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At least 19 recordsLinked to original sources

Development of a highly sensitive search strategy for the retrieval of reports of controlled trials using PubMed.

OBJECTIVE: To develop, through revision of the Cochrane Collaboration search strategy for OVID-MEDLINE, a highly sensitive search strategy to retrieve reports of controlled trials using PubMed. METHODS: The original highly sensitive Cochrane strategy was revised to take into account additional Medical Subject Headings (MeSH) and other terminology as well as the current unique features of PubMed. We compared the retrieval of the revised strategy with that of the original Cochrane strategy before and after translation of the strategies into PubMed format. Finally, we used a gold standard database of reports of controlled trials identified by electronic and hand search of selected journals to test the revised strategy in PubMed format. RESULTS: The revised strategy included a search statement modified for increased precision, and added 'Cross-over Studies' as a MeSH term and the term 'latin square' as a text word. Compared to the original Cochrane strategy, the revised strategy identified 53 additional reports of controlled trials accessing MEDLINE through OVID. When the revised strategy and original Cochrane strategy were translated into PubMed format, the revised strategy retrieved 90 reports of controlled trials not identified by the original strategy. Finally, the revised strategy in PubMed format retrieved all of the reports of controlled trials in the gold standard database. Ninety-eight per cent of the gold standard reports of controlled trials were retrieved by Phase 1 of the optimal PubMed search strategy. CONCLUSIONS: Failure to identify all relevant trials for systematic review could result in bias. We developed a highly sensitive search strategy for the retrieval of reports of controlled trials for use with PubMed that retrieves more relevant citations (greater sensitivity) and fewer non-relevant citations (greater precision) than the original Cochrane search strategy.

Bias↗

PubMed perspective of family medicine research: where does it stand?

OBJECTIVE: The aim of this study was to obtain a view of family medicine research by analyzing PubMed citations from 1960-2003. METHOD: Family practice (FP) citations in PubMed from 1960 to 2003 were downloaded in MEDLINE format. This was written into relation database using 'PubMed Grabber/Analyzer' software developed at University of Kelaniya, Sri Lanka. Search Query Language (SQL) and online PubMed queries were used for further analysis. RESULTS: There were 50288 FP citations from 80 countries. Of these, 33712 (67%) citations were from 15 FP journals. United Kingdom (18760), United States (13584), Australia (3262), Canada (1848), Germany-west (1340) were the five countries which had the most citations and 22 countries had less than 5 citations. Van Weel C (118), Geyman JP (116), Olesen F (87), Jones R (83) and Knottnerus JA (82) were numerically, the top five authors. Only 921 authors had more than 10 citations and the vast majority of authors had only one citation. Letters (5121), review (2715), editorial (2259), randomized controlled trials-RCT (1585) and Meta-analysis (44) were the top publication types. 40 citations found under 'qualitative research'. Discussion. The relatively few PubMed FP citations (50288) are by a small number of academics in developed countries. Citations showed an upsurge from the mid 1980s to the late 1990's but reached a plateau in the new millennium. Compared to PubMed citations from 1960-2003 in other specialties such as 2737655 for public health, 1151194 for cardiology & cardiovascular diseases and 318538 for medical informatics, the 50288 FP citations were paltry. Paucity of RCT (1585) and meta-analysis (44) was noted. The low 'qualitative research' citations (44) could have been due to the late introduction of the MeSH concept in 2003. CONCLUSIONS: Priority should be given to increase FP research and also to ensure the indexing of FP journals that are not currently indexed in PubMed. Efforts to increase citations in Medline may not give the desired results because of low priority given primary care specialties such as family medicine in the USA. Alternative solution of a separate bibliographic database for FP similar to PsycInfo may be too costly.

Family Practice↗

Three decades of the Ceylon Medical Journal--analysis using MEDLINE (PubMed).

INTRODUCTION: The Ceylon Medical Journal (CMJ) is the only Sri Lankan medical journal that is indexed in MEDLINE (PubMed). Publications in the CMJ from 1965 March to 2001 December were analysed using the PubMed interface of MEDLINE. METHOD: Using PubMed we downloaded the CMJ bibliography in MEDLINE format. Important tagged fields were written to a Microsoft-Access database using a PubMed Grabber/Analyser program. The analysis was done using Access-SQL and PubMed queries. RESULTS: There were 1472 citations by 1373 authors. 944 authors had only one and 176 had two articles. The top 10 authors contributed 8% and the top 25, 15.4% of the articles. Publications types were: 68.5% 'journal articles', 10.4% letters, 4.2% historical articles and 4.1% reviews. Controlled clinical trials, randomised controlled trials and clinical trials together totalled only 39 (2.1%). Articles were classified using 2 to 44 medical subject headings (MeSH; average 11.4, mode 9) from the MeSH vocabulary. CMJ articles classified using broad MeSH categories were (top five): infections 370(15 %), pathological conditions signs and symptoms 266( 10.8%), haemic, lymphatic and immunologic 199 (7.7%), endocrine, nutritional and metabolic 189 (7.7%), neoplasms 179(7.3%). DISCUSSION: For 938 (68%) authors, publishing in the CMJ was a one time affair. The top 50 authors contributed nearly a quarter (23.2%). A product of this research is an off-line CMJ searching system from 1965 to 2001 with menu driven search facilities which will be a useful tool for researchers.

