Sample records for public databases misannotation

  1. Using the structure-function linkage database to characterize functional domains in enzymes.

    PubMed

    Brown, Shoshana; Babbitt, Patricia

    2014-12-12

    The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

  2. Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea.

    PubMed

    Veloso, Felipe; Riadi, Gonzalo; Aliaga, Daniela; Lieph, Ryan; Holmes, David S

    2005-01-01

    Analysis of over 300,000 annotated genes in 105 bacterial and archaeal genomes reveals an unexpectedly high frequency of large (>300 nucleotides) alternate open reading frames (ORFs). Especially notable is the very high frequency of alternate ORFs in frames +3 and -1 (where the annotated gene is defined as frame +1). The occurrence of alternate ORFs is correlated with genomic G+C content and is strongly influenced by synonymous codon usage bias. The frequency of alternate ORFs in frame -1 is also influenced by the occurrence of codons encoding leucine and serine in frame +1. Although some alternate ORFs have been shown to encode proteins, many others are probably not expressed because they lack appropriate signals for transcription and translation. These latter can be mis-annotated by automatic gene finding programs leading to errors in public databases. Especially prone to mis-annotation is frame -1, because it exhibits a potential codon usage and theoretical capacity to encode proteins with an amino acid composition most similar to real genes. Some alternate ORFs are conserved across bacterial or archaeal species, and can give rise to misannotated "conserved hypothetical" genes, while others are unique to a genome and are misidentified as "hypothetical orphan" genes, contributing significantly to the orphan gene paradox.

  3. Evaluating Functional Annotations of Enzymes Using the Gene Ontology.

    PubMed

    Holliday, Gemma L; Davidson, Rebecca; Akiva, Eyal; Babbitt, Patricia C

    2017-01-01

    The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.

  4. Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification.

    PubMed

    Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Yaguchi, Takashi

    2016-01-01

    We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus .

  5. Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification

    PubMed Central

    Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Yaguchi, Takashi

    2016-01-01

    We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus. PMID:27843740

  6. ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea

    PubMed Central

    Paramasivam, Nagarajan; Linke, Dirk

    2011-01-01

    The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as the relatively high false-positive and false-negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing SCL prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative predictions. ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the SCL prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/ PMID:22073040

  7. VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data

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

    Peterson, Elena S.; McCue, Lee Ann; Rutledge, Alexandra C.

    2012-04-25

    Visual Exploration and Statistics to Promote Annotation (VESPA) is an interactive visual analysis software tool that facilitates the discovery of structural mis-annotations in prokaryotic genomes. VESPA integrates high-throughput peptide-centric proteomics data and oligo-centric or RNA-Seq transcriptomics data into a genomic context. The data may be interrogated via visual analysis across multiple levels of genomic resolution, linked searches, exports and interaction with BLAST to rapidly identify location of interest within the genome and evaluate potential mis-annotations.

  8. Finding approximate gene clusters with Gecko 3.

    PubMed

    Winter, Sascha; Jahn, Katharina; Wehner, Stefanie; Kuchenbecker, Leon; Marz, Manja; Stoye, Jens; Böcker, Sebastian

    2016-11-16

    Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography–Mass Spectrometry-Based Metabolomics

    DOE PAGES

    Xu, Yi-Fan; Lu, Wenyun; Rabinowitz, Joshua D.

    2015-01-15

    Liquid chromatography–mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. Furthermore, when analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, andmore » hexose-phosphates generate triose-phosphates. We also evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Finally and accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.« less

  10. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

    PubMed

    Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

    2012-04-05

    The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

  11. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

    PubMed Central

    2012-01-01

    Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

  12. LeadMine: a grammar and dictionary driven approach to entity recognition.

    PubMed

    Lowe, Daniel M; Sayle, Roger A

    2015-01-01

    Chemical entity recognition has traditionally been performed by machine learning approaches. Here we describe an approach using grammars and dictionaries. This approach has the advantage that the entities found can be directly related to a given grammar or dictionary, which allows the type of an entity to be known and, if an entity is misannotated, indicates which resource should be corrected. As recognition is driven by what is expected, if spelling errors occur, they can be corrected. Correcting such errors is highly useful when attempting to lookup an entity in a database or, in the case of chemical names, converting them to structures. Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of trivial chemical names (from PubChem) yields a better performing dictionary than the previously published Jochem dictionary. Our final system performs post-processing steps to modify the boundaries of entities and to detect abbreviations. These steps are shown to significantly improve performance (2.6% and 4.0% F1-score respectively). Our complete system, with incremental post-BioCreative workshop improvements, achieves 89.9% precision and 85.4% recall (87.6% F1-score) on the CHEMDNER test set. Grammar and dictionary approaches can produce results at least as good as the current state of the art in machine learning approaches. While machine learning approaches are commonly thought of as "black box" systems, our approach directly links the output entities to the input dictionaries and grammars. Our approach also allows correction of errors in detected entities, which can assist with entity resolution.

  13. LeadMine: a grammar and dictionary driven approach to entity recognition

    PubMed Central

    2015-01-01

    Background Chemical entity recognition has traditionally been performed by machine learning approaches. Here we describe an approach using grammars and dictionaries. This approach has the advantage that the entities found can be directly related to a given grammar or dictionary, which allows the type of an entity to be known and, if an entity is misannotated, indicates which resource should be corrected. As recognition is driven by what is expected, if spelling errors occur, they can be corrected. Correcting such errors is highly useful when attempting to lookup an entity in a database or, in the case of chemical names, converting them to structures. Results Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of trivial chemical names (from PubChem) yields a better performing dictionary than the previously published Jochem dictionary. Our final system performs post-processing steps to modify the boundaries of entities and to detect abbreviations. These steps are shown to significantly improve performance (2.6% and 4.0% F1-score respectively). Our complete system, with incremental post-BioCreative workshop improvements, achieves 89.9% precision and 85.4% recall (87.6% F1-score) on the CHEMDNER test set. Conclusions Grammar and dictionary approaches can produce results at least as good as the current state of the art in machine learning approaches. While machine learning approaches are commonly thought of as "black box" systems, our approach directly links the output entities to the input dictionaries and grammars. Our approach also allows correction of errors in detected entities, which can assist with entity resolution. PMID:25810776

  14. Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

    PubMed Central

    Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C.; Fiser, Andras

    2014-01-01

    The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins—including proteins for which reliable homology models can be generated—on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long. PMID:24567391

  15. Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.

    PubMed

    Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C; Fiser, Andras

    2014-03-11

    The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins--including proteins for which reliable homology models can be generated--on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long.

  16. Geoseq: a tool for dissecting deep-sequencing datasets.

    PubMed

    Gurtowski, James; Cancio, Anthony; Shah, Hardik; Levovitz, Chaya; George, Ajish; Homann, Robert; Sachidanandam, Ravi

    2010-10-12

    Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a) identify differential isoform expression in mRNA-seq datasets, b) identify miRNAs (microRNAs) in libraries, and identify mature and star sequences in miRNAS and c) to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

  17. Rapid Identification of Sequences for Orphan Enzymes to Power Accurate Protein Annotation

    PubMed Central

    Ojha, Sunil; Watson, Douglas S.; Bomar, Martha G.; Galande, Amit K.; Shearer, Alexander G.

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the “back catalog” of enzymology – “orphan enzymes,” those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme “back catalog” is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology’s “back catalog” another powerful tool to drive accurate genome annotation. PMID:24386392

  18. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    PubMed

    Ramkissoon, Kevin R; Miller, Jennifer K; Ojha, Sunil; Watson, Douglas S; Bomar, Martha G; Galande, Amit K; Shearer, Alexander G

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  19. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database containing...

  20. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database containing...

  1. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database containing...

  2. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database containing...

  3. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database containing...

  4. Resolving protein structure-function-binding site relationships from a binding site similarity network perspective.

    PubMed

    Mudgal, Richa; Srinivasan, Narayanaswamy; Chandra, Nagasuma

    2017-07-01

    Functional annotation is seldom straightforward with complexities arising due to functional divergence in protein families or functional convergence between non-homologous protein families, leading to mis-annotations. An enzyme may contain multiple domains and not all domains may be involved in a given function, adding to the complexity in function annotation. To address this, we use binding site information from bound cognate ligands and catalytic residues, since it can help in resolving fold-function relationships at a finer level and with higher confidence. A comprehensive database of 2,020 fold-function-binding site relationships has been systematically generated. A network-based approach is employed to capture the complexity in these relationships, from which different types of associations are deciphered, that identify versatile protein folds performing diverse functions, same function associated with multiple folds and one-to-one relationships. Binding site similarity networks integrated with fold, function, and ligand similarity information are generated to understand the depth of these relationships. Apart from the observed continuity in the functional site space, network properties of these revealed versatile families with topologically different or dissimilar binding sites and structural families that perform very similar functions. As a case study, subtle changes in the active site of a set of evolutionarily related superfamilies are studied using these networks. Tracing of such similarities in evolutionarily related proteins provide clues into the transition and evolution of protein functions. Insights from this study will be helpful in accurate and reliable functional annotations of uncharacterized proteins, poly-pharmacology, and designing enzymes with new functional capabilities. Proteins 2017; 85:1319-1335. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Structures of Saccharomyces cerevisiae D-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.

    PubMed

    Hu, Xiao-Qian; Guo, Peng-Chao; Ma, Jin-Di; Li, Wei-Fang

    2013-11-01

    The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 Å resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.

  6. Mining for Micropeptides.

    PubMed

    Makarewich, Catherine A; Olson, Eric N

    2017-09-01

    Advances in computational biology and large-scale transcriptome analyses have revealed that a much larger portion of the genome is transcribed than was previously recognized, resulting in the production of a diverse population of RNA molecules with both protein-coding and noncoding potential. Emerging evidence indicates that several RNA molecules have been mis-annotated as noncoding and in fact harbor short open reading frames (sORFs) that encode functional peptides and that have evaded detection until now due to their small size. sORF-encoded peptides (SEPs), or micropeptides, have been shown to have important roles in fundamental biological processes and in the maintenance of cellular homeostasis. These small proteins can act independently, for example as ligands or signaling molecules, or they can exert their biological functions by engaging with and modulating larger regulatory proteins. Given their small size, micropeptides may be uniquely suited to fine-tune complex biological systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. An integrated approach to characterize genetic interaction networks in yeast metabolism

    PubMed Central

    Szappanos, Balázs; Kovács, Károly; Szamecz, Béla; Honti, Frantisek; Costanzo, Michael; Baryshnikova, Anastasia; Gelius-Dietrich, Gabriel; Lercher, Martin J.; Jelasity, Márk; Myers, Chad L.; Andrews, Brenda J.; Boone, Charles; Oliver, Stephen G.; Pál, Csaba; Papp, Balázs

    2011-01-01

    Intense experimental and theoretical efforts have been made to globally map genetic interactions, yet we still do not understand how gene-gene interactions arise from the operation of biomolecular networks. To bridge the gap between empirical and computational studies, we: i) quantitatively measure genetic interactions between ~185,000 metabolic gene pairs in Saccharomyces cerevisiae, ii) superpose the data on a detailed systems biology model of metabolism, and iii) introduce a machine-learning method to reconcile empirical interaction data with model predictions. We systematically investigate the relative impacts of functional modularity and metabolic flux coupling on the distribution of negative and positive genetic interactions. We also provide a mechanistic explanation for the link between the degree of genetic interaction, pleiotropy, and gene dispensability. Last, we demonstrate the feasibility of automated metabolic model refinement by correcting misannotations in NAD biosynthesis and confirming them by in vivo experiments. PMID:21623372

  8. 76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-30

    ...] FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code Names... replaced non- informative code names with descriptive identifiers on its public database of products that... on our public database with non-informative code names. After careful consideration of this matter...

  9. NREL: Renewable Resource Data Center - Biomass Resource Publications

    Science.gov Websites

    Marginal Lands in APEC Economies NREL Publications Database For a comprehensive list of other NREL biomass resource publications, explore NREL's Publications Database. When searching the database, search on "

  10. Public variant databases: liability?

    PubMed

    Thorogood, Adrian; Cook-Deegan, Robert; Knoppers, Bartha Maria

    2017-07-01

    Public variant databases support the curation, clinical interpretation, and sharing of genomic data, thus reducing harmful errors or delays in diagnosis. As variant databases are increasingly relied on in the clinical context, there is concern that negligent variant interpretation will harm patients and attract liability. This article explores the evolving legal duties of laboratories, public variant databases, and physicians in clinical genomics and recommends a governance framework for databases to promote responsible data sharing.Genet Med advance online publication 15 December 2016.

  11. Database Support for Research in Public Administration

    ERIC Educational Resources Information Center

    Tucker, James Cory

    2005-01-01

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

  12. Berkeley Lab - Materials Sciences Division

    Science.gov Websites

    Postdoc Forum Research Highlights Awards Publications Database Events Calendar Newsletter Archive People Database Events Calendar Newsletter Archive Send us your research highlights. Reserch Highlight Template (powerpoint) Publications Database The MSD publications database has been updated to include all FY2014

  13. Public variant databases: liability?

    PubMed Central

    Thorogood, Adrian; Cook-Deegan, Robert; Knoppers, Bartha Maria

    2017-01-01

    Public variant databases support the curation, clinical interpretation, and sharing of genomic data, thus reducing harmful errors or delays in diagnosis. As variant databases are increasingly relied on in the clinical context, there is concern that negligent variant interpretation will harm patients and attract liability. This article explores the evolving legal duties of laboratories, public variant databases, and physicians in clinical genomics and recommends a governance framework for databases to promote responsible data sharing. Genet Med advance online publication 15 December 2016 PMID:27977006

  14. 16 CFR 1102.28 - Publication of reports of harm.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Procedural..., the Commission will publish reports of harm that meet the requirements for publication in the Database...(d) in the Database beyond the 10-business-day time frame set forth in paragraph (a) of this section...

  15. 49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

  16. 49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

  17. 49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

  18. 49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

  19. 49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

  20. LexisNexis

    EPA Pesticide Factsheets

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

  1. 76 FR 10044 - Notice of Proposed Information Collection for Public Comment Public Housing Assessment System...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-23

    ... Database Adjustments AGENCY: Office of the Assistant Secretary for Public and Indian Housing, HUD. ACTION...: Public Housing Assessment System Appeals, Technical Reviews and Database Adjustments. OMB Control Number..., at Sec. 902.24, a database adjustment if certain conditions are present. A technical review of the...

  2. Prototype Food and Nutrient Database for Dietary Studies: Branded Food Products Database for Public Health Proof of Concept

    USDA-ARS?s Scientific Manuscript database

    The Prototype Food and Nutrient Database for Dietary Studies (Prototype FNDDS) Branded Food Products Database for Public Health is a proof of concept database. The database contains a small selection of food products which is being used to exhibit the approach for incorporation of the Branded Food ...

  3. TabSQL: a MySQL tool to facilitate mapping user data to public databases.

    PubMed

    Xia, Xiao-Qin; McClelland, Michael; Wang, Yipeng

    2010-06-23

    With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.

  4. TabSQL: a MySQL tool to facilitate mapping user data to public databases

    PubMed Central

    2010-01-01

    Background With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. Results We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Conclusions TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data. PMID:20573251

  5. The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

    PubMed Central

    Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

    2005-01-01

    Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

  6. 16 CFR § 1102.10 - Reports of harm.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.10 Reports of... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

  7. MOXI Is a Mitochondrial Micropeptide That Enhances Fatty Acid β-Oxidation.

    PubMed

    Makarewich, Catherine A; Baskin, Kedryn K; Munir, Amir Z; Bezprozvannaya, Svetlana; Sharma, Gaurav; Khemtong, Chalermchai; Shah, Akansha M; McAnally, John R; Malloy, Craig R; Szweda, Luke I; Bassel-Duby, Rhonda; Olson, Eric N

    2018-06-26

    Micropeptide regulator of β-oxidation (MOXI) is a conserved muscle-enriched protein encoded by an RNA transcript misannotated as non-coding. MOXI localizes to the inner mitochondrial membrane where it associates with the mitochondrial trifunctional protein, an enzyme complex that plays a critical role in fatty acid β-oxidation. Isolated heart and skeletal muscle mitochondria from MOXI knockout mice exhibit a diminished ability to metabolize fatty acids, while transgenic MOXI overexpression leads to enhanced β-oxidation. Additionally, hearts from MOXI knockout mice preferentially oxidize carbohydrates over fatty acids in an isolated perfused heart system compared to wild-type (WT) animals. MOXI knockout mice also exhibit a profound reduction in exercise capacity, highlighting the role of MOXI in metabolic control. The functional characterization of MOXI provides insight into the regulation of mitochondrial metabolism and energy homeostasis and underscores the regulatory potential of additional micropeptides that have yet to be identified. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  8. PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.

    PubMed

    Gao, Yubang; Wang, Huiyuan; Zhang, Hangxiao; Wang, Yongsheng; Chen, Jinfeng; Gu, Lianfeng

    2018-05-01

    The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful. Here, we present a one-stop solution for Iso-Seq analysis, called PRAPI to analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. PRAPI is capable of combining Iso-Seq full-length isoforms with short read data, such as RNA-Seq or polyadenylation site sequencing (PAS-seq) for differential expression analysis of NAT, AS, APA and circRNAs. Furthermore, PRAPI can annotate new genes and correct mis-annotated genes when gene annotation is available. Finally, PRAPI generates high-quality vector graphics to visualize and highlight the Iso-Seq results. The Dockerfile of PRAPI is available at http://www.bioinfor.org/tool/PRAPI. lfgu@fafu.edu.cn.

  9. 76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-07

    ...: Notice of Public Web Conferences AGENCY: Consumer Product Safety Commission. ACTION: Notice. SUMMARY: The Consumer Product Safety Commission (``Commission,'' ``CPSC,'' or ``we'') is announcing two Web conferences... database (``Database''). The Web conferences will be webcast live from the Commission's headquarters in...

  10. Comprehensive Thematic T-matrix Reference Database: a 2013-2014 Update

    NASA Technical Reports Server (NTRS)

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

    2014-01-01

    This paper is the sixth update to the comprehensive thematic database of peer-reviewedT-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

  11. 78 FR 65293 - Collection of Information; Proposed Extension of Approval; Comment Request-Publicly Available...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-31

    ... Extension of Approval; Comment Request--Publicly Available Consumer Product Safety Information Database... Publicly Available Consumer Product Safety Information Database. The Commission will consider all comments... intention to seek extension of approval of a collection of information for a database on the safety of...

  12. 16 CFR 1102.28 - Publication of reports of harm.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

  13. 16 CFR 1102.28 - Publication of reports of harm.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

  14. Publications of Australian LIS Academics in Databases

    ERIC Educational Resources Information Center

    Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

    2011-01-01

    This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

  15. Publications - DDS 8 | Alaska Division of Geological & Geophysical Surveys

    Science.gov Websites

    DGGS DDS 8 Publication Details Title: Alaska Volcano Observatory geochemical database Authors: Cameron ., Snedigar, S.F., and Nye, C.J., 2014, Alaska Volcano Observatory geochemical database: Alaska Division of ://doi.org/10.14509/29120 Publication Products Interactive Interactive Database Alaska Volcano Observatory

  16. 76 FR 77533 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-13

    ... FEDERAL HOUSING FINANCE AGENCY [No. 2011-N-13] Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family Securitized Loan Data Fields and Technical Data Field..., regarding FHFA's adoption of an Order revising FHFA's Public Use Database matrices to include certain data...

  17. 16 CFR § 1102.28 - Publication of reports of harm.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

  18. Bibliographical database of radiation biological dosimetry and risk assessment: Part 1, through June 1988

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

    Straume, T.; Ricker, Y.; Thut, M.

    1988-08-29

    This database was constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on publication number, authors, key words, title, year, and journal name. Photocopies of all publications contained in the database are maintained in a file that is numerically arranged by citation number. This report of the database is provided as a useful reference and overview. Itmore » should be emphasized that the database will grow as new citations are added to it. With that in mind, we arranged this report in order of ascending citation number so that follow-up reports will simply extend this document. The database cite 1212 publications. Publications are from 119 different scientific journals, 27 of these journals are cited at least 5 times. It also contains reference to 42 books and published symposia, and 129 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed among the scientific literature, although a few journals clearly dominate. The four journals publishing the largest number of relevant papers are Health Physics, Mutation Research, Radiation Research, and International Journal of Radiation Biology. Publications in Health Physics make up almost 10% of the current database.« less

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

    PubMed

    Rosset, Saharon; Aharoni, Ehud; Neuvirth, Hani

    2014-07-01

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

  20. 19 CFR 351.304 - Establishing business proprietary treatment of information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... information. 351.304 Section 351.304 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE...) Electronic databases. In accordance with § 351.303(c)(3), an electronic database need not contain brackets... in the database. The public version of the database must be publicly summarized and ranged in...

  1. 19 CFR 351.304 - Establishing business proprietary treatment of information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... information. 351.304 Section 351.304 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE...) Electronic databases. In accordance with § 351.303(c)(3), an electronic database need not contain brackets... in the database. The public version of the database must be publicly summarized and ranged in...

  2. 19 CFR 351.304 - Establishing business proprietary treatment of information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... information. 351.304 Section 351.304 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE...) Electronic databases. In accordance with § 351.303(c)(3), an electronic database need not contain brackets... in the database. The public version of the database must be publicly summarized and ranged in...

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

    USGS Publications Warehouse

    Price, Curtis V.; Maupin, Molly A.

    2014-01-01

    The purpose of this report is to document the PSDB and explain the methods used to populate and update the data from the SDWIS, State datasets, and map and geospatial imagery. This report describes 3 data tables and 11 domain tables, including field contents, data sources, and relations between tables. Although the PSDB database is not available to the general public, this information should be useful for others who are developing other database systems to store and analyze public-supply system and facility data.

  4. Exploration of the Chemical Space of Public Genomic Databases

    EPA Science Inventory

    The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information.

  5. 75 FR 41180 - Notice of Order: Revisions to Enterprise Public Use Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-15

    ... Database AGENCY: Federal Housing Finance Agency. ACTION: Notice of order. SUMMARY: Section 1323(a)(1) of.... This responsibility to maintain a public use database (PUDB) for such mortgage data was transferred to... purpose of loan data field in these two databases. 4. Single-family Data Field 27 and Multifamily Data...

  6. 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

  7. NREL: U.S. Life Cycle Inventory Database - Publications

    Science.gov Websites

    Publications Planning Documents U.S. Life Cycle Inventory Database Roadmap, February 2009 U.S. Life Cycle Inventory User Survey, February 2009 U.S. LCI Database Factsheet, March 2005 User's Guide for Life

  8. 16 CFR 1102.24 - Designation of confidential information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural... allegedly confidential information is not placed in the database, a request for designation of confidential... publication in the Database until it makes a determination regarding confidential treatment. (e) Assistance...

  9. 16 CFR 1102.24 - Designation of confidential information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural... allegedly confidential information is not placed in the database, a request for designation of confidential... publication in the Database until it makes a determination regarding confidential treatment. (e) Assistance...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-28

    ... Database Incorporating High-Cost Single-Family Securitized Loan Data Fields and Technical Data Field... single-family matrix in FHFA's Public Use Database (PUDB) to include data fields for the high-cost single... of loan attributes in FHFA's databases that could be used, singularly or in some combination, to...

  11. 16 CFR 1102.12 - Manufacturer comments.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.12 Manufacturer... Database if such manufacturer comment meets the following requirements: (1) Manufacturer comment relates to... publication in the Database. (2) Unique identifier. A manufacturer comment must state the unique identifier...

  12. 16 CFR § 1102.24 - Designation of confidential information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural... allegedly confidential information is not placed in the database, a request for designation of confidential... publication in the Database until it makes a determination regarding confidential treatment. (e) Assistance...

  13. 16 CFR 1102.12 - Manufacturer comments.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Content Requirements... private labeler in the Database if such manufacturer comment meets the following requirements: (1... that is submitted for publication in the Database. (2) Unique identifier. A manufacturer comment must...

  14. 16 CFR 1102.12 - Manufacturer comments.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.12 Manufacturer... Database if such manufacturer comment meets the following requirements: (1) Manufacturer comment relates to... publication in the Database. (2) Unique identifier. A manufacturer comment must state the unique identifier...

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

    PubMed

    Yamamoto, Ryuichi

    2014-01-01

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

  16. Publications | Hydrogen and Fuel Cells | NREL

    Science.gov Websites

    , and demonstration activities in hydrogen and fuel cells. NREL Publications Database Access the full library of our publications. Search the database View all NREL publications about hydrogen and fuel cell research. Transportation and Hydrogen Newsletter Get semi-monthly updates on NREL's research, development

  17. Reporting discrepancies between the ClinicalTrials.gov results database and peer-reviewed publications.

    PubMed

    Hartung, Daniel M; Zarin, Deborah A; Guise, Jeanne-Marie; McDonagh, Marian; Paynter, Robin; Helfand, Mark

    2014-04-01

    ClinicalTrials.gov requires reporting of result summaries for many drug and device trials. To evaluate the consistency of reporting of trials that are registered in the ClinicalTrials.gov results database and published in the literature. ClinicalTrials.gov results database and matched publications identified through ClinicalTrials.gov and a manual search of 2 electronic databases. 10% random sample of phase 3 or 4 trials with results in the ClinicalTrials.gov results database, completed before 1 January 2009, with 2 or more groups. One reviewer extracted data about trial design and results from the results database and matching publications. A subsample was independently verified. Of 110 trials with results, most were industry-sponsored, parallel-design drug studies. The most common inconsistency was the number of secondary outcome measures reported (80%). Sixteen trials (15%) reported the primary outcome description inconsistently, and 22 (20%) reported the primary outcome value inconsistently. Thirty-eight trials inconsistently reported the number of individuals with a serious adverse event (SAE); of these, 33 (87%) reported more SAEs in ClinicalTrials.gov. Among the 84 trials that reported SAEs in ClinicalTrials.gov, 11 publications did not mention SAEs, 5 reported them as zero or not occurring, and 21 reported a different number of SAEs. Among 29 trials that reported deaths in ClinicalTrials.gov, 28% differed from the matched publication. Small sample that included earliest results posted to the database. Reporting discrepancies between the ClinicalTrials.gov results database and matching publications are common. Which source contains the more accurate account of results is unclear, although ClinicalTrials.gov may provide a more comprehensive description of adverse events than the publication. Agency for Healthcare Research and Quality.

  18. 16 CFR 1102.24 - Designation of confidential information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011... allegedly confidential information is not placed in the database, a request for designation of confidential... publication in the Database until it makes a determination regarding confidential treatment. (e) Assistance...

  19. 16 CFR § 1102.12 - Manufacturer comments.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.12 Manufacturer... Database if such manufacturer comment meets the following requirements: (1) Manufacturer comment relates to... publication in the Database. (2) Unique identifier. A manufacturer comment must state the unique identifier...

  20. Online vs. Print Publications: Users' Opinions.

    ERIC Educational Resources Information Center

    Wang, Chih

    The rapid expansion of online publications has raised some concerns about the use of online databases in comparison with using traditional print publications. To determine the opinions of end users about using Dialog online databases versus their corresponding print versions, three libraries in Atlanta, Georgia--Atlanta-Fulton Public Library,…

  1. 75 FR 29155 - Publicly Available Consumer Product Safety Information Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-24

    ...The Consumer Product Safety Commission (``Commission,'' ``CPSC,'' or ``we'') is issuing a notice of proposed rulemaking that would establish a publicly available consumer product safety information database (``database''). Section 212 of the Consumer Product Safety Improvement Act of 2008 (``CPSIA'') amended the Consumer Product Safety Act (``CPSA'') to require the Commission to establish and maintain a publicly available, searchable database on the safety of consumer products, and other products or substances regulated by the Commission. The proposed rule would interpret various statutory requirements pertaining to the information to be included in the database and also would establish provisions regarding submitting reports of harm; providing notice of reports of harm to manufacturers; publishing reports of harm and manufacturer comments in the database; and dealing with confidential and materially inaccurate information.

