Sample records for database search programs

  1. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

    PubMed

    Wang, Chunlin; Lefkowitz, Elliot J

    2004-10-28

    Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

  2. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

    PubMed Central

    Wang, Chunlin; Lefkowitz, Elliot J

    2004-01-01

    Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

  3. Algorithms for database-dependent search of MS/MS data.

    PubMed

    Matthiesen, Rune

    2013-01-01

    The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather than providing software user manuals. The process of database-dependent search can be divided into search strategy, peptide scoring, protein scoring, and finally protein inference. Most efforts in the literature have been put in to comparing results from different software rather than discussing the underlining algorithms. Such practical comparisons can be cluttered by suboptimal implementation and the observed differences are frequently caused by software parameters settings which have not been set proper to allow even comparison. In other words an algorithmic idea can still be worth considering even if the software implementation has been demonstrated to be suboptimal. The aim in this chapter is therefore to split the algorithms for database-dependent searching of MS/MS data into the above steps so that the different algorithmic ideas become more transparent and comparable. Most search engines provide good implementations of the first three data analysis steps mentioned above, whereas the final step of protein inference are much less developed for most search engines and is in many cases performed by an external software. The final part of this chapter illustrates how protein inference is built into the VEMS search engine and discusses a stand-alone program SIR for protein inference that can import a Mascot search result.

  4. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  5. LigandBox: A database for 3D structures of chemical compounds.

    PubMed

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

  6. National Rehabilitation Information Center

    MedlinePlus

    ... search the NARIC website or one of our databases Select a database or search for a webpage A NARIC webpage ... Projects conducting research and/or development (NIDILRR Program Database). Organizations, agencies, and online resources that support people ...

  7. Using "Reader's Guide to Periodical Literature" on CD-Rom To Teach Database Searching to High School Students.

    ERIC Educational Resources Information Center

    Kern, Joanne F.

    The lack of opportunity for high school sophomores to learn database searching was addressed by the implementation of a computerized magazine article search program. "Reader's Guide to Periodical Literature" on CD-ROM was used to train students in database searching during the time they were assigned to the library to do research papers…

  8. 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

  9. Archive of mass spectral data files on recordable CD-ROMs and creation and maintenance of a searchable computerized database.

    PubMed

    Amick, G D

    1999-01-01

    A database containing names of mass spectral data files generated in a forensic toxicology laboratory and two Microsoft Visual Basic programs to maintain and search this database is described. The data files (approximately 0.5 KB/each) were collected from six mass spectrometers during routine casework. Data files were archived on 650 MB (74 min) recordable CD-ROMs. Each recordable CD-ROM was given a unique name, and its list of data file names was placed into the database. The present manuscript describes the use of search and maintenance programs for searching and routine upkeep of the database and creation of CD-ROMs for archiving of data files.

  10. A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

    PubMed

    Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

    1996-03-01

    We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

  11. On the predictability of protein database search complexity and its relevance to optimization of distributed searches.

    PubMed

    Deciu, Cosmin; Sun, Jun; Wall, Mark A

    2007-09-01

    We discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as Linux cluster. Load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. The particular case of the Sequest program is considered here, but the general methodology should apply to any similar database search program. We show how the runtimes for Sequest searches of tandem mass spectral data can be predicted from profiles of previous representative searches, and how this information can be used for better load balancing of novel data. A well-known heuristic load balancing method is shown to be applicable to this problem, and its performance is analyzed for a variety of search parameters.

  12. Finding Protein and Nucleotide Similarities with FASTA

    PubMed Central

    Pearson, William R.

    2016-01-01

    The FASTA programs provide a comprehensive set of rapid similarity searching tools ( fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local and global similarity searches ( ssearch36, ggsearch36) and for searching with short peptides and oligonucleotides ( fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity (Unit 3.5). The FASTA programs can produce “BLAST-like” alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases (Unit 9.4). The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. PMID:27010337

  13. Finding Protein and Nucleotide Similarities with FASTA.

    PubMed

    Pearson, William R

    2016-03-24

    The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity. The FASTA programs can produce "BLAST-like" alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases. The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. Copyright © 2016 John Wiley & Sons, Inc.

  14. 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…

  15. BLAST and FASTA similarity searching for multiple sequence alignment.

    PubMed

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  16. MICA: desktop software for comprehensive searching of DNA databases

    PubMed Central

    Stokes, William A; Glick, Benjamin S

    2006-01-01

    Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

  17. 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

  18. 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

  19. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

    PubMed

    Jagtap, Pratik; Goslinga, Jill; Kooren, Joel A; McGowan, Thomas; Wroblewski, Matthew S; Seymour, Sean L; Griffin, Timothy J

    2013-04-01

    Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. System for Performing Single Query Searches of Heterogeneous and Dispersed Databases

    NASA Technical Reports Server (NTRS)

    Maluf, David A. (Inventor); Okimura, Takeshi (Inventor); Gurram, Mohana M. (Inventor); Tran, Vu Hoang (Inventor); Knight, Christopher D. (Inventor); Trinh, Anh Ngoc (Inventor)

    2017-01-01

    The present invention is a distributed computer system of heterogeneous databases joined in an information grid and configured with an Application Programming Interface hardware which includes a search engine component for performing user-structured queries on multiple heterogeneous databases in real time. This invention reduces overhead associated with the impedance mismatch that commonly occurs in heterogeneous database queries.

  1. --No Title--

    Science.gov Websites

    Search Search Home SH Reference Manual E19 Documentation Program Management Training/Drills Other Dataweb National Water Information System Database SH Reference Manual, E-19 Docs, Program Management

  2. Ocean Drilling Program: Web Site Access Statistics

    Science.gov Websites

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

  3. NBIC: National Ballast Information Clearinghouse

    Science.gov Websites

    Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database / Database Manager: Tami Huber Senior Analyst / Ecologist: Mark Minton Data Managers Ashley Arnwine Jessica Hardee Amanda Reynolds Database Design and Programming / Application Programming: Paul Winterbauer

  4. SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands

    NASA Astrophysics Data System (ADS)

    Ho, Chris M. W.; Marshall, Garland R.

    1993-12-01

    SPLICE is a program that processes partial query solutions retrieved from 3D, structural databases to generate novel, aggregate ligands. It is designed to interface with the database searching program FOUNDATION, which retrieves fragments containing any combination of a user-specified minimum number of matching query elements. SPLICE eliminates aspects of structures that are physically incapable of binding within the active site. Then, a systematic rule-based procedure is performed upon the remaining fragments to ensure receptor complementarity. All modifications are automated and remain transparent to the user. Ligands are then assembled by linking components into composite structures through overlapping bonds. As a control experiment, FOUNDATION and SPLICE were used to reconstruct a know HIV-1 protease inhibitor after it had been fragmented, reoriented, and added to a sham database of fifty different small molecules. To illustrate the capabilities of this program, a 3D search query containing the pharmacophoric elements of an aspartic proteinase-inhibitor crystal complex was searched using FOUNDATION against a subset of the Cambridge Structural Database. One hundred thirty-one compounds were retrieved, each containing any combination of at least four query elements. Compounds were automatically screened and edited for receptor complementarity. Numerous combinations of fragments were discovered that could be linked to form novel structures, containing a greater number of pharmacophoric elements than any single retrieved fragment.

  5. Developing a Systematic Patent Search Training Program

    ERIC Educational Resources Information Center

    Zhang, Li

    2009-01-01

    This study aims to develop a systematic patent training program using patent analysis and citation analysis techniques applied to patents held by the University of Saskatchewan. The results indicate that the target audience will be researchers in life sciences, and aggregated patent database searching and advanced search techniques should be…

  6. Citation Searching: Search Smarter & Find More

    ERIC Educational Resources Information Center

    Hammond, Chelsea C.; Brown, Stephanie Willen

    2008-01-01

    The staff at University of Connecticut are participating in Elsevier's Student Ambassador Program (SAmP) in which graduate students train their peers on "citation searching" research using Scopus and Web of Science, two tremendous citation databases. They are in the fourth semester of these training programs, and they are wildly successful: They…

  7. Home Page: Division of Mammals: Department of Vertebrate Zoology: NMNH

    Science.gov Websites

    Search Field: Search Submit: Submit {search_item} Advanced Search Plan Your Visit Exhibitions Education Resources Databases Marine Mammal Program Beaked Whale Identification Guide 3D Primates VZ Libraries Related

  8. Mass Spectral Library with Search Program, Data Version: NIST v17

    National Institute of Standards and Technology Data Gateway

    SRD 1A NIST/EPA/NIH Mass Spectral Library with Search Program, Data Version: NIST v17 (PC database for purchase)   Available with full-featured NIST MS Search Program for Windows integrated tools, the NIST '98 is a fully evaluated collection of electron-ionization mass spectra. (147,198 Compounds with Spectra; 147,194 Chemical Structures; 174,948 Spectra )

  9. BEAUTY-X: enhanced BLAST searches for DNA queries.

    PubMed

    Worley, K C; Culpepper, P; Wiese, B A; Smith, R F

    1998-01-01

    BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu

  10. Department of Pesticide Regulation Databases

    Science.gov Websites

    ; Safety Report an Illness | Food Safety | Risk Assessment & Mitigation | Human Health | Physicians Endangered Species Enforcement Food Safety Forms Human Health Laws Licensing Mill Assessment Permitting Pest Statewide search: Search Search Search this site: Search Search DPR California Home Programs Health &

  11. Assigning statistical significance to proteotypic peptides via database searches

    PubMed Central

    Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

    2011-01-01

    Querying MS/MS spectra against a database containing only proteotypic peptides reduces data analysis time due to reduction of database size. Despite the speed advantage, this search strategy is challenged by issues of statistical significance and coverage. The former requires separating systematically significant identifications from less confident identifications, while the latter arises when the underlying peptide is not present, due to single amino acid polymorphisms (SAPs) or post-translational modifications (PTMs), in the proteotypic peptide libraries searched. To address both issues simultaneously, we have extended RAId’s knowledge database to include proteotypic information, utilized RAId’s statistical strategy to assign statistical significance to proteotypic peptides, and modified RAId’s programs to allow for consideration of proteotypic information during database searches. The extended database alleviates the coverage problem since all annotated modifications, even those occurred within proteotypic peptides, may be considered. Taking into account the likelihoods of observation, the statistical strategy of RAId provides accurate E-value assignments regardless whether a candidate peptide is proteotypic or not. The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches. PMID:21055489

  12. Strategies for Introducing Databasing into Science.

    ERIC Educational Resources Information Center

    Anderson, Christopher L.

    1990-01-01

    Outlines techniques used in the context of a sixth grade science class to teach database structure and search strategies for science using the AppleWorks program. Provides templates and questions for class and element databases. (Author/YP)

  13. Development of program package for investigation and modeling of carbon nanostructures in diamond like carbon films with the help of Raman scattering and infrared absorption spectra line resolving

    NASA Astrophysics Data System (ADS)

    Hayrapetyan, David B.; Hovhannisyan, Levon; Mantashyan, Paytsar A.

    2013-04-01

    The analysis of complex spectra is an actual problem for modern science. The work is devoted to the creation of a software package, which analyzes spectrum in the different formats, possesses by dynamic knowledge database and self-study mechanism, performs automated analysis of the spectra compound based on knowledge database by application of certain algorithms. In the software package as searching systems, hyper-spherical random search algorithms, gradient algorithms and genetic searching algorithms were used. The analysis of Raman and IR spectrum of diamond-like carbon (DLC) samples were performed by elaborated program. After processing the data, the program immediately displays all the calculated parameters of DLC.

  14. muBLASTP: database-indexed protein sequence search on multicore CPUs.

    PubMed

    Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

    2016-11-04

    The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

  15. SEER Bibliography

    Cancer.gov

    Search this database of articles and other publications produced by cancer registry staff and Surveillance Research Program staff. Search by author, title, date, and organization. Provides links to PubMed and abstracts.

  16. Methods and means used in programming intelligent searches of technical documents

    NASA Technical Reports Server (NTRS)

    Gross, David L.

    1993-01-01

    In order to meet the data research requirements of the Safety, Reliability & Quality Assurance activities at Kennedy Space Center (KSC), a new computer search method for technical data documents was developed. By their very nature, technical documents are partially encrypted because of the author's use of acronyms, abbreviations, and shortcut notations. This problem of computerized searching is compounded at KSC by the volume of documentation that is produced during normal Space Shuttle operations. The Centralized Document Database (CDD) is designed to solve this problem. It provides a common interface to an unlimited number of files of various sizes, with the capability to perform any diversified types and levels of data searches. The heart of the CDD is the nature and capability of its search algorithms. The most complex form of search that the program uses is with the use of a domain-specific database of acronyms, abbreviations, synonyms, and word frequency tables. This database, along with basic sentence parsing, is used to convert a request for information into a relational network. This network is used as a filter on the original document file to determine the most likely locations for the data requested. This type of search will locate information that traditional techniques, (i.e., Boolean structured key-word searching), would not find.

  17. Choosing the Right Database Management Program.

    ERIC Educational Resources Information Center

    Vockell, Edward L.; Kopenec, Donald

    1989-01-01

    Provides a comparison of four database management programs commonly used in schools: AppleWorks, the DOS 3.3 and ProDOS versions of PFS, and MECC's Data Handler. Topics discussed include information storage, spelling checkers, editing functions, search strategies, graphs, printout formats, library applications, and HyperCard. (LRW)

  18. Structure elucidation of organic compounds aided by the computer program system SCANNET

    NASA Astrophysics Data System (ADS)

    Guzowska-Swider, B.; Hippe, Z. S.

    1992-12-01

    Recognition of chemical structure is a very important problem currently solved by molecular spectroscopy, particularly IR, UV, NMR and Raman spectroscopy, and mass spectrometry. Nowadays, solution of the problem is frequently aided by the computer. SCANNET is a computer program system for structure elucidation of organic compounds, developed by our group. The structure recognition of an unknown substance is made by comparing its spectrum with successive reference spectra of standard compounds, i.e. chemical compounds of known chemical structure, stored in a spectral database. The computer program system SCANNET consists of six different spectral databases for following the analytical methods: IR, UV, 13C-NMR, 1H-NMR and Raman spectroscopy, and mass spectrometry. A chemist, to elucidate a structure, can use one of these spectral methods or a combination of them and search the appropriate databases. As the result of searching each spectral database, the user obtains a list of chemical substances whose spectra are identical and/or similar to the spectrum input into the computer. The final information obtained from searching the spectral databases is in the form of a list of chemical substances having all the examined spectra, for each type of spectroscopy, identical or simlar to those of the unknown compound.

  19. Custom Search Engines: Tools & Tips

    ERIC Educational Resources Information Center

    Notess, Greg R.

    2008-01-01

    Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

  20. Fermilab Education Life Science Instructional Resources

    Science.gov Websites

    using SIMply Prairie and student plant population data (6-9) Databases: Birds - Butterflies - Frogs Fermilab's Nature and Ecology Search Programs - Search Science Adventures - Calendar - About - FAQ - Fermilab

  1. Multimedia explorer: image database, image proxy-server and search-engine.

    PubMed Central

    Frankewitsch, T.; Prokosch, U.

    1999-01-01

    Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval. PMID:10566463

  2. Multimedia explorer: image database, image proxy-server and search-engine.

    PubMed

    Frankewitsch, T; Prokosch, U

    1999-01-01

    Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval.

  3. Online Secondary Research in the Advertising Research Class: A Friendly Introduction to Computing.

    ERIC Educational Resources Information Center

    Adler, Keith

    In an effort to promote computer literacy among advertising students, an assignment was devised that required the use of online database search techniques to find secondary research materials. The search program, chosen for economical reasons, was "Classroom Instruction Program" offered by Dialog Information Services. Available for a…

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

    PubMed

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

    2017-08-01

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

  5. A practical approach for inexpensive searches of radiology report databases.

    PubMed

    Desjardins, Benoit; Hamilton, R Curtis

    2007-06-01

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

  6. Using Statistics for Database Management in an Academic Library.

    ERIC Educational Resources Information Center

    Hyland, Peter; Wright, Lynne

    1996-01-01

    Collecting statistical data about database usage by library patrons aids in the management of CD-ROM and database offerings, collection development, and evaluation of training programs. Two approaches to data collection are presented which should be used together: an automated or nonintrusive method which monitors search sessions while the…

  7. Ocean Drilling Program: Privacy Policy

    Science.gov Websites

    and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site ODP/TAMU Science Operator Home Ocean Drilling Program Privacy Policy The following is the privacy policy for the www-odp.tamu.edu web site. 1. Cookies are used in the Database portion of the web

  8. 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

  9. 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.

  10. POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs.

    PubMed

    Dayringer, H E; Sammons, S A

    1991-04-01

    Computer support for research in biotechnology has developed rapidly and has provided several tools to aid the researcher. This report describes the capabilities of new computer software developed in this laboratory to aid in the documentation and planning of experiments in molecular biology. The program, POLLUX, provides a graphical medium for the entry, edit and manipulation of DNA constructs and a textual format for display and edit of construct descriptive data. Program operation and procedures are designed to mimic the actual laboratory experiments with respect to capability and the order in which they are performed. Flexible control over the content of the computer-generated displays and program facilities is provided by a mouse-driven menu interface. Programmed facilities for mutagenesis, simulated cloning and searching of the database from networked workstations are described.

  11. PTSD Treatment Programs in the U.S. Department of Veterans Affairs

    MedlinePlus

    ... VA for Vets Performance Based Interviewing Clinical Trainees (Academic Affiliations) Employees & Contractors Talent Management System (TMS) VA ... stress. Search Pilots Search PILOTS *, the largest citation database on PTSD. What is PILOTS? Subscribe Sign up ...

  12. MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

    PubMed

    Yang, Chunguang G; Granite, Stephen J; Van Eyk, Jennifer E; Winslow, Raimond L

    2006-11-01

    Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

  13. Addition of a breeding database in the Genome Database for Rosaceae

    PubMed Central

    Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

    2013-01-01

    Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox PMID:24247530

  14. Addition of a breeding database in the Genome Database for Rosaceae.

    PubMed

    Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

    2013-01-01

    Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox.

  15. Accessibility and quality of online information for pediatric orthopaedic surgery fellowships.

    PubMed

    Davidson, Austin R; Murphy, Robert F; Spence, David D; Kelly, Derek M; Warner, William C; Sawyer, Jeffrey R

    2014-12-01

    Pediatric orthopaedic fellowship applicants commonly use online-based resources for information on potential programs. Two primary sources are the San Francisco Match (SF Match) database and the Pediatric Orthopaedic Society of North America (POSNA) database. We sought to determine the accessibility and quality of information that could be obtained by using these 2 sources. The online databases of the SF Match and POSNA were reviewed to determine the availability of embedded program links or external links for the included programs. If not available in the SF Match or POSNA data, Web sites for listed programs were located with a Google search. All identified Web sites were analyzed for accessibility, content volume, and content quality. At the time of online review, 50 programs, offering 68 positions, were listed in the SF Match database. Although 46 programs had links included with their information, 36 (72%) of them simply listed http://www.sfmatch.org as their unique Web site. Ten programs (20%) had external links listed, but only 2 (4%) linked directly to the fellowship web page. The POSNA database does not list any links to the 47 programs it lists, which offer 70 positions. On the basis of a Google search of the 50 programs listed in the SF Match database, web pages were found for 35. Of programs with independent web pages, all had a description of the program and 26 (74%) described their application process. Twenty-nine (83%) listed research requirements, 22 (63%) described the rotation schedule, and 12 (34%) discussed the on-call expectations. A contact telephone number and/or email address was provided by 97% of programs. Twenty (57%) listed both the coordinator and fellowship director, 9 (26%) listed the coordinator only, 5 (14%) listed the fellowship director only, and 1 (3%) had no contact information given. The SF Match and POSNA databases provide few direct links to fellowship Web sites, and individual program Web sites either do not exist or do not effectively convey information about the programs. Improved accessibility and accurate information online would allow potential applicants to obtain information about pediatric fellowships in a more efficient manner.

  16. The Next Linear Collider Program

    Science.gov Websites

    Navbar Other Address Books: Laboratory Phone/Email Web Directory SLAC SLAC Phonebook Entire SLAC Web FNAL Telephone Directory Fermilab Search LLNL Phone Book LLNL Web Servers LBNL Directory Services Web Search: A-Z Index KEK E-mail Database Research Projects NLC Website Search: Entire SLAC Web | Help

  17. 41. DISCOVERY, SEARCH, AND COMMUNICATION OF TEXTUAL KNOWLEDGE RESOURCES IN DISTRIBUTED SYSTEMS a. Discovering and Utilizing Knowledge Sources for Metasearch Knowledge Systems

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

    Zamora, Antonio

    Advanced Natural Language Processing Tools for Web Information Retrieval, Content Analysis, and Synthesis. The goal of this SBIR was to implement and evaluate several advanced Natural Language Processing (NLP) tools and techniques to enhance the precision and relevance of search results by analyzing and augmenting search queries and by helping to organize the search output obtained from heterogeneous databases and web pages containing textual information of interest to DOE and the scientific-technical user communities in general. The SBIR investigated 1) the incorporation of spelling checkers in search applications, 2) identification of significant phrases and concepts using a combination of linguisticmore » and statistical techniques, and 3) enhancement of the query interface and search retrieval results through the use of semantic resources, such as thesauri. A search program with a flexible query interface was developed to search reference databases with the objective of enhancing search results from web queries or queries of specialized search systems such as DOE's Information Bridge. The DOE ETDE/INIS Joint Thesaurus was processed to create a searchable database. Term frequencies and term co-occurrences were used to enhance the web information retrieval by providing algorithmically-derived objective criteria to organize relevant documents into clusters containing significant terms. A thesaurus provides an authoritative overview and classification of a field of knowledge. By organizing the results of a search using the thesaurus terminology, the output is more meaningful than when the results are just organized based on the terms that co-occur in the retrieved documents, some of which may not be significant. An attempt was made to take advantage of the hierarchy provided by broader and narrower terms, as well as other field-specific information in the thesauri. The search program uses linguistic morphological routines to find relevant entries regardless of whether terms are stored in singular or plural form. Implementation of additional inflectional morphology processes for verbs can enhance retrieval further, but this has to be balanced by the possibility of broadening the results too much. In addition to the DOE energy thesaurus, other sources of specialized organized knowledge such as the Medical Subject Headings (MeSH), the Unified Medical Language System (UMLS), and Wikipedia were investigated. The supporting role of the NLP thesaurus search program was enhanced by incorporating spelling aid and a part-of-speech tagger to cope with misspellings in the queries and to determine the grammatical roles of the query words and identify nouns for special processing. To improve precision, multiple modes of searching were implemented including Boolean operators, and field-specific searches. Programs to convert a thesaurus or reference file into searchable support files can be deployed easily, and the resulting files are immediately searchable to produce relevance-ranked results with builtin spelling aid, morphological processing, and advanced search logic. Demonstration systems were built for several databases, including the DOE energy thesaurus.« less

  18. SymDex: increasing the efficiency of chemical fingerprint similarity searches for comparing large chemical libraries by using query set indexing.

    PubMed

    Tai, David; Fang, Jianwen

    2012-08-27

    The large sizes of today's chemical databases require efficient algorithms to perform similarity searches. It can be very time consuming to compare two large chemical databases. This paper seeks to build upon existing research efforts by describing a novel strategy for accelerating existing search algorithms for comparing large chemical collections. The quest for efficiency has focused on developing better indexing algorithms by creating heuristics for searching individual chemical against a chemical library by detecting and eliminating needless similarity calculations. For comparing two chemical collections, these algorithms simply execute searches for each chemical in the query set sequentially. The strategy presented in this paper achieves a speedup upon these algorithms by indexing the set of all query chemicals so redundant calculations that arise in the case of sequential searches are eliminated. We implement this novel algorithm by developing a similarity search program called Symmetric inDexing or SymDex. SymDex shows over a 232% maximum speedup compared to the state-of-the-art single query search algorithm over real data for various fingerprint lengths. Considerable speedup is even seen for batch searches where query set sizes are relatively small compared to typical database sizes. To the best of our knowledge, SymDex is the first search algorithm designed specifically for comparing chemical libraries. It can be adapted to most, if not all, existing indexing algorithms and shows potential for accelerating future similarity search algorithms for comparing chemical databases.

  19. Web-based Electronic Sharing and RE-allocation of Assets

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

    Leverett, Dave; Miller, Robert A.; Berlin, Gary J.

    2002-09-09

    The Electronic Asses Sharing Program is a web-based application that provides the capability for complex-wide sharing and reallocation of assets that are excess, under utilized, or un-utilized. through a web-based fron-end and supporting has database with a search engine, users can search for assets that they need, search for assets needed by others, enter assets they need, and enter assets they have available for reallocation. In addition, entire listings of available assets and needed assets can be viewed. The application is written in Java, the hash database and search engine are in Object-oriented Java Database Management (OJDBM). The application willmore » be hosted on an SRS-managed server outside the Firewall and access will be controlled via a protected realm. An example of the application can be viewed at the followinig (temporary) URL: http://idgdev.srs.gov/servlet/srs.weshare.WeShare« less

  20. [Synthesis of 107 Workplace Literacy Programs.

    ERIC Educational Resources Information Center

    Bussert, Kathy M.

    A study examined information from 107 workplace literacy program descriptions from the United States and drew conclusions about joint partnerships, funding, and flexibility. Most of the program descriptions were found in an extensive search using the ERIC database. The programs described were from 1989 and 1990. Some of the findings were the…

  1. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

    PubMed

    Fourment, Mathieu; Gibbs, Mark J

    2008-02-05

    Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

  2. Parenting Interventions for Indigenous Child Psychosocial Functioning: A Scoping Review

    ERIC Educational Resources Information Center

    Macvean, Michelle; Shlonsky, Aron; Mildon, Robyn; Devine, Ben

    2017-01-01

    Objectives: To scope evaluations of Indigenous parenting programs designed to improve child psychosocial outcomes. Methods: Electronic databases, gray literature, Indigenous websites and journals, and reference lists were searched. The search was restricted to high-income countries with a history of colonialism. Results: Sixteen studies describing…

  3. Promising Practices for Home/School Partnerships.

    ERIC Educational Resources Information Center

    Salerno, Anne; Fink, Mary

    This report contains profiles of 18 innovative and successful parent involvement programs for migrant families. The programs were selected based on recommendations from State Directors of Migrant Education and migrant educators and on a search of the ERIC database. Each profile includes sponsoring institution or agency, program format, program…

  4. BIOPEP database and other programs for processing bioactive peptide sequences.

    PubMed

    Minkiewicz, Piotr; Dziuba, Jerzy; Iwaniak, Anna; Dziuba, Marta; Darewicz, Małgorzata

    2008-01-01

    This review presents the potential for application of computational tools in peptide science based on a sample BIOPEP database and program as well as other programs and databases available via the World Wide Web. The BIOPEP application contains a database of biologically active peptide sequences and a program enabling construction of profiles of the potential biological activity of protein fragments, calculation of quantitative descriptors as measures of the value of proteins as potential precursors of bioactive peptides, and prediction of bonds susceptible to hydrolysis by endopeptidases in a protein chain. Other bioactive and allergenic peptide sequence databases are also presented. Programs enabling the construction of binary and multiple alignments between peptide sequences, the construction of sequence motifs attributed to a given type of bioactivity, searching for potential precursors of bioactive peptides, and the prediction of sites susceptible to proteolytic cleavage in protein chains are available via the Internet as are other approaches concerning secondary structure prediction and calculation of physicochemical features based on amino acid sequence. Programs for prediction of allergenic and toxic properties have also been developed. This review explores the possibilities of cooperation between various programs.

  5. Leadership Curricula in Nursing Education: A Critical Literature Review and Gap Analysis.

    PubMed

    Morrow, Kelly J

    2015-07-01

    The Institute of Medicine's Future of Nursing report advises nursing education programs to integrate and embed leadership content within all areas of prelicensure nursing curriculum. This critical literature review synthesizes the state of the science of leadership curricula in prelicensure baccalaureate nursing education programs from 2008 to 2013. Gaps are identified and discussed. The Academic Search Premier and Health Source databases were searched, using the keywords baccalaureate nursing education and leadership. The CINAHL database was searched, using the keywords leadership, education, nursing, and baccalaureate. The 13 peer-reviewed articles identified for inclusion comprised descriptive articles (n = 8), mixed-methods studies (n = 2), quantitative studies (n = 2), and a qualitative study (n = 1). The underlying theme identified is the study and use of active learning strategies. Subthemes within this context were the use of reflection, peer learning, interdisciplinary teams, organizational partnerships, and curricular reform. Copyright 2015, SLACK Incorporated.

  6. MISSE in the Materials and Processes Technical Information System (MAPTIS )

    NASA Technical Reports Server (NTRS)

    Burns, DeWitt; Finckenor, Miria; Henrie, Ben

    2013-01-01

    Materials International Space Station Experiment (MISSE) data is now being collected and distributed through the Materials and Processes Technical Information System (MAPTIS) at Marshall Space Flight Center in Huntsville, Alabama. MISSE data has been instrumental in many programs and continues to be an important source of data for the space community. To facilitate great access to the MISSE data the International Space Station (ISS) program office and MAPTIS are working to gather this data into a central location. The MISSE database contains information about materials, samples, and flights along with pictures, pdfs, excel files, word documents, and other files types. Major capabilities of the system are: access control, browsing, searching, reports, and record comparison. The search capabilities will search within any searchable files so even if the desired meta-data has not been associated data can still be retrieved. Other functionality will continue to be added to the MISSE database as the Athena Platform is expanded

  7. NASA Image eXchange (NIX)

    NASA Technical Reports Server (NTRS)

    vonOfenheim. William H. C.; Heimerl, N. Lynn; Binkley, Robert L.; Curry, Marty A.; Slater, Richard T.; Nolan, Gerald J.; Griswold, T. Britt; Kovach, Robert D.; Corbin, Barney H.; Hewitt, Raymond W.

    1998-01-01

    This paper discusses the technical aspects of and the project background for the NASA Image exchange (NIX). NIX, which provides a single entry point to search selected image databases at the NASA Centers, is a meta-search engine (i.e., a search engine that communicates with other search engines). It uses these distributed digital image databases to access photographs, animations, and their associated descriptive information (meta-data). NIX is available for use at the following URL: http://nix.nasa.gov./NIX, which was sponsored by NASAs Scientific and Technical Information (STI) Program, currently serves images from seven NASA Centers. Plans are under way to link image databases from three additional NASA Centers. images and their associated meta-data, which are accessible by NIX, reside at the originating Centers, and NIX utilizes a virtual central site that communicates with each of these sites. Incorporated into the virtual central site are several protocols to support searches from a diverse collection of database engines. The searches are performed in parallel to ensure optimization of response times. To augment the search capability, browse functionality with pre-defined categories has been built into NIX, thereby ensuring dissemination of 'best-of-breed' imagery. As a final recourse, NIX offers access to a help desk via an on-line form to help locate images and information either within the scope of NIX or from available external sources.

  8. 48 CFR 19.703 - Eligibility requirements for participating in the program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... or Small Business Administration certification status of the ANC or Indian tribe. (ii) Where one or... accessing the Central Contractor Registration (CCR) database or by contacting the SBA. Options for contacting the SBA include— (i) HUBZone small business database search application Web page at http://dsbs...

  9. 48 CFR 19.703 - Eligibility requirements for participating in the program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... or Small Business Administration certification status of the ANC or Indian tribe. (ii) Where one or... accessing the Central Contractor Registration (CCR) database or by contacting the SBA. Options for contacting the SBA include— (i) HUBZone small business database search application Web page at http://dsbs...

  10. Automated Literature Searches for Longitudinal Tracking of Cancer Research Training Program Graduates.

    PubMed

    Padilla, Luz A; Desmond, Renee A; Brooks, C Michael; Waterbor, John W

    2018-06-01

    A key outcome measure of cancer research training programs is the number of cancer-related peer-reviewed publications after training. Because program graduates do not routinely report their publications, staff must periodically conduct electronic literature searches on each graduate. The purpose of this study is to compare findings of an innovative computer-based automated search program versus repeated manual literature searches to identify post-training peer-reviewed publications. In late 2014, manual searches for publications by former R25 students identified 232 cancer-related articles published by 112 of 543 program graduates. In 2016, a research assistant was instructed in performing Scopus literature searches for comparison with individual PubMed searches on our 543 program graduates. Through 2014, Scopus found 304 cancer publications, 220 of that had been retrieved manually plus an additional 84 papers. However, Scopus missed 12 publications found manually. Together, both methods found 316 publications. The automated method found 96.2 % of the 316 publications while individual searches found only 73.4 %. An automated search method such as using the Scopus database is a key tool for conducting comprehensive literature searches, but it must be supplemented with periodic manual searches to find the initial publications of program graduates. A time-saving feature of Scopus is the periodic automatic alerts of new publications. Although a training period is needed and initial costs can be high, an automated search method is worthwhile due to its high sensitivity and efficiency in the long term.

  11. The NSO FTS database program and archive (FTSDBM)

    NASA Technical Reports Server (NTRS)

    Lytle, D. M.

    1992-01-01

    Data from the NSO Fourier transform spectrometer is being re-archived from half inch tape onto write-once compact disk. In the process, information about each spectrum and a low resolution copy of each spectrum is being saved into an on-line database. FTSDBM is a simple database management program in the NSO external package for IRAF. A command language allows the FTSDBM user to add entries to the database, delete entries, select subsets from the database based on keyword values including ranges of values, create new database files based on these subsets, make keyword lists, examine low resolution spectra graphically, and make disk number/file number lists. Once the archive is complete, FTSDBM will allow the database to be efficiently searched for data of interest to the user and the compact disk format will allow random access to that data.

  12. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

    PubMed Central

    Fourment, Mathieu; Gibbs, Mark J

    2008-01-01

    Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically. PMID:18251994

  13. Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs).

    PubMed

    Rogozin, I B; Mayorov, V I; Lavrentieva, M V; Milanesi, L; Adkison, L R

    2000-09-01

    The presence of repetitive elements can create serious problems for sequence analysis, especially in the case of homology searches in nucleotide sequence databases. Repetitive elements should be treated carefully by using special programs and databases. In this paper, various aspects of SINE (short interspersed repetitive element) identification, analysis and evolution are discussed.

  14. Kangaroo – A pattern-matching program for biological sequences

    PubMed Central

    2002-01-01

    Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718

  15. Ocean Drilling Program: Publication Services: Online Manuscript Submission

    Science.gov Websites

    products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP/TAMU Science Operator Home ODP's main web site Publications Policy Author Instructions Scientific Results Manuscript use the submission and review forms available on the IODP-USIO publications web site. ODP | Search

  16. Tools to Ease Your Internet Adventures: Part I.

    ERIC Educational Resources Information Center

    Descy, Don E.

    1993-01-01

    This first of a two-part series highlights three tools that improve accessibility to Internet resources: (1) Alex, a database that accesses files in FTP (file transfer protocol) sites; (2) Archie, software that searches for file names with a user's search term; and (3) Gopher, a menu-driven program to access Internet sites. (LRW)

  17. A Critical Review of Research on the Alert Program®

    ERIC Educational Resources Information Center

    Gill, Kamaldeep; Thompson-Hodgetts, Sandra; Rasmussen, Carmen

    2018-01-01

    To evaluate the strength of evidence for the effectiveness, feasibility, and appropriateness of the Alert Program®. Multiple databases were systematically searched for peer-reviewed, English-language articles that evaluated the Alert Program®. Six articles met the inclusion criteria. The strength of evidence ranged from weak to moderate using the…

  18. The 21st Century Writing Program: Collaboration for the Common Good

    ERIC Educational Resources Information Center

    Moberg, Eric

    2010-01-01

    The purpose of this report is to review the literature on theoretical frameworks, best practices, and conceptual models for the 21st century collegiate writing program. Methods include electronic database searches for recent and historical peer-reviewed scholarly literature on collegiate writing programs. The author analyzed over 65 sources from…

  19. Decision making in family medicine: randomized trial of the effects of the InfoClinique and Trip database search engines.

    PubMed

    Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

    2013-10-01

    To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Randomized trial. Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Fifteen second-year family medicine residents. Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine's effect on the decision-making process in clinical practice. Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants' perceptions of each engine's effect on the decision-making process were very positive and similar for both search engines. Family medicine residents' ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care.

  20. Partial DNA sequencing of Douglas-fir cDNAs used in RFLP mapping

    Treesearch

    K.D. Jermstad; D.L. Bassoni; C.S. Kinlaw; D.B. Neale

    1998-01-01

    DNA sequences from 87 Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) cDNA RFLP probes were determined. Sequences were submitted to the GenBank dbEST database and searched for similarity against nucleotide and protein databases using the BLASTn and BLASTx programs. Twenty-one sequences (24%) were assigned putative functions; 18 of which...

  1. The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

    ERIC Educational Resources Information Center

    Machovec, George S., Ed.

    1995-01-01

    Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

  2. University Library Online Reference Service Program Plan, 1986/87.

    ERIC Educational Resources Information Center

    Koga, James S.

    This program plan for online reference service--the individualized assistance provided to a library patron using an online system--at California State Polytechnic University, Pomona, covers the areas of funding, eligibility for online services, search request eligibility, database eligibility, management of online services, reference faculty…

  3. The Technological Evolution in Schools: Reflections and Projections.

    ERIC Educational Resources Information Center

    Higgins, James E.

