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At least 19 recordsLinked to original sources

PubMed2005

PubMed Assistant: a biologist-friendly interface for enhanced PubMed search.

MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar and others that are lacking in PubMed.

Artificial Intelligence↗

PubMed2002

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↗

PubMed2005

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↗

PubMed2006

Increased expenditure on Australian health and medical research and changes in numbers of publications determined using PubMed.

OBJECTIVE: To determine temporal trends in PubMed publications for Australian authors compared with changes in funding for health and medical research (HMR). DESIGN: Retrospective observational study. SETTING: Internet-based bibliometric study that collated Australian HMR expenditure from the Australian Institute of Health and Welfare and Australian (and other) research publications from PubMed. MAIN OUTCOME MEASURES: Australian expenditure on HMR and numbers of PubMed-cited publications from 1980 to 2004, with subgroup analyses for universities, clinical trials, and genetic and biotechnology research, and comparison with similar results from the United Kingdom and New Zealand. RESULTS: From 1980-81 to 2003-04, Australian HMR expenditure increased from $66 million to $1503 million and total Australian PubMed publications increased from 844 to 13 836. From 1995-96 to 2003-04, Australian publications for university-derived research and for clinical trials increased at a fairly constant rate. Genetic and biotechnology publications increased about fivefold (49 to 277) between 1990-91 and 2003-04. Between 1990 and 2004, total publications increased from 1754 to 3288 for New Zealand and from 12 401 to 19 600 for the UK. CONCLUSIONS: There is an association between increased funding for HMR and increased publications, as determined using PubMed, in the past 10 years. Using PubMed may be a simple way to track output from HMR expenditure.

Australia↗

PubMed2007

A day in the life of PubMed: analysis of a typical day's query log.

OBJECTIVE: To characterize PubMed usage over a typical day and compare it to previous studies of user behavior on Web search engines. DESIGN: We performed a lexical and semantic analysis of 2,689,166 queries issued on PubMed over 24 consecutive hours on a typical day. MEASUREMENTS: We measured the number of queries, number of distinct users, queries per user, terms per query, common terms, Boolean operator use, common phrases, result set size, MeSH categories, used semantic measurements to group queries into sessions, and studied the addition and removal of terms from consecutive queries to gauge search strategies. RESULTS: The size of the result sets from a sample of queries showed a bimodal distribution, with peaks at approximately 3 and 100 results, suggesting that a large group of queries was tightly focused and another was broad. Like Web search engine sessions, most PubMed sessions consisted of a single query. However, PubMed queries contained more terms. CONCLUSION: PubMed's usage profile should be considered when educating users, building user interfaces, and developing future biomedical information retrieval systems.

Algorithms↗

PubMed2006

[Development of a geographic filter for PubMed to identify studies performed in Spain].

INTRODUCTION AND OBJECTIVES: The increasing size of the PubMed (Medline) database has made it necessary to develop specific tools for information retrieval (i.e., filters). The current configuration of the Limits option in PubMed does not enable searches to be limited according to geographic criteria. Our objectives, therefore, were a) to develop a geographic filter for the retrieval from PubMed of studies performed in the Spanish population, and b) to assess its performance. METHODS: A second-generation filter was constructed by reviewing previous strategies. It involved the selection of three types of record that included: a) the term Spain in different languages; b) Spanish place names (i.e., mainly those of autonomous regions and provinces), and c) acronyms for health services in autonomous regions. The performance of the filter (i.e., its sensitivity and specificity) was assessed in a representative sample (i.e., clinical trials indexed in PubMed under the MeSH term Myocardial Infarction) by comparison with the results of a manual search (the gold standard). In addition, the filter's performance was also evaluated by comparing it with a simple search for the term Spain[ad]. RESULTS: Use of the filter retrieved 74 (98.7%) of the relevant references. The sensitivity (88.1%) was higher than that of the simple search strategy (45.8%), and excellent specificity (100%) was achieved in both cases. CONCLUSIONS: A geographic filter has been developed for identifying studies in PubMed that involve the Spanish population.

Bibliometrics↗

PubMed2005

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↗

PubMed2006

PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines.

PubMed and HighWire Press are both useful medical literature search engines available for free to anyone on the internet. We measured retrieval accuracy, number of results generated, retrieval speed, features and search tools on HighWire Press and PubMed using the quick search features of each. We found that using HighWire Press resulted in a higher likelihood of retrieving the desired article and higher number of search results than the same search on PubMed. PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines.

Databases, Bibliographic↗

PubMed2006

The use of PubMed/Medline in psychiatry. 1: Presentation of NLM and PubMed.

