertzi, Kleoniki; Colombani, Nicolo; Mastrocicco, Micol; Ghirardini, Andrea; Castaldelli, Giuseppe; Fano, Elisa-Anna

2017-08-01

The objective of the study is to provide global grids (0.5°) of revised annual coefficients for the Priestley-Taylor (P-T) and Hargreaves-Samani (H-S) evapotranspiration methods after calibration based on the ASCE (American Society of Civil Engineers)-standardized Penman-Monteith method (the ASCE method includes two reference crops: short-clipped grass and tall alfalfa). The analysis also includes the development of a global grid of revised annual coefficients for solar radiation (Rs) estimations using the respective Rs formula of H-S. The analysis was based on global gridded climatic data of the period 1950-2000. The method for deriving annual coefficients of the P-T and H-S methods was based on partial weighted averages (PWAs) of their mean monthly values. This method estimates the annual values considering the amplitude of the parameter under investigation (ETo and Rs) giving more weight to the monthly coefficients of the months with higher ETo values (or Rs values for the case of the H-S radiation formula). The method also eliminates the effect of unreasonably high or low monthly coefficients that may occur during periods where ETo and Rs fall below a specific threshold. The new coefficients were validated based on data from 140 stations located in various climatic zones of the USA and Australia with expanded observations up to 2016. The validation procedure for ETo estimations of the short reference crop showed that the P-T and H-S methods with the new revised coefficients outperformed the standard methods reducing the estimated root mean square error (RMSE) in ETo values by 40 and 25 %, respectively. The estimations of Rs using the H-S formula with revised coefficients reduced the RMSE by 28 % in comparison to the standard H-S formula. Finally, a raster database was built consisting of (a) global maps for the mean monthly ETo values estimated by ASCE-standardized method for both reference crops, (b) global maps for the revised annual coefficients of the P-T and H-S evapotranspiration methods for both reference crops and a global map for the revised annual coefficient of the H-S radiation formula and (c) global maps that indicate the optimum locations for using the standard P-T and H-S methods and their possible annual errors based on reference values. The database can support estimations of ETo and solar radiation for locations where climatic data are limited and it can support studies which require such estimations on larger scales (e.g. country, continent, world). The datasets produced in this study are archived in the PANGAEA database (https://doi.org/10.1594/PANGAEA.868808) and in the ESRN database (http://www.esrn-database.org or http://esrn-database.weebly.com).

Bilateral key comparison SIM.T-K6.5 on humidity standards in the dew/frost-point temperature range from -30 °C to +20 °C

NASA Astrophysics Data System (ADS)

Meyer, C.; Solano, A.

2016-01-01

A Regional Metrology Organization (RMO) Key Comparison of dew/frost point temperatures was carried out by the National Institute of Standards and Technology (NIST, USA) and the Laboratorio Costarricense de Metrología (LACOMET, Costa Rica) between February 2015 and August 2015. The results of this comparison are reported here, along with descriptions of the humidity laboratory standards for NIST and LACOMET and the uncertainty budget for these standards. This report also describes the protocol for the comparison and presents the data acquired. The results are analyzed, determining degree of equivalence between the dew/frost-point standards of NIST and LACOMET. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Bilateral key comparison SIM.T-K6.2 on humidity standards in the dew/frost-point temperature range from -20 °c to 20 °c

NASA Astrophysics Data System (ADS)

Huang, P. H.; Meyer, C. W.; Martines-López, E.; Dávila Pacheco, J. A.; Méndez-Lango, E.

2014-01-01

A Regional Metrology Organization (RMO) Key Comparison of dew/frost point temperatures was carried out by the National Institute of Standards and Technology (NIST, USA) and the Centro Nacional de Metrologia (CENAM, Mexico) between July 2008 and December 2008. The results of this comparison are reported here, along with descriptions of the humidity laboratory standards for NIST and CENAM and the uncertainty budget for these standards. This report also describes the protocol for the comparison and presents the data acquired. The results are analyzed, determining degree of equivalence between the dew/frost-point standards of NIST and CENAM. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Final report: Bilateral key comparison SIM.T-K6.3 on humidity standards in the dew/frost-point temperature range from -30°C to 20°C

NASA Astrophysics Data System (ADS)

Huang, Peter; Meyer, Christopher; Brionizio, Julio D.

2015-01-01

A Regional Metrology Organization (RMO) Key Comparison of dew/frost point temperatures was carried out by the National Institute of Standards and Technology (NIST, USA) and the Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO, Brazil) between October 2009 and March 2010. The results of this comparison are reported here, along with descriptions of the humidity laboratory standards for NIST and INMETRO and the uncertainty budget for these standards. This report also describes the protocol for the comparison and presents the data acquired. The results are analyzed, determining degree of equivalence between the dew/frost-point standards of NIST and INMETRO. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Final report on AFRIMETS comparison of liquid in glass thermometer calibrations from -35 °C to 250 °C

NASA Astrophysics Data System (ADS)

Liedberg, Hans; Kebede Ejigu, Efrem; Madiba, Tshifhiwa; du Clou, Sven; Chibaya, Blessing; Mwazi, Victor; Kajane, Tebogo; Mundembe, Victor; Kwong, Christian Ng Ha; Madeleine, Gilbert

2017-01-01

A Regional Metrology Organization (RMO) supplementary comparison of liquid in glass thermometer (AFRIMETS.T-S5) was carried out by the National Metrology Institute of South Africa (NMISA), Zimbabwe Scientific & Industrial Research & Development Centre—National Metrology Institute (SIRDC-NMI), Zambia Bureau of Standards (ZABS), Botswana Bureau of Standards (BOBS), Namibian Standards Institute (NSI), Mauritius Standards Bureau (MSB) and Seychelles Bureau of Standards (SBS) between January and September 2016. The temperature range of the inter comparison is -35 °C to 250 °C. The results of this comparison are reported here, along with descriptions of the Artefacts used. This report also presents the uncertainty budget of each participant. The results are analysed and normalized error (En) values are reported. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Treatment of leydig cell tumours of the testis: Can testis-sparing surgery replace radical orchidectomy? Results of a systematic review.

PubMed

Bozzini, G; Ratti, D; Carmignani, L

2017-04-01

The gold standard for Leydig cell tumours (LCTs) is still considered radical orchidectomy, but testis sparing surgery (TSS) in conjunction with intraoperative frozen section (FSE) has been recently attempted with promising results. Studies were identified by searching electronic databases. A bibliographic search covering the period from January 1980 to December 2012 was conducted using PubMed/MEDLINE and EMBASE database. Studies were excluded if they were single case reports, meeting abstracts and conference proceedings. The present analysis is based on a total of 13 studies that fulfilled the predefined inclusion criteria. A total of 247 participants were included in the 13 studies examined in this systematic review. 145 were treated with radical orchiectomy and 102 with TSS. In the radical surgery group, the follow-up varied from 6 to 249 months). In the TSS group, the follow-up varied from 6 to 192 months. Frozen section was performed in a total of 96 patients. Sensitivity was 87.5%. None of the patients treated with TSS presented a metastatic recurrence, while in patients treated with radical orchiectomy three patients presented with metastatic recurrence In selected cases radical surgery appears excessive and the potential for a shift to TSS as the standard management is gathering momentum. The results confirm the favourable course of LCT treated with TSS. The results obtained are encouraging and the concept is attractive to become the standard therapy in all patients and not only in people affected by (sub)fertility or with solitary testis. Copyright © 2016 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

Standardization of Keyword Search Mode

ERIC Educational Resources Information Center

Su, Di

2010-01-01

In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

78 FR 40478 - Privacy Act of 1974; Notice of an Updated System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-05

... of MyUSA's programmatic interfaces, such as notifications, tasks, or events; (3) a history of third... Technology standards and information in the database is encrypted. Records are safeguarded in accordance with... algorithms and firewalls are compliant with National Institute of Standards and Technology standards...

A survey of the current status of web-based databases indexing Iranian journals.

PubMed

Merat, Shahin; Khatibzadeh, Shahab; Mesgarpour, Bita; Malekzadeh, Reza

2009-05-01

The scientific output of Iran is increasing rapidly during the recent years. Unfortunately, most papers are published in journals which are not indexed by popular indexing systems and many of them are in Persian without English translation. This makes the results of Iranian scientific research unavailable to other researchers, including Iranians. The aim of this study was to evaluate the quality of current web-based databases indexing scientific articles published in Iran. We identified web-based databases which indexed scientific journals published in Iran using popular search engines. The sites were then subjected to a series of tests to evaluate their coverage, search capabilities, stability, accuracy of information, consistency, accessibility, ease of use, and other features. Results were compared with each other to identify strengths and shortcomings of each site. Five web sites were indentified. None had a complete coverage on scientific Iranian journals. The search capabilities were less than optimal in most sites. English translations of research titles, author names, keywords, and abstracts of Persian-language articles did not follow standards. Some sites did not cover abstracts. Numerous typing errors make searches ineffective and citation indexing unreliable. None of the currently available indexing sites are capable of presenting Iranian research to the international scientific community. The government should intervene by enforcing policies designed to facilitate indexing through a systematic approach. The policies should address Iranian journals, authors, and indexing sites. Iranian journals should be required to provide their indexing data, including references, electronically; authors should provide correct indexing information to journals; and indexing sites should improve their software to meet standards set by the government.

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

EPA Science Inventory

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

Navigating spatial and temporal complexity in developing a long-term land use database for an agricultural watershed

USDA-ARS?s Scientific Manuscript database

No comprehensive protocols exist for the collection, standardization, and storage of agronomic management information into a database that preserves privacy, maintains data uncertainty, and translates everyday decisions into quantitative values. This manuscript describes the development of a databas...

The Ins and Outs of USDA Nutrient Composition

USDA-ARS?s Scientific Manuscript database

The USDA National Nutrient Database for Standard Reference (SR) is the major source of food composition data in the United States, providing the foundation for most food composition databases in the public and private sectors. Sources of data used in SR include analytical studies, food manufacturer...

Characterization of primary standards for use in the HPLC analysis of the procyanidin content of cocoa and chocolate containing products.

PubMed

Hurst, William J; Stanley, Bruce; Glinski, Jan A; Davey, Matthew; Payne, Mark J; Stuart, David A

2009-10-15

This report describes the characterization of a series of commercially available procyanidin standards ranging from dimers DP = 2 to decamers DP = 10 for the determination of procyanidins from cocoa and chocolate. Using a combination of HPLC with fluorescence detection and MALDI-TOF mass spectrometry, the purity of each standard was determined and these data were used to determine relative response factors. These response factors were compared with other response factors obtained from published methods. Data comparing the procyanidin analysis of a commercially available US dark chocolate calculated using each of the calibration methods indicates divergent results and demonstrate that previous methods may significantly underreport the procyanidins in cocoa-containing products. These results have far reaching implications because the previous calibration methods have been used to develop data for a variety of scientific reports, including food databases and clinical studies.

Flexible solution for interoperable cloud healthcare systems.

PubMed

Vida, Mihaela Marcella; Lupşe, Oana Sorina; Stoicu-Tivadar, Lăcrămioara; Bernad, Elena

2012-01-01

It is extremely important for the healthcare domain to have a standardized communication because will improve the quality of information and in the end the resulting benefits will improve the quality of patients' life. The standards proposed to be used are: HL7 CDA and CCD. For a better access to the medical data a solution based on cloud computing (CC) is investigated. CC is a technology that supports flexibility, seamless care, and reduced costs of the medical act. To ensure interoperability between healthcare information systems a solution creating a Web Custom Control is presented. The control shows the database tables and fields used to configure the two standards. This control will facilitate the work of the medical staff and hospital administrators, because they can configure the local system easily and prepare it for communication with other systems. The resulted information will have a higher quality and will provide knowledge that will support better patient management and diagnosis.

Designing testing service at baristand industri Medan’s liquid waste laboratory

NASA Astrophysics Data System (ADS)

Kusumawaty, Dewi; Napitupulu, Humala L.; Sembiring, Meilita T.