    1991-01-01

    Presents a first-person account of one teacher's experiences with computer hardware and software. The article discusses various programs and applications, such as integrated learning systems, database searching via CD-ROM, desktop publishing, authoring programs, and indicates future changes in instruction with increasing use of technology. (SM)

  4. Artificial Intelligence: Applications in Education.

    ERIC Educational Resources Information Center

    Thorkildsen, Ron J.; And Others

    1986-01-01

    Artificial intelligence techniques are used in computer programs to search out rapidly and retrieve information from very large databases. Programing advances have also led to the development of systems that provide expert consultation (expert systems). These systems, as applied to education, are the primary emphasis of this article. (LMO)

  5. Chiropractic: An Introduction

    MedlinePlus

    ... the sciences. Chiropractic training is a 4-year academic program that includes both classroom work and direct ... health approaches, including publications and searches of Federal databases of scientific and medical literature. The Clearinghouse does ...

  6. Nutrition Education and Body Mass Index in Grades K-12: A Systematic Review

    ERIC Educational Resources Information Center

    Price, Cayla; Cohen, Deborah; Pribis, Peter; Cerami, Jean

    2017-01-01

    Background: Overweight and obese body mass index (BMI) status affects an increasing number of children in the United States. The school setting has been identified as a focus area to implement obesity prevention programs. Methods: A database search of PubMed, Education Search Complete, and Cumulative Index to Nursing and Allied Health Literature…

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

    ERIC Educational Resources Information Center

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

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

  8. Development of a database system for near-future climate change projections under the Japanese National Project SI-CAT

    NASA Astrophysics Data System (ADS)

    Nakagawa, Y.; Kawahara, S.; Araki, F.; Matsuoka, D.; Ishikawa, Y.; Fujita, M.; Sugimoto, S.; Okada, Y.; Kawazoe, S.; Watanabe, S.; Ishii, M.; Mizuta, R.; Murata, A.; Kawase, H.

    2017-12-01

    Analyses of large ensemble data are quite useful in order to produce probabilistic effect projection of climate change. Ensemble data of "+2K future climate simulations" are currently produced by Japanese national project "Social Implementation Program on Climate Change Adaptation Technology (SI-CAT)" as a part of a database for Policy Decision making for Future climate change (d4PDF; Mizuta et al. 2016) produced by Program for Risk Information on Climate Change. Those data consist of global warming simulations and regional downscaling simulations. Considering that those data volumes are too large (a few petabyte) to download to a local computer of users, a user-friendly system is required to search and download data which satisfy requests of the users. We develop "a database system for near-future climate change projections" for providing functions to find necessary data for the users under SI-CAT. The database system for near-future climate change projections mainly consists of a relational database, a data download function and user interface. The relational database using PostgreSQL is a key function among them. Temporally and spatially compressed data are registered on the relational database. As a first step, we develop the relational database for precipitation, temperature and track data of typhoon according to requests by SI-CAT members. The data download function using Open-source Project for a Network Data Access Protocol (OPeNDAP) provides a function to download temporally and spatially extracted data based on search results obtained by the relational database. We also develop the web-based user interface for using the relational database and the data download function. A prototype of the database system for near-future climate change projections are currently in operational test on our local server. The database system for near-future climate change projections will be released on Data Integration and Analysis System Program (DIAS) in fiscal year 2017. Techniques of the database system for near-future climate change projections might be quite useful for simulation and observational data in other research fields. We report current status of development and some case studies of the database system for near-future climate change projections.

  9. RTECS database (on the internet). Online data

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

    NONE

    The Registry of Toxic Effects of Chemical Substances (RTECS (trademark)) is a database of toxicological information compiled, maintained, and updated by the National Institute for Occupational Safety and Health. The program is mandated by the Occupational Safety and Health Act of 1970. The original edition, known as the `Toxic Substances List,` was published on June 28, 1971, and included toxicologic data for approximately 5,000 chemicals. Since that time, the list has continuously grown and been updated, and its name changed to the current title, `Registry of Toxic Effects of Chemical Substances.` RTECS (trademark) now contains over 133,000 chemicals as NIOSHmore » strives to fulfill the mandate to list `all known toxic substances...and the concentrations at which...toxicity is known to occur.` This database is now available for searching through the Gov. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

  10. Accredited Orthopaedic Sports Medicine Fellowship Websites: An Updated Assessment of Accessibility and Content.

    PubMed

    Yayac, Michael; Javandal, Mitra; Mulcahey, Mary K

    2017-01-01

    A substantial number of orthopaedic surgeons apply for sports medicine fellowships after residency completion. The Internet is one of the most important resources applicants use to obtain information about fellowship programs, with the program website serving as one of the most influential sources. The American Orthopaedic Society for Sports Medicine (AOSSM), San Francisco Match (SFM), and Arthroscopy Association of North America (AANA) maintain databases of orthopaedic sports medicine fellowship programs. A 2013 study evaluated the content and accessibility of the websites for accredited orthopaedic sports medicine fellowships. To reassess these websites based on the same parameters and compare the results with those of the study published in 2013 to determine whether any improvement has been made in fellowship website content or accessibility. Cross-sectional study. We reviewed all existing websites for the 95 accredited orthopaedic sports medicine fellowships included in the AOSSM, SFM, and AANA databases. Accessibility of the websites was determined by performing a Google search for each program. A total of 89 sports fellowship websites were evaluated for overall content. Websites for the remaining 6 programs could not be identified, so they were not included in content assessment. Of the 95 accredited sports medicine fellowships, 49 (52%) provided links in the AOSSM database, 89 (94%) in the SFM database, and 24 (25%) in the AANA database. Of the 89 websites, 89 (100%) provided a description of the program, 62 (70%) provided selection process information, and 40 (45%) provided a link to the SFM website. Two searches through Google were able to identify links to 88% and 92% of all accredited programs. The majority of accredited orthopaedic sports medicine fellowship programs fail to utilize the Internet to its full potential as a resource to provide applicants with detailed information about the program, which could help residents in the selection and ranking process. Orthopaedic sports medicine fellowship websites that are easily accessible through the AOSSM, SFM, AANA, or Google and that provide all relevant information for applicants would simplify the process of deciding where to apply, interview, and ultimately how to rank orthopaedic sports medicine fellowship programs for the Orthopaedic Sports Medicine Fellowship Match.

  11. School-Based Sleep Education Programs for Short Sleep Duration in Adolescents: A Systematic Review and Meta-Analysis

    ERIC Educational Resources Information Center

    Chung, Ka-Fai; Chan, Man-Sum; Lam, Ying-Yin; Lai, Cindy Sin-Yee; Yeung, Wing-Fai

    2017-01-01

    Background: Insufficient sleep among students is a major school health problem. School-based sleep education programs tailored to reach large number of students may be one of the solutions. A systematic review and meta-analysis was conducted to summarize the programs' effectiveness and current status. Methods: Electronic databases were searched up…

  12. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

    PubMed Central

    Billoud, B; Kontic, M; Viari, A

    1996-01-01

    At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified. PMID:8628670

  13. Recruitment strategies for an osteoporosis clinical trial: analysis of effectiveness.

    PubMed

    Heard, Allison; March, Rachel; Maguire, Patricia; Reilly, Penny; Helmore, Joy; Cameron, Sheryl; Frampton, Christopher; Nicholls, Gary; Gilchrist, Nigel

    2012-09-01

    To examine the effectiveness of a planned rapid recruitment strategy in an osteoporosis clinical trial. Multiple recruitment methods were explored, including media advertising, searching bone density scan and X-ray results in specialist and primary practice databases, community initiatives, and generation of research centre and study-specific pamphlets. Of 246 women screened, 41 consenting to the study, only 14 were randomised. Thus, 232 (94%) volunteers were screen failures, ineligible or declined to participate. With regard to the cost-effectiveness of all recruitment strategies, searching the research centre database was the most successful, with four women randomised at a cost of approximately NZ$302 per volunteer. Other strategies were less cost-effective. Obtaining a specific study cohort can be achieved by a comprehensive, targeted, rapid recruitment program. A research centre database search was the most successful and cost-effective recruitment modality in this small study. © 2012 Canterbury Geriatric Medical Research Trust. Australasian Journal on Ageing © 2012 ACOTA.

  14. Systematic Review and Meta-Analysis of the "Skills for Social and Academic Success" ("SASS") Program

    ERIC Educational Resources Information Center

    Mychailyszyn, Matthew P.

    2017-01-01

    The purpose of this systematic review and meta-analysis was to synthesize the available research on the "Skills for Social and Academic Success" ("SASS") program, a school-based cognitive/behavioural intervention for adolescents with social anxiety disorder. A search of online databases, combined with reference list examination…

  15. Library Computing.

    ERIC Educational Resources Information Center

    Goodgion, Laurel; And Others

    1986-01-01

    Eight articles in special supplement to "Library Journal" and "School Library Journal" cover a computer program called "Byte into Books"; microcomputers and the small library; creating databases with students; online searching with a microcomputer; quality automation software; Meckler Publishing Company's…

  16. Database resources of the National Center for Biotechnology Information

    PubMed Central

    2015-01-01

    The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:25398906

  17. Database resources of the National Center for Biotechnology Information

    PubMed Central

    2016-01-01

    The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:26615191

  18. Evaluation of the Content and Accessibility of Web Sites for Accredited Orthopaedic Trauma Surgery Fellowships.

    PubMed

    Shaath, M Kareem; Yeranosian, Michael G; Ippolito, Joseph A; Adams, Mark R; Sirkin, Michael S; Reilly, Mark C

    2018-05-02

    Orthopaedic trauma fellowship applicants use online-based resources when researching information on potential U.S. fellowship programs. The 2 primary sources for identifying programs are the Orthopaedic Trauma Association (OTA) database and the San Francisco Match (SF Match) database. Previous studies in other orthopaedic subspecialty areas have demonstrated considerable discrepancies among fellowship programs. The purpose of this study was to analyze content and availability of information on orthopaedic trauma surgery fellowship web sites. The online databases of the OTA and SF Match were reviewed to determine the availability of embedded program links or external links for the included programs. Thereafter, a Google search was performed for each program individually by typing the program's name, followed by the term "orthopaedic trauma fellowship." All identified fellowship web sites were analyzed for accessibility and content. Web sites were evaluated for comprehensiveness in mentioning key components of the orthopaedic trauma surgery curriculum. By consensus, we refined the final list of variables utilizing the methodology of previous studies on the topic. We identified 54 OTA-accredited fellowship programs, offering 87 positions. The majority (94%) of programs had web sites accessible through a Google search. Of the 51 web sites found, all (100%) described their program. Most commonly, hospital affiliation (88%), operative experiences (76%), and rotation overview (65%) were listed, and, least commonly, interview dates (6%), selection criteria (16%), on-call requirements (20%), and fellow evaluation criteria (20%) were listed. Programs with ≥2 fellows provided more information with regard to education content (p = 0.0001) and recruitment content (p = 0.013). Programs with Accreditation Council for Graduate Medical Education (ACGME) accreditation status also provided greater information with regard to education content (odds ratio, 4.0; p = 0.0001). Otherwise, no differences were seen by region, residency affiliation, medical school affiliation, or hospital affiliation. The SF Match and OTA databases provide few direct links to fellowship web sites. Individual program web sites do not effectively and completely convey information about the programs. The Internet is an underused resource for fellow recruitment. The lack of information on these sites allows for future opportunity to optimize this resource.

  19. Decision making in family medicine

    PubMed Central

    Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

    2013-01-01

    Abstract Objective To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Design Randomized trial. Setting Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Participants Fifteen second-year family medicine residents. Intervention Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. Main outcome measures The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine’s effect on the decision-making process in clinical practice. Results Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants’ perceptions of each engine’s effect on the decision-making process were very positive and similar for both search engines. Conclusion Family medicine residents’ ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care. PMID:24130286

  20. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

    PubMed Central

    Liu, Yongchao; Maskell, Douglas L; Schmidt, Bertil

    2009-01-01

    Background The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware. Findings Our CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card) provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs. PMID:19416548

  1. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

    PubMed Central

    2013-01-01

    Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

  2. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

    PubMed

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

    2013-03-01

    Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

  3. SANSparallel: interactive homology search against Uniprot

    PubMed Central

    Somervuo, Panu; Holm, Liisa

    2015-01-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. PMID:25855811

  4. Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.

    PubMed

    Brandt, C; Nadkarni, P

    2001-01-01

    The Web is increasingly the medium of choice for multi-user application program delivery. Yet selection of an appropriate programming environment for rapid prototyping, code portability, and maintainability remain issues. We summarize our experience on the conversion of a LISP Web application, Search/SR to a new, functionally identical application, Search/SR-ASP using a relational database and active server pages (ASP) technology. Our results indicate that provision of easy access to database engines and external objects is almost essential for a development environment to be considered viable for rapid and robust application delivery. While LISP itself is a robust language, its use in Web applications may be hard to justify given that current vendor implementations do not provide such functionality. Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages.

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

    Clancey, P.; Logg, C.

    DEPOT has been developed to provide tracking for the Stanford Linear Collider (SLC) control system equipment. For each piece of equipment entered into the database, complete location, service, maintenance, modification, certification, and radiation exposure histories can be maintained. To facilitate data entry accuracy, efficiency, and consistency, barcoding technology has been used extensively. DEPOT has been an important tool in improving the reliability of the microsystems controlling SLC. This document describes the components of the DEPOT database, the elements in the database records, and the use of the supporting programs for entering data, searching the database, and producing reports from themore » information.« less

  6. COSMIC: Software catalog 1991 edition diskette format

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The PC edition of the annual COSMIC Software contains descriptions of the over 1,200 computer programs available for use within the United States as of January 1, 1991. By using the PC version of the catalog, it is possible to conduct extensive searches of the software inventory for programs that meet specific criteria. Elements such as program keywords, hardware specifications, source code languages, and title acronyms can be used for the basis of such searches. After isolating those programs that might be of best interest to the user, it is then possible to either view at the monitor, or generate a hardcopy listing of all information on those packages. In addition to the program elements that the user can search on, information such as total program size, distribution media, and program price, as well as extensive abstracts on the program, are also available to the user at this time. Another useful feature of the catalog allows for the retention of programs that meet certain search criteria between individual sessions of using the catalog. This allows users to save the information on those programs that are of interest to them in different areas of application. They can then recall a specific collection of programs for information retrieval or further search reduction if desired. In addition, this version of the catalog is adaptable to a network/shared resource environment, allowing multiple users access to a single copy of the catalog database simultaneously.

  7. A collection of open source applications for mass spectrometry data mining.

    PubMed

    Gallardo, Óscar; Ovelleiro, David; Gay, Marina; Carrascal, Montserrat; Abian, Joaquin

    2014-10-01

    We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Reading Programs for Gifted Readers. Learning Package No. 28.

    ERIC Educational Resources Information Center

    Collins, Norma, Comp.; Smith, Carl, Ed.

    Originally developed as part of a project for the Department of Defense Schools (DoDDS) system, this learning package on reading programs for gifted readers is designed for teachers who wish to upgrade or expand their teaching skills on their own. The package includes an overview of the project; a comprehensive search of the ERIC database; a…

  9. Literature searches on Ayurveda: An update.

    PubMed

    Aggithaya, Madhur G; Narahari, Saravu R

    2015-01-01

    The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches.

  10. Optics Toolbox: An Intelligent Relational Database System For Optical Designers

    NASA Astrophysics Data System (ADS)

    Weller, Scott W.; Hopkins, Robert E.

    1986-12-01

    Optical designers were among the first to use the computer as an engineering tool. Powerful programs have been written to do ray-trace analysis, third-order layout, and optimization. However, newer computing techniques such as database management and expert systems have not been adopted by the optical design community. For the purpose of this discussion we will define a relational database system as a database which allows the user to specify his requirements using logical relations. For example, to search for all lenses in a lens database with a F/number less than two, and a half field of view near 28 degrees, you might enter the following: FNO < 2.0 and FOV of 28 degrees ± 5% Again for the purpose of this discussion, we will define an expert system as a program which contains expert knowledge, can ask intelligent questions, and can form conclusions based on the answers given and the knowledge which it contains. Most expert systems store this knowledge in the form of rules-of-thumb, which are written in an English-like language, and which are easily modified by the user. An example rule is: IF require microscope objective in air and require NA > 0.9 THEN suggest the use of an oil immersion objective The heart of the expert system is the rule interpreter, sometimes called an inference engine, which reads the rules and forms conclusions based on them. The use of a relational database system containing lens prototypes seems to be a viable prospect. However, it is not clear that expert systems have a place in optical design. In domains such as medical diagnosis and petrology, expert systems are flourishing. These domains are quite different from optical design, however, because optical design is a creative process, and the rules are difficult to write down. We do think that an expert system is feasible in the area of first order layout, which is sufficiently diagnostic in nature to permit useful rules to be written. This first-order expert would emulate an expert designer as he interacted with a customer for the first time: asking the right questions, forming conclusions, and making suggestions. With these objectives in mind, we have developed the Optics Toolbox. Optics Toolbox is actually two programs in one: it is a powerful relational database system with twenty-one search parameters, four search modes, and multi-database support, as well as a first-order optical design expert system with a rule interpreter which has full access to the relational database. The system schematic is shown in Figure 1.

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

    PubMed

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

    2005-04-01

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

  12. 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.

  13. Evaluation of the content and accessibility of web sites for accredited orthopaedic sports medicine fellowships.

    PubMed

    Mulcahey, Mary K; Gosselin, Michelle M; Fadale, Paul D

    2013-06-19

    The Internet is a common source of information for orthopaedic residents applying for sports medicine fellowships, with the web sites of the American Orthopaedic Society for Sports Medicine (AOSSM) and the San Francisco Match serving as central databases. We sought to evaluate the web sites for accredited orthopaedic sports medicine fellowships with regard to content and accessibility. We reviewed the existing web sites of the ninety-five accredited orthopaedic sports medicine fellowships included in the AOSSM and San Francisco Match databases from February to March 2012. A Google search was performed to determine the overall accessibility of program web sites and to supplement information obtained from the AOSSM and San Francisco Match web sites. The study sample consisted of the eighty-seven programs whose web sites connected to information about the fellowship. Each web site was evaluated for its informational value. Of the ninety-five programs, fifty-one (54%) had links listed in the AOSSM database. Three (3%) of all accredited programs had web sites that were linked directly to information about the fellowship. Eighty-eight (93%) had links listed in the San Francisco Match database; however, only five (5%) had links that connected directly to information about the fellowship. Of the eighty-seven programs analyzed in our study, all eighty-seven web sites (100%) provided a description of the program and seventy-six web sites (87%) included information about the application process. Twenty-one web sites (24%) included a list of current fellows. Fifty-six web sites (64%) described the didactic instruction, seventy (80%) described team coverage responsibilities, forty-seven (54%) included a description of cases routinely performed by fellows, forty-one (47%) described the role of the fellow in seeing patients in the office, eleven (13%) included call responsibilities, and seventeen (20%) described a rotation schedule. Two Google searches identified direct links for 67% to 71% of all accredited programs. Most accredited orthopaedic sports medicine fellowships lack easily accessible or complete web sites in the AOSSM or San Francisco Match databases. Improvement in the accessibility and quality of information on orthopaedic sports medicine fellowship web sites would facilitate the ability of applicants to obtain useful information.

  14. Adjacency and Proximity Searching in the Science Citation Index and Google

    DTIC Science & Technology

    2005-01-01

    major database search engines , including commercial S&T database search engines (e.g., Science Citation Index (SCI), Engineering Compendex (EC...PubMed, OVID), Federal agency award database search engines (e.g., NSF, NIH, DOE, EPA, as accessed in Federal R&D Project Summaries), Web search Engines (e.g...searching. Some database search engines allow strict constrained co- occurrence searching as a user option (e.g., OVID, EC), while others do not (e.g., SCI

  15. Information Literacy for Users at the National Medical Library of Cuba: Cochrane Library Course for the Search of Best Evidence for Clinical Decisions

    ERIC Educational Resources Information Center

    Santana Arroyo, Sonia; del Carmen Gonzalez Rivero, Maria

    2012-01-01

    The National Medical Library of Cuba is currently developing an information literacy program to train users in the use of biomedical databases. This paper describes the experience with the course "Cochrane Library: Evidence-Based Medicine," which aims to teach users how to make the best use of this database, as well as the evidence-based…

  16. CampusGIS of the University of Cologne: a tool for orientation, navigation, and management

    NASA Astrophysics Data System (ADS)

    Baaser, U.; Gnyp, M. L.; Hennig, S.; Hoffmeister, D.; Köhn, N.; Laudien, R.; Bareth, G.

    2006-10-01

    The working group for GIS and Remote Sensing at the Department of Geography at the University of Cologne has established a WebGIS called CampusGIS of the University of Cologne. The overall task of the CampusGIS is the connection of several existing databases at the University of Cologne with spatial data. These existing databases comprise data about staff, buildings, rooms, lectures, and general infrastructure like bus stops etc. These information were yet not linked to their spatial relation. Therefore, a GIS-based method is developed to link all the different databases to spatial entities. Due to the philosophy of the CampusGIS, an online-GUI is programmed which enables users to search for staff, buildings, or institutions. The query results are linked to the GIS database which allows the visualization of the spatial location of the searched entity. This system was established in 2005 and is operational since early 2006. In this contribution, the focus is on further developments. First results of (i) including routing services in, (ii) programming GUIs for mobile devices for, and (iii) including infrastructure management tools in the CampusGIS are presented. Consequently, the CampusGIS is not only available for spatial information retrieval and orientation. It also serves for on-campus navigation and administrative management.

  17. Comet: an open-source MS/MS sequence database search tool.

    PubMed

    Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

    2013-01-01

    Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Database Search Engines: Paradigms, Challenges and Solutions.

    PubMed

    Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

  19. A bibliography of IRIS-related publications, 2000-2011

    NASA Astrophysics Data System (ADS)

    Muco, B.

    2012-12-01

    Citations and acknowledgements in scientific journals can be an indicator of the role an organization has on the research of that field. Since its formation and incorporation in May 1984, the IRIS Consortium (Incorporated Research Institutions for Seismology) is mentioned more and more as a valuable source of data, instruments and programs in the literature of earth sciences. As a large organization with more than 100 member domestic institutes and about 40 international affiliates, obviously IRIS has a direct impact on the earth sciences through all its programs, projects, workshops, symposia, and news¬letters and as a lively forum for exchanging ideas. In order to maintain support from National Science Foundation (NSF) and the research community, it is important to document the continued use of IRIS facilities in basic research programs. IRIS maintains a database of articles that are based on the use of IRIS facilities or which reference use of IRIS data and resources. Articles in this database have been either been provided to IRIS by the authors or selected through an annual search of a number of prominent journals. A text version of the full bibliographic database is available on the IRIS website and a version in EndNote format is also provided. To provide a more complete bibliography and a consistent evaluation of temporal tends in publications, a special annual search began in 2000 which focused on a subset of key seismology and Earth science journals: Bulletin of Seismological Society of America, Journal of Geophysical Research, Seismological Research Letters, Geophysical Research Letters, Earth and Planetary Science Letters, Physics of the Earth and Planetary Interiors, Tectonophysics, Geophysical Journal International, Nature, Science, Geology and EOS. Using different search engines as Scirus, ScienceDirect, GeoRef, OCLC First Search, EASI Search, NASA Abstract Service etc. for online journals and publishers' databases, we searched for key words (IRIS, GSN, DMS, PASSCAL, USArray etc) in titles, abstracts and text. Most of the selections found by this method were confirmed by reading through online texts or original journals. This bibliography of peer-reviewed articles (excluding abstracts) identified in these key journals for 2000-2011 includes approximately 1800 entries. As for American Geophysical Union (AGU) transaction, the bibliography of IRIS-related abstracts for the abovementioned period includes approximately 1400 abstracts. This study is a clear indicator of making intensive use by the seismological community of the resources that IRIS provides and of the paramount importance this organization has in advancement of seismological research worldwide.

  20. The new interactive CESAR

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

    Fox, P.B.; Yatabe, M.

    1987-01-01

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

  1. An approach in building a chemical compound search engine in oracle database.

    PubMed

    Wang, H; Volarath, P; Harrison, R

    2005-01-01

    A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

  2. EROS main image file - A picture perfect database for Landsat imagery and aerial photography

    NASA Technical Reports Server (NTRS)

    Jack, R. F.

    1984-01-01

    The Earth Resources Observation System (EROS) Program was established by the U.S. Department of the Interior in 1966 under the administration of the Geological Survey. It is primarily concerned with the application of remote sensing techniques for the management of natural resources. The retrieval system employed to search the EROS database is called INORAC (Inquiry, Ordering, and Accounting). A description is given of the types of images identified in EROS, taking into account Landsat imagery, Skylab images, Gemini/Apollo photography, and NASA aerial photography. Attention is given to retrieval commands, geographic coordinate searching, refinement techniques, various online functions, and questions regarding the access to the EROS Main Image File.

  3. Software Tools Streamline Project Management

    NASA Technical Reports Server (NTRS)

    2009-01-01

    Three innovative software inventions from Ames Research Center (NETMARK, Program Management Tool, and Query-Based Document Management) are finding their way into NASA missions as well as industry applications. The first, NETMARK, is a program that enables integrated searching of data stored in a variety of databases and documents, meaning that users no longer have to look in several places for related information. NETMARK allows users to search and query information across all of these sources in one step. This cross-cutting capability in information analysis has exponentially reduced the amount of time needed to mine data from days or weeks to mere seconds. NETMARK has been used widely throughout NASA, enabling this automatic integration of information across many documents and databases. NASA projects that use NETMARK include the internal reporting system and project performance dashboard, Erasmus, NASA s enterprise management tool, which enhances organizational collaboration and information sharing through document routing and review; the Integrated Financial Management Program; International Space Station Knowledge Management; Mishap and Anomaly Information Reporting System; and management of the Mars Exploration Rovers. Approximately $1 billion worth of NASA s projects are currently managed using Program Management Tool (PMT), which is based on NETMARK. PMT is a comprehensive, Web-enabled application tool used to assist program and project managers within NASA enterprises in monitoring, disseminating, and tracking the progress of program and project milestones and other relevant resources. The PMT consists of an integrated knowledge repository built upon advanced enterprise-wide database integration techniques and the latest Web-enabled technologies. The current system is in a pilot operational mode allowing users to automatically manage, track, define, update, and view customizable milestone objectives and goals. The third software invention, Query-Based Document Management (QBDM) is a tool that enables content or context searches, either simple or hierarchical, across a variety of databases. The system enables users to specify notification subscriptions where they associate "contexts of interest" and "events of interest" to one or more documents or collection(s) of documents. Based on these subscriptions, users receive notification when the events of interest occur within the contexts of interest for associated document or collection(s) of documents. Users can also associate at least one notification time as part of the notification subscription, with at least one option for the time period of notifications.

  4. The Impact of Online Bibliographic Databases on Teaching and Research in Political Science.

    ERIC Educational Resources Information Center

    Reichel, Mary

    The availability of online bibliographic databases greatly facilitates literature searching in political science. The advantages to searching databases online include combination of concepts, comprehensiveness, multiple database searching, free-text searching, currency, current awareness services, document delivery service, and convenience.…

  5. Integrating Variances into an Analytical Database

    NASA Technical Reports Server (NTRS)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  6. A web based relational database management system for filariasis control

    PubMed Central

    Murty, Upadhyayula Suryanarayana; Kumar, Duvvuri Venkata Rama Satya; Sriram, Kumaraswamy; Rao, Kadiri Madhusudhan; Bhattacharyulu, Chakravarthula Hayageeva Narasimha Venakata; Praveen, Bhoopathi; Krishna, Amirapu Radha

    2005-01-01

    The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface. Availability http://www.webfil.org (login and password can be obtained from the authors) PMID:17597846

  7. Flight Deck Interval Management Display. [Elements, Information and Annunciations Database User Guide

    NASA Technical Reports Server (NTRS)

    Lancaster, Jeff; Dillard, Michael; Alves, Erin; Olofinboba, Olu

    2014-01-01

    The User Guide details the Access Database provided with the Flight Deck Interval Management (FIM) Display Elements, Information, & Annunciations program. The goal of this User Guide is to support ease of use and the ability to quickly retrieve and select items of interest from the Database. The Database includes FIM Concepts identified in a literature review preceding the publication of this document. Only items that are directly related to FIM (e.g., spacing indicators), which change or enable FIM (e.g., menu with control buttons), or which are affected by FIM (e.g., altitude reading) are included in the database. The guide has been expanded from previous versions to cover database structure, content, and search features with voiced explanations.

  8. Evaluating the Progress of the School Reading Program. Learning Package No. 17.

    ERIC Educational Resources Information Center

    Nelson, Carol; Smith, Carl, Comp.

    Originally developed for the Department of Defense Schools (DoDDS) system, this learning package on evaluating the progress of the school reading program is designed for teachers who wish to upgrade or expand their teaching skills on their own. The package includes a comprehensive search of the ERIC database; a lecture giving an overview on the…

  9. Assisting Scientific and Technical Research Through Subject Oriented Bibliographies of NTIS Reports.

    ERIC Educational Resources Information Center

    Schwarzwalder, Robert N., Jr.

    A program combining cost-free searching of the National Technical Information Service (NTIS) database and document delivery to faculty members was offered at the Kansas State University Libraries. NTIS report usage was monitored from May 1987, five months prior to the onset of the study, until May 1988, at which time the program was terminated.…

  10. Nuclear data made easily accessible through the Notre Dame Nuclear Database

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  11. Specialized microbial databases for inductive exploration of microbial genome sequences

    PubMed Central

    Fang, Gang; Ho, Christine; Qiu, Yaowu; Cubas, Virginie; Yu, Zhou; Cabau, Cédric; Cheung, Frankie; Moszer, Ivan; Danchin, Antoine

    2005-01-01

    Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore , a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison. PMID:15698474

  12. HAEdb: a novel interactive, locus-specific mutation database for the C1 inhibitor gene.

    PubMed

    Kalmár, Lajos; Hegedüs, Tamás; Farkas, Henriette; Nagy, Melinda; Tordai, Attila

    2005-01-01

    Hereditary angioneurotic edema (HAE) is an autosomal dominant disorder characterized by episodic local subcutaneous and submucosal edema and is caused by the deficiency of the activated C1 esterase inhibitor protein (C1-INH or C1INH; approved gene symbol SERPING1). Published C1-INH mutations are represented in large universal databases (e.g., OMIM, HGMD), but these databases update their data rather infrequently, they are not interactive, and they do not allow searches according to different criteria. The HAEdb, a C1-INH gene mutation database (http://hae.biomembrane.hu) was created to contribute to the following expectations: 1) help the comprehensive collection of information on genetic alterations of the C1-INH gene; 2) create a database in which data can be searched and compared according to several flexible criteria; and 3) provide additional help in new mutation identification. The website uses MySQL, an open-source, multithreaded, relational database management system. The user-friendly graphical interface was written in the PHP web programming language. The website consists of two main parts, the freely browsable search function, and the password-protected data deposition function. Mutations of the C1-INH gene are divided in two parts: gross mutations involving DNA fragments >1 kb, and micro mutations encompassing all non-gross mutations. Several attributes (e.g., affected exon, molecular consequence, family history) are collected for each mutation in a standardized form. This database may facilitate future comprehensive analyses of C1-INH mutations and also provide regular help for molecular diagnostic testing of HAE patients in different centers.

  13. LIVIVO - the Vertical Search Engine for Life Sciences.

    PubMed

    Müller, Bernd; Poley, Christoph; Pössel, Jana; Hagelstein, Alexandra; Gübitz, Thomas

    2017-01-01

    The explosive growth of literature and data in the life sciences challenges researchers to keep track of current advancements in their disciplines. Novel approaches in the life science like the One Health paradigm require integrated methodologies in order to link and connect heterogeneous information from databases and literature resources. Current publications in the life sciences are increasingly characterized by the employment of trans-disciplinary methodologies comprising molecular and cell biology, genetics, genomic, epigenomic, transcriptional and proteomic high throughput technologies with data from humans, plants, and animals. The literature search engine LIVIVO empowers retrieval functionality by incorporating various literature resources from medicine, health, environment, agriculture and nutrition. LIVIVO is developed in-house by ZB MED - Information Centre for Life Sciences. It provides a user-friendly and usability-tested search interface with a corpus of 55 Million citations derived from 50 databases. Standardized application programming interfaces are available for data export and high throughput retrieval. The search functions allow for semantic retrieval with filtering options based on life science entities. The service oriented architecture of LIVIVO uses four different implementation layers to deliver search services. A Knowledge Environment is developed by ZB MED to deal with the heterogeneity of data as an integrative approach to model, store, and link semantic concepts within literature resources and databases. Future work will focus on the exploitation of life science ontologies and on the employment of NLP technologies in order to improve query expansion, filters in faceted search, and concept based relevancy rankings in LIVIVO.

  14. Ridge 2000 Data Management System

    NASA Astrophysics Data System (ADS)

    Goodwillie, A. M.; Carbotte, S. M.; Arko, R. A.; Haxby, W. F.; Ryan, W. B.; Chayes, D. N.; Lehnert, K. A.; Shank, T. M.

    2005-12-01

    Hosted at Lamont by the marine geoscience Data Management group, mgDMS, the NSF-funded Ridge 2000 electronic database, http://www.marine-geo.org/ridge2000/, is a key component of the Ridge 2000 multi-disciplinary program. The database covers each of the three Ridge 2000 Integrated Study Sites: Endeavour Segment, Lau Basin, and 8-11N Segment. It promotes the sharing of information to the broader community, facilitates integration of the suite of information collected at each study site, and enables comparisons between sites. The Ridge 2000 data system provides easy web access to a relational database that is built around a catalogue of cruise metadata. Any web browser can be used to perform a versatile text-based search which returns basic cruise and submersible dive information, sample and data inventories, navigation, and other relevant metadata such as shipboard personnel and links to NSF program awards. In addition, non-proprietary data files, images, and derived products which are hosted locally or in national repositories, as well as science and technical reports, can be freely downloaded. On the Ridge 2000 database page, our Data Link allows users to search the database using a broad range of parameters including data type, cruise ID, chief scientist, geographical location. The first Ridge 2000 field programs sailed in 2004 and, in addition to numerous data sets collected prior to the Ridge 2000 program, the database currently contains information on fifteen Ridge 2000-funded cruises and almost sixty Alvin dives. Track lines can be viewed using a recently- implemented Web Map Service button labelled Map View. The Ridge 2000 database is fully integrated with databases hosted by the mgDMS group for MARGINS and the Antarctic multibeam and seismic reflection data initiatives. Links are provided to partner databases including PetDB, SIOExplorer, and the ODP Janus system. Improved inter-operability with existing and new partner repositories continues to be strengthened. One major effort involves the gradual unification of the metadata across these partner databases. Standardised electronic metadata forms that can be filled in at sea are available from our web site. Interactive map-based exploration and visualisation of the Ridge 2000 database is provided by GeoMapApp, a freely-available Java(tm) application being developed within the mgDMS group. GeoMapApp includes high-resolution bathymetric grids for the 8-11N EPR segment and allows customised maps and grids for any of the Ridge 2000 ISS to be created. Vent and instrument locations can be plotted and saved as images, and Alvin dive photos are also available.

  15. SANSparallel: interactive homology search against Uniprot.

    PubMed

    Somervuo, Panu; Holm, Liisa

    2015-07-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Accessibility, availability, and quality of online information for US radiation oncology residencies.

    PubMed

    Wakefield, Daniel V; Manole, Bogdan A; Jethanandani, Amit; May, Michael E; Marcrom, Samuel R; Farmer, Michael R; Ballo, Matthew T; VanderWalde, Noam A

    2016-01-01

    Radiation oncology (RO) residency applicants commonly use Internet resources for information on residency programs. The purpose of this study is to assess the accessibility, availability, and quality of online information for RO graduate medical education. Accessibility of online information was determined by surveying databases for RO residency programs within the Fellowship Residency Electronic Interactive Data Access System (FREIDA) of the American Medical Association, the Accreditation Council for Graduate Medical Education (ACGME), and Google search. As of June 30, 2015, websites were assessed for presence, accessibility, and overall content availability based on a 55-item list of desired features based on 13 program features important to previously surveyed applicants. Quality scoring of available content was performed based on previously published Likert scale variables deemed desirable to RO applicants. Quality score labels were given based on percentage of desired information presented. FREIDA and ACGME databases listed 89% and 98% of program websites, respectively, but only 56% and 52% of links routed to a RO department-specific website, respectively. Google search obtained websites for 98% of programs and 95% of links routed to RO department-specific websites. The majority of websites had program descriptions (98%) and information on staff. However, resident information was more limited (total number [42%], education [47%], previous residents [28%], positions available [35%], contact information [13%]). Based on quality scoring, program websites contained only 47% of desired information on average. Only 13% of programs had superior websites containing 80% or more of desired information. Compared with Google, the FREIDA and ACGME program databases provide limited access to RO residency websites. The overall information availability and quality of information within RO residency websites varies widely. Applicants and programs may benefit from improved content accessibility and quality from US RO program websites in the residency application process. Copyright © 2016 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

  17. Literature searches on Ayurveda: An update

    PubMed Central

    Aggithaya, Madhur G.; Narahari, Saravu R.