Abstracting and Indexing↗

Worldwide access to evidence-based mental health literature: how useful is PubMed in Anglo-Saxon and non-Anglo-Saxon countries?

The aim of this study was to verify the presence of cultural variety among the psychiatric journals available on PubMed, the major online tool for accessing literature. Data for analysis were taken from a survey of the world psychiatric journals indexed in Index Medicus 1999 (IM), the alphabetical list used by PubMed, and from the mean impact factor (IF) values of the journals. Approximately 80% of international psychiatric literature available on PubMed is published in Anglo-Saxon countries, especially in the USA (59.8% of the total). The widespread use of the English language (94.9% of all the journals) further stresses the dominance of the Anglo-Saxon cultural model, as do the mean IF values of Anglo-Saxon journals compared to non-Anglo-Saxon publications (3.252 vs. 1.693; P=0.0079). The under-representation of non-Anglo-Saxon cultural models on PubMed plays a negative role for bringing about a truly multicultural literature in psychiatry.

Culture↗

A usability study of the PubMed on Tap user interface for PDAs.

Healthcare providers are challenged by the availability of information at the point of care. Overcoming these challenges requires access to current, reliable, and accurate information. The purpose of the PubMed on Tap project is to discover and implement design principles to facilitate healthcare practitioners' access to medical information at the point-of-care, related to user interface design, organization and performance. The PubMed on Tap prototype was developed for personal digital assistants (PDAs) as a testbed to study these design principles. Usability testing was used to derive conclusions regarding the functionality of PubMed on Tap. Participant events (n=323) mostly occurred in navigational ability (31%) and perceived functionality (33%). A strong correlation (r=0.87) was observed between total time and the sum of negative events in locating functions and navigational categories. Researchers concluded the basic functionality of the PubMed on Tap interface was valuable to users. However, there was room for improvement in the navigational and functional characteristics, such as placing labels on icons, which affected the users' ability to use the research tool.

Attitude to Computers↗

GoPubMed: exploring PubMed with the Gene Ontology.

The biomedical literature grows at a tremendous rate and PubMed comprises already over 15 000 000 abstracts. Finding relevant literature is an important and difficult problem. We introduce GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: first, it gives an overview of the literature abstracts by categorizing abstracts according to the GO and thus allowing users to quickly navigate through the abstracts by category. Second, it automatically shows general ontology terms related to the original query, which often do not even appear directly in the abstract. Third, it enables users to verify its classification because GO terms are highlighted in the abstracts and as each term is labelled with an accuracy percentage. Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org. Querying is currently limited to 100 papers per query.

Abstracting and Indexing↗

Searching the MEDLINE literature database through PubMed: a short guide.

The Medline database from the National Library of Medicine (NLM) contains more than 12 million bibliographic citations from over 4,600 international biomedical journals. One of the interfaces for searching Medline is PubMed, provided by the NLM for free access via the Internet (www.pubmed.gov). Also searchable with the PubMed interface are non-Medline citations, i.e. articles supplied by publishers to the NLM. Direct access to an electronic full text version is also possible if the article is available from a publisher or institution participating in Linkout (www.ncbi.nlm.nih.gov/entrez/linkout/). Some publishers provide free access to their journals. Other journals require an online license and are fee based. The following example demonstrates some of the most important search functions in PubMed. We will start out with a fast and simple approach without the use of specific searching techniques and then continue with a more sophisticated search that requires the knowledge of Medline search functions. This example will show how the application of Medline search tools and how the use of the controlled vocabulary of 'Medical Subject Headings' (MeSH) will influence the results in comparison with the fast and simple approach. Let's try to find the best evidence to answer the following question: Is a 30-year-old man with typical acid reflux symptoms for many years (gastroesophageal reflux disease, GERD) more likely to develop esophageal cancer than people without reflux symptoms? This question can be split into several components: -a patient with reflux symptoms (GERD), -esophageal cancer: etiology, risk, -study design for etiology studies: cohort studies, case-control studies.

Database Management Systems↗

Retrieval comparison of EndNote to search MEDLINE (Ovid and PubMed) versus searching them directly.

