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At least 127 records · Page 7Linked to original sources
PubMed1993

Factors affecting students' use of MEDLINE.

MEDLINE search transcripts by a class of third-year medical students were analyzed. The 184 students were divided into three groups according to their search experience in terms of the number of sessions logged at the time of a search assignment. A strong relation was found between the level of search experience and the frequency of use in the subsequent 5 months. Over 80% of the students were able to retrieve a few useful items for an emergency clinical situation. More experienced searchers were able to retrieve more relevant items than less experienced searchers. However, no relation was found between search effectiveness and clinical knowledge as indicated by two scores derived from the University of Michigan's Comprehensive Clinical Assessment examination and Part II of NBME. Similarly, clinical knowledge also did not appear to relate to MEDLINE search experience. More exposure to MEDLINE during medical school could play an important role in developing effective literature searching skills for lifelong learning, which is essential for today's health professionals.

Clinical Competence↗
PubMedDate not supplied

The completeness of MEDLINE for papers published and abstracted in the Journal of Emergency Medicine.

The purpose of this paper is to assess whether MEDLINE, a common source for reviewing the medical literature, is complete with regard to referencing papers published and abstracted in The Journal of Emergency Medicine (JEM) over a 10-year period. In that time, 1178 abstracts and 843 original contributions were included in JEM. All papers were reviewed and classified as either a review of subject, case report with review of literature, editorial, or prospective or retrospective original research. Results showed 98.5% of all original work published in JEM and 99.74% of all abstracts referenced in JEM were found in MEDLINE, thus supporting the hypothesis that MEDLINE is a complete and thorough database for current literature.

Abstracting and Indexing↗
PubMed2006

Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles.

Biomedical abbreviations and acronyms are widely used in biomedical literature. Since many of them represent important content in biomedical literature, information retrieval and extraction benefits from identifying the meanings of those terms. On the other hand, many abbreviations and acronyms are ambiguous, it would be important to map them to their full forms, which ultimately represent the meanings of the abbreviations. In this study, we present a semi-supervised method that applies MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. We first automatically generated from the MEDLINE abstracts a dictionary of abbreviation-full pairs based on a rule-based system that maps abbreviations to full forms when full forms are defined in the abstracts. We then trained on the MEDLINE abstracts and predicted the full forms of abbreviations in full-text journal articles by applying supervised machine-learning algorithms in a semi-supervised fashion. We report up to 92% prediction precision and up to 91% coverage.

Artificial Intelligence↗
PubMed2005

Selective exposure reporting and Medline indexing limited the search sensitivity for observational studies of the adverse effects of oral contraceptives.

OBJECTIVE: To explore development of possible approaches leading to a sensitive and precise Medline search to identify observational studies of the association between oral contraceptives and breast cancer, an adverse event. STUDY DESIGN AND SETTING: We compared the results of a series of Medline searches to a gold standard comprising 58 reports from a 1996 systematic review examining the relationship between oral contraceptives and the development of breast cancer. Sensitivity (the proportion of gold standard publications identified) and precision (the proportion of retrieved publications that were included in the gold standard) were calculated for each Medline search. RESULTS: We identified all 58 articles when the search was not limited by terms related to oral contraceptives, but precision was less than 1% (58 of 6,120). Indexing was problematic when oral contraceptives or hormones were not mentioned in the title or abstract (n = 8) or full text (n = 2). CONCLUSION: Search strategies identifying all relevant studies were possible but arguably impractical; additional research is needed to generalize our findings. Authors and editors should ensure that all interventions and outcomes examined are reported and indexers should make sure they are indexed. Central registration of observational studies and all variables they examined should be considered to assure identification of studies examining adverse events associated with health interventions.

Abstracting and Indexing↗
PubMedDate not supplied

Automatically identifying gene/protein terms in MEDLINE abstracts.

MOTIVATION: Natural language processing (NLP) techniques are used to extract information automatically from computer-readable literature. In biology, the identification of terms corresponding to biological substances (e.g., genes and proteins) is a necessary step that precedes the application of other NLP systems that extract biological information (e.g., protein-protein interactions, gene regulation events, and biochemical pathways). We have developed GPmarkup (for "gene/protein-full name mark up"), a software system that automatically identifies gene/protein terms (i.e., symbols or full names) in MEDLINE abstracts. As a part of marking up process, we also generated automatically a knowledge source of paired gene/protein symbols and full names (e.g., LARD for lymphocyte associated receptor of death) from MEDLINE. We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation. RESULTS: GPmarkup has 73% recall and 93% precision in identifying and marking up gene/protein terms in MEDLINE abstracts. AVAILABILITY: A random sample of gene/protein symbols and full names and a sample set of marked up abstracts can be viewed at http://www.cpmc.columbia.edu/homepages/yuh9001/GPmarkup/. Contact. hy52@columbia.edu. Voice: 212-939-7028; fax: 212-666-0140.