  2. 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,...

  3. 16 CFR 1102.10 - Reports of harm.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.10 Reports of harm. (a... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

  4. 16 CFR 1102.26 - Determination of materially inaccurate information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural... reviewing a report of harm or manufacturer comment, either before or after publication in the Database, may... manufacturer comment, be excluded from the Database or corrected by the Commission because it contains...

  5. 16 CFR 1102.26 - Determination of materially inaccurate information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural... reviewing a report of harm or manufacturer comment, either before or after publication in the Database, may... manufacturer comment, be excluded from the Database or corrected by the Commission because it contains...

  6. 16 CFR 1102.10 - Reports of harm.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.10 Reports of harm. (a... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

  7. 16 CFR 1102.10 - Reports of harm.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Content Requirements § 1102.10... they have a public safety purpose. (b) Manner of submission. To be entered into the Database, reports... Commission will publish in the Publicly Available Consumer Product Safety Information Database reports of...

  8. Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal - a case study from health science.

    PubMed

    Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

    2016-01-01

    Unique identifiers (UID) are seen as an effective key to match identical publications across databases or identify duplicates in a database. The objective of the present study is to investigate how well UIDs work as match keys in the integration between Pure and SciVal, based on a case with publications from the health sciences. We evaluate the matching process based on information about coverage, precision, and characteristics of publications matched versus not matched with UIDs as the match keys. We analyze this information to detect errors, if any, in the matching process. As an example we also briefly discuss how publication sets formed by using UIDs as the match keys may affect the bibliometric indicators number of publications, number of citations, and the average number of citations per publication.  The objective is addressed in a literature review and a case study. The literature review shows that only a few studies evaluate how well UIDs work as a match key. From the literature we identify four error types: Duplicate digital object identifiers (DOI), incorrect DOIs in reference lists and databases, DOIs not registered by the database where a bibliometric analysis is performed, and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation of average number of citations per publication. The use of UIDs as a match key in citation linking is implemented in many settings, and the availability of UIDs may become critical for the inclusion of a publication or a database in a bibliometric analysis.

  9. Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal – a case study from health science

    PubMed Central

    Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

    2016-01-01

    Unique identifiers (UID) are seen as an effective key to match identical publications across databases or identify duplicates in a database. The objective of the present study is to investigate how well UIDs work as match keys in the integration between Pure and SciVal, based on a case with publications from the health sciences. We evaluate the matching process based on information about coverage, precision, and characteristics of publications matched versus not matched with UIDs as the match keys. We analyze this information to detect errors, if any, in the matching process. As an example we also briefly discuss how publication sets formed by using UIDs as the match keys may affect the bibliometric indicators number of publications, number of citations, and the average number of citations per publication.  The objective is addressed in a literature review and a case study. The literature review shows that only a few studies evaluate how well UIDs work as a match key. From the literature we identify four error types: Duplicate digital object identifiers (DOI), incorrect DOIs in reference lists and databases, DOIs not registered by the database where a bibliometric analysis is performed, and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation of average number of citations per publication. The use of UIDs as a match key in citation linking is implemented in many settings, and the availability of UIDs may become critical for the inclusion of a publication or a database in a bibliometric analysis. PMID:27635223

  10. 16 CFR § 1102.26 - Determination of materially inaccurate information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PRODUCT SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural... reviewing a report of harm or manufacturer comment, either before or after publication in the Database, may... manufacturer comment, be excluded from the Database or corrected by the Commission because it contains...

  11. USDA Branded Food Products Database, Release 2

    USDA-ARS?s Scientific Manuscript database

    The USDA Branded Food Products Database is the ongoing result of a Public-Private Partnership (PPP), whose goal is to enhance public health and the sharing of open data by complementing the USDA National Nutrient Database for Standard Reference (SR) with nutrient composition of branded foods and pri...

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

    PubMed Central

    Machado, Helena; Silva, Susana

    2015-01-01

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

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

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

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

    2003-11-01

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

  14. Academic impact of a public electronic health database: bibliometric analysis of studies using the general practice research database.

    PubMed

    Chen, Yu-Chun; Wu, Jau-Ching; Haschler, Ingo; Majeed, Azeem; Chen, Tzeng-Ji; Wetter, Thomas

    2011-01-01

    Studies that use electronic health databases as research material are getting popular but the influence of a single electronic health database had not been well investigated yet. The United Kingdom's General Practice Research Database (GPRD) is one of the few electronic health databases publicly available to academic researchers. This study analyzed studies that used GPRD to demonstrate the scientific production and academic impact by a single public health database. A total of 749 studies published between 1995 and 2009 with 'General Practice Research Database' as their topics, defined as GPRD studies, were extracted from Web of Science. By the end of 2009, the GPRD had attracted 1251 authors from 22 countries and been used extensively in 749 studies published in 193 journals across 58 study fields. Each GPRD study was cited 2.7 times by successive studies. Moreover, the total number of GPRD studies increased rapidly, and it is expected to reach 1500 by 2015, twice the number accumulated till the end of 2009. Since 17 of the most prolific authors (1.4% of all authors) contributed nearly half (47.9%) of GPRD studies, success in conducting GPRD studies may accumulate. The GPRD was used mainly in, but not limited to, the three study fields of "Pharmacology and Pharmacy", "General and Internal Medicine", and "Public, Environmental and Occupational Health". The UK and United States were the two most active regions of GPRD studies. One-third of GRPD studies were internationally co-authored. A public electronic health database such as the GPRD will promote scientific production in many ways. Data owners of electronic health databases at a national level should consider how to reduce access barriers and to make data more available for research.

  15. 48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  16. 16 CFR 1102.26 - Determination of materially inaccurate information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10... publication in the Database, may request that the report of harm or manufacturer comment, or portions of such report of harm or manufacturer comment, be excluded from the Database or corrected by the Commission...

  17. 48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  18. Influencing Database Use in Public Libraries.

    ERIC Educational Resources Information Center

    Tenopir, Carol

    1999-01-01

    Discusses results of a survey of factors influencing database use in public libraries. Highlights the importance of content; ease of use; and importance of instruction. Tabulates importance indications for number and location of workstations, library hours, availability of remote login, usefulness and quality of content, lack of other databases,…

  19. Systematic Analysis of Splice-Site-Creating Mutations in Cancer

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

    Jayasinghe, Reyka G.; Cao, Song; Gao, Qingsong

    For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared tomore » missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.« less

  20. Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

    PubMed

    Jayasinghe, Reyka G; Cao, Song; Gao, Qingsong; Wendl, Michael C; Vo, Nam Sy; Reynolds, Sheila M; Zhao, Yanyan; Climente-González, Héctor; Chai, Shengjie; Wang, Fang; Varghese, Rajees; Huang, Mo; Liang, Wen-Wei; Wyczalkowski, Matthew A; Sengupta, Sohini; Li, Zhi; Payne, Samuel H; Fenyö, David; Miner, Jeffrey H; Walter, Matthew J; Vincent, Benjamin; Eyras, Eduardo; Chen, Ken; Shmulevich, Ilya; Chen, Feng; Ding, Li

    2018-04-03

    For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  1. Systematic Analysis of Splice-Site-Creating Mutations in Cancer

    DOE PAGES

    Jayasinghe, Reyka G.; Cao, Song; Gao, Qingsong; ...

    2018-04-05

    For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared tomore » missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.« less

  2. On-Line Database of Vibration-Based Damage Detection Experiments

    NASA Technical Reports Server (NTRS)

    Pappa, Richard S.; Doebling, Scott W.; Kholwad, Tina D.

    2000-01-01

    This paper describes a new, on-line bibliographic database of vibration-based damage detection experiments. Publications in the database discuss experiments conducted on actual structures as well as those conducted with simulated data. The database can be searched and sorted in many ways, and it provides photographs of test structures when available. It currently contains 100 publications, which is estimated to be about 5-10% of the number of papers written to date on this subject. Additional entries are forthcoming. This database is available for public use on the Internet at the following address: http://sdbpappa-mac.larc.nasa.gov. Click on the link named "dd_experiments.fp3" and then type "guest" as the password. No user name is required.

  3. GenderMedDB: an interactive database of sex and gender-specific medical literature.

    PubMed

    Oertelt-Prigione, Sabine; Gohlke, Björn-Oliver; Dunkel, Mathias; Preissner, Robert; Regitz-Zagrosek, Vera

    2014-01-01

    Searches for sex and gender-specific publications are complicated by the absence of a specific algorithm within search engines and by the lack of adequate archives to collect the retrieved results. We previously addressed this issue by initiating the first systematic archive of medical literature containing sex and/or gender-specific analyses. This initial collection has now been greatly enlarged and re-organized as a free user-friendly database with multiple functions: GenderMedDB (http://gendermeddb.charite.de). GenderMedDB retrieves the included publications from the PubMed database. Manuscripts containing sex and/or gender-specific analysis are continuously screened and the relevant findings organized systematically into disciplines and diseases. Publications are furthermore classified by research type, subject and participant numbers. More than 11,000 abstracts are currently included in the database, after screening more than 40,000 publications. The main functions of the database include searches by publication data or content analysis based on pre-defined classifications. In addition, registrants are enabled to upload relevant publications, access descriptive publication statistics and interact in an open user forum. Overall, GenderMedDB offers the advantages of a discipline-specific search engine as well as the functions of a participative tool for the gender medicine community.

  4. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.16 Additional... in the Database any additional information it determines to be in the public interest, consistent...

  5. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.16 Additional... in the Database any additional information it determines to be in the public interest, consistent...

  6. 16 CFR § 1102.30 - Publication of manufacturer comments.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural....26, the Commission will publish in the Database manufacturer comments submitted in response to a...

  7. The Latin American Social Medicine database

    PubMed Central

    Eldredge, Jonathan D; Waitzkin, Howard; Buchanan, Holly S; Teal, Janis; Iriart, Celia; Wiley, Kevin; Tregear, Jonathan

    2004-01-01

    Background Public health practitioners and researchers for many years have been attempting to understand more clearly the links between social conditions and the health of populations. Until recently, most public health professionals in English-speaking countries were unaware that their colleagues in Latin America had developed an entire field of inquiry and practice devoted to making these links more clearly understood. The Latin American Social Medicine (LASM) database finally bridges this previous gap. Description This public health informatics case study describes the key features of a unique information resource intended to improve access to LASM literature and to augment understanding about the social determinants of health. This case study includes both quantitative and qualitative evaluation data. Currently the LASM database at The University of New Mexico brings important information, originally known mostly within professional networks located in Latin American countries to public health professionals worldwide via the Internet. The LASM database uses Spanish, Portuguese, and English language trilingual, structured abstracts to summarize classic and contemporary works. Conclusion This database provides helpful information for public health professionals on the social determinants of health and expands access to LASM. PMID:15627401

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

    PubMed

    Powell, Kimberly R; Peterson, Shenita R

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

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

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

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

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

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

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

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

  11. Publishing Your Database on CD-ROM for Profit: The FISHLIT and NISC Experience.

    ERIC Educational Resources Information Center

    Crampton, Margaret

    1995-01-01

    Details the development of the FISHLIT bibliographic database at the JLB Smith Institute of Ichthyology Library at Rhodes University (South Africa), and the subsequent CD-ROM publication of the database by NISC (National Information Services Corporation). Discusses the advantages of CD-ROM publication, costs and information service provision,…

  12. A Public-Use, Full-Screen Interface for SPIRES Databases.

    ERIC Educational Resources Information Center

    Kriz, Harry M.

    This paper describes the techniques for implementing a full-screen, custom SPIRES interface for a public-use library database. The database-independent protocol that controls the system is described in detail. Source code for an entire working application using this interface is included. The protocol, with less than 170 lines of procedural code,…

  13. 48 CFR 504.605-70 - Federal Procurement Data System-Public access to data.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  14. 48 CFR 504.605-70 - Federal Procurement Data System-Public access to data.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  15. 48 CFR 504.605-70 - Federal Procurement Data System-Public access to data.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  16. 16 CFR § 1102.16 - Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.16 Additional... in the Database any additional information it determines to be in the public interest, consistent...

  17. 16 CFR 1102.30 - Publication of manufacturer comments.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011....24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in...

  18. Chinese journals: a guide for epidemiologists

    PubMed Central

    Fung, Isaac CH

    2008-01-01

    Chinese journals in epidemiology, preventive medicine and public health contain much that is of potential international interest. However, few non-Chinese speakers are acquainted with this literature. This article therefore provides an overview of the contemporary scene in Chinese biomedical journal publication, Chinese bibliographic databases and Chinese journals in epidemiology, preventive medicine and public health. The challenge of switching to English as the medium of publication, the development of publishing bibliometric data from Chinese databases, the prospect of an Open Access publication model in China, the issue of language bias in literature reviews and the quality of Chinese journals are discussed. Epidemiologists are encouraged to search the Chinese bibliographic databases for Chinese journal articles. PMID:18826604

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

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

    Yesley, M.S.

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

  20. Comprehensive T-matrix Reference Database: A 2009-2011 Update

    NASA Technical Reports Server (NTRS)

    Zakharova, Nadezhda T.; Videen, G.; Khlebtsov, Nikolai G.

    2012-01-01

    The T-matrix method is one of the most versatile and efficient theoretical techniques widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of peer-reviewed T-matrix publications compiled by us previously and includes the publications that appeared since 2009. It also lists several earlier publications not included in the original database.

  1. 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.

  2. NCCDPHP PUBLICATION DATABASE

    EPA Science Inventory

    This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

  3. ClinicalTrials.gov

    MedlinePlus

    ... Terms and Conditions Disclaimer ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted ... world. ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of ...

  4. Ocean Drilling Program: Mirror Sites

    Science.gov Websites

    Publication services and products Drilling services and tools Online Janus database Search the ODP/TAMU web information, see www.iodp-usio.org. ODP | Search | Database | Drilling | Publications | Science | Cruise Info

  5. Ocean Drilling Program: TAMU Staff Directory

    Science.gov Websites

    products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site Employment Opportunities ODP | Search | Database | Drilling | Publications | Science | Cruise Info | Public

  6. Health Information-Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease.

    PubMed

    Pesälä, Samuli; Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

    2017-11-06

    People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician's Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs' queries, and what causes possible differences in behavior. The aim of our study was to evaluate how the general public's and HCPs' information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public's information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician's Databases, were used. We compared the general public's article openings on Lyme disease from Health Library to HCPs' article openings on Lyme disease from Physician's Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Both databases, Health Library and Physician's Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Lyme disease-related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public's article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public's access to Health Library. ©Samuli Pesälä, Mikko J Virtanen, Jussi Sane, Pekka Mustonen, Minna Kaila, Otto Helve. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.11.2017.

  7. A Chronostratigraphic Relational Database Ontology

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

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

  8. National Library of Medicine

    MedlinePlus

    ... Disasters and Public Health Emergencies The NLM Disaster Information Management Research Center has tools, guides, and databases to ... Disasters and Public Health Emergencies The NLM Disaster Information Management Research Center has tools, guides, and databases to ...

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

    PubMed

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

    2008-01-01

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

  10. Production and distribution of scientific and technical databases - Comparison among Japan, US and Europe

    NASA Astrophysics Data System (ADS)

    Onodera, Natsuo; Mizukami, Masayuki

    This paper estimates several quantitative indice on production and distribution of scientific and technical databases based on various recent publications and attempts to compare the indice internationally. Raw data used for the estimation are brought mainly from the Database Directory (published by MITI) for database production and from some domestic and foreign study reports for database revenues. The ratio of the indice among Japan, US and Europe for usage of database is similar to those for general scientific and technical activities such as population and R&D expenditures. But Japanese contributions to production, revenue and over-countory distribution of databases are still lower than US and European countries. International comparison of relative database activities between public and private sectors is also discussed.

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

    EPA Science Inventory


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

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  13. Comprehensive T-Matrix Reference Database: A 2007-2009 Update

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

    The T-matrix method is among the most versatile, efficient, and widely used theoretical techniques for the numerically exact computation of electromagnetic scattering by homogeneous and composite particles, clusters of particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of T-matrix publications compiled by us previously and includes the publications that appeared since 2007. It also lists several earlier publications not included in the original database.

  14. ECOTOX database; new additions and future direction

    EPA Science Inventory

    The ECOTOXicology database (ECOTOX) is a comprehensive, publicly available knowledgebase developed and maintained by ORD/NHEERL. It is used for environmental toxicity data on aquatic life, terrestrial plants and wildlife. Publications are identified for potential applicability af...

  15. BioQ: tracing experimental origins in public genomic databases using a novel data provenance model.

    PubMed

    Saccone, Scott F; Quan, Jiaxi; Jones, Peter L

    2012-04-15

    Public genomic databases, which are often used to guide genetic studies of human disease, are now being applied to genomic medicine through in silico integrative genomics. These databases, however, often lack tools for systematically determining the experimental origins of the data. We introduce a new data provenance model that we have implemented in a public web application, BioQ, for assessing the reliability of the data by systematically tracing its experimental origins to the original subjects and biologics. BioQ allows investigators to both visualize data provenance as well as explore individual elements of experimental process flow using precise tools for detailed data exploration and documentation. It includes a number of human genetic variation databases such as the HapMap and 1000 Genomes projects. BioQ is freely available to the public at http://bioq.saclab.net.

  16. 19 CFR 351.303 - Filing, document identification, format, translation, service, and certification of documents.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... submit a public version of a database in pdf format. The public version of the database must be publicly... interested party that files with the Department a request for an expedited antidumping review, an..., whichever is later. If the interested party that files the request is unable to locate a particular exporter...

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

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

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

    2004-12-01

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

  18. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

    PubMed Central

    Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

    2010-01-01

    We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

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

    PubMed

    Machado, Helena; Silva, Susana

    2015-10-01

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

  20. ICRP Publication 107. Nuclear decay data for dosimetric calculations.

    PubMed

    Eckerman, K; Endo, A

    2008-01-01

    In this report, the Commission provides an electronic database of the physical data needed in calculations of radionuclide-specific protection and operational quantities. This database supersedes the data of Publication 38 (ICRP, 1983), and will be used in future ICRP publications of dose coefficients for the intake of or exposure to radionuclides in the workplace and the environment.The database contains information on the half-lives, decay chains, and yields and energies of radiations emitted in nuclear transformations of 1252 radionuclides of 97 elements. The CD accompanying the publication provides electronic access to complete tables of the emitted radiations, as well as the beta and neutron spectra. The database has been constructed such that user-developed software can extract the data needed for further calculations of a radionuclide of interest. A Windows-based application is provided to display summary information on a user-specified radionuclide, as well as the general characterisation of the nuclides contained in the database. In addition, the application provides a means by which the user can export the emissions of a specified radionuclide for use in subsequent calculations.

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

    PubMed

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

    2014-10-01

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

  2. 16 CFR 1102.44 - Applicability of sections 6(a) and (b) of the CPSA.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PRODUCT SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan... publication in § 1102.10(d) in the Database. (b) Limitation on construction. Section 1102.44(a) shall not be...

  3. Academic Impact of a Public Electronic Health Database: Bibliometric Analysis of Studies Using the General Practice Research Database

    PubMed Central

    Chen, Yu-Chun; Wu, Jau-Ching; Haschler, Ingo; Majeed, Azeem; Chen, Tzeng-Ji; Wetter, Thomas

    2011-01-01

    Background Studies that use electronic health databases as research material are getting popular but the influence of a single electronic health database had not been well investigated yet. The United Kingdom's General Practice Research Database (GPRD) is one of the few electronic health databases publicly available to academic researchers. This study analyzed studies that used GPRD to demonstrate the scientific production and academic impact by a single public health database. Methodology and Findings A total of 749 studies published between 1995 and 2009 with ‘General Practice Research Database’ as their topics, defined as GPRD studies, were extracted from Web of Science. By the end of 2009, the GPRD had attracted 1251 authors from 22 countries and been used extensively in 749 studies published in 193 journals across 58 study fields. Each GPRD study was cited 2.7 times by successive studies. Moreover, the total number of GPRD studies increased rapidly, and it is expected to reach 1500 by 2015, twice the number accumulated till the end of 2009. Since 17 of the most prolific authors (1.4% of all authors) contributed nearly half (47.9%) of GPRD studies, success in conducting GPRD studies may accumulate. The GPRD was used mainly in, but not limited to, the three study fields of “Pharmacology and Pharmacy”, “General and Internal Medicine”, and “Public, Environmental and Occupational Health”. The UK and United States were the two most active regions of GPRD studies. One-third of GRPD studies were internationally co-authored. Conclusions A public electronic health database such as the GPRD will promote scientific production in many ways. Data owners of electronic health databases at a national level should consider how to reduce access barriers and to make data more available for research. PMID:21731733

  4. Publication proportions for registered breast cancer trials: before and following the introduction of the ClinicalTrials.gov results database.

    PubMed

    Asiimwe, Innocent Gerald; Rumona, Dickson

    2016-01-01

    To limit selective and incomplete publication of the results of clinical trials, registries including ClinicalTrials.gov were introduced. The ClinicalTrials.gov registry added a results database in 2008 to enable researchers to post the results of their trials as stipulated by the Food and Drug Administration Amendment Act of 2007. This study aimed to determine the direction and magnitude of any change in publication proportions of registered breast cancer trials that occurred since the inception of the ClinicalTrials.gov results database. A cross-sectional study design was employed using ClinicalTrials.gov, a publicly available registry/results database as the primary data source. Registry contents under the subcategories 'Breast Neoplasms' and 'Breast Neoplasms, Male' were downloaded on 1 August 2015. A literature search for included trials was afterwards conducted using MEDLINE and DISCOVER databases to determine publication status of the registered breast cancer trials. Nearly half (168/340) of the listed trials had been published, with a median time to publication of 24 months (Q1 = 14 months, Q3 = 42 months). Only 86 trials were published within 24 months of completion. There was no significant increase in publication proportions of trials that were completed before the introduction of the results database compared to those completed after (OR = 1.00, 95 % CI = .61 to 1.63; adjusted OR = 0.84, 95 % CI = .51 to 1.39). Characteristics associated with publication included trial type (observational versus interventional adjusted OR = .28, 95 % CI = .10 to .74) and completion/termination status (terminated versus completed adjusted OR = .22, 95 % CI = .09 to .51). Less than a half of breast cancer trials registered in ClinicalTrials.gov are published in peer-reviewed journals.

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

    PubMed

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

    2012-11-01

    Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery. © 2012 John Wiley & Sons A/S.

  6. GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

    PubMed

    Riviere, Guillaume; Klopp, Christophe; Ibouniyamine, Nabihoudine; Huvet, Arnaud; Boudry, Pierre; Favrel, Pascal

    2015-12-02

    The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

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

    ERIC Educational Resources Information Center

    Adams, Michael Q.

    1986-01-01

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

  8. PoMaMo--a comprehensive database for potato genome data.

    PubMed

    Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

    2005-01-01

    A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes.

  9. PoMaMo—a comprehensive database for potato genome data

    PubMed Central

    Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

    2005-01-01

    A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes. PMID:15608284

  10. 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.

  11. A Novel Approach: Chemical Relational Databases, and the ...

    EPA Pesticide Factsheets

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as

  12. The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

    DTIC Science & Technology

    2016-09-20

    31 diagnostics for the identification of bacterial pathogens. To do this effectively, 32 genomics databases must be comprehensive to identify the...diverse B. 118 pseudomallei/mallei strains were sequenced, assembled, and deposited in public 119 databases (Supplemental Table 1); these genomes were...combined with 160 B. 120 pseudomallei/mallei genome assemblies already in public databases . Most of the 121 genomes (n=779) in this study were

  13. TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University

    PubMed Central

    Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

    2010-01-01

    We developed, TNAURice: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx. PMID:21364829

  14. TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

    PubMed

    Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

    2010-11-27

    WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

  15. Hawaii bibliographic database

    USGS Publications Warehouse

    Wright, T.L.; Takahashi, T.J.

    1998-01-01

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

  16. The Protein Information Resource: an integrated public resource of functional annotation of proteins

    PubMed Central

    Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

    2002-01-01

    The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

  17. On-Line Databases in Mexico.

    ERIC Educational Resources Information Center

    Molina, Enzo

    1986-01-01

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

  18. Village Green Project: Web-accessible Database

    EPA Science Inventory

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

  19. BioQ: tracing experimental origins in public genomic databases using a novel data provenance model

    PubMed Central

    Saccone, Scott F.; Quan, Jiaxi; Jones, Peter L.

    2012-01-01

    Motivation: Public genomic databases, which are often used to guide genetic studies of human disease, are now being applied to genomic medicine through in silico integrative genomics. These databases, however, often lack tools for systematically determining the experimental origins of the data. Results: We introduce a new data provenance model that we have implemented in a public web application, BioQ, for assessing the reliability of the data by systematically tracing its experimental origins to the original subjects and biologics. BioQ allows investigators to both visualize data provenance as well as explore individual elements of experimental process flow using precise tools for detailed data exploration and documentation. It includes a number of human genetic variation databases such as the HapMap and 1000 Genomes projects. Availability and implementation: BioQ is freely available to the public at http://bioq.saclab.net Contact: ssaccone@wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22426342

  20. [The theme of disaster in health care: profile of technical and scientific production in the specialized database on disasters of the Virtual Health Library - VHL].

    PubMed

    Rocha, Vania; Ximenes, Elisa Francioli; Carvalho, Mauren Lopes de; Alpino, Tais de Moura Ariza; Freitas, Carlos Machado de

    2014-09-01

    In the specialized database of the Virtual Health Library (VHL), the DISASTER database highlights the importance of the theme for the health sector. The scope of this article is to identify the profiles of technical and scientific publications in the specialized database. Based on systematic searches and the analysis of results it is possible to determine: the type of publication; the main topics addressed; the most common type of disasters mentioned in published materials, countries and regions as subjects, historic periods with the most publications and the current trend of publications. When examining the specialized data in detail, it soon becomes clear that the number of major topics is very high, making a specific search process in this database a challenging exercise. On the other hand, it is encouraging that the disaster topic is discussed and assessed in a broad and diversified manner, associated with different aspects of the natural and social sciences. The disaster issue requires the production of interdisciplinary knowledge development to reduce the impacts of disasters and for risk management. In this way, since the health sector is a interdisciplinary area, it can contribute to knowledge production.

  1. The Alaska Volcano Observatory Website a Tool for Information Management and Dissemination

    NASA Astrophysics Data System (ADS)

    Snedigar, S. F.; Cameron, C. E.; Nye, C. J.

    2006-12-01

    The Alaska Volcano Observatory's (AVO's) website served as a primary information management tool during the 2006 eruption of Augustine Volcano. The AVO website is dynamically generated from a database back- end. This system enabled AVO to quickly and easily update the website, and provide content based on user- queries to the database. During the Augustine eruption, the new AVO website was heavily used by members of the public (up to 19 million hits per day), and this was largely because the AVO public pages were an excellent source of up-to-date information. There are two different, yet fully integrated parts of the website. An external, public site (www.avo.alaska.edu) allows the general public to track eruptive activity by viewing the latest photographs, webcam images, webicorder graphs, and official information releases about activity at the volcano, as well as maps, previous eruption information, bibliographies, and rich information about other Alaska volcanoes. The internal half of the website hosts diverse geophysical and geological data (as browse images) in a format equally accessible by AVO staff in different locations. In addition, an observation log allows users to enter information about anything from satellite passes to seismic activity to ash fall reports into a searchable database. The individual(s) on duty at the watch office use forms on the internal website to post a summary of the latest activity directly to the public website, ensuring that the public website is always up to date. The internal website also serves as a starting point for monitoring Alaska's volcanoes. AVO's extensive image database allows AVO personnel to upload many photos, diagrams, and videos which are then available to be browsed by anyone in the AVO community. Selected images are viewable from the public page. The primary webserver is housed at the University of Alaska Fairbanks, and holds a MySQL database with over 200 tables and several thousand lines of php code gluing the database and website together. The database currently holds 95 GB of data. Webcam images and webicorder graphs are pulled from servers in Anchorage every few minutes. Other servers in Fairbanks generate earthquake location plots and spectrograms.