A comprehensive view of the available literature on a psychiatric problem can be found in the large electronic databases. Medline at the National Library of Medicine (NLM) in USA is the largest medical database. PubMed is the searchable database at the NLM, having Medline as its major content. PubMed is free of charge, barrier-free and always accessible via the Internet. This paper describes the NLM, Medline and PubMed. The indexing of scientific papers in Medline is based on Medical Subject Headings, the MeSH terms. The hierarchic tree structure of MeSH is the basis of the search and retrieval system. The present paper is the first in a series of three, intended as a tutorial on the use of PubMed for inexperienced users. Information and examples on the MeSH system, together with exercises in its use, are presented in an appendix.

Abstracting and Indexing↗

PubMed2006

The use of PubMed/Medline in psychiatry. 2: The PubMed search window: a description and a tutorial.

A previous paper, in a series of three, presented the National Library of Medicine, Medline, PubMed and the MeSH system. Connection to PubMed via the Internet opens the PubMed search window that is the tool for retrieving references to scientific medical literature. This paper is intended as a tutorial for an inexperienced visitor to PubMed, and describes the search window in some detail. Several proposals for exercises in its use are given in the text, while explanations and comments to the exercises are presented in an appendix. The following procedures are described: retrieving references, ways to see the abstract, ways of displaying, sorting and showing the references, together with how to produce lists, import references to your own computer, and ways to get the full text of a paper.

MEDLINE↗

PubMed2006

Finding the evidence for protein-protein interactions from PubMed abstracts.

MOTIVATION: Protein-protein interactions play critical roles in biological processes, and many biologists try to find or to predict crucial information concerning these interactions. Before verifying interactions in biological laboratory work, validating them from previous research is necessary. Although many efforts have been made to create databases that store verified information in a structured form, much interaction information still remains as unstructured text. As the amount of new publications has increased rapidly, a large amount of research has sought to extract interactions from the text automatically. However, there remain various difficulties associated with the process of applying automatically generated results into manually annotated databases. For interactions that are not found in manually stored databases, researchers attempt to search for abstracts or full papers. RESULTS: As a result of a search for two proteins, PubMed frequently returns hundreds of abstracts. In this paper, a method is introduced that validates protein-protein interactions from PubMed abstracts. A query is generated from two given proteins automatically and abstracts are then collected from PubMed. Following this, target proteins and their synonyms are recognized and their interaction information is extracted from the collection. It was found that 67.37% of the interactions from DIP-PPI corpus were found from the PubMed abstracts and 87.37% of interactions were found from the given full texts. AVAILABILITY: Contact authors.

Abstracting and Indexing↗

PubMed2005

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↗

PubMed2006

Searching for observational studies: what does citation tracking add to PubMed? A case study in depression and coronary heart disease.

BACKGROUND: PubMed is the most widely used method for searches of the medical literature, but fails to identify many relevant articles. Electronic citation tracking offers an alternative search method. METHODS: Articles investigating the role of depression in the aetiology and prognosis of coronary heart disease were sought through two methods: a) PubMed, and b) citation tracking where Science Citation Index was searched for all articles which cited ("forward citation tracking") or were cited by ("backward citation tracking") any of the articles in an index review. The number and quality of eligible articles identified by the two methods were compared. RESULTS: 50 articles that were not already included in the index review met our inclusion criteria; 11 were identified through Science Citation Index alone, 8 through PubMed alone, and 31 through both methods. Articles identified by Science Citation Index alone were published in higher impact factor journals, were larger and were less likely to show a positive association. CONCLUSION: Science Citation Index identified more eligible articles than PubMed, and these differed qualitatively. Failing to use citation tracking in a systematic review of observational studies may result in bias.

Abstracting and Indexing↗

PubMed2004

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↗

PubMed2006

Literature search using PubMed: an essential tool for practicing evidence- based medicine.

Efficient literature search is essential to the practice of Evidence-Based Medicine. PubMed provides free access to one of the largest searchable biomedical databases. Efficient literature search using PubMed requires a good understanding of the available search strategies and tools. In this article we present a step-by-step approach for performing literature search using PubMed. Several PubMed tools including 'Single Citation Matcher', 'Clinical Queries', 'Clipboard', 'Field Tags', and 'Cubby' are highlighted using case based scenarios.

Abstracting and Indexing↗

PubMed2006

The use of PubMed/Medline in psychiatry. 3: Searching PubMed.

This paper is the third in a series of three, intended as a tutorial in the use of PubMed/Medline for an inexperienced user. The papers have the following contents: I--a description of NLM, Medline, PubMed and the system of Medical Subject Headings (MeSH), which form the basis for the indexing of scientific articles, books and other items at NLM. II--A description and a tutorial of the PubMed search window. III--The present article deals mainly with the searching for references in PubMed. Ways of restricting and concentrating the search are presented, and exercises are proposed. A reader may also find guidance for a search for medical books in the NLM Catalog, and in the use of tools like Related Articles, Bookshelf, and Index. With eating disorders as an example, more information is presented on the use of MeSH terms.

MEDLINE↗

PubMed2005

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↗

PubMed2005

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↗