SEARCH · PubMed Health

Results for “Search Engine”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 307 records · Page 17Linked to original sources

PubMed1997

Information mining on the Internet.

As with most software, developers tend to create interfaces which seem logical and user-friendly. The only problem is that 'logical' to one person is confusing to another. The best approach is try out several search engines and spend enough time trying sample searches that you get a feel for the degree to which it satisfies your needs. All of these sites have adequate help areas and should be your first stop. Hopefully, these tools will help you to spend less time aimlessly surfing and more time realizing the potential of the Internet.

Computer Communication Networks↗

PubMed1996

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

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.

Computer Communication Networks↗

PubMed2025

OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem.

SUMMARY: The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently, there has been a significant increase in the size and complexity of ontologies due to new scales of biological knowledge, such as spatial transcriptomics, new ontology development methodologies, and curation on an increased scale. Existing Web-based tools for ontology browsing such as BioPortal and OntoBee do not support the full range of definitions used by today's ontologies. In order to support the community going forward, we have developed OLS4, implementing the complete OWL2 specification, internationalization support for multiple languages, and a new user interface with UX enhancements such as links out to external databases. OLS4 has replaced OLS3 in production at EMBL-EBI and has a backward compatible API supporting users of OLS3 to transition. AVAILABILITY AND IMPLEMENTATION: The source code of OLS is available at https://github.com/EBISPOT/ols4 and DOI 10.5281/zenodo.14960290 with Apache 2.0 License. A freely available implementation is accessible at https://www.ebi.ac.uk/ols4.

Biological Ontologies↗

PubMed2005

Combined vitamin B6-magnesium treatment in autism spectrum disorder.

BACKGROUND: The use of mega-vitamin intervention began in the 1950s with the treatment of schizophrenic patients. Pyroxidine (vitamin B6) was first used with children diagnosed with "autism syndrome" when speech and language improvement was observed in some children as a result of large doses of B6. A number of studies attempted to assess the effects of vitamin B6-Magnesium (Mg) was found to reduce undesirable side effects from B6) on characteristics such as verbal communication, non-verbal communication, interpersonal skills, and physiological function, in individuals with autism. OBJECTIVES: To determine the efficacy of vitamin B6 and magnesium (B6-Mg) for treating social, communication, and behavioural responses of children and adults with autism. SEARCH STRATEGY: We searched the Cochrane Controlled Trials Register (Cochrane Library, Issue 2, 2002), MEDLINE (1966 to January 2002), EMBASE (1980 to January 2002), PsycINFO (1887 to January 2002), Dissertation Abstracts International (1861 to January 2002). The search engine FirstSearch was also used (January 2002). All searches were updated in April 2005. Reference lists for all the obtained studies and other review articles were examined for additional studies. SELECTION CRITERIA: All studies in which the participants had been diagnosed with autistic spectrum disorder were randomly allocated prior to intervention and in which outcomes were compared to either a placebo or non-treated group were included. DATA COLLECTION AND ANALYSIS: Two reviewers independently evaluated and extracted data from all potential studies identified for inclusion. MAIN RESULTS: This update includes a new trial (Kuriyama 2002) to bring the total of included studies to three (total n=33). One study, which used a cross-over design (Tolbert 1993) provided insufficient data to conduct an analysis. Another crossover study (Findling 1997) yielded no significant differences between treatment and placebo group performances following the B6 intervention on measures of social interaction, communication, compulsivity, impulsivity, or hyperactivity. The latest study (Kuriyama 2002) was motivated by evidence from epilepsy research and was focussed on a subgroup of children with pervasive developmental disorders (PDDs) who exhibited clinical features similar to those with pyroxidine-dependent epilepsy. This small study (n=8) only measured IQ and 'Social Quotient' and found a statistically significant benefit for IQ (5.2, 95% CI = [0.2 to 10.3]) when in the treated group, by using change scores. AUTHORS' CONCLUSIONS: Due to the small number of studies, the methodological quality of studies, and small sample sizes, no recommendation can be advanced regarding the use of B6-Mg as a treatment for autism.

Adult↗

PubMed2005

Can we trust cancer information on the Internet?--A comparison of interactive cancer risk sites.