  2. Quality control of EUVE databases

    NASA Technical Reports Server (NTRS)

    John, L. M.; Drake, J.

    1992-01-01

    The publicly accessible databases for the Extreme Ultraviolet Explorer include: the EUVE Archive mailserver; the CEA ftp site; the EUVE Guest Observer Mailserver; and the Astronomical Data System node. The EUVE Performance Assurance team is responsible for verifying that these public EUVE databases are working properly, and that the public availability of EUVE data contained therein does not infringe any data rights which may have been assigned. In this poster, we describe the Quality Assurance (QA) procedures we have developed from the approach of QA as a service organization, thus reflecting the overall EUVE philosophy of Quality Assurance integrated into normal operating procedures, rather than imposed as an external, post facto, control mechanism.

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

    PubMed

    Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

    2014-08-15

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

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

    EPA Science Inventory

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

  5. NASA STI Database, Aerospace Database and ARIN coverage of 'space law'

    NASA Technical Reports Server (NTRS)

    Buchan, Ronald L.

    1992-01-01

    The space-law coverage provided by the NASA STI Database, the Aerospace Database, and ARIN is briefly described. Particular attention is given to the space law content of the two Databases and of ARIN, the NASA Thesauras space law terminology, space law publication forms, and the availability of the space law literature.

  6. MetPetDB: A database for metamorphic geochemistry

    NASA Astrophysics Data System (ADS)

    Spear, Frank S.; Hallett, Benjamin; Pyle, Joseph M.; Adalı, Sibel; Szymanski, Boleslaw K.; Waters, Anthony; Linder, Zak; Pearce, Shawn O.; Fyffe, Matthew; Goldfarb, Dennis; Glickenhouse, Nickolas; Buletti, Heather

    2009-12-01

    We present a data model for the initial implementation of MetPetDB, a geochemical database specific to metamorphic rock samples. The database is designed around the concept of preservation of spatial relationships, at all scales, of chemical analyses and their textural setting. Objects in the database (samples) represent physical rock samples; each sample may contain one or more subsamples with associated geochemical and image data. Samples, subsamples, geochemical data, and images are described with attributes (some required, some optional); these attributes also serve as search delimiters. All data in the database are classified as published (i.e., archived or published data), public or private. Public and published data may be freely searched and downloaded. All private data is owned; permission to view, edit, download and otherwise manipulate private data may be granted only by the data owner; all such editing operations are recorded by the database to create a data version log. The sharing of data permissions among a group of collaborators researching a common sample is done by the sample owner through the project manager. User interaction with MetPetDB is hosted by a web-based platform based upon the Java servlet application programming interface, with the PostgreSQL relational database. The database web portal includes modules that allow the user to interact with the database: registered users may save and download public and published data, upload private data, create projects, and assign permission levels to project collaborators. An Image Viewer module provides for spatial integration of image and geochemical data. A toolkit consisting of plotting and geochemical calculation software for data analysis and a mobile application for viewing the public and published data is being developed. Future issues to address include population of the database, integration with other geochemical databases, development of the analysis toolkit, creation of data models for derivative data, and building a community-wide user base. It is believed that this and other geochemical databases will enable more productive collaborations, generate more efficient research efforts, and foster new developments in basic research in the field of solid earth geochemistry.

  7. The National Institute on Disability, Independent Living, and Rehabilitation Research Burn Model System: Twenty Years of Contributions to Clinical Service and Research.

    PubMed

    Goverman, Jeremy; Mathews, Katie; Holavanahalli, Radha K; Vardanian, Andrew; Herndon, David N; Meyer, Walter J; Kowalske, Karen; Fauerbach, Jim; Gibran, Nicole S; Carrougher, Gretchen J; Amtmann, Dagmar; Schneider, Jeffrey C; Ryan, Colleen M

    The National Institute on Disability, Independent Living, and Rehabilitation Research (NIDILRR) established the Burn Model System (BMS) in 1993 to improve the lives of burn survivors. The BMS program includes 1) a multicenter longitudinal database describing the functional and psychosocial recovery of burn survivors; 2) site-specific burn-related research; and 3) a knowledge dissemination component directed toward patients and providers. Output from each BMS component was analyzed. Database structure, content, and access procedures are described. Publications using the database were identified and categorized to illustrate the content area of the work. Unused areas of the database were identified for future study. Publications related to site-specific projects were cataloged. The most frequently cited articles are summarized to illustrate the scope of these projects. The effectiveness of dissemination activities was measured by quantifying website hits and information downloads. There were 25 NIDILRR-supported publications that utilized the database. These articles covered topics related to psychological outcomes, functional outcomes, community reintegration, and burn demographics. There were 172 site-specific publications; highly cited articles demonstrate a wide scope of study. For information dissemination, visits to the BMS website quadrupled between 2013 and 2014, with 124,063 downloads of educational material in 2014. The NIDILRR BMS program has played a major role in defining the course of burn recovery, and making that information accessible to the general public. The accumulating information in the database serves as a rich resource to the burn community for future study. The BMS is a model for collaborative research that is multidisciplinary and outcome focused.

  8. A knowledge base for tracking the impact of genomics on population health.

    PubMed

    Yu, Wei; Gwinn, Marta; Dotson, W David; Green, Ridgely Fisk; Clyne, Mindy; Wulf, Anja; Bowen, Scott; Kolor, Katherine; Khoury, Muin J

    2016-12-01

    We created an online knowledge base (the Public Health Genomics Knowledge Base (PHGKB)) to provide systematically curated and updated information that bridges population-based research on genomics with clinical and public health applications. Weekly horizon scanning of a wide variety of online resources is used to retrieve relevant scientific publications, guidelines, and commentaries. After curation by domain experts, links are deposited into Web-based databases. PHGKB currently consists of nine component databases. Users can search the entire knowledge base or search one or more component databases directly and choose options for customizing the display of their search results. PHGKB offers researchers, policy makers, practitioners, and the general public a way to find information they need to understand the complicated landscape of genomics and population health.Genet Med 18 12, 1312-1314.

  9. Investigating Evolutionary Questions Using Online Molecular Databases.

    ERIC Educational Resources Information Center

    Puterbaugh, Mary N.; Burleigh, J. Gordon

    2001-01-01

    Recommends using online molecular databases as teaching tools to illustrate evolutionary questions and concepts while introducing students to public molecular databases. Provides activities in which students make molecular comparisons between species. (YDS)

  10. The Data Base and Decision Making in Public Schools.

    ERIC Educational Resources Information Center

    Hedges, William D.

    1984-01-01

    Describes generic types of databases--file management systems, relational database management systems, and network/hierarchical database management systems--with their respective strengths and weaknesses; discusses factors to be considered in determining whether a database is desirable; and provides evaluative criteria for use in choosing…

  11. 75 FR 60460 - Proposed Data Collections Submitted for Public Comment and Recommendations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... one integrated database. The mission of the SEPDPO is to prepare an applied public health workforce... candidates, maintaining a current alumni database, documenting the impact of the fellowships on alumni's... to the questions in the online application; submission of academic transcripts and letters of...

  12. Governing Software: Networks, Databases and Algorithmic Power in the Digital Governance of Public Education

    ERIC Educational Resources Information Center

    Williamson, Ben

    2015-01-01

    This article examines the emergence of "digital governance" in public education in England. Drawing on and combining concepts from software studies, policy and political studies, it identifies some specific approaches to digital governance facilitated by network-based communications and database-driven information processing software…

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  15. Measuring Academic Performance for Healthcare Researchers with the H Index: Which Search Tool Should Be Used?

    PubMed Central

    Patel, Vanash M.; Ashrafian, Hutan; Almoudaris, Alex; Makanjuola, Jonathan; Bucciarelli-Ducci, Chiara; Darzi, Ara; Athanasiou, Thanos

    2013-01-01

    Objectives To compare H index scores for healthcare researchers returned by Google Scholar, Web of Science and Scopus databases, and to assess whether a researcher's age, country of institutional affiliation and physician status influences calculations. Subjects and Methods One hundred and ninety-five Nobel laureates in Physiology and Medicine from 1901 to 2009 were considered. Year of first and last publications, total publications and citation counts, and the H index for each laureate were calculated from each database. Cronbach's alpha statistics was used to measure the reliability of H index scores between the databases. Laureate characteristic influence on the H index was analysed using linear regression. Results There was no concordance between the databases when considering the number of publications and citations count per laureate. The H index was the most reliably calculated bibliometric across the three databases (Cronbach's alpha = 0.900). All databases returned significantly higher H index scores for younger laureates (p < 0.0001). Google Scholar and Web of Science returned significantly higher H index for physician laureates (p = 0.025 and p = 0.029, respectively). Country of institutional affiliation did not influence the H index in any database. Conclusion The H index appeared to be the most consistently calculated bibliometric between the databases for Nobel laureates in Physiology and Medicine. Researcher-specific characteristics constituted an important component of objective research assessment. The findings of this study call to question the choice of current and future academic performance databases. PMID:22964880

  16. Analysis of commercial and public bioactivity databases.

    PubMed

    Tiikkainen, Pekka; Franke, Lutz

    2012-02-27

    Activity data for small molecules are invaluable in chemoinformatics. Various bioactivity databases exist containing detailed information of target proteins and quantitative binding data for small molecules extracted from journals and patents. In the current work, we have merged several public and commercial bioactivity databases into one bioactivity metabase. The molecular presentation, target information, and activity data of the vendor databases were standardized. The main motivation of the work was to create a single relational database which allows fast and simple data retrieval by in-house scientists. Second, we wanted to know the amount of overlap between databases by commercial and public vendors to see whether the former contain data complementing the latter. Third, we quantified the degree of inconsistency between data sources by comparing data points derived from the same scientific article cited by more than one vendor. We found that each data source contains unique data which is due to different scientific articles cited by the vendors. When comparing data derived from the same article we found that inconsistencies between the vendors are common. In conclusion, using databases of different vendors is still useful since the data overlap is not complete. It should be noted that this can be partially explained by the inconsistencies and errors in the source data.

  17. Multiple imputation as one tool to provide longitudinal databases for modelling human height and weight development.

    PubMed

    Aßmann, C

    2016-06-01

    Besides large efforts regarding field work, provision of valid databases requires statistical and informational infrastructure to enable long-term access to longitudinal data sets on height, weight and related issues. To foster use of longitudinal data sets within the scientific community, provision of valid databases has to address data-protection regulations. It is, therefore, of major importance to hinder identifiability of individuals from publicly available databases. To reach this goal, one possible strategy is to provide a synthetic database to the public allowing for pretesting strategies for data analysis. The synthetic databases can be established using multiple imputation tools. Given the approval of the strategy, verification is based on the original data. Multiple imputation by chained equations is illustrated to facilitate provision of synthetic databases as it allows for capturing a wide range of statistical interdependencies. Also missing values, typically occurring within longitudinal databases for reasons of item non-response, can be addressed via multiple imputation when providing databases. The provision of synthetic databases using multiple imputation techniques is one possible strategy to ensure data protection, increase visibility of longitudinal databases and enhance the analytical potential.

  18. NREL: U.S. Life Cycle Inventory Database - About the LCI Database Project

    Science.gov Websites

    About the LCI Database Project The U.S. Life Cycle Inventory (LCI) Database is a publicly available data collection and analysis methods. Finding consistent and transparent LCI data for life cycle and maintain the database. The 2009 U.S. Life Cycle Inventory (LCI) Data Stakeholder meeting was an

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

    ERIC Educational Resources Information Center

    Tomblin, J. Bruce

    2010-01-01

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

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

    EPA Science Inventory

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

  1. 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...

  2. Publication rates of public health theses in international and national peer-review journals in Turkey.

    PubMed

    Sipahi, H; Durusoy, R; Ergin, I; Hassoy, H; Davas, A; Karababa, Ao

    2012-01-01

    Thesis is an important part of specialisation and doctorate education and requires intense work. The aim of this study was to investigate the publication rates of Turkish Public Health Doctorate Theses (PHDT) and Public Health Specialization (PHST) theses in international and Turkish national peer-review journals and to analyze the distribution of research areas. List of all theses upto 30 September 2009 were retrieved from theses database of the Council of Higher Education of the Republic of Turkey. The publication rates of these theses were found by searching PubMed, Science Citation Index-Expanded, Turkish Academic Network and Information Center (ULAKBIM) Turkish Medical Database, and Turkish Medline databases for the names of thesis author and mentor. The theses which were published in journals indexed either in PubMed or SCI-E were considered as international publications. Our search yielded a total of 538 theses (243 PHDT, 295 PHST). It was found that the overall publication rate in Turkish national journals was 18%. The overall publication rate in international journals was 11.9%. Overall the most common research area was occupational health. Publication rates of Turkish PHDT and PHST are low. A better understanding of factors affecting this publication rate is important for public health issues where national data is vital for better intervention programs and develop better public health policies.

  3. Publication Rates of Public Health Theses in International and National Peer-Review Journals in Turkey

    PubMed Central

    Sipahi, H; Durusoy, R; Ergin, I; Hassoy, H; Davas, A; Karababa, AO

    2012-01-01

    Background: Thesis is an important part of specialisation and doctorate education and requires intense work. The aim of this study was to investigate the publication rates of Turkish Public Health Doctorate Theses (PHDT) and Public Health Specialization (PHST) theses in international and Turkish national peer-review journals and to analyze the distribution of research areas. Methods: List of all theses upto 30 September 2009 were retrieved from theses database of the Council of Higher Education of the Republic of Turkey. The publication rates of these theses were found by searching PubMed, Science Citation Index-Expanded, Turkish Academic Network and Information Center (ULAKBIM) Turkish Medical Database, and Turkish Medline databases for the names of thesis author and mentor. The theses which were published in journals indexed either in PubMed or SCI-E were considered as international publications. Results: Our search yielded a total of 538 theses (243 PHDT, 295 PHST). It was found that the overall publication rate in Turkish national journals was 18%. The overall publication rate in international journals was 11.9%. Overall the most common research area was occupational health. Conclusion: Publication rates of Turkish PHDT and PHST are low. A better understanding of factors affecting this publication rate is important for public health issues where national data is vital for better intervention programs and develop better public health policies. PMID:23193503

  4. Health Information–Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease

    PubMed Central

    Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

    2017-01-01

    Background People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician’s Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs’ queries, and what causes possible differences in behavior. Objective The aim of our study was to evaluate how the general public’s and HCPs’ information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public’s information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Methods Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician’s Databases, were used. We compared the general public’s article openings on Lyme disease from Health Library to HCPs’ article openings on Lyme disease from Physician’s Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Results Both databases, Health Library and Physician’s Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Conclusions Lyme disease–related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public’s article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public’s access to Health Library. PMID:29109071

  5. 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

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

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

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

    2002-01-01

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

  7. Release of ToxCastDB and ExpoCastDB databases

    EPA Science Inventory

    EPA has released two databases - the Toxicity Forecaster database (ToxCastDB) and a database of chemical exposure studies (ExpoCastDB) - that scientists and the public can use to access chemical toxicity and exposure data. ToxCastDB users can search and download data from over 50...

  8. 32 CFR 105.15 - Defense Sexual Assault Incident Database (DSAID).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 1 2013-07-01 2013-07-01 false Defense Sexual Assault Incident Database (DSAID... Sexual Assault Incident Database (DSAID). (a) Purpose. (1) In accordance with section 563 of Public Law... activities. It shall serve as a centralized, case-level database for the collection and maintenance of...

  9. 40 CFR 1400.13 - Read-only database.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  10. 42 CFR 455.436 - Federal database checks.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 4 2012-10-01 2012-10-01 false Federal database checks. 455.436 Section 455.436....436 Federal database checks. The State Medicaid agency must do all of the following: (a) Confirm the... databases. (b) Check the Social Security Administration's Death Master File, the National Plan and Provider...

  11. 42 CFR 455.436 - Federal database checks.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Federal database checks. 455.436 Section 455.436....436 Federal database checks. The State Medicaid agency must do all of the following: (a) Confirm the... databases. (b) Check the Social Security Administration's Death Master File, the National Plan and Provider...

  12. 32 CFR 105.15 - Defense Sexual Assault Incident Database (DSAID).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 1 2014-07-01 2014-07-01 false Defense Sexual Assault Incident Database (DSAID... Sexual Assault Incident Database (DSAID). (a) Purpose. (1) In accordance with section 563 of Public Law... activities. It shall serve as a centralized, case-level database for the collection and maintenance of...

  13. 40 CFR 1400.13 - Read-only database.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

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

  14. 42 CFR 455.436 - Federal database checks.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 4 2014-10-01 2014-10-01 false Federal database checks. 455.436 Section 455.436....436 Federal database checks. The State Medicaid agency must do all of the following: (a) Confirm the... databases. (b) Check the Social Security Administration's Death Master File, the National Plan and Provider...

  15. 40 CFR 1400.13 - Read-only database.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

  16. 42 CFR 455.436 - Federal database checks.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 4 2013-10-01 2013-10-01 false Federal database checks. 455.436 Section 455.436....436 Federal database checks. The State Medicaid agency must do all of the following: (a) Confirm the... databases. (b) Check the Social Security Administration's Death Master File, the National Plan and Provider...

  17. 40 CFR 1400.13 - Read-only database.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  18. 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<...

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

    ERIC Educational Resources Information Center

    Rice, James

    1988-01-01

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

  20. 75 FR 18837 - Office of Public Health and Science, Office of Minority Health; Privacy Act of 1974; Report of a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-13

    ... collected on members of the general public, health professionals, faculty of academic institutions, students... peers on healthy living and pre-conception care. 5. Organizational Databases: Business contact... to work. 3. Organizational Databases: Name of organization and key contact person, business address...

  1. Building a Faculty Publications Database: A Case Study

    ERIC Educational Resources Information Center

    Tabaei, Sara; Schaffer, Yitzchak; McMurray, Gregory; Simon, Bashe

    2013-01-01

    This case study shares the experience of building an in-house faculty publications database that was spearheaded by the Touro College and University System library in 2010. The project began with the intention of contributing to the college by collecting the research accomplishments of our faculty and staff, thereby also increasing library…

  2. Online Public Access Catalogs. ERIC Fact Sheet.

    ERIC Educational Resources Information Center

    Cochrane, Pauline A.

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

  3. Extending the Online Public Access Catalog into the Microcomputer Environment.

    ERIC Educational Resources Information Center

    Sutton, Brett

    1990-01-01

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

  4. “NaKnowBase”: A Nanomaterials Relational Database

    EPA Science Inventory

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

  5. Advancements in web-database applications for rabies surveillance.

    PubMed

    Rees, Erin E; Gendron, Bruno; Lelièvre, Frédérick; Coté, Nathalie; Bélanger, Denise

    2011-08-02

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

  6. Advancements in web-database applications for rabies surveillance

    PubMed Central

    2011-01-01

    Background Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. Results RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include 1) automatic integration of multi-agency data and diagnostic results on a daily basis; 2) a web-based data editing interface that enables authorized users to add, edit and extract data; and 3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. Conclusions RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response. PMID:21810215

  7. An open experimental database for exploring inorganic materials

    DOE PAGES

    Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; ...

    2018-04-03

    The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half ofmore » these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.« less

  8. Variations in clinicopathologic characteristics of thyroid cancer among racial ethnic groups: analysis of a large public city hospital and the SEER database.

    PubMed

    Moo-Young, Tricia A; Panergo, Jessel; Wang, Chih E; Patel, Subhash; Duh, Hong Yan; Winchester, David J; Prinz, Richard A; Fogelfeld, Leon

    2013-11-01

    Clinicopathologic variables influence the treatment and prognosis of patients with thyroid cancer. A retrospective analysis of public hospital thyroid cancer database and the Surveillance, Epidemiology and End Results 17 database was conducted. Demographic, clinical, and pathologic data were compared across ethnic groups. Within the public hospital database, Hispanics versus non-Hispanic whites were younger and had more lymph node involvement (34% vs 17%, P < .001). Median tumor size was not statistically different across ethnic groups. Similar findings were demonstrated within the Surveillance, Epidemiology and End Results database. African Americans aged <45 years had the largest tumors but were least likely to have lymph node involvement. Asians had the most stage IV disease despite having no differences in tumor size, lymph node involvement, and capsular invasion. There is considerable variability in the clinical presentation of thyroid cancer across ethnic groups. Such disparities persist within an equal-access health care system. These findings suggest that factors beyond socioeconomics may contribute to such differences. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. An open experimental database for exploring inorganic materials.

    PubMed

    Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; Perkins, John D; White, Robert; Munch, Kristin; Tumas, William; Phillips, Caleb

    2018-04-03

    The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.

  10. An open experimental database for exploring inorganic materials

    PubMed Central

    Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; Perkins, John D.; White, Robert; Munch, Kristin; Tumas, William; Phillips, Caleb

    2018-01-01

    The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource. PMID:29611842

  11. An open experimental database for exploring inorganic materials

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

    Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus

    The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half ofmore » these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.« less

  12. Public health research in Denmark in the years 1995--2005.

    PubMed

    Gulis, G; Eriksen, M L; Aro, A R

    2010-02-01

    The objective of this study was to find out the number of publications (in Danish) and research projects (including grey literature) either carried out or ongoing within the field of public health in Denmark, using the same criteria as the SPHERE project, but looking at Danish research databases. The Danish research database served as the main resource for the study supported by national research reports. There is an increasing trend in the number of public health research projects and publications. Compared with public health research projects published in English there are differences in some categories. Overall, public health research in Denmark seems to contribute around 4.8%-6.5% of the total amount of health research. Public health research has a relatively low share of overall health research in Denmark.

  13. Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

    PubMed

    Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

    2016-07-04

    The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

  14. Mental health and psychiatry research in Brazil: scientific production from 1999 to 2003.

    PubMed

    Razzouk, Denise; Zorzetto, Ricardo; Dubugras, Maria Thereza; Gerolin, Jerônimo; Mari, Jair de Jesus

    2006-08-01

    To assess the extent of mental health scientific production in Brazil from 1999 to 2003, and to identify the nature of the publications generated, their sources of finance and the ways of publicly disseminating the research findings. Searches for publications were conducted in the Medline and PsychInfo databases for the period 1999-2003. A semi-structured questionnaire developed by an international team was applied to 626 mental health researchers, covering each interviewee's educational background, research experience, access to funding sources, public impact and research priorities. The sample was composed by 626 mental health researchers identified from 792 publications indexed on Medline and PsychInfo databases for the period above, and from a list of reviewers of Revista Brasileira de Psiquiatria. In Brazil, 792 publications were produced by 525 authors between 1999 and 2003 (441 indexed in Medline and 398 in the ISI database). The main topics were: depression (29.1%), substance misuse (14.6%), psychoses (10%), childhood disorders (7%) and dementia (6.7%). Among the 626 Brazilian mental health researchers, 329 answered the questionnaire. There were steadily increasing numbers of Brazilian articles on mental health published in foreign journals from 1999 to 2003: the number of articles in Medline tripled and it doubled in the ISI database. The content of these articles corresponded to the priorities within mental health, but there is a need for better interlinking between researchers and mental health policymakers.

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

    PubMed Central

    Cousineau, J; Girard, N; Monardes, C; Leroux, T; Jean, M Stanton

    2012-01-01

    Because many diseases are multifactorial disorders, the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State’s role and authority on matters related to public health, in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec). Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec, as examples of key tools framing public health decision-making process. We observed that State powers in public health, are not, in Quebec, well adapted to the expansion of genomics research. We propose that the scope of the concept of research in public health should be clear and include the following characteristics: a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up, consent, etc.). We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters. PMID:23113174

  16. Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian

    PubMed Central

    Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

    2008-01-01

    Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today. PMID:18826570

  17. Clinical Variant Classification: A Comparison of Public Databases and a Commercial Testing Laboratory.

    PubMed

    Gradishar, William; Johnson, KariAnne; Brown, Krystal; Mundt, Erin; Manley, Susan

    2017-07-01

    There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, the well-documented limitations of these databases call into question how often clinicians will encounter discordant variant classifications that may introduce uncertainty into patient management. Here, we evaluate discordance in BRCA1 and BRCA2 variant classifications between a single commercial testing laboratory and a public database commonly consulted in clinical practice. BRCA1 and BRCA2 variant classifications were obtained from ClinVar and compared with the classifications from a reference laboratory. Full concordance and discordance were determined for variants whose ClinVar entries were of the same pathogenicity (pathogenic, benign, or uncertain). Variants with conflicting ClinVar classifications were considered partially concordant if ≥1 of the listed classifications agreed with the reference laboratory classification. Four thousand two hundred and fifty unique BRCA1 and BRCA2 variants were available for analysis. Overall, 73.2% of classifications were fully concordant and 12.3% were partially concordant. The remaining 14.5% of variants had discordant classifications, most of which had a definitive classification (pathogenic or benign) from the reference laboratory compared with an uncertain classification in ClinVar (14.0%). Here, we show that discrepant classifications between a public database and single reference laboratory potentially account for 26.7% of variants in BRCA1 and BRCA2 . The time and expertise required of clinicians to research these discordant classifications call into question the practicality of checking all test results against a database and suggest that discordant classifications should be interpreted with these limitations in mind. With the increasing use of clinical genetic testing for hereditary cancer risk, accurate variant classification is vital to ensuring appropriate medical management. There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, we show that up to 26.7% of variants in BRCA1 and BRCA2 have discordant classifications between ClinVar and a reference laboratory. The findings presented in this paper serve as a note of caution regarding the utility of database consultation. © AlphaMed Press 2017.

  18. RESPIRATORY INFECTIONS RESEARCH IN AFGHANISTAN: BIBLIOMETRIC ANALYSIS WITH THE DATABASE PUBMED.

    PubMed

    Pilsczek, Florian H

    2015-01-01

    Infectious diseases research in a low-income country like Afghanistan is important. In this study an internet-based database Pubmed was used for bibliometric analysis of infectious diseases research activity. Research publications entries in PubMed were analysed according to number of publications, topic, publication type, and country of investigators. Between 2002-2011, 226 (77.7%) publications with the following research topics were identified: respiratory infections 3 (1.3%); parasites 8 (3.5%); diarrhoea 10 (4.4%); tuberculosis 10 (4.4%); human immunodeficiency virus (HIV) 11 (4.9%); multi-drug resistant bacteria (MDR) 18 (8.0%); polio 31 (13.7%); leishmania 31 (13.7%); malaria 46 (20.4%). From 2002-2011, 11 (4.9%) publications were basic science laboratory-based research studies. Between 2002-2011, 8 (3.5%) publications from Afghan institutions were identified. In conclusion, the internet-based database Pubmed can be consulted to collect data for guidance of infectious diseases research activity of low-income countries. The presented data suggest that infectious diseases research in Afghanistan is limited for respiratory infections research, has few studies conducted by Afghan institutions, and limited laboratory-based research contributions.

  19. “NaKnowBase”: A Nanomaterials Relational Database

    EPA Science Inventory

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

  20. Annual Review of Database Development: 1992.

    ERIC Educational Resources Information Center

    Basch, Reva

    1992-01-01

    Reviews recent trends in databases and online systems. Topics discussed include new access points for established databases; acquisitions, consolidations, and competition between vendors; European coverage; international services; online reference materials, including telephone directories; political and legal materials and public records;…

  1. Publications of the Western Geologic Mapping Team 1997-1998

    USGS Publications Warehouse

    Stone, Paul; Powell, C.L.