2018-03-01

Baristand Industri Medan is a technical implementation unit under the Industrial and Research and Development Agency, the Ministry of Industry. One of the services often used in Baristand Industri Medan is liquid waste testing service. The company set the standard of service is nine working days for testing services. At 2015, 89.66% on testing services liquid waste does not meet the specified standard of services company because of many samples accumulated. The purpose of this research is designing online services to schedule the coming the liquid waste sample. The method used is designing an information system that consists of model design, output design, input design, database design and technology design. The results of designing information system of testing liquid waste online consist of three pages are pages to the customer, the recipient samples and laboratory. From the simulation results with scheduled samples, then the standard services a minimum of nine working days can be reached.

IDD Info: a software to manage surveillance data of Iodine Deficiency Disorders.

PubMed

Liu, Peng; Teng, Bai-Jun; Zhang, Shu-Bin; Su, Xiao-Hui; Yu, Jun; Liu, Shou-Jun

2011-08-01

IDD info, a new software for managing survey data of Iodine Deficiency Disorders (IDD), is presented in this paper. IDD Info aims to create IDD project databases, process, analyze various national or regional surveillance data and form final report. It has series measures of choosing database from existing ones, revising it, choosing indicators from pool to establish database and adding indicators to pool. It also provides simple tools to scan one database and compare two databases, to set IDD standard parameters, to analyze data by single indicator and multi-indicators, and finally to form typeset report with content customized. IDD Info was developed using Chinese national IDD surveillance data of 2005. Its validity was evaluated by comparing with survey report given by China CDC. The IDD Info is a professional analysis tool, which succeeds in speeding IDD data analysis up to about 14.28% with respect to standard reference routines. It consequently enhances analysis performance and user compliance. IDD Info is a practical and accurate means of managing the multifarious IDD surveillance data that can be widely used by non-statisticians in national and regional IDD surveillance. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Implementation of an open adoption research data management system for clinical studies.

PubMed

Müller, Jan; Heiss, Kirsten Ingmar; Oberhoffer, Renate

2017-07-06

Research institutions need to manage multiple studies with individual data sets, processing rules and different permissions. So far, there is no standard technology that provides an easy to use environment to create databases and user interfaces for clinical trials or research studies. Therefore various software solutions are being used-from custom software, explicitly designed for a specific study, to cost intensive commercial Clinical Trial Management Systems (CTMS) up to very basic approaches with self-designed Microsoft ® databases. The technology applied to conduct those studies varies tremendously from study to study, making it difficult to evaluate data across various studies (meta-analysis) and keeping a defined level of quality in database design, data processing, displaying and exporting. Furthermore, the systems being used to collect study data are often operated redundantly to systems used in patient care. As a consequence the data collection in studies is inefficient and data quality may suffer from unsynchronized datasets, non-normalized database scenarios and manually executed data transfers. With OpenCampus Research we implemented an open adoption software (OAS) solution on an open source basis, which provides a standard environment for state-of-the-art research database management at low cost.

Recent advances in the compilation of holocene relative Sea-level database in North America

NASA Astrophysics Data System (ADS)

Horton, B.; Vacchi, M.; Engelhart, S. E.; Nikitina, D.

2015-12-01

Reconstruction of relative sea level (RSL) has implications for investigation of crustal movements, calibration of earth rheology models and the reconstruction of ice sheets. In recent years, efforts were made to create RSL databases following a standardized methodology. These regional databases provided a framework for developing our understanding of the primary mechanisms of RSL change since the Last Glacial Maximum and a long-term baseline against which to gauge changes in sea-level during the 20th century and forecasts for the 21st. Here we present two quality-controlled Holocene RSL database compiled for North America. Along the Pacific coast of North America (British Columbia, Canada to California, USA), our re-evaluation of sea-level indicators from geological and archaeological investigations yield 841 RSL data-points mainly from salt and freshwater wetlands or adjacent estuarine sediment as well as from isolation basin. Along the Atlantic coast of North America (Hudson Bay, Canada to South Carolina, USA), we are currently compiling a database including more than 2000 RSL data-points from isolation basin, salt and freshwater wetlands, beach ridges and intratidal deposits. We outline the difficulties and solutions we made to compile databases in such different depostional environment. We address complex tectonics and the framework to compare such large variability of RSL data-point. We discuss the implications of our results for the glacio-isostatic adjustment (GIA) models in the two studied regions.

Appropriateness of the food-pics image database for experimental eating and appetite research with adolescents.

PubMed

Jensen, Chad D; Duraccio, Kara M; Barnett, Kimberly A; Stevens, Kimberly S

2016-12-01

Research examining effects of visual food cues on appetite-related brain processes and eating behavior has proliferated. Recently investigators have developed food image databases for use across experimental studies examining appetite and eating behavior. The food-pics image database represents a standardized, freely available image library originally validated in a large sample primarily comprised of adults. The suitability of the images for use with adolescents has not been investigated. The aim of the present study was to evaluate the appropriateness of the food-pics image library for appetite and eating research with adolescents. Three hundred and seven adolescents (ages 12-17) provided ratings of recognizability, palatability, and desire to eat, for images from the food-pics database. Moreover, participants rated the caloric content (high vs. low) and healthiness (healthy vs. unhealthy) of each image. Adolescents rated approximately 75% of the food images as recognizable. Approximately 65% of recognizable images were correctly categorized as high vs. low calorie and 63% were correctly classified as healthy vs. unhealthy in 80% or more of image ratings. These results suggest that a smaller subset of the food-pics image database is appropriate for use with adolescents. With some modifications to included images, the food-pics image database appears to be appropriate for use in experimental appetite and eating-related research conducted with adolescents. Copyright © 2016 Elsevier Ltd. All rights reserved.

MP3C - the Minor Planet Physical Properties Catalogue: a New VO Service For Multi-database Query

NASA Astrophysics Data System (ADS)

Tanga, Paolo; Delbo, M.; Gerakis, J.

2013-10-01

In the last few years we witnessed a large growth in the number of asteroids for which we have physical properties. However, these data are dispersed in a multiplicity of catalogs. Extracting data and combining them for further analysis requires custom tools, a situation further complicated by the variety of data sources, some of them standardized (Planetary Data System) others not. With these problems in mind, we created a new Virtual Observatory service named “Minor Planet Physical Properties Catalogue” (abbreviated as MP3C - http://mp3c.oca.eu/). MP3C is not a new database, but rather a portal allowing the user to access selected properties of objects by easy SQL query, even from different sources. At present, such diverse data as orbital parameters, photometric and light curve parameters, sizes and albedos derived by IRAS, AKARI and WISE, SDSS colors, SMASS taxonomy, family membership, satellite data, stellar occultation results, are included. Other data sources will be added in the near future. The physical properties output of the MP3C can be tuned by the users by query criteria based upon ranges of values of the ingested quantities. The resulting list of object can be used for interactive plots through standard VO tools such as TOPCAT. Also, their ephemerids and visibilities from given sites can be computed. We are targeting full VO compliance for providing a new standardized service to the community.

Curating and Preserving the Big Canopy Database System: an Active Curation Approach using SEAD

NASA Astrophysics Data System (ADS)

Myers, J.; Cushing, J. B.; Lynn, P.; Weiner, N.; Ovchinnikova, A.; Nadkarni, N.; McIntosh, A.

2015-12-01

Modern research is increasingly dependent upon highly heterogeneous data and on the associated cyberinfrastructure developed to organize, analyze, and visualize that data. However, due to the complexity and custom nature of such combined data-software systems, it can be very challenging to curate and preserve them for the long term at reasonable cost and in a way that retains their scientific value. In this presentation, we describe how this challenge was met in preserving the Big Canopy Database (CanopyDB) system using an agile approach and leveraging the Sustainable Environment - Actionable Data (SEAD) DataNet project's hosted data services. The CanopyDB system was developed over more than a decade at Evergreen State College to address the needs of forest canopy researchers. It is an early yet sophisticated exemplar of the type of system that has become common in biological research and science in general, including multiple relational databases for different experiments, a custom database generation tool used to create them, an image repository, and desktop and web tools to access, analyze, and visualize this data. SEAD provides secure project spaces with a semantic content abstraction (typed content with arbitrary RDF metadata statements and relationships to other content), combined with a standards-based curation and publication pipeline resulting in packaged research objects with Digital Object Identifiers. Using SEAD, our cross-project team was able to incrementally ingest CanopyDB components (images, datasets, software source code, documentation, executables, and virtualized services) and to iteratively define and extend the metadata and relationships needed to document them. We believe that both the process, and the richness of the resultant standards-based (OAI-ORE) preservation object, hold lessons for the development of best-practice solutions for preserving scientific data in association with the tools and services needed to derive value from it.

New design and facilities for the International Database for Absolute Gravity Measurements (AGrav): A support for the Establishment of a new Global Absolute Gravity Reference System

NASA Astrophysics Data System (ADS)

Wziontek, Hartmut; Falk, Reinhard; Bonvalot, Sylvain; Rülke, Axel

2017-04-01

After about 10 years of successful joint operation by BGI and BKG, the International Database for Absolute Gravity Measurements "AGrav" (see references hereafter) was under a major revision. The outdated web interface was replaced by a responsive, high level web application framework based on Python and built on top of Pyramid. Functionality was added, like interactive time series plots or a report generator and the interactive map-based station overview was updated completely, comprising now clustering and the classification of stations. Furthermore, the database backend was migrated to PostgreSQL for better support of the application framework and long-term availability. As comparisons of absolute gravimeters (AG) become essential to realize a precise and uniform gravity standard, the database was extended to document the results on international and regional level, including those performed at monitoring stations equipped with SGs. By this it will be possible to link different AGs and to trace their equivalence back to the key comparisons under the auspices of International Committee for Weights and Measures (CIPM) as the best metrological realization of the absolute gravity standard. In this way the new AGrav database accommodates the demands of the new Global Absolute Gravity Reference System as recommended by the IAG Resolution No. 2 adopted in Prague 2015. The new database will be presented with focus on the new user interface and new functionality, calling all institutions involved in absolute gravimetry to participate and contribute with their information to built up a most complete picture of high precision absolute gravimetry and improve its visibility. A Digital Object Identifier (DOI) will be provided by BGI to contributors to give a better traceability and facilitate the referencing of their gravity surveys. Links and references: BGI mirror site : http://bgi.obs-mip.fr/data-products/Gravity-Databases/Absolute-Gravity-data/ BKG mirror site: http://agrav.bkg.bund.de/agrav-meta/ Wilmes, H., H. Wziontek, R. Falk, S. Bonvalot (2009). AGrav - the New Absolute Gravity Database and a Proposed Cooperation with the GGP Project. J. of Geodynamics, 48, pp. 305-309. doi:10.1016/j.jog.2009.09.035. Wziontek, H., H. Wilmes, S. Bonvalot (2011). AGrav: An international database for absolute gravity measurements. In Geodesy for Planet Earth (S. Kenyon at al. eds). IAG Symposia, 136, 1035-1040, Springer, Berlin. 2011. doi:10.1007/978-3-642-20338-1_130.

Testing the Capacity of a Multi-Nutrient Profiling System to Guide Food and Beverage Reformulation: Results from Five National Food Composition Databases.

PubMed

Combet, Emilie; Vlassopoulos, Antonis; Mölenberg, Famke; Gressier, Mathilde; Privet, Lisa; Wratten, Craig; Sharif, Sahar; Vieux, Florent; Lehmann, Undine; Masset, Gabriel

2017-04-21

Nutrient profiling ranks foods based on their nutrient composition, with applications in multiple aspects of food policy. We tested the capacity of a category-specific model developed for product reformulation to improve the average nutrient content of foods, using five national food composition datasets (UK, US, China, Brazil, France). Products ( n = 7183) were split into 35 categories based on the Nestlé Nutritional Profiling Systems (NNPS) and were then classified as NNPS 'Pass' if all nutrient targets were met (energy (E), total fat (TF), saturated fat (SFA), sodium (Na), added sugars (AS), protein, calcium). In a modelling scenario, all NNPS Fail products were 'reformulated' to meet NNPS standards. Overall, a third (36%) of all products achieved the NNPS standard/pass (inter-country and inter-category range: 32%-40%; 5%-72%, respectively), with most products requiring reformulation in two or more nutrients. The most common nutrients to require reformulation were SFA (22%-44%) and TF (23%-42%). Modelled compliance with NNPS standards could reduce the average content of SFA, Na and AS (10%, 8% and 6%, respectively) at the food supply level. Despite the good potential to stimulate reformulation across the five countries, the study highlights the need for better data quality and granularity of food composition databases.