    2015-01-01

    Introduction: The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. Aims: To update on Ayurveda literature search and strategy to retrieve maximum publications. Methods: Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Results: Five among 46 databases are now relevant – AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. “The Researches in Ayurveda” and “Ayurvedic Research Database” (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. Conclusion: AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches. PMID:27313409

  18. Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

    ERIC Educational Resources Information Center

    Fitzgibbons, Megan; Meert, Deborah

    2010-01-01

    The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

  19. Cloud parallel processing of tandem mass spectrometry based proteomics data.

    PubMed

    Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

    2012-10-05

    Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

  20. National Weather- RFC Development Management

    Science.gov Websites

    Map News Organization Search NWS ALL NOAA Go RFC Development Management Presentations Projects & ; Plans RFC Development Program RFC Archive Database Documentation Outline Workshops Contact Us resources and services. Description Graphic The RFC Development Management component of the Office of

  1. Bibliographies without Tears: Bibliography-Managers Round-Up.

    ERIC Educational Resources Information Center

    Science Software Quarterly, 1984

    1984-01-01

    Reviews and compares "Sci-Mate,""Reference Manager," and "BIBLIOPHILE" software packages used for storage and retrieval tasks involving bibliographic data. Each program handles search tasks well; major differences are in the amount of flexibility in customizing the database structure, their import and export…

  2. De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes

    PubMed Central

    Gulvik, Christopher A.; Effler, T. Chad; Wilhelm, Steven W.; Buchan, Alison

    2012-01-01

    Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications. PMID:23189198

  3. Flight Test Hazard Planning Near the Speed of Light

    NASA Technical Reports Server (NTRS)

    Henwood, Bart; Huete, Rod

    2007-01-01

    A viewgraph presentation describing flight test safety near the speed of light is shown. The topics include: 1) Concept; 2) Portal Content; 3) Activity to Date; 4) FTS Database Updatd FAA Program; 5) FAA Flight Test Risk Management; 6) CFR 14 Part 21.35 Current and proposed changes; 7) An Online Resource for Flight Test Safety Planning; 8) Data Gathering; 9) NTPS Role; 10) Example Maturation; 11) Many Varied Inputs; 12) Matured Stall Hazards; 13) Loss of Control Mitigations; 14) FAA Access; 15) NASA PBMA Website Link; 16) FAR Reference Search; 17) Record Field Search; 18) Keyword Search; and 19) Results of FAR Reference Search.

  4. DPS Planetary Science Graduate Programs Listing: A Resource for Students and Advisors

    NASA Astrophysics Data System (ADS)

    Klassen, David R.; Roman, Anthony; Meinke, Bonnie

    2015-11-01

    We began a web page on the DPS Education site in 2013 listing all the graduate programs we could find that can lead to a PhD with a planetary science focus. Since then the static page has evolved into a database-driven, filtered-search site. It is intended to be a useful resource for both undergraduate students and undergraduate advisers, allowing them to find and compare programs across a basic set of search criteria. From the filtered list users can click on links to get a "quick look" at the database information and follow links to the program main site.The reason for such a list is because planetary science is a heading that covers an extremely diverse set of disciplines. The usual case is that planetary scientists are housed in a discipline-placed department so that finding them is typically not easy—undergraduates cannot look for a Planetary Science department, but must (somehow) know to search for them in all their possible places. This can overwhelm even determined undergraduate student, and even many advisers!We present here the updated site and a walk-through of the basic features. In addition we ask for community feedback on additional features to make the system more usable for them. Finally, we call upon those mentoring and advising undergraduates to use this resource, and program admission chairs to continue to review their entry and provide us with the most up-to-date information.The URL for our site is http://dps.aas.org/education/graduate-schools.

  5. DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

    PubMed

    Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

    2018-01-04

    The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

  6. Analysis of human serum phosphopeptidome by a focused database searching strategy.

    PubMed

    Zhu, Jun; Wang, Fangjun; Cheng, Kai; Song, Chunxia; Qin, Hongqiang; Hu, Lianghai; Figeys, Daniel; Ye, Mingliang; Zou, Hanfa

    2013-01-14

    As human serum is an important source for early diagnosis of many serious diseases, analysis of serum proteome and peptidome has been extensively performed. However, the serum phosphopeptidome was less explored probably because the effective method for database searching is lacking. Conventional database searching strategy always uses the whole proteome database, which is very time-consuming for phosphopeptidome search due to the huge searching space resulted from the high redundancy of the database and the setting of dynamic modifications during searching. In this work, a focused database searching strategy using an in-house collected human serum pro-peptidome target/decoy database (HuSPep) was established. It was found that the searching time was significantly decreased without compromising the identification sensitivity. By combining size-selective Ti (IV)-MCM-41 enrichment, RP-RP off-line separation, and complementary CID and ETD fragmentation with the new searching strategy, 143 unique endogenous phosphopeptides and 133 phosphorylation sites (109 novel sites) were identified from human serum with high reliability. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Conformational flexibility of two RNA trimers explored by computational tools and database search.

    PubMed

    Fadrná, Eva; Koca, Jaroslav

    2003-04-01

    Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data. Registry numbers: adenylyl-(3' --> 5')-adenylyl-(3' --> 5')-adenosine [917-44-2] adenylyl-(3' --> 5')-uridylyl-(3' --> 5')-guanosine [3494-35-7].

  8. Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.

    PubMed

    Li, Honglan; Joh, Yoon Sung; Kim, Hyunwoo; Paek, Eunok; Lee, Sang-Won; Hwang, Kyu-Baek

    2016-12-22

    Proteogenomics is a promising approach for various tasks ranging from gene annotation to cancer research. Databases for proteogenomic searches are often constructed by adding peptide sequences inferred from genomic or transcriptomic evidence to reference protein sequences. Such inflation of databases has potential of identifying novel peptides. However, it also raises concerns on sensitive and reliable peptide identification. Spurious peptides included in target databases may result in underestimated false discovery rate (FDR). On the other hand, inflation of decoy databases could decrease the sensitivity of peptide identification due to the increased number of high-scoring random hits. Although several studies have addressed these issues, widely applicable guidelines for sensitive and reliable proteogenomic search have hardly been available. To systematically evaluate the effect of database inflation in proteogenomic searches, we constructed a variety of real and simulated proteogenomic databases for yeast and human tandem mass spectrometry (MS/MS) data, respectively. Against these databases, we tested two popular database search tools with various approaches to search result validation: the target-decoy search strategy (with and without a refined scoring-metric) and a mixture model-based method. The effect of separate filtering of known and novel peptides was also examined. The results from real and simulated proteogenomic searches confirmed that separate filtering increases the sensitivity and reliability in proteogenomic search. However, no one method consistently identified the largest (or the smallest) number of novel peptides from real proteogenomic searches. We propose to use a set of search result validation methods with separate filtering, for sensitive and reliable identification of peptides in proteogenomic search.

  9. A pseudo MS3 approach for identification of disulfide-bonded proteins: uncommon product ions and database search.

    PubMed

    Chen, Jianzhong; Shiyanov, Pavel; Schlager, John J; Green, Kari B

    2012-02-01

    It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs. © American Society for Mass Spectrometry, 2011

  10. Blended Synchronous Delivery Mode in Graduate Programs: A Literature Review and Its Implementation in the Master Teacher Program

    ERIC Educational Resources Information Center

    Lakhal, Sawsen; Bateman, Dianne; Bédard, Janie

    2017-01-01

    The aim of this study is to present a narrative literature review of advantages, challenges, and conditions for the success of blended synchronous course delivery mode. For this purpose, we searched the database EditLib and analyzed 16 existing papers from 2001 to 2016. The conditions for success were operationalized in the Master Teacher Program…

  11. Technology in Science and Mathematics Education.

    ERIC Educational Resources Information Center

    Buccino, Alphonse

    Provided are several perspectives on technology, addressing changes in learners related to technology, changes in contemporary life related to technology, and changes in subject areas related to technology (indicating that technology has created such new tools for inquiry as computer programming, word processing, online database searches, and…

  12. Science in Afterschool Literature Review

    ERIC Educational Resources Information Center

    Falkenberg, Karen; McClure, Patricia; McComb, Errin M.

    2006-01-01

    In considering science in afterschool, research was reviewed and is presented in this document on how students learn science; how science is assessed, particularly inquiry science; recommended practices for afterschool science; and current afterschool science programs. Databases such as ERIC, Wilson Web, and PsychINFO were searched using…

  13. DOE technology information management system database study report

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

    Widing, M.A.; Blodgett, D.W.; Braun, M.D.

    1994-11-01

    To support the missions of the US Department of Energy (DOE) Special Technologies Program, Argonne National Laboratory is defining the requirements for an automated software system that will search electronic databases on technology. This report examines the work done and results to date. Argonne studied existing commercial and government sources of technology databases in five general areas: on-line services, patent database sources, government sources, aerospace technology sources, and general technology sources. First, it conducted a preliminary investigation of these sources to obtain information on the content, cost, frequency of updates, and other aspects of their databases. The Laboratory then performedmore » detailed examinations of at least one source in each area. On this basis, Argonne recommended which databases should be incorporated in DOE`s Technology Information Management System.« less

  14. Software for Managing Inventory of Flight Hardware

    NASA Technical Reports Server (NTRS)

    Salisbury, John; Savage, Scott; Thomas, Shirman

    2003-01-01

    The Flight Hardware Support Request System (FHSRS) is a computer program that relieves engineers at Marshall Space Flight Center (MSFC) of most of the non-engineering administrative burden of managing an inventory of flight hardware. The FHSRS can also be adapted to perform similar functions for other organizations. The FHSRS affords a combination of capabilities, including those formerly provided by three separate programs in purchasing, inventorying, and inspecting hardware. The FHSRS provides a Web-based interface with a server computer that supports a relational database of inventory; electronic routing of requests and approvals; and electronic documentation from initial request through implementation of quality criteria, acquisition, receipt, inspection, storage, and final issue of flight materials and components. The database lists both hardware acquired for current projects and residual hardware from previous projects. The increased visibility of residual flight components provided by the FHSRS has dramatically improved the re-utilization of materials in lieu of new procurements, resulting in a cost savings of over $1.7 million. The FHSRS includes subprograms for manipulating the data in the database, informing of the status of a request or an item of hardware, and searching the database on any physical or other technical characteristic of a component or material. The software structure forces normalization of the data to facilitate inquiries and searches for which users have entered mixed or inconsistent values.

  15. Application of ChemDraw NMR Tool: Correlation of Program-Generated 13C Chemical Shifts and pKa Values of para-Substituted Benzoic Acids

    NASA Astrophysics Data System (ADS)

    Wang, Hongyi

    2005-09-01

    An application of ChemDraw NMR Tool was demonstrated by correlation of program-generated 13 C NMR chemical shifts and p K a values of para-substituted benzoic acids. Experimental 13 C NMR chemical shifts were analyzed in the same way for comparison. The project can be used as an assignment at the end of the first-year organic chemistry course to review topics or explore new techniques: Hammett equation, acid base equilibrium theory, electronic nature of functional groups, inductive and resonance effects, structure reactivity relationship, NMR spectroscopy, literature search, database search, and ChemDraw software.

  16. Database resources of the National Center for Biotechnology Information

    PubMed Central

    Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Kenton, David L.; Khovayko, Oleg; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Sherry, Stephen T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Suzek, Tugba O.; Tatusov, Roman; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

    2006-01-01

    In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840

  17. Database resources of the National Center for Biotechnology Information.

    PubMed

    Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

    2012-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

  18. The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

    PubMed

    Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

    2012-03-01

    The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  19. Database resources of the National Center for Biotechnology Information

    PubMed Central

    Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

    2014-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429

  20. PHASS99: A software program for retrieving and decoding the radiometric ages of igneous rocks from the international database IGBADAT

    NASA Astrophysics Data System (ADS)

    Al-Mishwat, Ali T.

    2016-05-01

    PHASS99 is a FORTRAN program designed to retrieve and decode radiometric and other physical age information of igneous rocks contained in the international database IGBADAT (Igneous Base Data File). In the database, ages are stored in a proprietary format using mnemonic representations. The program can handle up to 99 ages in an igneous rock specimen and caters to forty radiometric age systems. The radiometric age alphanumeric strings assigned to each specimen description in the database consist of four components: the numeric age and its exponential modifier, a four-character mnemonic method identification, a two-character mnemonic name of analysed material, and the reference number in the rock group bibliography vector. For each specimen, the program searches for radiometric age strings, extracts them, parses them, decodes the different age components, and converts them to high-level English equivalents. IGBADAT and similarly-structured files are used for input. The output includes three files: a flat raw ASCII text file containing retrieved radiometric age information, a generic spreadsheet-compatible file for data import to spreadsheets, and an error file. PHASS99 builds on the old program TSTPHA (Test Physical Age) decoder program and expands greatly its capabilities. PHASS99 is simple, user friendly, fast, efficient, and does not require users to have knowledge of programing.

  1. EasyKSORD: A Platform of Keyword Search Over Relational Databases

    NASA Astrophysics Data System (ADS)

    Peng, Zhaohui; Li, Jing; Wang, Shan

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

  2. Database resources of the National Center for Biotechnology Information.

    PubMed

    2016-01-04

    The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  3. Database resources of the National Center for Biotechnology Information.

    PubMed

    2015-01-01

    The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  4. Using SQL Databases for Sequence Similarity Searching and Analysis.

    PubMed

    Pearson, William R; Mackey, Aaron J

    2017-09-13

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

  5. Evaluation of scientific periodicals and the Brazilian production of nursing articles.

    PubMed

    Erdmann, Alacoque Lorenzini; Marziale, Maria Helena Palucci; Pedreira, Mavilde da Luz Gonçalves; Lana, Francisco Carlos Félix; Pagliuca, Lorita Marlena Freitag; Padilha, Maria Itayra; Fernandes, Josicelia Dumêt

    2009-01-01

    This study aimed to identify nursing journals edited in Brazil indexed in the main bibliographic databases in the areas of health and nursing. It also aimed to classify the production of nursing graduate programs in 2007 according to the QUALIS/CAPES criteria used to classify scientific periodicals that disseminate the intellectual production of graduate programs in Brazil. This exploratory study used data from reports and documents available from CAPES to map scientific production and from searching the main international and national indexing databases. The findings from this research can help students, professors and coordinators of graduate programs in several ways: to understand the criteria of classifying periodicals; to be aware of the current production of graduate programs in the area of nursing; and to provide information that authors can use to select periodicals in which to publish their articles.

  6. Biosequence Similarity Search on the Mercury System

    PubMed Central

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described. PMID:18846267

  7. Universal neonatal hearing screening program in Shanghai, China: An inter-regional and international comparison.

    PubMed

    Fang, Xingang; Li, Xi; Zhang, Qi; Wan, Jin; Sun, Mei; Chang, Fengshui; Lü, Jun; Chen, Gang

    2016-11-01

    By comparing the Universal Neonatal Hearing Screening (UNHS) program as implemented in Shanghai and other regions in China and countries around the world, this study makes an assessment of the Shanghai model and summarizes the experiences implementing the UNHS program, so as to provide a valuable reference for other countries or regions to carry out UNHS more effectively. Since Shanghai is one of the most developed regions in China, we also examined the relationship between economic development and the UNHS starting year and coverage rate. The study conducted a systematic review of published studies in Chinese and English on the program status of neonatal hearing screening to compare and analyze the implementation of the UNHS program in 20 cities or provinces in China and 24 regions or countries around the world. The literature search in Chinese was conducted in the three most authoritative publication databases, CNKI (China National Knowledge Infrastructure), WANFANGDATA, and CQVIP (http://www.cqvip.com/). We searched all publications in those databases with the keywords "neonatal hearing screening" (in Chinese) between 2005 and 2014. English literature was searched using the same keywords (in English). The publication database included Medline and Web of Science, and the search time period was 2000-2014. Shanghai was one of the first regions in China to implement UNHS, and its coverage rate was among the top regions by international comparison. The starting time of the UNHS program had no relationship with the Gross Domestic Product (GDP) per capita in the same year. Economic level serves as a threshold for carrying out UNHS but is not a linear contributor to the exact starting time of such a program. The screening coverage rate generally showed a rising trend with the increasing GDP per capita in China, but it had no relationship with the area's GDP per capita in selected regions and countries around the world. The system design of UNHS is the key factor influencing screening coverage. Policy makers, program administrators, and cost-sharing structures are important factors that influence the coverage rates of UNHS. When to carry out a UNHS program is determined by the willingness and preference of the local government, which is influenced by the area's social, political and cultural conditions. Mandatory hearing screening and minimal-cost to no-cost intervention are two pillars for a good coverage rate of UNHS. In terms of system design, decision-making, implementation, funding and the concrete implementation plan are all important factors affecting the implementation of the UNHS. Copyright © 2016 The Author(s). Published by Elsevier Ireland Ltd.. All rights reserved.

  8. Physical-chemical property based sequence motifs and methods regarding same

    DOEpatents

    Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

    2008-09-09

    A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

  9. Staff - April M. Woolery | Alaska Division of Geological & Geophysical

    Science.gov Websites

    SurveysA> Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic Geologic Mapping Advisory Board STATEMAP Publications Geophysics Program Information Geophysical Survey

  10. Native Health Research Database

    MedlinePlus

    ... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

  11. Database resources of the National Center for Biotechnology Information

    PubMed Central

    Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

    2008-01-01

    In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

  12. 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;…

  13. Elementary software for the hand lens identification of some common iranian woods

    Treesearch

    Vahidreza Safdari; Margaret S. Devall

    2009-01-01

    A computer program, “Hyrcania”, has been developed for identifying some common woods (26 hardwoods and 6 softwoods) from the Hyrcanian forest type of Iran. The program has been written in JavaScript and is usable with computers as well as mobile phones. The databases use anatomical characteristics (visible with a hand lens) and wood colour, and can be searched in...

  14. Quality Assessment of Published Articles in Iranian Journals Related to Economic Evaluation in Health Care Programs Based on Drummond's Checklist: A Narrative Review.

    PubMed

    Rezapour, Aziz; Jafari, Abdosaleh; Mirmasoudi, Kosha; Talebianpour, Hamid

    2017-09-01

    Health economic evaluation research plays an important role in selecting cost-effective interventions. The purpose of this study was to assess the quality of published articles in Iranian journals related to economic evaluation in health care programs based on Drummond's checklist in terms of numbers, features, and quality. In the present review study, published articles (Persian and English) in Iranian journals related to economic evaluation in health care programs were searched using electronic databases. In addition, the methodological quality of articles' structure was analyzed by Drummond's standard checklist. Based on the inclusion criteria, the search of databases resulted in 27 articles that fully covered economic evaluation in health care programs. A review of articles in accordance with Drummond's criteria showed that the majority of studies had flaws. The most common methodological weakness in the articles was in terms of cost calculation and valuation. Considering such methodological faults in these studies, it is anticipated that these studies would not provide an appropriate feedback to policy makers to allocate health care resources correctly and select suitable cost-effective interventions. Therefore, researchers are required to comply with the standard guidelines in order to better execute and report on economic evaluation studies.

  15. Quality Assessment of Published Articles in Iranian Journals Related to Economic Evaluation in Health Care Programs Based on Drummond’s Checklist: A Narrative Review

    PubMed Central

    Rezapour, Aziz; Jafari, Abdosaleh; Mirmasoudi, Kosha; Talebianpour, Hamid

    2017-01-01

    Health economic evaluation research plays an important role in selecting cost-effective interventions. The purpose of this study was to assess the quality of published articles in Iranian journals related to economic evaluation in health care programs based on Drummond’s checklist in terms of numbers, features, and quality. In the present review study, published articles (Persian and English) in Iranian journals related to economic evaluation in health care programs were searched using electronic databases. In addition, the methodological quality of articles’ structure was analyzed by Drummond’s standard checklist. Based on the inclusion criteria, the search of databases resulted in 27 articles that fully covered economic evaluation in health care programs. A review of articles in accordance with Drummond’s criteria showed that the majority of studies had flaws. The most common methodological weakness in the articles was in terms of cost calculation and valuation. Considering such methodological faults in these studies, it is anticipated that these studies would not provide an appropriate feedback to policy makers to allocate health care resources correctly and select suitable cost-effective interventions. Therefore, researchers are required to comply with the standard guidelines in order to better execute and report on economic evaluation studies. PMID:29234174

  16. HOWDY: an integrated database system for human genome research

    PubMed Central

    Hirakawa, Mika

    2002-01-01

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

  17. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

    PubMed

    Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

    2017-01-01

    Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

  18. Based on a True Story? The Portrayal of ECT in International Movies and Television Programs.

    PubMed

    Sienaert, Pascal

    Movies and television (TV) programs are an important source of public information about ECT. To narratively review the portrayal of ECT in international movies and TV programs from 1948 until present. Several Internet movie databases and a database of phrases appearing in movies and TV programs were searched, supplemented with a Medline-search. No language restrictions were applied. ECT was portrayed in 52 movies (57 scenes), 21 TV programs (23 scenes), and 2 animated sitcoms (2 scenes). In movies, the main indication for ECT is behavioral control or torture (17/57, 29.8%), whereas in TV programs, the most frequent indication is erasing memories (7/25, 28%). In most scenes (47/82; 57.3%) ECT is given without consent, and without anesthesia (59/82; 72%). Unmodified ECT is depicted more frequently in American scenes (48/64, 75%), as opposed to scenes from other countries (11/18; 64.7%). Bilateral electrode placement is used in almost all (89%, 73/82) scenes. The vast majority of movies (46/57, 80.7%) and TV programs (18/25, 72%) show a negative and inaccurate image of the treatment. In the majority of scenes, ECT is used as a metaphor for repression, mind and behavior control, and is shown as a memory-erasing, painful and damaging treatment, adding to the stigma already associated with ECT. Only a few exceptions paint a truthful picture of this indispensable treatment in modern psychiatry. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Does gamification increase engagement with online programs? A systematic review.

    PubMed

    Looyestyn, Jemma; Kernot, Jocelyn; Boshoff, Kobie; Ryan, Jillian; Edney, Sarah; Maher, Carol

    2017-01-01

    Engagement in online programs is difficult to maintain. Gamification is the recent trend that offers to increase engagement through the inclusion of game-like features like points and badges, in non-game contexts. This review will answer the following question, 'Are gamification strategies effective in increasing engagement in online programs?' Eight databases (Web of Science, PsycINFO, Medline, INSPEC, ERIC, Cochrane Library, Business Source Complete and ACM Digital Library) were searched from 2010 to the 28th of October 2015 using a comprehensive search strategy. Eligibility criteria was based on the PICOS format, where "population" included adults, "intervention" involved an online program or smart phone application that included at least one gamification feature. "Comparator" was a control group, "outcomes" included engagement and "downstream" outcomes which occurred as a result of engagement; and "study design" included experimental studies from peer-reviewed sources. Effect sizes (Cohens d and 95% confidence intervals) were also calculated. 1017 studies were identified from database searches following the removal of duplicates, of which 15 met the inclusion criteria. The studies involved a total of 10,499 participants, and were commonly undertaken in tertiary education contexts. Engagement metrics included time spent (n = 5), volume of contributions (n = 11) and occasions visited to the software (n = 4); as well as downstream behaviours such as performance (n = 4) and healthy behaviours (n = 1). Effect sizes typically ranged from medium to large in direct engagement and downstream behaviours, with 12 out of 15 studies finding positive significant effects in favour of gamification. Gamification is effective in increasing engagement in online programs. Key recommendations for future research into gamification are provided. In particular, rigorous study designs are required to fully examine gamification's effects and determine how to best achieve sustained engagement.

  20. Towards computational improvement of DNA database indexing and short DNA query searching.

    PubMed

    Stojanov, Done; Koceski, Sašo; Mileva, Aleksandra; Koceska, Nataša; Bande, Cveta Martinovska

    2014-09-03

    In order to facilitate and speed up the search of massive DNA databases, the database is indexed at the beginning, employing a mapping function. By searching through the indexed data structure, exact query hits can be identified. If the database is searched against an annotated DNA query, such as a known promoter consensus sequence, then the starting locations and the number of potential genes can be determined. This is particularly relevant if unannotated DNA sequences have to be functionally annotated. However, indexing a massive DNA database and searching an indexed data structure with millions of entries is a time-demanding process. In this paper, we propose a fast DNA database indexing and searching approach, identifying all query hits in the database, without having to examine all entries in the indexed data structure, limiting the maximum length of a query that can be searched against the database. By applying the proposed indexing equation, the whole human genome could be indexed in 10 hours on a personal computer, under the assumption that there is enough RAM to store the indexed data structure. Analysing the methodology proposed by Reneker, we observed that hits at starting positions [Formula: see text] are not reported, if the database is searched against a query shorter than [Formula: see text] nucleotides, such that [Formula: see text] is the length of the DNA database words being mapped and [Formula: see text] is the length of the query. A solution of this drawback is also presented.

  1. Data-Base Software For Tracking Technological Developments

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  2. Information Retrieval Using ADABAS-NATURAL (with Applications for Television and Radio).

    ERIC Educational Resources Information Center

    Silbergeld, I.; Kutok, P.

    1984-01-01

    Describes use of the software ADABAS (general purpose database management system) and NATURAL (interactive programing language) in development and implementation of an information retrieval system for the National Television and Radio Network of Israel. General design considerations, files contained in each archive, search strategies, and keywords…

  3. Southwell's Relaxation Search in Computer Aided Advising: An Intelligent Information System.

    ERIC Educational Resources Information Center

    Song, Xueshu

    1992-01-01

    Describes the development and validation of a microcomputer software system that enhances undergraduate students' interests in becoming engineering graduate students. The development of a database with information on engineering graduate programs is discussed, and a model that matches individual and institutional needs using Southwell's Relaxation…

  4. School Gardens Enhance Academic Performance and Dietary Outcomes in Children

    ERIC Educational Resources Information Center

    Berezowitz, Claire K.; Bontrager Yoder, Andrea B.; Schoeller, Dale A.

    2015-01-01

    Background: Schools face increasing demands to provide education on healthy living and improve core academic performance. Although these appear to be competing concerns, they may interact beneficially. This article focuses on school garden programs and their effects on students' academic and dietary outcomes. Methods: Database searches in CABI,…

  5. School-Based First Aid Training Programs: A Systematic Review

    ERIC Educational Resources Information Center

    Reveruzzi, Bianca; Buckley, Lisa; Sheehan, Mary

    2016-01-01

    Background: This review examines the breadth of first aid training delivered to school students and the components that are age appropriate to adolescents. Method: Eligible studies included school-based first aid interventions targeting students aged between 10 and 18 years. Online databases were searched, for peer-reviewed publications available…

  6. Using dBASE II for Bibliographic Files.

    ERIC Educational Resources Information Center

    Sullivan, Jeanette

    1985-01-01

    Describes use of a database management system (dBASE II, produced by Ashton-Tate), noting best features and disadvantages. Highlights include data entry, multiple access points available, training requirements, use of dBASE for a bibliographic application, auxiliary software, and dBASE updates. Sample searches, auxiliary programs, and requirements…

  7. Rapid identification of anonymous subjects in large criminal databases: problems and solutions in IAFIS III/FBI subject searches

    NASA Astrophysics Data System (ADS)

    Kutzleb, C. D.

    1997-02-01

    The high incidence of recidivism (repeat offenders) in the criminal population makes the use of the IAFIS III/FBI criminal database an important tool in law enforcement. The problems and solutions employed by IAFIS III/FBI criminal subject searches are discussed for the following topics: (1) subject search selectivity and reliability; (2) the difficulty and limitations of identifying subjects whose anonymity may be a prime objective; (3) database size, search workload, and search response time; (4) techniques and advantages of normalizing the variability in an individual's name and identifying features into identifiable and discrete categories; and (5) the use of database demographics to estimate the likelihood of a match between a search subject and database subjects.

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

    PubMed

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

    1998-01-01

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

  9. Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

    PubMed

    Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

    2011-06-03

    Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

  10. What is lost when searching only one literature database for articles relevant to injury prevention and safety promotion?

    PubMed

    Lawrence, D W

    2008-12-01

    To assess what is lost if only one literature database is searched for articles relevant to injury prevention and safety promotion (IPSP) topics. Serial textword (keyword, free-text) searches using multiple synonym terms for five key IPSP topics (bicycle-related brain injuries, ethanol-impaired driving, house fires, road rage, and suicidal behaviors among adolescents) were conducted in four of the bibliographic databases that are most used by IPSP professionals: EMBASE, MEDLINE, PsycINFO, and Web of Science. Through a systematic procedure, an inventory of articles on each topic in each database was conducted to identify the total unduplicated count of all articles on each topic, the number of articles unique to each database, and the articles available if only one database is searched. No single database included all of the relevant articles on any topic, and the database with the broadest coverage differed by topic. A search of only one literature database will return 16.7-81.5% (median 43.4%) of the available articles on any of five key IPSP topics. Each database contributed unique articles to the total bibliography for each topic. A literature search performed in only one database will, on average, lead to a loss of more than half of the available literature on a topic.

  11. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

    PubMed Central

    2011-01-01

    Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance. PMID:21631914

  12. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

    PubMed

    Rognes, Torbjørn

    2011-06-01

    The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

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

    ERIC Educational Resources Information Center

    Meyer, Daniel E.; And Others

    1983-01-01

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

  14. Computerized literature reference system: use of an optical scanner and optical character recognition software.

    PubMed

    Lossef, S V; Schwartz, L H

    1990-09-01

    A computerized reference system for radiology journal articles was developed by using an IBM-compatible personal computer with a hand-held optical scanner and optical character recognition software. This allows direct entry of scanned text from printed material into word processing or data-base files. Additionally, line diagrams and photographs of radiographs can be incorporated into these files. A text search and retrieval software program enables rapid searching for keywords in scanned documents. The hand scanner and software programs are commercially available, relatively inexpensive, and easily used. This permits construction of a personalized radiology literature file of readily accessible text and images requiring minimal typing or keystroke entry.

  15. Content based information retrieval in forensic image databases.

    PubMed

    Geradts, Zeno; Bijhold, Jurrien

    2002-03-01

    This paper gives an overview of the various available image databases and ways of searching these databases on image contents. The developments in research groups of searching in image databases is evaluated and compared with the forensic databases that exist. Forensic image databases of fingerprints, faces, shoeprints, handwriting, cartridge cases, drugs tablets, and tool marks are described. The developments in these fields appear to be valuable for forensic databases, especially that of the framework in MPEG-7, where the searching in image databases is standardized. In the future, the combination of the databases (also DNA-databases) and possibilities to combine these can result in stronger forensic evidence.

  16. FunSimMat: a comprehensive functional similarity database

    PubMed Central

    Schlicker, Andreas; Albrecht, Mario

    2008-01-01

    Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML–RPC interface gives automatic online access to FunSimMat for programs and remote services. PMID:17932054

  17. Prescription drug monitoring programs in the United States of America

    PubMed Central

    Félix, Sausan El Burai; Mack, Karin

    2015-01-01

    SYNOPSIS Since the late 1990s, the number of opioid analgesic overdose deaths has quadrupled in the United States of America (from 4 030 deaths in 1999 to 16 651 in 2010). The objectives of this article are to provide an overview of the problem of prescription drug overdose in the United States and to discuss actions that could help reduce the problem, with particular attention to the characteristics of prescription drug monitoring programs (PDMPs). These programs consist of state-level databases that monitor controlled substances. The information compiled in the databases is at the disposal of authorized persons (e.g., physicians, pharmacists, and other health-care providers) and may be used only for professional purposes. Suppliers can use such information to prevent interaction with other drugs or therapeutic duplication, or to identify drug-search behavior. Law enforcement agencies can use these programs to identify improper drug prescription or dispensing patterns, or drug diversion. PMID:25563153

  18. RAG-3D: A search tool for RNA 3D substructures

    DOE PAGES

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  19. RAG-3D: a search tool for RNA 3D substructures

    PubMed Central

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  20. RAG-3D: A search tool for RNA 3D substructures

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

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  1. Searching for religion and mental health studies required health, social science, and grey literature databases.

    PubMed

    Wright, Judy M; Cottrell, David J; Mir, Ghazala

    2014-07-01

    To determine the optimal databases to search for studies of faith-sensitive interventions for treating depression. We examined 23 health, social science, religious, and grey literature databases searched for an evidence synthesis. Databases were prioritized by yield of (1) search results, (2) potentially relevant references identified during screening, (3) included references contained in the synthesis, and (4) included references that were available in the database. We assessed the impact of databases beyond MEDLINE, EMBASE, and PsycINFO by their ability to supply studies identifying new themes and issues. We identified pragmatic workload factors that influence database selection. PsycINFO was the best performing database within all priority lists. ArabPsyNet, CINAHL, Dissertations and Theses, EMBASE, Global Health, Health Management Information Consortium, MEDLINE, PsycINFO, and Sociological Abstracts were essential for our searches to retrieve the included references. Citation tracking activities and the personal library of one of the research teams made significant contributions of unique, relevant references. Religion studies databases (Am Theo Lib Assoc, FRANCIS) did not provide unique, relevant references. Literature searches for reviews and evidence syntheses of religion and health studies should include social science, grey literature, non-Western databases, personal libraries, and citation tracking activities. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. New Technologies and the World Ahead: The Top 20 Plus 5

    DTIC Science & Technology

    2011-01-01

    Specialized Agent Software Programs. Bots represent the next great milestone in soft- ware development. The general deployment of bots is projected to be in...knowledge and areas of interest. Powerful personal- agent 206 Moving from Vision to Action programs will search the Internet and its databases based on...language- capable chatbot and avatar interfaces that can control electronic data and also change and manipulate things in the physical world. These

  3. Proposal of Network-Based Multilingual Space Dictionary Database System

    NASA Astrophysics Data System (ADS)

    Yoshimitsu, T.; Hashimoto, T.; Ninomiya, K.

    2002-01-01

    The International Academy of Astronautics (IAA) is now constructing a multilingual dictionary database system of space-friendly terms. The database consists of a lexicon and dictionaries of multiple languages. The lexicon is a table which relates corresponding terminology in different languages. Each language has a dictionary which contains terms and their definitions. The database assumes the use on the internet. Updating and searching the terms and definitions are conducted via the network. Maintaining the database is conducted by the international cooperation. A new word arises day by day, thus to easily input new words and their definitions to the database is required for the longstanding success of the system. The main key of the database is an English term which is approved at the table held once or twice with the working group members. Each language has at lease one working group member who is responsible of assigning the corresponding term and the definition of the term of his/her native language. Inputting and updating terms and their definitions can be conducted via the internet from the office of each member which may be located at his/her native country. The system is constructed by freely distributed database server program working on the Linux operating system, which will be installed at the head office of IAA. Once it is installed, it will be open to all IAA members who can search the terms via the internet. Currently the authors are constructing the prototype system which is described in this paper.

  4. Database resources of the National Center for Biotechnology Information

    PubMed Central

    Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

    2012-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104

  5. Database resources of the National Center for Biotechnology Information

    PubMed Central

    2013-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

  6. Database resources of the National Center for Biotechnology Information.

    PubMed

    Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

    2007-01-01

    In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

  7. Database resources of the National Center for Biotechnology Information.

    PubMed

    Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene; Ye, Jian

    2009-01-01

    In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

  8. Shuttle-Data-Tape XML Translator

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Osborne, Richard N.

    2005-01-01

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

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

    PubMed Central

    2013-01-01

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

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

    PubMed

    Kiener, Joos

    2013-12-11

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

  11. Craniofacial Surgery Fellowship Websites.

    PubMed

    Silvestre, Jason; Agarwal, Divyansh; Taylor, Jesse A

    2016-06-01

    Applicants for craniofacial surgery fellowships utilize Internet-based resources like the San Francisco (SF) Match to manage applications. The purpose of this study was to evaluate the accessibility and content of craniofacial surgery fellowship websites (CSFWs). A list of available craniofacial surgery fellowships was compiled from directories of the American Society of Craniofacial Surgery (ACSFS) and SF Match. Accessibility of CSFWs was assessed via links from these directories and a Google search. Craniofacial surgery fellowship websites were evaluated on education and recruitment content and compared via program characteristics. Twenty-four of the 28 US-based craniofacial surgery fellowship programs had a CSFW (86%). The ACSFS and SF Match databases had limited CSFW accessibility, but a Google search revealed most CSFWs had the top search result (76%). In total, CSFWs provided an average of 39% of education and recruitment variables. While most programs provided fellowship program descriptions (96%), application links (96%), and faculty listings (83%), relatively few provided rotation schedules (13%), fellow selection process information (13%), or interview dates (8%). CSFW content did not vary by program location, faculty size, accreditation status, or institutional affiliations (P > 0.05). Craniofacial surgery fellowships often lack readily accessible websites from national program lists and have limited information for interested applicants. The consistent lack of online information across programs suggests future opportunities exist to improve these educational resources.

  12. Large-scale feature searches of collections of medical imagery

    NASA Astrophysics Data System (ADS)

    Hedgcock, Marcus W.; Karshat, Walter B.; Levitt, Tod S.; Vosky, D. N.

    1993-09-01

    Large scale feature searches of accumulated collections of medical imagery are required for multiple purposes, including clinical studies, administrative planning, epidemiology, teaching, quality improvement, and research. To perform a feature search of large collections of medical imagery, one can either search text descriptors of the imagery in the collection (usually the interpretation), or (if the imagery is in digital format) the imagery itself. At our institution, text interpretations of medical imagery are all available in our VA Hospital Information System. These are downloaded daily into an off-line computer. The text descriptors of most medical imagery are usually formatted as free text, and so require a user friendly database search tool to make searches quick and easy for any user to design and execute. We are tailoring such a database search tool (Liveview), developed by one of the authors (Karshat). To further facilitate search construction, we are constructing (from our accumulated interpretation data) a dictionary of medical and radiological terms and synonyms. If the imagery database is digital, the imagery which the search discovers is easily retrieved from the computer archive. We describe our database search user interface, with examples, and compare the efficacy of computer assisted imagery searches from a clinical text database with manual searches. Our initial work on direct feature searches of digital medical imagery is outlined.

  13. Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

    PubMed

    Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

    2015-04-01

    To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments

    PubMed Central

    Linder, Suzanne K.; Kamath, Geetanjali R.; Pratt, Gregory F.; Saraykar, Smita S.; Volk, Robert J.