    1999-01-01

    The Western Geologic Mapping Team (WGMT) of the U.S. Geological Survey, Geologic Division (USGS, GD), conducts geologic mapping and related topical earth-science studies in the western United States. This work is focused on areas where modern geologic maps and associated earth-science data are needed to address key societal and environmental issues such as ground-water quality, potential geologic hazards, and land-use decisions. Areas of primary emphasis currently include southern California, the San Francisco Bay region, the Pacific Northwest, the Las Vegas urban corridor, and selected National Park lands. The team has its headquarters in Menlo Park, California, and maintains smaller field offices at several other locations in the western United States. The results of research conducted by the WGMT are released to the public as a variety of databases, maps, text reports, and abstracts, both through the internal publication system of the USGS and in diverse external publications such as scientific journals and books. This report lists publications of the WGMT released in calendar years 1997 and 1998. Most of the publications listed were authored or coauthored by WGMT staff. However, the list also includes some publications authored by formal non-USGS cooperators with the WGMT, as well as some authored by USGS staff outside the WGMT in cooperation with WGMT projects. Several of the publications listed are available on the World Wide Web; for these, URL addresses are provided. Most of these Web publications are USGS open-file reports that contain large digital databases of geologic map and related information. For these, the bibliographic citation refers specifically to an explanatory pamphlet containing information about the content and accessibility of the database, not to the actual map or related information comprising the database itself.

  2. 77 FR 39269 - Submission for OMB Review, Comment Request, Proposed Collection: IMLS Museum Web Database...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ..., Proposed Collection: IMLS Museum Web Database: MuseumsCount.gov AGENCY: Institute of Museum and Library... general public. Information such as name, address, phone, email, Web site, staff size, program details... Museum Web Database: MuseumsCount.gov collection. The 60-day notice for the IMLS Museum Web Database...

  3. Scientific Communication of Geochemical Data and the Use of Computer Databases.

    ERIC Educational Resources Information Center

    Le Bas, M. J.; Durham, J.

    1989-01-01

    Describes a scheme in the United Kingdom that coordinates geochemistry publications with a computerized geochemistry database. The database comprises not only data published in the journals but also the remainder of the pertinent data set. The discussion covers the database design; collection, storage and retrieval of data; and plans for future…

  4. 78 FR 2363 - Notification of Deletion of a System of Records; Automated Trust Funds Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-11

    ... Database AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice of deletion of a system... establishing the Automated Trust Funds (ATF) database system of records. The Federal Information Security... Integrity Act of 1982, Public Law 97-255, provided authority for the system. The ATF database has been...

  5. USGS cold-water coral geographic database-Gulf of Mexico and western North Atlantic Ocean, version 1.0

    USGS Publications Warehouse

    Scanlon, Kathryn M.; Waller, Rhian G.; Sirotek, Alexander R.; Knisel, Julia M.; O'Malley, John; Alesandrini, Stian

    2010-01-01

    The USGS Cold-Water Coral Geographic Database (CoWCoG) provides a tool for researchers and managers interested in studying, protecting, and/or utilizing cold-water coral habitats in the Gulf of Mexico and western North Atlantic Ocean.  The database makes information about the locations and taxonomy of cold-water corals available to the public in an easy-to-access form while preserving the scientific integrity of the data.  The database includes over 1700 entries, mostly from published scientific literature, museum collections, and other databases.  The CoWCoG database is easy to search in a variety of ways, and data can be quickly displayed in table form and on a map by using only the software included with this publication.  Subsets of the database can be selected on the basis of geographic location, taxonomy, or other criteria and exported to one of several available file formats.  Future versions of the database are being planned to cover a larger geographic area and additional taxa.

  6. MEDLINE versus EMBASE and CINAHL for telemedicine searches.

    PubMed

    Bahaadinbeigy, Kambiz; Yogesan, Kanagasingam; Wootton, Richard

    2010-10-01

    Researchers in the domain of telemedicine throughout the world tend to search multiple bibliographic databases to retrieve the highest possible number of publications when conducting review projects. Medical Literature Analysis and Retrieval System Online (MEDLINE), Excerpta Medica Database (EMBASE), and Cumulative Index to Nursing and Allied Health Literature (CINAHL) are three popular databases in the discipline of biomedicine that are used for conducting reviews. Access to the MEDLINE database is free and easy, whereas EMBASE and CINAHL are not free and sometimes not easy to access for researchers in small research centers. This project sought to compare MEDLINE with EMBASE and CINAHL to estimate what proportion of potentially relevant publications would be missed when only MEDLINE is used in a review project, in comparison to when EMBASE and CINAHL are also used. Twelve simple keywords relevant to 12 different telemedicine applications were searched using all three databases, and the results were compared. About 9%-18% of potentially relevant articles would have been missed if MEDLINE had been the only database used. It is preferable if all three or more databases are used when conducting a review in telemedicine. Researchers from developing countries or small research institutions could rely on only MEDLINE, but they would loose 9%-18% of the potentially relevant publications. Searching MEDLINE alone is not ideal, but in a resource-constrained situation, it is definitely better than nothing.

  7. EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

    PubMed Central

    Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

    2017-01-01

    Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

  8. How to locate and appraise qualitative research in complementary and alternative medicine

    PubMed Central

    2013-01-01

    Background The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Methods Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. Results 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. Conclusions This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies. PMID:23731997

  9. How to locate and appraise qualitative research in complementary and alternative medicine.

    PubMed

    Franzel, Brigitte; Schwiegershausen, Martina; Heusser, Peter; Berger, Bettina

    2013-06-03

    The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies.

  10. Use of existing data for public health planning: a study of the prevalence of hepatitis B surface antigen and core antibody in Al Ain Medical District, United Arab Emirates.

    PubMed Central

    al-Owais, A.; al-Suwaidi, K.; Amiri, N.; Carter, A. O.; Hossain, M. M.; Sheek-Hussein, M. M.

    2000-01-01

    INTRODUCTION: Hepatitis B is of major public health importance. Accurate information on its occurrence, with particular reference to the prevalence of immunity and chronic infection (marked by the presence of hepatitis B core antibody and surface antigen, respectively, in serum), is essential for planning public health programmes for the control of the disease. The generation of marker prevalence data through serological surveys is costly and time-consuming. The present study in Al Ain Medical District, United Arab Emirates, investigated the possibility of obtaining sufficiently accurate marker prevalence estimates from existing data to plan public health programmes. METHODS: Two antenatal screening databases, one student serological survey database, one immunization programme database and one pre-marriage screening database containing information on marker prevalence were identified. Epidemiological data were abstracted from these databases and analysed. RESULTS: The data showed that the prevalence of hepatitis B surface antigen and the prevalence of core antibody in young citizens in 1998 were approximately 2% and 14% respectively, that any immunization campaign aimed at citizens of the United Arab Emirates should target teenagers as they had the highest risk of acquiring the disease, and that pre-immunization screening of young adults would be wasteful. However, the data did not yield information on the prevalence of hepatitis B surface antigen and core antibody in other population subgroups of public health significance. DISCUSSION: While data generated by the study are sufficient to support a hepatitis B immunization programme targeted at teenaged citizens, more accurate data, generated by a well-designed serological survey, would be essential for optimal public health planning. PMID:11143192

  11. Development of a Publications and Conferences Data Base in the Mexican Electric Power Research Institute.

    ERIC Educational Resources Information Center

    Ripoll, C. Lopez Cerdan; And Others

    This paper describes the development by the Mexican Electric Power Research Institute (Instituto de Investigaciones Electricas or IIE) over a 10-year period of a publications and conferences database (PCDB) of research and development output of the institute. The paper begins by listing the objectives of the database and describing data coverage…

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

    ERIC Educational Resources Information Center

    Nemeth, Erik

    2010-01-01

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

  13. Toward a public analysis database for LHC new physics searches using M ADA NALYSIS 5

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  14. Horse Racing at the Library: How One Library System Increased the Usage of Some of Its Online Databases

    ERIC Educational Resources Information Center

    Kurhan, Scott H.; Griffing, Elizabeth A.

    2011-01-01

    Reference services in public libraries are changing dramatically. The Internet, online databases, and shrinking budgets are all making it necessary for non-traditional reference staff to become familiar with online reference tools. Recognizing the need for cross-training, Chesapeake Public Library (CPL) developed a program called the Database…

  15. Publications - MP 141 | Alaska Division of Geological & Geophysical Surveys

    Science.gov Websites

    DGGS MP 141 Publication Details Title: Quaternary faults and folds in Alaska: A digital database Combellick, R.A., 2012, Quaternary faults and folds in Alaska: A digital database, in Koehler, R.D Quaternary faults, scale 1:3,700,000 (63.0 M) Digital Geospatial Data Digital Geospatial Data Quaternary

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

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

    The T-matrix method is one of the most versatile, efficient, and accurate theoretical techniques widely used for numerically exact computer calculations of electromagnetic scattering by single and composite particles, discrete random media, and particles imbedded in complex environments. This paper presents the fifth update to the comprehensive database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2012. It also lists several earlier publications not incorporated in the original database, including Peter Waterman's reports from the 1960s illustrating the history of the T-matrix approach and demonstrating that John Fikioris and Peter Waterman were the true pioneers of the multi-sphere method otherwise known as the generalized Lorenz - Mie theory.

  17. Going public: accessing urban data and producing population estimates using the urban FIA database

    Treesearch

    Chris Edgar; Mark Hatfield

    2015-01-01

    In this presentation we describe the urban forest inventory database (U-FIADB) and demonstrate how to use the database to produce population estimates. Examples from the recently completed City of Austin inventory will be used to demonstrate the capabilities of the database. We will identify several features of U-FIADB that are different from the FIA database (FIADB)...

  18. 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.

  19. Drinking Water Treatability Database (Database)

    EPA Science Inventory

    The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

  20. 16 CFR 1102.6 - Definitions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Background and Definitions § 1102.6 Definitions. (a... Database. (2) Commission or CPSC means the Consumer Product Safety Commission. (3) Consumer product means a... private labeler. (7) Publicly Available Consumer Product Safety Information Database, also referred to as...

  1. 16 CFR 1102.6 - Definitions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Background and Definitions § 1102.6 Definitions. (a... Database. (2) Commission or CPSC means the Consumer Product Safety Commission. (3) Consumer product means a... private labeler. (7) Publicly Available Consumer Product Safety Information Database, also referred to as...

  2. Physiological Parameters Database for PBPK Modeling (External Review Draft)

    EPA Science Inventory

    EPA released for public comment a physiological parameters database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence. It also contains similar data for an...

  3. Information technologies in public health management: a database on biocides to improve quality of life.

    PubMed

    Roman, C; Scripcariu, L; Diaconescu, Rm; Grigoriu, A

    2012-01-01

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

  4. Patenting of university and non-university public research organisations in Germany: evidence from patent applications for medical research results.

    PubMed

    Tinnemann, Peter; Ozbay, Jonas; Saint, Victoria A; Willich, Stefan N

    2010-11-18

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

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

    PubMed Central

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

    2010-01-01

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

  6. The MAR databases: development and implementation of databases specific for marine metagenomics

    PubMed Central

    Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen

    2018-01-01

    Abstract We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. PMID:29106641

  7. Tree chemistry database (version 1.0)

    Treesearch

    Linda H. Pardo; Molly Robin-Abbott; Natasha Duarte; Eric K. Miller

    2005-01-01

    The Tree Chemistry Database is a relational database of C, N, P, K, Ca, Mg, Mn, and Al concentrations in bole bark, bole wood, branches, twigs, and foliage. Compiled from data in 218 articles and publications, the database contains reported nutrient and biomass values for tree species in the Northeastern United States. Nutrient data can be sorted on parameters such as...

  8. The radiopurity.org material database

    NASA Astrophysics Data System (ADS)

    Cooley, J.; Loach, J. C.; Poon, A. W. P.

    2018-01-01

    The database at http://www.radiopurity.org is the world's largest public database of material radio-purity mea-surements. These measurements are used by members of the low-background physics community to build experiments that search for neutrinos, neutrinoless double-beta decay, WIMP dark matter, and other exciting physics. This paper summarizes the current status and the future plan of this database.

  9. Northern Forest Futures reporting tools and database guide

    Treesearch

    Patrick D. Miles; Robert J. Huggett; W. Keith Moser

    2015-01-01

    The Northern Forest Futures database (NFFDB) supports the reporting of both current and projected future forest conditions for the 20 states that make up the U.S. North, an area bounded by Maine, Maryland, Missouri, and Minnesota. The NFFDB database and attendant reporting tools are available to the public as a Microsoft AccessTM database. The...

  10. An analysis of current pharmaceutical industry practices for making clinical trial results publicly accessible.

    PubMed

    Viereck, Christopher; Boudes, Pol

    2009-07-01

    We compared the clinical trial transparency practices of US/European pharma by analyzing the publicly-accessible clinical trial results databases of major drugs (doripenem, varenicline, lapatinib, zoledronic acid, adalimumab, insulin glargine, raltegravir, gefitinib). We evaluated their accessibility and utility from the perspective of the lay public. We included databases on company websites, http://www.clinicalstudyresults.org, http://www.clinicaltrials.gov and http://clinicaltrials.ifpma.org. Only 2 of 8 company homepages provide a direct link to the results. While the use of common terms on company search engines led to results for 5 of the 8 drugs following 2-4 clicks, no logical pathway was identified. The number of clinical trials in the databases was inconsistent: 0 for doripenem to 45 for insulin glargine. Results from all phases of clinical development were provided for 2 (insulin glargine and gefitinib) of the 8 drugs. Analyses of phase III reports revealed that most critical elements of the International Conference of Harmonization E3 Structure and Content of Synopses for Clinical Trial Reports were provided for 2 (varenicline, lapatinib) of the 8 drugs. For adalimumab and zoledronic acid, only citations were provided, which the lay public would be unable to access. None of the clinical trial reports was written in lay language. User-friendly support, when provided, was of marginal benefit. Only 1 of the databases (gefitinib) permitted the user to find the most recently updated reports. None of the glossaries included explanations for adverse events or statistical methodology. In conclusion, our study indicates that the public faces significant hurdles in finding and understanding clinical trial results databases.

  11. The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index.

    PubMed

    Larsen, Peder Olesen; von Ins, Markus

    2010-09-01

    The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source.

  12. The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index

    PubMed Central

    von Ins, Markus

    2010-01-01

    The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source. PMID:20700371

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

    USDA-ARS?s Scientific Manuscript database

    The Dietary Supplement Ingredient Database (DSID) is a federally-funded, publically-accessible dietary supplement database that currently contains analytically derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in di...

  14. 24 CFR 902.24 - Database adjustment.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false Database adjustment. 902.24 Section 902.24 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN DEVELOPMENT (CONTINUED... PUBLIC HOUSING ASSESSMENT SYSTEM Physical Condition Indicator § 902.24 Database adjustment. (a...

  15. 24 CFR 902.24 - Database adjustment.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false Database adjustment. 902.24 Section 902.24 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN DEVELOPMENT (CONTINUED... PUBLIC HOUSING ASSESSMENT SYSTEM Physical Condition Indicator § 902.24 Database adjustment. (a...

  16. 24 CFR 902.24 - Database adjustment.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Database adjustment. 902.24 Section 902.24 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN DEVELOPMENT (CONTINUED... PUBLIC HOUSING ASSESSMENT SYSTEM Physical Condition Indicator § 902.24 Database adjustment. (a...

  17. 16 CFR § 1102.6 - Definitions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Background and Definitions § 1102.6 Definitions. (a... Database. (2) Commission or CPSC means the Consumer Product Safety Commission. (3) Consumer product means a... private labeler. (7) Publicly Available Consumer Product Safety Information Database, also referred to as...

  18. 24 CFR 902.24 - Database adjustment.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false Database adjustment. 902.24 Section 902.24 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN DEVELOPMENT (CONTINUED... PUBLIC HOUSING ASSESSMENT SYSTEM Physical Condition Indicator § 902.24 Database adjustment. (a...

  19. NBIC: National Ballast Information Clearinghouse

    Science.gov Websites

    Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database | NBIC Research & Development | NBIC News | Home Cite NBIC Database as: National Ballast Information Clearinghouse 2016. NBIC Online Database. Electronic publication, Smithsonian Environmental Research Center &

  20. Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

    PubMed

    Richard, Ann M; Williams, ClarLynda R

    2002-01-29

    The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.

  1. Software Classifications: Trends in Literacy Software Publication and Marketing.

    ERIC Educational Resources Information Center

    Balajthy, Ernest

    First in a continuing series of reports on trends in marketing and publication of software for literacy education, a study explored the development of a database to track the trends and reported on trends seen in 1995. The final version of the 1995 database consisted of 1011 software titles, 165 of which had been published in 1995 and 846…

  2. Mass-Spectrometry Based Structure Identification of "Known-Unknowns" Using the EPA's CompTox Dashboard (ACS Spring National Meeting) 4 of 7

    EPA Science Inventory

    The CompTox Dashboard is a publicly accessible database provided by the National Center for Computational Toxicology at the US-EPA. The dashboard provides access to a database containing ~720,000 chemicals and integrates a number of our public-facing projects (e.g. ToxCast and Ex...

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

    Cancer.gov

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

  4. The igmspec database of public spectra probing the intergalactic medium

    NASA Astrophysics Data System (ADS)

    Prochaska, J. X.

    2017-04-01

    We describe v02 of igmspec, a database of publicly available ultraviolet, optical, and near-infrared spectra that probe the intergalactic medium (IGM). This database, a child of the specdb repository in the specdb github organization, comprises 403 277 unique sources and 434 686 spectra obtained with the world's greatest observatories. All of these data are distributed in a single ≈ 25GB HDF5 file maintained at the University of California Observatories and the University of California, Santa Cruz. The specdb software package includes Python scripts and modules for searching the source catalog and spectral datasets, and software links to the linetools package for spectral analysis. The repository also includes software to generate private spectral datasets that are compliant with International Virtual Observatory Alliance (IVOA) protocols and a Python-based interface for IVOA Simple Spectral Access queries. Future versions of igmspec will ingest other sources (e.g. gamma-ray burst afterglows) and other surveys as they become publicly available. The overall goal is to include every spectrum that effectively probes the IGM. Future databases of specdb may include publicly available galaxy spectra (exgalspec) and published supernovae spectra (snspec). The community is encouraged to join the effort on github: https://github.com/specdb.

  5. Vehicle Thermal Management Publications | Transportation Research | NREL

    Science.gov Websites

    Publications Vehicle Thermal Management Publications Explore NREL's recent publications about light - and heavy-duty vehicle thermal management. For the complete collection of NREL's vehicle thermal management publications, search the NREL Publications Database. All Light-Duty Electric-Drive Light-Duty

  6. NREL: Renewable Resource Data Center - Geothermal Resource Publications

    Science.gov Websites

    Publications For a list of Geothermal publications, go to Geothermal Technologies Publication page . For a list of legacy Geothermal publications, check out Geothermal Technologies Legacy Collection . NREL Publications Database For a comprehensive list of other NREL geothermal resource publications

  7. Using the Proteomics Identifications Database (PRIDE).

    PubMed

    Martens, Lennart; Jones, Phil; Côté, Richard

    2008-03-01

    The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer-reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE.

  8. Efficient bibliographic searches on allergy using ISI databases.

    PubMed

    Sáez Gómez, J M; Annan, J W; Negro Alvarez, J M; Guillen-Grima, F; Bozzola, C M; Ivancevich, J C; Aguinaga Ontoso, E

    2008-01-01

    The aim of this article is to provide an introduction to using databases from the Thomson ISI Web of Knowledge, with special reference to Citation Indexes as an analysis tool for publications, and also to explain the meaning of the well-known Impact Factor. We present the partially modified new Consultation Interface to enhance information search routines of these databases. It introduces distinctive methods in search bibliography, including the correct application of analysis tools, paying particular attention to Journal Citation Reports and Impact Factor. We finish this article with comment on the consequences of using the Impact Factor as a quality indicator for the assessment of journals and publications, and how to ensure measures for indexing in the Thomson ISI Databases.

  9. Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G

    PubMed Central

    2011-01-01

    Background Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea. Results We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A. Conclusions The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated. PMID:21569248

  10. Improving the annotation of the Heterorhabditis bacteriophora genome.

    PubMed

    McLean, Florence; Berger, Duncan; Laetsch, Dominik R; Schwartz, Hillel T; Blaxter, Mark

    2018-04-01

    Genome assembly and annotation remain exacting tasks. As the tools available for these tasks improve, it is useful to return to data produced with earlier techniques to assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes. We revisited the H. bacteriophora genome assembly and gene predictions to determine whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant. Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species' genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published genome assemblies.

  11. PROGRESS REPORT ON THE DSSTOX DATABASE NETWORK: NEWLY LAUNCHED WEBSITE, APPLICATIONS, FUTURE PLANS

    EPA Science Inventory

    Progress Report on the DSSTox Database Network: Newly Launched Website, Applications, Future Plans

    Progress will be reported on development of the Distributed Structure-Searchable Toxicity (DSSTox) Database Network and the newly launched public website that coordinates and...

  12. DEVELOPMENT AND APPLICATION OF THE DORIAN (DOSE-RESPONSE INFORMATION ANALYSIS) SYSTEM

    EPA Science Inventory

    • Migration of ArrayTrack from the proprietary Oracle database to open source Postgres database.
    • Making the public version of the ebKB available with provisions for soliciting input from collaborators and outside users.
    • Continued development ...

    • Data tables for the 1993 National Transit Database section 15 report year

      DOT National Transportation Integrated Search

      1994-12-01

      The Data Tables For the 1993 National Transit Database Section 15 Report Year is one of three publications comprising the 1993 Annual Report. Also referred to as the National Transit Database Reporting System, it is administered by the Federal Transi...

    • Data base management system for lymphatic filariasis--a neglected tropical disease.

      PubMed

      Upadhyayula, Suryanaryana Murty; Mutheneni, Srinivasa Rao; Kadiri, Madhusudhan Rao; Kumaraswamy, Sriram; Nelaturu, Sarat Chandra Babu

      2012-01-01

      Researchers working in the area of Public Health are being confronted with large volumes of data on various aspects of entomology and epidemiology. To obtain the relevant information out of these data requires particular database management system. In this paper, we have described about the usages of our developed database on lymphatic filariasis. This database application is developed using Model View Controller (MVC) architecture, with MySQL as database and a web based interface. We have collected and incorporated the data on filariasis in the database from Karimnagar, Chittoor, East and West Godavari districts of Andhra Pradesh, India. The importance of this database is to store the collected data, retrieve the information and produce various combinational reports on filarial aspects which in turn will help the public health officials to understand the burden of disease in a particular locality. This information is likely to have an imperative role on decision making for effective control of filarial disease and integrated vector management operations.

    • The Génolevures database.

      PubMed

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

      2011-01-01

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

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

      PubMed

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

      2014-03-01

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

    • Accessing the public MIMIC-II intensive care relational database for clinical research.

      PubMed

      Scott, Daniel J; Lee, Joon; Silva, Ikaro; Park, Shinhyuk; Moody, George B; Celi, Leo A; Mark, Roger G

      2013-01-10

      The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge "Predicting mortality of ICU Patients". QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database.

    • The LISS--a public database of common imaging signs of lung diseases for computer-aided detection and diagnosis research and medical education.

      PubMed

      Han, Guanghui; Liu, Xiabi; Han, Feifei; Santika, I Nyoman Tenaya; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

      2015-02-01

      Lung computed tomography (CT) imaging signs play important roles in the diagnosis of lung diseases. In this paper, we review the significance of CT imaging signs in disease diagnosis and determine the inclusion criterion of CT scans and CT imaging signs of our database. We develop the software of abnormal regions annotation and design the storage scheme of CT images and annotation data. Then, we present a publicly available database of lung CT imaging signs, called LISS for short, which contains 271 CT scans and 677 abnormal regions in them. The 677 abnormal regions are divided into nine categories of common CT imaging signs of lung disease (CISLs). The ground truth of these CISLs regions and the corresponding categories are provided. Furthermore, to make the database publicly available, all private data in CT scans are eliminated or replaced with provisioned values. The main characteristic of our LISS database is that it is developed from a new perspective of CT imaging signs of lung diseases instead of commonly considered lung nodules. Thus, it is promising to apply to computer-aided detection and diagnosis research and medical education.

    • Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

      PubMed

      Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

      2018-04-06

      Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

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

      PubMed

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

      2013-02-01

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

  1. 45 CFR 1356.80 - Scope of the National Youth in Transition Database.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Scope of the National Youth in Transition Database... REQUIREMENTS APPLICABLE TO TITLE IV-E § 1356.80 Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through 1356.86 of this part apply...

  2. 45 CFR 1356.80 - Scope of the National Youth in Transition Database.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Scope of the National Youth in Transition Database... REQUIREMENTS APPLICABLE TO TITLE IV-E § 1356.80 Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through 1356.86 of this part apply...

  3. 45 CFR 1356.80 - Scope of the National Youth in Transition Database.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Scope of the National Youth in Transition Database... REQUIREMENTS APPLICABLE TO TITLE IV-E § 1356.80 Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through 1356.86 of this part apply...

  4. 45 CFR 1356.80 - Scope of the National Youth in Transition Database.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Scope of the National Youth in Transition Database... REQUIREMENTS APPLICABLE TO TITLE IV-E § 1356.80 Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through 1356.86 of this part apply...

  5. 45 CFR 1356.80 - Scope of the National Youth in Transition Database.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Scope of the National Youth in Transition Database... REQUIREMENTS APPLICABLE TO TITLE IV-E § 1356.80 Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through 1356.86 of this part apply...

  6. How can the research potential of the clinical quality databases be maximized? The Danish experience.

    PubMed

    Nørgaard, M; Johnsen, S P

    2016-02-01

    In Denmark, the need for monitoring of clinical quality and patient safety with feedback to the clinical, administrative and political systems has resulted in the establishment of a network of more than 60 publicly financed nationwide clinical quality databases. Although primarily devoted to monitoring and improving quality of care, the potential of these databases as data sources in clinical research is increasingly being recognized. In this review, we describe these databases focusing on their use as data sources for clinical research, including their strengths and weaknesses as well as future concerns and opportunities. The research potential of the clinical quality databases is substantial but has so far only been explored to a limited extent. Efforts related to technical, legal and financial challenges are needed in order to take full advantage of this potential. © 2016 The Association for the Publication of the Journal of Internal Medicine.

  7. Aviation Safety Issues Database

    NASA Technical Reports Server (NTRS)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

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

    PubMed

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

    2017-01-13

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

  9. The Vocational Guidance Research Database: A Scientometric Approach

    ERIC Educational Resources Information Center

    Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

    2012-01-01

    The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the…

  10. Library Instruction and Online Database Searching.

    ERIC Educational Resources Information Center

    Mercado, Heidi

    1999-01-01

    Reviews changes in online database searching in academic libraries. Topics include librarians conducting all searches; the advent of end-user searching and the need for user instruction; compact disk technology; online public catalogs; the Internet; full text databases; electronic information literacy; user education and the remote library user;…

  11. Berkeley Lab - Materials Sciences Division

    Science.gov Websites

    Postdoc Forum Research Highlights Awards Publications Database Events Calendar Newsletter Archive People Database Events Calendar Newsletter Archive Send us your research highlights. Reserch Highlight Template

  12. Progress in development of an integrated dietary supplement ingredient database at the NIH Office of Dietary Supplements

    PubMed Central

    Dwyer, Johanna T.; Picciano, Mary Frances; Betz, Joseph M.; Fisher, Kenneth D.; Saldanha, Leila G.; Yetley, Elizabeth A.; Coates, Paul M.; Radimer, Kathy; Bindewald, Bernadette; Sharpless, Katherine E.; Holden, Joanne; Andrews, Karen; Zhao, Cuiwei; Harnly, James; Wolf, Wayne R.; Perry, Charles R.