Asbestos Exposure Assessment Database

NASA Technical Reports Server (NTRS)

Arcot, Divya K.

2010-01-01

Exposure to particular hazardous materials in a work environment is dangerous to the employees who work directly with or around the materials as well as those who come in contact with them indirectly. In order to maintain a national standard for safe working environments and protect worker health, the Occupational Safety and Health Administration (OSHA) has set forth numerous precautionary regulations. NASA has been proactive in adhering to these regulations by implementing standards which are often stricter than regulation limits and administering frequent health risk assessments. The primary objective of this project is to create the infrastructure for an Asbestos Exposure Assessment Database specific to NASA Johnson Space Center (JSC) which will compile all of the exposure assessment data into a well-organized, navigable format. The data includes Sample Types, Samples Durations, Crafts of those from whom samples were collected, Job Performance Requirements (JPR) numbers, Phased Contrast Microscopy (PCM) and Transmission Electron Microscopy (TEM) results and qualifiers, Personal Protective Equipment (PPE), and names of industrial hygienists who performed the monitoring. This database will allow NASA to provide OSHA with specific information demonstrating that JSC s work procedures are protective enough to minimize the risk of future disease from the exposures. The data has been collected by the NASA contractors Computer Sciences Corporation (CSC) and Wyle Laboratories. The personal exposure samples were collected from devices worn by laborers working at JSC and by building occupants located in asbestos-containing buildings.

Physiological closed-loop control in intelligent oxygen therapy: A review.

PubMed

Sanchez-Morillo, Daniel; Olaby, Osama; Fernandez-Granero, Miguel Angel; Leon-Jimenez, Antonio

2017-07-01

Oxygen therapy has become a standard care for the treatment of patients with chronic obstructive pulmonary disease and other hypoxemic chronic lung diseases. In current systems, manually continuous adjustment of O 2 flow rate is a time-consuming task, often unsuccessful, that requires experienced staff. The primary aim of this systematic review is to collate and report on the principles, algorithms and accuracy of autonomous physiological close-loop controlled oxygen devices as well to present recommendations for future research and studies in this area. A literature search was performed on medical database MEDLINE, engineering database IEEE-Xplore and wide-raging scientific databases Scopus and Web of Science. A narrative synthesis of the results was carried out. A summary of the findings of this review suggests that when compared to the conventional manual practice, the closed-loop controllers maintain higher saturation levels, spend less time below the target saturation, and save oxygen resources. Nonetheless, despite of their potential, autonomous oxygen therapy devices are scarce in real clinical applications. Robustness of control algorithms, fail-safe mechanisms, limited reliability of sensors, usability issues and the need for standardized evaluating methods of assessing risks can be among the reasons for this lack of matureness and need to be addressed before the wide spreading of a new generation of automatic oxygen devices. Copyright © 2017 Elsevier B.V. All rights reserved.

The Effect of Relational Database Technology on Administrative Computing at Carnegie Mellon University.

ERIC Educational Resources Information Center

Golden, Cynthia; Eisenberger, Dorit

1990-01-01

Carnegie Mellon University's decision to standardize its administrative system development efforts on relational database technology and structured query language is discussed and its impact is examined in one of its larger, more widely used applications, the university information system. Advantages, new responsibilities, and challenges of the…

Thematic Accuracy Assessment of the 2011 National Land Cover Database (NLCD)

EPA Science Inventory

Accuracy assessment is a standard protocol of National Land Cover Database (NLCD) mapping. Here we report agreement statistics between map and reference labels for NLCD 2011, which includes land cover for ca. 2001, ca. 2006, and ca. 2011. The two main objectives were assessment o...

Public Opinion Poll Question Databases: An Evaluation

ERIC Educational Resources Information Center

Woods, Stephen

2007-01-01

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

Update of NDL’s list of key foods based on the 2007-2008 WWEIA-NHANES

USDA-ARS?s Scientific Manuscript database

The Nutrient Data Laboratory is responsible for developing authoritative nutrient databases that contain a wide range of food composition values of the nation's food supply. This requires updating and revising the USDA Nutrient Database for Standard Reference (SR) and developing various special int...

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR CODING: FIELD FORMS (UA-D-37.0)

EPA Science Inventory

The purpose of this SOP is to define the coding strategy for selected field forms. Forms addressed here will be scanned into databases; databases are created because the forms contain critical values needed to calculate pollutant concentrations. Other forms not addressed by thi...

The Virtual Observatory Service TheoSSA: Establishing a Database of Synthetic Stellar Flux Standards I. NLTE Spectral Analysis of the DA-Type White Dwarf G191-B2B *,**,***,****

NASA Technical Reports Server (NTRS)

Rauch, T.; Werner, K.; Bohlin, R.; Kruk, J. W.

2013-01-01

Hydrogen-rich, DA-type white dwarfs are particularly suited as primary standard stars for flux calibration. State-of-the-art NLTE models consider opacities of species up to trans-iron elements and provide reliable synthetic stellar-atmosphere spectra to compare with observations. Aims. We will establish a database of theoretical spectra of stellar flux standards that are easily accessible via a web interface. Methods. In the framework of the Virtual Observatory, the German Astrophysical Virtual Observatory developed the registered service TheoSSA. It provides easy access to stellar spectral energy distributions (SEDs) and is intended to ingest SEDs calculated by any model-atmosphere code. In case of the DA white dwarf G191-B2B, we demonstrate that the model reproduces not only its overall continuum shape but also the numerous metal lines exhibited in its ultraviolet spectrum. Results. TheoSSA is in operation and contains presently a variety of SEDs for DA-type white dwarfs. It will be extended in the near future and can host SEDs of all primary and secondary flux standards. The spectral analysis of G191-B2B has shown that our hydrostatic models reproduce the observations best at Teff =60 000 +/- 2000K and log g=7.60 +/- 0.05.We newly identified Fe vi, Ni vi, and Zn iv lines. For the first time, we determined the photospheric zinc abundance with a logarithmic mass fraction of -4.89 (7.5 × solar). The abundances of He (upper limit), C, N, O, Al, Si, O, P, S, Fe, Ni, Ge, and Sn were precisely determined. Upper abundance limits of about 10% solar were derived for Ti, Cr, Mn, and Co. Conclusions. The TheoSSA database of theoretical SEDs of stellar flux standards guarantees that the flux calibration of all astronomical data and cross-calibration between different instruments can be based on the same models and SEDs calculated with different model-atmosphere codes and are easy to compare.

S-World: A high resolution global soil database for simulation modelling (Invited)

NASA Astrophysics Data System (ADS)

Stoorvogel, J. J.

2013-12-01

There is an increasing call for high resolution soil information at the global level. A good example for such a call is the Global Gridded Crop Model Intercomparison carried out within AgMIP. While local studies can make use of surveying techniques to collect additional techniques this is practically impossible at the global level. It is therefore important to rely on legacy data like the Harmonized World Soil Database. Several efforts do exist that aim at the development of global gridded soil property databases. These estimates of the variation of soil properties can be used to assess e.g., global soil carbon stocks. However, they do not allow for simulation runs with e.g., crop growth simulation models as these models require a description of the entire pedon rather than a few soil properties. This study provides the required quantitative description of pedons at a 1 km resolution for simulation modelling. It uses the Harmonized World Soil Database (HWSD) for the spatial distribution of soil types, the ISRIC-WISE soil profile database to derive information on soil properties per soil type, and a range of co-variables on topography, climate, and land cover to further disaggregate the available data. The methodology aims to take stock of these available data. The soil database is developed in five main steps. Step 1: All 148 soil types are ordered on the basis of their expected topographic position using e.g., drainage, salinization, and pedogenesis. Using the topographic ordering and combining the HWSD with a digital elevation model allows for the spatial disaggregation of the composite soil units. This results in a new soil map with homogeneous soil units. Step 2: The ranges of major soil properties for the topsoil and subsoil of each of the 148 soil types are derived from the ISRIC-WISE soil profile database. Step 3: A model of soil formation is developed that focuses on the basic conceptual question where we are within the range of a particular soil property at a particular location given a specific soil type. The soil properties are predicted for each grid cell based on the soil type, the corresponding ranges of soil properties, and the co-variables. Step 4: Standard depth profiles are developed for each of the soil types using the diagnostic criteria of the soil types and soil profile information from the ISRIC-WISE database. The standard soil profiles are combined with the the predicted values for the topsoil and subsoil yielding unique soil profiles at each location. Step 5: In a final step, additional soil properties are added to the database using averages for the soil types and pedo-transfer functions. The methodology, denominated S-World (Soils of the World), results in readily available global maps with quantitative pedon data for modelling purposes. It forms the basis for the Global Gridded Crop Model Intercomparison carried out within AgMIP.

A Public Database of Immersive VR Videos with Corresponding Ratings of Arousal, Valence, and Correlations between Head Movements and Self Report Measures.

PubMed

Li, Benjamin J; Bailenson, Jeremy N; Pines, Adam; Greenleaf, Walter J; Williams, Leanne M

2017-01-01

Virtual reality (VR) has been proposed as a methodological tool to study the basic science of psychology and other fields. One key advantage of VR is that sharing of virtual content can lead to more robust replication and representative sampling. A database of standardized content will help fulfill this vision. There are two objectives to this study. First, we seek to establish and allow public access to a database of immersive VR video clips that can act as a potential resource for studies on emotion induction using virtual reality. Second, given the large sample size of participants needed to get reliable valence and arousal ratings for our video, we were able to explore the possible links between the head movements of the observer and the emotions he or she feels while viewing immersive VR. To accomplish our goals, we sourced for and tested 73 immersive VR clips which participants rated on valence and arousal dimensions using self-assessment manikins. We also tracked participants' rotational head movements as they watched the clips, allowing us to correlate head movements and affect. Based on past research, we predicted relationships between the standard deviation of head yaw and valence and arousal ratings. Results showed that the stimuli varied reasonably well along the dimensions of valence and arousal, with a slight underrepresentation of clips that are of negative valence and highly arousing. The standard deviation of yaw positively correlated with valence, while a significant positive relationship was found between head pitch and arousal. The immersive VR clips tested are available online as supplemental material.

Gulf Arabic nouns and verbs: A standardized set of 319 object pictures and 141 action pictures, with predictors of naming latencies.

PubMed

Khwaileh, Tariq; Mustafawi, Eiman; Herbert, Ruth; Howard, David

2018-02-15

Standardized pictorial stimuli and predictors of successful picture naming are not readily available for Gulf Arabic. On the basis of data obtained from Qatari Arabic, a variety of Gulf Arabic, the present study provides norms for a set of 319 object pictures and a set of 141 action pictures. Norms were collected from healthy speakers, using a picture-naming paradigm and rating tasks. Norms for naming latencies, name agreement, visual complexity, image agreement, imageability, age of acquisition, and familiarity were established. Furthermore, the database includes other intrinsic factors, such as syllable length and phoneme length. It also includes orthographic frequency values (extracted from Aralex; Boudelaa & Marslen-Wilson, 2010). These factors were then examined for their impact on picture-naming latencies in object- and action-naming tasks. The analysis showed that the primary determinants of naming latencies in both nouns and verbs are (in descending order) image agreement, name agreement, familiarity, age of acquisition, and imageability. These results indicate no evidence that noun- and verb-naming processes in Gulf Arabic are influenced in different ways by these variables. This is the first database for Gulf Arabic, and therefore the norms collected from the present study will be of paramount importance for researchers and clinicians working with speakers of this variety of Arabic. Due to the similarity of the Arabic varieties spoken in the Gulf, these different varieties are grouped together under the label "Gulf Arabic" in the literature. The normative databases and the standardized pictures from this study can be downloaded from http://qufaculty.qu.edu.qa/tariq-khwaileh/download-center/ .

A Public Database of Immersive VR Videos with Corresponding Ratings of Arousal, Valence, and Correlations between Head Movements and Self Report Measures

PubMed Central

Li, Benjamin J.; Bailenson, Jeremy N.; Pines, Adam; Greenleaf, Walter J.; Williams, Leanne M.