    2015-01-01

    Objective To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a healthcare decision-making instrument commonly used in clinical settings. Study Design & Setting We searched the literature using two methods: 1) keyword searching using variations of “control preferences scale” and 2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Results Keyword searches in bibliographic databases yielded high average precision (90%), but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45–54%), but precision ranged from 35–75% with Scopus being the most precise. Conclusion Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time and resources should dictate the combination of which methods and databases are used. PMID:25554521

  15. VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, N.; Sellis, Timos

    1992-01-01

    One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

  16. Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.

    PubMed

    Park, Gun Wook; Hwang, Heeyoun; Kim, Kwang Hoe; Lee, Ju Yeon; Lee, Hyun Kyoung; Park, Ji Yeong; Ji, Eun Sun; Park, Sung-Kyu Robin; Yates, John R; Kwon, Kyung-Hoon; Park, Young Mok; Lee, Hyoung-Joo; Paik, Young-Ki; Kim, Jin Young; Yoo, Jong Shin

    2016-11-04

    In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein level, using an integrated proteomic pipeline (IPP) that consists of four engrailed steps as follows. First, using three different search engines, SEQUEST, MASCOT, and MS-GF+, individual proteomic searches were performed against the neXtProt database. Second, the search results from the PSMs were combined using statistical evaluation tools including DTASelect and Percolator. Third, the peptide search scores were converted into E-scores normalized using an in-house program. Last, ProteinInferencer was used to filter the proteins containing two or more peptides with a controlled FDR of 1.0% at the protein level. Finally, we compared the performance of the IPP to a conventional proteomic pipeline (CPP) for protein identification using a controlled FDR of <1% at the protein level. Using the IPP, a total of 5756 proteins (vs 4453 using the CPP) including 477 alternative splicing variants (vs 182 using the CPP) were identified from human hippocampal tissue. In addition, a total of 10 missing proteins (vs 7 using the CPP) were identified with two or more unique peptides, and their tryptic peptides were validated using MS/MS spectral pattern from a repository database or their corresponding synthetic peptides. This study shows that the IPP effectively improved the identification of proteins, including alternative splicing variants and missing proteins, in human hippocampal tissues for the C-HPP. All RAW files used in this study were deposited in ProteomeXchange (PXD000395).

  17. Chesapeake Bay Program Water Quality Database

    EPA Pesticide Factsheets

    The Chesapeake Information Management System (CIMS), designed in 1996, is an integrated, accessible information management system for the Chesapeake Bay Region. CIMS is an organized, distributed library of information and software tools designed to increase basin-wide public access to Chesapeake Bay information. The information delivered by CIMS includes technical and public information, educational material, environmental indicators, policy documents, and scientific data. Through the use of relational databases, web-based programming, and web-based GIS a large number of Internet resources have been established. These resources include multiple distributed on-line databases, on-demand graphing and mapping of environmental data, and geographic searching tools for environmental information. Baseline monitoring data, summarized data and environmental indicators that document ecosystem status and trends, confirm linkages between water quality, habitat quality and abundance, and the distribution and integrity of biological populations are also available. One of the major features of the CIMS network is the Chesapeake Bay Program's Data Hub, providing users access to a suite of long- term water quality and living resources databases. Chesapeake Bay mainstem and tidal tributary water quality, benthic macroinvertebrates, toxics, plankton, and fluorescence data can be obtained for a network of over 800 monitoring stations.

  18. Food & Nutrition | National Agricultural Library

    Science.gov Websites

    News Contact Us Search  Log inRegister Home Home Food & Nutrition Data from: The data of change years. Ag Data Commons 2x zip html National Animal Nutrition Program (NANP) Feed Composition Database degrees related to agriculture; USDA partner institution snapshots; Food and nutrition research; 4-H

  19. Evaluation of Federated Searching Options for the School Library

    ERIC Educational Resources Information Center

    Abercrombie, Sarah E.

    2008-01-01

    Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

  20. Telescope Bibliography Cookbook: Creating a Database of Scientific Papers that Use Observational Data

    NASA Astrophysics Data System (ADS)

    Kitt, S.; Grothkopf, U.

    2010-10-01

    This paper explains the procedures involved in creating a database of scientific papers that use observational data and linking the records to the observations residing in a data archive. Based on our experiences with the ESO Telescope Bibliography, we describe the workflow we apply in order to retrieve relevant articles, assign tags to describe the observing facilities that generated the data, and identify the correct program identification numbers (IDs). These program identifiers are particularly important as they link the published papers and the underlying data and enable scientists to access the data for new studies. With the understanding that the difficulty of compiling correct and complete data varies, depending on the information readily provided in the published literature, this paper proposes an evolution of search options for finding appropriate ID numbers. To explore the process and its various stages, we use the analogy of the "cookbook." These search methodologies might be labeled fast, medium, and slow heat recipes within our culinary theme. We provide a step-by-step guide in order to assist other bibliography compilers, in particular those who are new to the field.

  1. 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

  2. Online Patent Searching: The Realities.

    ERIC Educational Resources Information Center

    Kaback, Stuart M.

    1983-01-01

    Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

  3. Multilevel library instruction for emerging nursing roles.

    PubMed

    Francis, B W; Fisher, C C

    1995-10-01

    As new nursing roles emerge that involve greater decision making than in the past, added responsibility for outcomes and cost control, and increased emphasis on primary care, the information-seeking skills needed by nurses change. A search of library and nursing literature indicates that there is little comprehensive library instruction covering all levels of nursing programs: undergraduate, returning registered nurses, and graduate students. The University of Florida is one of the few places that has such a multilevel, course-integrated curriculum in place for all entrants into the nursing program. Objectives have been developed for each stage of learning. The courses include instruction in the use of the online public access catalog, printed resources, and electronic databases. A library classroom equipped with the latest technology enables student interaction with electronic databases. This paper discusses the program and several methods used to evaluate it.

  4. Application of kernel functions for accurate similarity search in large chemical databases.

    PubMed

    Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

    2010-04-29

    Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

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

    PubMed

    Mackey, Aaron J; Pearson, William R

    2004-10-01

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

  6. DNA profiles, computer searches, and the Fourth Amendment.

    PubMed

    Kimel, Catherine W

    2013-01-01

    Pursuant to federal statutes and to laws in all fifty states, the United States government has assembled a database containing the DNA profiles of over eleven million citizens. Without judicial authorization, the government searches each of these profiles one-hundred thousand times every day, seeking to link database subjects to crimes they are not suspected of committing. Yet, courts and scholars that have addressed DNA databasing have focused their attention almost exclusively on the constitutionality of the government's seizure of the biological samples from which the profiles are generated. This Note fills a gap in the scholarship by examining the Fourth Amendment problems that arise when the government searches its vast DNA database. This Note argues that each attempt to match two DNA profiles constitutes a Fourth Amendment search because each attempted match infringes upon database subjects' expectations of privacy in their biological relationships and physical movements. The Note further argues that database searches are unreasonable as they are currently conducted, and it suggests an adaptation of computer-search procedures to remedy the constitutional deficiency.

  7. Protein structural similarity search by Ramachandran codes

    PubMed Central

    Lo, Wei-Cheng; Huang, Po-Jung; Chang, Chih-Hung; Lyu, Ping-Chiang

    2007-01-01

    Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era. PMID:17716377

  8. Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

    NASA Astrophysics Data System (ADS)

    Kent, B. R.; Greene, G. R.

    The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

  9. Barriers for Nonparticipation and Dropout of Women in Cardiac Rehabilitation Programs: A Systematic Review.

    PubMed

    Resurrección, Davinia M; Motrico, Emma; Rigabert, Alina; Rubio-Valera, Maria; Conejo-Cerón, Sonia; Pastor, Luis; Moreno-Peral, Patricia

    2017-08-01

    Cardiovascular disease (CVD) is a major health problem worldwide. Cardiac rehabilitation (CR) programs are effective in reducing mortality and improving the quality of life of patients with CVD. Women are under-represented in CR and have a higher dropout rate than men. We aimed to systematically review the literature on barriers perceived by women with CVD affecting their nonparticipation in and/or dropping out from CR programs. Systematic review was done using MEDLINE, Embase, Scopus, Open Grey, and Cochrane Database from inception to September 2016. Search terms included (1) heart disease and other cardiac conditions, (2) CR and secondary prevention, and (3) nonparticipation in and/or dropout. Databases were searched following the "participants, interventions, comparisons, outcomes, and study design" method. A total of 24 studies (17 descriptive, 6 qualitative, and 1 randomized controlled trial) reporting several barriers were grouped into five broad categories: intrapersonal barriers (self-reported health, health beliefs, lack of time, motivation, and religious reasons); interpersonal barriers (lack of family/social support and work conflicts); logistical barriers (transport, distance, and availability of personal/community resources); CR program barriers (services offered, group format, exercise component, and CR sessions); and health system barriers (lack of referral, cost, negative experiences with the health system, and language). We found differences between the barriers related to nonparticipation in and dropout from CR programs. Women reported multilevel barriers for nonparticipation in and dropout from CR programs. Future clinical guidelines should evaluate and eliminate these barriers to improve adherence to CR programs in women. In addition, understanding the barriers for nonparticipation and dropout may be beneficial for future intervention trials.

  10. Virtual Reality Applications for Stress Management Training in the Military.

    PubMed

    Pallavicini, Federica; Argenton, Luca; Toniazzi, Nicola; Aceti, Luciana; Mantovani, Fabrizia

    2016-12-01

    Stress Management Training programs are increasingly being adopted in the military field for resilience empowerment and primary stress prevention. In the last several years, advanced technologies (virtual reality in particular) have been integrated in order to develop more innovative and effective stress training programs for military personnel, including soldiers, pilots, and other aircrew professionals. This systematic review describes experimental studies that have been conducted in recent years to test the effectiveness of virtual reality-based Stress Management Training programs developed for military personnel. This promising state-of-the-art technology has the potential to be a successful new approach in empowering soldiers and increasing their resilience to stress. To provide an overview from 2001 to 2016 of the application of virtual reality for Stress Management Training programs developed for the military, a computer-based search for relevant publications was performed in several databases. Databases used in the search were PsycINFO, Web of Science (Web of Knowledge), PubMed, and Medline. The search string was: ("Virtual Reality") AND ("Military") AND ["Stress Training" OR ("Stress Management")]. There were 14 studies that met the inclusion criteria and were included in the review. The main observation to be drawn from this review is that virtual reality can provide interactive Stress Management Training to decrease levels of perceived stress and negative affect in military personnel. This technology appears to be a promising tool for assessing individuals' resilience to stress and for identifying the impact that stress can have on physiological reactivity and performance.Pallavicini F, Argenton L, Toniazzi N, Aceti L, Mantovani F. Virtual realtiy applications for stress management training in the military. Aerosp Med Hum Perform. 2016; 87(12):1021-1030.

  11. Structured sedation programs in the emergency department, hospital and other acute settings: protocol for systematic review of effects and events.

    PubMed

    McCoy, Siobhán; Wakai, Abel; Blackburn, Carol; Barrett, Michael; Murphy, Adrian; Brenner, Maria; Larkin, Philip; Crispino-O'Connell, Gloria; Ratnapalan, Savithiri; O'Sullivan, Ronan

    2013-10-01

    The use of procedural sedation outside the operating theatre has increased in hospital settings and has gained popularity among non-anesthesiologists. Sedative agents used for procedural pain, although effective, also pose significant risks to the patient if used incorrectly. There is currently no universally accepted program of education for practitioners using or introducing procedural sedation into their practice. There is emerging literature identifying structured procedural sedation programs (PSPs) as a method of ensuring a standardized level of competency among staff and reducing risks to the patient. We hypothesize that programs of education for healthcare professionals using procedural sedation outside the operating theatre are beneficial in improving patient care, safety, practitioner competence and reducing adverse event rates. Electronic databases will be systematically searched for studies (randomized and non-randomized) examining the effectiveness of structured PSPs from 1966 to present. Database searches will be supplemented by contact with experts, reference and citation checking, and a grey literature search. No language restriction will be imposed. Screening of titles and abstracts, and data extraction will be performed by two independent reviewers. All disagreements will be resolved by discussion with an independent third party. Data analysis will be completed adhering to procedures outlined in the Cochrane Handbook of Systematic Reviews of Interventions. If the data allows, a meta-analysis will be performed. This review will cohere evidence on the effectiveness of structured PSPs on sedation events and patient outcomes within the hospital and other acute care settings. In addition, it will examine key components identified within a PSP associated with patient safety and improved patient outcomes. PROSPERO registration number: CRD42013003851.

  12. Alternative Databases for Anthropology Searching.

    ERIC Educational Resources Information Center

    Brody, Fern; Lambert, Maureen

    1984-01-01

    Examines online search results of sample questions in several databases covering linguistics, cultural anthropology, and physical anthropology in order to determine if and where any overlap in results might occur, and which files have greatest number of relevant hits. Search results by database are given for each subject area. (EJS)

  13. New software for statistical analysis of Cambridge Structural Database data

    PubMed Central

    Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

    2011-01-01

    A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

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

    NASA Astrophysics Data System (ADS)

    McCutchan, Elizabeth

    2017-01-01

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

  15. Winnowing sequences from a database search.

    PubMed

    Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

    2000-01-01

    In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

  16. When is a search not a search? A comparison of searching the AMED complementary health database via EBSCOhost, OVID and DIALOG.

    PubMed

    Younger, Paula; Boddy, Kate

    2009-06-01

    The researchers involved in this study work at Exeter Health library and at the Complementary Medicine Unit, Peninsula School of Medicine and Dentistry (PCMD). Within this collaborative environment it is possible to access the electronic resources of three institutions. This includes access to AMED and other databases using different interfaces. The aim of this study was to investigate whether searching different interfaces to the AMED allied health and complementary medicine database produced the same results when using identical search terms. The following Internet-based AMED interfaces were searched: DIALOG DataStar; EBSCOhost and OVID SP_UI01.00.02. Search results from all three databases were saved in an endnote database to facilitate analysis. A checklist was also compiled comparing interface features. In our initial search, DIALOG returned 29 hits, OVID 14 and Ebsco 8. If we assume that DIALOG returned 100% of potential hits, OVID initially returned only 48% of hits and EBSCOhost only 28%. In our search, a researcher using the Ebsco interface to carry out a simple search on AMED would miss over 70% of possible search hits. Subsequent EBSCOhost searches on different subjects failed to find between 21 and 86% of the hits retrieved using the same keywords via DIALOG DataStar. In two cases, the simple EBSCOhost search failed to find any of the results found via DIALOG DataStar. Depending on the interface, the number of hits retrieved from the same database with the same simple search can vary dramatically. Some simple searches fail to retrieve a substantial percentage of citations. This may result in an uninformed literature review, research funding application or treatment intervention. In addition to ensuring that keywords, spelling and medical subject headings (MeSH) accurately reflect the nature of the search, database users should include wildcards and truncation and adapt their search strategy substantially to retrieve the maximum number of appropriate citations possible. Librarians should be aware of these differences when making purchasing decisions, carrying out literature searches and planning user education.

  17. AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts.

    PubMed

    Lavorgna, Giovanni; Triunfo, Riccardo; Santoni, Federico; Orfanelli, Ugo; Noci, Sara; Bulfone, Alessandro; Zanetti, Gianluigi; Casari, Giorgio

    2005-07-01

    An increasing number of eukaryotic and prokaryotic genes are being found to have natural antisense transcripts (NATs). There is also growing evidence to suggest that antisense transcription could play a key role in many human diseases. Consequently, there have been several recent attempts to set up computational procedures aimed at identifying novel NATs. Our group has developed the AntiHunter program for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, the program requires a genomic sequence plus an associated list of transcript names and coordinates of the genomic region. After masking the repeated regions, the program carries out a BLASTN search of this sequence in the selected EST database, reporting via email the EST entries that reveal an antisense transcript according to the user-supplied list. Here, we present the newly developed version 2.0 of the AntiHunter tool. Several improvements have been added to this version of the program in order to increase its ability to detect a larger number of antisense ESTs. As a result, AntiHunter can now detect, on average, >45% more antisense ESTs with little or no increase in the percentage of the false positives. We also raised the maximum query size to 3 Mb (previously 1 Mb). Moreover, we found that a reasonable trade-off between the program search sensitivity and the maximum allowed size of the input-query sequence could be obtained by querying the database with the MEGABLAST program, rather than by using the BLAST one. We now offer this new opportunity to users, i.e. if choosing the MEGABLAST option, users can input a query sequence up to 30 Mb long, thus considerably improving the possibility to analyze longer query regions. The AntiHunter tool is freely available at http://bioinfo.crs4.it/AH2.0.

  18. A systematic review of the literature to support an evidence-based precepting program.

    PubMed

    Mann-Salinas, Elizabeth; Hayes, Elizabeth; Robbins, Johnnie; Sabido, Jean; Feider, Laura; Allen, David; Yoder, Linda

    2014-05-01

    To provide a systematic review of the literature regarding development of an evidence-based Precepting Program for nurses transitioning to burn specialty practice. Burned patients are admitted to specialty Burn Centers where highly complex nursing care is provided. Successful orientation and integration into such a specialized work environment is a fundamental component of a nurse's ability to provide safe and holistic patient care. A systematic review of the literature was performed for the period 1995-2011 using electronic databases within PUBMED and Ovid search engines. Databases included Medline, CINHAL, ProQuest for Dissertations and Thesis, and Cochran Collaboration using key search terms: preceptor, preceptee, preceptorship, precept*, nurs*, critical care, personality types, competency-based education, and learning styles. Nurses graded the level and quality of evidence of the included articles using a modified 7-level rating system and the Johns Hopkins Nursing Quality of Evidence Appraisal during journal-club meetings. A total of 43 articles related to competency (n=8), knowledge acquisition and personality characteristics (n=8), learning style (n=5), preceptor development (n=7), and Precepting Programs (n=14). A significant clinical gap existed between the scientific evidence and actual precepting practice of experienced nurses at the Burn Center. Based on this extensive review of the literature, it was determined that a sufficient evidence base existed for development of an evidence-based Precepting Program. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

  19. 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.

  20. VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, N.; Sellis, Timos

    1993-01-01

    One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image datasets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate database search.

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

    PubMed

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

    2016-10-01

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

  2. Environmental Factor(tm) system: RCRA hazardous waste handler information (on cd-rom). Database

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

    NONE

    1996-04-01

    Environmental Factor(tm) RCRA Hazardous Waste Handler Information on CD-ROM unleashes the invaluable information found in two key EPA data sources on hazardous waste handlers and offers cradle-to-grave waste tracking. It`s easy to search and display: (1) Permit status, design capacity and compliance history for facilities found in the EPA Resource Conservation and Recovery Information System (RCRIS) program tracking database; (2) Detailed information on hazardous wastes generation, management and minimization by companies who are large quantity generators, and (3) Data on the waste management practices of treatment, storage and disposal (TSD) facilities from the EPA Biennial Reporting System which is collectedmore » every other year. Environmental Factor`s powerful database retrieval system lets you: (1) Search for RCRA facilities by permit type, SIC code, waste codes, corrective action or violation information, TSD status, generator and transporter status and more; (2) View compliance information - dates of evaluation, violation, enforcement and corrective action; (3) Lookup facilities by waste processing categories of marketing, transporting, processing and energy recovery; (4) Use owner/operator information and names, titles and telephone numbers of project managers for prospecting; and (5) Browse detailed data on TSD facility and large quantity generators` activities such as onsite waste treatment, disposal, or recycling, offsite waste received, and waste generation and management. The product contains databases, search and retrieval software on two CD-ROMs, an installation diskette and User`s Guide. Environmental Factor has online context-sensitive help from any screen and a printed User`s Guide describing installation and step-by-step procedures for searching, retrieving and exporting. Hotline support is also available for no additional charge.« less

  3. Methamphetamine use and treatment in Iran: A systematic review from the most populated Persian Gulf country.

    PubMed

    Alam-mehrjerdi, Zahra; Mokri, Azarakhsh; Dolan, Kate

    2015-08-01

    Methamphetamine use is a new health concern in Iran, the most populated Persian Gulf country. However, there is no well-documented literature. The current study objectives were to systematically review all published English and Persian studies of the prevalence of methamphetamine use, the general physical and psychiatric-related harms and the availability of methamphetamine treatment and harm reduction services for adult users in Iran. A comprehensive search of the international peer-reviewed and gray literature was undertaken. Multiple electronic and scientific English and Persian databases were systematically searched from January 2002 to September 2014. Additionally, English and Persian gray literature on methamphetamine use was sought using online gray literature databases, library databases and general online searches over the same period of time. Nineteen thousand and two hundred and eight studies, reports and conference papers were identified but only 42 studies were relevant to the study objectives. They were mainly published in 2010-2014. The search results confirmed the seizures of methamphetamine (six studies), the prevalence of methamphetamine use among the general population (three studies), drug users (four studies), women (nine studies) and opiate users in opiate treatment programs (five studies). In addition, methamphetamine use had resulted in blood-borne viral infections (one study), psychosis and intoxication (ten studies). Different reasons had facilitated methamphetamine use. However, the Matrix Model, community therapy and harm reduction services (four studies) had been provided for methamphetamine users in some cities. The current situation of methamphetamine use necessitates more research on the epidemiology and health-related implications. These studies should help in identifying priorities for designing and implementing prevention and educational programs. More active models of engagement with Persian methamphetamine users and the provision of services that meet their specific treatment needs are required. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Fast parallel tandem mass spectral library searching using GPU hardware acceleration

    PubMed Central

    Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K.; Martin, Daniel B.

    2011-01-01

    Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment. PMID:21545112

  5. Prevention and Periodontal Treatment in Down Syndrome Patients: A Systematic Review

    PubMed Central

    Greghi, Sebastião Luiz Aguiar; de Resende, Maria Lúcia Rubo; Sant’Ana, Adriana Campos Passanezi; Damante, Carla Andreotti

    2016-01-01

    The aim of this systematic literature review was to evaluate which type of periodontal preventive and therapeutic approaches presents superior outcomes in patients with Down syndrome (DS). Studies reporting different methods of periodontal care from DS patients were considered eligible. Included clinical studies should indicate at least two periodontal parameters in different periods of assessment. Screening of the articles, data extraction and quality assessment were conducted independently and in duplicate. Electronic search according to the PICO search, with both Key-words and MESH terms were conducted in MEDLINE, EMBASE and CENTRAL databases until March 2016. Manual search was conducted in four journals, namely Journal of Periodontology, Journal of Clinical Periodontology, Journal of Periodontal Research and Special Care in Dentistry and their electronic databases were searched. Electronic and manual search resulted in 763 papers, and of them 744 were excluded after title/abstract assessment. The full text of 19 potentially eligible publications was screened and 9 studies met inclusion criteria. The results demonstrated the importance to introduce youngest DS patients in preventive programs, as well as participation of parents, caregivers or institutional attendants in supervising/performing oral hygiene. In studies with higher frequency of attendance, all age groups presented superior preventive and therapeutic results, irrespective of the therapeutic approach used (surgical/nonsurgical/periodontal care program). The important factors for reducing periodontal parameters were the frequency of the appointments and association with chlorhexidine/plaque disclosing agents as adjuvant treatment. This systematic review demonstrated that early introduction in periodontal care, participation of parents/caregivers/institutional attendants, frequency of attendance and association with chemical adjuvants (independently of the periodontal treatment adopted) seems to improve periodontal outcomes in preventive and periodontal treatment of DS patients. Registration number (Prospero): CRD42016038433. PMID:27355338

  6. Database Searching by Managers.

    ERIC Educational Resources Information Center

    Arnold, Stephen E.

    Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

  7. Constructing Effective Search Strategies for Electronic Searching.

    ERIC Educational Resources Information Center

    Flanagan, Lynn; Parente, Sharon Campbell

    Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

  8. Subject searching of monographs online in the medical literature.

    PubMed

    Brahmi, F A

    1988-01-01

    Searching by subject for monographic information online in the medical literature is a challenging task. The NLM database of choice is CATLINE. Other NLM databases of interest are BIOTHICSLINE, CANCERLIT, HEALTH, POPLINE, and TOXLINE. Ten BRS databases are also discussed. Of these, Books in Print, Bookinfo, and OCLC are explored further. The databases are compared as to number of total records and number and percentage of monographs. Three topics were searched on CROSS to compare hits on BBIP, BOOK, and OCLC. The same searches were run on CATLINE. The parameters of time coverage and language were equalized and the resulting citations were compared and analyzed for duplication and uniqueness. With the input of CATLINE tapes into OCLC, OCLC has become the database of choice for searching by subject for medical monographs.

  9. mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

    PubMed

    Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

    2018-05-21

    With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

  10. Ability of HIV Advocacy to Modify Behavioral Norms and Treatment Impact: A Systematic Review.

    PubMed

    Sunguya, Bruno F; Munisamy, Murallitharan; Pongpanich, Sathirakorn; Yasuoka, Junko; Jimba, Masamine

    2016-08-01

    HIV advocacy programs are partly responsible for the global community's success in reducing the burden of HIV. The rising wave of the global burden of noncommunicable diseases (NCDs) has prompted the World Health Organization to espouse NCD advocacy efforts as a possible preventive strategy. HIV and NCDs share some similarities in their chronicity and risky behaviors, which are their associated etiology. Therefore, pooled evidence on the effectiveness of HIV advocacy programs and ideas shared could be replicated and applied during the conceptualization of NCD advocacy programs. Such evidence, however, has not been systematically reviewed to address the effectiveness of HIV advocacy programs, particularly programs that aimed at changing public behaviors deemed as risk factors. To determine the effectiveness of HIV advocacy programs and draw lessons from those that are effective to strengthen future noncommunicable disease advocacy programs. We searched for evidence regarding the effectiveness of HIV advocacy programs in medical databases: PubMed, The Cumulative Index to Nursing and Allied Health Literature Plus, Educational Resources and Information Center, and Web of Science, with articles dated from 1994 to 2014. Search criteria. The review protocol was registered before this review. The inclusion criteria were studies on advocacy programs or interventions. We selected studies with the following designs: randomized controlled design studies, pre-post intervention studies, cohorts and other longitudinal studies, quasi-experimental design studies, and cross-sectional studies that reported changes in outcome variables of interest following advocacy programs. We constructed Boolean search terms and used them in PubMed as well as other databases, in line with a population, intervention, comparator, and outcome question. The flow of evidence search and reporting followed the standard Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. We selected 2 outcome variables (i.e., changing social norms and a change in impact) out of 6 key outcomes of advocacy interventions. We assessed the risk of bias for all selected studies by using the Cochrane risk-of-bias tool for randomized studies and using the Risk of Bias for Nonrandomized Observational Studies for observational studies. We did not grade the collective quality of evidence because of differences between the studies, with regard to methods, study designs, and context. Moreover, we could not carry out meta-analyses because of heterogeneity and the diverse study designs; thus, we used a narrative synthesis to report the findings. A total of 25 studies were eligible, of the 1463 studies retrieved from selected databases. Twenty-two of the studies indicated a shift in social norms as a result of HIV advocacy programs, and 3 indicated a change in impact. We drew 6 lessons from these programs that may be useful for noncommunicable disease advocacy: (1) involving at-risk populations in advocacy programs, (2) working with laypersons and community members, (3) working with peer advocates and activists, (4) targeting specific age groups and asking support from celebrities, (5) targeting several, but specific, risk factors, and (6) using an evidence-based approach through formative research. Author conclusions. HIV advocacy programs have been effective in shifting social norms and facilitating a change in impact. The lessons learned from these effective programs could be used to improve the design and implementation of future noncommunicable disease advocacy programs.

  11. Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

    PubMed

    Okuma, E

    1994-01-01

    With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program.

  12. Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

    PubMed Central

    Okuma, E

    1994-01-01

    With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program. PMID:8136757

  13. A systematic review of evaluated suicide prevention programs targeting indigenous youth.

    PubMed

    Harlow, Alyssa F; Bohanna, India; Clough, Alan

    2014-01-01

    Indigenous young people have significantly higher suicide rates than their non-indigenous counterparts. There is a need for culturally appropriate and effective suicide prevention programs for this demographic. This review assesses suicide prevention programs that have been evaluated for indigenous youth in Australia, Canada, New Zealand, and the United States. The databases MEDLINE and PsycINFO were searched for publications on suicide prevention programs targeting indigenous youth that include reports on evaluations and outcomes. Program content, indigenous involvement, evaluation design, program implementation, and outcomes were assessed for each article. The search yielded 229 articles; 90 abstracts were assessed, and 11 articles describing nine programs were reviewed. Two Australian programs and seven American programs were included. Programs were culturally tailored, flexible, and incorporated multiple-levels of prevention. No randomized controlled trials were found, and many programs employed ad hoc evaluations, poor program description, and no process evaluation. Despite culturally appropriate content, the results of the review indicate that more controlled study designs using planned evaluations and valid outcome measures are needed in research on indigenous youth suicide prevention. Such changes may positively influence the future of research on indigenous youth suicide prevention as the outcomes and efficacy will be more reliable.

  14. Search Fermilab Plant Database

    Science.gov Websites

    Select the characteristics of the plant you want to find below and click the Search button. To see Plants to see all the prairie plants in the database. Click Search All Plants at Fermilab to search for reflects observations at Fermilab. If you need a more sophisticated search, try the Advanced Search. Search

  15. Care plan program reduces the number of visits for challenging psychiatric patients in the ED.

    PubMed

    Abello, Arthur; Brieger, Ben; Dear, Kim; King, Ben; Ziebell, Chris; Ahmed, Atheer; Milling, Truman J

    2012-09-01

    A small number of patients representing a significant demand on emergency department (ED) services present regularly for a variety of reasons, including psychiatric or behavioral complaints and lack of access to other services. A care plan program was created as a database of ED high users and patients of concern, as identified by ED staff and approved by program administrators to improve care and mitigate ED strain. A list of medical record numbers was assembled by searching the care plan program database for adult patients initially enrolled between the dates of November 1, 2006, and October 21, 2007. Inclusion criteria were the occurrence of a psychiatric International Classification Diseases, Ninth Revision, code in their medical record and a care plan level implying a serious psychiatric disorder causing harmful behavior. Additional data about these patients were acquired using an indigent care tracking database and electronic medical records. Variables collected from these sources were analyzed for changes before and after program enrollment. Of 501 patients in the database in the period studied, 48 patients fulfilled the criteria for the cohort. There was a significant reduction in the number of visits to the ED from the year before program enrollment to the year after enrollment (8.9, before; 5.9, after; P < .05). There was also an increase in psychiatric hospital visits (2%, before; 25%, after; P < .05). An alert program that identifies challenging ED patients with psychiatric conditions and creates a care plan appears to reduce visits and lead to more appropriate use of other resources. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Reducing process delays for real-time earthquake parameter estimation - An application of KD tree to large databases for Earthquake Early Warning

    NASA Astrophysics Data System (ADS)

    Yin, Lucy; Andrews, Jennifer; Heaton, Thomas

    2018-05-01

    Earthquake parameter estimations using nearest neighbor searching among a large database of observations can lead to reliable prediction results. However, in the real-time application of Earthquake Early Warning (EEW) systems, the accurate prediction using a large database is penalized by a significant delay in the processing time. We propose to use a multidimensional binary search tree (KD tree) data structure to organize large seismic databases to reduce the processing time in nearest neighbor search for predictions. We evaluated the performance of KD tree on the Gutenberg Algorithm, a database-searching algorithm for EEW. We constructed an offline test to predict peak ground motions using a database with feature sets of waveform filter-bank characteristics, and compare the results with the observed seismic parameters. We concluded that large database provides more accurate predictions of the ground motion information, such as peak ground acceleration, velocity, and displacement (PGA, PGV, PGD), than source parameters, such as hypocenter distance. Application of the KD tree search to organize the database reduced the average searching process by 85% time cost of the exhaustive method, allowing the method to be feasible for real-time implementation. The algorithm is straightforward and the results will reduce the overall time of warning delivery for EEW.

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

    PubMed Central

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

    1997-01-01

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

  18. Lunar e-Library: Putting Space History to Work

    NASA Technical Reports Server (NTRS)

    McMahan, Tracy A.; Shea, Charlotte A.; Finckenor, Miria

    2006-01-01

    As NASA plans and implements the Vision for Space Exploration, managers, engineers, and scientists need historically important information that is readily available and easily accessed. The Lunar e-Library - a searchable collection of 1100 electronic (.PDF) documents - makes it easy to find critical technical data and lessons learned and put space history knowledge in action. The Lunar e-Library, a DVD knowledge database, was developed by NASA to shorten research time and put knowledge at users' fingertips. Funded by NASA's Space Environments and Effects (SEE) Program headquartered at Marshall Space Flight Center (MSFC) and the MSFC Materials and Processes Laboratory, the goal of the Lunar e- Library effort was to identify key lessons learned from Apollo and other lunar programs and missions and to provide technical information from those programs in an easy-to-use format. The SEE Program began distributing the Lunar e-Library knowledge database in 2006. This paper describes the Lunar e-Library development process (including a description of the databases and resources used to acquire the documents) and the contents of the DVD product, demonstrates its usefulness with focused searches, and provides information on how to obtain this free resource.

  19. Interactive searching of facial image databases

    NASA Astrophysics Data System (ADS)

    Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

    1995-09-01

    A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

  20. Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

    ERIC Educational Resources Information Center

    Tenopir, Carol

    1985-01-01

    This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

  1. A Systematic Review of Sound-Based Intervention Programs to Improve Participation in Education for Children with Sensory Processing and Integration Challenges

    ERIC Educational Resources Information Center

    Villasenor, Romana F.; Smith, Sarah L.; Jewell, Vanessa D.

    2018-01-01

    This systematic review evaluates current evidence for using sound-based interventions (SBIs) to improve educational participation for children with challenges in sensory processing and integration. Databases searched included CINAHL, MEDLINE Complete, PsychINFO, ERIC, Web of Science, and Cochrane. No studies explicitly measured participation-level…

  2. In search of the emotional face: anger versus happiness superiority in visual search.

    PubMed

    Savage, Ruth A; Lipp, Ottmar V; Craig, Belinda M; Becker, Stefanie I; Horstmann, Gernot

    2013-08-01

    Previous research has provided inconsistent results regarding visual search for emotional faces, yielding evidence for either anger superiority (i.e., more efficient search for angry faces) or happiness superiority effects (i.e., more efficient search for happy faces), suggesting that these results do not reflect on emotional expression, but on emotion (un-)related low-level perceptual features. The present study investigated possible factors mediating anger/happiness superiority effects; specifically search strategy (fixed vs. variable target search; Experiment 1), stimulus choice (Nimstim database vs. Ekman & Friesen database; Experiments 1 and 2), and emotional intensity (Experiment 3 and 3a). Angry faces were found faster than happy faces regardless of search strategy using faces from the Nimstim database (Experiment 1). By contrast, a happiness superiority effect was evident in Experiment 2 when using faces from the Ekman and Friesen database. Experiment 3 employed angry, happy, and exuberant expressions (Nimstim database) and yielded anger and happiness superiority effects, respectively, highlighting the importance of the choice of stimulus materials. Ratings of the stimulus materials collected in Experiment 3a indicate that differences in perceived emotional intensity, pleasantness, or arousal do not account for differences in search efficiency. Across three studies, the current investigation indicates that prior reports of anger or happiness superiority effects in visual search are likely to reflect on low-level visual features associated with the stimulus materials used, rather than on emotion. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  3. Embedding strategies for effective use of information from multiple sequence alignments.

    PubMed Central

    Henikoff, S.; Henikoff, J. G.

    1997-01-01

    We describe a new strategy for utilizing multiple sequence alignment information to detect distant relationships in searches of sequence databases. A single sequence representing a protein family is enriched by replacing conserved regions with position-specific scoring matrices (PSSMs) or consensus residues derived from multiple alignments of family members. In comprehensive tests of these and other family representations, PSSM-embedded queries produced the best results overall when used with a special version of the Smith-Waterman searching algorithm. Moreover, embedding consensus residues instead of PSSMs improved performance with readily available single sequence query searching programs, such as BLAST and FASTA. Embedding PSSMs or consensus residues into a representative sequence improves searching performance by extracting multiple alignment information from motif regions while retaining single sequence information where alignment is uncertain. PMID:9070452

  4. Genetic Testing Registry

    MedlinePlus

    ... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

  5. The Effectiveness of Suicide Prevention Education Programs for Nurses.

    PubMed

    Ferguson, Monika S; Reis, Julie A; Rabbetts, Lyn; Ashby, Heather-Jean; Bayes, Miriam; McCracken, Tara; Ross, Christine; Procter, Nicholas G

    2018-03-01

    Education to improve health professionals' responses to suicide is considered an important suicide prevention strategy. However, the effectiveness of this approach for nurses is unclear. To systematically review the peer-reviewed literature regarding the effectiveness of suicide prevention education programs for nurses. Nine academic databases (CINAHL, Cochrane Reviews & Trials, Embase, Informit Health Collection, Joanna Briggs Institute, Medline, PsycINFO, Scopus, and Web of Science) were searched in November 2016, utilizing search terms related to suicide, education, and nurses, with no limits placed on publication date or study design. The search yielded 5,456 identified articles, 11 of which met the inclusion criteria. Studies were primarily quantitative (RCTs n = 3; quasi-experimental n = 6; qualitative n = 2), and involved nurses (range = 16-561) working in a diversity of settings, particularly hospitals (n = 9). Studies revealed positive changes in nurses' competence, knowledge, and attitudes associated with training over the short term. The heterogeneity of education programs and methodological weaknesses of included studies limit the conclusions drawn. There is a moderate body of evidence to support the effectiveness of suicide prevention education programs for nurses. Future research should examine longer-term changes in clinical practice and strategies for continuing education, with more rigorous study designs.