Using EndNote version 7.0, the authors tested the search capabilities of the EndNote search engine for retrieving citations from MEDLINE for importation into EndNote, a citation management software package. Ovid MEDLINE and PubMed were selected for the comparison. Several searches were performed on Ovid MEDLINE and PubMed using EndNote as the search engine, and the same searches were run on both Ovid and PubMed directly. Findings indicate that it is preferable to search MEDLINE directly rather than using EndNote. The publishers of EndNote do warn its users about the limitations of their product as a search engine when searching external databases. In this article, the limitations of EndNote as a search engine for searching MEDLINE were explored as related to MeSH, non-MeSH, citation verification, and author searching.

Database Management Systems↗

PubMed enhancements: fulfilling the promise of a great product.

There have been many recent changes to PubMed to enhance its usefulness. Those changes include: LinkOut Libraries (local holding field), PubMed Central (full-text articles archived by the National Library of Medicine), and LinkOut (access to full-text articles right from the PubMed citation). Medical librarians should be aware of how these features work to best assist their clients. These new features offer the possibility of true desktop access for library patrons. Not only will patrons appreciate these new features, but their use in libraries will literally change what we do, who does it, and how it is done.

Consumer Behavior↗

Using advanced search tools on PubMed for citation retrieval.

PubMed (www.pubmed.gov) provides health care professionals with free access to one of the largest searchable biomedical databases available. However, attempting to find relevant literature in PubMed without an understanding of basic search strategies and tools may be daunting and frustrating. In a previous issue of the Mayo Clinic Proceedings, we presented an overview of searching in PubMed and introduced its basic features. In this article, we build on this foundation and present advanced search tools designed to assist clinicians in performing efficient and focused literature searches.

Information Storage and Retrieval↗

Searching the medical literature using PubMed: a tutorial.

Staying current with advances in medicine is becoming a major challenge for clinicians. Access to updated repositories of medical information and the expertise to locate relevant information within them are becoming necessary clinical skills. PubMed (http://www.pubmedgov) provides free access to the largest biomedical resource available and is updated daily. Clinicians can use this resource to find answers to focused clinical questions quickly and efficiently. The purpose of this article is to assist clinicians in the development of the basic skills required to use PubMed to make informed clinical decisions.

Clinical Competence↗

[Spanish pediatric publications in PubMed between 1996 and 2001].

OBJECTIVES: To assess and compare the scientific pediatric production of Spanish authors in Pubmed and Journal Citation Reports (JCR) between 1996 and 2001. MATERIAL AND METHODS: We reviewed the first 200 articles that appeared in PubMed between 1996 and 2001 on childhood ("newborn OR neonate OR children OR child OR infant") by Spanish authors (Spain [affiliation]). We compared the quality of study design, sample sizes, subject of the article, impact factor and the authors' specialty, using the chi-squared and/or Student's t-test. The factors related to publication in journals with an impact factor of more than 2 were analyzed using logistic regression analysis. RESULTS: Only 35 % of the articles selected were performed exclusively in children. Between 1996 and 2001, Spanish pediatric publications included in the Journal Impact Factor increased by 37.5 %. The impact factor between these two years was similar (1.776 vs 1.823; p: NS). An impact factor of more than 2 was related to articles published in non-pediatric journals (OR: 3, 95 % CI: 1.17-7.69, p 0.018), publications including multiple regression analysis in the statistical analysis (OR: 3.27; 95 % CI: 1.12-9.56; p 0.028), multicenter studies (OR: 4.2, 95 % CI: 1.1-22.4, p 0.048) and articles on immunology or molecular biology (OR: 2.45; 95 % CI: 1.01-5.92; p 0.044). CONCLUSIONS: In the last 5 years Spanish pediatric publications in journals included in the JCR increased by 37.5 %. We should promote publications with larger sample sizes, multicentric studies and those with high quality design (clinical trials and cohort studies).

Bibliometrics↗

Research methodology search filters: are they effective for locating research for evidence-based veterinary medicine in PubMed?

OBJECTIVE: The study examined the effectiveness of research methodology search filters developed by Haynes and colleagues and utilized by the Clinical Query feature of PubMed for locating literature for evidence-based veterinary medicine (EBVM). METHODS: A manual review of articles published in 6 commonly read veterinary journals was conducted. Articles were classified by format (original study, review, general article, conference report, decision analysis, and case report) and purpose category (etiology, prognosis, diagnosis, and treatment). Search strategies listed in PubMed's Clinical Query feature were then tested and compared to the manually reviewed data to calculate sensitivity, specificity, and precision. RESULTS: The author manually reviewed 914 articles to identify 702 original studies. Search #1 included terms determined to have the highest sensitivity and returned acceptable sensitivities over 75% for diagnosis and treatment. Search #2 included terms identified as providing the highest specificity and returned results with specificities over 75% for etiology, prognosis, and treatment. DISCUSSION: The low precision for each search prompts the question: Are research methodology search filters practical for locating literature for the practice of EBVM? A study examining terms related to appropriate research methodologies for advanced clinical veterinary research is necessary to develop filters designed to locate literature for EBVM.