2017-01-01

Virtual reality (VR) has been proposed as a methodological tool to study the basic science of psychology and other fields. One key advantage of VR is that sharing of virtual content can lead to more robust replication and representative sampling. A database of standardized content will help fulfill this vision. There are two objectives to this study. First, we seek to establish and allow public access to a database of immersive VR video clips that can act as a potential resource for studies on emotion induction using virtual reality. Second, given the large sample size of participants needed to get reliable valence and arousal ratings for our video, we were able to explore the possible links between the head movements of the observer and the emotions he or she feels while viewing immersive VR. To accomplish our goals, we sourced for and tested 73 immersive VR clips which participants rated on valence and arousal dimensions using self-assessment manikins. We also tracked participants' rotational head movements as they watched the clips, allowing us to correlate head movements and affect. Based on past research, we predicted relationships between the standard deviation of head yaw and valence and arousal ratings. Results showed that the stimuli varied reasonably well along the dimensions of valence and arousal, with a slight underrepresentation of clips that are of negative valence and highly arousing. The standard deviation of yaw positively correlated with valence, while a significant positive relationship was found between head pitch and arousal. The immersive VR clips tested are available online as supplemental material. PMID:29259571

Application of ISO standard 27048: dose assessment for the monitoring of workers for internal radiation exposure.

PubMed

Henrichs, K

2011-03-01

Besides ongoing developments in the dosimetry of incorporated radionuclides, there are various efforts to improve the monitoring of workers for potential or real intakes of radionuclides. The disillusioning experience with numerous intercomparison projects identified substantial differences between national regulations, concepts, applied programmes and methods, and dose assessment procedures. Measured activities were not directly comparable because of significant differences between measuring frequencies and methods, but also results of case studies for dose assessments revealed differences of orders of magnitude. Besides the general common interest in reliable monitoring results, at least the cross-border activities of workers (e.g. nuclear power plant services) require consistent approaches and comparable results. The International Standardization Organization therefore initiated projects to standardise programmes for the monitoring of workers, the requirements for measuring laboratories and the processes for the quantitative evaluation of monitoring results in terms of internal assessed doses. The strength of the concepts applied by the international working group consists in a unified approach defining the requirements, databases and processes. This paper is intended to give a short introduction into the standardization project followed by a more detailed description of the dose assessment standard, which will be published in the very near future.

Structure elucidation of organic compounds aided by the computer program system SCANNET

NASA Astrophysics Data System (ADS)

Guzowska-Swider, B.; Hippe, Z. S.

1992-12-01

Recognition of chemical structure is a very important problem currently solved by molecular spectroscopy, particularly IR, UV, NMR and Raman spectroscopy, and mass spectrometry. Nowadays, solution of the problem is frequently aided by the computer. SCANNET is a computer program system for structure elucidation of organic compounds, developed by our group. The structure recognition of an unknown substance is made by comparing its spectrum with successive reference spectra of standard compounds, i.e. chemical compounds of known chemical structure, stored in a spectral database. The computer program system SCANNET consists of six different spectral databases for following the analytical methods: IR, UV, 13C-NMR, 1H-NMR and Raman spectroscopy, and mass spectrometry. A chemist, to elucidate a structure, can use one of these spectral methods or a combination of them and search the appropriate databases. As the result of searching each spectral database, the user obtains a list of chemical substances whose spectra are identical and/or similar to the spectrum input into the computer. The final information obtained from searching the spectral databases is in the form of a list of chemical substances having all the examined spectra, for each type of spectroscopy, identical or simlar to those of the unknown compound.

Updates to the Virtual Atomic and Molecular Data Centre

NASA Astrophysics Data System (ADS)

Hill, Christian; Tennyson, Jonathan; Gordon, Iouli E.; Rothman, Laurence S.; Dubernet, Marie-Lise

2014-06-01

The Virtual Atomic and Molecular Data Centre (VAMDC) has established a set of standards for the storage and transmission of atomic and molecular data and an SQL-based query language (VSS2) for searching online databases, known as nodes. The project has also created an online service, the VAMDC Portal, through which all of these databases may be searched and their results compared and aggregated. Since its inception four years ago, the VAMDC e-infrastructure has grown to encompass over 40 databases, including HITRAN, in more than 20 countries and engages actively with scientists in six continents. Associated with the portal are a growing suite of software tools for the transformation of data from its native, XML-based, XSAMS format, to a range of more convenient human-readable (such as HTML) and machinereadable (such as CSV) formats. The relational database for HITRAN1, created as part of the VAMDC project is a flexible and extensible data model which is able to represent a wider range of parameters than the current fixed-format text-based one. Over the next year, a new online interface to this database will be tested, released and fully documented - this web application, HITRANonline2, will fully replace the ageing and incomplete JavaHAWKS software suite.

Normal Databases for the Relative Quantification of Myocardial Perfusion

PubMed Central

Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S.; Slomka, Piotr J.

2016-01-01

Purpose of review Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. Recent findings New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Summary Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied. PMID:28138354

An Updating System for the Gridded Population Database of China Based on Remote Sensing, GIS and Spatial Database Technologies.

PubMed

Yang, Xiaohuan; Huang, Yaohuan; Dong, Pinliang; Jiang, Dong; Liu, Honghui

2009-01-01

The spatial distribution of population is closely related to land use and land cover (LULC) patterns on both regional and global scales. Population can be redistributed onto geo-referenced square grids according to this relation. In the past decades, various approaches to monitoring LULC using remote sensing and Geographic Information Systems (GIS) have been developed, which makes it possible for efficient updating of geo-referenced population data. A Spatial Population Updating System (SPUS) is developed for updating the gridded population database of China based on remote sensing, GIS and spatial database technologies, with a spatial resolution of 1 km by 1 km. The SPUS can process standard Moderate Resolution Imaging Spectroradiometer (MODIS L1B) data integrated with a Pattern Decomposition Method (PDM) and an LULC-Conversion Model to obtain patterns of land use and land cover, and provide input parameters for a Population Spatialization Model (PSM). The PSM embedded in SPUS is used for generating 1 km by 1 km gridded population data in each population distribution region based on natural and socio-economic variables. Validation results from finer township-level census data of Yishui County suggest that the gridded population database produced by the SPUS is reliable.

32 CFR 2001.42 - Standards for security equipment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... OVERSIGHT OFFICE, NATIONAL ARCHIVES AND RECORDS ADMINISTRATION CLASSIFIED NATIONAL SECURITY INFORMATION... Administration (GSA) shall, in coordination with agency heads originating classified information, establish and publish uniform standards, specifications, qualified product lists or databases, and supply schedules for...

15 CFR 995.4 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE QUALITY ASSURANCE AND CERTIFICATION... of the 1974 SOLAS Convention. Electronic Navigational Chart (ENC) means a database, standardized as... National Oceanic and Atmospheric Administration. NOAA ENC files comply with the IHO S-57 standard, Edition...

15 CFR 995.4 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE QUALITY ASSURANCE AND CERTIFICATION... of the 1974 SOLAS Convention. Electronic Navigational Chart (ENC) means a database, standardized as... National Oceanic and Atmospheric Administration. NOAA ENC files comply with the IHO S-57 standard, Edition...

32 CFR 2001.42 - Standards for security equipment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... OVERSIGHT OFFICE, NATIONAL ARCHIVES AND RECORDS ADMINISTRATION CLASSIFIED NATIONAL SECURITY INFORMATION... Administration (GSA) shall, in coordination with agency heads originating classified information, establish and publish uniform standards, specifications, qualified product lists or databases, and supply schedules for...

15 CFR 995.4 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE QUALITY ASSURANCE AND CERTIFICATION... of the 1974 SOLAS Convention. Electronic Navigational Chart (ENC) means a database, standardized as... National Oceanic and Atmospheric Administration. NOAA ENC files comply with the IHO S-57 standard, Edition...

15 CFR 995.4 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE QUALITY ASSURANCE AND CERTIFICATION... of the 1974 SOLAS Convention. Electronic Navigational Chart (ENC) means a database, standardized as... National Oceanic and Atmospheric Administration. NOAA ENC files comply with the IHO S-57 standard, Edition...

32 CFR 2001.42 - Standards for security equipment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... OVERSIGHT OFFICE, NATIONAL ARCHIVES AND RECORDS ADMINISTRATION CLASSIFIED NATIONAL SECURITY INFORMATION... Administration (GSA) shall, in coordination with agency heads originating classified information, establish and publish uniform standards, specifications, qualified product lists or databases, and supply schedules for...

32 CFR 2001.42 - Standards for security equipment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... OVERSIGHT OFFICE, NATIONAL ARCHIVES AND RECORDS ADMINISTRATION CLASSIFIED NATIONAL SECURITY INFORMATION... Administration (GSA) shall, in coordination with agency heads originating classified information, establish and publish uniform standards, specifications, qualified product lists or databases, and supply schedules for...

Lessons Learned and Technical Standards: A Logical Marriage for Future Space Systems Design

NASA Technical Reports Server (NTRS)

Gill, Paul S.; Garcia, Danny; Vaughan, William W.; Parker, Nelson C. (Technical Monitor)

2002-01-01

A comprehensive database of engineering lessons learned that corresponds with relevant technical standards will be a valuable asset to those engaged in studies on future space vehicle developments, especially for structures, materials, propulsion, control, operations and associated elements. In addition, this will enable the capturing of technology developments applicable to the design, development, and operation of future space vehicles as planned in the Space Launch Initiative. Using the time-honored tradition of passing on lessons learned while utilizing the newest information technology, NASA has launched an intensive effort to link lessons learned acquired through various Internet databases with applicable technical standards. This paper will discuss the importance of lessons learned, the difficulty in finding relevant lessons learned while engaged in a space vehicle development, and the new NASA effort to relate them to technical standards that can help alleviate this difficulty.

The financial attractiveness assessment of large waste management projects registered as clean development mechanism

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

Bufoni, André Luiz, E-mail: bufoni@facc.ufrj.br; Oliveira, Luciano Basto; Rosa, Luiz Pinguelli

Highlights: • Projects are not financially attractive without registration as CDMs. • WM benchmarks and indicators are converging and reducing in variance. • A sensitivity analysis reveal that revenue has more of an effect on the financial results. • Results indicate that an extensive database would reduce WM project risk and capital costs. • Disclosure standards would make information more comparable worldwide. - Abstract: This study illustrates the financial analyses for demonstration and assessment of additionality presented in the project design (PDD) and enclosed documents of the 431 large Clean Development Mechanisms (CDM) classified as the ‘waste handling and disposalmore » sector’ (13) over the past ten years (2004–2014). The expected certified emissions reductions (CER) of these projects total 63.54 million metric tons of CO{sub 2}eq, where eight countries account for 311 projects and 43.36 million metric tons. All of the projects declare themselves ‘not financially attractive’ without CER with an estimated sum of negative results of approximately a half billion US$. The results indicate that WM benchmarks and indicators are converging and reducing in variance, and the sensitivity analysis reveals that revenues have a greater effect on the financial results. This work concludes that an extensive financial database with simple standards for disclosure would greatly diminish statement problems and make information more comparable, reducing the risk and capital costs of WM projects.« less

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.

Digital Dental X-ray Database for Caries Screening

NASA Astrophysics Data System (ADS)

Rad, Abdolvahab Ehsani; Rahim, Mohd Shafry Mohd; Rehman, Amjad; Saba, Tanzila

2016-06-01

Standard database is the essential requirement to compare the performance of image analysis techniques. Hence the main issue in dental image analysis is the lack of available image database which is provided in this paper. Periapical dental X-ray images which are suitable for any analysis and approved by many dental experts are collected. This type of dental radiograph imaging is common and inexpensive, which is normally used for dental disease diagnosis and abnormalities detection. Database contains 120 various Periapical X-ray images from top to bottom jaw. Dental digital database is constructed to provide the source for researchers to use and compare the image analysis techniques and improve or manipulate the performance of each technique.

A standards-based clinical information system for HIV/AIDS.