    2013-01-01

    Several activities of the Office of Dietary Supplements (ODS) at the National Institutes of Health involve enhancement of dietary supplement databases. These include an initiative with US Department of Agriculture to develop an analytically substantiated dietary supplement ingredient database (DSID) and collaboration with the National Center for Health Statistics to enhance the dietary supplement label database in the National Health and Nutrition Examination Survey (NHANES). The many challenges that must be dealt with in developing an analytically supported DSID include categorizing product types in the database, identifying nutrients, and other components of public health interest in these products and prioritizing which will be entered in the database first. Additional tasks include developing methods and reference materials for quantifying the constituents, finding qualified laboratories to measure the constituents, developing appropriate sample handling procedures, and finally developing representative sampling plans. Developing the NHANES dietary supplement label database has other challenges such as collecting information on dietary supplement use from NHANES respondents, constant updating and refining of information obtained, developing default values that can be used if the respondent cannot supply the exact supplement or strength that was consumed, and developing a publicly available label database. Federal partners and the research community are assisting in making an analytically supported dietary supplement database a reality. PMID:25309034

  13. Curation accuracy of model organism databases

    PubMed Central

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

    2014-01-01

    Manual extraction of information from the biomedical literature—or biocuration—is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org// PMID:24923819

  14. The MAR databases: development and implementation of databases specific for marine metagenomics.

    PubMed

    Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

    2018-01-04

    We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. EVpedia: a community web portal for extracellular vesicles research.

    PubMed

    Kim, Dae-Kyum; Lee, Jaewook; Kim, Sae Rom; Choi, Dong-Sic; Yoon, Yae Jin; Kim, Ji Hyun; Go, Gyeongyun; Nhung, Dinh; Hong, Kahye; Jang, Su Chul; Kim, Si-Hyun; Park, Kyong-Su; Kim, Oh Youn; Park, Hyun Taek; Seo, Ji Hye; Aikawa, Elena; Baj-Krzyworzeka, Monika; van Balkom, Bas W M; Belting, Mattias; Blanc, Lionel; Bond, Vincent; Bongiovanni, Antonella; Borràs, Francesc E; Buée, Luc; Buzás, Edit I; Cheng, Lesley; Clayton, Aled; Cocucci, Emanuele; Dela Cruz, Charles S; Desiderio, Dominic M; Di Vizio, Dolores; Ekström, Karin; Falcon-Perez, Juan M; Gardiner, Chris; Giebel, Bernd; Greening, David W; Gross, Julia Christina; Gupta, Dwijendra; Hendrix, An; Hill, Andrew F; Hill, Michelle M; Nolte-'t Hoen, Esther; Hwang, Do Won; Inal, Jameel; Jagannadham, Medicharla V; Jayachandran, Muthuvel; Jee, Young-Koo; Jørgensen, Malene; Kim, Kwang Pyo; Kim, Yoon-Keun; Kislinger, Thomas; Lässer, Cecilia; Lee, Dong Soo; Lee, Hakmo; van Leeuwen, Johannes; Lener, Thomas; Liu, Ming-Lin; Lötvall, Jan; Marcilla, Antonio; Mathivanan, Suresh; Möller, Andreas; Morhayim, Jess; Mullier, François; Nazarenko, Irina; Nieuwland, Rienk; Nunes, Diana N; Pang, Ken; Park, Jaesung; Patel, Tushar; Pocsfalvi, Gabriella; Del Portillo, Hernando; Putz, Ulrich; Ramirez, Marcel I; Rodrigues, Marcio L; Roh, Tae-Young; Royo, Felix; Sahoo, Susmita; Schiffelers, Raymond; Sharma, Shivani; Siljander, Pia; Simpson, Richard J; Soekmadji, Carolina; Stahl, Philip; Stensballe, Allan; Stępień, Ewa; Tahara, Hidetoshi; Trummer, Arne; Valadi, Hadi; Vella, Laura J; Wai, Sun Nyunt; Witwer, Kenneth; Yáñez-Mó, María; Youn, Hyewon; Zeidler, Reinhard; Gho, Yong Song

    2015-03-15

    Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

    EPA Pesticide Factsheets

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

  17. Geographical and temporal distribution of basic research experiments in homeopathy.

    PubMed

    Clausen, Jürgen; van Wijk, Roeland; Albrecht, Henning

    2014-07-01

    The database HomBRex (Homeopathy Basic Research experiments) was established in 2002 to provide an overview of the basic research already done on homeopathy (http://www.carstens-stiftung.de/hombrex). By this means, it facilitates the exploration of the Similia Principle and the working mechanism of homeopathy. Since 2002, the total number of experiments listed has almost doubled. The current review reports the history of basic research in homeopathy as evidenced by publication dates and origin of publications. In July 2013, the database held 1868 entries. Most publications were reported from France (n = 267), followed by Germany (n = 246) and India (n = 237). In the last ten years, the number of publications from Brazil dramatically increased from n = 13 (before 2004) to n = 164 (compared to n = 251 published in France before 2004, and n = 16 between 2004 and 2013). The oldest database entry was from Germany (1832). Copyright © 2014 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

  18. Publications - AR 2015 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic publication sales page for more information. Quadrangle(s): Alaska General Bibliographic Reference DGGS Staff

  19. Publications - GMC 280 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic please see our publication sales page for more information. Bibliographic Reference Piggott, Neil, and

  20. Usefulness of Canadian Public Health Insurance Administrative Databases to Assess Breast and Ovarian Cancer Screening Imaging Technologies for BRCA1/2 Mutation Carriers.

    PubMed

    Larouche, Geneviève; Chiquette, Jocelyne; Plante, Marie; Pelletier, Sylvie; Simard, Jacques; Dorval, Michel

    2016-11-01

    In Canada, recommendations for clinical management of hereditary breast and ovarian cancer among individuals carrying a deleterious BRCA1 or BRCA2 mutation have been available since 2007. Eight years later, very little is known about the uptake of screening and risk-reduction measures in this population. Because Canada's public health care system falls under provincial jurisdictions, using provincial health care administrative databases appears a valuable option to assess management of BRCA1/2 mutation carriers. The objective was to explore the usefulness of public health insurance administrative databases in British Columbia, Ontario, and Quebec to assess management after BRCA1/2 genetic testing. Official public health insurance documents were considered potentially useful if they had specific procedure codes, and pertained to procedures performed in the public and private health care systems. All 3 administrative databases have specific procedures codes for mammography and breast ultrasounds. Only Quebec and Ontario have a specific procedure code for breast magnetic resonance imaging. It is impossible to assess, on an individual basis, the frequency of others screening exams, with the exception of CA-125 testing in British Columbia. Screenings done in private practice are excluded from the administrative databases unless covered by special agreements for reimbursement, such as all breast imaging exams in Ontario and mammograms in British Columbia and Quebec. There are no specific procedure codes for risk-reduction surgeries for breast and ovarian cancer. Population-based assessment of breast and ovarian cancer risk management strategies other than mammographic screening, using only administrative data, is currently challenging in the 3 Canadian provinces studied. Copyright © 2016 Canadian Association of Radiologists. Published by Elsevier Inc. All rights reserved.

  1. Citations and the h index of soil researchers and journals in the Web of Science, Scopus, and Google Scholar

    PubMed Central

    Hartemink, Alfred E.; McBratney, Alex; Jang, Ho-Jun

    2013-01-01

    Citation metrics and h indices differ using different bibliometric databases. We compiled the number of publications, number of citations, h index and year since the first publication from 340 soil researchers from all over the world. On average, Google Scholar has the highest h index, number of publications and citations per researcher, and the Web of Science the lowest. The number of papers in Google Scholar is on average 2.3 times higher and the number of citations is 1.9 times higher compared to the data in the Web of Science. Scopus metrics are slightly higher than that of the Web of Science. The h index in Google Scholar is on average 1.4 times larger than Web of Science, and the h index in Scopus is on average 1.1 times larger than Web of Science. Over time, the metrics increase in all three databases but fastest in Google Scholar. The h index of an individual soil scientist is about 0.7 times the number of years since his/her first publication. There is a large difference between the number of citations, number of publications and the h index using the three databases. From this analysis it can be concluded that the choice of the database affects widely-used citation and evaluation metrics but that bibliometric transfer functions exist to relate the metrics from these three databases. We also investigated the relationship between journal’s impact factor and Google Scholar’s h5-index. The h5-index is a better measure of a journal’s citation than the 2 or 5 year window impact factor. PMID:24167778

  2. Citations and the h index of soil researchers and journals in the Web of Science, Scopus, and Google Scholar.

    PubMed

    Minasny, Budiman; Hartemink, Alfred E; McBratney, Alex; Jang, Ho-Jun

    2013-01-01

    Citation metrics and h indices differ using different bibliometric databases. We compiled the number of publications, number of citations, h index and year since the first publication from 340 soil researchers from all over the world. On average, Google Scholar has the highest h index, number of publications and citations per researcher, and the Web of Science the lowest. The number of papers in Google Scholar is on average 2.3 times higher and the number of citations is 1.9 times higher compared to the data in the Web of Science. Scopus metrics are slightly higher than that of the Web of Science. The h index in Google Scholar is on average 1.4 times larger than Web of Science, and the h index in Scopus is on average 1.1 times larger than Web of Science. Over time, the metrics increase in all three databases but fastest in Google Scholar. The h index of an individual soil scientist is about 0.7 times the number of years since his/her first publication. There is a large difference between the number of citations, number of publications and the h index using the three databases. From this analysis it can be concluded that the choice of the database affects widely-used citation and evaluation metrics but that bibliometric transfer functions exist to relate the metrics from these three databases. We also investigated the relationship between journal's impact factor and Google Scholar's h5-index. The h5-index is a better measure of a journal's citation than the 2 or 5 year window impact factor.

  3. Sequencing artifacts in the type A influenza databases and attempts to correct them.

    PubMed

    Suarez, David L; Chester, Nikki; Hatfield, Jason

    2014-07-01

    There are over 276 000 influenza gene sequences in public databases, with the quality of the sequences determined by the contributor. As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate. Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on sequences with additional nucleotides upstream or downstream of the highly conserved non-coding ends of the viral segments. A total of 1081 sequences were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer sequence wasn't removed from the sequence; PCR product was cloned and plasmid sequence was included in the sequence; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide sequence were also commonly observed, but in many cases it was unclear if the sequence was correct or actually contained an error. A total of 215 sequences, or 22.8% of the suspect sequences, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional sequences with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of sequences submitted to public databases is needed to fully reap the benefits of these large data sets. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

  4. Development and application of a database of food ingredient fraud and economically motivated adulteration from 1980 to 2010.

    PubMed

    Moore, Jeffrey C; Spink, John; Lipp, Markus

    2012-04-01

    Food ingredient fraud and economically motivated adulteration are emerging risks, but a comprehensive compilation of information about known problematic ingredients and detection methods does not currently exist. The objectives of this research were to collect such information from publicly available articles in scholarly journals and general media, organize into a database, and review and analyze the data to identify trends. The results summarized are a database that will be published in the US Pharmacopeial Convention's Food Chemicals Codex, 8th edition, and includes 1305 records, including 1000 records with analytical methods collected from 677 references. Olive oil, milk, honey, and saffron were the most common targets for adulteration reported in scholarly journals, and potentially harmful issues identified include spices diluted with lead chromate and lead tetraoxide, substitution of Chinese star anise with toxic Japanese star anise, and melamine adulteration of high protein content foods. High-performance liquid chromatography and infrared spectroscopy were the most common analytical detection procedures, and chemometrics data analysis was used in a large number of reports. Future expansion of this database will include additional publically available articles published before 1980 and in other languages, as well as data outside the public domain. The authors recommend in-depth analyses of individual incidents. This report describes the development and application of a database of food ingredient fraud issues from publicly available references. The database provides baseline information and data useful to governments, agencies, and individual companies assessing the risks of specific products produced in specific regions as well as products distributed and sold in other regions. In addition, the report describes current analytical technologies for detecting food fraud and identifies trends and developments. © 2012 US Pharmacupia Journal of Food Science © 2012 Institute of Food Technologistsreg;

  5. CottonGen: a genomics, genetics and breeding database for cotton research

    USDA-ARS?s Scientific Manuscript database

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

  6. Market Pressure and Government Intervention in the Administration and Development of Molecular Databases.

    ERIC Educational Resources Information Center

    Sillince, J. A. A.; Sillince, M.

    1993-01-01

    Discusses molecular databases and the role that government and private companies play in their administration and development. Highlights include copyright and patent issues relating to public databases and the information contained in them; data quality; data structures and technological questions; the international organization of molecular…

  7. Sequencing artifacts in the type A influenza database and attempts to correct them

    USDA-ARS?s Scientific Manuscript database

    Currently over 300,000 Type A influenza gene sequences representing over 50,000 strains are available in publicly available databases. However, the quality of the sequences submitted are determined by the contributor and many sequence errors are present in the databases, which can affect the result...

  8. Characteristics of Resources Represented in the OCLC CORC Database.

    ERIC Educational Resources Information Center

    Connell, Tschera Harkness; Prabha, Chandra

    2002-01-01

    Examines the characteristics of Web resources in Online Computer Library Center's (OCLC) Cooperative Online Resource Catalog (CORC) in terms of subject matter, source of content, publication patterns, and units of information chosen for representation in the database. Suggests that the ability to successfully use a database depends on…

  9. NREL Opens Large Database of Inorganic Thin-Film Materials | News | NREL

    Science.gov Websites

    Inorganic Thin-Film Materials April 3, 2018 An extensive experimental database of inorganic thin-film Energy Laboratory (NREL) is now publicly available. The High Throughput Experimental Materials (HTEM Schroeder / NREL) "All existing experimental databases either contain many entries or have all this

  10. 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...

  11. 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...

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

    USDA-ARS?s Scientific Manuscript database

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

  13. 14 CFR 221.180 - Requirements for electronic filing of tariffs.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... of Transportation, for the maintenance and security of the on-line tariff database. (b) No carrier or... to its on-line tariff database. The filer shall be responsible for the transportation, installation... installation or maintenance. (3) The filer shall provide public access to its on-line tariff database, at...

  14. 14 CFR 221.180 - Requirements for electronic filing of tariffs.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... of Transportation, for the maintenance and security of the on-line tariff database. (b) No carrier or... to its on-line tariff database. The filer shall be responsible for the transportation, installation... installation or maintenance. (3) The filer shall provide public access to its on-line tariff database, at...

  15. 77 FR 21618 - 60-Day Notice of Proposed Information Collection: Civilian Response Corps Database In-Processing...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-10

    ... DEPARTMENT OF STATE [Public Notice 7843] 60-Day Notice of Proposed Information Collection: Civilian Response Corps Database In-Processing Electronic Form, OMB Control Number 1405-0168, Form DS-4096... Collection: Civilian Response Corps Database In-Processing Electronic Form. OMB Control Number: 1405-0168...

  16. 14 CFR 221.180 - Requirements for electronic filing of tariffs.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... of Transportation, for the maintenance and security of the on-line tariff database. (b) No carrier or... to its on-line tariff database. The filer shall be responsible for the transportation, installation... installation or maintenance. (3) The filer shall provide public access to its on-line tariff database, at...

  17. 14 CFR 221.180 - Requirements for electronic filing of tariffs.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... of Transportation, for the maintenance and security of the on-line tariff database. (b) No carrier or... to its on-line tariff database. The filer shall be responsible for the transportation, installation... installation or maintenance. (3) The filer shall provide public access to its on-line tariff database, at...

  18. 14 CFR 221.180 - Requirements for electronic filing of tariffs.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... of Transportation, for the maintenance and security of the on-line tariff database. (b) No carrier or... to its on-line tariff database. The filer shall be responsible for the transportation, installation... installation or maintenance. (3) The filer shall provide public access to its on-line tariff database, at...

  19. 77 FR 47690 - 30-Day Notice of Proposed Information Collection: Civilian Response Corps Database In-Processing...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-09

    ... DEPARTMENT OF STATE [Public Notice 7976] 30-Day Notice of Proposed Information Collection: Civilian Response Corps Database In-Processing Electronic Form, OMB Control Number 1405-0168, Form DS-4096.... Title of Information Collection: Civilian Response Corps Database In-Processing Electronic Form. OMB...

  20. PrimateLit: About the Project

    Science.gov Websites

    Info Center WI Regional Primate Resource Center About the Project The PrimateLit database provides communities. Coverage of the database spans 1940 to present and includes all publication categories (articles will also be found in a search of the whole database. Books Received includes review copies of books

  1. Correlates of Access to Business Research Databases

    ERIC Educational Resources Information Center

    Gottfried, John C.

    2010-01-01

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

  2. Go Figure: Computer Database Adds the Personal Touch.

    ERIC Educational Resources Information Center

    Gaffney, Jean; Crawford, Pat

    1992-01-01

    A database for recordkeeping for a summer reading club was developed for a public library system using an IBM PC and Microsoft Works. Use of the database resulted in more efficient program management, giving librarians more time to spend with patrons and enabling timely awarding of incentives. (LAE)

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

    Riemer, R.L.

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

  4. Sports medicine clinical trial research publications in academic medical journals between 1996 and 2005: an audit of the PubMed MEDLINE database.

    PubMed

    Nichols, A W

    2008-11-01

    To identify sports medicine-related clinical trial research articles in the PubMed MEDLINE database published between 1996 and 2005 and conduct a review and analysis of topics of research, experimental designs, journals of publication and the internationality of authorships. Sports medicine research is international in scope with improving study methodology and an evolution of topics. Structured review of articles identified in a search of a large electronic medical database. PubMed MEDLINE database. Sports medicine-related clinical research trials published between 1996 and 2005. Review and analysis of articles that meet inclusion criteria. Articles were examined for study topics, research methods, experimental subject characteristics, journal of publication, lead authors and journal countries of origin and language of publication. The search retrieved 414 articles, of which 379 (345 English language and 34 non-English language) met the inclusion criteria. The number of publications increased steadily during the study period. Randomised clinical trials were the most common study type and the "diagnosis, management and treatment of sports-related injuries and conditions" was the most popular study topic. The knee, ankle/foot and shoulder were the most frequent anatomical sites of study. Soccer players and runners were the favourite study subjects. The American Journal of Sports Medicine had the highest number of publications and shared the greatest international diversity of authorships with the British Journal of Sports Medicine. The USA, Australia, Germany and the UK produced a good number of the lead authorships. In all, 91% of articles and 88% of journals were published in English. Sports medicine-related research is internationally diverse, clinical trial publications are increasing and the sophistication of research design may be improving.

  5. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Content Requirements... notices, the CPSC shall include in the Database any additional information it determines to be in the...

  6. [Relevance of the hemovigilance regional database for the shared medical file identity server].

    PubMed

    Doly, A; Fressy, P; Garraud, O

    2008-11-01

    The French Health Products Safety Agency coordinates the national initiative of computerization of blood products traceability within regional blood banks and public and private hospitals. The Auvergne-Loire Regional French Blood Service, based in Saint-Etienne, together with a number of public hospitals set up a transfusion data network named EDITAL. After four years of progressive implementation and experimentation, a software enabling standardized data exchange has built up a regional nominative database, endorsed by the Traceability Computerization National Committee in 2004. This database now provides secured web access to a regional transfusion history enabling biologists and all hospital and family practitioners to take in charge the patient follow-up. By running independently from the softwares of its partners, EDITAL database provides reference for the regional identity server.

  7. GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

    PubMed Central

    Samson, Delphine; Legeai, Fabrice; Karsenty, Emmanuelle; Reboux, Sébastien; Veyrieras, Jean-Baptiste; Just, Jeremy; Barillot, Emmanuel

    2003-01-01

    Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/. PMID:12519976

  8. Publications - AR 2008 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic ; Geophysical Surveys Ordering Info: Download below or please see our publication sales page for more

  9. Publications - AR 2007 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic ; Geophysical Surveys Ordering Info: Download below or please see our publication sales page for more

  10. Publications - AR 2001 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic ; Geophysical Surveys Ordering Info: Download below or please see our publication sales page for more

  11. Publications - GMC 379 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic Info: Download below or please see our publication sales page for more information. Quadrangle(s

  12. Publications - AR 2002 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic ; Geophysical Surveys Ordering Info: Download below or please see our publication sales page for more

  13. A public HTLV-1 molecular epidemiology database for sequence management and data mining.

    PubMed

    Araujo, Thessika Hialla Almeida; Souza-Brito, Leandro Inacio; Libin, Pieter; Deforche, Koen; Edwards, Dustin; de Albuquerque-Junior, Antonio Eduardo; Vandamme, Anne-Mieke; Galvao-Castro, Bernardo; Alcantara, Luiz Carlos Junior

    2012-01-01

    It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/. All data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient. The HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.

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

    PubMed Central

    Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

    2016-01-01

    Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

  15. Predicting Host Level Reachability via Static Analysis of Routing Protocol Configuration

    DTIC Science & Technology

    2007-09-01

    check_function_bodies = false; SET client_min_messages = warning; -- -- Name: SCHEMA public; Type: COMMENT; Schema: -; Owner: postgres -- COMMENT...public; Owner: mcmanst -- -- -- Name: public; Type: ACL; Schema: -; Owner: postgres -- REVOKE ALL ON SCHEMA public FROM PUBLIC; REVOKE...ALL ON SCHEMA public FROM postgres ; GRANT ALL ON SCHEMA public TO postgres ; GRANT ALL ON SCHEMA public TO PUBLIC; -- -- PostgreSQL database

  16. ACToR: Aggregated Computational Toxicology Resource (T) ...

    EPA Pesticide Factsheets

    The EPA Aggregated Computational Toxicology Resource (ACToR) is a set of databases compiling information on chemicals in the environment from a large number of public and in-house EPA sources. ACToR has 3 main goals: (1) The serve as a repository of public toxicology information on chemicals of interest to the EPA, and in particular to be a central source for the testing data on all chemicals regulated by all EPA programs; (2) To be a source of in vivo training data sets for building in vitro to in vivo computational models; (3) To serve as a central source of chemical structure and identity information for the ToxCastTM and Tox21 programs. There are 4 main databases, all linked through a common set of chemical information and a common structure linking chemicals to assay data: the public ACToR system (available at http://actor.epa.gov), the ToxMiner database holding ToxCast and Tox21 data, along with results form statistical analyses on these data; the Tox21 chemical repository which is managing the ordering and sample tracking process for the larger Tox21 project; and the public version of ToxRefDB. The public ACToR system contains information on ~500K compounds with toxicology, exposure and chemical property information from >400 public sources. The web site is visited by ~1,000 unique users per month and generates ~1,000 page requests per day on average. The databases are built on open source technology, which has allowed us to export them to a number of col

  17. Comparison of reporting phase I trial results in ClinicalTrials.gov and matched publications.

    PubMed

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

    2017-12-01

    Background Data on completeness of reporting of phase I cancer clinical trials in publications are lacking. Methods The ClinicalTrials.gov database was searched for completed adult phase I cancer trials with reported results. PubMed was searched for matching primary publications published prior to November 1, 2016. Reporting in primary publications was compared with the ClinicalTrials.gov database using a 28-point score (2=complete; 1=partial; 0=no reporting) for 14 items related to study design, outcome measures and safety profile. Inconsistencies between primary publications and ClinicalTrials.gov were recorded. Linear regression was used to identify factors associated with incomplete reporting. Results After a review of 583 trials in ClinicalTrials.gov , 163 matching primary publications were identified. Publications reported outcomes that did not appear in ClinicalTrials.gov in 25% of trials. Outcomes were upgraded, downgraded or omitted in publications in 47% of trials. The overall median reporting score was 23/28 (interquartile range 21-25). Incompletely reported items in >25% publications were: inclusion criteria (29%), primary outcome definition (26%), secondary outcome definitions (53%), adverse events (71%), serious adverse events (80%) and dates of study start and database lock (91%). Higher reporting scores were associated with phase I (vs phase I/II) trials (p<0.001), multicenter trials (p<0.001) and publication in journals with lower impact factor (p=0.004). Conclusions Reported results in primary publications for early phase cancer trials are frequently inconsistent or incomplete compared with ClinicalTrials.gov entries. ClinicalTrials.gov may provide more comprehensive data from new cancer drug trials.

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

    Cancer.gov

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

  19. Description of the MHS Health Level 7 Chemistry Laboratory for Public Health Surveillance

    DTIC Science & Technology

    2012-09-01

    document provides a history of the HL7 chemistry database and its contents, explains the creation of chemistry/serology records, describes the pathway...in health surveillance activities. This technical document discusses the chemistry database by providing a history of the dataset and its contents...source for its usefulness in public health surveillance. While HL7 data also includes radiology, anatomic pathology reports and pharmacy transactions

  20. GigaDB: announcing the GigaScience database.

    PubMed

    Sneddon, Tam P; Li, Peter; Edmunds, Scott C

    2012-07-12

    With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience's goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.

  1. Publications - GMC 322 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic Ordering Info: Download below or please see our publication sales page for more information. Quadrangle(s

  2. A Case Study: Testing in the Albuquerque Public Schools.

    ERIC Educational Resources Information Center

    Robinson, Carol

    1983-01-01

    This case study of testing in the Albuquerque public schools highlights improvement of test results dissemination and use through cooperative planning, integrated database development, and a partnership with public media. (Author)

  3. 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

  4. Analysis of Antisense Expression by Whole Genome Tiling Microarrays and siRNAs Suggests Mis-Annotation of Arabidopsis Orphan Protein-Coding Genes

    PubMed Central

    Richardson, Casey R.; Luo, Qing-Jun; Gontcharova, Viktoria; Jiang, Ying-Wen; Samanta, Manoj; Youn, Eunseog; Rock, Christopher D.

    2010-01-01

    Background MicroRNAs (miRNAs) and trans-acting small-interfering RNAs (tasi-RNAs) are small (20–22 nt long) RNAs (smRNAs) generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs) are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery. Principal Findings We explored rice (Oryza sativa) sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans) and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis ‘orphan’ hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM) was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the “ancient” (deeply conserved) class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for “new” rapidly-evolving MIRNA genes. Conclusions Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non-coding RNAs in plants and potentially other kingdoms, which can provide insight into antisense transcription, miRNA evolution, and post-transcriptional gene regulation. PMID:20520764

  5. Development of a Consumer Product Ingredient Database for ...

    EPA Pesticide Factsheets

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed Central

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

    2018-01-01

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

  9. Accessing the public MIMIC-II intensive care relational database for clinical research

    PubMed Central

    2013-01-01

    Background The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. Results QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge “Predicting mortality of ICU Patients”. Conclusions QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database. PMID:23302652

  10. Aptamer Database

    PubMed Central

    Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

    2004-01-01

    The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

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

    PubMed

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

    2011-01-01

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

  12. IEEE Conference Publications in Libraries.

    ERIC Educational Resources Information Center

    Johnson, Karl E.

    1984-01-01

    Conclusions of surveys (63 libraries, OCLC database, University of Rhode Island users) assessing handling of Institute of Electrical and Electronics Engineers (IEEE) conference publications indicate that most libraries fully catalog these publications using LC cataloging, and library patrons frequently require series access to publications. Eight…

  13. DEFINING THE CHEMICAL SPACE OF PUBLIC GENOMIC DATA (S)

    EPA Science Inventory

    The current project aims to chemically index the genomics content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. By defining the chemical space of public genomic data, it is possibl...

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

    ERIC Educational Resources Information Center

    Friedman, Debra; Hoffman, Phillip

    2001-01-01

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

  15. 76 FR 54807 - Notice of Proposed Information Collection: IMLS Museum Web Database: MuseumsCount.gov

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-02

    ...: IMLS Museum Web Database: MuseumsCount.gov AGENCY: Institute of Museum and Library Services, National..., and the general public. Information such as name, address, phone, e-mail, Web site, congressional...: IMLS Museum Web Database, MuseumsCount.gov . OMB Number: To be determined. Agency Number: 3137...

  16. Ionic Liquids Database- (ILThermo)

    National Institute of Standards and Technology Data Gateway

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

  17. The Forest Inventory and Analysis Database Version 4.0: Database Description and Users Manual for Phase 3

    Treesearch

    Christopher W. Woodall; Barbara L. Conkling; Michael C. Amacher; John W. Coulston; Sarah Jovan; Charles H. Perry; Beth Schulz; Gretchen C. Smith; Susan Will Wolf

    2010-01-01

    Describes the structure of the Forest Inventory and Analysis Database (FIADB) 4.0 for phase 3 indicators. The FIADB structure provides a consistent framework for storing forest health monitoring data across all ownerships for the entire United States. These data are available to the public.

