Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Reference database”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81Linked to original sources
PubMed1998

Latin American biomedical publications: the case of Colombia in Medline.

Latin America generates a low proportion of the references quoted in Medline, the most popular health-related literature search database in the world. This paper explores references from and about Colombia in Medline during the period 1987-1996. Topics addressed, patterns of authorship and research locations are established. The number of Latin American journals indexed in Medline has been progressively reduced during this 10-year period, with Colombian journals completely excluded since 1991. During this 10-year period, the total output of Colombian research institutions in foreign journals consisted of 531 articles, 41% (219) of which come from the four leading universities. These figures are substantially lower than those from other countries of the region such as Venezuela or Chile. Despite some governmental efforts, Colombia continues to have a low scientific output and has yet to attract the interest of foreign researchers. Alternatives for development of Latin American research and publications are offered.

Colombia↗
PubMed2003

Gene indexing: characterization and analysis of NLM's GeneRIFs.

We present an initial analysis of the National Library of Medicine's (NLM) Gene Indexing initiative. Gene Indexing occurs at the time of indexing for all 4600 journals and over 500,000 articles added to PubMed/MEDLINE each year. Gene Indexing links articles about the basic biology of a gene or protein within eight model organisms to a specific record in the NLM's LocusLink database of gene products. The result is an entry called a Gene Reference Into Function (GeneRIF) within the LocusLink database. We analyzed the numbers of GeneRIFs produced in the first year of GeneRIF production. 27,645 GeneRIFs were produced, pertaining to 9126 loci over eight model organisms. 60% of these were associated with human genes and 27% with mouse genes. About 80% discuss genes with an established MeSH Heading or other MeSH term. We developed a prototype functional alerting system for researchers based on the GeneRIFs, and a strategy to find all of the literature related to genes. We conclude that the Gene Indexing initiative adds considerable value to the life sciences research community.

Abstracting and Indexing↗
PubMed2005

Effectiveness of different databases in identifying studies for systematic reviews: experience from the WHO systematic review of maternal morbidity and mortality.

BACKGROUND: Failure to be comprehensive can distort the results of a systematic review. Conversely, extensive searches may yield unmanageable number of citations of which only few may be relevant. Knowledge of usefulness of each source of information may help to tailor search strategies in systematic reviews. METHODS: We conducted a systematic review of prevalence/incidence of maternal mortality and morbidities from 1997 to 2002. The search strategy included electronic databases, hand searching, screening of reference lists, congress abstract books, contacting experts active in the field and web sites from less developed countries. We evaluated the effectiveness of each source of data and discuss limitations and implications for future research on this topic. RESULTS: Electronic databases identified 64098 different citations of which 2093 were included. Additionally 487 citations were included from other sources. MEDLINE had the highest yield identifying about 62% of the included citations. BIOSIS was the most precise with 13.2% of screened citations included. Considering electronic citations alone (2093), almost 20% were identified uniquely by MEDLINE (400), 7.4% uniquely by EMBASE (154), and 5.6% uniquely by LILACS (117). About 60% of the electronic citations included were identified by two or more databases. CONCLUSIONS: This analysis confirms the need for extending the search to other sources beyond well-known electronic databases in systematic reviews of maternal mortality and morbidity prevalence/incidence. These include regional databases such as LILACS and other topic specific sources such as hand searching of relevant journals not indexed in electronic databases. Guidelines for search strategies for prevalence/incidence studies need to be developed.

Female↗
PubMed2005

Rice proteome analysis: a step toward functional analysis of the rice genome.

The technique of proteome analysis using 2-DE has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this review, we describe construction of the rice proteome database, the cataloging of rice proteins, and the functional characterization of some of the proteins identified. Initially, proteins extracted from various tissues and organelles were separated by 2-DE and an image analyzer was used to construct a display or reference map of the proteins. The rice proteome database currently contains 23 reference maps based on 2-DE of proteins from different rice tissues and subcellular compartments. These reference maps comprise 13 129 rice proteins, and the amino acid sequences of 5092 of these proteins are entered in the database. Major proteins involved in growth or stress responses have been identified by using a proteomics approach and some of these proteins have unique functions. Furthermore, initial work has also begun on analyzing the phosphoproteome and protein-protein interactions in rice. The information obtained from the rice proteome database will aid in the molecular cloning of rice genes and in predicting the function of unknown proteins.