PubMed

Stitt, F W

1995-01-01

To create a clinical data repository to interface the Veteran's Administration (VA) Decentralized Hospital Computer Program (DHCP) and a departmental clinical information system for the management of HIV patients. This system supports record-keeping, decision-making, reporting, and analysis. The database development was designed to overcome two impediments to successful implementations of clinical databases: (i) lack of a standard reference data model, and; (ii) lack of a universal standard for medical concept representation. Health Level Seven (HL7) is a standard protocol that specifies the implementation of interfaces between two computer applications (sender and receiver) from different vendors or sources of electronic data exchange in the health care environment. This eliminates or substantially reduces the custom interface programming and program maintenance that would otherwise be required. HL7 defines the data to be exchanged, the timing of the interchange, and the communication of errors to the application. The formats are generic in nature and must be configured to meet the needs of the two applications involved. The standard conceptually operates at the seventh level of the ISO model for Open Systems Interconnection (OSI). The OSI simply defines the data elements that are exchanged as abstract messages, and does not prescribe the exact bit stream of the messages that flow over the network. Lower level network software developed according to the OSI model may be used to encode and decode the actual bit stream. The OSI protocols are not universally implemented and, therefore, a set of encoding rules for defining the exact representation of a message must be specified. The VA has created an HL7 module to assist DHCP applications in exchanging health care information with other applications using the HL7 protocol. The DHCP HL7 module consists of a set of utility routines and files that provide a generic interface to the HL7 protocol for all DHCP applications. The VA's DHCP core modules are in standard use at 169 hospitals, and the role of the VA system in health care delivery has been discussed elsewhere. This development was performed at the Miami VA Medical Center Special Immunology Unit, where a database was created for an HIV patient registry in 1987. Over 2,300 patient have been entered into a database that supports a problem-oriented summary of the patient's clinical record. The interface to the VA DHCP was designed and implemented to capture information from the patient treatment file, pharmacy, laboratory, radiology, and other modules. We obtained a suite of programs for implementing the HL7 encoding rules from Columbia-Presbyterian Medical Center in New York, written in ANSI C. This toolkit isolates our application programs from the details of the HL7 encoding rules, and allows them to deal with abstract messages and the programming level. While HL7 has become a standard for healthcare message exchange, SQL (Structured Query Language) is the standard for database definition, data manipulation, and query. The target database (Stitt F.W. The Problem-Oriented Medical Synopsis: a patient-centered clinical information system. Proc 17 SCAMC. 1993:88-93) provides clinical workstation functionality. Medical concepts are encoded using a preferred terminology derived from over 15 sources that include the Unified Medical Language System and SNOMed International ( Stitt F.W. The Problem-Oriented Medical Synopsis: coding, indexing, and classification sub-model. Proc 18 SCAMC, 1994: in press). The databases were modeled using the Information Engineering CASE tools, and were written using relational database utilities, including embedded SQL in C (ESQL/C). We linked ESQL/C programs to the HL7 toolkit to allow data to be inserted, deleted, or updated, under transaction control. A graphical format will be used to display the entity-rel

GeneSigDB—a curated database of gene expression signatures

PubMed Central

Culhane, Aedín C.; Schwarzl, Thomas; Sultana, Razvan; Picard, Kermshlise C.; Picard, Shaita C.; Lu, Tim H.; Franklin, Katherine R.; French, Simon J.; Papenhausen, Gerald; Correll, Mick; Quackenbush, John

2010-01-01

The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats. PMID:19934259

A comprehensive clinical research database based on CDISC ODM and i2b2.

PubMed

Meineke, Frank A; Stäubert, Sebastian; Löbe, Matthias; Winter, Alfred

2014-01-01

We present a working approach for a clinical research database as part of an archival information system. The CDISC ODM standard is target for clinical study and research relevant routine data, thus decoupling the data ingest process from the access layer. The presented research database is comprehensive as it covers annotating, mapping and curation of poorly annotated source data. Besides a conventional relational database the medical data warehouse i2b2 serves as main frontend for end-users. The system we developed is suitable to support patient recruitment, cohort identification and quality assurance in daily routine.

Solutions for medical databases optimal exploitation

PubMed Central

Branescu, I; Purcarea, VL; Dobrescu, R

2014-01-01

The paper discusses the methods to apply OLAP techniques for multidimensional databases that leverage the existing, performance-enhancing technique, known as practical pre-aggregation, by making this technique relevant to a much wider range of medical applications, as a logistic support to the data warehousing techniques. The transformations have practically low computational complexity and they may be implemented using standard relational database technology. The paper also describes how to integrate the transformed hierarchies in current OLAP systems, transparently to the user and proposes a flexible, “multimodel" federated system for extending OLAP querying to external object databases. PMID:24653769

Freva - Freie Univ Evaluation System Framework for Scientific Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Schartner, Thomas; Kirchner, Ingo; Rust, Henning W.; Cubasch, Ulrich; Ulbrich, Uwe

2016-04-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science. Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitation of the provision and usage of tools and climate data automatically increases the number of scientists working with the data sets and identifying discrepancies. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Therefore, plugged-in tools benefit from transparency and reproducibility. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Freva - Freie Univ Evaluation System Framework for Scientific HPC Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Schartner, T.; Grieger, J.; Kirchner, I.; Rust, H.; Cubasch, U.; Ulbrich, U.

2017-12-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science (e.g. www-miklip.dkrz.de, cmip-eval.dkrz.de). Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Glocal Clinical Registries: Pacemaker Registry Design and Implementation for Global and Local Integration – Methodology and Case Study

PubMed Central

da Silva, Kátia Regina; Costa, Roberto; Crevelari, Elizabeth Sartori; Lacerda, Marianna Sobral; de Moraes Albertini, Caio Marcos; Filho, Martino Martinelli; Santana, José Eduardo; Vissoci, João Ricardo Nickenig; Pietrobon, Ricardo; Barros, Jacson V.

2013-01-01

Background The ability to apply standard and interoperable solutions for implementing and managing medical registries as well as aggregate, reproduce, and access data sets from legacy formats and platforms to advanced standard formats and operating systems are crucial for both clinical healthcare and biomedical research settings. Purpose Our study describes a reproducible, highly scalable, standard framework for a device registry implementation addressing both local data quality components and global linking problems. Methods and Results We developed a device registry framework involving the following steps: (1) Data standards definition and representation of the research workflow, (2) Development of electronic case report forms using REDCap (Research Electronic Data Capture), (3) Data collection according to the clinical research workflow and, (4) Data augmentation by enriching the registry database with local electronic health records, governmental database and linked open data collections, (5) Data quality control and (6) Data dissemination through the registry Web site. Our registry adopted all applicable standardized data elements proposed by American College Cardiology / American Heart Association Clinical Data Standards, as well as variables derived from cardiac devices randomized trials and Clinical Data Interchange Standards Consortium. Local interoperability was performed between REDCap and data derived from Electronic Health Record system. The original data set was also augmented by incorporating the reimbursed values paid by the Brazilian government during a hospitalization for pacemaker implantation. By linking our registry to the open data collection repository Linked Clinical Trials (LinkedCT) we found 130 clinical trials which are potentially correlated with our pacemaker registry. Conclusion This study demonstrates how standard and reproducible solutions can be applied in the implementation of medical registries to constitute a re-usable framework. Such approach has the potential to facilitate data integration between healthcare and research settings, also being a useful framework to be used in other biomedical registries. PMID:23936257

Accuracy of LightCycler(R) SeptiFast for the detection and identification of pathogens in the blood of patients with suspected sepsis: a systematic review protocol.

PubMed

Dark, Paul; Wilson, Claire; Blackwood, Bronagh; McAuley, Danny F; Perkins, Gavin D; McMullan, Ronan; Gates, Simon; Warhurst, Geoffrey

2012-01-01

Background There is growing interest in the potential utility of molecular diagnostics in improving the detection of life-threatening infection (sepsis). LightCycler® SeptiFast is a multipathogen probe-based real-time PCR system targeting DNA sequences of bacteria and fungi present in blood samples within a few hours. We report here the protocol of the first systematic review of published clinical diagnostic accuracy studies of this technology when compared with blood culture in the setting of suspected sepsis. Methods/design Data sources: the Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects (DARE), the Health Technology Assessment Database (HTA), the NHS Economic Evaluation Database (NHSEED), The Cochrane Library, MEDLINE, EMBASE, ISI Web of Science, BIOSIS Previews, MEDION and the Aggressive Research Intelligence Facility Database (ARIF). diagnostic accuracy studies that compare the real-time PCR technology with standard culture results performed on a patient's blood sample during the management of sepsis. three reviewers, working independently, will determine the level of evidence, methodological quality and a standard data set relating to demographics and diagnostic accuracy metrics for each study. Statistical analysis/data synthesis: heterogeneity of studies will be investigated using a coupled forest plot of sensitivity and specificity and a scatter plot in Receiver Operator Characteristic (ROC) space. Bivariate model method will be used to estimate summary sensitivity and specificity. The authors will investigate reporting biases using funnel plots based on effective sample size and regression tests of asymmetry. Subgroup analyses are planned for adults, children and infection setting (hospital vs community) if sufficient data are uncovered. Dissemination Recommendations will be made to the Department of Health (as part of an open-access HTA report) as to whether the real-time PCR technology has sufficient clinical diagnostic accuracy potential to move forward to efficacy testing during the provision of routine clinical care. Registration PROSPERO-NIHR Prospective Register of Systematic Reviews (CRD42011001289).

Carbon-14 Measurements in Atmospheric CO2 from Northern and Southern Hemisphere Sites, 1962-1993 (NDP-057)

DOE Data Explorer

Nydal, Reidar [Radiological Dating Laboratory, The Norwegian Institute of Technology, Trondheim, Norway; Lovseth, Knut [Radiological Dating Laboratory, The Norwegian Institute of Technology, Trondheim, Norway; Boden, Thomas A. [CDIAC, Oak Ridge National Laboratory, Oak Ridge TN (USA); World Data Center A - Atmospheric Trace Gases; Zumbrunn, Virgene [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)

1996-01-01

In the 1960s, thermonuclear bomb tests released significant pulses of radioactive 14C into the atmosphere. This major perturbation allowed scientists to study the dynamics of the global carbon cycle by measuring and observing rates of isotopic exchange. The Radiological Dating Laboratory at the Norwegian Institute of Technology performed 14C measurements in atmospheric CO2 from 1962 to 1993 at a network of ground stations in the Northern and Southern hemispheres. These measurements were supplemented during 1965 with high-altitude (9-12.6 km) air samples collected using aircraft from the Norwegian Air Force. The resulting database, coupled with other 14C data sets, provides a greater understanding of the dynamic carbon reservoir and a crude picture of anomalous sources and sinks at different geographical latitudes. This database is outstanding for its inclusion of early 14C measurements, broad spatial coverage of sampling, consistency of sampling method, and 14C calculation results corrected for isotopic fractionation and radioactive decay. This database replaces previous versions published by the authors and the Radiological Dating Laboratory. Fourteen stations spanning latitudes from Spitsbergen (78° N) to Madagascar (21° S) were used for sampling during the lifetime of the Norwegian program. Some of the stations have data for only a brief period, while others have measurements through 1993. Sampling stations subject to local industrial CO2 contamination were avoided. The sites have sufficient separation to describe the latitudinal distribution of 14C in atmospheric models. The sampling procedure for all the surface (10-2400 m asl) 14C measurements in this database consisted of quantitative absorption of atmospheric CO2 in carbonate-free 0.5 N NaOH solution. The 14C measurements were made in a CO2 proportional counter and calculated (14C) as per mil excess above the normal 14C level defined by the US National Institute of Standards and Technology (NIST). Atmospheric 14C content is finally expressed as 14C, which is the relative deviation of the measured 14C activity from the NIST oxalic acid standard activity, after correction for isotopic fractionation and radioactive decay related to age. The data are organized by sampling station, and each record of the database contains the sampling dates; values for 14C excess (14C) relative to the NIST standard, fractionation 13C (13C) relative to the Pee Dee Belemnite (PDB) standard, and corrected 14C ( 14C) excess; and the standard deviation for 14C. The 14C calculation results presented here are thus corrected for isotopic fractionation and radioactive decay, and constitute the final product of a research effort that has spanned three decades. The 14C station data show a sharp increase in tropospheric radiocarbon levels in the early 1960s and then a decline after the majority of nuclear tests came to an end on August 5, 1963 (Test Ban Treaty). The sharp peaks in tropospheric radiocarbon in the early 1960s are more pronounced in the Northern Hemisphere, reflecting the location of most atomic weapons tests. The measurements show large seasonal variations in the 14C level during the early 1960s mainly as a result of springtime transport of bomb 14C from the stratosphere. During the 1970s, the seasonal variations are smaller and due partly to seasonal variations in CO2 from fossil-fuel emissions. The rate of decrease of atmospheric radiocarbon provides a check on the exchange constants of the atmosphere and ocean. This report and all data it describes are available from the Carbon Dioxide Information Analysis Center (CDIAC) without charge. The Nydal and Lövseth atmospheric 14C database comprises 21 data files totaling 0.2 megabytes in size. The following report describes the sampling methods and analysis. In addition, the report includes a complete discussion of CDIAC's data-processing efforts, the contents and format of the data files, and a reprint of a Nydal and Lövseth journal article.