Abstracting and Indexing↗
PubMed1995

The quality and impact of MEDLINE searches performed by end users.

Evidence suggests that MEDLINE is becoming an important clinical tool that can improve the care and health of patients. Efforts to improve the quality and impact of end-user searching are needed and ongoing. End users are completing many MEDLINE searches. They appreciate and value training along with feedback on their searching techniques. Practice, is however, the biggest single factor in improving the quality of searching. Key roles for the library in end-user searching include, providing the most effective MEDLINE access possible to the maximum number of users, and providing training that includes feedback and practice opportunities. System-wide advances in structured abstracts, indexing, system design, informatics research and the literature itself will make searching easier and more effective in the future. More important than the quality of search results per se is the impact that end-user searches have on patient care and patient outcomes. Growing evidence shows that both patient care and patient outcomes are improved by end-user searches.

Abstracting and Indexing↗
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↗
PubMed2002

Finding relevant references to genes and proteins in Medline using a Bayesian approach.

MOTIVATION: Mining the biomedical literature for references to genes and proteins always involves a tradeoff between high precision with false negatives, and high recall with false positives. Having a reliable method for assessing the relevance of literature mining results is crucial to finding ways to balance precision and recall, and for subsequently building automated systems to analyze these results. We hypothesize that abstracts and titles that discuss the same gene or protein use similar words. To validate this hypothesis, we built a dictionary- and rule-based system to mine Medline for references to genes and proteins, and used a Bayesian metric for scoring the relevance of each reference assignment. RESULTS: We analyzed the entire set of Medline records from 1966 to late 2001, and scored each gene and protein reference using a Bayesian estimated probability (EP) based on word frequency in a training set of 137837 known assignments from 30594 articles to 36197 gene and protein symbols. Two test sets of 148 and 150 randomly chosen assignments, respectively, were hand-validated and categorized as either good or bad. The distributions of EP values, when plotted on a log-scale histogram, are shown to markedly differ between good and bad assignments. Using EP values, recall was 100% at 61% precision (EP=2 x 10(-5)), 63% at 88% precision (EP=0.008), and 10% at 100% precision (EP=0.1). These results show that Medline entries discussing the same gene or protein have similar word usage, and that our method of assessing this similarity using EP values is valid, and enables an EP cutoff value to be determined that accurately and reproducibly balances precision and recall, allowing automated analysis of literature mining results. .

Abstracting and Indexing↗
PubMed2001

Benchmarking the endodontic literature on MEDLINE.

The purpose of this study was to identify and quantify the endodontic literature available for clinical decision making. A search strategy based on Medical Subject Headings for endodontics was developed to examine MEDLINE. The identified articles were limited to human subjects and English. Sensitive and specific methodological search filters identified four categories of information: etiology, diagnosis, therapy, and prognosis. The results were then subdivided by year to identify trends. Between 1990 and 1998 MEDLINE identified 3,152 articles published in English on endodontics in humans. The number of articles per year (mean +/- SD) for sensitive and specific searches was etiology (28+/-10, 1+/-2), diagnosis (38+/-11, 1+/-1), therapy (59+/-15, 3+/-3), and prognosis (40+/-13, 10+/-5), respectively. The number of articles in each category increased by 1 to 3% each year. There were 150 articles/yr in endodontics in at least 120 journals cited on MEDLINE on which to base clinical decisions.

Analysis of Variance↗
PubMed2005

Optimal search strategies for retrieving scientifically strong studies of treatment from Medline: analytical survey.