  6. Current Abstracts Nuclear Reactors and Technology

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

    Bales, J.D.; Hicks, S.C.

    1993-01-01

    This publication Nuclear Reactors and Technology (NRT) announces on a monthly basis the current worldwide information available from the open literature on nuclear reactors and technology, including all aspects of power reactors, components and accessories, fuel elements, control systems, and materials. This publication contains the abstracts of DOE reports, journal articles, conference papers, patents, theses, and monographs added to the Energy Science and Technology Database during the past month. Also included are US information obtained through acquisition programs or interagency agreements and international information obtained through acquisition programs or interagency agreements and international information obtained through the International Energy Agency`smore » Energy Technology Data Exchange or government-to-government agreements. The digests in NRT and other citations to information on nuclear reactors back to 1948 are available for online searching and retrieval on the Energy Science and Technology Database and Nuclear Science Abstracts (NSA) database. Current information, added daily to the Energy Science and Technology Database, is available to DOE and its contractors through the DOE Integrated Technical Information System. Customized profiles can be developed to provide current information to meet each user`s needs.« less

  7. Database Search Strategies & Tips. Reprints from the Best of "ONLINE" [and]"DATABASE."

    ERIC Educational Resources Information Center

    Online, Inc., Weston, CT.

    Reprints of 17 articles presenting strategies and tips for searching databases online appear in this collection, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1)…

  8. Shapefile for Coastal Zone Management Program counties of the United States and its territories, 2009 (CZMP_counties_2009.shp)

    USGS Publications Warehouse

    Hartwell, Stephen R.; Wingfield, Dana K.; Allwardt, Alan O.; Wong, Florence L.; Lightsom, Frances L.

    2013-01-01

    A shapefile of 492 Coastal Zone Management Program counties of the United States and its territories, current for the ground condition in 2009, has been extracted from the U.S. Census Bureau MAF/TIGER database. Geospatial information systems with the capability to search user-defined, polygonal geographic areas will be able to utilize this shapefile or secondary products derived from it, such as well-known text representations of the individual polygons within the shapefile.

  9. Cysteine-containing peptides having antioxidant properties

    DOEpatents

    Bielicki, John K [Castro Valley, CA

    2007-05-15

    The term "homology" or "homologous" means an amino acid similarity measured by the program, BLAST (Altschul et al (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:33 89 3402), and expressed as --(% identity n/n). In measuring homology between a peptide and a protein of greater size, homology is measured only in the corresponding region; that is, the protein is regarded as only having the same general length as the peptide, allowing for gaps and insertions.

  10. The RAND Online Measure Repository for Evaluating Psychological Health and Traumatic Brain Injury Programs. The RAND Toolkit, Volume 2

    DTIC Science & Technology

    2014-01-01

    tempo may raise the risk for mental health challenges. During this time, the U.S. Department of Defense (DoD) has implemented numerous programs to...and were based on the constraints of each electronic database. However, most searches were variations on a basic three-category format: The first...Gerontology, 1983, 38: 111–116. Iannuzzo RW, Jaeger J, Goldberg JF, Kafantaris V, Sublette ME. “Development and Reliability of the Ham-D/MADRS

  11. Availability and Diversity of Training Programs for Responders to International Disasters and Complex Humanitarian Emergencies

    PubMed Central

    Jacquet, Gabrielle A.; Obi, Chioma C.; Chang, Mary P.; Bayram, Jamil D.

    2014-01-01

    Introduction: Volunteers and members of relief organizations increasingly seek formal training prior to international field deployment. This paper identifies training programs for personnel responding to international disasters and complex humanitarian emergencies, and provides concise information – if available- regarding the founding organization, year established, location, cost, duration of training, participants targeted, and the content of each program. Methods: An environmental scan was conducted through a combination of a peer-reviewed literature search and an open Internet search for the training programs. Literature search engines included EMBASE, Cochrane, Scopus, PubMed, Web of Science databases using the search terms “international,” “disaster,” “complex humanitarian emergencies,” “training,” and “humanitarian response”. Both searches were conducted between January 2, 2013 and September 12, 2013. Results: 14 peer-reviewed articles mentioned or described eight training programs, while open Internet search revealed 13 additional programs. In total, twenty-one training programs were identified as currently available for responders to international disasters and CHE. Each of the programs identified has different goals and objectives, duration, expenses, targeted trainees and modules. Each of the programs identified has different goals and objectives, duration, expenses, targeted trainees and modules. Seven programs (33%) are free of charge and four programs (19%) focus on the mental aspects of disasters. The mean duration for each training program is 5 to 7 days. Fourteen of the trainings are conducted in multiple locations (66%), two in Cuba (9%) and two in Australia (9%). The cost-reported in US dollars- ranges from $100 to $2,400 with a mean cost of $480 and a median cost of $135. Most of the programs are open to the public, but some are only available by invitation only, such as the International Mobilization Preparation for Action (IMPACT) and the United Nations Humanitarian Civil-Military Coordination (UN-CMCoord) Field Course. Conclusions: A variety of training programs are available for responders to disasters and complex humanitarian emergencies. These programs vary in their objectives, audiences, modules, geographical locations, eligibility and financial cost. This paper presents an overview of available programs and serves as a resource for potential responders interested in capacity-building training prior to deployment. PMID:24987573

  12. Histoplasma capsulatum proteome response to decreased iron availability

    PubMed Central

    Winters, Michael S; Spellman, Daniel S; Chan, Qilin; Gomez, Francisco J; Hernandez, Margarita; Catron, Brittany; Smulian, Alan G; Neubert, Thomas A; Deepe, George S

    2008-01-01

    Background A fundamental pathogenic feature of the fungus Histoplasma capsulatum is its ability to evade innate and adaptive immune defenses. Once ingested by macrophages the organism is faced with several hostile environmental conditions including iron limitation. H. capsulatum can establish a persistent state within the macrophage. A gap in knowledge exists because the identities and number of proteins regulated by the organism under host conditions has yet to be defined. Lack of such knowledge is an important problem because until these proteins are identified it is unlikely that they can be targeted as new and innovative treatment for histoplasmosis. Results To investigate the proteomic response by H. capsulatum to decreasing iron availability we have created H. capsulatum protein/genomic databases compatible with current mass spectrometric (MS) search engines. Databases were assembled from the H. capsulatum G217B strain genome using gene prediction programs and expressed sequence tag (EST) libraries. Searching these databases with MS data generated from two dimensional (2D) in-gel digestions of proteins resulted in over 50% more proteins identified compared to searching the publicly available fungal databases alone. Using 2D gel electrophoresis combined with statistical analysis we discovered 42 H. capsulatum proteins whose abundance was significantly modulated when iron concentrations were lowered. Altered proteins were identified by mass spectrometry and database searching to be involved in glycolysis, the tricarboxylic acid cycle, lysine metabolism, protein synthesis, and one protein sequence whose function was unknown. Conclusion We have created a bioinformatics platform for H. capsulatum and demonstrated the utility of a proteomic approach by identifying a shift in metabolism the organism utilizes to cope with the hostile conditions provided by the host. We have shown that enzyme transcripts regulated by other fungal pathogens in response to lowering iron availability are also regulated in H. capsulatum at the protein level. We also identified H. capsulatum proteins sensitive to iron level reductions which have yet to be connected to iron availability in other pathogens. These data also indicate the complexity of the response by H. capsulatum to nutritional deprivation. Finally, we demonstrate the importance of a strain specific gene/protein database for H. capsulatum proteomic analysis. PMID:19108728

  13. CEBS: a comprehensive annotated database of toxicological data

    PubMed Central

    Lea, Isabel A.; Gong, Hui; Paleja, Anand; Rashid, Asif; Fostel, Jennifer

    2017-01-01

    The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/databases/cebs/. PMID:27899660

  14. Database resources of the National Center for Biotechnology Information.

    PubMed

    Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

    2011-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

  15. National Center for Biotechnology Information

    MedlinePlus

    ... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

  16. Information sources for obesity prevention policy research: a review of systematic reviews.

    PubMed

    Hanneke, Rosie; Young, Sabrina K

    2017-08-08

    Systematic identification of evidence in health policy can be time-consuming and challenging. This study examines three questions pertaining to systematic reviews on obesity prevention policy, in order to identify the most efficient search methods: (1) What percentage of the primary studies selected for inclusion in the reviews originated in scholarly as opposed to gray literature? (2) How much of the primary scholarly literature in this topic area is indexed in PubMed/MEDLINE? (3) Which databases index the greatest number of primary studies not indexed in PubMed, and are these databases searched consistently across systematic reviews? We identified systematic reviews on obesity prevention policy and explored their search methods and citations. We determined the percentage of scholarly vs. gray literature cited, the most frequently cited journals, and whether each primary study was indexed in PubMed. We searched 21 databases for all primary study articles not indexed in PubMed to determine which database(s) indexed the highest number of these relevant articles. In total, 21 systematic reviews were identified. Ten of the 21 systematic reviews reported searching gray literature, and 12 reviews ultimately included gray literature in their analyses. Scholarly articles accounted for 577 of the 649 total primary study papers. Of these, 495 (76%) were indexed in PubMed. Google Scholar retrieved the highest number of the remaining 82 non-PubMed scholarly articles, followed by Scopus and EconLit. The Journal of the American Dietetic Association was the most-cited journal. Researchers can maximize search efficiency by searching a small yet targeted selection of both scholarly and gray literature resources. A highly sensitive search of PubMed and those databases that index the greatest number of relevant articles not indexed in PubMed, namely multidisciplinary and economics databases, could save considerable time and effort. When combined with a gray literature search and additional search methods, including cited reference searching and consulting with experts, this approach could help maintain broad retrieval of relevant studies while improving search efficiency. Findings also have implications for designing specialized databases for public health research.

  17. Implementation of a Big Data Accessing and Processing Platform for Medical Records in Cloud.

    PubMed

    Yang, Chao-Tung; Liu, Jung-Chun; Chen, Shuo-Tsung; Lu, Hsin-Wen

    2017-08-18

    Big Data analysis has become a key factor of being innovative and competitive. Along with population growth worldwide and the trend aging of population in developed countries, the rate of the national medical care usage has been increasing. Due to the fact that individual medical data are usually scattered in different institutions and their data formats are varied, to integrate those data that continue increasing is challenging. In order to have scalable load capacity for these data platforms, we must build them in good platform architecture. Some issues must be considered in order to use the cloud computing to quickly integrate big medical data into database for easy analyzing, searching, and filtering big data to obtain valuable information.This work builds a cloud storage system with HBase of Hadoop for storing and analyzing big data of medical records and improves the performance of importing data into database. The data of medical records are stored in HBase database platform for big data analysis. This system performs distributed computing on medical records data processing through Hadoop MapReduce programming, and to provide functions, including keyword search, data filtering, and basic statistics for HBase database. This system uses the Put with the single-threaded method and the CompleteBulkload mechanism to import medical data. From the experimental results, we find that when the file size is less than 300MB, the Put with single-threaded method is used and when the file size is larger than 300MB, the CompleteBulkload mechanism is used to improve the performance of data import into database. This system provides a web interface that allows users to search data, filter out meaningful information through the web, and analyze and convert data in suitable forms that will be helpful for medical staff and institutions.

  18. Transterm—extended search facilities and improved integration with other databases

    PubMed Central

    Jacobs, Grant H.; Stockwell, Peter A.; Tate, Warren P.; Brown, Chris M.

    2006-01-01

    Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3′ and 5′ flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at . PMID:16381889

  19. Fast and efficient search for MPEG-4 video using adjacent pixel intensity difference quantization histogram feature

    NASA Astrophysics Data System (ADS)

    Lee, Feifei; Kotani, Koji; Chen, Qiu; Ohmi, Tadahiro

    2010-02-01

    In this paper, a fast search algorithm for MPEG-4 video clips from video database is proposed. An adjacent pixel intensity difference quantization (APIDQ) histogram is utilized as the feature vector of VOP (video object plane), which had been reliably applied to human face recognition previously. Instead of fully decompressed video sequence, partially decoded data, namely DC sequence of the video object are extracted from the video sequence. Combined with active search, a temporal pruning algorithm, fast and robust video search can be realized. The proposed search algorithm has been evaluated by total 15 hours of video contained of TV programs such as drama, talk, news, etc. to search for given 200 MPEG-4 video clips which each length is 15 seconds. Experimental results show the proposed algorithm can detect the similar video clip in merely 80ms, and Equal Error Rate (ERR) of 2 % in drama and news categories are achieved, which are more accurately and robust than conventional fast video search algorithm.

  20. Quantum search of a real unstructured database

    NASA Astrophysics Data System (ADS)

    Broda, Bogusław

    2016-02-01

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

  1. Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

    PubMed Central

    Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, Hanno

    2012-01-01

    Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis. PMID:22493179

  2. The MAO NASU Plate Archive Database. Current Status and Perspectives

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

  3. Does gamification increase engagement with online programs? A systematic review

    PubMed Central

    Looyestyn, Jemma; Kernot, Jocelyn; Boshoff, Kobie; Ryan, Jillian; Edney, Sarah; Maher, Carol

    2017-01-01

    Background Engagement in online programs is difficult to maintain. Gamification is the recent trend that offers to increase engagement through the inclusion of game-like features like points and badges, in non-game contexts. This review will answer the following question, ‘Are gamification strategies effective in increasing engagement in online programs?’ Method Eight databases (Web of Science, PsycINFO, Medline, INSPEC, ERIC, Cochrane Library, Business Source Complete and ACM Digital Library) were searched from 2010 to the 28th of October 2015 using a comprehensive search strategy. Eligibility criteria was based on the PICOS format, where “population” included adults, “intervention” involved an online program or smart phone application that included at least one gamification feature. “Comparator” was a control group, “outcomes” included engagement and “downstream” outcomes which occurred as a result of engagement; and “study design” included experimental studies from peer-reviewed sources. Effect sizes (Cohens d and 95% confidence intervals) were also calculated. Results 1017 studies were identified from database searches following the removal of duplicates, of which 15 met the inclusion criteria. The studies involved a total of 10,499 participants, and were commonly undertaken in tertiary education contexts. Engagement metrics included time spent (n = 5), volume of contributions (n = 11) and occasions visited to the software (n = 4); as well as downstream behaviours such as performance (n = 4) and healthy behaviours (n = 1). Effect sizes typically ranged from medium to large in direct engagement and downstream behaviours, with 12 out of 15 studies finding positive significant effects in favour of gamification. Conclusion Gamification is effective in increasing engagement in online programs. Key recommendations for future research into gamification are provided. In particular, rigorous study designs are required to fully examine gamification’s effects and determine how to best achieve sustained engagement. PMID:28362821

  4. Teaching-skills training programs for family medicine residents: systematic review of formats, content, and effects of existing programs.

    PubMed

    Lacasse, Miriam; Ratnapalan, Savithiri

    2009-09-01

    To review the literature on teaching-skills training programs for family medicine residents and to identify formats and content of these programs and their effects. Ovid MEDLINE (1950 to mid-July 2008) and the Education Resources Information Center database (pre-1966 to mid-July 2008) were searched using and combining the MeSH terms teaching, internship and residency, and family practice; and teaching, graduate medical education, and family practice. The initial MEDLINE and Education Resources Information Center database searches identified 362 and 33 references, respectively. Titles and abstracts were reviewed and studies were included if they described the format or content of a teaching-skills program or if they were primary studies of the effects of a teaching-skills program for family medicine residents or family medicine and other specialty trainees. The bibliographies of those articles were reviewed for unidentified studies. A total of 8 articles were identified for systematic review. Selection was limited to articles published in English. Teaching-skills training programs for family medicine residents vary from half-day curricula to a few months of training. Their content includes leadership skills, effective clinical teaching skills, technical teaching skills, as well as feedback and evaluation skills. Evaluations mainly assessed the programs' effects on teaching behaviour, which was generally found to improve following participation in the programs. Evaluations of learner reactions and learning outcomes also suggested that the programs have positive effects. Family medicine residency training programs differ from all other residency training programs in their shorter duration, usually 2 years, and the broader scope of learning within those 2 years. Few studies on teaching-skills training, however, were designed specifically for family medicine residents. Further studies assessing the effects of teaching-skills training in family medicine residents are needed to stimulate development of adapted programs for the discipline. Future research should also assess how residents' teaching-skills training can affect their learners' clinical training and eventually patient care.

  5. Adaptation of Decoy Fusion Strategy for Existing Multi-Stage Search Workflows

    NASA Astrophysics Data System (ADS)

    Ivanov, Mark V.; Levitsky, Lev I.; Gorshkov, Mikhail V.

    2016-09-01

    A number of proteomic database search engines implement multi-stage strategies aiming at increasing the sensitivity of proteome analysis. These approaches often employ a subset of the original database for the secondary stage of analysis. However, if target-decoy approach (TDA) is used for false discovery rate (FDR) estimation, the multi-stage strategies may violate the underlying assumption of TDA that false matches are distributed uniformly across the target and decoy databases. This violation occurs if the numbers of target and decoy proteins selected for the second search are not equal. Here, we propose a method of decoy database generation based on the previously reported decoy fusion strategy. This method allows unbiased TDA-based FDR estimation in multi-stage searches and can be easily integrated into existing workflows utilizing popular search engines and post-search algorithms.

  6. Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies.

    PubMed

    Delaney, Aogán; Tamás, Peter A

    2018-03-01

    Despite recognition that database search alone is inadequate even within the health sciences, it appears that reviewers in fields that have adopted systematic review are choosing to rely primarily, or only, on database search for information retrieval. This commentary reminds readers of factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It then discusses alternative methods for information retrieval that require development, formalisation, and evaluation. Our goals are to encourage reviewers to reflect critically and transparently on their choice of information retrieval methods and to encourage investment in research on alternatives. Copyright © 2017 John Wiley & Sons, Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

  9. Smoking cessation support for pregnant women: role of mobile technology

    PubMed Central

    Heminger, Christina L; Schindler-Ruwisch, Jennifer M; Abroms, Lorien C

    2016-01-01

    Background Smoking during pregnancy has deleterious health effects for the fetus and mother. Given the high risks associated with smoking in pregnancy, smoking cessation programs that are designed specifically for pregnant smokers are needed. This paper summarizes the current landscape of mHealth cessation programs aimed at pregnant smokers and where available reviews evidence to support their use. Methods A search strategy was conducted in June–August 2015 to identify mHealth programs with at least one component or activity that was explicitly directed at smoking cessation assistance for pregnant women. The search for text messaging programs and applications included keyword searches within public health and medical databases of peer-reviewed literature, Google Play/iTunes stores, and gray literature via Google. Results Five unique short message service programs and two mobile applications were identified and reviewed. Little evidence was identified to support their use. Common tools and features identified included the ability to set your quit date, ability to track smoking status, ability to get help during cravings, referral to quitline, and tailored content for the individual participant. The theoretical approach utilized was varied, and approximately half of the programs included pregnancy-related content, in addition to cessation content. With one exception, the mHealth programs identified were found to have low enrollment. Conclusion Globally, there are a handful of applications and text-based mHealth programs available for pregnant smokers. Future studies are needed that examine the efficacy of such programs, as well as strategies to best promote enrollment. PMID:27110146

  10. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

    PubMed Central

    Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

    2016-01-01

    Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs. PMID:27929431

  11. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

    PubMed

    Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

    2016-12-06

    Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

  12. Rhinoplasty perioperative database using a personal digital assistant.

    PubMed

    Kotler, Howard S

    2004-01-01

    To construct a reliable, accurate, and easy-to-use handheld computer database that facilitates the point-of-care acquisition of perioperative text and image data specific to rhinoplasty. A user-modified database (Pendragon Forms [v.3.2]; Pendragon Software Corporation, Libertyville, Ill) and graphic image program (Tealpaint [v.4.87]; Tealpaint Software, San Rafael, Calif) were used to capture text and image data, respectively, on a Palm OS (v.4.11) handheld operating with 8 megabytes of memory. The handheld and desktop databases were maintained secure using PDASecure (v.2.0) and GoldSecure (v.3.0) (Trust Digital LLC, Fairfax, Va). The handheld data were then uploaded to a desktop database of either FileMaker Pro 5.0 (v.1) (FileMaker Inc, Santa Clara, Calif) or Microsoft Access 2000 (Microsoft Corp, Redmond, Wash). Patient data were collected from 15 patients undergoing rhinoplasty in a private practice outpatient ambulatory setting. Data integrity was assessed after 6 months' disk and hard drive storage. The handheld database was able to facilitate data collection and accurately record, transfer, and reliably maintain perioperative rhinoplasty data. Query capability allowed rapid search using a multitude of keyword search terms specific to the operative maneuvers performed in rhinoplasty. Handheld computer technology provides a method of reliably recording and storing perioperative rhinoplasty information. The handheld computer facilitates the reliable and accurate storage and query of perioperative data, assisting the retrospective review of one's own results and enhancement of surgical skills.

  13. The Internet as a communication tool for orthopedic spine fellowships in the United States.

    PubMed

    Silvestre, Jason; Guzman, Javier Z; Skovrlj, Branko; Overley, Samuel C; Cho, Samuel K; Qureshi, Sheeraz A; Hecht, Andrew C

    2015-04-01

    Orthopedic residents seeking additional training in spine surgery commonly use the Internet to manage their fellowship applications. Although studies have assessed the accessibility and content of Web sites in other medical specialties, none have looked at orthopedic spine fellowship Web sites (SFWs). The purpose of this study was to evaluate the accessibility of information from commonly used databases and assess the content of SFWs. This was a Web site accessibility and content evaluation study. A comprehensive list of available orthopedic spine fellowship programs was compiled by accessing program lists from the SF Match, North American Spine Society, Fellowship and Residency Electronic Interactive Database (FREIDA), and Orthopaedicsone.com (Ortho1). These databases were assessed for accessibility of information including viable links to SFWs and responsive program contacts. A Google search was used to identify SFWs not readily available on these national databases. SFWs were evaluated based on online education and recruitment content. Evaluators found 45 SFWs of 63 active programs (71%). Available SFWs were often not readily accessible from national program lists, and no program afforded a direct link to their SFW from SF Match. Approximately half of all programs responded via e-mail. Although many programs described surgical experience (91%) and research requirements (87%) during the fellowship, less than half mentioned didactic instruction (46%), journal clubs (41%), and national meetings or courses attended (28%). Evaluators found an average 45% of fellow recruitment content. Comparison of SFWs by program characteristics revealed three significant differences. Programs with greater than one fellowship position had greater online education content than programs with a single fellow (p=.022). Spine fellowships affiliated with an orthopedic residency program maintained greater education (p=.006) and recruitment (p=.046) content on their SFWs. Most orthopedic spine surgery programs underuse the Internet for fellow education and recruitment. The inaccessibility of information and paucity of content on SFWs allow for future opportunity to optimize these resources. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Searching for Controlled Trials of Complementary and Alternative Medicine: A Comparison of 15 Databases

    PubMed Central

    Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

    2011-01-01

    This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records—these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases. PMID:19468052

  15. Searching for controlled trials of complementary and alternative medicine: a comparison of 15 databases.

    PubMed

    Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

    2011-01-01

    This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records-these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases.

  16. End User Information Searching on the Internet: How Do Users Search and What Do They Search For? (SIG USE)

    ERIC Educational Resources Information Center

    Saracevic, Tefko

    2000-01-01

    Summarizes a presentation that discussed findings and implications of research projects using an Internet search service and Internet-accessible vendor databases, representing the two sides of public database searching: query formulation and resource utilization. Presenters included: Tefko Saracevic, Amanda Spink, Dietmar Wolfram and Hong Xie.…

  17. Assessment of Metabolome Annotation Quality: A Method for Evaluating the False Discovery Rate of Elemental Composition Searches

    PubMed Central

    Matsuda, Fumio; Shinbo, Yoko; Oikawa, Akira; Hirai, Masami Yokota; Fiehn, Oliver; Kanaya, Shigehiko; Saito, Kazuki

    2009-01-01

    Background In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. Methodology/Principal Findings The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30–50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. Conclusions/Significance High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data. PMID:19847304

  18. 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 "

  19. An assessment of the efficacy of searching in biomedical databases beyond MEDLINE in identifying studies for a systematic review on ward closures as an infection control intervention to control outbreaks.

    PubMed

    Kwon, Yoojin; Powelson, Susan E; Wong, Holly; Ghali, William A; Conly, John M

    2014-11-11

    The purpose of our study is to determine the value and efficacy of searching biomedical databases beyond MEDLINE for systematic reviews. We analyzed the results from a systematic review conducted by the authors and others on ward closure as an infection control practice. Ovid MEDLINE including In-Process & Other Non-Indexed Citations, Ovid Embase, CINAHL Plus, LILACS, and IndMED were systematically searched for articles of any study type discussing ward closure, as were bibliographies of selected articles and recent infection control conference abstracts. Search results were tracked, recorded, and analyzed using a relative recall method. The sensitivity of searching in each database was calculated. Two thousand ninety-five unique citations were identified and screened for inclusion in the systematic review: 2,060 from database searching and 35 from hand searching and other sources. Ninety-seven citations were included in the final review. MEDLINE and Embase searches each retrieved 80 of the 97 articles included, only 4 articles from each database were unique. The CINAHL search retrieved 35 included articles, and 4 were unique. The IndMED and LILACS searches did not retrieve any included articles, although 75 of the included articles were indexed in LILACS. The true value of using regional databases, particularly LILACS, may lie with the ability to search in the language spoken in the region. Eight articles were found only through hand searching. Identifying studies for a systematic review where the research is observational is complex. The value each individual study contributes to the review cannot be accurately measured. Consequently, we could not determine the value of results found from searching beyond MEDLINE, Embase, and CINAHL with accuracy. However, hand searching for serendipitous retrieval remains an important aspect due to indexing and keyword challenges inherent in this literature.

  20. US and foreign alloy cross-reference database

    NASA Technical Reports Server (NTRS)

    Springer, John M.; Morgan, Steven H.

    1991-01-01

    Marshall Space Flight Center and other NASA installations have a continuing requirement for materials data from other countries involved with the development of joint international Spacelab experiments and other hardware. This need includes collecting data for common alloys to ascertain composition, physical properties, specifications, and designations. This data is scattered throughout a large number of specification statements, standards, handbooks, and other technical literature which make a manual search both tedious and often limited in extent. In recognition of this problem, a computerized database of information on alloys was developed along with the software necessary to provide the desired functions to access this data. The intention was to produce an initial database covering aluminum alloys, along with the program to provide a user-interface to the data, and then later to extend and refine the database to include other nonferrous and ferrous alloys.

  1. Should we search Chinese biomedical databases when performing systematic reviews?

    PubMed

    Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M

    2015-03-06

    Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.

  2. NBIC: Search Ballast Report Database

    Science.gov Websites

    Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database developed an online database that can be queried through our website. Data are accessible for all coastal Lakes, have been incorporated into the NBIC database as of August 2004. Information on data availability

  3. Using the TIGR gene index databases for biological discovery.

    PubMed

    Lee, Yuandan; Quackenbush, John

    2003-11-01

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

  4. Reverse screening methods to search for the protein targets of chemopreventive compounds

    NASA Astrophysics Data System (ADS)

    Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

    2018-05-01

    This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.

  5. Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds.

    PubMed

    Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

    2018-01-01

    This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.

  6. Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds

    PubMed Central

    Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

    2018-01-01

    This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction. PMID:29868550

  7. Influence of a Hospital-Based, Internal Leadership Development Program on Leadership Effectiveness

    ERIC Educational Resources Information Center

    Welch-Carre, Elizabeth

    2017-01-01

    A search on Amazon revealed more than 6,000 books related to leadership development. The Business Source database has more than 700 articles with the word leadership in the title, published between 2005 and 2015. This suggests that leadership is a topic in which many are interested. Clearly, leadership makes a difference in an organization's…

  8. Database resources of the National Center for Biotechnology Information: 2002 update

    PubMed Central

    Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

    2002-01-01

    In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:11752242

  9. Establishing homologies in protein sequences

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.; Barker, W. C.; Hunt, L. T.

    1983-01-01

    Computer-based statistical techniques used to determine homologies between proteins occurring in different species are reviewed. The technique is based on comparison of two protein sequences, either by relating all segments of a given length in one sequence to all segments of the second or by finding the best alignment of the two sequences. Approaches discussed include selection using printed tabulations, identification of very similar sequences, and computer searches of a database. The use of the SEARCH, RELATE, and ALIGN programs (Dayhoff, 1979) is explained; sample data are presented in graphs, diagrams, and tables and the construction of scoring matrices is considered.

  10. Publication search and retrieval system

    USGS Publications Warehouse

    Winget, Elizabeth A.

    1981-01-01

    The publication search and retrieval system of the Branch of Atlantic-Gulf of Mexico Geology, U.S. Geological Survey, Woods Hole, Mass., is a procedure for listing and describing branch-sponsored publications. It is designed for maintenance and retrieval by those having limited knowledge of computer languages and programs. Because this branch currently utilizes the Hewlett-Packard HP-1000 computer with RTE-IVB operating system, database entry and maintenance is performed in accordance with the TE-IVB Terminal User’s Reference Manual (Hewlett-Packard Company, 1980) and within the constraints of GRASP (Bowen and Botbol, 1975) and WOLF (Evenden, 1978).

  11. An Online Resource for Flight Test Safety Planning

    NASA Technical Reports Server (NTRS)

    Lewis, Greg

    2007-01-01

    A viewgraph presentation describing an online database for flight test safety techniques is shown. The topics include: 1) Goal; 2) Test Hazard Analyses; 3) Online Database Background; 4) Data Gathering; 5) NTPS Role; 6) Organizations; 7) Hazard Titles; 8) FAR Paragraphs; 9) Maneuver Name; 10) Identified Hazard; 11) Matured Hazard Titles; 12) Loss of Control Causes; 13) Mitigations; 14) Database Now Open to the Public; 15) FAR Reference Search; 16) Record Field Search; 17) Keyword Search; and 18) Results of FAR Reference Search.

  12. Searching Databases without Query-Building Aids: Implications for Dyslexic Users

    ERIC Educational Resources Information Center

    Berget, Gerd; Sandnes, Frode Eika

    2015-01-01

    Introduction: Few studies document the information searching behaviour of users with cognitive impairments. This paper therefore addresses the effect of dyslexia on information searching in a database with no tolerance for spelling errors and no query-building aids. The purpose was to identify effective search interface design guidelines that…

  13. Conducting a Web Search.

    ERIC Educational Resources Information Center

    Miller-Whitehead, Marie

    Keyword and text string searches of online library catalogs often provide different results according to library and database used and depending upon how books and journals are indexed. For this reason, online databases such as ERIC often provide tutorials and recommendations for searching their site, such as how to use Boolean search strategies.…

  14. Evaluating Dermatology Residency Program Websites.

    PubMed

    Ashack, Kurt A; Burton, Kyle A; Soh, Jonathan M; Lanoue, Julien; Boyd, Anne H; Milford, Emily E; Dunnick, Cory; Dellavalle, Robert P

    2016-03-16

    Internet resources play an important role in how medical students access information related to residency programs.Evaluating program websites is necessary in order to provide accurate information for applicants and provide information regarding areas of website improvement for programs. To date, dermatology residency websites (D  WS) have not been evaluated.This paper evaluates dermatology residency websites based on availability of predefined measures. Using the FREIDA (Fellowship and Residency Electronic Interactive Database) Online database, authors searched forall accredited dermatology program websites. Eligible programs were identified through the FREIDA Online database and had a functioning website. Two authors independently extracted data with consensus or third researcher resolution of differences. This data was accessed and archived from July 15th to July 17th, 2015.Primary outcomes measured were presence of content on education, resident and faculty information, program environment, applicant recruitment, schedule, salary, and website quality evaluated using an online tool (WooRank.com). Out of 117 accredited dermatology residencies, 115 had functioning webpages. Of these, 76.5% (75) had direct links found on the FRIEDA Online database. Most programs contained information on education, faculty, program environment, and applicant recruitment. However, website quality and marketing effectiveness were highly variable; most programs were deemed to need improvements in the functioning of their webpages. Also, additional information on current residents and about potential away rotations were lacking from most websites with only 52.2% (60) and 41.7% (48) of programs providing this content, respectively. A majority of dermatology residency websites contained adequate information on many of the factors we evaluated. However, many were lacking in areas that matter to applicants. We hope this report will encourage dermatology residencyprograms to improve their websites and provide adequate content to attract the top residents for their respective programs.

  15. Citation searching: a systematic review case study of multiple risk behaviour interventions

    PubMed Central

    2014-01-01

    Background The value of citation searches as part of the systematic review process is currently unknown. While the major guides to conducting systematic reviews state that citation searching should be carried out in addition to searching bibliographic databases there are still few studies in the literature that support this view. Rather than using a predefined search strategy to retrieve studies, citation searching uses known relevant papers to identify further papers. Methods We describe a case study about the effectiveness of using the citation sources Google Scholar, Scopus, Web of Science and OVIDSP MEDLINE to identify records for inclusion in a systematic review. We used the 40 included studies identified by traditional database searches from one systematic review of interventions for multiple risk behaviours. We searched for each of the included studies in the four citation sources to retrieve the details of all papers that have cited these studies. We carried out two analyses; the first was to examine the overlap between the four citation sources to identify which citation tool was the most useful; the second was to investigate whether the citation searches identified any relevant records in addition to those retrieved by the original database searches. Results The highest number of citations was retrieved from Google Scholar (1680), followed by Scopus (1173), then Web of Science (1095) and lastly OVIDSP (213). To retrieve all the records identified by the citation tracking searching all four resources was required. Google Scholar identified the highest number of unique citations. The citation tracking identified 9 studies that met the review’s inclusion criteria. Eight of these had already been identified by the traditional databases searches and identified in the screening process while the ninth was not available in any of the databases when the original searches were carried out. It would, however, have been identified by two of the database search strategies if searches had been carried out later. Conclusions Based on the results from this investigation, citation searching as a supplementary search method for systematic reviews may not be the best use of valuable time and resources. It would be useful to verify these findings in other reviews. PMID:24893958

  16. DECADE Web Portal: Integrating MaGa, EarthChem and GVP Will Further Our Knowledge on Earth Degassing

    NASA Astrophysics Data System (ADS)

    Cardellini, C.; Frigeri, A.; Lehnert, K. A.; Ash, J.; McCormick, B.; Chiodini, G.; Fischer, T. P.; Cottrell, E.

    2014-12-01

    The release of gases from the Earth's interior to the exosphere takes place in both volcanic and non-volcanic areas of the planet. Fully understanding this complex process requires the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. We are developing interoperability between three of those, which will support more powerful synoptic studies of degassing. The three data systems that will make their data accessible via the DECADE portal are: (1) the Smithsonian Institution's Global Volcanism Program database (GVP) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. These databases are developed and maintained by institutions or groups of experts in a specific field, and data are archived in formats specific to these databases. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing a web portal that will create a powerful search engine of these databases from a single entry point. The portal will return comprehensive multi-component datasets, based on the search criteria selected by the user. For example, a single geographic or temporal search will return data relating to compositions of emitted gases and erupted products, the age of the erupted products, and coincident activity at the volcano. The development of this level of capability for the DECADE Portal requires complete synergy between these databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process. Other data systems can be easily plugged in using the existing framework. Our vision is to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

  17. Coverage of Google Scholar, Scopus, and Web of Science: a case study of the h-index in nursing.

    PubMed

    De Groote, Sandra L; Raszewski, Rebecca

    2012-01-01

    This study compares the articles cited in CINAHL, Scopus, Web of Science (WOS), and Google Scholar and the h-index ratings provided by Scopus, WOS, and Google Scholar. The publications of 30 College of Nursing faculty at a large urban university were examined. Searches by author name were executed in Scopus, WOS, and POP (Publish or Perish, which searches Google Scholar), and the h-index for each author from each database was recorded. In addition, the citing articles of their published articles were imported into a bibliographic management program. This data was used to determine an aggregated h-index for each author. Scopus, WOS, and Google Scholar provided different h-index ratings for authors and each database found unique and duplicate citing references. More than one tool should be used to calculate the h-index for nursing faculty because one tool alone cannot be relied on to provide a thorough assessment of a researcher's impact. If researchers are interested in a comprehensive h-index, they should aggregate the citing references located by WOS and Scopus. Because h-index rankings differ among databases, comparisons between researchers should be done only within a specified database. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. A comparative study of six European databases of medically oriented Web resources.

    PubMed

    Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

    2005-10-01

    The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

  19. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

    PubMed

    Verheggen, Kenneth; Raeder, Helge; Berven, Frode S; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

    2017-09-13

    Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

  20. Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra.

    PubMed

    Wang, Jianqi; Zhang, Yajie; Yu, Yonghao

    2015-07-01

    A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L- and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm.

  1. On-line searching: costly or cost effective? A marketing perspective.

    PubMed

    Dunn, R G; Boyle, H F

    1984-05-01

    The value of acquiring and using information is not well understood. Decisions to purchase information are made on the basis of the perceived need for the information, the anticipated benefit of using it, and the price. The current pricing of on-line information services, which emphasizes the connect hour as the unit of price, does not relate the price of a search to the value of a search, and the education programs of on-line vendors and database suppliers concentrate on the mechanics of information retrieval rather than on the application of information to the customer's problem. The on-line information industry needs to adopt a strong marketing orientation that focuses on the needs of customers rather than the needs of suppliers or vendors.

  2. Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.

    PubMed

    Khashan, Raed S

    2015-01-01

    As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.