A novel method for efficient archiving and retrieval of biomedical images using MPEG-7

NASA Astrophysics Data System (ADS)

Meyer, Joerg; Pahwa, Ash

2004-10-01

Digital archiving and efficient retrieval of radiological scans have become critical steps in contemporary medical diagnostics. Since more and more images and image sequences (single scans or video) from various modalities (CT/MRI/PET/digital X-ray) are now available in digital formats (e.g., DICOM-3), hospitals and radiology clinics need to implement efficient protocols capable of managing the enormous amounts of data generated daily in a typical clinical routine. We present a method that appears to be a viable way to eliminate the tedious step of manually annotating image and video material for database indexing. MPEG-7 is a new framework that standardizes the way images are characterized in terms of color, shape, and other abstract, content-related criteria. A set of standardized descriptors that are automatically generated from an image is used to compare an image to other images in a database, and to compute the distance between two images for a given application domain. Text-based database queries can be replaced with image-based queries using MPEG-7. Consequently, image queries can be conducted without any prior knowledge of the keys that were used as indices in the database. Since the decoding and matching steps are not part of the MPEG-7 standard, this method also enables searches that were not planned by the time the keys were generated.

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

NASA Astrophysics Data System (ADS)

Bono, Andrea

2007-01-01

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

A Database of Herbaceous Vegetation Responses to Elevated Atmospheric CO2 (NDP-073)

DOE Data Explorer

Jones, Michael H [The Ohio State Univ., Columbus, OH (United States); Curtis, Peter S [The Ohio State Univ., Columbus, OH (United States); Cushman, Robert M [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brenkert, Antoinette L [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

1999-01-01

To perform a statistically rigorous meta-analysis of research results on the response by herbaceous vegetation to increased atmospheric CO2 levels, a multiparameter database of responses was compiled from the published literature. Seventy-eight independent CO2-enrichment studies, covering 53 species and 26 response parameters, reported mean response, sample size, and variance of the response (either as standard deviation or standard error). An additional 43 studies, covering 25 species and 6 response parameters, did not report variances. This numeric data package accompanies the Carbon Dioxide Information Analysis Center's (CDIAC's) NDP- 072, which provides similar information for woody vegetation. This numeric data package contains a 30-field data set of CO2- exposure experiment responses by herbaceous plants (as both a flat ASCII file and a spreadsheet file), files listing the references to the CO2-exposure experiments and specific comments relevant to the data in the data sets, and this documentation file (which includes SAS and Fortran codes to read the ASCII data file; SAS is a registered trademark of the SAS Institute, Inc., Cary, North Carolina 27511).

A comparison of operative outcomes between standard and robotic laparoscopic surgery for endometrial cancer: A systematic review and meta‐analysis

PubMed Central

Laios, Alex; Hacking, Matthew; Nobbenhuis, Marielle

2017-01-01

Abstract Background Evidence has been systematically assessed comparing robotic with standard laparoscopy for treatment of endometrial cancer. Methods A search of Medline, Embase and Cochrane databases was performed until 30th October 2016. Results Thirty‐six papers including 33 retrospective studies, two matched case–control studies and one randomized controlled study were used in a meta‐analysis. Information from a further seven registry/database studies were assessed descriptively. There were no differences in the duration of surgery but days stay in hospital were shorter in the robotic arm (0.46 days, 95%CI 0.26 to 0.66). A robotic approach had less blood loss (57.74 mL, 95%CI 38.29 to 77.20), less conversions to laparotomy (RR = 0.41, 95%CI 0.29 to 0.59), and less overall complications (RR = 0.82, 95%CI 0.72 to 0.93). A robotic approach had higher costs ($1746.20, 95%CI $63.37 to $3429.03). Conclusion A robotic approach has favourable clinical outcomes but is more expensive. PMID:28762635

Assured crew return vehicle man-systems integration standards

NASA Technical Reports Server (NTRS)

1991-01-01

This is Volume 6 of the Man-Systems Integration Standards (MSIS) family of documents, which is contained in several volumes and a relational database. Each volume has a specific purpose, and each has been assembled from the data contained in the relational database. Volume 6 serves as the Assured Crew Return Vehicle project man-systems integration design requirements. The data in this document is a subset of the data found in Volume 1 and defines the requirements which are pertinent to the Assured Crew Return Vehicle as defined in the SPRD. Additional data and guidelines are provided to assist in the design.

Designing and Developing a NASA Research Projects Knowledge Base and Implementing Knowledge Management and Discovery Techniques

NASA Astrophysics Data System (ADS)

Dabiru, L.; O'Hara, C. G.; Shaw, D.; Katragadda, S.; Anderson, D.; Kim, S.; Shrestha, B.; Aanstoos, J.; Frisbie, T.; Policelli, F.; Keblawi, N.

2006-12-01

The Research Project Knowledge Base (RPKB) is currently being designed and will be implemented in a manner that is fully compatible and interoperable with enterprise architecture tools developed to support NASA's Applied Sciences Program. Through user needs assessment, collaboration with Stennis Space Center, Goddard Space Flight Center, and NASA's DEVELOP Staff personnel insight to information needs for the RPKB were gathered from across NASA scientific communities of practice. To enable efficient, consistent, standard, structured, and managed data entry and research results compilation a prototype RPKB has been designed and fully integrated with the existing NASA Earth Science Systems Components database. The RPKB will compile research project and keyword information of relevance to the six major science focus areas, 12 national applications, and the Global Change Master Directory (GCMD). The RPKB will include information about projects awarded from NASA research solicitations, project investigator information, research publications, NASA data products employed, and model or decision support tools used or developed as well as new data product information. The RPKB will be developed in a multi-tier architecture that will include a SQL Server relational database backend, middleware, and front end client interfaces for data entry. The purpose of this project is to intelligently harvest the results of research sponsored by the NASA Applied Sciences Program and related research program results. We present various approaches for a wide spectrum of knowledge discovery of research results, publications, projects, etc. from the NASA Systems Components database and global information systems and show how this is implemented in SQL Server database. The application of knowledge discovery is useful for intelligent query answering and multiple-layered database construction. Using advanced EA tools such as the Earth Science Architecture Tool (ESAT), RPKB will enable NASA and partner agencies to efficiently identify the significant results for new experiment directions and principle investigators to formulate experiment directions for new proposals.

Computational Thermochemistry of Jet Fuels and Rocket Propellants

NASA Technical Reports Server (NTRS)

Crawford, T. Daniel

2002-01-01

The design of new high-energy density molecules as candidates for jet and rocket fuels is an important goal of modern chemical thermodynamics. The NASA Glenn Research Center is home to a database of thermodynamic data for over 2000 compounds related to this goal, in the form of least-squares fits of heat capacities, enthalpies, and entropies as functions of temperature over the range of 300 - 6000 K. The chemical equilibrium with applications (CEA) program written and maintained by researchers at NASA Glenn over the last fifty years, makes use of this database for modeling the performance of potential rocket propellants. During its long history, the NASA Glenn database has been developed based on experimental results and data published in the scientific literature such as the standard JANAF tables. The recent development of efficient computational techniques based on quantum chemical methods provides an alternative source of information for expansion of such databases. For example, it is now possible to model dissociation or combustion reactions of small molecules to high accuracy using techniques such as coupled cluster theory or density functional theory. Unfortunately, the current applicability of reliable computational models is limited to relatively small molecules containing only around a dozen (non-hydrogen) atoms. We propose to extend the applicability of coupled cluster theory- often referred to as the 'gold standard' of quantum chemical methods- to molecules containing 30-50 non-hydrogen atoms. The centerpiece of this work is the concept of local correlation, in which the description of the electron interactions- known as electron correlation effects- are reduced to only their most important localized components. Such an advance has the potential to greatly expand the current reach of computational thermochemistry and thus to have a significant impact on the theoretical study of jet and rocket propellants.

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

Creation of clinical research databases in the 21st century: a practical algorithm for HIPAA Compliance.

PubMed

Schell, Scott R

2006-02-01

Enforcement of the Health Insurance Portability and Accountability Act (HIPAA) began in April, 2003. Designed as a law mandating health insurance availability when coverage was lost, HIPAA imposed sweeping and broad-reaching protections of patient privacy. These changes dramatically altered clinical research by placing sizeable regulatory burdens upon investigators with threat of severe and costly federal and civil penalties. This report describes development of an algorithmic approach to clinical research database design based upon a central key-shared data (CK-SD) model allowing researchers to easily analyze, distribute, and publish clinical research without disclosure of HIPAA Protected Health Information (PHI). Three clinical database formats (small clinical trial, operating room performance, and genetic microchip array datasets) were modeled using standard structured query language (SQL)-compliant databases. The CK database was created to contain PHI data, whereas a shareable SD database was generated in real-time containing relevant clinical outcome information while protecting PHI items. Small (< 100 records), medium (< 50,000 records), and large (> 10(8) records) model databases were created, and the resultant data models were evaluated in consultation with an HIPAA compliance officer. The SD database models complied fully with HIPAA regulations, and resulting "shared" data could be distributed freely. Unique patient identifiers were not required for treatment or outcome analysis. Age data were resolved to single-integer years, grouping patients aged > 89 years. Admission, discharge, treatment, and follow-up dates were replaced with enrollment year, and follow-up/outcome intervals calculated eliminating original data. Two additional data fields identified as PHI (treating physician and facility) were replaced with integer values, and the original data corresponding to these values were stored in the CK database. Use of the algorithm at the time of database design did not increase cost or design effort. The CK-SD model for clinical database design provides an algorithm for investigators to create, maintain, and share clinical research data compliant with HIPAA regulations. This model is applicable to new projects and large institutional datasets, and should decrease regulatory efforts required for conduct of clinical research. Application of the design algorithm early in the clinical research enterprise does not increase cost or the effort of data collection.

A novel approach for medical research on lymphomas

PubMed Central

Conte, Cécile; Palmaro, Aurore; Grosclaude, Pascale; Daubisse-Marliac, Laetitia; Despas, Fabien; Lapeyre-Mestre, Maryse

2018-01-01

Abstract The use of claims database to study lymphomas in real-life conditions is a crucial issue in the future. In this way, it is essential to develop validated algorithms for the identification of lymphomas in these databases. The aim of this study was to assess the validity of diagnosis codes in the French health insurance database to identify incident cases of lymphomas according to results of a regional cancer registry, as the gold standard. Between 2010 and 2013, incident lymphomas were identified in hospital data through 2 algorithms of selection. The results of the identification process and characteristics of incident lymphomas cases were compared with data from the Tarn Cancer Registry. Each algorithm's performance was assessed by estimating sensitivity, predictive positive value, specificity (SPE), and negative predictive value. During the period, the registry recorded 476 incident cases of lymphomas, of which 52 were Hodgkin lymphomas and 424 non-Hodgkin lymphomas. For corresponding area and period, algorithm 1 provides a number of incident cases close to the Registry, whereas algorithm 2 overestimated the number of incident cases by approximately 30%. Both algorithms were highly specific (SPE = 99.9%) but moderately sensitive. The comparative analysis illustrates that similar distribution and characteristics are observed in both sources. Given these findings, the use of claims database can be consider as a pertinent and powerful tool to conduct medico-economic or pharmacoepidemiological studies in lymphomas. PMID:29480830

Architecture for biomedical multimedia information delivery on the World Wide Web

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

1997-10-01

Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

PubMed

Wang, Yingfeng; Kora, Guruprasad; Bowen, Benjamin P; Pan, Chongle

2014-10-07

A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.