  18. 47 CFR 101.1523 - Sharing and coordination among non-government licensees and between non-government and government...

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Wireless Telecommunications Bureau announces by public notice the implementation of a third-party database...) Provide an electronic copy of an interference analysis to the third-party database manager which...-party database managers shall receive and retain the interference analyses electronically and make them...

  19. 47 CFR 101.1523 - Sharing and coordination among non-government licensees and between non-government and government...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Wireless Telecommunications Bureau announces by public notice the implementation of a third-party database...) Provide an electronic copy of an interference analysis to the third-party database manager which...-party database managers shall receive and retain the interference analyses electronically and make them...

  20. 47 CFR 101.1523 - Sharing and coordination among non-government licensees and between non-government and government...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Wireless Telecommunications Bureau announces by public notice the implementation of a third-party database...) Provide an electronic copy of an interference analysis to the third-party database manager which...-party database managers shall receive and retain the interference analyses electronically and make them...

  1. 47 CFR 101.1523 - Sharing and coordination among non-government licensees and between non-government and government...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Wireless Telecommunications Bureau announces by public notice the implementation of a third-party database...) Provide an electronic copy of an interference analysis to the third-party database manager which...-party database managers shall receive and retain the interference analyses electronically and make them...

  2. 47 CFR 101.1523 - Sharing and coordination among non-government licensees and between non-government and government...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Wireless Telecommunications Bureau announces by public notice the implementation of a third-party database...) Provide an electronic copy of an interference analysis to the third-party database manager which...-party database managers shall receive and retain the interference analyses electronically and make them...

  3. CiteAb: a searchable antibody database that ranks antibodies by the number of times they have been cited

    PubMed Central

    2014-01-01

    Background Research antibodies are used by thousands of scientists working in diverse disciplines, but it is common to hear concerns about antibody quality. This means that researchers need to carefully choose the antibodies they use to avoid wasting time and money. A well accepted way of selecting a research antibody is to identify one which has been used previously, where the associated data has been peer-reviewed and the results published. Description CiteAb is a searchable database which ranks antibodies by the number of times they have been cited. This allows researchers to easily find antibodies that have been used in peer-reviewed publications and the accompanying citations are listed, so users can check the data contained within the publications. This makes CiteAb a useful resource for identifying antibodies for experiments and also for finding information to demonstrate antibody validation. The database currently contains 1,400,000 antibodies which are from 90 suppliers, including 87 commercial companies and 3 academic resources. Associated with these antibodies are 140,000 publications which provide 306,000 antibody citations. In addition to searching, users can also browse through the antibodies and add their own publications to the CiteAb database. Conclusions CiteAb provides a new way for researchers to find research antibodies that have been used successfully in peer-reviewed publications. It aims to assist these researchers and will hopefully help promote progress in many areas of life science research. PMID:24528853

  4. Publication trend, resource utilization, and impact of the US National Cancer Database: A systematic review.

    PubMed

    Su, Chang; Peng, Cuiying; Agbodza, Ena; Bai, Harrison X; Huang, Yuqian; Karakousis, Giorgos; Zhang, Paul J; Zhang, Zishu

    2018-03-01

    The utilization and impact of the studies published using the National Cancer Database (NCDB) is currently unclear. In this study, we aim to characterize the published studies, and identify relatively unexplored areas for future investigations. A literature search was performed using PubMed in January 2017 to identify all papers published using NCDB data. Characteristics of the publications were extracted. Citation frequencies were obtained through the Web of Science. Three hundred 2 articles written by 230 first authors met the inclusion criteria. The number of publications grew exponentially since 2013, with 108 articles published in 2016. Articles were published in 86 journals. The majority of the published papers focused on digestive system cancer, while bone and joints, eye and orbit, myeloma, mesothelioma, and Kaposi Sarcoma were never studied. Thirteen institutions in the United States were associated with more than 5 publications. The papers have been cited for a total of 9858 times since the publication of the first paper in 1992. Frequently appearing keywords congregated into 3 clusters: "demographics," "treatments and survival," and "statistical analysis method." Even though the main focuses of the articles captured a extremely wide range, they can be classified into 2 main categories: survival analysis and characterization. Other focuses include database(s) analysis and/or comparison, and hospital reporting. The surging interest in the use of NCDB is accompanied by unequal utilization of resources by individuals and institutions. Certain areas were relatively understudied and should be further explored.

  5. The annotation-enriched non-redundant patent sequence databases.

    PubMed

    Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

    2013-01-01

    The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/

  6. The Annotation-enriched non-redundant patent sequence databases

    PubMed Central

    Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

    2013-01-01

    The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/ PMID:23396323

  7. The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

    PubMed

    Nishio, Shin-Ya; Usami, Shin-Ichi

    2017-03-01

    Recent advances in next-generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease-specific databases. Here, we report a new database development tool, named the "Clinical NGS Database," for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two-feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity-based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database. © 2016 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

  8. Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds.

    PubMed

    Southan, Christopher; Várkonyi, Péter; Muresan, Sorel

    2009-07-06

    Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding. This work updates a previous comparative study of databases chosen because of their bioactive content, availability of downloads and facility to select informative subsets. Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate standardised comparisons typically reduced source counts by between 5% and 30%. The pair-wise overlaps between 23 databases and subsets were determined, as well as changes between 2006 and 2008. While all compound sets have increased, PubChem has doubled to 14.2 million. The 2008 comparison matrix shows not only overlap but also unique content across all sources. Many of the detailed differences could be attributed to individual strategies for data selection and extraction. While there was a big increase in patent-derived structures entering PubChem since 2006, GVKBIO contains over 0.8 million unique structures from this source. Venn diagrams showed extensive overlap between compounds extracted by independent expert curation from journals by GVKBIO, WOMBAT (both commercial) and BindingDB (public) but each included unique content. In contrast, the approved drug collections from GVKBIO, MDDR (commercial) and DrugBank (public) showed surprisingly low overlap. Aggregating all commercial sources established that while 1 million compounds overlapped with PubChem 1.2 million did not. On the basis of chemical structure content per se public sources have covered an increasing proportion of commercial databases over the last two years. However, commercial products included in this study provide links between compounds and information from patents and journals at a larger scale than current public efforts. They also continue to capture a significant proportion of unique content. Our results thus demonstrate not only an encouraging overall expansion of data-supported bioactive chemical space but also that both commercial and public sources are complementary for its exploration.

  9. Fun Databases: My Top Ten.

    ERIC Educational Resources Information Center

    O'Leary, Mick

    1992-01-01

    Provides reviews of 10 online databases: Consumer Reports; Public Opinion Online; Encyclopedia of Associations; Official Airline Guide Adventure Atlas and Events Calendar; CENDATA; Hollywood Hotline; Fearless Taster; Soap Opera Summaries; and Human Sexuality. (LRW)

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

    The T-matrix method is one of the most versatile and efficient direct computer solvers of the macroscopic Maxwell equations and is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper is the seventh update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists a number of earlier publications overlooked previously.

  11. State and Local Government Publications.

    ERIC Educational Resources Information Center

    Nakata, Yuri; Kopec, Karen

    1980-01-01

    Reviews trends in library programs for state and local government publications and documents the increased interest in microforms and databases. Discussion focuses on publication distribution and control, and efforts to support interstate networking. There are 28 references. (RAA)

  12. DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY ...

    EPA Pesticide Factsheets

    The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, SAR model development, or building of chemical relational databases (CRD). The Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: 1) to adopt and encourage the use of a common standard file format (SDF) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; 2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data s

  13. 14 CFR 158.20 - Submission of required documents.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... due to the security process. (b) Once the database development is completed with air carrier capability, public agencies and air carriers may use the FAA's national PFC database to post their required...

  14. 14 CFR 158.20 - Submission of required documents.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... due to the security process. (b) Once the database development is completed with air carrier capability, public agencies and air carriers may use the FAA's national PFC database to post their required...

  15. 14 CFR 158.20 - Submission of required documents.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... due to the security process. (b) Once the database development is completed with air carrier capability, public agencies and air carriers may use the FAA's national PFC database to post their required...

  16. 14 CFR 158.20 - Submission of required documents.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... due to the security process. (b) Once the database development is completed with air carrier capability, public agencies and air carriers may use the FAA's national PFC database to post their required...

  17. 14 CFR 158.20 - Submission of required documents.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... due to the security process. (b) Once the database development is completed with air carrier capability, public agencies and air carriers may use the FAA's national PFC database to post their required...

  18. Applying Knowledge Discovery in Databases in Public Health Data Set: Challenges and Concerns

    PubMed Central

    Volrathongchia, Kanittha

    2003-01-01

    In attempting to apply Knowledge Discovery in Databases (KDD) to generate a predictive model from a health care dataset that is currently available to the public, the first step is to pre-process the data to overcome the challenges of missing data, redundant observations, and records containing inaccurate data. This study will demonstrate how to use simple pre-processing methods to improve the quality of input data. PMID:14728545

  19. GigaDB: announcing the GigaScience database

    PubMed Central

    2012-01-01

    With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience’s goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond. PMID:23587345

  20. A publication database for optical long baseline interferometry

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  1. McMaster Optimal Aging Portal: an evidence-based database for geriatrics-focused health professionals.

    PubMed

    Barbara, Angela M; Dobbins, Maureen; Brian Haynes, R; Iorio, Alfonso; Lavis, John N; Raina, Parminder; Levinson, Anthony J

    2017-07-11

    The objective of this work was to provide easy access to reliable health information based on good quality research that will help health care professionals to learn what works best for seniors to stay as healthy as possible, manage health conditions and build supportive health systems. This will help meet the demands of our aging population that clinicians provide high quality care for older adults, that public health professionals deliver disease prevention and health promotion strategies across the life span, and that policymakers address the economic and social need to create a robust health system and a healthy society for all ages. The McMaster Optimal Aging Portal's (Portal) professional bibliographic database contains high quality scientific evidence about optimal aging specifically targeted to clinicians, public health professionals and policymakers. The database content comes from three information services: McMaster Premium LiteratUre Service (MacPLUS™), Health Evidence™ and Health Systems Evidence. The Portal is continually updated, freely accessible online, easily searchable, and provides email-based alerts when new records are added. The database is being continually assessed for value, usability and use. A number of improvements are planned, including French language translation of content, increased linkages between related records within the Portal database, and inclusion of additional types of content. While this article focuses on the professional database, the Portal also houses resources for patients, caregivers and the general public, which may also be of interest to geriatric practitioners and researchers.

  2. Stability and Longevity in the Publication Careers of U.S. Doctorate Recipients

    PubMed Central

    Waaijer, Cathelijn J. F.; Macaluso, Benoît; Sugimoto, Cassidy R.; Larivière, Vincent

    2016-01-01

    Since the 1950s, the number of doctorate recipients has risen dramatically in the United States. In this paper, we investigate whether the longevity of doctorate recipients’ publication careers has changed. This is achieved by matching 1951–2010 doctorate recipients with rare names in astrophysics, chemistry, economics, genetics and psychology in the dissertation database ProQuest to their publications in the publication database Web of Science. Our study shows that pre-PhD publication careers have changed: the median year of first publication has shifted from after the PhD to several years before PhD in most of the studied fields. In contrast, post-PhD publication career spans have not changed much in most fields. The share of doctorate recipients who have published for more than twenty years has remained stable over time; the shares of doctorate recipients publishing for shorter periods also remained almost unchanged. Thus, though there have been changes in pre-PhD publication careers, post-PhD career spans remained quite stable. PMID:27128633

  3. Acupuncture for treating sciatica: a systematic review protocol

    PubMed Central

    Qin, Zongshi; Liu, Xiaoxu; Yao, Qin; Zhai, Yanbing; Liu, Zhishun

    2015-01-01

    Introduction This systematic review aims to assess the effectiveness and safety of acupuncture for treating sciatica. Methods The following nine databases will be searched from their inception to 30 October 2014: MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), the Chinese Biomedical Literature Database (CBM), the Chinese Medical Current Content (CMCC), the Chinese Scientific Journal Database (VIP database), the Wan-Fang Database, the China National Knowledge Infrastructure (CNKI) and Citation Information by National Institute of Informatics (CiNii). Randomised controlled trials (RCTs) of acupuncture for sciatica in English, Chinese or Japanese without restriction of publication status will be included. Two researchers will independently undertake study selection, extraction of data and assessment of study quality. Meta-analysis will be conducted after screening of studies. Data will be analysed using risk ratio for dichotomous data, and standardised mean difference or weighted mean difference for continuous data. Dissemination This systematic review will be disseminated electronically through a peer-reviewed publication or conference presentations. Trial registration number PROSPERO CRD42014015001. PMID:25922105

  4. Space medicine research publications: 1983-1984

    NASA Technical Reports Server (NTRS)

    Solberg, J. L.; Pleasant, L. G.

    1984-01-01

    A list of publications supported by the Space Medicine Program, Office of Space Science and Applications is given. Included are publications entered into the Life Sciences Bibliographic Database by The George Washington University as of October 1, 1984.

  5. GlycomeDB – integration of open-access carbohydrate structure databases

    PubMed Central

    Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

    2008-01-01

    Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

  6. The Publications Tracking and Metrics Program at NOAO: Challenges and Opportunities

    NASA Astrophysics Data System (ADS)

    Hunt, Sharon

    2015-08-01

    The National Optical Astronomy Observatory (NOAO) is the U.S. national research and development center for ground-based nighttime astronomy. The NOAO librarian manages the organization’s publications tracking and metrics program, which consists of three components: identifying publications, organizing citation data, and disseminating publications information. We are developing methods to streamline these tasks, better organize our data, provide greater accessibility to publications data, and add value to our services.Our publications tracking process is complex, as we track refereed publications citing data from several sources: NOAO telescopes at two observatory sites, telescopes of consortia in which NOAO participates, the NOAO Science Archive, and NOAO-granted community-access time on non-NOAO telescopes. We also identify and document our scientific staff publications. In addition, several individuals contribute publications data.In the past year, we made several changes in our publications tracking and metrics program. To better organize our data and streamline the creation of reports and metrics, we created a MySQL publications database. When designing this relational database, we considered ease of use, the ability to incorporate data from various sources, efficiency in data inputting and sorting, and potential for growth. We also considered the types of metrics we wished to generate from our publications data based on our target audiences and the messages we wanted to convey. To increase accessibility and dissemination of publications information, we developed a publications section on the library’s website, with citation lists, acknowledgements guidelines, and metrics. We are now developing a searchable online database for our website using PHP.The publications tracking and metrics program has provided many opportunities for the library to market its services and contribute to the organization’s mission. As we make decisions on collecting, organizing, and disseminating publications information and metrics, we add to the visibility of the library, gain professional recognition, and produce a value-added service.

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

    PubMed Central

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

    2009-01-01

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

  8. EarthRef.org: Exploring aspects of a Cyber Infrastructure in Earth Science and Education

    NASA Astrophysics Data System (ADS)

    Staudigel, H.; Koppers, A.; Tauxe, L.; Constable, C.; Helly, J.

    2004-12-01

    EarthRef.org is the common host and (co-) developer of a range of earth science databases and IT resources providing a test bed for a Cyberinfrastructure in Earth Science and Education (CIESE). EarthRef.org data base efforts include in particular the Geochemical Earth Reference Model (GERM), the Magnetics Information Consortium (MagIC), the Educational Resources for Earth Science Education (ERESE) project, the Seamount Catalog, the Mid-Ocean Ridge Catalog, the Radio-Isotope Geochronology (RiG) initiative for CHRONOS, and the Microbial Observatory for Fe oxidizing microbes on Loihi Seamount (FeMO; the most recent development). These diverse databases are developed under a single database umbrella and webserver at the San Diego Supercomputing Center. All the data bases have similar structures, with consistent metadata concepts, a common database layout, and automated upload wizards. Shared resources include supporting databases like an address book, a reference/publication catalog, and a common digital archive making database development and maintenance cost-effective, while guaranteeing interoperability. The EarthRef.org CIESE provides a common umbrella for synthesis information as well as sample-based data, and it bridges the gap between science and science education in middle and high schools, validating the potential for a system wide data infrastructure in a CIESE. EarthRef.org experiences have shown that effective communication with the respective communities is a key part of a successful CIESE facilitating both utility and community buy-in. GERM has been particularly successful at developing a metadata scheme for geochemistry and in the development of a new electronic journal (G-cubed) that has made much progress in data publication and linkages between journals and community data bases. GERM also has worked, through editors and publishers, towards interfacing databases with the publication process, to accomplish a more scholarly and database friendly data publication environment, and to interface with the respective science communities. MagIC has held several workshops that have resulted in an integrated data archival environment using metadata that are interchangeable with the geochemical metadata. MagIC archives a wide array of paleo and rock magnetic directional, intensity and magnetic property data as well as integrating computational tools. ERESE brought together librarians, teachers, and scientists to create an educational environment that supports inquiry driven education and the use of science data. Experiences in EarthRef.org demonstrates the feasibility of an effective, community wide CIESE for data publication, archival and modeling, as well as the outreach to the educational community.

  9. Development of DHQ II Nutrient & Food Group Database | EGRP/DCCPS/NCI/NIH

    Cancer.gov

    Links to publications describing methods used to create values for the Diet History Questionnaire II (DHQ II) database using NHANES data and the addition of nutrients from the University of Minnesota’s Nutrition Data System for Research (NDS-R). The process used to create the Canadian DHQ II database is also described.

  10. Database Creation and Statistical Analysis: Finding Connections Between Two or More Secondary Storage Device

    DTIC Science & Technology

    2017-09-01

    NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS DATABASE CREATION AND STATISTICAL ANALYSIS: FINDING CONNECTIONS BETWEEN TWO OR MORE SECONDARY...BLANK ii Approved for public release. Distribution is unlimited. DATABASE CREATION AND STATISTICAL ANALYSIS: FINDING CONNECTIONS BETWEEN TWO OR MORE...Problem and Motivation . . . . . . . . . . . . . . . . . . . 1 1.2 DOD Applicability . . . . . . . . . . . . . . . . .. . . . . . . 2 1.3 Research

  11. 75 FR 10552 - Sixth Meeting-RTCA Special Committee 217: Joint With EUROCAE WG-44 Terrain and Airport Mapping...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-08

    ... 217: Joint With EUROCAE WG- 44 Terrain and Airport Mapping Databases AGENCY: Federal Aviation... Airport Mapping Databases. SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA Special Committee 217: Joint with EUROCAE WG-44 Terrain and Airport Mapping Databases. DATES: The...

  12. 76 FR 27744 - Eighth Meeting-RTCA Special Committee 217: Joint With EUROCAE WG-44 Terrain and Airport Mapping...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-12

    ... Committee 217: Joint With EUROCAE WG-44 Terrain and Airport Mapping Databases AGENCY: Federal Aviation... Airport Mapping Databases. SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA Special Committee 217: Joint with EUROCAE WG-44 Terrain and Airport Mapping Databases. DATES: The...

  13. 16 CFR 1102.20 - Transmission of reports of harm to the identified manufacturer or private labeler.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... INFORMATION DATABASE Procedural Requirements § 1102.20 Transmission of reports of harm to the identified..., provided such report meets the minimum requirements for publication in the Database, to the manufacturer or... harm, or otherwise, then it will not post the report of harm on the Database but will maintain the...

  14. 49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  15. 76 FR 54527 - Ninth Meeting-RTCA Special Committee 217: Joint With EUROCAE WG-44 Terrain and Airport Mapping...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-01

    ... 217: Joint With EUROCAE WG- 44 Terrain and Airport Mapping Databases AGENCY: Federal Aviation... Airport Mapping Databases. SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA Special Committee 217: Joint with EUROCAE WG-44 Terrain and Airport Mapping Databases. DATES: The...

  16. 16 CFR 1102.20 - Transmission of reports of harm to the identified manufacturer or private labeler.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... INFORMATION DATABASE Procedural Requirements § 1102.20 Transmission of reports of harm to the identified..., provided such report meets the minimum requirements for publication in the Database, to the manufacturer or... harm, or otherwise, then it will not post the report of harm on the Database but will maintain the...

  17. Consumer Product Category Database

    EPA Pesticide Factsheets

    The Chemical and Product Categories database (CPCat) catalogs the use of over 40,000 chemicals and their presence in different consumer products. The chemical use information is compiled from multiple sources while product information is gathered from publicly available Material Safety Data Sheets (MSDS). EPA researchers are evaluating the possibility of expanding the database with additional product and use information.

  18. 76 FR 6179 - Eighth Meeting-RTCA Special Committee 217: Joint With EUROCAE WG-44 Terrain and Airport Mapping...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-03

    ... Committee 217: Joint With EUROCAE WG-44 Terrain and Airport Mapping Databases AGENCY: Federal Aviation... Airport Mapping Databases. SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA Special Committee 217: Joint with EUROCAE WG-44 Terrain and Airport Mapping Databases. DATES: The...

  19. 49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  20. Computer Cataloging of Electronic Journals in Unstable Aggregator Databases: The Hong Kong Baptist University Library Experience.

    ERIC Educational Resources Information Center

    Li, Yiu-On; Leung, Shirley W.

    2001-01-01

    Discussion of aggregator databases focuses on a project at the Hong Kong Baptist University library to integrate full-text electronic journal titles from three unstable aggregator databases into its online public access catalog (OPAC). Explains the development of the electronic journal computer program (EJCOP) to generate MARC records for…

  1. 49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  2. 49 CFR 1570.13 - False statements regarding security background checks by public transportation agency or railroad...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  3. Ocean Drilling Program: Science Operator Search Engine

    Science.gov Websites

    and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main -USIO site, plus IODP, ODP, and DSDP Publications, together or separately. ODP | Search | Database

  4. Utilization of accident databases and fuzzy sets to estimate frequency of HazMat transport accidents.

    PubMed

    Qiao, Yuanhua; Keren, Nir; Mannan, M Sam

    2009-08-15

    Risk assessment and management of transportation of hazardous materials (HazMat) require the estimation of accident frequency. This paper presents a methodology to estimate hazardous materials transportation accident frequency by utilizing publicly available databases and expert knowledge. The estimation process addresses route-dependent and route-independent variables. Negative binomial regression is applied to an analysis of the Department of Public Safety (DPS) accident database to derive basic accident frequency as a function of route-dependent variables, while the effects of route-independent variables are modeled by fuzzy logic. The integrated methodology provides the basis for an overall transportation risk analysis, which can be used later to develop a decision support system.

  5. Development of a gene expression database and related analysis programs for evaluation of anticancer compounds.

    PubMed

    Ushijima, Masaru; Mashima, Tetsuo; Tomida, Akihiro; Dan, Shingo; Saito, Sakae; Furuno, Aki; Tsukahara, Satomi; Seimiya, Hiroyuki; Yamori, Takao; Matsuura, Masaaki

    2013-03-01

    Genome-wide transcriptional expression analysis is a powerful strategy for characterizing the biological activity of anticancer compounds. It is often instructive to identify gene sets involved in the activity of a given drug compound for comparison with different compounds. Currently, however, there is no comprehensive gene expression database and related application system that is; (i) specialized in anticancer agents; (ii) easy to use; and (iii) open to the public. To develop a public gene expression database of antitumor agents, we first examined gene expression profiles in human cancer cells after exposure to 35 compounds including 25 clinically used anticancer agents. Gene signatures were extracted that were classified as upregulated or downregulated after exposure to the drug. Hierarchical clustering showed that drugs with similar mechanisms of action, such as genotoxic drugs, were clustered. Connectivity map analysis further revealed that our gene signature data reflected modes of action of the respective agents. Together with the database, we developed analysis programs that calculate scores for ranking changes in gene expression and for searching statistically significant pathways from the Kyoto Encyclopedia of Genes and Genomes database in order to analyze the datasets more easily. Our database and the analysis programs are available online at our website (http://scads.jfcr.or.jp/db/cs/). Using these systems, we successfully showed that proteasome inhibitors are selectively classified as endoplasmic reticulum stress inducers and induce atypical endoplasmic reticulum stress. Thus, our public access database and related analysis programs constitute a set of efficient tools to evaluate the mode of action of novel compounds and identify promising anticancer lead compounds. © 2012 Japanese Cancer Association.

  6. The use and misuse of biomedical data: is bigger really better?

    PubMed

    Hoffman, Sharona; Podgurski, Andy

    2013-01-01

    Very large biomedical research databases, containing electronic health records (EHR) and genomic data from millions of patients, have been heralded recently for their potential to accelerate scientific discovery and produce dramatic improvements in medical treatments. Research enabled by these databases may also lead to profound changes in law, regulation, social policy, and even litigation strategies. Yet, is "big data" necessarily better data? This paper makes an original contribution to the legal literature by focusing on what can go wrong in the process of biomedical database research and what precautions are necessary to avoid critical mistakes. We address three main reasons for approaching such research with care and being cautious in relying on its outcomes for purposes of public policy or litigation. First, the data contained in biomedical databases is surprisingly likely to be incorrect or incomplete. Second, systematic biases, arising from both the nature of the data and the preconceptions of investigators, are serious threats to the validity of research results, especially in answering causal questions. Third, data mining of biomedical databases makes it easier for individuals with political, social, or economic agendas to generate ostensibly scientific but misleading research findings for the purpose of manipulating public opinion and swaying policymakers. In short, this paper sheds much-needed light on the problems of credulous and uninformed acceptance of research results derived from biomedical databases. An understanding of the pitfalls of big data analysis is of critical importance to anyone who will rely on or dispute its outcomes, including lawyers, policymakers, and the public at large. The Article also recommends technical, methodological, and educational interventions to combat the dangers of database errors and abuses.

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

    Yesley, M.S.; Ossorio, P.N.

    This report updates and expands the second edition of the ELSI Bibliography, published in 1993. The Bibliography and Supplement provides a comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. The Bibliography and Supplement are extracted from a database compiled at Los Alamos National Laboratory with the support of the Office of Energy Research, US Department of Energy. The second edition of the ELSI Bibliography was dated May 1993 but included publications added to the database until fall 1993. This Supplement reflects approximately 1,000 entries addedmore » to the database during the past year, bringing the total to approximately 7,000 entries. More than half of the new entries were published in the last year, and the remainder are earlier publications not previously included in the database. Most of the new entries were published in the academic and professional literature. The remainder are press reports from newspapers of record and scientific journals. The topical listing of the second edition has been followed in the Supplement, with a few changes. The topics of Cystic Fibrosis, Huntington`s Disease, and Sickle Cell Anemia have been combined in a single topic, Disorders. Also, all the entries published in the past year are included in a new topic, Publications: September 1993--September 1994, which provides a comprehensive view of recent reporting and commentary on the science and ELSI of genetics.« less

  8. Toward public volume database management: a case study of NOVA, the National Online Volumetric Archive

    NASA Astrophysics Data System (ADS)

    Fletcher, Alex; Yoo, Terry S.

    2004-04-01

    Public databases today can be constructed with a wide variety of authoring and management structures. The widespread appeal of Internet search engines suggests that public information be made open and available to common search strategies, making accessible information that would otherwise be hidden by the infrastructure and software interfaces of a traditional database management system. We present the construction and organizational details for managing NOVA, the National Online Volumetric Archive. As an archival effort of the Visible Human Project for supporting medical visualization research, archiving 3D multimodal radiological teaching files, and enhancing medical education with volumetric data, our overall database structure is simplified; archives grow by accruing information, but seldom have to modify, delete, or overwrite stored records. NOVA is being constructed and populated so that it is transparent to the Internet; that is, much of its internal structure is mirrored in HTML allowing internet search engines to investigate, catalog, and link directly to the deep relational structure of the collection index. The key organizational concept for NOVA is the Image Content Group (ICG), an indexing strategy for cataloging incoming data as a set structure rather than by keyword management. These groups are managed through a series of XML files and authoring scripts. We cover the motivation for Image Content Groups, their overall construction, authorship, and management in XML, and the pilot results for creating public data repositories using this strategy.