OBJECTIVE: To investigate the prevalence and quality of interactive cancer risk sites on the Internet. METHODS: A cancer risk site was defined as a website that gave an estimate of the individual risk of developing cancer. Six search engines and one Meta crawler were used to search the Internet for cancer risk sites (including breast, prostate, colon, and lung cancer). A set of defined quality criteria for health related websites was used to evaluate the websites during 2001 and 2002. RESULTS: The number of cancer risk sites, as defined above, increased by 50% between 2001 and 2002. Only two out of 22 cancer risk sites fulfilled the quality criteria adequately. No signs of a change in trend (with regard to the quality criteria met) were noted in January 2005. CONCLUSIONS: The overall quality of the documentation on the cancer risk sites was poor and no improvement was seen during the study period. The majority of the cancer risk sites do not give reliable risk estimates.

Humans↗

PubMed2000

PIR: a new resource for bioinformatics.

UNLABELLED: The Protein Information Resource (PIR) has greatly expanded its Web site and developed a set of interactive search and analysis tools to facilitate the analysis, annotation, and functional identification of proteins. New search engines have been implemented to combine sequence similarity search results with database annotation information. The new PIR search systems have proved very useful in providing enriched functional annotation of protein sequences, determining protein superfamily-domain relationships, and detecting annotation errors in genomic database archives. AVAILABILITY: http://pir.georgetown.edu/. CONTACT: mcgarvey@nbrf.georgetown.edu

Animals↗

PubMedDate not supplied

Intraspinal use of morphine.

OBJECTIVE: To compare the different sterility standards and the cost issues involved when choosing an opioid product for intraspinal administration. DATA SOURCES: Literature accessed through MEDLINE and other Internet search engines (September 2002-April 2003) was evaluated. Key search terms included epidural/intrathecal, opioids, sterility, and compounding. DATA SYNTHESIS: Intraspinal use is prevalent in the area of pain management. Product selection is of utmost importance when administering through the intraspinal route. An evaluation of guidelines on sterility and a cost comparison were conducted. CONCLUSIONS: The preservative-free commercially available products that are indicated for intrathecal/epidural use are the best alternative due to proper outside testing and stringent quality assurance. The generic morphine preservative-free product may also be considered if proper steps are taken to ensure that the final product is diluted properly.

Analgesics, Opioid↗

PubMed2005

The Internet for pathologists: a simple schema for evaluating pathology-related Web sites and a catalog of sites useful for practicing pathologists.

CONTEXT: With the increasing popularity of the Internet as a primary medical information source, it is critical for pathologists to be able to use and evaluate both general medical- and pathology-related Web sites. Several published models for evaluating Web sites prove cumbersome to use and often involve computer- or statistic-based algorithms. OBJECTIVES: To develop a simple group of scoring criteria to objectively evaluate medical Web sites and provide a list of the highest-scoring pathology-related sites that will be useful to the practicing pathologist. DESIGN: Using 11 commonly used Internet search engines, the top 50 "hits" retrieved from the search term websites for pathologists were scored using 5 criteria, including accuracy, ease of navigation, relevance, updates, and completeness. A possible 6 to 12 points per area were awarded, and the total score was summated. RESULTS: Scores obtained ranged from 12 to 21. Thirty-five Web sites, all scoring 15 or higher based on these criteria, were listed as most useful. CONCLUSION: A simple, easy-to-use, 5-category scoring system can prove useful in evaluating pathology- and medical-related Web sites.

Evaluation Studies as Topic↗

PubMed2002

RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, identifies proteins via in silico database searching, then stores the processed data and search results in a relational database suitable for customized reporting. The system is robust, used in 24/7 operation, accessible to multiple users of an intranet through a web browser, may be monitored by Virtual Private Network, and is secure. RADARS is scalable for use on one or many computers, and is suited to multiple processor systems. It can incorporate any local database in FASTA format, and can search protein and DNA databases online. A key feature is a suite of visualisation tools (many available gratis), allowing facile manipulation of spectra, by hand annotation, reanalysis, and access to all procedures. We also described the use of Sonar MS/MS, a novel, rapid search engine requiring 40 MB RAM per process for searches against a genomic or EST database translated in all six reading frames. RADARS reduces the cost of analysis by its efficient algorithms: Sonar MS/MS can identifiy proteins without accurate knowledge of the parent ion mass and without protein tags. Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user.