OBJECTIVE: To develop and test optimal Medline search strategies for retrieving sound clinical studies on prevention or treatment of health disorders. DESIGN: Analytical survey. DATA SOURCES: 161 clinical journals indexed in Medline for the year 2000. MAIN OUTCOME MEASURES: Sensitivity, specificity, precision, and accuracy of 4862 unique terms in 18 404 combinations. RESULTS: Only 1587 (24.2%) of 6568 articles on treatment met criteria for testing clinical interventions. Combinations of search terms reached peak sensitivities of 99.3% (95% confidence interval 98.7% to 99.8%) at a specificity of 70.4% (69.8% to 70.9%). Compared with best single terms, best multiple terms increased sensitivity for sound studies by 4.1% (absolute increase), but with substantial loss of specificity (absolute difference 23.7%) when sensitivity was maximised. When terms were combined to maximise specificity, 97.4% (97.3% to 97.6%) was achieved, about the same as that achieved by the best single term (97.6%, 97.4% to 97.7%). The strategies newly reported in this paper outperformed other validated search strategies except for two strategies that had slightly higher specificity (98.1% and 97.6% v 97.4%) but lower sensitivity (42.0% and 92.8% v 93.1%). CONCLUSION: New empirical search strategies have been validated to optimise retrieval from Medline of articles reporting high quality clinical studies on prevention or treatment of health disorders.

Information Storage and Retrieval↗
PubMedDate not supplied

MEDLINE: the options for health professionals.

The bibliographic database MEDLINE, produced by the National Library of Medicine (NLM), is a computerized index to the world's biomedical literature. The database can be searched back to 1966 and contains 6.8 million records. The various means of access are divided, for the purposes of this article, into three categories: logging onto a remote host computer by telephone and modem or by the Internet; subscribing to part or all of the database on compact disc (CD-ROM); and leasing the data on a transport medium such as magnetic tape or CDs for loading on a local host computer. Decisions about which method is preferable in a given situation depend on cost, availability of hardware and software, local expertise, and the size of the intended user population. Trends include increased access to the Internet by health professionals, increased network speed, links from MEDLINE records to full-text databases or online journals, and integration of MEDLINE into wider health information systems.

CD-ROM↗
PubMedDate not supplied

Retrieval feedback in MEDLINE.

OBJECTIVE: To investigate a new approach for query expansion based on retrieval feedback. The first objective in this study was to examine alternative query-expansion methods within the same retrieval-feedback framework. The three alternatives proposed are: expansion on the MeSH query field alone, expansion on the free-text field alone, and expansion on both the MeSH and the free-text fields. The second objective was to gain further understanding of retrieval feedback by examining possible dependencies on relevant documents during the feedback cycle. DESIGN: Comparative study of retrieval effectiveness using the original unexpanded and the alternative expanded user queries on a MEDLINE test collection of 75 queries and 2,334 MEDLINE citations. MEASUREMENTS: Retrieval effectivenesses of the original unexpanded and the alternative expanded queries were compared using 11-point-average precision scores (11-AvgP). These are averages of precision scores obtained at 11 standard recall points. RESULTS: All three expansion strategies significantly improved the original queries in terms of retrieval effectiveness. Expansion on MeSH alone was equivalent to expansion on both MeSH and the free-text fields. Expansion on the free-text field alone improved the queries significantly less than did the other two strategies. The second part of the study indicated that retrieval-feedback-based expansion yields significant performance improvements independent of the availability of relevant documents for feedback information. CONCLUSIONS: Retrieval feedback offers a robust procedure for query expansion that is most effective for MEDLINE when applied to the MeSH field.

Feedback↗
PubMed2005

CoPub Mapper: mining MEDLINE based on search term co-publication.

BACKGROUND: High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned. RESULTS: MEDLINE search strings for 15,621 known genes and 3,731 keywords were generated and validated. PubMed IDs were retrieved from MEDLINE and relative probability of co-occurrences of all gene-gene and gene-keyword pairs determined. To assess gene clustering according to literature co-publication, 150 genes consisting of 8 sets with known connections (same pathway, same protein complex, or same cellular localization, etc.) were run through the program. Receiver operator characteristics (ROC) analyses showed that most gene sets were clustered much better than expected by random chance. To test grouping of genes from real microarray data, 221 differentially expressed genes from a microarray experiment were analyzed with CoPub Mapper, which resulted in several relevant clusters of genes with biological process and disease keywords. In addition, all genes versus keywords were hierarchical clustered to reveal a complete grouping of published genes based on co-occurrence. CONCLUSION: The CoPub Mapper program allows for quick and versatile querying of co-published genes and keywords and can be successfully used to cluster predefined groups of genes and microarray data.

Algorithms↗
PubMed2006

Optimizing search strategies to identify randomized controlled trials in MEDLINE.