  3. Laptop Computer - Based Facial Recognition System Assessment

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

    R. A. Cain; G. B. Singleton

    2001-03-01

    The objective of this project was to assess the performance of the leading commercial-off-the-shelf (COTS) facial recognition software package when used as a laptop application. We performed the assessment to determine the system's usefulness for enrolling facial images in a database from remote locations and conducting real-time searches against a database of previously enrolled images. The assessment involved creating a database of 40 images and conducting 2 series of tests to determine the product's ability to recognize and match subject faces under varying conditions. This report describes the test results and includes a description of the factors affecting the results.more » After an extensive market survey, we selected Visionics' FaceIt{reg_sign} software package for evaluation and a review of the Facial Recognition Vendor Test 2000 (FRVT 2000). This test was co-sponsored by the US Department of Defense (DOD) Counterdrug Technology Development Program Office, the National Institute of Justice, and the Defense Advanced Research Projects Agency (DARPA). Administered in May-June 2000, the FRVT 2000 assessed the capabilities of facial recognition systems that were currently available for purchase on the US market. Our selection of this Visionics product does not indicate that it is the ''best'' facial recognition software package for all uses. It was the most appropriate package based on the specific applications and requirements for this specific application. In this assessment, the system configuration was evaluated for effectiveness in identifying individuals by searching for facial images captured from video displays against those stored in a facial image database. An additional criterion was that the system be capable of operating discretely. For this application, an operational facial recognition system would consist of one central computer hosting the master image database with multiple standalone systems configured with duplicates of the master operating in remote locations. Remote users could perform real-time searches where network connectivity is not available. As images are enrolled at the remote locations, periodic database synchronization is necessary.« less

  4. Environmental factor(tm) system: RCRA hazardous waste handler information (on CD-ROM). Data file

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

    NONE

    1995-11-01

    Environmental Factor(trademark) RCRA Hazardous Waste Handler Information on CD-ROM unleashes the invaluable information found in two key EPA data sources on hazardous waste handlers and offers cradle-to-grave waste tracking. It`s easy to search and display: (1) Permit status, design capacity, and compliance history for facilities found in the EPA Research Conservation and Recovery Information System (RCRIS) program tracking database; (2) Detailed information on hazardous wastes generation, management, and minimization by companies who are large quantity generators; and (3) Data on the waste management practices of treatment, storage, and disposal (TSD) facilities from the EPA Biennial Reporting System which is collectedmore » every other year. Environmental Factor`s powerful database retrieval system lets you: (1) Search for RCRA facilities by permit type, SIC code, waste codes, corrective action, or violation information, TSD status, generator and transporter status, and more. (2) View compliance information - dates of evaluation, violation, enforcement, and corrective action. (3) Lookup facilities by waste processing categories of marketing, transporting, processing, and energy recovery. (4) Use owner/operator information and names, titles, and telephone numbers of project managers for prospecting. (5) Browse detailed data on TSD facility and large quantity generators` activities such as onsite waste treatment, disposal, or recycling, offsite waste received, and waste generation and management. The product contains databases, search and retrieval software on two CD-ROMs, an installation diskette and User`s Guide. Environmental Factor has online context-sensitive help from any screen and a printed User`s Guide describing installation and step-by-step procedures for searching, retrieving, and exporting.« less

  5. Teaching-skills training programs for family medicine residents

    PubMed Central

    Lacasse, Miriam; Ratnapalan, Savithiri

    2009-01-01

    ABSTRACT OBJECTIVE To review the literature on teaching-skills training programs for family medicine residents and to identify formats and content of these programs and their effects. DATA SOURCES Ovid MEDLINE (1950 to mid-July 2008) and the Education Resources Information Center database (pre-1966 to mid-July 2008) were searched using and combining the MeSH terms teaching, internship and residency, and family practice; and teaching, graduate medical education, and family practice. STUDY SELECTION The initial MEDLINE and Education Resources Information Center database searches identified 362 and 33 references, respectively. Titles and abstracts were reviewed and studies were included if they described the format or content of a teaching-skills program or if they were primary studies of the effects of a teaching-skills program for family medicine residents or family medicine and other specialty trainees. The bibliographies of those articles were reviewed for unidentified studies. A total of 8 articles were identified for systematic review. Selection was limited to articles published in English. SYNTHESIS Teaching-skills training programs for family medicine residents vary from half-day curricula to a few months of training. Their content includes leadership skills, effective clinical teaching skills, technical teaching skills, as well as feedback and evaluation skills. Evaluations mainly assessed the programs’ effects on teaching behaviour, which was generally found to improve following participation in the programs. Evaluations of learner reactions and learning outcomes also suggested that the programs have positive effects. CONCLUSION Family medicine residency training programs differ from all other residency training programs in their shorter duration, usually 2 years, and the broader scope of learning within those 2 years. Few studies on teaching-skills training, however, were designed specifically for family medicine residents. Further studies assessing the effects of teaching-skills training in family medicine residents are needed to stimulate development of adapted programs for the discipline. Future research should also assess how residents’ teaching-skills training can affect their learners’ clinical training and eventually patient care. PMID:19752261

  6. Privacy-preserving search for chemical compound databases.

    PubMed

    Shimizu, Kana; Nuida, Koji; Arai, Hiromi; Mitsunari, Shigeo; Attrapadung, Nuttapong; Hamada, Michiaki; Tsuda, Koji; Hirokawa, Takatsugu; Sakuma, Jun; Hanaoka, Goichiro; Asai, Kiyoshi

    2015-01-01

    Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources. In order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation. We proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information.

  7. Privacy-preserving search for chemical compound databases

    PubMed Central

    2015-01-01

    Background Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources. Results In order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation. Conclusion We proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information. PMID:26678650

  8. Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

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

    Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division

    2007-01-01

    The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, themore » necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.« less

  9. [Profile of a systematic search. Search areas, databases and reports].

    PubMed

    Korsbek, Lisa; Bendix, Ane Friis; Kidholm, Kristian

    2006-04-03

    Systematic literature search is a fundamental in evidence-based medicine. But systematic literature search is not yet a very well used way of retrieving evidence-based information. This article profiles a systematic literature search for evidence-based literature. It goes through the most central databases and gives an example of how to document the literature search. The article also sums up the literature search in all reviews in Ugeskrift for Laeger in the year 2004.

  10. University Faculty Use of Computerized Databases: An Assessment of Needs and Resources.

    ERIC Educational Resources Information Center

    Borgman, Christine L.; And Others

    1985-01-01

    Results of survey indicate that: academic faculty are unaware of range of databases available; few recognize need for databases in research; most delegate searching to librarian or assistant, rather than perform searching themselves; and 39 database guides identified tended to be descriptive rather than evaluative. A comparison of the guides is…

  11. Sagace: A web-based search engine for biomedical databases in Japan

    PubMed Central

    2012-01-01

    Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

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

    PubMed

    Rijnbeek, Mark; Steinbeck, Christoph

    2009-10-22

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

  13. Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

    PubMed

    Wang, Penghao; Wilson, Susan R

    2013-01-01

    Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

  14. 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

  15. Term Relevance Feedback and Mediated Database Searching: Implications for Information Retrieval Practice and Systems Design.

    ERIC Educational Resources Information Center

    Spink, Amanda

    1995-01-01

    This study uses the human approach to examine the sources and effectiveness of search terms selected during 40 mediated interactive database searches and focuses on determining the retrieval effectiveness of search terms identified by users and intermediaries from retrieved items during term relevance feedback. (Author/JKP)

  16. The Weaknesses of Full-Text Searching

    ERIC Educational Resources Information Center

    Beall, Jeffrey

    2008-01-01

    This paper provides a theoretical critique of the deficiencies of full-text searching in academic library databases. Because full-text searching relies on matching words in a search query with words in online resources, it is an inefficient method of finding information in a database. This matching fails to retrieve synonyms, and it also retrieves…

  17. DNAStat, version 2.1--a computer program for processing genetic profile databases and biostatistical calculations.

    PubMed

    Berent, Jarosław

    2010-01-01

    This paper presents the new DNAStat version 2.1 for processing genetic profile databases and biostatistical calculations. The popularization of DNA studies employed in the judicial system has led to the necessity of developing appropriate computer programs. Such programs must, above all, address two critical problems, i.e. the broadly understood data processing and data storage, and biostatistical calculations. Moreover, in case of terrorist attacks and mass natural disasters, the ability to identify victims by searching related individuals is very important. DNAStat version 2.1 is an adequate program for such purposes. The DNAStat version 1.0 was launched in 2005. In 2006, the program was updated to 1.1 and 1.2 versions. There were, however, slight differences between those versions and the original one. The DNAStat version 2.0 was launched in 2007 and the major program improvement was an introduction of the group calculation options with the potential application to personal identification of mass disasters and terrorism victims. The last 2.1 version has the option of language selection--Polish or English, which will enhance the usage and application of the program also in other countries.

  18. Literature searching for clinical and cost-effectiveness studies used in health technology assessment reports carried out for the National Institute for Clinical Excellence appraisal system.

    PubMed

    Royle, P; Waugh, N

    2003-01-01

    To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. A sample of 20 recent TARs. All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.

  19. Evidence-based librarianship: searching for the needed EBL evidence.

    PubMed

    Eldredge, J D

    2000-01-01

    This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

  20. MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

    PubMed

    Wang, Yingfeng; Kora, Guruprasad; Bowen, Benjamin P; Pan, Chongle

    2014-10-07

    A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.

  1. Investigations into mirror fabrication metrology analysis

    NASA Technical Reports Server (NTRS)

    Dimmock, John O.

    1994-01-01

    This final report describes the work performed under this delivery order from June 1993 through August 1994. The scope of work included three distinct tasks in support of the AXAF-I program. The objective of the first task was to perform investigations of the grinding and polishing characteristics of the zerodur material by fabricating several samples. The second task was to continue the development of the integrated optical performance modeling software for AXAF-I. The purpose of third and final task was to develop and update the database of AXAF technical documents for an easy and rapid access. The MSFC optical and metrology shops were relocated from the B-wing of Building 4487 to Room BC 144 of Building 4466 in the beginning of this contract. This included dismantling, packing, and moving the equipment from its old location, and then reassembling it at the new location. A total of 65 zerodur samples, measuring 1 inch x 2 inches x 6 inches were ground and polished to a surface figure of lambda/10 p-v, and a surface finish of 5A rms were fabricated for coating tests. A number of special purpose tools and metal mirrors were also fabricated to support various AXAF-I development activities. In the metrology area, the ZYGO Mark 4 interferometer was relocated and also upgraded with a faster and more powerful processor. Surface metrology work was also performed on the coating samples and other optics using ZYGO interferometer and WYKO profilometer. A number of new features have been added to the GRAZTRACE program to enhance its analysis and modeling capabilities. A number of new commands have been added to the command mode GRAZTRACE program to provide a better control to the user on the program execution and data manipulation. Some commands and parameter entries have been reorganized for a uniform format. The command mode version of the convolution program CONVOLVE has been developed. An on-line help system and a user's manual have also been developed for the benefit of the users. The database of AXAF technical documents continues to progress. The titles, company name, date, and location of over 390 documents have been entered in this database. This database provides both a data search and retrieval function, and a data adding function. These functions allow a user to quickly search the data files for documents or add new information. A detailed user's guide has also been prepared. This user guide includes a document classification guide, a list of abbreviations, and a list of acronyms, which have been used in compiling this database of AXAF-I technical documents.

  2. School-based Yoga Programs in the United States: A Survey

    PubMed Central

    Butzer, Bethany; Ebert, Marina; Telles, Shirley; Khalsa, Sat Bir S.

    2016-01-01

    Context Substantial interest has begun to emerge around the implementation of yoga interventions in schools. Researchers have found that yoga practices may enhance skills such as self-regulation and prosocial behavior, and lead to improvements in students’ performance. These researchers, therefore, have proposed that contemplative practices have the potential to play a crucial role in enhancing the quality of US public education. Objective The purpose of the present study was to provide a summary and comparison of school-based yoga programs in the United States. Design Online, listserv, and database searches were conducted to identify programs, and information was collected regarding each program’s scope of work, curriculum characteristics, teacher-certification and training requirements, implementation models, modes of operation, and geographical regions. Setting The online, listserv, and database searches took place in Boston, MA, USA, and New Haven, CT, USA. Results Thirty-six programs were identified that offer yoga in more than 940 schools across the United States, and more than 5400 instructors have been trained by these programs to offer yoga in educational settings. Despite some variability in the exact mode of implementation, training requirements, locations served, and grades covered, the majority of the programs share a common goal of teaching 4 basic elements of yoga: (1) physical postures, (2) breathing exercises, (3) relaxation techniques, and (4) mindfulness and meditation practices. The programs also teach a variety of additional educational, social-emotional, and didactic techniques to enhance students’ mental and physical health and behavior. Conclusions The fact that the present study was able to find a relatively large number of formal, school-based yoga programs currently being implemented in the United States suggests that the programs may be acceptable and feasible to implement. The results also suggest that the popularity of school-based yoga programs may continue to grow. PMID:26535474

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

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

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

  4. System, method and apparatus for conducting a keyterm search

    NASA Technical Reports Server (NTRS)

    McGreevy, Michael W. (Inventor)

    2004-01-01

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

  5. System, method and apparatus for conducting a phrase search

    NASA Technical Reports Server (NTRS)

    McGreevy, Michael W. (Inventor)

    2004-01-01

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

  6. On Building a Search Interface Discovery System

    NASA Astrophysics Data System (ADS)

    Shestakov, Denis

    A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  8. A review on quantum search algorithms

    NASA Astrophysics Data System (ADS)

    Giri, Pulak Ranjan; Korepin, Vladimir E.

    2017-12-01

    The use of superposition of states in quantum computation, known as quantum parallelism, has significant advantage in terms of speed over the classical computation. It is evident from the early invented quantum algorithms such as Deutsch's algorithm, Deutsch-Jozsa algorithm and its variation as Bernstein-Vazirani algorithm, Simon algorithm, Shor's algorithms, etc. Quantum parallelism also significantly speeds up the database search algorithm, which is important in computer science because it comes as a subroutine in many important algorithms. Quantum database search of Grover achieves the task of finding the target element in an unsorted database in a time quadratically faster than the classical computer. We review Grover's quantum search algorithms for a singe and multiple target elements in a database. The partial search algorithm of Grover and Radhakrishnan and its optimization by Korepin called GRK algorithm are also discussed.

  9. Mathematical Notation in Bibliographic Databases.

    ERIC Educational Resources Information Center

    Pasterczyk, Catherine E.

    1990-01-01

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

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

    USGS Publications Warehouse

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

    1998-01-01

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

  11. Center for Nanoscale Science and Technology

    National Institute of Standards and Technology Data Gateway

    NIST Center for Nanoscale Science and Technology (Program website, free access)   Currently there is no database matching your keyword search, but the NIST Center for Nanoscale Science and Technology website may be of interest. The Center for Nanoscale Science and Technology enables science and industry by providing essential measurement methods, instrumentation, and standards to support all phases of nanotechnology development, from discovery to production.

  12. Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

    PubMed

    Su, Xiaoquan; Xu, Jian; Ning, Kang

    2012-10-01

    It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples. ningkang@qibebt.ac.cn Supplementary data are available at Bioinformatics online.

  13. GenBank

    PubMed Central

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

    2007-01-01

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

  14. The Boolean Is Dead, Long Live the Boolean! Natural Language versus Boolean Searching in Introductory Undergraduate Instruction

    ERIC Educational Resources Information Center

    Lowe, M. Sara; Maxson, Bronwen K.; Stone, Sean M.; Miller, Willie; Snajdr, Eric; Hanna, Kathleen

    2018-01-01

    Boolean logic can be a difficult concept for first-year, introductory students to grasp. This paper compares the results of Boolean and natural language searching across several databases with searches created from student research questions. Performance differences between databases varied. Overall, natural search language is at least as good as…

  15. A taxonomy for community-based care programs focused on HIV/AIDS prevention, treatment, and care in resource-poor settings

    PubMed Central

    Rachlis, Beth; Sodhi, Sumeet; Burciul, Barry; Orbinski, James; Cheng, Amy H.Y.; Cole, Donald

    2013-01-01

    Community-based care (CBC) can increase access to key services for people affected by HIV/AIDS through the mobilization of community interests and resources and their integration with formal health structures. Yet, the lack of a systematic framework for analysis of CBC focused on HIV/AIDS impedes our ability to understand and study CBC programs. We sought to develop taxonomy of CBC programs focused on HIV/AIDS in resource-limited settings in an effort to understand their key characteristics, uncover any gaps in programming, and highlight the potential roles they play. Our review aimed to systematically identify key CBC programs focused on HIV/AIDS in resource-limited settings. We used both bibliographic database searches (Medline, CINAHL, and EMBASE) for peer-reviewed literature and internet-based searches for gray literature. Our search terms were ‘HIV’ or ‘AIDS’ and ‘community-based care’ or ‘CBC’. Two co-authors developed a descriptive taxonomy through an iterative, inductive process using the retrieved program information. We identified 21 CBC programs useful for developing taxonomy. Extensive variation was observed within each of the nine categories identified: region, vision, characteristics of target populations, program scope, program operations, funding models, human resources, sustainability, and monitoring and evaluation strategies. While additional research may still be needed to identify the conditions that lead to overall program success, our findings can help to inform our understanding of the various aspects of CBC programs and inform potential logic models for CBC programming in the context of HIV/AIDS in resource-limited settings. Importantly, the findings of the present study can be used to develop sustainable HIV/AIDS-service delivery programs in regions with health resource shortages. PMID:23594416

  16. A taxonomy for community-based care programs focused on HIV/AIDS prevention, treatment, and care in resource-poor settings.

    PubMed

    Rachlis, Beth; Sodhi, Sumeet; Burciul, Barry; Orbinski, James; Cheng, Amy H Y; Cole, Donald

    2013-04-16

    Community-based care (CBC) can increase access to key services for people affected by HIV/AIDS through the mobilization of community interests and resources and their integration with formal health structures. Yet, the lack of a systematic framework for analysis of CBC focused on HIV/AIDS impedes our ability to understand and study CBC programs. We sought to develop taxonomy of CBC programs focused on HIV/AIDS in resource-limited settings in an effort to understand their key characteristics, uncover any gaps in programming, and highlight the potential roles they play. Our review aimed to systematically identify key CBC programs focused on HIV/AIDS in resource-limited settings. We used both bibliographic database searches (Medline, CINAHL, and EMBASE) for peer-reviewed literature and internet-based searches for gray literature. Our search terms were 'HIV' or 'AIDS' and 'community-based care' or 'CBC'. Two co-authors developed a descriptive taxonomy through an iterative, inductive process using the retrieved program information. We identified 21 CBC programs useful for developing taxonomy. Extensive variation was observed within each of the nine categories identified: region, vision, characteristics of target populations, program scope, program operations, funding models, human resources, sustainability, and monitoring and evaluation strategies. While additional research may still be needed to identify the conditions that lead to overall program success, our findings can help to inform our understanding of the various aspects of CBC programs and inform potential logic models for CBC programming in the context of HIV/AIDS in resource-limited settings. Importantly, the findings of the present study can be used to develop sustainable HIV/AIDS-service delivery programs in regions with health resource shortages.

  17. A comprehensive and scalable database search system for metaproteomics.

    PubMed

    Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

    2016-08-16

    Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

  18. Network meta-analyses could be improved by searching more sources and by involving a librarian.

    PubMed

    Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

    2014-09-01

    Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Effectiveness of two interventions in preventing traffic accidents: a systematic review.

    PubMed

    Porchia, B R; Baldasseroni, A; Dellisanti, C; Lorini, C; Bonaccorsi, G

    2014-01-01

    The prevention of road traffic accidents should be considered a serious public health concern, since they are the eighth leading cause of death globally and the main cause of death for young people aged 15-29. Evidences from many countries show that successes in preventing road traffic injuries can be achieved through concerted efforts at national level. The aim of our study was to assess the effectiveness of two interventions to prevent road traffic accidents: the introduction of graduated driver licensing (GDL) and the interventions to improve pedestrian and cyclist visibility. Our search started with a scoping review on the interventions to prevent road traffic accidents to allow the development of a logical framework of traffic accidents. Specific and answerable questions formulated according to PICO scheme and combinations of keywords were used to perform a systematic search in the following databases: Pubmed, Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effects (DARE), Health Evidence, Transport Research International Documentation (TRID) and Google. References of selected papers were searched. Only systematic reviews and meta-analyses were eligible. No temporal limits or linguistic filters were applied. 160 systematic reviews and meta-analyses were found for the question of the introduction of GDL program and 188 on the improvement of visibility in cyclists and pedestrians. After selection, four papers were included in qualitative synthesis for each question. All included studies underwent quality evaluation. GDL programs seem to be effective in reducing crash rates among young drivers, in particular in 16 year-old. Programs with more restrictions seem also to reduce fatal events. To improve visibility of pedestrians and cyclists, street lighting has been suggested as an intervention able to improve driver's visual capabilities and ability to detect roadway hazards and to prevent car crashes. Visibility aids (fluorescent materials, lamps, flashing lights and retroreflective materials) have the potential to increase visibility and enable drivers to detect pedestrians and cyclists earlier. The two interventions seem to be effective, but further examinations are needed to measure long-term effects. It is necessary to provide feasible studies in local context to estimate the impact of introduction of GDL programs or of some of their components and to improve interventions to increase visibility of pedestrians and cyclists.

  20. Systematic review of the effectiveness of training programs in writing for scholarly publication, journal editing, and manuscript peer review (protocol).

    PubMed

    Galipeau, James; Moher, David; Skidmore, Becky; Campbell, Craig; Hendry, Paul; Cameron, D William; Hébert, Paul C; Palepu, Anita

    2013-06-17

    An estimated $100 billion is lost to 'waste' in biomedical research globally, annually, much of which comes from the poor quality of published research. One area of waste involves bias in reporting research, which compromises the usability of published reports. In response, there has been an upsurge in interest and research in the scientific process of writing, editing, peer reviewing, and publishing (that is, journalology) of biomedical research. One reason for bias in reporting and the problem of unusable reports could be due to authors lacking knowledge or engaging in questionable practices while designing, conducting, or reporting their research. Another might be that the peer review process for journal publication has serious flaws, including possibly being ineffective, and having poorly trained and poorly motivated reviewers. Similarly, many journal editors have limited knowledge related to publication ethics. This can ultimately have a negative impact on the healthcare system. There have been repeated calls for better, more numerous training opportunities in writing for publication, peer review, and publishing. However, little research has taken stock of journalology training opportunities or evaluations of their effectiveness. We will conduct a systematic review to synthesize studies that evaluate the effectiveness of training programs in journalology. A comprehensive three-phase search approach will be employed to identify evaluations of training opportunities, involving: 1) forward-searching using the Scopus citation database, 2) a search of the MEDLINE In-Process and Non-Indexed Citations, MEDLINE, Embase, ERIC, and PsycINFO databases, as well as the databases of the Cochrane Library, and 3) a grey literature search. This project aims to provide evidence to help guide the journalological training of authors, peer reviewers, and editors. While there is ample evidence that many members of these groups are not getting the necessary training needed to excel at their respective journalology-related tasks, little is known about the characteristics of existing training opportunities, including their effectiveness. The proposed systematic review will provide evidence regarding the effectiveness of training, therefore giving potential trainees, course designers, and decision-makers evidence to help inform their choices and policies regarding the merits of specific training opportunities or types of training.

  1. A critical review: early life nutrition and prenatal programming for adult disease.

    PubMed

    Carolan-Olah, Mary; Duarte-Gardea, Maria; Lechuga, Julia

    2015-12-01

    To present the evidence in relation to early life nutrition and foetal programming for adult disease. Epigenetics is a new and growing area of study investigating the impact of the intrauterine environment on the lifelong health of individuals. Discursive paper. Searches were conducted in a range of electronic health databases. Hand searches located additional articles for review. Maternal search terms included: pregnancy; nutrition; diet; obesity; over nutrition; under nutrition. Offspring related search terms included: macrosomia; intrauterine growth restriction; epigenetics; foetal programming; childhood obesity; adolescent obesity; adolescent type 2 diabetes. Results indicate that foetal programming for adult disease occurs in response to particular insults during vulnerable developmental periods. Four main areas of foetal exposure were identified in this review: (1) under nutrition; (2) over nutrition; (3) gestational diabetes mellitus; and (4) infant catch-up growth. Numerous studies also described the trans-generational nature of foetal programming. Overall, foetal exposure to excess or insufficient nutrition during vulnerable developmental periods appears to result in a lifelong predisposition to obesity and adult disease, such as type 2 diabetes and cardiac disease. For the infant who has been undernourished during early life, a predisposition to renal disease also occurs. Pregnancy is a time when women are engaged in health systems and are receptive to health messages. These factors suggest that pregnancy may be an optimal time for dietary education and intervention. There is a particular need for education on healthy diet and for interventions which aim to limit over consumption of calories. © 2015 John Wiley & Sons Ltd.

  2. Implant dentistry curriculum in undergraduate education: part 1-a literature review.

    PubMed

    Kroeplin, Birgit S; Strub, Joerg R

    2011-01-01

    The aim of this literature review was to evaluate to what extent oral implant dentistry was integrated into undergraduate educational programs worldwide. An online search of PubMed (MEDLINE and additional life science journals) was performed for articles published from 1966 to January 2010 using combinations of select medical subject headings. Additionally, the ISI Web of Knowledge database (MEDLINE: 1950 to present, Web of Science: 1945 to present) was searched using "education" and "implant" as search terms. The online search was supplemented with a manual search of dental journals in the fields of education, prosthodontics, and implant dentistry and of the reference lists of selected full-text articles. Surveys comparing different undergraduate dental implant curricula and articles describing the undergraduate dental implant curriculum of a single university were identified. Postgraduate or continuing education programs for dental practitioners or master and specialist programs were excluded. Twenty-five articles met the inclusion criteria of this review. The percentage of universities that included implant dentistry in undergraduate education increased from 51% in 1974 to 97% in 2006 for universities in the United States and to 100% for surveyed European universities. All curricula included lectures (mostly 1 to 20 hours) and 30% to 42% included laboratory courses, but the level of clinical experience differed greatly between surveyed universities. Because oral implant dentistry has become a standard treatment alternative, the undergraduate dental curricula should include its application in treatment planning, observation of placing and restoring implants, and treating patients with implant-retained or -supported restorations.

  3. Teaching Data Base Search Strategies.

    ERIC Educational Resources Information Center

    Hannah, Larry

    1987-01-01

    Discusses database searching as a method for developing thinking skills, and describes an activity suitable for fifth grade through high school using a president's and vice president's database. Teaching methods are presented, including student team activities, and worksheets designed for the AppleWorks database are included. (LRW)

  4. Optimizing literature search in systematic reviews - are MEDLINE, EMBASE and CENTRAL enough for identifying effect studies within the area of musculoskeletal disorders?

    PubMed

    Aagaard, Thomas; Lund, Hans; Juhl, Carsten

    2016-11-22

    When conducting systematic reviews, it is essential to perform a comprehensive literature search to identify all published studies relevant to the specific research question. The Cochrane Collaborations Methodological Expectations of Cochrane Intervention Reviews (MECIR) guidelines state that searching MEDLINE, EMBASE and CENTRAL should be considered mandatory. The aim of this study was to evaluate the MECIR recommendations to use MEDLINE, EMBASE and CENTRAL combined, and examine the yield of using these to find randomized controlled trials (RCTs) within the area of musculoskeletal disorders. Data sources were systematic reviews published by the Cochrane Musculoskeletal Review Group, including at least five RCTs, reporting a search history, searching MEDLINE, EMBASE, CENTRAL, and adding reference- and hand-searching. Additional databases were deemed eligible if they indexed RCTs, were in English and used in more than three of the systematic reviews. Relative recall was calculated as the number of studies identified by the literature search divided by the number of eligible studies i.e. included studies in the individual systematic reviews. Finally, cumulative median recall was calculated for MEDLINE, EMBASE and CENTRAL combined followed by the databases yielding additional studies. Deemed eligible was twenty-three systematic reviews and the databases included other than MEDLINE, EMBASE and CENTRAL was AMED, CINAHL, HealthSTAR, MANTIS, OT-Seeker, PEDro, PsychINFO, SCOPUS, SportDISCUS and Web of Science. Cumulative median recall for combined searching in MEDLINE, EMBASE and CENTRAL was 88.9% and increased to 90.9% when adding 10 additional databases. Searching MEDLINE, EMBASE and CENTRAL was not sufficient for identifying all effect studies on musculoskeletal disorders, but additional ten databases did only increase the median recall by 2%. It is possible that searching databases is not sufficient to identify all relevant references, and that reviewers must rely upon additional sources in their literature search. However further research is needed.

  5. A Web-based Tool for SDSS and 2MASS Database Searches

    NASA Astrophysics Data System (ADS)

    Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

    We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

  6. Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

    PubMed

    Sherwin, Trevor; Gilhotra, Amardeep K

    2006-02-01

    Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

  7. [Effects of Family Support Programs for Caregivers of People with Dementia - Caregiving Burden, Depression, and Stress: Systematic Review and Meta-analysis].

    PubMed

    Park, Seyeon; Park, Myonghwa

    2015-10-01

    The objective of this systematic review was to assess the effects of family support programs on caregiving burden, depression, and stress in family caregivers of people with dementia. A literature search was conducted of electronic databases to identify randomized controlled studies with family support programs done between 2000 and 2014. Studies published in English and/or Korean were included for the analysis with search strategies adapted from the Cochrane Dementia and Cognitive Improvement Group. Studies were rated for quality assessment by two independent reviewers using the appraisal checklist developed by Cochrane Reviews and Dissemination. Of 8,334 articles identified in the literature search, full texts of 76 articles that met the inclusion criteria were reviewed and 38 were found to include relevant outcomes. Results from selected studies were pooled in statistical meta-analysis using Review Manager Software and heterogeneity between combined studies was assessed using the Chi-square test. Meta-analysis showed that the effect sizes of family caregiver support programs were small to medium for categories of caregiving burden (Hedge's g=-0.17, 95% CI=-0.30~-0.04), depression (Hedge's g=-0.30, 95% CI=-0.40~-0.20), and stress (Hedge's g=-0.39, 95% CI=-0.52~-0.25). The review results indicate that a support programs can assist family caregivers in reducing their psycho-emotional distress.

  8. Literature review of teaching skills programs for junior medical officers.

    PubMed

    Dannaway, Jasan; Ng, Heryanto; Schoo, Adrian

    2016-01-31

    The aim of this review was to assess the current evidence regarding the efficacy of teaching skills programs for junior medical officers. We aimed to compare and contrast these results with findings from previous literature reviews, the last of which were published in 2009. In order to capture studies since the last published literature reviews, five databases and grey literature were searched for publications from January 2008 to January 2015. A search for literature reviews without using the timeframe limitation was also performed. The search from January 2008 to January 2015 resulted in the inclusion of 12 studies. Five systematic reviews of the topic were found which included 39 individual studies that were also analysed. Nearly all studies reported positive effects. Twenty nine studies reported change in attitudes, 28 reported modification in knowledge, 28 reported change in behaviour, 6 reported change in the organisation and two reported change in program participant's students. There were substantial threats of bias present. The literature reviewed demonstrated many positive effects of teaching skills programs, which supports their utilization. However, high level outcomes need to be evaluated over longer periods of time to establish their true impact. An organisation specific approach to these programs needs to occur using sound course design principles, and they need to be reported in evaluation trials that are designed with robust methodology.

  9. DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

    PubMed Central

    Sebestyén, Endre; Nagy, Tibor; Suhai, Sándor; Barta, Endre

    2009-01-01

    Background The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). Results We have developed a new tool called DoOPSearch for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. Conclusion We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes. PMID:19534755

  10. Evaluation of DNA mixtures from database search.

    PubMed

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

    2010-03-01

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

  11. Faster sequence homology searches by clustering subsequences.

    PubMed

    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2015-04-15

    Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  12. Search Filter Precision Can Be Improved By NOTing Out Irrelevant Content

    PubMed Central

    Wilczynski, Nancy L.; McKibbon, K. Ann; Haynes, R. Brian

    2011-01-01

    Background: Most methodologic search filters developed for use in large electronic databases such as MEDLINE have low precision. One method that has been proposed but not tested for improving precision is NOTing out irrelevant content. Objective: To determine if search filter precision can be improved by NOTing out the text words and index terms assigned to those articles that are retrieved but are off-target. Design: Analytic survey. Methods: NOTing out unique terms in off-target articles and testing search filter performance in the Clinical Hedges Database. Main Outcome Measures: Sensitivity, specificity, precision and number needed to read (NNR). Results: For all purpose categories (diagnosis, prognosis and etiology) except treatment and for all databases (MEDLINE, EMBASE, CINAHL and PsycINFO), constructing search filters that NOTed out irrelevant content resulted in substantive improvements in NNR (over four-fold for some purpose categories and databases). Conclusion: Search filter precision can be improved by NOTing out irrelevant content. PMID:22195215

  13. Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis.

    PubMed

    Kremer, Lukas P M; Leufken, Johannes; Oyunchimeg, Purevdulam; Schulze, Stefan; Fufezan, Christian

    2016-03-04

    Proteomics data integration has become a broad field with a variety of programs offering innovative algorithms to analyze increasing amounts of data. Unfortunately, this software diversity leads to many problems as soon as the data is analyzed using more than one algorithm for the same task. Although it was shown that the combination of multiple peptide identification algorithms yields more robust results, it is only recently that unified approaches are emerging; however, workflows that, for example, aim to optimize search parameters or that employ cascaded style searches can only be made accessible if data analysis becomes not only unified but also and most importantly scriptable. Here we introduce Ursgal, a Python interface to many commonly used bottom-up proteomics tools and to additional auxiliary programs. Complex workflows can thus be composed using the Python scripting language using a few lines of code. Ursgal is easily extensible, and we have made several database search engines (X!Tandem, OMSSA, MS-GF+, Myrimatch, MS Amanda), statistical postprocessing algorithms (qvality, Percolator), and one algorithm that combines statistically postprocessed outputs from multiple search engines ("combined FDR") accessible as an interface in Python. Furthermore, we have implemented a new algorithm ("combined PEP") that combines multiple search engines employing elements of "combined FDR", PeptideShaker, and Bayes' theorem.

  14. A statistical view of FMRFamide neuropeptide diversity.

    PubMed

    Espinoza, E; Carrigan, M; Thomas, S G; Shaw, G; Edison, A S

    2000-01-01

    FMRFamide-like peptide (FLP) amino acid sequences have been collected and statistically analyzed. FLP amino acid composition as a function of position in the peptide is graphically presented for several major phyla. Results of total amino acid composition and frequencies of pairs of FLP amino acids have been computed and compared with corresponding values from the entire GenBank protein sequence database. The data for pairwise distributions of amino acids should help in future structure-function studies of FLPs. To aid in future peptide discovery, a computer program and search protocol was developed to identify FLPs from the GenBank protein database without the use of keywords.

  15. Master Metadata Repository and Metadata-Management System

    NASA Technical Reports Server (NTRS)

    Armstrong, Edward; Reed, Nate; Zhang, Wen

    2007-01-01

    A master metadata repository (MMR) software system manages the storage and searching of metadata pertaining to data from national and international satellite sources of the Global Ocean Data Assimilation Experiment (GODAE) High Resolution Sea Surface Temperature Pilot Project [GHRSSTPP]. These sources produce a total of hundreds of data files daily, each file classified as one of more than ten data products representing global sea-surface temperatures. The MMR is a relational database wherein the metadata are divided into granulelevel records [denoted file records (FRs)] for individual satellite files and collection-level records [denoted data set descriptions (DSDs)] that describe metadata common to all the files from a specific data product. FRs and DSDs adhere to the NASA Directory Interchange Format (DIF). The FRs and DSDs are contained in separate subdatabases linked by a common field. The MMR is configured in MySQL database software with custom Practical Extraction and Reporting Language (PERL) programs to validate and ingest the metadata records. The database contents are converted into the Federal Geographic Data Committee (FGDC) standard format by use of the Extensible Markup Language (XML). A Web interface enables users to search for availability of data from all sources.

  16. ProtaBank: A repository for protein design and engineering data.

    PubMed

    Wang, Connie Y; Chang, Paul M; Ary, Marie L; Allen, Benjamin D; Chica, Roberto A; Mayo, Stephen L; Olafson, Barry D

    2018-03-25

    We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  17. GenBank.

    PubMed

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

    2008-01-01

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

  18. GenBank

    PubMed Central

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

    2008-01-01

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

  19. Footprint Database and web services for the Herschel space observatory

    NASA Astrophysics Data System (ADS)

    Verebélyi, Erika; Dobos, László; Kiss, Csaba

    2015-08-01

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

  20. The Use of AJAX in Searching a Bibliographic Database: A Case Study of the Italian Biblioteche Oggi Database

    ERIC Educational Resources Information Center

    Cavaleri, Piero

    2008-01-01

    Purpose: The purpose of this paper is to describe the use of AJAX for searching the Biblioteche Oggi database of bibliographic records. Design/methodology/approach: The paper is a demonstration of how bibliographic database single page interfaces allow the implementation of more user-friendly features for social and collaborative tasks. Findings:…

  1. Description of 'REQUEST-KYUSHYU' for KYUKEICHO regional data base

    NASA Astrophysics Data System (ADS)

    Takimoto, Shin'ichi

    Kyushu Economic Research Association (a foundational juridical person) initiated the regional database services, ' REQUEST-Kyushu ' recently. It is the full scale databases compiled based on the information and know-hows which the Association has accumulated over forty years. It covers the regional information database for journal and newspaper articles, and statistical information database for economic statistics. As to the former database it is searched on a personal computer and then a search result (original text) is sent through a facsimile. As to the latter, it is also searched on a personal computer where the data is processed, edited or downloaded. This paper describes characteristics, content and the system outline of 'REQUEST-Kyushu'.