  9. NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1987-1990

    NASA Technical Reports Server (NTRS)

    1991-01-01

    This catalog lists 783 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into NASA Scientific and Technical Information Database during the year's 1987 through 1990. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  10. NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1989

    NASA Technical Reports Server (NTRS)

    1990-01-01

    This catalog lists 190 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA scientific and technical information database during accession year 1989. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  11. NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1991-1992

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This catalog lists 458 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information database during accession year 1991 through 1992. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  12. NASA scientific and technical publications: A catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1987

    NASA Technical Reports Server (NTRS)

    1988-01-01

    This catalog lists 239 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered in the NASA scientific and technical information database during accession year 1987. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  13. Immunization Program | Department of Public Health and Social Services

    Science.gov Websites

    Skip to main content logo Department of Public Health & Social Services Dipattamenton Salut of Public Health Division of Public Welfare Division of Environmental Health Division of Senior Recordings Health Inspection Database Healthy Vending Machine Calculator Photo Galleries Videos Medical

  14. 16 CFR 1102.44 - Applicability of sections 6(a) and (b) of the CPSA.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... PRODUCT SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Notice and...) in the Database. (b) Limitation on construction. Section 1102.44(a) shall not be construed to exempt...

  15. 16 CFR 1102.44 - Applicability of sections 6(a) and (b) of the CPSA.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PRODUCT SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Notice and...) in the Database. (b) Limitation on construction. Section 1102.44(a) shall not be construed to exempt...

  16. Data mining and visualization of the Alabama accident database

    DOT National Transportation Integrated Search

    2000-08-01

    The Alabama Department of Public Safety has developed and maintains a centralized database that contain traffic accident data collected from crash report completed by local police officers and state troopers. The Critical Analysis Reporting Environme...

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

    NASA Technical Reports Server (NTRS)

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

    2017-01-01

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

  18. Comprehensive thematic T-matrix reference database: A 2015-2017 update

    NASA Astrophysics Data System (ADS)

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

    2017-11-01

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

  19. Terrorism reports: The tip of the iceberg.

    PubMed

    Ellenberg, Eytan; Taragin, Mark; Bar-On, Zvia; Cohen, Osnat; Ostfeld, Ishay

    2017-01-01

    Medical impact of terror is a public health issue as the threat is growing all over the world. Our objective was to compare the number of injured and incidents in the three different databases and reports [Global Terrorism Database (GTD), Israeli Security Agency (ISA) and National Insurance Institute (NII)] in Israel. Retrospective study. Analyses of three different databases (GTD, ISA and NII) and basic comparison. The victims reimbursed for medical expenses are the largest population. The number of injured as described by GTD and ISA database are less important. The 2010-2013 years are marked by more incidents recognized in Israel vs GTD assessment (except in 2014). The number of victims being reimbursed for medical and mental health services is radically different from the GTD and the ISA reports. Public Health specialists should be advised of this phenomenon to deliver their right approach (including mental health) to growing threat and develop new definition of victim of terror.

  20. Building a genome database using an object-oriented approach.

    PubMed

    Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

    2002-01-01

    GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

  1. Tackling community concerns about commercialisation and genetic research: a modest interdisciplinary proposal.

    PubMed

    Haddow, Gillian; Laurie, Graeme; Cunningham-Burley, Sarah; Hunter, Kathryn G

    2007-01-01

    In recent years, there has been a rise in the creation of DNA databases promising a range of health benefits to individuals and populations. This development has been accompanied by an interest in, and concern for the ethical, legal and social aspects of such collections. In terms of policy solutions, much of the focus of these debates has been on issues of consent, confidentiality and research governance. However, there are broader concerns, such as those associated with commercialisation, which cannot be adequately addressed by these foci. In this article, we focus on the health-wealth benefits that DNA databases promise by considering the views of 10 focus groups on Generation Scotland, Scotland's first national genetic database. As in previous studies, our qualitative research on public/s and stakeholders' views of DNA databases show the prospect of utilising donated samples and information derived for wealth-related ends (i.e. for private profit), irrespective of whether there is an associated health-related benefit, arouses considerable reaction. While health-wealth benefits are not mutually exclusive ideals, the tendency has been to cast 'public' benefits as exclusively health-related, while 'private' commercial benefits for funders and/or researchers are held out as a necessary pay-off. We argue for a less polarised approach that reconsiders what is meant by 'public benefits' and questions the exclusivity of commercial interests. We believe accommodation can be achieved via the mobilisation of a grass roots solution known as 'benefit-sharing' or a 'profit pay-off'. We propose a sociologically informed model that has a pragmatic, legal framework, which responds seriously to public concerns.

  2. Machine Learning Techniques for the Detection of Shockable Rhythms in Automated External Defibrillators

    PubMed Central

    Irusta, Unai; Morgado, Eduardo; Aramendi, Elisabete; Ayala, Unai; Wik, Lars; Kramer-Johansen, Jo; Eftestøl, Trygve; Alonso-Atienza, Felipe

    2016-01-01

    Early recognition of ventricular fibrillation (VF) and electrical therapy are key for the survival of out-of-hospital cardiac arrest (OHCA) patients treated with automated external defibrillators (AED). AED algorithms for VF-detection are customarily assessed using Holter recordings from public electrocardiogram (ECG) databases, which may be different from the ECG seen during OHCA events. This study evaluates VF-detection using data from both OHCA patients and public Holter recordings. ECG-segments of 4-s and 8-s duration were analyzed. For each segment 30 features were computed and fed to state of the art machine learning (ML) algorithms. ML-algorithms with built-in feature selection capabilities were used to determine the optimal feature subsets for both databases. Patient-wise bootstrap techniques were used to evaluate algorithm performance in terms of sensitivity (Se), specificity (Sp) and balanced error rate (BER). Performance was significantly better for public data with a mean Se of 96.6%, Sp of 98.8% and BER 2.2% compared to a mean Se of 94.7%, Sp of 96.5% and BER 4.4% for OHCA data. OHCA data required two times more features than the data from public databases for an accurate detection (6 vs 3). No significant differences in performance were found for different segment lengths, the BER differences were below 0.5-points in all cases. Our results show that VF-detection is more challenging for OHCA data than for data from public databases, and that accurate VF-detection is possible with segments as short as 4-s. PMID:27441719

  3. Machine Learning Techniques for the Detection of Shockable Rhythms in Automated External Defibrillators.

    PubMed

    Figuera, Carlos; Irusta, Unai; Morgado, Eduardo; Aramendi, Elisabete; Ayala, Unai; Wik, Lars; Kramer-Johansen, Jo; Eftestøl, Trygve; Alonso-Atienza, Felipe

    2016-01-01

    Early recognition of ventricular fibrillation (VF) and electrical therapy are key for the survival of out-of-hospital cardiac arrest (OHCA) patients treated with automated external defibrillators (AED). AED algorithms for VF-detection are customarily assessed using Holter recordings from public electrocardiogram (ECG) databases, which may be different from the ECG seen during OHCA events. This study evaluates VF-detection using data from both OHCA patients and public Holter recordings. ECG-segments of 4-s and 8-s duration were analyzed. For each segment 30 features were computed and fed to state of the art machine learning (ML) algorithms. ML-algorithms with built-in feature selection capabilities were used to determine the optimal feature subsets for both databases. Patient-wise bootstrap techniques were used to evaluate algorithm performance in terms of sensitivity (Se), specificity (Sp) and balanced error rate (BER). Performance was significantly better for public data with a mean Se of 96.6%, Sp of 98.8% and BER 2.2% compared to a mean Se of 94.7%, Sp of 96.5% and BER 4.4% for OHCA data. OHCA data required two times more features than the data from public databases for an accurate detection (6 vs 3). No significant differences in performance were found for different segment lengths, the BER differences were below 0.5-points in all cases. Our results show that VF-detection is more challenging for OHCA data than for data from public databases, and that accurate VF-detection is possible with segments as short as 4-s.

  4. Publication trend, resource utilization, and impact of the US National Cancer Database

    PubMed Central

    Su, Chang; Peng, Cuiying; Agbodza, Ena; Bai, Harrison X.; Huang, Yuqian; Karakousis, Giorgos; Zhang, Paul J.; Zhang, Zishu

    2018-01-01

    Abstract Background: The utilization and impact of the studies published using the National Cancer Database (NCDB) is currently unclear. In this study, we aim to characterize the published studies, and identify relatively unexplored areas for future investigations. Methods: A literature search was performed using PubMed in January 2017 to identify all papers published using NCDB data. Characteristics of the publications were extracted. Citation frequencies were obtained through the Web of Science. Results: Three hundred 2 articles written by 230 first authors met the inclusion criteria. The number of publications grew exponentially since 2013, with 108 articles published in 2016. Articles were published in 86 journals. The majority of the published papers focused on digestive system cancer, while bone and joints, eye and orbit, myeloma, mesothelioma, and Kaposi Sarcoma were never studied. Thirteen institutions in the United States were associated with more than 5 publications. The papers have been cited for a total of 9858 times since the publication of the first paper in 1992. Frequently appearing keywords congregated into 3 clusters: “demographics,” “treatments and survival,” and “statistical analysis method.” Even though the main focuses of the articles captured a extremely wide range, they can be classified into 2 main categories: survival analysis and characterization. Other focuses include database(s) analysis and/or comparison, and hospital reporting. Conclusion: The surging interest in the use of NCDB is accompanied by unequal utilization of resources by individuals and institutions. Certain areas were relatively understudied and should be further explored. PMID:29489679

  5. 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

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

    PubMed

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

    2018-01-04

    The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. FARME DB: a functional antibiotic resistance element database

    PubMed Central

    Wallace, James C.; Port, Jesse A.; Smith, Marissa N.; Faustman, Elaine M.

    2017-01-01

    Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates. Database URL: http://staff.washington.edu/jwallace/farme PMID:28077567

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

    PubMed Central

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

    2011-01-01

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

  9. DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS ...

    EPA Pesticide Factsheets

    DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction ModelsAnn M. RichardUS Environmental Protection Agency, Research Triangle Park, NC, USADistributed: Decentralized set of standardized, field-delimited databases, each separatelyauthored and maintained, that are able to accommodate diverse toxicity data content;Structure-Searchable: Standard format (SDF) structure-data files that can be readily imported into available chemical relational databases and structure-searched;Tox: Toxicity data as it exists in widely disparate forms in current public databases, spanning diverse toxicity endpoints, test systems, levels of biological content, degrees of summarization, and information content.INTRODUCTIONThe economic and social pressures to reduce the need for animal testing and to better anticipate the potential for human and eco-toxicity of environmental, industrial, or pharmaceutical chemicals are as pressing today as at any time prior. However, the goal of predicting chemical toxicity in its many manifestations, the `T' in 'ADMET' (adsorption, distribution, metabolism, elimination, toxicity), remains one of the most difficult and largely unmet challenges in a chemical screening paradigm [1]. It is widely acknowledged that the single greatest hurdle to improving structure-activity relationship (SAR) toxicity prediction capabilities, in both the pharmaceutical and environmental regulation arenas, is the lack of suffici

  10. All Information Is Not Equal: Using the Literature Databases PubMed and The Cochrane Library for Identifying the Evidence on Granulocyte Transfusion Therapy.

    PubMed

    Metzendorf, Maria-Inti; Schulz, Manuela; Braun, Volker

    2014-10-01

    To be able to take well-informed decisions or carry out sound research, clinicians and researchers alike require specific information seeking skills matching their respective information needs. Biomedical information is traditionally available via different literature databases. This article gives an introduction to two diverging sources, PubMed (23 million references) and The Cochrane Library (800,000 references), both of which offer sophisticated instruments for searching an increasing amount of medical publications of varied quality and ambition. Whereas PubMed as an unfiltered source of primary literature comprises all different kinds of publication types occurring in academic journals, The Cochrane Library is a pre-filtered source which offers access to either synthesized publication types or critically appraised and carefully selected references. A search approach has to be carried out deliberately and requires a good knowledge on the scope and features of the databases as well as on the ability to build a search strategy in a structured way. We present a specific and a sensitive search approach, making use of both databases within two application case scenarios in order to identify the evidence on granulocyte transfusions for infections in adult patients with neutropenia.

  11. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

    PubMed Central

    Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2015-01-01

    Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. PMID:25158685

  12. Large-scale Health Information Database and Privacy Protection.

    PubMed

    Yamamoto, Ryuichi

    2016-09-01

    Japan was once progressive in the digitalization of healthcare fields but unfortunately has fallen behind in terms of the secondary use of data for public interest. There has recently been a trend to establish large-scale health databases in the nation, and a conflict between data use for public interest and privacy protection has surfaced as this trend has progressed. Databases for health insurance claims or for specific health checkups and guidance services were created according to the law that aims to ensure healthcare for the elderly; however, there is no mention in the act about using these databases for public interest in general. Thus, an initiative for such use must proceed carefully and attentively. The PMDA projects that collect a large amount of medical record information from large hospitals and the health database development project that the Ministry of Health, Labour and Welfare (MHLW) is working on will soon begin to operate according to a general consensus; however, the validity of this consensus can be questioned if issues of anonymity arise. The likelihood that researchers conducting a study for public interest would intentionally invade the privacy of their subjects is slim. However, patients could develop a sense of distrust about their data being used since legal requirements are ambiguous. Nevertheless, without using patients' medical records for public interest, progress in medicine will grind to a halt. Proper legislation that is clear for both researchers and patients will therefore be highly desirable. A revision of the Act on the Protection of Personal Information is currently in progress. In reality, however, privacy is not something that laws alone can protect; it will also require guidelines and self-discipline. We now live in an information capitalization age. I will introduce the trends in legal reform regarding healthcare information and discuss some basics to help people properly face the issue of health big data and privacy protection with a sense of ownership.

  13. Large-scale Health Information Database and Privacy Protection*1

    PubMed Central

    YAMAMOTO, Ryuichi

    2016-01-01

    Japan was once progressive in the digitalization of healthcare fields but unfortunately has fallen behind in terms of the secondary use of data for public interest. There has recently been a trend to establish large-scale health databases in the nation, and a conflict between data use for public interest and privacy protection has surfaced as this trend has progressed. Databases for health insurance claims or for specific health checkups and guidance services were created according to the law that aims to ensure healthcare for the elderly; however, there is no mention in the act about using these databases for public interest in general. Thus, an initiative for such use must proceed carefully and attentively. The PMDA*2 projects that collect a large amount of medical record information from large hospitals and the health database development project that the Ministry of Health, Labour and Welfare (MHLW) is working on will soon begin to operate according to a general consensus; however, the validity of this consensus can be questioned if issues of anonymity arise. The likelihood that researchers conducting a study for public interest would intentionally invade the privacy of their subjects is slim. However, patients could develop a sense of distrust about their data being used since legal requirements are ambiguous. Nevertheless, without using patients’ medical records for public interest, progress in medicine will grind to a halt. Proper legislation that is clear for both researchers and patients will therefore be highly desirable. A revision of the Act on the Protection of Personal Information is currently in progress. In reality, however, privacy is not something that laws alone can protect; it will also require guidelines and self-discipline. We now live in an information capitalization age. I will introduce the trends in legal reform regarding healthcare information and discuss some basics to help people properly face the issue of health big data and privacy protection with a sense of ownership. PMID:28299244

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis.

    PubMed

    Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

    2004-02-25

    Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups.

  17. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

    PubMed Central

    Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

    2004-01-01

    Background Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. Results To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. Conclusion A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups. PMID:15113403

  18. Database System Design and Implementation for Marine Air-Traffic-Controller Training

    DTIC Science & Technology

    2017-06-01

    NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. DATABASE SYSTEM DESIGN AND...thesis 4. TITLE AND SUBTITLE DATABASE SYSTEM DESIGN AND IMPLEMENTATION FOR MARINE AIR-TRAFFIC-CONTROLLER TRAINING 5. FUNDING NUMBERS 6. AUTHOR(S...12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This project focused on the design , development, and implementation of a centralized

  19. 16 CFR 1102.20 - Transmission of reports of harm to the identified manufacturer or private labeler.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... INFORMATION DATABASE (Eff. Jan. 10, 2011) Procedural Requirements § 1102.20 Transmission of reports of harm to... report of harm, provided such report meets the minimum requirements for publication in the Database, to... labeler is from the report of harm, or otherwise, then it will not post the report of harm on the Database...

  20. 16 CFR § 1102.20 - Transmission of reports of harm to the identified manufacturer or private labeler.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... SAFETY INFORMATION DATABASE Procedural Requirements § 1102.20 Transmission of reports of harm to the... of harm, provided such report meets the minimum requirements for publication in the Database, to the... report of harm, or otherwise, then it will not post the report of harm on the Database but will maintain...

  1. How Intrusion Detection Can Improve Software Decoy Applications

    DTIC Science & Technology

    2003-03-01

    THIS PAGE INTENTIONALLY LEFT BLANK 41 V. DISCUSSION Military history suggests it is best to employ a layered, defense-in...database: alert, postgresql , user=snort dbname=snort # output database: log, unixodbc, user=snort dbname=snort # output database: log, mssql, dbname...Threat Monitoring and Surveillance, James P. Anderson Co., Fort Washington. PA, April 1980. URL http://csrc.nist.gov/publications/ history /ande80

  2. Protecting patient privacy by quantifiable control of disclosures in disseminated databases.

    PubMed

    Ohno-Machado, Lucila; Silveira, Paulo Sérgio Panse; Vinterbo, Staal

    2004-08-01

    One of the fundamental rights of patients is to have their privacy protected by health care organizations, so that information that can be used to identify a particular individual is not used to reveal sensitive patient data such as diagnoses, reasons for ordering tests, test results, etc. A common practice is to remove sensitive data from databases that are disseminated to the public, but this can make the disseminated database useless for important public health purposes. If the degree of anonymity of a disseminated data set could be measured, it would be possible to design algorithms that can assure that the desired level of confidentiality is achieved. Privacy protection in disseminated databases can be facilitated by the use of special ambiguation algorithms. Most of these algorithms are aimed at making one individual indistinguishable from one or more of his peers. However, even in databases considered "anonymous", it may still be possible to obtain sensitive information about some individuals or groups of individuals with the use of pattern recognition algorithms. In this article, we study the problem of determining the degree of ambiguation in disseminated databases and discuss its implications in the development and testing of "anonymization" algorithms.

  3. HepSEQ: International Public Health Repository for Hepatitis B

    PubMed Central

    Gnaneshan, Saravanamuttu; Ijaz, Samreen; Moran, Joanne; Ramsay, Mary; Green, Jonathan

    2007-01-01

    HepSEQ is a repository for an extensive library of public health and molecular data relating to hepatitis B virus (HBV) infection collected from international sources. It is hosted by the Centre for Infections, Health Protection Agency (HPA), England, United Kingdom. This repository has been developed as a web-enabled, quality-controlled database to act as a tool for surveillance, HBV case management and for research. The web front-end for the database system can be accessed from . The format of the database system allows for comprehensive molecular, clinical and epidemiological data to be deposited into a functional database, to search and manipulate the stored data and to extract and visualize the information on epidemiological, virological, clinical, nucleotide sequence and mutational aspects of HBV infection through web front-end. Specific tools, built into the database, can be utilized to analyse deposited data and provide information on HBV genotype, identify mutations with known clinical significance (e.g. vaccine escape, precore and antiviral-resistant mutations) and carry out sequence homology searches against other deposited strains. Further mechanisms are also in place to allow specific tailored searches of the database to be undertaken. PMID:17130143

  4. Perceptions of the uses of routine general practice data beyond individual care in England: a qualitative study.

    PubMed

    Wyatt, David; Cook, Jenny; McKevitt, Christopher

    2018-01-08

    To investigate how different lay and professional groups perceive and understand the use of routinely collected general practice patient data for research, public health, service evaluation and commissioning. We conducted a multimethod, qualitative study. This entailed participant observation of the design and delivery of a series of deliberative engagement events about a local patient database made of routine primary care data. We also completed semistructured interviews with key professionals involved in the database. Qualitative data were thematically analysed. The research took place in an inner city borough in England. Of the community groups who participated in the six engagement events (111 individual citizens), five were health focused. It was difficult to recruit other types of organisations. Participants supported the uses of the database, but it was unclear how well they understood its scope and purpose. They had concerns about transparency, security and the potential misuse of data. Overall, they were more focused on the need for immediate investment in primary care capacity than data infrastructures to improve future health. The 10 interviewed professionals identified the purpose of the database in different ways, according to their interests. They emphasised the promise of the database as a resource in health research in its own right and in linking it to other datasets. Findings demonstrate positivity to the uses of this local database, but a disconnect between the long-term purposes of the database and participants' short-term priorities for healthcare quality. Varying understandings of the database and the potential for it to be used in multiple different ways in the future cement a need for systematic and routine public engagement to develop and maintain public awareness. Problems recruiting community groups signal a need to consider how we engage wider audiences more effectively. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  5. Perceptions of the uses of routine general practice data beyond individual care in England: a qualitative study

    PubMed Central

    Cook, Jenny; McKevitt, Christopher

    2018-01-01

    Objective To investigate how different lay and professional groups perceive and understand the use of routinely collected general practice patient data for research, public health, service evaluation and commissioning. Design, method, participants and setting We conducted a multimethod, qualitative study. This entailed participant observation of the design and delivery of a series of deliberative engagement events about a local patient database made of routine primary care data. We also completed semistructured interviews with key professionals involved in the database. Qualitative data were thematically analysed. The research took place in an inner city borough in England. Results Of the community groups who participated in the six engagement events (111 individual citizens), five were health focused. It was difficult to recruit other types of organisations. Participants supported the uses of the database, but it was unclear how well they understood its scope and purpose. They had concerns about transparency, security and the potential misuse of data. Overall, they were more focused on the need for immediate investment in primary care capacity than data infrastructures to improve future health. The 10 interviewed professionals identified the purpose of the database in different ways, according to their interests. They emphasised the promise of the database as a resource in health research in its own right and in linking it to other datasets. Conclusions Findings demonstrate positivity to the uses of this local database, but a disconnect between the long-term purposes of the database and participants’ short-term priorities for healthcare quality. Varying understandings of the database and the potential for it to be used in multiple different ways in the future cement a need for systematic and routine public engagement to develop and maintain public awareness. Problems recruiting community groups signal a need to consider how we engage wider audiences more effectively. PMID:29317420

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

    PubMed

    Weirick, Tyler; John, David; Uchida, Shizuka

    2017-03-01

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

  7. 14 CFR 298.70 - Public disclosure of data.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS EXEMPTIONS FOR AIR TAXI AND COMMUTER AIR CARRIER OPERATIONS Public... available immediately following the Department's determination that the database is complete, but no earlier...

  8. 14 CFR 298.70 - Public disclosure of data.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS EXEMPTIONS FOR AIR TAXI AND COMMUTER AIR CARRIER OPERATIONS Public... available immediately following the Department's determination that the database is complete, but no earlier...

  9. 14 CFR 298.70 - Public disclosure of data.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS EXEMPTIONS FOR AIR TAXI AND COMMUTER AIR CARRIER OPERATIONS Public... available immediately following the Department's determination that the database is complete, but no earlier...

  10. 14 CFR 298.70 - Public disclosure of data.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS EXEMPTIONS FOR AIR TAXI AND COMMUTER AIR CARRIER OPERATIONS Public... available immediately following the Department's determination that the database is complete, but no earlier...

  11. 14 CFR 298.70 - Public disclosure of data.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS EXEMPTIONS FOR AIR TAXI AND COMMUTER AIR CARRIER OPERATIONS Public... available immediately following the Department's determination that the database is complete, but no earlier...

  12. 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.

  13. Anabaena sp. strain PCC 7120 conR contains a LytR-CpsA-Psr domain, is developmentally regulated, and is essential for diazotrophic growth and heterocyst morphogenesis.

    PubMed

    Mella-Herrera, Rodrigo A; Neunuebel, M Ramona; Golden, James W

    2011-03-01

    The conR (all0187) gene of the filamentous cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120 is predicted to be part of a family of proteins that contain the LytR-CpsA-Psr domain associated with septum formation and cell wall maintenance. The conR gene was originally misannotated as a transcription regulator. Northern RNA blot analysis showed that conR expression was upregulated 8 h after nitrogen step-down. Fluorescence microscopy of a P(conR)-gfp reporter strain revealed increased GFP fluorescence in proheterocysts and heterocysts beginning 9 h after nitrogen step-down. Insertional inactivation of conR caused a septum-formation defect of vegetative cells grown in nitrate-containing medium. In nitrate-free medium, mutant filaments formed abnormally long heterocysts and were defective for diazotrophic growth. Septum formation between heterocysts and adjacent vegetative cells was abnormal, often with one or both poles of the heterocysts appearing partially open. In a conR mutant, expression of nifH was delayed after nitrogen step-down and nitrogenase activity was approximately 70 % of wild-type activity, indicating that heterocysts of the conR mutant strain are partially functional. We hypothesize that the diazotrophic growth defect is caused by an inability of the heterocysts to transport fixed nitrogen to the neighbouring vegetative cells.

  14. Evaluation of a National Call Center and a Local Alerts System for Detection of New Cases of Ebola Virus Disease - Guinea, 2014-2015.

    PubMed

    Lee, Christopher T; Bulterys, Marc; Martel, Lise D; Dahl, Benjamin A

    2016-03-11

    The epidemic of Ebola virus disease (Ebola) in West Africa began in Guinea in late 2013 (1), and on August 8, 2014, the World Health Organization (WHO) declared the epidemic a Public Health Emergency of International Concern (2). Guinea was declared Ebola-free on December 29, 2015, and is under a 90 day period of enhanced surveillance, following 3,351 confirmed and 453 probable cases of Ebola and 2,536 deaths (3). Passive surveillance for Ebola in Guinea has been conducted principally through the use of a telephone alert system. Community members and health facilities report deaths and suspected Ebola cases to local alert numbers operated by prefecture health departments or to a national toll-free call center. The national call center additionally functions as a source of public health information by responding to questions from the public about Ebola. To evaluate the sensitivity of the two systems and compare the sensitivity of the national call center with the local alerts system, the CDC country team performed probabilistic record linkage of the combined prefecture alerts database, as well as the national call center database, with the national viral hemorrhagic fever (VHF) database; the VHF database contains records of all known confirmed Ebola cases. Among 17,309 alert calls analyzed from the national call center, 71 were linked to 1,838 confirmed Ebola cases in the VHF database, yielding a sensitivity of 3.9%. The sensitivity of the national call center was highest in the capital city of Conakry (11.4%) and lower in other prefectures. In comparison, the local alerts system had a sensitivity of 51.1%. Local public health infrastructure plays an important role in surveillance in an epidemic setting.

  15. IRIS Toxicological Review of Benzo[a]pyrene (Public ...

    EPA Pesticide Factsheets

    EPA is developing an Integrated Risk Information System (IRIS) assessment of benzo[a]pyrene and has released the draft assessment for public comment and external peer review. When final, the assessment will appear on the IRIS database. EPA is undertaking an update of the Integrated Risk Information System (IRIS) health assessment for benzo[a]pyrene (BaP). The outcome of this project is an updated Toxicological Review and IRIS Summary for BaP that will be entered into the IRIS database.

  16. LiverTox: Clinical and Research Information on Drug-Induced Liver Injury

    MedlinePlus

    ... News Information Resources Glossary Abbreviations SEARCH THE LIVERTOX DATABASE Search for a specific medication, herbal or supplement: ... About Us . Disclaimer. Information presented in the LiverTox database is derived from the scientific literature and public ...

  17. 16 CFR § 1102.44 - Applicability of sections 6(a) and (b) of the CPSA.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... CONSUMER PRODUCT SAFETY ACT REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE... § 1102.10(d) in the Database. (b) Limitation on construction. Section 1102.44(a) shall not be construed...