Calreticulin↗
PubMed2004

Searching multiple databases for systematic reviews: added value or diminishing returns?

OBJECTIVE: To explore whether searching specialised bibliographic databases identified additional relevant papers to those located by a Medline search for a systematic review of exercise therapy. METHOD: Searches were performed in Medline, two further generalised medical databases (Embase, Cochrane Library) and four specialised databases (CancerLit, Cinahl, PsychInfo, SportDiscus) to identify controlled trials of exercise interventions for cancer patients. RESULTS: A total of 749 different publications were located through the search, of which 18 met inclusion criteria. Fifteen (83%) of these were identified through Medline and three (17%) from three individual specialised databases. A further seven studies meeting inclusion criteria were located through reference lists and contact with experts. CONCLUSION: In this example, searching Medline and additional specialised databases along with checking reference lists and contacting experts was the most effective means of ensuring that all relevant papers were included in the review. Searching Medline alone for systematic reviews of exercise or other unconventional therapies is likely to be inadequate.

Databases, Bibliographic↗
PubMed2006

ISfinder: the reference centre for bacterial insertion sequences.

ISfinder (www-is.biotoul.fr) is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.

DNA Transposable Elements↗
PubMed1983

Selection of scientific periodicals to monitor drug safety information using Excerpta Medica and Japicdoc in the post marketing surveillance of drugs.

In order to select important journals to be monitored for efficient collection of literature information on drug safety, a retrospective search was made of the safety information in the Excerpta Medica (EM) database between 1979 and 1981. The search provided 54,005 references to drug safety, which were found in a total of 2,536 journals. Fifty percent of the references appeared in only 148 journals, or 6% of all journals surveyed. A similar search, carried out using the Japicdoc (JD) database, provided 9,268 references in 172 journals. To cover all the necessary information appearing in overseas journals, however, a retrospective search of a bibliographic database is required as a cost-effective means to improve the comprehensiveness of the collection of information. In domestic journals, because JD includes fewer journals than EM, all of the 172 journals can be monitored for the collection of drug safety information.

Consumer Product Safety↗
PubMed2000

Tyrosine supplementation for phenylketonuria.

BACKGROUND: Phenylketonuria is an inherited disease for which the main treatment is the dietary restriction of the amino acid phenylalanine. The diet has to be initiated in the neonatal period to prevent or reduce mental handicap however the diet is very restrictive and unpalatable and can be difficult to follow. A deficiency of the amino acid tyrosine has been suggested as a cause of some of the neuropsychological problems exhibited in PKU. Therefore, this review aims to assess the efficasy of tyrosine supplementation for phenylketonuria. OBJECTIVES: To assess the effects of tyrosine supplementation alongside or instead of phenylalanine restricted diet for patients with phenylketonuria who commenced on diet at diagnosis and either continued on the diet or relaxed the diet later in life. To assess the evidence that tyrosine supplementation alongside, or instead of phenylalanine restricted diet improves intelligence, neuropsychological performance, growth and nutritional status, mortality rate and quality of life. SEARCH STRATEGY: We searched the Cochrane Cystic Fibrosis and Genetic Disorders Trials Register which is a specialist trials register which comprises references identified from comprehensive electronic database searches, handsearching relevant journals and handsearching abstract books of conference proceedings. Additional studies were identified from handsearching the Journal of Inherited Metabolic Disease (from inception, 1978, to 1998). The manufacturers of prescribable dietary products used in the treatment of phenylketonuria were also contacted for further references. Date of the most recent search of the Group's specialised register: November 1999. SELECTION CRITERIA: All randomised or pseudo-randomised trials investigating the use of tyrosine supplementation versus placebo in patients with phenylketonuria in addition to, or instead of, a phenylalanine restricted diet. Patients treated for maternal phenylketonuria were excluded. DATA COLLECTION AND ANALYSIS: Two reviewers independently assessed the trial eligibility, methodological quality and extracted the data. MAIN RESULTS: Two trials were included with a total of 47 patients. The blood tyrosine concentrations were significantly higher in the patients receiving tyrosine supplements than those in the placebo group (weighted mean difference 22.526, 95% Confidence interval (CI) 12.182 - 32.870). No significant differences were found between any of the other outcomes measured. REVIEWER'S CONCLUSIONS: From the available evidence no recommendations can be made about whether tyrosine supplementation should be introduced into routine clinical practice. Further randomised controlled studies are required to provide further evidence.