  2. OrChem - An open source chemistry search engine for Oracle®

    PubMed Central

    2009-01-01

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

  3. Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis.

    PubMed

    Iwata, Y; Arisawa, M; Hamada, R; Kita, Y; Mizutani, M Y; Tomioka, N; Itai, A; Miyamoto, S

    2001-05-24

    Aldose reductase (AR) has been implicated in the etiology of diabetic complications. Due to the limited number of currently available drugs for the treatment of diabetic complications, we have carried out structure-based drug design and synthesis in an attempt to find new types of AR inhibitors. With the ADAM&EVE program, a three-dimensional database (ACD3D) was searched using the ligand binding site of the AR crystal structure. Out of 179 compounds selected through this search followed by visual inspection, 36 compounds were purchased and subjected to a biological assay. Ten compounds showed more than 40% inhibition of AR at a 15 microg/mL concentration. In a subsequent lead optimization, a series of analogues of the most active compound were synthesized based on the docking mode derived by ADAM&EVE. Many of these congeners exhibited higher activities compared to the mother compound. Indeed, the most potent, synthesized compound showed an approximately 20-fold increase in inhibitory activity (IC(50) = 0.21 vs 4.3 microM). Furthermore, a hydrophobic subsite was newly inferred, which would be useful for the design of inhibitors with improved affinity for AR.

  4. The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

    Bouckk John; Michael McLeod; Kim Worley

    1999-09-10

    The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

  5. The CIS Database: Occupational Health and Safety Information Online.

    ERIC Educational Resources Information Center

    Siegel, Herbert; Scurr, Erica

    1985-01-01

    Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

  6. Federated Search Tools in Fusion Centers: Bridging Databases in the Information Sharing Environment

    DTIC Science & Technology

    2012-09-01

    considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases...centers, when considering integrating federated search tools; by evaluating the importance of the planning, requirements gathering, selection and...acquisition processes for integrating federated search tools; by acknowledging the challenges faced by some fusion centers during these integration processes

  7. SIMBAD : a sequence-independent molecular-replacement pipeline

    DOE PAGES

    Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

    2018-06-08

    The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

  8. SIMBAD : a sequence-independent molecular-replacement pipeline

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

    Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

    The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

  9. Managing Content in a Matter of Minutes

    NASA Technical Reports Server (NTRS)

    2004-01-01

    NASA software created to help scientists expeditiously search and organize their research documents is now aiding compliance personnel, law enforcement investigators, and the general public in their efforts to search, store, manage, and retrieve documents more efficiently. Developed at Ames Research Center, NETMARK software was designed to manipulate vast amounts of unstructured and semi-structured NASA documents. NETMARK is both a relational and object-oriented technology built on an Oracle enterprise-wide database. To ensure easy user access, Ames constructed NETMARK as a Web-enabled platform utilizing the latest in Internet technology. One of the significant benefits of the program was its ability to store and manage mission-critical data.

  10. Alternative treatment technology information center computer database system

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

    Sullivan, D.

    1995-10-01

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

  11. 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

  12. 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.

  13. Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

    PubMed Central

    2013-01-01

    Background It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. Results We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. Conclusions The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator. PMID:23865810

  14. Applying systematic review search methods to the grey literature: a case study examining guidelines for school-based breakfast programs in Canada.

    PubMed

    Godin, Katelyn; Stapleton, Jackie; Kirkpatrick, Sharon I; Hanning, Rhona M; Leatherdale, Scott T

    2015-10-22

    Grey literature is an important source of information for large-scale review syntheses. However, there are many characteristics of grey literature that make it difficult to search systematically. Further, there is no 'gold standard' for rigorous systematic grey literature search methods and few resources on how to conduct this type of search. This paper describes systematic review search methods that were developed and applied to complete a case study systematic review of grey literature that examined guidelines for school-based breakfast programs in Canada. A grey literature search plan was developed to incorporate four different searching strategies: (1) grey literature databases, (2) customized Google search engines, (3) targeted websites, and (4) consultation with contact experts. These complementary strategies were used to minimize the risk of omitting relevant sources. Since abstracts are often unavailable in grey literature documents, items' abstracts, executive summaries, or table of contents (whichever was available) were screened. Screening of publications' full-text followed. Data were extracted on the organization, year published, who they were developed by, intended audience, goal/objectives of document, sources of evidence/resources cited, meals mentioned in the guidelines, and recommendations for program delivery. The search strategies for identifying and screening publications for inclusion in the case study review was found to be manageable, comprehensive, and intuitive when applied in practice. The four search strategies of the grey literature search plan yielded 302 potentially relevant items for screening. Following the screening process, 15 publications that met all eligibility criteria remained and were included in the case study systematic review. The high-level findings of the case study systematic review are briefly described. This article demonstrated a feasible and seemingly robust method for applying systematic search strategies to identify web-based resources in the grey literature. The search strategy we developed and tested is amenable to adaptation to identify other types of grey literature from other disciplines and answering a wide range of research questions. This method should be further adapted and tested in future research syntheses.

  15. Biomedical Requirements for High Productivity Computing Systems

    DTIC Science & Technology

    2005-04-01

    server at http://www.ncbi.nlm.nih.gov/BLAST/. There are many variants of BLAST, including: 1. BLASTN - Compares a DNA query to a DNA database. Searches ...database (3 reading frames from each strand of the DNA) searching . 13 4. TBLASTN - Compares a protein query to a DNA database, in the 6 possible...the molecular during this phase. After eliminating molecules that could not match the query , an atom-by-atom search for the molecules in conducted

  16. Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

    ERIC Educational Resources Information Center

    Angier, Jennifer J.; Epstein, Barbara A.

    1980-01-01

    Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

  17. Subject Specific Databases: A Powerful Research Tool

    ERIC Educational Resources Information Center

    Young, Terrence E., Jr.

    2004-01-01

    Subject specific databases, or vortals (vertical portals), are databases that provide highly detailed research information on a particular topic. They are the smallest, most focused search tools on the Internet and, in recent years, they've been on the rise. Currently, more of the so-called "mainstream" search engines, subject directories, and…

  18. Subject Retrieval from Full-Text Databases in the Humanities

    ERIC Educational Resources Information Center

    East, John W.

    2007-01-01

    This paper examines the problems involved in subject retrieval from full-text databases of secondary materials in the humanities. Ten such databases were studied and their search functionality evaluated, focusing on factors such as Boolean operators, document surrogates, limiting by subject area, proximity operators, phrase searching, wildcards,…

  19. Environmental Factor{trademark} system: RCRA hazardous waste handler information

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

    NONE

    1999-03-01

    Environmental Factor{trademark} RCRA Hazardous Waste Handler Information on CD-ROM unleashes the invaluable information found in two key EPA data sources on hazardous waste handlers and offers cradle-to-grave waste tracking. It`s easy to search and display: (1) Permit status, design capacity and compliance history for facilities found in the EPA Resource Conservation and Recovery Information System (RCRIS) program tracking database; (2) Detailed information on hazardous wastes generation, management and minimization by companies who are large quantity generators, and (3) Data on the waste management practices of treatment, storage and disposal (TSD) facilities from the EPA Biennial Reporting System which is collectedmore » every other year. Environmental Factor`s powerful database retrieval system lets you: (1) Search for RCRA facilities by permit type, SIC code, waste codes, corrective action or violation information, TSD status, generator and transporter status and more; (2) View compliance information -- dates of evaluation, violation, enforcement and corrective action; (3) Lookup facilities by waste processing categories of marketing, transporting, processing and energy recovery; (4) Use owner/operator information and names, titles and telephone numbers of project managers for prospecting; and (5) Browse detailed data on TSD facility and large quantity generators` activities such as onsite waste treatment, disposal, or recycling, offsite waste received, and waste generation and management. The product contains databases, search and retrieval software on two CD-ROMs, an installation diskette and User`s Guide. Environmental Factor has online context-sensitive help from any screen and a printed User`s Guide describing installation and step-by-step procedures for searching, retrieving and exporting. Hotline support is also available for no additional charge.« less

  20. Exploring experienced nurses' attitudes, views and expectations of new graduate nurses: a critical review.

    PubMed

    Freeling, Michelle; Parker, Steve

    2015-02-01

    This critical review evaluates the existing primary research literature to identify experienced registered nurses' attitudes, views and expectations of graduate nurses which may create a barrier for optimal graduate nurse performance. Relevant primary studies were identified by searching online databases using a wide variety of appropriate keyword combinations. Online databases including Cumulative Index to Nursing and Allied Health Literature (CINAHL), Scopus, PsycINFO and Google Scholar were comprehensively searched for relevant research. The selected studies were subjected to a rigorous critical appraisal to evaluate the studies and to determine if the findings were applicable to practice. A manual method of thematic analysis was conducted to highlight explicit and implicit themes from the reviewed studies. Themes were grouped and continually reduced until only essential themes remain. Themes and subthemes emerged which were then compared and contrasted to analyse results. The four major themes identified include nursing skills, inadequate preparation during academic program, attitudes and ward culture and concerns with confidence. Subthemes were identified within these categories. Findings indicate experienced registered nurses discussed themes including 'nursing skills', 'inadequate preparation during academic program', 'attitudes and ward culture' and 'concerns with confidence'. Concerns were raised including the value of traditional training versus tertiary education programs, coping with unprofessional behaviour and inadequate preparation for practice. Further research is required to fully address management of the theory-practice gap, as well as the attitudes of experienced registered nurses educated in traditional programs versus those in tertiary education programs. Nurse managers should be aware of the possible occurrence of unprofessional behaviour, and increased workplace training regarding lateral violence would assist in raising awareness regarding negative and unacceptable behaviour. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. A Framework for Cloudy Model Optimization and Database Storage

    NASA Astrophysics Data System (ADS)

    Calvén, Emilia; Helton, Andrew; Sankrit, Ravi

    2018-01-01

    We present a framework for producing Cloudy photoionization models of the nebular emission from novae ejecta and storing a subset of the results in SQL database format for later usage. The database can be searched for models best fitting observed spectral line ratios. Additionally, the framework includes an optimization feature that can be used in tandem with the database to search for and improve on models by creating new Cloudy models while, varying the parameters. The database search and optimization can be used to explore the structures of nebulae by deriving their properties from the best-fit models. The goal is to provide the community with a large database of Cloudy photoionization models, generated from parameters reflecting conditions within novae ejecta, that can be easily fitted to observed spectral lines; either by directly accessing the database using the framework code or by usage of a website specifically made for this purpose.

  2. General surgery residency program websites: usefulness and usability for resident applicants.

    PubMed

    Reilly, Eugene F; Leibrandt, Thomas J; Zonno, Alan J; Simpson, Mary Christina; Morris, Jon B

    2004-01-01

    To assess the content of general surgery residency program websites, the websites' potential as tools in resident recruitment, and their "usability." The homepages of general surgery residency programs were evaluated for accessibility, ease-of-use, adherence to established principles of website design, and content. Investigators completed a questionnaire on aspects of their online search, including number of mouse-clicks used, number of errors encountered, and number of returns to the residency homepage. The World Wide Web listings on the Fellowship and Residency Electronic Interactive Database (FREIDA) of the American Medical Association (AMA). A total of 251 ACGME-accredited general surgery residency programs. One hundred sixty-seven programs (67%) provided a viable link to the program's website. Evaluators found an average of 5.9 of 16 content items; 2 (1.2%) websites provided as many as 12 content items. Five of the 16 content items (program description, conference schedules, listing of faculty, caseload, and salary) were found on more than half of the sites. An average of 24 mouse-clicks was required to complete the questionnaire for each site. Forty-six sites (28%) generated at least 1 error during our search. The residency homepage was revisited an average of 5 times during each search. On average, programs adhered to 6 of the 10 design principles; only 6 (3.6%) sites adhered to all 10 design principles. Two of the 10 design principles (use of familiar fonts, absence of frames) were adhered to in more than half of the sites. Our overall success rate when searching residency websites was 38%. General surgery residency programs do not use the World Wide Web optimally, particularly for users who are potential residency candidates. The usability of these websites could be increased by providing relevant content, making that content easier to find, and adhering to established web design principles.

  3. Mitigation of Fluorosis - A Review

    PubMed Central

    Dodamani, Arun S.; Jadhav, Harish C.; Naik, Rahul G.; Deshmukh, Manjiri A.

    2015-01-01

    Fluoride is required for normal development and growth of the body. It is found in plentiful quantity in environment and fluoride content in drinking water is largest contributor to the daily fluoride intake. The behaviour of fluoride ions in the human organism can be regarded as that of “double-edged sword”. Fluoride is beneficial in small amounts but toxic in large amounts. Excessive consumption of fluorides in various forms leads to development of fluorosis. Fluorosis is major health problem in 24 countries, including India, which lies in the geographical fluoride belt. Various technologies are being used to remove fluoride from water but still the problem has not been rooted out. The purpose of this paper is to review the available treatment modalities for fluorosis, available technologies for fluoride removal from water and ongoing fluorosis mitigation programs based on literature survey. Medline was the primary database used in the literature search. Other databases included: PubMed, Web of Science, Google Scholar, WHO, Ebscohost, Science Direct, Google Search Engine, etc. PMID:26266235

  4. Effectiveness of Motivational Interviewing Interventions for Adolescent Substance Use Behavior Change: A Meta-Analytic Review

    ERIC Educational Resources Information Center

    Jensen, Chad D.; Cushing, Christopher C.; Aylward, Brandon S.; Craig, James T.; Sorell, Danielle M.; Steele, Ric G.

    2011-01-01

    Objective: This study was designed to quantitatively evaluate the effectiveness of motivational interviewing (MI) interventions for adolescent substance use behavior change. Method: Literature searches of electronic databases were undertaken in addition to manual reference searches of identified review articles. Databases searched include…

  5. Volcanoes of México: An Interactive CD-ROM From the Smithsonian's Global Volcanism Program

    NASA Astrophysics Data System (ADS)

    Siebert, L.; Kimberly, P.; Calvin, C.; Luhr, J. F.; Kysar, G.

    2002-12-01

    The Smithsonian Institution's Global Volcanism Program is nearing completion of an interactive CD-ROM, the Volcanoes of México. This CD is the second in a series sponsored by the U.S. Department of Energy Office of Geothermal Technologies to collate Smithsonian data on Quaternary volcanism as a resource for the geothermal community. It also has utility for those concerned with volcanic hazard and risk mitgation as well as an educational tool for those interested in Mexican volcanism. We acknowledge the significant contributions of many Mexican volcanologists to the eruption reports, data, and images contained in this CD, in particular those contributions of the Centro Nacional de Prevencion de Desastres (CENAPRED), the Colima Volcano Observatory of the University of Colima, and the Universidad Nacional Autónoma de México (UNAM). The Volcanoes of México CD has a format similar to that of an earlier Smithsonian CD, the Volcanoes of Indonesia, but also shows Pleistocene volcanic centers and additional data on geothermal sites. A clickable map of México shows both Holocene and Pleistocene volcanic centers and provides access to individual pages on 67 volcanoes ranging from Cerro Prieto in Baja California to Tacaná on the Guatemalan border. These include geographic and geologic data on individual volcanoes (as well as a brief paragraph summarizing the geologic history) along with tabular eruption chronologies, eruptive characteristics, and eruptive volumes, when known. Volcano data are accessible from both geographical and alphabetical searches. A major component of the CD is more than 400 digitized images illustrating the morphology of volcanic centers and eruption processes and deposits, providing a dramatic visual primer to the country's volcanoes. Images of specific eruptions can be directly linked to from the eruption chronology tables. The Volcanoes of México CD includes monthly reports and associated figures and tables cataloging volcanic activity in México from the Bulletin of the Global Volcanism Network and its predecessor, the Scientific Event Alert Network Bulletin, as well as early event-card notices of the Smithsonian's Center for Short-Lived Phenomena. An extensive petrologic database contains major-element analyses and other petrological and geochemical data for 1776 samples. The user also has access to a database of the Global Volcanism Program's map archives. Another option on the CD views earthquake hypocenters and volcanic eruptions from 1960 to the present plotted sequentially on a map of México and Central America. A bibliography of Mexican volcanism and geothermal research includes references cited in the Smithsonian's volcano database as well as those obtained from a search of the Georef bibliographic database. For more advanced queries and searches both the petrologic database and volcanic activity reports can be uploaded from the CD.

  6. Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping

    PubMed Central

    Matthiesen, Rune; Kirpekar, Finn

    2009-01-01

    The idea of identifying or characterizing an RNA molecule based on a mass spectrum of specifically generated RNA fragments has been used in various forms for well over a decade. We have developed software—named RRM for ‘RNA mass mapping’—which can search whole prokaryotic genomes or RNA FASTA sequence databases to identify the origin of a given RNA based on a mass spectrum of RNA fragments. As input, the program uses the masses of specific RNase cleavage of the RNA under investigation. RNase T1 digestion is used here as a demonstration of the usability of the method for RNA identification. The concept for identification is that the masses of the digestion products constitute a specific fingerprint, which characterize the given RNA. The search algorithm is based on the same principles as those used in peptide mass fingerprinting, but has here been extended to work for both RNA sequence databases and for genome searches. A simple and powerful probability model for ranking RNA matches is proposed. We demonstrate viability of the entire setup by identifying the DNA template of a series of RNAs of biological and of in vitro transcriptional origin in complete microbial genomes and by identifying authentic 16S ribosomal RNAs in a ‘small ribosomal subunit RNA’ database. Thus, we present a new tool for a rapid identification of unknown RNAs using only a few picomoles of starting material. PMID:19264806

  7. The LAILAPS search engine: a feature model for relevance ranking in life science databases.

    PubMed

    Lange, Matthias; Spies, Karl; Colmsee, Christian; Flemming, Steffen; Klapperstück, Matthias; Scholz, Uwe

    2010-03-25

    Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

  8. 77 FR 6535 - Notice of Intent To Seek Approval To Collect Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-08

    ... information from participants: Contact information, affiliation, and database searching experience... and fax numbers, and email address. Six questions are asked regarding: database searching experience...

  9. Database resources of the National Center for Biotechnology Information

    PubMed Central

    Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

    2001-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:11125038

  10. Database resources of the National Center for Biotechnology

    PubMed Central

    Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

    2003-01-01

    In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941

  11. SoyFN: a knowledge database of soybean functional networks.

    PubMed

    Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

    2014-01-01

    Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

  12. Searching mixed DNA profiles directly against profile databases.

    PubMed

    Bright, Jo-Anne; Taylor, Duncan; Curran, James; Buckleton, John

    2014-03-01

    DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead. In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  13. Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

    PubMed Central

    Lee, Taein; Cheng, Chun-Huai; Ficklin, Stephen; Yu, Jing; Humann, Jodi; Main, Dorrie

    2017-01-01

    Abstract Tripal is an open-source database platform primarily used for development of genomic, genetic and breeding databases. We report here on the release of the Chado Loader, Chado Data Display and Chado Search modules to extend the functionality of the core Tripal modules. These new extension modules provide additional tools for (1) data loading, (2) customized visualization and (3) advanced search functions for supported data types such as organism, marker, QTL/Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their respective metadata. The Chado Loader module provides data collection templates in Excel with defined metadata and data loaders with front end forms. The Chado Data Display module contains tools to visualize each data type and the metadata which can be used as is or customized as desired. The Chado Search module provides search and download functionality for the supported data types. Also included are the tools to visualize map and species summary. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with different metadata types to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGen (cottongen.org), Citrus Genome Database (citrusgenomedb.org), Genome Database for Vaccinium (vaccinium.org) and the Cool Season Food Legume Database (coolseasonfoodlegume.org). Database URL: https://www.citrusgenomedb.org/, https://www.coolseasonfoodlegume.org/, https://www.cottongen.org/, https://www.rosaceae.org/, https://www.vaccinium.org/

  14. Difficulties and challenges associated with literature searches in operating room management, complete with recommendations.

    PubMed

    Wachtel, Ruth E; Dexter, Franklin

    2013-12-01

    The purpose of this article is to teach operating room managers, financial analysts, and those with a limited knowledge of search engines, including PubMed, how to locate articles they need in the areas of operating room and anesthesia group management. Many physicians are unaware of current literature in their field and evidence-based practices. The most common source of information is colleagues. Many people making management decisions do not read published scientific articles. Databases such as PubMed are available to search for such articles. Other databases, such as citation indices and Google Scholar, can be used to uncover additional articles. Nevertheless, most people who do not know how to use these databases are reluctant to utilize help resources when they do not know how to accomplish a task. Most people are especially reluctant to use on-line help files. Help files and search databases are often difficult to use because they have been designed for users already familiar with the field. The help files and databases have specialized vocabularies unique to the application. MeSH terms in PubMed are not useful alternatives for operating room management, an important limitation, because MeSH is the default when search terms are entered in PubMed. Librarians or those trained in informatics can be valuable assets for searching unusual databases, but they must possess the domain knowledge relative to the subject they are searching. The search methods we review are especially important when the subject area (e.g., anesthesia group management) is so specific that only 1 or 2 articles address the topic of interest. The materials are presented broadly enough that the reader can extrapolate the findings to other areas of clinical and management issues in anesthesiology.

  15. HBVPathDB: a database of HBV infection-related molecular interaction network.

    PubMed

    Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

    2005-03-21

    To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

  16. VIOLIN: vaccine investigation and online information network.

    PubMed

    Xiang, Zuoshuang; Todd, Thomas; Ku, Kim P; Kovacic, Bethany L; Larson, Charles B; Chen, Fang; Hodges, Andrew P; Tian, Yuying; Olenzek, Elizabeth A; Zhao, Boyang; Colby, Lesley A; Rush, Howard G; Gilsdorf, Janet R; Jourdian, George W; He, Yongqun

    2008-01-01

    Vaccines are among the most efficacious and cost-effective tools for reducing morbidity and mortality caused by infectious diseases. The vaccine investigation and online information network (VIOLIN) is a web-based central resource, allowing easy curation, comparison and analysis of vaccine-related research data across various human pathogens (e.g. Haemophilus influenzae, human immunodeficiency virus (HIV) and Plasmodium falciparum) of medical importance and across humans, other natural hosts and laboratory animals. Vaccine-related peer-reviewed literature data have been downloaded into the database from PubMed and are searchable through various literature search programs. Vaccine data are also annotated, edited and submitted to the database through a web-based interactive system that integrates efficient computational literature mining and accurate manual curation. Curated information includes general microbial pathogenesis and host protective immunity, vaccine preparation and characteristics, stimulated host responses after vaccination and protection efficacy after challenge. Vaccine-related pathogen and host genes are also annotated and available for searching through customized BLAST programs. All VIOLIN data are available for download in an eXtensible Markup Language (XML)-based data exchange format. VIOLIN is expected to become a centralized source of vaccine information and to provide investigators in basic and clinical sciences with curated data and bioinformatics tools for vaccine research and development. VIOLIN is publicly available at http://www.violinet.org.

  17. The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

    EPA Pesticide Factsheets

    The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati

  18. Multi-source and ontology-based retrieval engine for maize mutant phenotypes

    PubMed Central

    Green, Jason M.; Harnsomburana, Jaturon; Schaeffer, Mary L.; Lawrence, Carolyn J.; Shyu, Chi-Ren

    2011-01-01

    Model Organism Databases, including the various plant genome databases, collect and enable access to massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc, as well as textual descriptions of many of these entities. While a variety of basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of phenotypic data, next-generation search mechanisms that allow querying and ranking of text descriptions are much less common. In addition, the plant community needs an innovative way to leverage the existing links in these databases to search groups of text descriptions simultaneously. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing these issues, we have developed a unique search engine for mutant phenotypes from MaizeGDB. This advanced search mechanism integrates various text description sources in MaizeGDB to aid a user in retrieving desired mutant phenotype information. Currently, descriptions of mutant phenotypes, loci and gene products are utilized collectively for each search, though expansion of the search mechanism to include other sources is straightforward. The retrieval engine, to our knowledge, is the first engine to exploit the content and structure of available domain ontologies, currently the Plant and Gene Ontologies, to expand and enrich retrieval results in major plant genomic databases. Database URL: http:www.PhenomicsWorld.org/QBTA.php PMID:21558151

  19. Concentrations of indoor pollutants database: User's manual

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

    Not Available

    1992-05-01

    This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author's last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user's needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

  20. Concentrations of indoor pollutants database: User`s manual

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

    Not Available

    1992-05-01

    This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author`s last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user`s needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

  1. Web-based flood database for Colorado, water years 1867 through 2011

    USGS Publications Warehouse

    Kohn, Michael S.; Jarrett, Robert D.; Krammes, Gary S.; Mommandi, Amanullah

    2013-01-01

    In order to provide a centralized repository of flood information for the State of Colorado, the U.S. Geological Survey, in cooperation with the Colorado Department of Transportation, created a Web-based geodatabase for flood information from water years 1867 through 2011 and data for paleofloods occurring in the past 5,000 to 10,000 years. The geodatabase was created using the Environmental Systems Research Institute ArcGIS JavaScript Application Programing Interface 3.2. The database can be accessed at http://cwscpublic2.cr.usgs.gov/projects/coflood/COFloodMap.html. Data on 6,767 flood events at 1,597 individual sites throughout Colorado were compiled to generate the flood database. The data sources of flood information are indirect discharge measurements that were stored in U.S. Geological Survey offices (water years 1867–2011), flood data from indirect discharge measurements referenced in U.S. Geological Survey reports (water years 1884–2011), paleoflood studies from six peer-reviewed journal articles (data on events occurring in the past 5,000 to 10,000 years), and the U.S. Geological Survey National Water Information System peak-discharge database (water years 1883–2010). A number of tests were performed on the flood database to ensure the quality of the data. The Web interface was programmed using the Environmental Systems Research Institute ArcGIS JavaScript Application Programing Interface 3.2, which allows for display, query, georeference, and export of the data in the flood database. The data fields in the flood database used to search and filter the database include hydrologic unit code, U.S. Geological Survey station number, site name, county, drainage area, elevation, data source, date of flood, peak discharge, and field method used to determine discharge. Additional data fields can be viewed and exported, but the data fields described above are the only ones that can be used for queries.

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

    PubMed

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

    2011-10-01

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

  3. The EMBL-EBI bioinformatics web and programmatic tools framework.

    PubMed

    Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

    2015-07-01

    Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

    PubMed

    Tamimi, Ahmad; Ashhab, Yaqoub; Tamimi, Hashem

    2016-01-01

    Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

  5. THGS: a web-based database of Transmembrane Helices in Genome Sequences

    PubMed Central

    Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

    2004-01-01

    Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

  6. Engineering the object-relation database model in O-Raid

    NASA Technical Reports Server (NTRS)

    Dewan, Prasun; Vikram, Ashish; Bhargava, Bharat

    1989-01-01

    Raid is a distributed database system based on the relational model. O-raid is an extension of the Raid system and will support complex data objects. The design of O-Raid is evolutionary and retains all features of relational data base systems and those of a general purpose object-oriented programming language. O-Raid has several novel properties. Objects, classes, and inheritance are supported together with a predicate-base relational query language. O-Raid objects are compatible with C++ objects and may be read and manipulated by a C++ program without any 'impedance mismatch'. Relations and columns within relations may themselves be treated as objects with associated variables and methods. Relations may contain heterogeneous objects, that is, objects of more than one class in a certain column, which can individually evolve by being reclassified. Special facilities are provided to reduce the data search in a relation containing complex objects.

  7. The Peer Education Approach in Adolescents- Narrative Review Article.

    PubMed

    Abdi, Fatemeh; Simbar, Masoumeh

    2013-11-01

    Adolescence is an important stage of human life span, which crucial developmental processes occur. Since peers play a critical role in the psychosocial development of most adolescents, peer education is currently considered as a health promotion strategy in adolescents. Peer education is defined as a system of delivering knowledge that improves social learning and provides psychosocial support. As identifying the outcomes of different educational approaches will be beneficial in choosing the most effective programs for training adolescents, the present article reviewed the impact of the peer education approach on adolescents. In this review, databases such as PubMed, EMBASE, ISI, and Iranian databases, from 1999 to 2013, were searched using a number of keywords. Peer education is an effective tool for promoting healthy behaviors among adolescents. The development of this social process depends on the settings, context, and the values and expectations of the participants. Therefore, designing such programs requires proper preparation, training, supervision, and evaluation.

  8. Data-driven indexing mechanism for the recognition of polyhedral objects

    NASA Astrophysics Data System (ADS)

    McLean, Stewart; Horan, Peter; Caelli, Terry M.

    1992-02-01

    This paper is concerned with the problem of searching large model databases. To date, most object recognition systems have concentrated on the problem of matching using simple searching algorithms. This is quite acceptable when the number of object models is small. However, in the future, general purpose computer vision systems will be required to recognize hundreds or perhaps thousands of objects and, in such circumstances, efficient searching algorithms will be needed. The problem of searching a large model database is one which must be addressed if future computer vision systems are to be at all effective. In this paper we present a method we call data-driven feature-indexed hypothesis generation as one solution to the problem of searching large model databases.

  9. Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

    PubMed

    Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

    2011-12-01

    The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

  10. Comparison of CINAHL, EMBASE, and MEDLINE databases for the nurse researcher.

    PubMed

    Burnham, J; Shearer, B

    1993-01-01

    The purpose of this research was to determine which of three databases, CINAHL, EMBASE or MEDLINE, should be accessed when researching nursing topics. The three databases were searched for citations on topics selected by three nurse researchers and the results were compared. For the search of nursing care literature on a medical condition, it was helpful to search both CINAHL and MEDLINE. CINAHL provided the majority of relevant articles for the second search, on computers and privacy, but inclusion of MEDLINE and EMBASE enhanced retrieval somewhat. The search on substance abuse in pregnancy, not restricted to nursing literature, retrieved better results when searching both MEDLINE and EMBASE. Due to the nature and distribution of the nursing literature, it is especially important for the searcher to understand and respond to the focus of the researcher.

  11. Choosing a Database for Social Work: A Comparison of Social Work Abstracts and Social Service Abstracts

    ERIC Educational Resources Information Center

    Flatley, Robert K.; Lilla, Rick; Widner, Jack

    2007-01-01

    This study compared Social Work Abstracts and Social Services Abstracts databases in terms of indexing, journal coverage, and searches. The authors interviewed editors, analyzed journal coverage, and compared searches. It was determined that the databases complement one another more than compete. The authors conclude with some considerations.

  12. The Philip Morris Information Network: A Library Database on an In-House Timesharing System.

    ERIC Educational Resources Information Center

    DeBardeleben, Marian Z.; And Others

    1983-01-01

    Outlines a database constructed at Philip Morris Research Center Library which encompasses holdings and circulation and acquisitions records for all items in the library. Host computer (DECSYSTEM-2060), software (BASIC), database design, search methodology, cataloging, and accessibility are noted; sample search, circ-in profile, end user profiles,…

  13. How Many People Search the ERIC Database Each Day?

    ERIC Educational Resources Information Center

    Rudner, Lawrence

    This study estimated the number of people searching the ERIC database each day. The Educational Resources Information Center (ERIC) is a national information system designed to provide ready access to an extensive body of education-related literature. Federal funds traditionally have paid for the development of the database, but not the…

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

    ERIC Educational Resources Information Center

    Koehler, Wallace; Mincey, Danielle

    1996-01-01

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

  15. Digging Deeper: The Deep Web.

    ERIC Educational Resources Information Center

    Turner, Laura

    2001-01-01

    Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

  16. An Integrative Review of Pain Resource Nurse Programs.

    PubMed

    Crawford, Cecelia L; Boller, Jan; Jadalla, Ahlam; Cuenca, Emma

    2016-01-01

    Mismanaged pain challenges health care systems. In the early 1990s, pain resource nurse programs were developed by Ferrell and colleagues. Variations of the model have existed for more than 20 years. While results of these programs have been disseminated, conclusive evidence has not been examined via a synthesis of the literature. A structured systematic search using multiple databases was conducted for research studies published 2005-2012. The search identified 11 studies on effective use of a pain resource nurse and/or a pain resource nurse program. The results revealed wide variations existing in program design, research methodology, practice settings, and reported outcomes. Overall, the strength of the evidence on pain resource nurse programs was determined to range from low to moderate quality for making generalizable conclusions. However, 4 key elements were identified as integral to effective pain resource nurse programs and useful for the program design and development: leadership commitment and active involvement in embedding a culture of effective pain management throughout the organization; addressing staff-related and organization-related challenges and barriers to pain management; a combination of strategies to overcome these barriers; and collaborative multidisciplinary teamwork and communication. Specific recommendations are provided for program implementation. Although the evidence was inconclusive, useful information exists to create the design of effective pain resource nurse programs. Collaborative multisite studies on the long-term effects of pain resource nurse programs are recommended.

  17. Vehicle-triggered video compression/decompression for fast and efficient searching in large video databases

    NASA Astrophysics Data System (ADS)

    Bulan, Orhan; Bernal, Edgar A.; Loce, Robert P.; Wu, Wencheng

    2013-03-01

    Video cameras are widely deployed along city streets, interstate highways, traffic lights, stop signs and toll booths by entities that perform traffic monitoring and law enforcement. The videos captured by these cameras are typically compressed and stored in large databases. Performing a rapid search for a specific vehicle within a large database of compressed videos is often required and can be a time-critical life or death situation. In this paper, we propose video compression and decompression algorithms that enable fast and efficient vehicle or, more generally, event searches in large video databases. The proposed algorithm selects reference frames (i.e., I-frames) based on a vehicle having been detected at a specified position within the scene being monitored while compressing a video sequence. A search for a specific vehicle in the compressed video stream is performed across the reference frames only, which does not require decompression of the full video sequence as in traditional search algorithms. Our experimental results on videos captured in a local road show that the proposed algorithm significantly reduces the search space (thus reducing time and computational resources) in vehicle search tasks within compressed video streams, particularly those captured in light traffic volume conditions.

  18. 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.

  19. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

    PubMed

    Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

    2010-08-01

    The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

  20. DOE Research and Development Accomplishments Website Policies/Important

    Science.gov Websites

    Links RSS Archive Videos XML DOE R&D Accomplishments DOE R&D Accomplishments searchQuery × Find searchQuery x Find DOE R&D Acccomplishments Navigation dropdown arrow The Basics Stories Snapshots R&D Nuggets Database dropdown arrow Search Tag Cloud Browse Reports Database Help

  1. Pre-Service Teachers' Use of Library Databases: Some Insights

    ERIC Educational Resources Information Center

    Lamb, Janeen; Howard, Sarah; Easey, Michael

    2014-01-01

    The aim of this study is to investigate if providing mathematics education pre-service teachers with animated library tutorials on library and database searches changes their searching practices. This study involved the completion of a survey by 138 students and seven individual interviews before and after library search demonstration videos were…

  2. A Web interface generator for molecular biology programs in Unix.

    PubMed

    Letondal, C

    2001-01-01

    Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration. The program has been used for three years by about 15000 users throughout the world; it has recently been installed on other sites and evaluated as a standard user interface for EMBOSS programs.

  3. Overview of Faculty Development Programs for Interprofessional Education.

    PubMed

    Ratka, Anna; Zorek, Joseph A; Meyer, Susan M

    2017-06-01

    Objectives. To describe characteristics of faculty development programs designed to facilitate interprofessional education, and to compile recommendations for development, delivery, and assessment of such faculty development programs. Methods. MEDLINE, CINAHL, ERIC, and Web of Science databases were searched using three keywords: faculty development, interprofessional education, and health professions. Articles meeting inclusion criteria were analyzed for emergent themes, including program design, delivery, participants, resources, and assessment. Results. Seventeen articles were identified for inclusion, yielding five characteristics of a successful program: institutional support; objectives and outcomes based on interprofessional competencies; focus on consensus-building and group facilitation skills; flexibility based on institution- and participant-specific characteristics; and incorporation of an assessment strategy. Conclusion. The themes and characteristics identified in this literature overview may support development of faculty development programs for interprofessional education. An advanced evidence base for interprofessional education faculty development programs is needed.

  4. ExoDat Information System at CeSAM

    NASA Astrophysics Data System (ADS)

    Agneray, F.; Moreau, C.; Chabaud, P.; Damiani, C.; Deleuil, M.

    2014-05-01

    CoRoT (Convection Rotation and planetary transits) is a space based mission led by French space agency (CNES) in association with French and international laboratories. One of CoRoT's goal is to detect exoplanets by the transit method. The Exoplanet Database (Exodat) is a VO compliant information system for the CoRoT exoplanet program. The main functions of ExoDat are to provide a source catalog for the observation fields and targets selection; to characterize the CoRoT targets (spectral type, variability , contamination...);and to support follow up programs. ExoDat is built using the AstroNomical Information System (ANIS) developed by the CeSAM (Centre de donneeS Astrophysique de Marseille). It offers download of observation catalogs and additional services like: search, extract and display data by using a combination of criteria, object list, and cone-search interfaces. Web services have been developed to provide easy access for user's softwares and pipelines.

  5. [A survey of the best bibliographic searching system in occupational medicine and discussion of its implementation].