Animals↗

Analysis of current nuclear cardiology literature in MEDLINE database: a study of gated SPECT imaging using PubMed.

BACKGROUND: Easy access to relevant clinical information is necessary for physicians to make the best decisions for patient management. The increasing amount of information available has made it difficult for physicians to retrieve up-to-date information efficiently. We sought to determine the accessibility and accuracy of indexing in the nuclear cardiology literature by conducting sample searches in the MEDLINE database on the topic of gated single photon emission computed tomography (SPECT) imaging. METHODS AND RESULTS: The MEDLINE database was initially searched by use of both a primary and a comprehensive search strategy on PubMed for publications in English from 1994 to 2000. A total of 260 papers were retrieved from the primary search and 306 additional papers from the comprehensive search. Only 204 of the 566 citations from the combined electronic searches were truly relevant to gated SPECT. The resulting specificity index (precision) was 36%. A hand search was conducted in 11 top journals from 1994 to 2000. It yielded 81 additional citations that were missed by the PubMed search. The sensitivity index (recall) was calculated for all 11 journals. The Journal of Nuclear Cardiology had the highest rate of publication but the lowest rate of recall (44%). The clinical nuclear cardiology terminology and classifications were compared with the available Medical Subject Headings (MeSH) and MeSH Trees used for indexing in MEDLINE. CONCLUSIONS: There are 6 nuclear cardiology techniques, including gated SPECT and myocardial perfusion imaging, that are not specifically indexed in the current MEDLINE database. The lack of specific MeSH headings and indexing structure results in low recall and precision for retrieval of nuclear cardiology literature. We recommend 2 additions to the MeSH Tree Structure and 6 new MeSH headings.

Cardiology↗

[Bibliography search in biology and medicine: a tutorial for Medline PubMed use].

To be informed about the last publications recently published or to produce a bibliography in a given thematic field is essential for researchers in the biomedical field. If the use of Internet information searching tools such as "Google" or "Alltheweb" makes possible to discover a great part of the grey literature, bibliographic databases like Embase, Current Contents, Biosis or Medline via PubMed are essential tools to locate scientific articles. Among these bibliographic databases, Medline PubMed, thanks to its free access, is the most used. However, a correct utilization of the various functionalities proposed (thesaurus MeSH, systematization of bibliographic searches...), and consequently the quality of bibliographic researches carried out in this database, requires to master elementary knowledge which are exposed in this article.

Biology↗

Searching MEDLINE free on the Internet using the National Library of Medicine's PubMed.

Searching MEDLINE, the National Library of Medicine's premier bibliographic database covering the fields of medicine, nursing, dental medicine, the healthcare system, veterinary medicine, and the preclinical sciences, is now available free on the Internet through PubMed. This retrieval system allows users of all skill levels to obtain important medical information. Additionally, through the National Network of Libraries of Medicine (NN/LM) program, a division of NLM, user support in the form of phone, e-mail, and training is available free of charge. Those interested in having a training session for PubMed at their facility may contact the NN/LM to make arrangements.

Computer User Training↗

Updating a bibliography using the related articles function within PubMed.

Comprehensive bibliographies are useful for conducting reviews of the literature, and for assessing the progress within a field. These bibliographies may be broad and inclusive, or focused and precise in their inclusion criteria. In either case, the task of maintaining a complete bibliography within a particular area of research is made difficult by the diversity, complexity and huge volume of newly published literature. In an effort to effectively and automatically retrieve relevant literature, different search strategies and indexing tools have been developed, including the RELATED ARTICLES function provided with the PubMed system. In this paper, we report a program for incremental updates of a bibliography using the PubMed RELATED ARTICLES function. Given a highly specialized starting bibliography of experimental measurements of the structure of the 30S bacterial ribosomal subunit, the system was applied to find additional relevant references. For this particular task, the system has a recall of 75%, a strict precision of 32% and a partial precision of 42%. Our results are notable because although the RELATED ARTICLES function is purely statistical, it is nonetheless able to select a very narrowly defined set of articles from the literature. We discuss the tradeoffs between having a user to evaluate many articles of possible interest in a single session, versus asking a user to evaluate a small set of articles on a periodic basis.

Bacteria↗

A tool for gene expression based PubMed search through combining data sources.

UNLABELLED: We present a new tool for the semi-automated querying of PubMed using a batch of tens to thousands of GenBank accession numbers or UniGene cluster ids. By combining information from UniGene and SWISS-PROT, microGENIE obtains information on the biological relevance of expressed genes, as identified by micro-array experiments, with minimal user intervention and time investment. AVAILABILITY: microGENIE is freely available from http://www.cs.vu.nl/microgenie SUPPLEMENTARY INFORMATION: The web site above supplies examples of input and output files.

Database Management Systems↗