Amino Acid Sequence↗

PubMed2006

The role of cognition in tinnitus.

CONCLUSIONS: The role of cognition in tinnitus is difficult to ignore. First, tinnitus is likely to disrupt cognitive functioning, and there are some indications that tinnitus patients have impaired capacity to perform certain cognitive tasks. Second, evidence is emerging that tinnitus patients show cognitive bias in the way they handle information. Such information processing style suggests either depressive functioning, or anxious vigilance, or both. Finally, self-report measures of tinnitus distress all require conscious recollection of how tinnitus is perceived and the consequences of tinnitus. Such reports necessitate cognitive capacity. OBJECTIVES: To review the literature on the interface between cognitive function and tinnitus, with special regard to the role of different levels of information processing. MATERIALS AND METHODS: A selective systematic literature search was conducted using the search engines of Medline and Psychological Abstracts, and by hand search of conference proceedings. RESULTS: There are yet relatively few published studies on cognitive functioning in tinnitus patients. Most research has been conducted by a few separate research groups. However, the available studies clearly implicate an important role of cognitive processes at different levels from basic cognitive function to more conscious appraisal of the consequences of tinnitus. Finally, a tentative model of the road from tinnitus generation to annoyance via cognitive function is suggested.

Cognition Disorders↗

PubMed2003

The patient's dilemma: prostate cancer treatment choices.

PURPOSE: We summarize the literature addressing factors that influence treatment decisions made by men with prostate cancer. MATERIALS AND METHODS: A MEDLINE search of the English language literature published between 1969 and 2000, using the combined MESH key words "prostatic neoplasms," "patient participation," "Internet" and "decision making," generated 181 abstracts. Only 23 of these publications addressed factors influencing treatment decisions made by men with prostate cancer. Nine additional relevant studies were identified from references in the original 23 articles. Subsequently a search for the term "prostate cancer" using several popular Internet search engines yielded more than 1 million hits. A further search was performed using the key words "prostate cancer" and "prostate" within on-line archives of the United Kingdom television channels BBC, ITV, and channels 4 and 5, and newspapers The Sun, The Daily Mail, The Observer, The Guardian and The Times. RESULTS: When there is poor quality evidence or little professional consensus to support a particular treatment over another, no clinical guidelines regarding treatment are possible. Patients are faced with a series of options, and the data reveal that the process of choosing between these options is based on input from a large number of sources. These sources differ in the way that benefits of treatment are emphasized over harms and vice versa. We identified little evidence regarding which type of input exerts the greatest influence on patients. It may be that the sources associated with the most bias have the greatest influence. CONCLUSIONS: There is a paucity of information on how patients with prostate cancer use different types of input in the treatment decision making process. The physician, as principal caregiver, still appears to have the most direct influence on patient choice. Just how long this status will continue is uncertain.

Compact Disks↗

PubMed2005

Rectocele repair using biomaterial augmentation: current documentation and clinical experience.

UNLABELLED: Although the etiology of rectocele remains debated, surgical innovations are currently promoted to improve anatomic outcome while avoiding dyspareunia and alleviating rectal emptying difficulties following rectocele surgery. Use of biomaterials in rectocele repair has become widespread in a short time, but the clinical documentation of their effectiveness and complications is limited. Medline and the Cochrane database were searched electronically from 1964 to May 2005 using the Pubmed and Ovid search engines. All English language publications including any of the search terms "rectocele," "implant," "mesh," "biomaterial," "prolapse," "synthetical," "pelvic floor," "biological," and "compatibility" were reviewed. This review outlines the basic principles for use of biomaterials in pelvic reconstructive surgery and provides a condensation of peer-reviewed articles describing clinical use of biomaterials in rectocele surgery. Historical and new concepts in rectocele surgery are discussed. Factors of importance for human in vivo biomaterial compatibility are presented together with current knowledge from clinical studies. Potential risks and problems associated with the use of biomaterials in rectocele and pelvic reconstructive surgery in general are described. Although use of biomaterials in rectocele and other pelvic organ prolapse surgery offers exciting possibilities, it raises treatment costs and may be associated with unknown and potentially severe complications at short and long term. Clinical benefits are currently unknown and need to be proven in clinical studies. TARGET AUDIENCE: Obstetricians & Gynecologists, Family Physicians TARGET AUDIENCE: After completion of this article, the reader should be able to explain that the objective of surgical treatment is to improve anatomic outcome and alleviate rectal emptying difficulties, describe the efficacy of biomaterials in rectocele repair, and summarize the potential risks and problems associated with use of biomaterials in rectocele and pelvic reconstructive surgery.