Dietary Supplements↗
PubMed2005

Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard.

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

Databases as Topic↗
PubMed2003

Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases.

The increasing popularity of DNA chip technology for the study of gene expression is producing, for each experiment, a sizable quantity of numerical data to analyse and an accompanying large number of gene identifiers that should be associated with the relevant biological annotation. We describe here a website at IFOM (FIRC Institute of Molecular Oncology) where we release regularly updated annotation tables for the most used Affymetrix oligonucleotide DNA chips and for the whole Research Genetics 46K clone collection for cDNA arrays. These tables are synchronised with every new release of the mouse and human UniGene databases (NCBI; National Center for Biotechnology Information), allowing fast and easy preliminary annotation of DNA array experiments. We also report some comparative evidence about the importance of biological database synchronisation and cross-references in the process of generating annotation tables for DNA chips.

Abstracting and Indexing↗
PubMed2000

MITOP, the mitochondrial proteome database: 2000 update.

MITOP (http://www.mips.biochem.mpg.de/proj/medgen/mitop/) is a comprehensive database for genetic and functional information on both nuclear- and mitochondrial-encoded proteins and their genes. The five species files--Saccharomyces cerevisiae, Mus musculus, Caenorhabditis elegans, Neurospora crassa and Homo sapiens--include annotated data derived from a variety of online resources and the literature. A wide spectrum of search facilities is given in the overlapping sections 'Gene catalogues', 'Protein catalogues', 'Homologies', 'Pathways and metabolism' and 'Human disease catalogue' including extensive references and hyperlinks to other databases. Central features are the results of various homology searches, which should facilitate the investigations into interspecies relationships. Precomputed FASTA searches using all the MITOP yeast protein entries and a list of the best human EST hits with graphical cluster alignments related to the yeast reference sequence are presented. The orthologue tables with cross-listings to all the protein entries for each species in MITOP have been expanded by adding the genomes of Rickettsia prowazeckii and Escherichia coli. To find new mitochondrial proteins the complete yeast genome has been analyzed using the MITOPROT program which identifies mitochondrial targeting sequences. The 'Human disease catalogue' contains tables with a total of 110 human diseases related to mitochondrial protein abnormalities, sorted by clinical criteria and age of onset. MITOP should contribute to the systematic genetic characterization of the mitochondrial proteome in relation to human disease.

Animals↗
PubMed2003

TSGDB: a database system for tumor suppressor genes.

UNLABELLED: A Web-based database system was constructed and implemented that contains 174 tumor suppressor genes. The database homepage was created to accommodate these genes in a pull-down window so that each gene can be viewed individually in a separate Web page. Information displayed on each page includes gene name, aliases, source organism, chromosome location, expression cells/tissues, gene structure, protein size, gene functions and major reference sources. Queries to the database can be conducted through a user-friendly interface, and query results are returned in the HTML format on dynamically generated web pages. AVAILABILITY: The database is available at http://www.cise.ufl.edu/~yy1/HTML-TSGDB/Homepage.html (data files also at http://www.patcar.org/Databases/Tumor_Suppressor_Genes)

Abstracting and Indexing↗
PubMed2006

The influence of contrasting suspended particulate matter transport regimes on the bias and precision of flux estimates.