    PubMed

    Inoue, J

    1991-12-01

    When occupational health personnel, especially occupational physicians search bibliographies, they usually have to search bibliographies by themselves. Also, if a library is not available because of the location of their work place, they might have to rely on online databases. Although there are many commercial databases in the world, people who seldom use them, will have problems with on-line searching, such as user-computer interface, keywords, and so on. The present study surveyed the best bibliographic searching system in the field of occupational medicine by questionnaire through the use of DIALOG OnDisc MEDLINE as a commercial database. In order to ascertain the problems involved in determining the best bibliographic searching system, a prototype bibliographic searching system was constructed and then evaluated. Finally, solutions for the problems were discussed. These led to the following conclusions: to construct the best bibliographic searching system at the present time, 1) a concept of micro-to-mainframe links (MML) is needed for the computer hardware network; 2) multi-lingual font standards and an excellent common user-computer interface are needed for the computer software; 3) a short course and education of database management systems, and support of personal information processing for retrieved data are necessary for the practical use of the system.

  6. Development of a One-Stop Data Search and Discovery Engine using Ontologies for Semantic Mappings (HydroSeek)

    NASA Astrophysics Data System (ADS)

    Piasecki, M.; Beran, B.

    2007-12-01

    Search engines have changed the way we see the Internet. The ability to find the information by just typing in keywords was a big contribution to the overall web experience. While the conventional search engine methodology worked well for textual documents, locating scientific data remains a problem since they are stored in databases not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different databases, especially for interdisciplinary research it is typically necessary to work with multiple data sources. These sources can be federal agencies which generally offer national coverage or regional sources which cover a smaller area with higher detail. However for a given geographic area of interest there often exists more than one database with relevant data. Thus being able to query multiple databases simultaneously is a desirable feature that would be tremendously useful for scientists. Development of such a search engine requires dealing with various heterogeneity issues. In scientific databases, systems often impose controlled vocabularies which ensure that they are generally homogeneous within themselves but are semantically heterogeneous when moving between different databases. This defines the boundaries of possible semantic related problems making it easier to solve than with the conventional search engines that deal with free text. We have developed a search engine that enables querying multiple data sources simultaneously and returns data in a standardized output despite the aforementioned heterogeneity issues between the underlying systems. This application relies mainly on metadata catalogs or indexing databases, ontologies and webservices with virtual globe and AJAX technologies for the graphical user interface. Users can trigger a search of dozens of different parameters over hundreds of thousands of stations from multiple agencies by providing a keyword, a spatial extent, i.e. a bounding box, and a temporal bracket. As part of this development we have also added an environment that allows users to do some of the semantic tagging, i.e. the linkage of a variable name (which can be anything they desire) to defined concepts in the ontology structure which in turn provides the backbone of the search engine.

  7. A Systematic Review of the Effects of Continuing Education Programs on Providing Clinical Community Pharmacy Services

    PubMed Central

    Marques dos Reis, Tiago; Guidoni, Camilo Molino; Girotto, Edmarlon; Guerra, Marisabelle Lima; de Oliveira Baldoni, André; Leira Pereira, Leonardo Régis

    2016-01-01

    Objective. To summarize the effects of media methods used in continuing education (CE) programs on providing clinical community pharmacy services and the methods used to evaluate the effectiveness of these programs. Methods. A systematic review was performed using Medline, SciELO, and Scopus databases. The timeline of the search was 1990 to 2013. Searches were conducted in English, Portuguese, and Spanish. Results. Nineteen articles of 3990 were included. Fourteen studies used only one media method, and the live method (n=11) was the most frequent (alone or in combination). Only two studies found that the CE program was ineffective or partially effective; these studies used only the live method. Most studies used nonrobust, nonvalidated, and nonstandardized methods to measure effectiveness. The majority of studies focused on the effect of the CE program on modifying the knowledge and skills of the pharmacists. One study assessed the CE program’s benefits to patients or clients. Conclusion. No evidence was obtained regarding which media methods are the most effective. Robust and validated methods, as well as assessment standardization, are required to clearly determine whether a particular media method is effective. PMID:27402991

  8. What Searches Do Users Run on PEDro? An Analysis of 893,971 Search Commands Over a 6-Month Period.

    PubMed

    Stevens, Matthew L; Moseley, Anne; Elkins, Mark R; Lin, Christine C-W; Maher, Chris G

    2016-08-05

    Clinicians must be able to search effectively for relevant research if they are to provide evidence-based healthcare. It is therefore relevant to consider how users search databases of evidence in healthcare, including what information users look for and what search strategies they employ. To date such analyses have been restricted to the PubMed database. Although the Physiotherapy Evidence Database (PEDro) is searched millions of times each year, no studies have investigated how users search PEDro. To assess the content and quality of searches conducted on PEDro. Searches conducted on the PEDro website over 6 months were downloaded and the 'get' commands and page-views extracted. The following data were tabulated: the 25 most common searches; the number of search terms used; the frequency of use of simple and advanced searches, including the use of each advanced search field; and the frequency of use of various search strategies. Between August 2014 and January 2015, 893,971 search commands were entered on PEDro. Fewer than 18 % of these searches used the advanced search features of PEDro. 'Musculoskeletal' was the most common subdiscipline searched, while 'low back pain' was the most common individual search. Around 20 % of all searches contained errors. PEDro is a commonly used evidence resource, but searching appears to be sub-optimal in many cases. The effectiveness of searches conducted by users needs to improve, which could be facilitated by methods such as targeted training and amending the search interface.

  9. SPACE 365: Upgraded App for Aviation and Space-Related Information and Program Planning

    NASA Astrophysics Data System (ADS)

    Williams, S.; Maples, J. E.; Castle, C. E.

    2014-12-01

    Foreknowledge of upcoming events and anniversary dates can be extraordinarily valuable in the planning and preparation of a variety of aviation and Space-related educational programming. Alignment of programming with items "newsworthy" enough to attract media attention on their own can result in effective program promotion at low/no cost. Similarly, awareness and avoidance of dates upon which media and public attention will likely be elsewhere can keep programs from being lost in the noise.NASA has created a useful and entertaining app called "SPACE 365" to help supply that foreknowledge. The app contains an extensive database of historical aviation and Space exploration-related events, along with other events and birthdays to provide socio-historical context, as well as an extensive file of present and future space missions, complete with images and videos. The user can search by entry topic category, date, and key words. Upcoming Events allows the user to plan, participate, and engage in significant "don't miss" happenings.The historical database was originally developed for use at the National Air and Space Museum, then expanded significantly to include more NASA-related information. The CIMA team at NASA MSFC, sponsored by the Planetary Science Division, added NASA current events and NASA educational programming information, and are continually adding new information and improving the functionality and features of the app. Features of SPACE 365 now include: NASA Image of the Day, Upcoming NASA Events, Event Save, Do Not Miss, and Ask Dr. Steve functions, and the CIMA team recently added a new start page and added improved search and navigation capabilities. App users can now socialize the Images of the Day via Twitter, Pinterest, Facebook, and other social media outlets.SPACE 365 is available at no cost from both the Apple appstore and GooglePlay, and has helped NASA, NASM, and other educators plan and schedule programming events. It could help you, too!

  10. The Giardia genome project database.

    PubMed

    McArthur, A G; Morrison, H G; Nixon, J E; Passamaneck, N Q; Kim, U; Hinkle, G; Crocker, M K; Holder, M E; Farr, R; Reich, C I; Olsen, G E; Aley, S B; Adam, R D; Gillin, F D; Sogin, M L

    2000-08-15

    The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.

  11. A Review of Databases Used in Orthopaedic Surgery Research and an Analysis of Database Use in Arthroscopy: The Journal of Arthroscopic and Related Surgery.

    PubMed

    Weinreb, Jeffrey H; Yoshida, Ryu; Cote, Mark P; O'Sullivan, Michael B; Mazzocca, Augustus D

    2017-01-01

    The purpose of this study was to evaluate how database use has changed over time in Arthroscopy: The Journal of Arthroscopic and Related Surgery and to inform readers about available databases used in orthopaedic literature. An extensive literature search was conducted to identify databases used in Arthroscopy and other orthopaedic literature. All articles published in Arthroscopy between January 1, 2006, and December 31, 2015, were reviewed. A database was defined as a national, widely available set of individual patient encounters, applicable to multiple patient populations, used in orthopaedic research in a peer-reviewed journal, not restricted by encounter setting or visit duration, and with information available in English. Databases used in Arthroscopy included PearlDiver, the American College of Surgeons National Surgical Quality Improvement Program, the Danish Common Orthopaedic Database, the Swedish National Knee Ligament Register, the Hospital Episodes Statistics database, and the National Inpatient Sample. Database use increased significantly from 4 articles in 2013 to 11 articles in 2015 (P = .012), with no database use between January 1, 2006, and December 31, 2012. Database use increased significantly between January 1, 2006, and December 31, 2015, in Arthroscopy. Level IV, systematic review of Level II through IV studies. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  12. Increasing access to program information: a strategy for improving adolescent health.

    PubMed

    Brindis, Claire D; Hair, Elizabeth C; Cochran, Stephanie; Cleveland, Kevin; Valderrama, L Teresa; Park, M Jane

    2007-01-01

    To identify existing programs serving 11- to 15-year-olds that aim to improve adolescent health in the areas of Health & Well-being, Fitness, Family & Peer Relationships, School Environment, Smoking, Alcohol Use, and Violence and to assess the utility of readily available resources in providing detailed program information. In Phase 1, publicly available program databases were searched to identify potential programs serving the target population. In Phase 2, an in-depth search of a limited sample of programs meeting the content and age criteria was performed to identify program descriptors. Over 1,000 program names were identified in Phase 1. Information regarding programs is becoming more readily available through the internet; however, the program information that was publicly available only begins to draw the picture. Phase 2 revealed that a broad array of efforts are underway in all seven content areas, but found information on the program descriptors to be limited. Investment in programming is not enough; an upfront investment in communication and information sharing is critical in order to maximize the resources dedicated to the improvement of adolescent health. A well-publicized centralized program repository offered in conjunction with technical assistance would provide an efficient mechanism for this information sharing. We further suggest that the inherent gap between research and practice can be lessened by building a new body of practice knowledge. This would require improved program data collection by programs, the incorporation of program participation information in national surveys and enhanced evaluation efforts.

  13. Database for Safety-Oriented Tracking of Chemicals

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

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

  14. The Existing Approaches to Sexuality Education Targeting Children: A Review Article

    PubMed Central

    GANJI, Jila; EMAMIAN, Mohammad Hassan; MAASOUMI, Raziyeh; KERAMAT, Afsanah; MERGHATI KHOEI, Effat

    2017-01-01

    Background: We aimed to assess what is already known about sexuality education (SE)-related policy or practical issues using review methods to search and critically appraise the existing SE approaches targeting children under age 12 yr. Methods: We completed the data collection by an extensive search of the English and Persian published and unpublished literature, evidence from experts in the topic, and by searching citations. The MeSH-terms were sexuality and training, sexuality education and programs or approaches, sexuality and children, sexuality education and parents, sex or sexuality education, sex education and parents or caregivers. A systematic search of medical and health-related databases, the Cochrane Library and Web of Science was undertaken for the years 1970–2015 together with citation searching, reference list checking and recommendations from stakeholders to identify evidence for SE. Results: According to the inclusion criteria, 20 documents were identified. They were synthesized into three main categories as sexuality-related knowledge, attitudes, and parents’ skills to manage children’s sexual behavior and related education. Employed approaches to children’s sexuality were reported to be effective in developing healthy sexual behavior in children. Education was identified as the primary focus of the included packages and guidelines. Parents were recognized as first line educators in SE. However, interventions aiming to improve parents’ skills in SE for children were limited. In other words, developing skills in parents, and their competency in children’s sexual behavior management were not specified in the existing programs. Conclusion: Parents’ skill-building must be the focus of SE programs in order to address children’ sexual development goals. PMID:28845399

  15. The Existing Approaches to Sexuality Education Targeting Children: A Review Article.

    PubMed

    Ganji, Jila; Emamian, Mohammad Hassan; Maasoumi, Raziyeh; Keramat, Afsanah; Merghati Khoei, Effat

    2017-07-01

    We aimed to assess what is already known about sexuality education (SE)-related policy or practical issues using review methods to search and critically appraise the existing SE approaches targeting children under age 12 yr. We completed the data collection by an extensive search of the English and Persian published and unpublished literature, evidence from experts in the topic, and by searching citations. The MeSH-terms were sexuality and training, sexuality education and programs or approaches, sexuality and children, sexuality education and parents, sex or sexuality education, sex education and parents or caregivers. A systematic search of medical and health-related databases, the Cochrane Library and Web of Science was undertaken for the years 1970-2015 together with citation searching, reference list checking and recommendations from stakeholders to identify evidence for SE. According to the inclusion criteria, 20 documents were identified. They were synthesized into three main categories as sexuality-related knowledge, attitudes, and parents' skills to manage children's sexual behavior and related education. Employed approaches to children's sexuality were reported to be effective in developing healthy sexual behavior in children. Education was identified as the primary focus of the included packages and guidelines. Parents were recognized as first line educators in SE. However, interventions aiming to improve parents' skills in SE for children were limited. In other words, developing skills in parents, and their competency in children's sexual behavior management were not specified in the existing programs. Parents' skill-building must be the focus of SE programs in order to address children' sexual development goals.

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

    PubMed

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

    2017-06-01

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

  17. Characterizing the genetic structure of a forensic DNA database using a latent variable approach.

    PubMed

    Kruijver, Maarten

    2016-07-01

    Several problems in forensic genetics require a representative model of a forensic DNA database. Obtaining an accurate representation of the offender database can be difficult, since databases typically contain groups of persons with unregistered ethnic origins in unknown proportions. We propose to estimate the allele frequencies of the subpopulations comprising the offender database and their proportions from the database itself using a latent variable approach. We present a model for which parameters can be estimated using the expectation maximization (EM) algorithm. This approach does not rely on relatively small and possibly unrepresentative population surveys, but is driven by the actual genetic composition of the database only. We fit the model to a snapshot of the Dutch offender database (2014), which contains close to 180,000 profiles, and find that three subpopulations suffice to describe a large fraction of the heterogeneity in the database. We demonstrate the utility and reliability of the approach with three applications. First, we use the model to predict the number of false leads obtained in database searches. We assess how well the model predicts the number of false leads obtained in mock searches in the Dutch offender database, both for the case of familial searching for first degree relatives of a donor and searching for contributors to three-person mixtures. Second, we study the degree of partial matching between all pairs of profiles in the Dutch database and compare this to what is predicted using the latent variable approach. Third, we use the model to provide evidence to support that the Dutch practice of estimating match probabilities using the Balding-Nichols formula with a native Dutch reference database and θ=0.03 is conservative. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

    PubMed

    Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

    2015-01-01

    In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

  19. A portal for the ocean biogeographic information system

    USGS Publications Warehouse

    Zhang, Yunqing; Grassle, J. F.

    2002-01-01

    Since its inception in 1999 the Ocean Biogeographic Information System (OBIS) has developed into an international science program as well as a globally distributed network of biogeographic databases. An OBIS portal at Rutgers University provides the links and functional interoperability among member database systems. Protocols and standards have been established to support effective communication between the portal and these functional units. The portal provides distributed data searching, a taxonomy name service, a GIS with access to relevant environmental data, biological modeling, and education modules for mariners, students, environmental managers, and scientists. The portal will integrate Census of Marine Life field projects, national data archives, and other functional modules, and provides for network-wide analyses and modeling tools.

  20. Is Library Database Searching a Language Learning Activity?

    ERIC Educational Resources Information Center

    Bordonaro, Karen

    2010-01-01

    This study explores how non-native speakers of English think of words to enter into library databases when they begin the process of searching for information in English. At issue is whether or not language learning takes place when these students use library databases. Language learning in this study refers to the use of strategies employed by…

  1. Parallel database search and prime factorization with magnonic holographic memory devices

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

    Khitun, Alexander

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploitmore » wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.« less

  2. Parallel database search and prime factorization with magnonic holographic memory devices

    NASA Astrophysics Data System (ADS)

    Khitun, Alexander

    2015-12-01

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

  3. Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

    PubMed

    Deutsch, Eric W; Sun, Zhi; Campbell, David S; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S; Moritz, Robert L

    2016-11-04

    The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .

  4. Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

    PubMed Central

    Deutsch, Eric W.; Sun, Zhi; Campbell, David S.; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S.; Moritz, Robert L.

    2016-01-01

    The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances – a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ~20,000 primary isoforms plus contaminants to a very large database that includes almost all non-redundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/. PMID:27577934

  5. STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

    PubMed

    Piehowski, Paul D; Petyuk, Vladislav A; Sandoval, John D; Burnum, Kristin E; Kiebel, Gary R; Monroe, Matthew E; Anderson, Gordon A; Camp, David G; Smith, Richard D

    2013-03-01

    For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. GWFASTA: server for FASTA search in eukaryotic and microbial genomes.

    PubMed

    Issac, Biju; Raghava, G P S

    2002-09-01

    Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists.

  7. Analysis of Users' Searches of CD-ROM Databases in the National and University Library in Zagreb.

    ERIC Educational Resources Information Center

    Jokic, Maja

    1997-01-01

    Investigates the search behavior of CD-ROM database users in Zagreb (Croatia) libraries: one group needed a minimum of technical assistance, and the other was completely independent. Highlights include the use of questionnaires and transaction log analysis and the need for end-user education. The questionnaire and definitions of search process…

  8. JBEI Registry

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

    Ham, Timothy

    2008-12-01

    The JBEI Registry is a software to store and manage to a database of biological parts. It is intended to be used as a web service that is accessed via a web browser. It is also capable of running as a desktop program for a single user. The registry software stores, indexes, categories, and allows users to enter, search, retrieve, and contruct biological constructs in silico. It is also able to communicate with other Registries for data sharing and exchange.

  9. Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

    PubMed Central

    Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

    2012-01-01

    Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

  10. ESTree db: a Tool for Peach Functional Genomics

    PubMed Central

    Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Stella, Alessandra; Milanesi, Luciano; Pozzi, Carlo

    2005-01-01

    Background The ESTree db represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. Results The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. Conclusion The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig. PMID:16351742

  11. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    PubMed

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. ESTree db: a tool for peach functional genomics.

    PubMed

    Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Stella, Alessandra; Milanesi, Luciano; Pozzi, Carlo

    2005-12-01

    The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.

  13. PIPI: PTM-Invariant Peptide Identification Using Coding Method.

    PubMed

    Yu, Fengchao; Li, Ning; Yu, Weichuan

    2016-12-02

    In computational proteomics, the identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process. Alternatively, the other group of methods named unrestricted tools (including MS-Alignment, ProteinProspector, and MODa) avoids enumerating PTM patterns with an alignment-based approach to localizing and characterizing modified amino acids. However, because of the large search space and PTM localization issue, the sensitivity of these unrestricted tools is low. This paper proposes a novel method named PIPI to achieve PTM-invariant peptide identification. PIPI belongs to the category of unrestricted tools. It first codes peptide sequences into Boolean vectors and codes experimental spectra into real-valued vectors. For each coded spectrum, it then searches the coded sequence database to find the top scored peptide sequences as candidates. After that, PIPI uses dynamic programming to localize and characterize modified amino acids in each candidate. We used simulation experiments and real data experiments to evaluate the performance in comparison with restricted tools (i.e., Mascot, Comet, and MS-GF+) and unrestricted tools (i.e., Mascot with error tolerant search, MS-Alignment, ProteinProspector, and MODa). Comparison with restricted tools shows that PIPI has a close sensitivity and running speed. Comparison with unrestricted tools shows that PIPI has the highest sensitivity except for Mascot with error tolerant search and ProteinProspector. These two tools simplify the task by only considering up to one modified amino acid in each peptide, which results in a higher sensitivity but has difficulty in dealing with multiple modified amino acids. The simulation experiments also show that PIPI has the lowest false discovery proportion, the highest PTM characterization accuracy, and the shortest running time among the unrestricted tools.

  14. A methodological survey identified eight proposed frameworks for the adaptation of health related guidelines.

    PubMed

    Darzi, Andrea; Abou-Jaoude, Elias A; Agarwal, Arnav; Lakis, Chantal; Wiercioch, Wojtek; Santesso, Nancy; Brax, Hneine; El-Jardali, Fadi; Schünemann, Holger J; Akl, Elie A

    2017-06-01

    Our objective was to identify and describe published frameworks for adaptation of clinical, public health, and health services guidelines. We included reports describing methods of adaptation of guidelines in sufficient detail to allow its reproducibility. We searched Medline and EMBASE databases. We also searched personal files, as well manuals and handbooks of organizations and professional societies that proposed methods of adaptation and adoption of guidelines. We followed standard systematic review methodology. Our search captured 12,021 citations, out of which we identified eight proposed methods of guidelines adaptation: ADAPTE, Adapted ADAPTE, Alberta Ambassador Program adaptation phase, GRADE-ADOLOPMENT, MAGIC, RAPADAPTE, Royal College of Nursing (RCN), and Systematic Guideline Review (SGR). The ADAPTE framework consists of a 24-step process to adapt guidelines to a local context taking into consideration the needs, priorities, legislation, policies, and resources. The Alexandria Center for Evidence-Based Clinical Practice Guidelines updated one of ADAPTE's tools, modified three tools, and added three new ones. In addition, they proposed optionally using three other tools. The Alberta Ambassador Program adaptation phase consists of 11 steps and focused on adapting good-quality guidelines for nonspecific low back pain into local context. GRADE-ADOLOPMENT is an eight-step process based on the GRADE Working Group's Evidence to Decision frameworks and applied in 22 guidelines in the context of national guideline development program. The MAGIC research program developed a five-step adaptation process, informed by ADAPTE and the GRADE approach in the context of adapting thrombosis guidelines. The RAPADAPTE framework consists of 12 steps based on ADAPTE and using synthesized evidence databases, retrospectively derived from the experience of producing a high-quality guideline for the treatment of breast cancer with limited resources in Costa Rica. The RCN outlines five key steps strategy for adaptation of guidelines to the local context. The SGR method consists of nine steps and takes into consideration both methodological gaps and context-specific normative issues in source guidelines. We identified through searching personal files two abandoned methods. We identified and described eight proposed frameworks for the adaptation of health-related guidelines. There is a need to evaluate these different frameworks to assess rigor, efficiency, and transparency of their proposed processes. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. A Systematic Review of Extramural Presentations and Publications from Pharmacy Student Research Programs

    PubMed Central

    Martin, Jennifer; Worede, Leah; Islam, Sameer

    2016-01-01

    Objective. To conduct a systematic review of reports of pharmacy student research programs that describes the programs and resulting publications or presentations. Methods. To be eligible for the review, reports had to be in English and indicate that students were required to collect, analyze data, and report or present findings. The outcome variables were extramural posters/presentations and publications. Results. Database searches resulted in identification of 13 reports for 12 programs. Two-thirds were reports of projects required for a course or for graduation, and the remaining third were elective (participation was optional). Extramural posters resulted from 75% of the programs and publications from 67%. Conclusion. Although reporting on the outcomes of student research programs is limited, three-quarters of the programs indicated that extramural presentations, publications, or both resulted from student research. Additional research is needed to identify relevant outcomes of student research programs in pharmacy. PMID:27667837

  16. A Systematic Review of Extramural Presentations and Publications from Pharmacy Student Research Programs.

    PubMed

    Slack, Marion K; Martin, Jennifer; Worede, Leah; Islam, Sameer

    2016-08-25

    Objective. To conduct a systematic review of reports of pharmacy student research programs that describes the programs and resulting publications or presentations. Methods. To be eligible for the review, reports had to be in English and indicate that students were required to collect, analyze data, and report or present findings. The outcome variables were extramural posters/presentations and publications. Results. Database searches resulted in identification of 13 reports for 12 programs. Two-thirds were reports of projects required for a course or for graduation, and the remaining third were elective (participation was optional). Extramural posters resulted from 75% of the programs and publications from 67%. Conclusion. Although reporting on the outcomes of student research programs is limited, three-quarters of the programs indicated that extramural presentations, publications, or both resulted from student research. Additional research is needed to identify relevant outcomes of student research programs in pharmacy.

  17. Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

    PubMed Central

    Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

    2012-01-01

    The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

  18. Healing the community to heal the individual: literature review of aboriginal community-based alcohol and substance abuse programs.

    PubMed

    Jiwa, Ashifa; Kelly, Len; Pierre-Hansen, Natalie

    2008-07-01

    To understand the development of culturally based and community-based alcohol and substance abuse treatment programs for aboriginal patients in an international context. MEDLINE, HealthSTAR, and PsycINFO databases and government documents were searched from 1975 to 2007. MeSH headings included the following: Indians, North American, Pacific ancestry group, aboriginal, substance-related disorders, alcoholism, addictive behaviour, community health service, and indigenous health. The search produced 150 articles, 34 of which were relevant; most of the literature comprised opinion pieces and program descriptions (level III evidence). Substance abuse in some aboriginal communities is a complex problem requiring culturally appropriate, multidimensional approaches. One promising perspective supports community-based programs or community mobile treatment. These programs ideally cover prevention, harm reduction, treatment, and aftercare. They often eliminate the need for people to leave their remote communities. They become focuses of community development, as the communities become the treatment facilities. Success requires solutions developed within communities, strong community interest and engagement, leadership, and sustainable funding. Community-based addictions programs are appropriate alternatives to treatment at distant residential addictions facilities. The key components of success appear to be strong leadership in this area; strong community-member engagement; funding for programming and organizing; and the ability to develop infrastructure for longterm program sustainability. Programs require increased documentation of their inroads in this developing field.

  19. The impact of residency programs on new nurse graduates' clinical decision-making and leadership skills: a systematic review.

    PubMed

    AL-Dossary, Reem; Kitsantas, Panagiota; Maddox, P J

    2014-06-01

    Health care institutions have adapted residency programs to help new graduate nurses to become fully competent and transition from a student nurse to an independent practicing nurse and a bedside leader. The study's aim is to review the literature on the impact of residency programs on new graduate nurses' clinical decision-making and leadership skills. An electronic search was conducted between 1980 and 2013 using databases of the scientific literature in Medline, PubMed, Cochrane EPOC, Cumulative Index to Nursing & Allied Health Literature database guide (CINAHL), and PsychInfo using a range of keywords. Information gathered was evaluated for relevance. Thirteen studies that met the inclusion criteria were used in this systematic review. In several studies considered in this review, residency programs were developed to improve new graduates skills and promote their transition into the nursing workforce. In fact, the transition programs reduced turnover in that first year of practice and promoted professional growth of the new graduate such as hand-on nursing skills, clinical decision-making and leadership skills, satisfaction, and retention. There is a need for effective residency programs that are designed to prepare new graduate nurses in providing safe, competent and effective patient care. © 2013.

  20. Tautomerism in chemical information management systems

    NASA Astrophysics Data System (ADS)

    Warr, Wendy A.

    2010-06-01

    Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.

  1. GenBank.

    PubMed

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

    2007-01-01

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

  2. GenBank.

    PubMed

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

    2005-01-01

    GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

  3. GenBank.

    PubMed

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

    2006-01-01

    GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  5. Analysis Tool Web Services from the EMBL-EBI.

    PubMed

    McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

    2013-07-01

    Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

  6. Analysis Tool Web Services from the EMBL-EBI

    PubMed Central

    McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

    2013-01-01

    Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

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

    PubMed

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

    2009-02-01

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

  8. TRENDS: A flight test relational database user's guide and reference manual

    NASA Technical Reports Server (NTRS)

    Bondi, M. J.; Bjorkman, W. S.; Cross, J. L.

    1994-01-01

    This report is designed to be a user's guide and reference manual for users intending to access rotocraft test data via TRENDS, the relational database system which was developed as a tool for the aeronautical engineer with no programming background. This report has been written to assist novice and experienced TRENDS users. TRENDS is a complete system for retrieving, searching, and analyzing both numerical and narrative data, and for displaying time history and statistical data in graphical and numerical formats. This manual provides a 'guided tour' and a 'user's guide' for the new and intermediate-skilled users. Examples for the use of each menu item within TRENDS is provided in the Menu Reference section of the manual, including full coverage for TIMEHIST, one of the key tools. This manual is written around the XV-15 Tilt Rotor database, but does include an appendix on the UH-60 Blackhawk database. This user's guide and reference manual establishes a referrable source for the research community and augments NASA TM-101025, TRENDS: The Aeronautical Post-Test, Database Management System, Jan. 1990, written by the same authors.

  9. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2010-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov.

  10. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2009-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

  11. PubChemSR: A search and retrieval tool for PubChem

    PubMed Central

    Hur, Junguk; Wild, David J

    2008-01-01

    Background Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR. Implementation PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem. Results and Discussion The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. PMID:18482452

  12. Searching for alien artifacts on the moon

    NASA Astrophysics Data System (ADS)

    Davies, P. C. W.; Wagner, R. V.

    2013-08-01

    The Search for Extraterrestrial Intelligence (SETI) has a low probability of success, but it would have a high impact if successful. Therefore it makes sense to widen the search as much as possible within the confines of the modest budget and limited resources currently available. To date, SETI has been dominated by the paradigm of seeking deliberately beamed radio messages. However, indirect evidence for extraterrestrial intelligence could come from any incontrovertible signatures of non-human technology. Existing searchable databases from astronomy, biology, earth and planetary sciences all offer low-cost opportunities to seek a footprint of extraterrestrial technology. In this paper we take as a case study one particular new and rapidly-expanding database: the photographic mapping of the Moon's surface by the Lunar Reconnaissance Orbiter (LRO) to 0.5 m resolution. Although there is only a tiny probability that alien technology would have left traces on the moon in the form of an artifact or surface modification of lunar features, this location has the virtue of being close, and of preserving traces for an immense duration. Systematic scrutiny of the LRO photographic images is being routinely conducted anyway for planetary science purposes, and this program could readily be expanded and outsourced at little extra cost to accommodate SETI goals, after the fashion of the SETI@home and Galaxy Zoo projects.

  13. Beyond the "I" in the obesity epidemic: a review of social relational and network interventions on obesity.

    PubMed

    Leroux, Janette S; Moore, Spencer; Dubé, Laurette

    2013-01-01

    Recent research has shown the importance of networks in the spread of obesity. Yet, the translation of research on social networks and obesity into health promotion practice has been slow. To review the types of obesity interventions targeting social relational factors. Six databases were searched in January 2013. A Boolean search was employed with the following sets of terms: (1) social dimensions: social capital, cohesion, collective efficacy, support, social networks, or trust; (2) intervention type: intervention, experiment, program, trial, or policy; and (3) obesity in the title or abstract. Titles and abstracts were reviewed. Articles were included if they described an obesity intervention with the social relational component central. Articles were assessed on the social relational factor(s) addressed, social ecological level(s) targeted, the intervention's theoretical approach, and the conceptual placement of the social relational component in the intervention. Database searches and final article screening yielded 30 articles. Findings suggested that (1) social support was most often targeted; (2) few interventions were beyond the individual level; (3) most interventions were framed on behaviour change theories; and (4) the social relational component tended to be conceptually ancillary to the intervention. Theoretically and practically, social networks remain marginal to current interventions addressing obesity.

  14. Predicting Glycerophosphoinositol Identities in Lipidomic Datasets Using VaLID (Visualization and Phospholipid Identification)—An Online Bioinformatic Search Engine

    PubMed Central

    McDowell, Graeme S. V.; Taylor, Graeme P.; Fai, Stephen; Bennett, Steffany A. L.

    2014-01-01

    The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID) bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid classes: glycerophosphates, glyceropyrophosphates, glycerophosphocholines, glycerophosphoethanolamines, glycerophosphoglycerols, glycerophosphoglycerophosphates, glycerophosphoserines, and cytidine 5′-diphosphate 1,2-diacyl-sn-glycerols to be searched for any mass to charge value (with adjustable tolerance levels) under a variety of mass spectrometry conditions. Here, we describe an update that now includes all possible glycerophosphoinositols, glycerophosphoinositol monophosphates, glycerophosphoinositol bisphosphates, and glycerophosphoinositol trisphosphates. This update expands the total number of lipid species represented in the VaLID v2.0.0 database to 1,473,168 phospholipids. Each phospholipid can be generated in skeletal representation. A subset of species curated by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL) team is provided as an array of high-resolution structures. VaLID is freely available and responds to all users through the CTPNL resources web site. PMID:24701584

  15. Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine.

    PubMed

    McDowell, Graeme S V; Blanchard, Alexandre P; Taylor, Graeme P; Figeys, Daniel; Fai, Stephen; Bennett, Steffany A L

    2014-01-01

    The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID) bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid classes: glycerophosphates, glyceropyrophosphates, glycerophosphocholines, glycerophosphoethanolamines, glycerophosphoglycerols, glycerophosphoglycerophosphates, glycerophosphoserines, and cytidine 5'-diphosphate 1,2-diacyl-sn-glycerols to be searched for any mass to charge value (with adjustable tolerance levels) under a variety of mass spectrometry conditions. Here, we describe an update that now includes all possible glycerophosphoinositols, glycerophosphoinositol monophosphates, glycerophosphoinositol bisphosphates, and glycerophosphoinositol trisphosphates. This update expands the total number of lipid species represented in the VaLID v2.0.0 database to 1,473,168 phospholipids. Each phospholipid can be generated in skeletal representation. A subset of species curated by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL) team is provided as an array of high-resolution structures. VaLID is freely available and responds to all users through the CTPNL resources web site.

  16. The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

    PubMed

    Orsini, Massimiliano; Carcangiu, Simone; Cuccuru, Gianmauro; Uva, Paolo; Tramontano, Anna

    2013-01-01

    BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.

  17. Risk factors, incidence, consequences and prevention strategies for falls and fall-injury within older indigenous populations: a systematic review.

    PubMed

    Lukaszyk, Caroline; Harvey, Lara; Sherrington, Cathie; Keay, Lisa; Tiedemann, Anne; Coombes, Julieann; Clemson, Lindy; Ivers, Rebecca

    2016-12-01

    To examine the risk factors, incidence, consequences and existing prevention strategies for falls and fall-related injury in older indigenous people. Relevant literature was identified through searching 14 electronic databases, a range of institutional websites, online search engines and government databases, using search terms pertaining to indigenous status, injury and ageing. Thirteen studies from Australia, the United States, Central America and Canada were identified. Few studies reported on fall rates but two reported that around 30% of indigenous people aged 45 years and above experienced at least one fall during the past year. The most common hospitalised fall injuries among older indigenous people were hip fracture and head injury. Risk factors significantly associated with falls within indigenous populations included poor mobility, a history of stroke, epilepsy, head injury, poor hearing and urinary incontinence. No formally evaluated, indigenous-specific fall prevention interventions were identified. Falls are a significant and growing health issue for older indigenous people worldwide that can lead to severe health consequences and even death. No fully-evaluated, indigenous-specific fall prevention programs were identified. Implications for Public Health: Research into fall patterns and fall-related injury among indigenous people is necessary for the development of appropriate fall prevention interventions. © 2016 Public Health Association of Australia.

  18. A Search for Transiting Neptune-Mass Extrasolar Planets in High-Precision Photometry of Solar-Type Stars

    NASA Technical Reports Server (NTRS)

    Henry, Stephen M.; Gillman, Amelie r.; Henry, Gregory W.

    2005-01-01

    Tennessee State University operates several automatic photometric telescopes (APTs) at Fairborn Observatory in southern Arizona. Four 0.8 m APTs have been dedicated to measuring subtle luminosity variations that accompany magnetic cycles in solar-type stars. Over 1000 program and comparison stars have been observed every clear night in this program for up to 12 years with a precision of approximately 0.0015 mag for a single observation. We have developed a transit-search algorithm, based on fitting a computed transit template for each trial period, and have used it to search our photometric database for transits of unknown companions. Extensive simulations with the APT data have shown that we can reliably recover transits with periods under 10 days as long as the transits have a depth of at least 0.0024 mag, or about 1.6 times the scatter in the photometric observations. Thus, due to our high photometric precision, we are sensitive to transits of possible short-period Neptune-mass planets that likely would have escaped detection by current radial velocity techniques. Our search of the APT data sets for 1087 program and comparison stars revealed no new transiting planets. However, the detection of several unknown grazing eclipsing binaries from among our comparison stars, with eclipse depths of only a few millimags, illustrates the success of our technique. We have used this negative result to place limits on the frequency of Neptune-mass planets in close orbits around solar-type stars in the Sun's vicinity.

  19. G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases.

    PubMed

    Wang, Xiaohong; Smalter, Aaron; Huan, Jun; Lushington, Gerald H

    2009-01-01

    Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML documents, among others.Most of the current graph indexing methods focus on subgraph query processing, i.e. determining the set of database graphs that contains the query graph and hence do not directly support similarity search. In data mining and machine learning, various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models for supervised learning, graph kernel functions have (i) high computational complexity and (ii) non-trivial difficulty to be indexed in a graph database.Our objective is to bridge graph kernel function and similarity search in graph databases by proposing (i) a novel kernel-based similarity measurement and (ii) an efficient indexing structure for graph data management. Our method of similarity measurement builds upon local features extracted from each node and their neighboring nodes in graphs. A hash table is utilized to support efficient storage and fast search of the extracted local features. Using the hash table, a graph kernel function is defined to capture the intrinsic similarity of graphs and for fast similarity query processing. We have implemented our method, which we have named G-hash, and have demonstrated its utility on large chemical graph databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Most importantly, the new similarity measurement and the index structure is scalable to large database with smaller indexing size, faster indexing construction time, and faster query processing time as compared to state-of-the-art indexing methods such as C-tree, gIndex, and GraphGrep.

  20. Cost and Search Result Comparisons of BRS After Dark and Knowledge Index.

    ERIC Educational Resources Information Center

    Cloud, Gayla Staples; Hambric, Jacqueline

    This two-part study was designed (1) to determine differences in the costs of searching BRS After Dark (BRS AD) and Knowledge Index (KI) generally and across ten selected databases, and (2) to determine whether there is a difference in the citations retrieved when the same search is conducted on the same database in both systems. Study methodology…

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