  18. 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...

  19. Using Online Databases in Corporate Issues Management.

    ERIC Educational Resources Information Center

    Thomsen, Steven R.

    1995-01-01

    Finds that corporate public relations practitioners felt they were able, using online database and information services, to intercept issues earlier in the "issue cycle" and thus enable their organizations to develop more "proactionary" or "catalytic" issues management repose strategies. (SR)

  20. Result Publication of Chinese Trials in World Health Organization Primary Registries

    PubMed Central

    Xuemei, Liu; Youping, Li; Senlin, Yin; Shangqi, Song

    2010-01-01

    Background Result publication is the key step to improve the transparency of clinical trials. Objective To investigate the result publication rate of Chinese trials registered in World Health Organization (WHO) primary registries. Method We searched 11 WHO primary registries for Chinese trials records. The progress of each trial was analyzed. We searched for the full texts of result publications cited in the registration records. For completed trials without citations, we searched PubMed, Embase, Chinese Biomedical Literature Database (Chinese), China Knowledge Resource Integrated Database, and Chinese Science and Technology Periodicals Database for result publications. The search was conducted on July 14, 2009. We also called the investigators of completed trials to ask about results publication. Results We identified 1294 Chinese trials records (428 in ChiCTR,743 in clinicaltrials.gov,55 in ISRCTN, 21 in ACTRN). A total of 443 trials had been completed. The publication rate of the Chinese trials in WHO primary registries is 35.2%(156/443).The publication rate of Chinese trials in clinicaltrials.gov, ChiCTR, ISRCTN, and ACRTN was 36.5% (53/145), 36.3% (89/245), 26.0%(9/44), and 55.6%(5/9), respectively. The publication rate of trials sponsored by industry(23.8%) was lower than that of sponsored by central and local government(31.7%), hospital(35.1%), and universities (40.7%). The publication rate for randomized trials was higher than that of cohort study and case-control study (33.2% versus 16.7%, 22.2%). The publication rate for interventional studies and observational studies was similar(33.4% versus 33.3%). Conclusion The publication rate of the registered Chinese trials was low, with no significant difference between ChiCTR and clinicaltrials.gov. An effective mechanism is needed to promote publication of results for registered trials in China. PMID:20856888

  1. IRIS Toxicological Review of Tert-Butyl Alcohol (Tert-Butanol) ...

    EPA Pesticide Factsheets

    On April 29, 2016, the Toxicological Review of tert-Butyl Alcohol (tert-Butanol) (Public Comment Draft) was released for public comment. The draft Toxicological Review and charge were reviewed internally by EPA and by other federal agencies and the Executive Office of the President during Step 3 (Interagency Science Consultation) before public release. As part of the IRIS process, all written interagency comments on IRIS assessments will be made publicly available. Accordingly, interagency comments with EPA's response and the interagency science consultation drafts of the IRIS Toxicological Review of tert-Butanol and charge to external peer reviewers are posted on this site. EPA is undertaking a new health assessment for t-butyl alcohol (tert-butanol) for the Integrated Risk Information System (IRIS). The outcome of this project will be a Toxicological Review and IRIS and IRIS Summary of TBA that will be entered on the IRIS database. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information to evaluate potential public health risks associated with environmental contaminants. The IRIS database is relied on for the development of risk assessments, site-specific environmental decisions, and rule making.

  2. IRIS Toxicological Review of Biphenyl (Interagency Science ...

    EPA Pesticide Factsheets

    On September 30, 2011, the draft Toxicological Review of Biphenyl and the charge to external peer reviewers were released for external peer review and public comment. The Toxicological Review and charge were reviewed internally by EPA and by other federal agencies and White House Offices before public release. In the new IRIS process (May 2009), introduced by the EPA Administrator, all written comments on IRIS assessments submitted by other federal agencies and White House Offices will be made publicly available. Accordingly, interagency comments and the interagency science consultation draft of the IRIS Toxicological Review of Biphenyl and the charge to external peer reviewers are posted on this site. EPA is undertaking a new health assessment for biphenyl for the Integrated Risk Information System (IRIS). The outcome of this project will be a Toxicological Review and IRIS and IRIS Summary of biohenyl that will be entered on the IRIS database. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information to evaluate potential public health risks associated with exposure assessment information to evaluate potential public health risks associated with environmental contaminants. The IRIS database is relied on for the development of risk ass

  3. 79 FR 77522 - Public Review of the Draft Part 2 (Revision), Digital Orthoimagery, of the Federal Geographic...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2014-12-24

    ... for the semantic content of orthoimagery databases for public agencies and private enterprises. It... to the public on the FGDC Web site, www.fgdc.gov . DATES: Comments on the draft Part 2 (revision...

  4. Financing a future for public biological data.

    PubMed

    Ellis, L B; Kalumbi, D

    1999-09-01

    The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available; database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions. This study examines the finances and use statistics of a few of these organizations in more depth, and reviews several economic models that may help sustain them. Six organizations were studied. Their administrative overhead is fairly low; non-administrative personnel and computer-related costs account for 77% of expenses. One smaller, more specialized US database, in 1997, had 60% of total access from US domains; a majority (56%) of its US accesses came from commercial domains, although only 2% of the 153 databases originally studied received any industrial support. The most popular model used to gain industrial support is asymmetric pricing: preferentially charging the commercial users of a database. At least five biological databases have recently begun using this model. Advertising is another model which may be useful for the more general, more heavily used sites. Microcommerce has promise, especially for databases that do not attract advertisers, but needs further testing. The least income reported for any of the databases studied was $50,000/year; applying this rate to 400 biological databases (a lower limit of the number of such databases, many of which require far larger resources) would mean annual support need of at least $20 million. To obtain this level of support is challenging, yet failure to accept the challenge could be catastrophic. lynda@tc.umn. edu

  5. Technology in the Public Library: Results from the 1992 PLDS Survey of Technology.

    ERIC Educational Resources Information Center

    Fidler, Linda M.; Johnson, Debra Wilcox

    1994-01-01

    Discusses and compares the incorporation of technology by larger public libraries in Canada and the United States. Technology mentioned includes online public access catalogs; remote and local online database searching; microcomputers and software for public use; and fax, voice mail, and Telecommunication Devices for the Deaf and Teletype writer…

  6. There Is a Significant Discrepancy Between "Big Data" Database and Original Research Publications on Hip Arthroscopy Outcomes: A Systematic Review.

    PubMed

    Sochacki, Kyle R; Jack, Robert A; Safran, Marc R; Nho, Shane J; Harris, Joshua D

    2018-06-01

    The purpose of this study was to compare (1) major complication, (2) revision, and (3) conversion to arthroplasty rates following hip arthroscopy between database studies and original research peer-reviewed publications. A systematic review was performed using PRISMA guidelines. PubMed, SCOPUS, SportDiscus, and Cochrane Central Register of Controlled Trials were searched for studies that investigated major complication (dislocation, femoral neck fracture, avascular necrosis, fluid extravasation, septic arthritis, death), revision, and hip arthroplasty conversion rates following hip arthroscopy. Major complication, revision, and conversion to hip arthroplasty rates were compared between original research (single- or multicenter therapeutic studies) and database (insurance database using ICD-9/10 and/or current procedural terminology coding terminology) publishing studies. Two hundred seven studies (201 original research publications [15,780 subjects; 54% female] and 6 database studies [20,825 subjects; 60% female]) were analyzed (mean age, 38.2 ± 11.6 years old; mean follow-up, 2.7 ± 2.9 years). The database studies had a significantly higher age (40.6 + 2.8 vs 35.4 ± 11.6), body mass index (27.4 ± 5.6 vs 24.9 ± 3.1), percentage of females (60.1% vs 53.8%), and longer follow-up (3.1 ± 1.6 vs 2.7 ± 3.0) compared with original research (P < .0001 for all). Ninety-seven (0.6%) major complications occurred in the individual studies, and 95 (0.8%) major complications occurred in the database studies (P = .029; relative risk [RR], 1.3). There was a significantly higher rate of femoral neck fracture (0.24% vs 0.03%; P < .0001; RR, 8.0), and hip dislocation (0.17% vs 0.06%; P = .023; RR, 2.2) in the database studies. Reoperations occurred at a significantly higher rate in the database studies (11.1% vs 7.3%; P < .001; RR, 1.5). There was a significantly higher rate of conversion to arthroplasty in the database studies (8.0% vs 3.7%; P < .001; RR, 2.2). Database studies report significantly increased major complication, revision, and conversion to hip arthroplasty rates compared with original research investigations of hip arthroscopy outcomes. Level IV, systematic review of Level I-IV studies. Copyright © 2018 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  7. Lynx: a database and knowledge extraction engine for integrative medicine.

    PubMed

    Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T Conrad; Maltsev, Natalia

    2014-01-01

    We have developed Lynx (http://lynx.ci.uchicago.edu)--a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.

  8. Tympanometry in infants: a study of the sensitivity and specificity of 226-Hz and 1,000-Hz probe tones.

    PubMed

    Carmo, Michele Picanço; Costa, Nayara Thais de Oliveira; Momensohn-Santos, Teresa Maria

    2013-10-01

    Introduction For infants under 6 months, the literature recommends 1,000-Hz tympanometry, which has a greater sensitivity for the correct identification of middle ear disorders in this population. Objective To systematically analyze national and international publications found in electronic databases that used tympanometry with 226-Hz and 1,000-Hz probe tones. Data Synthesis Initially, we identified 36 articles in the SciELO database, 11 in the Latin American and Caribbean Literature on the Health Sciences (LILACS) database, 199 in MEDLINE, 0 in the Cochrane database, 16 in ISI Web of Knowledge, and 185 in the Scopus database. We excluded 433 articles because they did not fit the selection criteria, leaving 14 publications that were analyzed in their entirety. Conclusions The 1,000-Hz tone test has greater sensitivity and specificity for the correct identification of tympanometric curve changes. However, it is necessary to clarify the doubts that still exist regarding the use of this test frequency. Improved methods for rating curves, standardization of normality criteria, and the types of curves found in infants should be addressed.

  9. Tympanometry in Infants: A Study of the Sensitivity and Specificity of 226-Hz and 1,000-Hz Probe Tones

    PubMed Central

    Carmo, Michele Picanço; Costa, Nayara Thais de Oliveira; Momensohn-Santos, Teresa Maria

    2013-01-01

    Introduction For infants under 6 months, the literature recommends 1,000-Hz tympanometry, which has a greater sensitivity for the correct identification of middle ear disorders in this population. Objective To systematically analyze national and international publications found in electronic databases that used tympanometry with 226-Hz and 1,000-Hz probe tones. Data Synthesis Initially, we identified 36 articles in the SciELO database, 11 in the Latin American and Caribbean Literature on the Health Sciences (LILACS) database, 199 in MEDLINE, 0 in the Cochrane database, 16 in ISI Web of Knowledge, and 185 in the Scopus database. We excluded 433 articles because they did not fit the selection criteria, leaving 14 publications that were analyzed in their entirety. Conclusions The 1,000-Hz tone test has greater sensitivity and specificity for the correct identification of tympanometric curve changes. However, it is necessary to clarify the doubts that still exist regarding the use of this test frequency. Improved methods for rating curves, standardization of normality criteria, and the types of curves found in infants should be addressed. PMID:25992044

  10. BioModels Database: a repository of mathematical models of biological processes.

    PubMed

    Chelliah, Vijayalakshmi; Laibe, Camille; Le Novère, Nicolas

    2013-01-01

    BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

  11. Interactive bibliographical database on color

    NASA Astrophysics Data System (ADS)

    Caivano, Jose L.

    2002-06-01

    The paper describes the methodology and results of a project under development, aimed at the elaboration of an interactive bibliographical database on color in all fields of application: philosophy, psychology, semiotics, education, anthropology, physical and natural sciences, biology, medicine, technology, industry, architecture and design, arts, linguistics, geography, history. The project is initially based upon an already developed bibliography, published in different journals, updated in various opportunities, and now available at the Internet, with more than 2,000 entries. The interactive database will amplify that bibliography, incorporating hyperlinks and contents (indexes, abstracts, keywords, introductions, or eventually the complete document), and devising mechanisms for information retrieval. The sources to be included are: books, doctoral dissertations, multimedia publications, reference works. The main arrangement will be chronological, but the design of the database will allow rearrangements or selections by different fields: subject, Decimal Classification System, author, language, country, publisher, etc. A further project is to develop another database, including color-specialized journals or newsletters, and articles on color published in international journals, arranged in this case by journal name and date of publication, but allowing also rearrangements or selections by author, subject and keywords.

  12. LMSD: LIPID MAPS structure database

    PubMed Central

    Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

    2007-01-01

    The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

  13. Central Appalachian basin natural gas database: distribution, composition, and origin of natural gases

    USGS Publications Warehouse

    Román Colón, Yomayra A.; Ruppert, Leslie F.

    2015-01-01

    The U.S. Geological Survey (USGS) has compiled a database consisting of three worksheets of central Appalachian basin natural gas analyses and isotopic compositions from published and unpublished sources of 1,282 gas samples from Kentucky, Maryland, New York, Ohio, Pennsylvania, Tennessee, Virginia, and West Virginia. The database includes field and reservoir names, well and State identification number, selected geologic reservoir properties, and the composition of natural gases (methane; ethane; propane; butane, iso-butane [i-butane]; normal butane [n-butane]; iso-pentane [i-pentane]; normal pentane [n-pentane]; cyclohexane, and hexanes). In the first worksheet, location and American Petroleum Institute (API) numbers from public or published sources are provided for 1,231 of the 1,282 gas samples. A second worksheet of 186 gas samples was compiled from published sources and augmented with public location information and contains carbon, hydrogen, and nitrogen isotopic measurements of natural gas. The third worksheet is a key for all abbreviations in the database. The database can be used to better constrain the stratigraphic distribution, composition, and origin of natural gas in the central Appalachian basin.

  14. 14 CFR 291.60 - Public disclosure of data.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS CARGO OPERATIONS IN INTERSTATE AIR TRANSPORTATION Public Disclosure of Data... following the Department's determination that the database is complete, but no earlier than six months after...

  15. 14 CFR 291.60 - Public disclosure of data.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS CARGO OPERATIONS IN INTERSTATE AIR TRANSPORTATION Public Disclosure of Data... following the Department's determination that the database is complete, but no earlier than six months after...

  16. 14 CFR 291.60 - Public disclosure of data.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS CARGO OPERATIONS IN INTERSTATE AIR TRANSPORTATION Public Disclosure of Data... following the Department's determination that the database is complete, but no earlier than six months after...

  17. 14 CFR Sec. 19-6 - Public disclosure of traffic data.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS UNIFORM SYSTEM OF ACCOUNTS AND REPORTS FOR LARGE CERTIFICATED AIR CARRIERS..., shall be publicly available immediately following the Department's determination that the database is...

  18. 14 CFR 291.60 - Public disclosure of data.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PROCEEDINGS) ECONOMIC REGULATIONS CARGO OPERATIONS IN INTERSTATE AIR TRANSPORTATION Public Disclosure of Data... following the Department's determination that the database is complete, but no earlier than six months after...

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

    PubMed

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

    2011-05-01

    This communication analyzed research publications in dentistry in the Institute of Scientific Information Web of Science databases of 10 dental faculties in the Association of South-East Asian Nations (ASEAN) from 2000 to 2009. The term used for the "all-document types" search was "Faculty of Dentistry/College of Dentistry." Abstracts presented at regional meetings were also included in the analysis. The Times Higher Education System QS World University Rankings showed that universities in the region fare poorly in world university rankings. Only the National University of Singapore and Nanyang Technological University appeared in the top 100 in 2009; 19 universities in the region, including Indonesia, Malaysia, the Philippines, Singapore, and Thailand, appeared in the top 500. Data from the databases showed that research publications by dental institutes in the region fall short of their Asian counterparts. Singapore and Thailand are the most active in dental research of the ASEAN countries. © 2011 Blackwell Publishing Asia Pty Ltd.

  20. THE DRINKING WATER TREATABILITY DATABASE (Slides)

    EPA Science Inventory

    The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

  1. 78 FR 55081 - Circulatory System Devices Panel of the Medical Devices Advisory Committee; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-09

    ... measurements to a database for review by medical professionals. The database is a Web-based server that... review by medical professionals. FDA intends to make background material available to the public no later...

  2. Data tables for the 1994 National Transit Database report year

    DOT National Transportation Integrated Search

    1995-12-01

    The Data Tables For the 1994 National Transit Database Report Year is one of three publications also referred to as the National Transit Databse Reporting System. The report provides detailed summaries of financial and operating data submitted to FTA...

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

    NASA Technical Reports Server (NTRS)

    Lulla, Kamlesh

    1994-01-01

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

  4. Database Changes (Post-Publication). ERIC Processing Manual, Section X.

    ERIC Educational Resources Information Center

    Brandhorst, Ted, Ed.

    The purpose of this section is to specify the procedure for making changes to the ERIC database after the data involved have been announced in the abstract journals RIE or CIJE. As a matter of general ERIC policy, a document or journal article is not re-announced or re-entered into the database as a new accession for the purpose of accomplishing a…

  5. 37 CFR 2.122 - Matters in evidence.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... registration, or by a current printout of information from the electronic database records of the USPTO showing... publications, such as books and periodicals, available to the general public in libraries or of general.... The notice shall specify the printed publication (including information sufficient to identify the...

  6. A spatial national health facility database for public health sector planning in Kenya in 2008.

    PubMed

    Noor, Abdisalan M; Alegana, Victor A; Gething, Peter W; Snow, Robert W

    2009-03-06

    Efforts to tackle the enormous burden of ill-health in low-income countries are hampered by weak health information infrastructures that do not support appropriate planning and resource allocation. For health information systems to function well, a reliable inventory of health service providers is critical. The spatial referencing of service providers to allow their representation in a geographic information system is vital if the full planning potential of such data is to be realized. A disparate series of contemporary lists of health service providers were used to update a public health facility database of Kenya last compiled in 2003. These new lists were derived primarily through the national distribution of antimalarial and antiretroviral commodities since 2006. A combination of methods, including global positioning systems, was used to map service providers. These spatially-referenced data were combined with high-resolution population maps to analyze disparity in geographic access to public health care. The updated 2008 database contained 5,334 public health facilities (67% ministry of health; 28% mission and nongovernmental organizations; 2% local authorities; and 3% employers and other ministries). This represented an overall increase of 1,862 facilities compared to 2003. Most of the additional facilities belonged to the ministry of health (79%) and the majority were dispensaries (91%). 93% of the health facilities were spatially referenced, 38% using global positioning systems compared to 21% in 2003. 89% of the population was within 5 km Euclidean distance to a public health facility in 2008 compared to 71% in 2003. Over 80% of the population outside 5 km of public health service providers was in the sparsely settled pastoralist areas of the country. We have shown that, with concerted effort, a relatively complete inventory of mapped health services is possible with enormous potential for improving planning. Expansion in public health care in Kenya has resulted in significant increases in geographic access although several areas of the country need further improvements. This information is key to future planning and with this paper we have released the digital spatial database in the public domain to assist the Kenyan Government and its partners in the health sector.

  7. The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

    NASA Astrophysics Data System (ADS)

    Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

    2018-01-01

    We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

  8. The ClinicalTrials.gov results database--update and key issues.

    PubMed

    Zarin, Deborah A; Tse, Tony; Williams, Rebecca J; Califf, Robert M; Ide, Nicholas C

    2011-03-03

    The ClinicalTrials.gov trial registry was expanded in 2008 to include a database for reporting summary results. We summarize the structure and contents of the results database, provide an update of relevant policies, and show how the data can be used to gain insight into the state of clinical research. We analyzed ClinicalTrials.gov data that were publicly available between September 2009 and September 2010. As of September 27, 2010, ClinicalTrials.gov received approximately 330 new and 2000 revised registrations each week, along with 30 new and 80 revised results submissions. We characterized the 79,413 registry and 2178 results of trial records available as of September 2010. From a sample cohort of results records, 78 of 150 (52%) had associated publications within 2 years after posting. Of results records available publicly, 20% reported more than two primary outcome measures and 5% reported more than five. Of a sample of 100 registry record outcome measures, 61% lacked specificity in describing the metric used in the planned analysis. In a sample of 700 results records, the mean number of different analysis populations per study group was 2.5 (median, 1; range, 1 to 25). Of these trials, 24% reported results for 90% or less of their participants. ClinicalTrials.gov provides access to study results not otherwise available to the public. Although the database allows examination of various aspects of ongoing and completed clinical trials, its ultimate usefulness depends on the research community to submit accurate, informative data.

  9. Performance-Oriented Privacy-Preserving Data Integration

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

    Pon, R K; Critchlow, T

    2004-09-15

    Current solutions to integrating private data with public data have provided useful privacy metrics, such as relative information gain, that can be used to evaluate alternative approaches. Unfortunately, they have not addressed critical performance issues, especially when the public database is very large. The use of hashes and noise yields better performance than existing techniques while still making it difficult for unauthorized entities to distinguish which data items truly exist in the private database. As we show here, leveraging the uncertainty introduced by collisions caused by hashing and the injection of noise, we present a technique for performing a relationalmore » join operation between a massive public table and a relatively smaller private one.« less

  10. Déjà vu: a database of highly similar citations in the scientific literature

    PubMed Central

    Errami, Mounir; Sun, Zhaohui; Long, Tara C.; George, Angela C.; Garner, Harold R.

    2009-01-01

    In the scientific research community, plagiarism and covert multiple publications of the same data are considered unacceptable because they undermine the public confidence in the scientific integrity. Yet, little has been done to help authors and editors to identify highly similar citations, which sometimes may represent cases of unethical duplication. For this reason, we have made available Déjà vu, a publicly available database of highly similar Medline citations identified by the text similarity search engine eTBLAST. Following manual verification, highly similar citation pairs are classified into various categories ranging from duplicates with different authors to sanctioned duplicates. Déjà vu records also contain user-provided commentary and supporting information to substantiate each document's categorization. Déjà vu and eTBLAST are available to authors, editors, reviewers, ethicists and sociologists to study, intercept, annotate and deter questionable publication practices. These tools are part of a sustained effort to enhance the quality of Medline as ‘the’ biomedical corpus. The Déjà vu database is freely accessible at http://spore.swmed.edu/dejavu. The tool eTBLAST is also freely available at http://etblast.org. PMID:18757888

  11. Deja vu: a database of highly similar citations in the scientific literature.

    PubMed

    Errami, Mounir; Sun, Zhaohui; Long, Tara C; George, Angela C; Garner, Harold R

    2009-01-01

    In the scientific research community, plagiarism and covert multiple publications of the same data are considered unacceptable because they undermine the public confidence in the scientific integrity. Yet, little has been done to help authors and editors to identify highly similar citations, which sometimes may represent cases of unethical duplication. For this reason, we have made available Déjà vu, a publicly available database of highly similar Medline citations identified by the text similarity search engine eTBLAST. Following manual verification, highly similar citation pairs are classified into various categories ranging from duplicates with different authors to sanctioned duplicates. Déjà vu records also contain user-provided commentary and supporting information to substantiate each document's categorization. Déjà vu and eTBLAST are available to authors, editors, reviewers, ethicists and sociologists to study, intercept, annotate and deter questionable publication practices. These tools are part of a sustained effort to enhance the quality of Medline as 'the' biomedical corpus. The Déjà vu database is freely accessible at http://spore.swmed.edu/dejavu. The tool eTBLAST is also freely available at http://etblast.org.

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

    PubMed

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

    2016-01-01

    Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

  13. Digital database of the geologic map of the island of Hawai'i [Hawaii

    USGS Publications Warehouse

    Trusdell, Frank A.; Wolfe, Edward W.; Morris, Jean

    2006-01-01

    This online publication (DS 144) provides the digital database for the printed map by Edward W. Wolfe and Jean Morris (I-2524-A; 1996). This digital database contains all the information used to publish U.S. Geological Survey Geologic Investigations Series I-2524-A (available only in paper form; see http://pubs.er.usgs.gov/pubs/i/i2524A). The database contains the distribution and relationships of volcanic and surficial-sedimentary deposits on the island of Hawai‘i. This dataset represents the geologic history for the five volcanoes that comprise the Island of Hawai'i. The volcanoes are Kohala, Mauna Kea, Hualalai, Mauna Loa and Kīlauea.This database of the geologic map contributes to understanding the geologic history of the Island of Hawai‘i and provides the basis for understanding long-term volcanic processes in an intra-plate ocean island volcanic system. In addition the database also serves as a basis for producing volcanic hazards assessment for the island of Hawai‘i. Furthermore it serves as a base layer to be used for interdisciplinary research.This online publication consists of a digital database of the geologic map, an explanatory pamphlet, description of map units, correlation of map units diagram, and images for plotting. Geologic mapping was compiled at a scale of 1:100,000 for the entire mapping area. The geologic mapping was compiled as a digital geologic database in ArcInfo GIS format.

  14. THE DRINKING WATER TREATABILITY DATABASE (Conference Paper)

    EPA Science Inventory

    The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

  15. 16 CFR § 1102.2 - Purpose.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Background and Definitions § 1102.2 Purpose. This... establishment and maintenance of a Publicly Available Consumer Product Safety Information Database (also referred to as the “Database”) on the safety of consumer products and other products or substances...

  16. 16 CFR 1102.2 - Purpose.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Background and Definitions § 1102.2... establishment and maintenance of a Publicly Available Consumer Product Safety Information Database (also referred to as the “Database”) on the safety of consumer products and other products or substances...

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

    PubMed

    Zhavoronkov, Alex; Cantor, Charles R

    2011-01-01

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

  18. BioCarian: search engine for exploratory searches in heterogeneous biological databases.

    PubMed

    Zaki, Nazar; Tennakoon, Chandana

    2017-10-02

    There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

  19. 77 FR 37558 - Disclosure of Certain Credit Card Complaint Data

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-22

    ... publication of a public consumer complaint database that, instead of aiding complainants, enables data mining... Certain Credit Card Complaint Data AGENCY: Bureau of Consumer Financial Protection. ACTION: Notice of... Bureau plans to exercise its discretion to publicly disclose certain credit card complaint data that do...

  20. Privacy protection and public goods: building a genetic database for health research in Newfoundland and Labrador

    PubMed Central

    Pullman, Daryl; Perrot-Daley, Astrid; Hodgkinson, Kathy; Street, Catherine; Rahman, Proton

    2013-01-01

    Objective To provide a legal and ethical analysis of some of the implementation challenges faced by the Population Therapeutics Research Group (PTRG) at Memorial University (Canada), in using genealogical information offered by individuals for its genetics research database. Materials and methods This paper describes the unique historical and genetic characteristics of the Newfoundland and Labrador founder population, which gave rise to the opportunity for PTRG to build the Newfoundland Genealogy Database containing digitized records of all pre-confederation (1949) census records of the Newfoundland founder population. In addition to building the database, PTRG has developed the Heritability Analytics Infrastructure, a data management structure that stores genotype, phenotype, and pedigree information in a single database, and custom linkage software (KINNECT) to perform pedigree linkages on the genealogy database. Discussion A newly adopted legal regimen in Newfoundland and Labrador is discussed. It incorporates health privacy legislation with a unique research ethics statute governing the composition and activities of research ethics boards and, for the first time in Canada, elevating the status of national research ethics guidelines into law. The discussion looks at this integration of legal and ethical principles which provides a flexible and seamless framework for balancing the privacy rights and welfare interests of individuals, families, and larger societies in the creation and use of research data infrastructures as public goods. Conclusion The complementary legal and ethical frameworks that now coexist in Newfoundland and Labrador provide the legislative authority, ethical legitimacy, and practical flexibility needed to find a workable balance between privacy interests and public goods. Such an approach may also be instructive for other jurisdictions as they seek to construct and use biobanks and related research platforms for genetic research. PMID:22859644

Some links on this page may take you to non-federal websites. Their policies may differ from this site.
Top