Biocompatible Materials↗

PubMed2001

Kaiser Permanente's "metadata-driven" national clinical intranet.

This paper describes the approach taken to build Kaiser Permanente's national clinical intranet. A primary objective for the site is to facilitate resource discovery, which is enabled by the use of "metadata", or data (fields and field values) that describe the various resources available. Users can perform full text queries and/or fielded searching against the metadata. Metadata serves as the organizing principle of the site--it is used to index documents, sort search results, and structure the site's table of contents. The site's use of metadata--what it is, how it is created, how it is applied to documents, how it is indexed, how it is presented to the user in the search and the search results interface, and how it is used to construct the table of contents for the web site--will be discussed in detail. The result is that KP's national clinical intranet has coupled the power of Internet-like full text search engines with the power of MedLine-like fielded searching in order to maximize search precision and recall. Organizing content on the site in accordance with the metadata promotes overall consistency. Issues currently under investigation include how to better exploit the power of the controlled terminology within the metadata; whether the value gained is worth the cost of collecting metadata; and how automatic classification algorithms might obviate the need for manual document indexing.

Computer Communication Networks↗

PubMed2004

CASRdb: calcium-sensing receptor locus-specific database for mutations causing familial (benign) hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia.

Familial hypocalciuric hypercalcemia (FHH) is caused by heterozygous loss-of-function mutations in the calcium-sensing receptor (CASR), in which the lifelong hypercalcemia is generally asymptomatic. Homozygous loss-of-function CASR mutations manifest as neonatal severe hyperparathyroidism (NSHPT), a rare disorder characterized by extreme hypercalcemia and the bony changes of hyperparathyroidism, which occur in infancy. Activating mutations in the CASR gene have been identified in several families with autosomal dominant hypocalcemia (ADH), autosomal dominant hypoparathyroidism, or hypocalcemic hypercalciuria. Individuals with ADH may have mild hypocalcemia and relatively few symptoms. However, in some cases seizures can occur, especially in younger patients, and these often happen during febrile episodes due to intercurrent infection. Thus far, 112 naturally-occurring mutations in the human CASR gene have been reported, of which 80 are unique and 32 are recurrent. To better understand the mutations causing defects in the CASR gene and to define specific regions relevant for ligand-receptor interaction and other receptor functions, the data on mutations were collected and the information was centralized in the CASRdb (www.casrdb.mcgill.ca), which is easily and quickly accessible by search engines for retrieval of specific information. The information can be searched by mutation, genotype-phenotype, clinical data, in vitro analyses, and authors of publications describing the mutations. CASRdb is regularly updated for new mutations and it also provides a mutation submission form to ensure up-to-date information. The home page of this database provides links to different web pages that are relevant to the CASR, as well as disease clinical pages, sequence of the CASR gene exons, and position of mutations in the CASR. The CASRdb will help researchers to better understand and analyze the mutations, and aid in structure-function analyses.

Database Management Systems↗

PubMed2003

The quality of information about laparoscopic bariatric surgery on the Internet.