36 CFR 1235.50 - What specifications and standards for transfer apply to electronic records?

Code of Federal Regulations, 2011 CFR

2011-07-01

... characters and other non-data characters removed. Agencies must consult with the National Archives and... Road, College Park, MD 20740, phone number (301) 837-1578 to initiate transfer discussions. (b) Data files and databases. Data files and databases must be transferred to the National Archives of the United...

36 CFR 1235.50 - What specifications and standards for transfer apply to electronic records?

Code of Federal Regulations, 2010 CFR

2010-07-01

... characters and other non-data characters removed. Agencies must consult with the National Archives and... Road, College Park, MD 20740, phone number (301) 837-1578 to initiate transfer discussions. (b) Data files and databases. Data files and databases must be transferred to the National Archives of the United...

Protein, fat, moisture, and cooking yields from a nationwide study of retail beef cuts.

USDA-ARS?s Scientific Manuscript database

Nutrient data from the U.S. Department of Agriculture (USDA) are an important resource for U.S. and international databases. To ensure the data for retail beef cuts in USDA’s National Nutrient Database for Standard Reference (SR) are current, a comprehensive, nationwide, multiyear study was conducte...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR CODING: FIELD FORMS (UA-D-37.0)

EPA Science Inventory

The purpose of this SOP is to define the coding strategy for selected field forms. Forms addressed here will be scanned into databases. Databases are created because the forms contain critical values needed to calculate pollutant concentrations. Other forms not addressed by th...

EPA Tribal Areas (4 of 4): Alaska Native Allotments

EPA Pesticide Factsheets

This dataset is a spatial representation of the Public Land Survey System (PLSS) in Alaska, generated from land survey records. The data represents a seamless spatial portrayal of native allotment land parcels, their legal descriptions, corner positioning and markings, and survey measurements. This data is intended for mapping purposes only and is not a substitute or replacement for the legal land survey records or other legal documents.Measurement and attribute data are collected from survey records using data entry screens into a relational database. The database design is based upon the FGDC Cadastral Content Data Standard. Corner positions are derived by geodetic calculations using measurement records. Closure and edgematching are applied to produce a seamless dataset. The resultant features do not preserve the original geometry of survey measurements, but the record measurements are reported as attributes. Additional boundary data are derived by spatial capture, protraction and GIS processing. The spatial features are stored and managed within the relational database, with active links to the represented measurement and attribute data.

Analysis of prescription database extracted from standard textbooks of traditional Dai medicine

PubMed Central

2012-01-01

Background Traditional Dai Medicine (TDM) is one of the four major ethnomedicine of China. In 2007 a group of experts produced a set of seven Dai medical textbooks on this subject. The first two were selected as the main data source to analyse well recognized prescriptions. Objective To quantify patterns of prescriptions, common ingredients, indications and usages of TDM. Methods A relational database linking the prescriptions, ingredients, herb names, indications, and usages was set up. Frequency of pattern of combination and common ingredients were tabulated. Results A total of 200 prescriptions and 402 herbs were compiled. Prescriptions based on "wind" disorders, a detoxification theory that most commonly deals with symptoms of digestive system diseases, accounted for over one third of all prescriptions. The major methods of preparations mostly used roots and whole herbs. Conclusion The information extracted from the relational database may be useful for understanding symptomatic treatments. Antidote and detoxification theory deserves further research. PMID:22931752

Lead exposure in US worksites: A literature review and development of an occupational lead exposure database from the published literature

PubMed Central

Koh, Dong-Hee; Locke, Sarah J.; Chen, Yu-Cheng; Purdue, Mark P.; Friesen, Melissa C.

2016-01-01

Background Retrospective exposure assessment of occupational lead exposure in population-based studies requires historical exposure information from many occupations and industries. Methods We reviewed published US exposure monitoring studies to identify lead exposure measurement data. We developed an occupational lead exposure database from the 175 identified papers containing 1,111 sets of lead concentration summary statistics (21% area air, 47% personal air, 32% blood). We also extracted ancillary exposure-related information, including job, industry, task/location, year collected, sampling strategy, control measures in place, and sampling and analytical methods. Results Measurements were published between 1940 and 2010 and represented 27 2-digit standardized industry classification codes. The majority of the measurements were related to lead-based paint work, joining or cutting metal using heat, primary and secondary metal manufacturing, and lead acid battery manufacturing. Conclusions This database can be used in future statistical analyses to characterize differences in lead exposure across time, jobs, and industries. PMID:25968240

Seabird databases and the new paradigm for scientific publication and attribution

USGS Publications Warehouse

Hatch, Scott A.

2010-01-01

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

FIREDOC users manual, 3rd edition

NASA Astrophysics Data System (ADS)

Jason, Nora H.

1993-12-01

FIREDOC is the on-line bibliographic database which reflects the holdings (published reports, journal articles, conference proceedings, books, and audiovisual items) of the Fire Research Information Services (FRIS) at the Building and Fire Research Laboratory (BFRL), National Institute of Standards and Technology (NIST). This manual provides step-by-step procedures for entering and exiting the database via telecommunication lines, as well as a number of techniques for searching the database and processing the results of the searches. This Third Edition is necessitated by the change to a UNIX platform. The new computer allows for faster response time if searching via a modem and, in addition, offers internet accessibility. FIREDOC may be used with personal computers, using DOS or Windows, or with Macintosh computers and workstations. A new section on how to access Internet is included, and one on how to obtain the references of interest to you. Appendix F: Quick Guide to Getting Started will be useful to both modem and Internet users.

KEY COMPARISON Comparison of the standards of air kerma of the ENEA-INMRI and the BIPM for 137Cs gamma rays

NASA Astrophysics Data System (ADS)

Allisy-Roberts, P. J.; Kessler, C.; Toni, M.; Bovi, M.

2010-01-01

A comparison of the standards of air kerma of the Istituto Nazionale di Metrologia delle Radiazioni Ionizzanti of the Ente per le Nuove Tecnologie, l'Energia e l'Ambiente, Italy (ENEA-INMRI) and of the Bureau International des Poids et Mesures (BIPM) was carried out in 137Cs radiation in 1998. The comparison result, updated for changes in the standards in 2003 and 2009, is 0.9927 (0.0067) and demonstrates that the ENEA-INMRI and BIPM standards are in agreement within the uncertainties. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI Section I, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

International energy: Research organizations, 1986--1990

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

Hendricks, P.; Jordan, S.

The International Energy: Research Organizations publication contains the standardized names of energy research organizations used in energy information databases. Involved in this cooperative task are (1) the technical staff of the USDOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the Energy Technology Data Exchange (ETDE) and (2) the International Nuclear Information System (INIS). This publication identifies current organizations doing research in all energy fields, standardizes the format for recording these organization names in bibliographic citations, assigns a numeric code to facilitate data entry, and identifies report number prefixes assigned by these organizations. Thesemore » research organization names may be used in searching the databases Energy Science Technology'' on DIALOG and Energy'' on STN International. These organization names are also used in USDOE databases on the Integrated Technical Information System. Research organizations active in the past five years, as indicated by database records, were identified to form this publication. This directory includes approximately 34,000 organizations that reported energy-related literature from 1986 to 1990 and updates the DOE Energy Data Base: Corporate Author Entries.« less

Design and Implementation of a Metadata-rich File System

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

Ames, S; Gokhale, M B; Maltzahn, C

2010-01-19

Despite continual improvements in the performance and reliability of large scale file systems, the management of user-defined file system metadata has changed little in the past decade. The mismatch between the size and complexity of large scale data stores and their ability to organize and query their metadata has led to a de facto standard in which raw data is stored in traditional file systems, while related, application-specific metadata is stored in relational databases. This separation of data and semantic metadata requires considerable effort to maintain consistency and can result in complex, slow, and inflexible system operation. To address thesemore » problems, we have developed the Quasar File System (QFS), a metadata-rich file system in which files, user-defined attributes, and file relationships are all first class objects. In contrast to hierarchical file systems and relational databases, QFS defines a graph data model composed of files and their relationships. QFS incorporates Quasar, an XPATH-extended query language for searching the file system. Results from our QFS prototype show the effectiveness of this approach. Compared to the de facto standard, the QFS prototype shows superior ingest performance and comparable query performance on user metadata-intensive operations and superior performance on normal file metadata operations.« less

Indoor tanning injuries: an evaluation of FDA adverse event reporting data.

PubMed

Dowdy, John C; Sayre, Robert M; Shepherd, James G

2009-08-01

In 1979 the Food and Drug Administration (FDA) designated indoor tanning units would be regulated medical devices and that each must have an exposure timer. In 1985 FDA added a scheduled series of doses designed to allow tanning with little risk of concomitant sunburn. Subsequently FDA/CDRH maintained databases in which medical device associated injuries were reported. The databases, MAUDE and its predecessor MDR, are available online. While these records, in part, are not intended for evaluation of adverse event rates, analysis provides insight into the etiology of UV-related tanning injuries. We compiled 142 records reported for 1985-2006 including 22% noninjury malfunctions. Of the reported injuries approximately 50% resulted from UV exposure, an average of <1/year resulted in hospitalization. At least 36% of the UV-related injuries were attributable to various (user/operator) noncompliance with FDA sunlamp guidance policies. During 1985-1995 there were six times more UV injuries than 1996-2006, presumably reflecting cessation of much mandatory reporting in 1996. Injury reports declined steady from 1997 to 2006. FDA guidance appears most efficacious in injury prevention and we encourage its incorporation into the enforceable performance standard. We also advise that tanning industry professional training programs seek standardization/accreditation of their personnel certifications through recognized accreditation bodies such as ANSI or ISO/IEC.

THE ART OF DATA MINING THE MINEFIELDS OF TOXICITY ...

EPA Pesticide Factsheets

Toxicity databases have a special role in predictive toxicology, providing ready access to historical information throughout the workflow of discovery, development, and product safety processes in drug development as well as in review by regulatory agencies. To provide accurate information within a hypothesesbuilding environment, the content of the databases needs to be rigorously modeled using standards and controlled vocabulary. The utilitarian purposes of databases widely vary, ranging from a source for (Q)SAR datasets for modelers to a basis for

Inter Annual Variability of the Acoustic Propagation in the Yellow Sea Identified from a Synoptic Monthly Gridded Database as Compared with GDEM

DTIC Science & Technology

2016-09-01

the world climate is in fact warming due to anthropogenic causes (Anderegg et al. 2010; Solomon et al. 2009). To put this in terms for this research ...2006). The present research uses a 0.5’ resolution. B. SEDIMENTS DATABASE There are four openly available sediment databases: Enhanced, Standard...DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This research investigates the inter-annual acoustic variability in the Yellow Sea identified from

Algorithm for detection the QRS complexes based on support vector machine

NASA Astrophysics Data System (ADS)

Van, G. V.; Podmasteryev, K. V.

2017-11-01

The efficiency of computer ECG analysis depends on the accurate detection of QRS-complexes. This paper presents an algorithm for QRS complex detection based of support vector machine (SVM). The proposed algorithm is evaluated on annotated standard databases such as MIT-BIH Arrhythmia database. The QRS detector obtained a sensitivity Se = 98.32% and specificity Sp = 95.46% for MIT-BIH Arrhythmia database. This algorithm can be used as the basis for the software to diagnose electrical activity of the heart.

Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

NASA Astrophysics Data System (ADS)

Ehlmann, Bryon K.

Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

The Primate Life History Database: A unique shared ecological data resource

PubMed Central

Strier, Karen B.; Altmann, Jeanne; Brockman, Diane K.; Bronikowski, Anne M.; Cords, Marina; Fedigan, Linda M.; Lapp, Hilmar; Liu, Xianhua; Morris, William F.; Pusey, Anne E.; Stoinski, Tara S.; Alberts, Susan C.