A large database (507 station-years) of daily suspended particulate matter (SPM) concentration and discharge data from 36 stations on river basins ranging from 600 km(2) to 600,000 km(2) in size (USA and Europe) was collected to assess the effects of SPM transport regime on bias and imprecision of flux estimates when using infrequent surveys and the discharge-weighted mean concentration method. By extracting individual SPM concentrations and corresponding discharge values from the database, sampling frequencies from 12 to 200 per year were simulated using Monte Carlo techniques. The resulting estimates of yearly SPM fluxes were compared to reference fluxes derived from the complete database. For each station and given frequency, bias was measured by the median of relative errors between estimated and reference fluxes, and imprecision by the difference between the upper and lower deciles of relative errors. Results show that the SPM transport regime of rivers affects the bias and imprecision of fluxes estimated by the discharge-weighted mean concentration method for given sampling frequencies (e.g. weekly, bimonthly, monthly). The percentage of annual SPM flux discharged in 2% of time (Ms(2)) is a robust indicator of SPM transport regime directly related to bias and imprecision. These errors are linked to the Ms(2) indicator for various sampling frequencies within a specific nomograph. For instance, based on a deviation of simulated flux estimates from reference fluxes lower than +/-20% and a bias lower than 1% or 2%, the required sampling intervals are less than 3 days for rivers with Ms(2) greater than 40% (basin size<10,000 km(2)), between 3 and 5 days for rivers with Ms(2) between 30 and 40% (basin size between 10,000 and 50,000 km(2)), between 5 and 12 days for Ms(2) from 20% to 30% (basin size between 50,000 and 200,000 km(2)), 12-20 days for Ms(2) in the 15-20% range (basin size between 200,000 and 500,000 km(2)).

France↗
PubMed2000

The European small subunit ribosomal RNA database.

The European database of the Small Subunit (SSU) Ribosomal RNA is a curated database that strives to collect all information about the primary and secondary structure of completely or nearly-completely sequenced rRNAs. Furthermore, the database compiles additional information such as literature references and taxonomic status of the organism the sequence was derived from. The database can be consulted via the WWW at URL http://rrna.uia.ac.be/ssu/. Through the WWW, sequences can be easily selected either one by one, by taxonomic group, or by a combination of both, and can be retrieved in different sequence and alignment formats.

Databases, Factual↗
PubMed2005

Vitamin K for upper gastrointestinal bleeding in patients with liver diseases.

BACKGROUND: Upper gastrointestinal bleeding is one of the most frequent causes of morbidity and mortality in the course of liver cirrhosis. Several treatments are used for upper gastrointestinal bleeding in patients with liver diseases. However, supplementary interventions are often used as well. One of them is vitamin K administration, but it is unknown whether it benefits or harms patients with liver disease and upper gastrointestinal bleeding. OBJECTIVES: To assess the beneficial and harmful effects of vitamin K for patients with liver disease and upper gastrointestinal bleeding. SEARCH STRATEGY: We searched The Cochrane Hepato-Biliary Group Controlled Trials Register (February 2004), which comprises references identified from comprehensive electronic database searches and handsearching of relevant journals and abstract books of conference proceedings, The Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library (Issue 1, 2004), MEDLINE (1966 to March 2004), EMBASE (1988 to March 2004), and LILACS (1982 to March 2004). Additional randomised trials were sought from the reference lists of the trials found and reviews identified by the electronic searches. SELECTION CRITERIA: We intended to include randomised clinical trials. DATA COLLECTION AND ANALYSIS: We intended to summarise data by standard Cochrane Collaboration methodologies. MAIN RESULTS: We could not find any randomised trials on vitamin K for upper gastrointestinal bleeding in patients with liver diseases. AUTHORS' CONCLUSIONS: We were unable to identify randomised trials on the safety and efficacy of vitamin K for upper gastrointestinal bleeding in patients with liver diseases. The effects of vitamin K need to be tested in randomised clinical trials.

Antifibrinolytic Agents↗
PubMedDate not supplied

[Changes in nursing administration in supporting transplantation in Brazil].

This historical and bibliographic study aimed to understand how Nursing was organized to support care in transplantation. The HISA, LILACS, BDENF, PERIENF and DEDALUS databases were consulted, and thirteen references were found, ten of which were scientific articles, two were master's dissertations and one was a doctoral thesis. The span of time chosen for study ranges from the date of the first kidney transplant in Brazil (1965), to the date of publication of the last scientific article found in the databases mentioned above (2003). After reading these articles, the ones that were similar in topic were grouped together, thus creating the thematic axis for the presentation of the results. The results showed that the Nursing profession has played an important and active role in transplants ever since the first procedure in 1965.

Brazil↗
PubMedDate not supplied

Design and realization of an on-line database for multidimensional microscopic images of biological specimens.

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.

Animals↗