BACKGROUND: Although easy access to the Internet can provide much information for patients, the quality and accuracy of information are uncertain. This investigation evaluated information concerning laparoscopic bariatric surgery available via the Internet. METHODS: Searches on the six most popular search engines and two metasearch engines were performed. The first 20 "hits" for each separate search were included in the study. RESULTS: A total of 602 "hits" were found. Only 119 unique Web sites were found. Although 63 of the 119 sites discussed some procedure related to laparoscopic obesity surgery, 18 of the 63 had biased or misleading information, 30 did not discuss the details of the procedure, 37 did not discuss other procedures, 30 did not discuss complications, 37 did not discuss death as a risk, and 7 did not discuss laparoscopic procedure as an option. Only 89 of the original 602 "hits" led to Web sites that discussed laparoscopic obesity surgery, details of the procedure, and complications in an unbiased manner. CONCLUSIONS: A large amount of information is available via the Internet. However, it is difficult for the patient to identify the unbiased information. The Internet is not a dependable source of information for patients.

Humans↗

PubMed2002

Benchmarking the clinical prosthetic dental literature on MEDLINE.

STATEMENT OF PROBLEM: The utility of evidence-based clinical prosthetic dental decision making is, in part, predicated on the availability of high-quality clinical trials and the use of current best evidence. With literature or outcomes continually evolving, it is difficult to know how much information is available, how fast it changes, or where it is located. PURPOSE: This study identified and quantified the availability of high-quality prosthetic dental clinical trials, determined the dynamics of literature increase, and identified the location of relevant literature published within a specific decade. MATERIAL AND METHODS: A search strategy based on the Medical Subject Headings (MeSH) vocabulary for prosthetic dentistry was developed to examine MEDLINE with use of the Ovid Web Gateway search engine between the years 1990-1999. Specific and sensitive methodologic search filters identified 4 categories of information: etiology, diagnosis, therapy, and prognosis. The identified studies were limited to human subjects and to articles written in English. The results were subdivided by year to identify trends and location of the literature. This evaluation did not include the following: (1) other databases or languages or (2) an evaluation of the validity or clinical applicability of the literature. The first factor would increase the estimated number of relevant articles, whereas the second factor would decrease it. RESULTS: Between 1990 and 1999, MEDLINE identified 10,258 articles published in English on human prosthodontic issues. When subdivided by clinical category, the number of articles per year (mean +/- SD) for specific and sensitive searches, respectively, was as follows: etiology, 10 +/- 6 and 95 +/- 27; diagnosis, 11 +/- 5 and 77 +/- 21; therapy, 6 +/- 2 and 153 +/- 52; and prognosis, 13 +/- 6 and 91 +/- 27. For sensitive searches, this amounted to approximately 416 articles per year. The time-course analysis indicated that the number of articles in each category increased by approximately 7% per year. The articles were published in more than 60 different journals: approximately 50% of the articles were published in 14 journals, whereas the remaining articles were published in 46 journals. CONCLUSION: There appears to be substantial clinical prosthetic dental literature upon which to base clinical decisions. With the sensitive search strategy used as an estimate, to stay current, one would need to read and absorb approximately 8 articles per week, 52 weeks per year, across 60 different journals. Increases in the volume of literature each year make access even more difficult. These trends suggest the need for computer-based clinical knowledge systems.

Analysis of Variance↗

PubMed2003

Preprocessing of tandem mass spectrometric data to support automatic protein identification.

Liquid chromatography tandem mass spectrometry is a major tool for identifying proteins. The fragment spectra of peptides can be interpreted automatically in conjunction with a sequence database search. With the development of powerful automatic search engines, research now focuses on optimizing the result returned from database searches. We present a series of preprocessing steps for fragment spectra to increase the accuracy and specificity of automatic database searches. After processing, the correct amino acid sequences from the database can be related better to the fragment spectra. This increases the sensitivity and reliability of protein identifications, especially with very large genomic databanks, and can be important for the systematic characterization of post-translational modifications.

Algorithms↗

PubMed2000

MMDB: 3D structure data in Entrez.

Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure and be able to use this information to infer structure-function properties. The goal of Entrez's 3D structure database is to make this information accessible and useful to molecular biologists. To this end, Entrez's search engine provides three powerful features: (i) Links between databases; one may search by term matching in Medline((R)), for example, and link to 3D structures reported in these articles. (ii) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view a combined molecular-graphic and alignment display, to infer approximate 3D structure. Entrez's MMDB (Molecular Modeling DataBase) may be accessed at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html

Amino Acid Sequence↗