2011-01-01

Summary The importance of data archiving, data sharing, and public access to data has received considerable attention. Awareness is growing among scientists that collaborative databases can facilitate these activities.We provide a detailed description of the collaborative life history database developed by our Working Group at the National Evolutionary Synthesis Center (NESCent) to address questions about life history patterns and the evolution of mortality and demographic variability in wild primates.Examples from each of the seven primate species included in our database illustrate the range of data incorporated and the challenges, decision-making processes, and criteria applied to standardize data across diverse field studies. In addition to the descriptive and structural metadata associated with our database, we also describe the process metadata (how the database was designed and delivered) and the technical specifications of the database.Our database provides a useful model for other researchers interested in developing similar types of databases for other organisms, while our process metadata may be helpful to other groups of researchers interested in developing databases for other types of collaborative analyses. PMID:21698066

Specialized microbial databases for inductive exploration of microbial genome sequences

PubMed Central

Fang, Gang; Ho, Christine; Qiu, Yaowu; Cubas, Virginie; Yu, Zhou; Cabau, Cédric; Cheung, Frankie; Moszer, Ivan; Danchin, Antoine

2005-01-01

Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore , a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison. PMID:15698474

Simple re-instantiation of small databases using cloud computing.

PubMed

Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M

2013-01-01

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Supplement to the Carcinogenic Potency Database (CPDB): Results ofanimal bioassays published in the general literature through 1997 and bythe National Toxicology Program in 1997-1998

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

Gold, Lois Swirsky; Manley, Neela B.; Slone, Thomas H.

2005-04-08

The Carcinogenic Potency Database (CPDB) is a systematic and unifying resource that standardizes the results of chronic, long-term animal cancer tests which have been conducted since the 1950s. The analyses include sufficient information on each experiment to permit research into many areas of carcinogenesis. Both qualitative and quantitative information is reported on positive and negative experiments that meet a set of inclusion criteria. A measure of carcinogenic potency, TD50 (daily dose rate in mg/kg body weight/day to induce tumors in half of test animals that would have remained tumor-free at zero dose), is estimated for each tissue-tumor combination reported. Thismore » article is the ninth publication of a chronological plot of the CPDB; it presents results on 560 experiments of 188 chemicals in mice, rats, and hamsters from 185 publications in the general literature updated through 1997, and from 15 Reports of the National Toxicology Program in 1997-1998. The test agents cover a wide variety of uses and chemical classes. The CPDB Web Site(http://potency.berkeley.edu/) presents the combined database of all published plots in a variety of formats as well as summary tables by chemical and by target organ, supplemental materials on dosing and survival, a detailed guide to using the plot formats, and documentation of methods and publications. The overall CPDB, including the results in this article, presents easily accessible results of 6153 experiments on 1485 chemicals from 1426 papers and 429 NCI/NTP (National Cancer Institute/National Toxicology program) Technical Reports. A tab-separated format of the full CPDB for reading the data into spreadsheets or database applications is available on the Web Site.« less

Illinois Occupational Skill Standards: Information Technology Operate Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document contains Illinois Occupational Skill Standards for occupations in the Information Technology Operate Cluster (help desk support, computer maintenance and technical support technician, systems operator, application and computer support specialist, systems administrator, network administrator, and database administrator). The skill…

Catalogue of UV sources in the Galaxy

NASA Astrophysics Data System (ADS)

Beitia-Antero, L.; Gómez de Castro, A. I.

2017-03-01

The Galaxy Evolution Explorer (GALEX) ultraviolet (UV) database contains the largest photometric catalogue in the ultraviolet range; as a result GALEX photometric bands, Near UV band (NUV) and the Far UV band (FUV), have become standards. Nevertheless, the GALEX catalogue does not include bright UV sources due to the high sensitivity of its detectors, neither sources in the Galactic plane. In order to extend the GALEX database for future UV missions, we have obtained synthetic FUV and NUV photometry using the database of UV spectra generated by the International Ultraviolet Explorer (IUE). This database contains 63,755 spectra in the low dispersion mode (λ / δ λ ˜ 300) obtained during its 18-year lifetime. For stellar sources in the IUE database, we have selected spectra with high Signal-To-NoiseRatio (SNR) and computed FUV and NUV magnitudes using the GALEX transmission curves along with the conversion equations between flux and magnitudes provided by the mission. Besides, we have performed variability tests to determine whether the sources were variable (during the IUE observations). As a result, we have generated two different catalogues: one for non-variable stars and another one for variable sources. The former contains FUV and NUV magnitudes, while the latter gives the basic information and the FUV magnitude for each observation. The consistency of the magnitudes has been tested using White Dwarfs contained in both GALEX and IUE samples. The catalogues are available through the Centre des Donées Stellaires. The sources are distributed throughout the whole sky, with a special coverage of the Galactic plane.

Metal oxide based multisensor array and portable database for field analysis of antioxidants

PubMed Central

Sharpe, Erica; Bradley, Ryan; Frasco, Thalia; Jayathilaka, Dilhani; Marsh, Amanda; Andreescu, Silvana

2014-01-01

We report a novel chemical sensing array based on metal oxide nanoparticles as a portable and inexpensive paper-based colorimetric method for polyphenol detection and field characterization of antioxidant containing samples. Multiple metal oxide nanoparticles with various polyphenol binding properties were used as active sensing materials to develop the sensor array and establish a database of polyphenol standards that include epigallocatechin gallate, gallic acid, resveratrol, and Trolox among others. Unique charge-transfer complexes are formed between each polyphenol and each metal oxide on the surface of individual sensors in the array, creating distinct optically detectable signals which have been quantified and logged into a reference database for polyphenol identification. The field-portable Pantone/X-Rite© CapSure® color reader was used to create this database and to facilitate rapid colorimetric analysis. The use of multiple metal-oxide sensors allows for cross-validation of results and increases accuracy of analysis. The database has enabled successful identification and quantification of antioxidant constituents within real botanical extractions including green tea. Formation of charge-transfer complexes is also correlated with antioxidant activity exhibiting electron transfer capabilities of each polyphenol. The antioxidant activity of each sample was calculated and validated against the oxygen radical absorbance capacity (ORAC) assay showing good comparability. The results indicate that this method can be successfully used for a more comprehensive analysis of antioxidant containing samples as compared to conventional methods. This technology can greatly simplify investigations into plant phenolics and make possible the on-site determination of antioxidant composition and activity in remote locations. PMID:24610993

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

PubMed

Yokochi, Masashi; Kobayashi, Naohiro; Ulrich, Eldon L; Kinjo, Akira R; Iwata, Takeshi; Ioannidis, Yannis E; Livny, Miron; Markley, John L; Nakamura, Haruki; Kojima, Chojiro; Fujiwara, Toshimichi

2016-05-05

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

GMOMETHODS: the European Union database of reference methods for GMO analysis.

PubMed

Bonfini, Laura; Van den Bulcke, Marc H; Mazzara, Marco; Ben, Enrico; Patak, Alexandre

2012-01-01

In order to provide reliable and harmonized information on methods for GMO (genetically modified organism) analysis we have published a database called "GMOMETHODS" that supplies information on PCR assays validated according to the principles and requirements of ISO 5725 and/or the International Union of Pure and Applied Chemistry protocol. In addition, the database contains methods that have been verified by the European Union Reference Laboratory for Genetically Modified Food and Feed in the context of compliance with an European Union legislative act. The web application provides search capabilities to retrieve primers and probes sequence information on the available methods. It further supplies core data required by analytical labs to carry out GM tests and comprises information on the applied reference material and plasmid standards. The GMOMETHODS database currently contains 118 different PCR methods allowing identification of 51 single GM events and 18 taxon-specific genes in a sample. It also provides screening assays for detection of eight different genetic elements commonly used for the development of GMOs. The application is referred to by the Biosafety Clearing House, a global mechanism set up by the Cartagena Protocol on Biosafety to facilitate the exchange of information on Living Modified Organisms. The publication of the GMOMETHODS database can be considered an important step toward worldwide standardization and harmonization in GMO analysis.

An image database management system for conducting CAD research

NASA Astrophysics Data System (ADS)

Gruszauskas, Nicholas; Drukker, Karen; Giger, Maryellen L.

2007-03-01

The development of image databases for CAD research is not a trivial task. The collection and management of images and their related metadata from multiple sources is a time-consuming but necessary process. By standardizing and centralizing the methods in which these data are maintained, one can generate subsets of a larger database that match the specific criteria needed for a particular research project in a quick and efficient manner. A research-oriented management system of this type is highly desirable in a multi-modality CAD research environment. An online, webbased database system for the storage and management of research-specific medical image metadata was designed for use with four modalities of breast imaging: screen-film mammography, full-field digital mammography, breast ultrasound and breast MRI. The system was designed to consolidate data from multiple clinical sources and provide the user with the ability to anonymize the data. Input concerning the type of data to be stored as well as desired searchable parameters was solicited from researchers in each modality. The backbone of the database was created using MySQL. A robust and easy-to-use interface for entering, removing, modifying and searching information in the database was created using HTML and PHP. This standardized system can be accessed using any modern web-browsing software and is fundamental for our various research projects on computer-aided detection, diagnosis, cancer risk assessment, multimodality lesion assessment, and prognosis. Our CAD database system stores large amounts of research-related metadata and successfully generates subsets of cases that match the user's desired search criteria.

Italian Present-day Stress Indicators: IPSI Database

NASA Astrophysics Data System (ADS)

Mariucci, M. T.; Montone, P.

2017-12-01

In Italy, since the 90s of the last century, researches concerning the contemporary stress field have been developing at Istituto Nazionale di Geofisica e Vulcanologia (INGV) with local and regional scale studies. Throughout the years many data have been analysed and collected: now they are organized and available for an easy end-use online. IPSI (Italian Present-day Stress Indicators) database, is the first geo-referenced repository of information on the crustal present-day stress field maintained at INGV through a web application database and website development by Gabriele Tarabusi. Data consist of horizontal stress orientations analysed and compiled in a standardized format and quality-ranked for reliability and comparability on a global scale with other database. Our first database release includes 855 data records updated to December 2015. Here we present an updated version that will be released in 2018, after new earthquake data entry up to December 2017. The IPSI web site (http://ipsi.rm.ingv.it/) allows accessing data on a standard map viewer and choose which data (category and/or quality) to plot easily. The main information of each single element (type, quality, orientation) can be viewed simply going over the related symbol, all the information appear by clicking the element. At the same time, simple basic information on the different data type, tectonic regime assignment, quality ranking method are available with pop-up windows. Data records can be downloaded in some common formats, moreover it is possible to download a file directly usable with SHINE, a web based application to interpolate stress orientations (http://shine.rm.ingv.it). IPSI is mainly conceived for those interested in studying the characters of Italian peninsula and surroundings although Italian data are part of the World Stress Map (http://www.world-stress-map.org/) as evidenced by many links that redirect to this database for more details on standard practices in this field.

Agricultural Education. Missouri's Show-Me Standards and Vocational Education Competencies. Cross Reference. Main Report [and] Mini Report.

ERIC Educational Resources Information Center

Missouri Univ., Columbia. Instructional Materials Lab.

These two documents deal with the relationship between Missouri's Show-Me Standards (the standards defining what all Missouri students should know upon graduation from high school) with the vocational competencies taught in secondary-level agricultural education courses. The first document, which is a database documenting the common ground that…

Business Education. Missouri's Show-Me Standards and Vocational Education Competencies Cross Reference. Main Report [and] Mini Report.

ERIC Educational Resources Information Center

Tieman, Rebecca; Burns, Stacey

This publication consists of the main and mini reports for Missouri's Show-Me Standards and vocational education competencies for business education. This database documents the common ground between academic skills and vocational competencies. Both components of the Show-Me Standards--knowledge (content) and performance (process)--have been…

Industrial Education. Missouri's Show-Me Standards and Vocational Education Competencies Cross Reference. Main Report [and] Mini Report.

ERIC Educational Resources Information Center

Missouri Univ., Columbia. Instructional Materials Lab.

This publication consists of the main and mini reports for Missouri's Show-Me Standards and vocational education competencies for industrial education. This database documents the common ground between academic skills and vocational competencies. Both components of the Show-Me Standards--knowledge (content) and performance (process)--have been…