BACKGROUND: The Cochrane Highly Sensitive Search Strategy (HSSS), which contains three phases, is widely used to identify Randomized Controlled Trials (RCTs) in MEDLINE. Lefebvre and Clarke suggest that reviewers might consider using four revisions of the HSSS. The objective of this study is to validate these four revisions: combining the free text terms volunteer, crossover, versus, and the Medical Subject Heading CROSS-OVER STUDIES with the top two phases of the HSSS, respectively. METHODS: We replicated the subject search for 61 Cochrane reviews. The included studies of each review that were indexed in MEDLINE were pooled together by review and then combined with the subject search and each of the four proposed search strategies, the top two phases of the HSSS, and all three phases of the HSSS. These retrievals were used to calculate the sensitivity and precision of each of the six search strategies for each review. RESULTS: Across the 61 reviews, the search term versus combined with the top two phases of the HSSS was able to find 3 more included studies than the top two phases of the HSSS alone, or in combination with any of the other proposed search terms, but at the expense of missing 56 relevant articles that would be found if all three phases of the HSSS were used. The estimated time needed to finish a review is 1086 hours for all three phases of the HSSS, 823 hours for the strategy versus, 818 hours for the first two phases of the HSSS or any of the other three proposed strategies. CONCLUSION: This study shows that compared to the first two phases of the HSSS, adding the term versus to the top two phases of the HSSS balances the sensitivity and precision in the reviews studied here to some extent but the differences are very small. It is well known that missing relevant studies may result in bias in systematic reviews. Reviewers need to weigh the trade-offs when selecting the search strategies for identifying RCTs in MEDLINE.

Abstracting and Indexing↗
PubMedDate not supplied

Creating an online dictionary of abbreviations from MEDLINE.

OBJECTIVE: The growth of the biomedical literature presents special challenges for both human readers and automatic algorithms. One such challenge derives from the common and uncontrolled use of abbreviations in the literature. Each additional abbreviation increases the effective size of the vocabulary for a field. Therefore, to create an automatically generated and maintained lexicon of abbreviations, we have developed an algorithm to match abbreviations in text with their expansions. DESIGN: Our method uses a statistical learning algorithm, logistic regression, to score abbreviation expansions based on their resemblance to a training set of human-annotated abbreviations. We applied it to Medstract, a corpus of MEDLINE abstracts in which abbreviations and their expansions have been manually annotated. We then ran the algorithm on all abstracts in MEDLINE, creating a dictionary of biomedical abbreviations. To test the coverage of the database, we used an independently created list of abbreviations from the China Medical Tribune. MEASUREMENTS: We measured the recall and precision of the algorithm in identifying abbreviations from the Medstract corpus. We also measured the recall when searching for abbreviations from the China Medical Tribune against the database. RESULTS: On the Medstract corpus, our algorithm achieves up to 83% recall at 80% precision. Applying the algorithm to all of MEDLINE yielded a database of 781,632 high-scoring abbreviations. Of all the abbreviations in the list from the China Medical Tribune, 88% were in the database. CONCLUSION: We have developed an algorithm to identify abbreviations from text. We are making this available as a public abbreviation server at \url[http://abbreviation.stanford.edu/].

Abbreviations as Topic↗
PubMed2000

Free MEDLINE and implications for library operations.

The widespread availability of free MEDLINE systems on the Internet raises issues about the continued need to allocate library funds for commercial, fee-for-service MEDLINE vendors. This paper explores the evolution and acceptance of free MEDLINE, looking in particular at NLM's PubMed system. Results of a survey on librarian perceptions of PubMed are discussed. The new generation of PubMed software is evaluated in the context of end-user needs and educational goals of medical libraries.

Fee-for-Service Plans↗
PubMed2000

PubMed, Internet Grateful Med, and Ovid: a comparison of three MEDLINE Internet interfaces.

Three MEDLINE Internet interfaces are compared: PubMed, Internet Grateful Med, and Ovid MEDLINE. Although these interfaces all search MEDLINE, significant differences exist in terms of their search interfaces, presentation of results, and special features. This paper examines these variations and explores some of the advantages and disadvantages of the three interfaces.

Information Storage and Retrieval↗
PubMed2004

Comparing the self-described searching knowledge of first-year medical and dental students before and after a MEDLINE class.

Do students need MEDLINE instruction? Do self-described knowledge and search skills match actual ability? To address these questions, librarians developed an assessment tool, a self-administered pre-test/post-test of eighteen skills and concepts taught in the MEDLINE class. By their own assessment, 70% or more of the medical and dental students learned something about each concept taught during the workshop. The study convinced faculty and students that the MEDLINE class is necessary. Librarians and associated faculty agree that the class is important and should continue to be mandatory.

Curriculum↗