Evaluation of a new method for librarian-mediated literature searches for systematic reviews.
Ontology highlight
ABSTRACT: Methods
Single-line search strategies were prepared in a text document. Term completeness was ensured with a novel optimization technique. Macros in MS Word converted the syntaxes between databases and interfaces almost automatically. We compared search characteristics, such as number of search terms and databases, and outcomes, such as number of included and retrieved references and precision, from ESM searches and other Dutch academic hospitals identified by searching PubMed for systematic reviews published between 2014 and 2016. We compared time to perform the ESM with a secondary comparator of recorded search times from published literature and contact with authors to acquire unpublished data.Results
We identified 73 published Erasmus MC systematic reviews and 258 published by other Dutch academic hospitals meeting our criteria. We pooled search time data from 204 other systematic reviews. The ESM searches differed by using 2 times more databases, retrieving 44% more references, including 20% more studies in the final systematic review, but the time needed for the search was 8% of that of the control group. Similarities between methods include precision and the number of search terms.Conclusions
The evaluated similarities and differences suggest that the ESM is a highly efficient way to locate more references meeting the specified selection criteria in systematic reviews than traditional search methods. Further prospective research is required.
SUBMITTER: Bramer WM
PROVIDER: S-EPMC5920798 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BACKGROUND:Within systematic reviews, when searching for relevant references, it is advisable to use multiple databases. However, searching databases is laborious and time-consuming, as syntax of search strategies are database specific. We aimed to determine the optimal combination of databases needed to conduct efficient searches in systematic reviews and whether the current practice in published reviews is appropriate. While previous studies determined the coverage of databases, we analyzed the actual retrieval from the original searches for systematic reviews. METHODS:Since May 2013, the first author prospectively recorded results from systematic review searches that he performed at his institution. PubMed was used to identify systematic reviews published using our search strategy results. For each published systematic review, we extracted the references of the included studies. Using the prospectively recorded results and the studies included in the publications, we calculated recall, precision, and number needed to read for single databases and databases in combination. We assessed the frequency at which databases and combinations would achieve varying levels of recall (i.e., 95%). For a sample of 200 recently published systematic reviews, we calculated how many had used enough databases to ensure 95% recall. RESULTS:A total of 58 published systematic reviews were included, totaling 1746 relevant references identified by our database searches, while 84 included references had been retrieved by other search methods. Sixteen percent of the included references (291 articles) were only found in a single database; Embase produced the most unique references (n?=?132). The combination of Embase, MEDLINE, Web of Science Core Collection, and Google Scholar performed best, achieving an overall recall of 98.3 and 100% recall in 72% of systematic reviews. We estimate that 60% of published systematic reviews do not retrieve 95% of all available relevant references as many fail to search important databases. Other specialized databases, such as CINAHL or PsycINFO, add unique references to some reviews where the topic of the review is related to the focus of the database. CONCLUSIONS:Optimal searches in systematic reviews should search at least Embase, MEDLINE, Web of Science, and Google Scholar as a minimum requirement to guarantee adequate and efficient coverage.
| S-EPMC5718002 | biostudies-literature
Project description:ObjectiveThe research evaluated the perceived quality of librarian-mediated literature searching services at one of Canada's largest acute care teaching hospitals for the purpose of continuous quality improvement and investigation of relationships between variables that can impact user satisfaction.MethodsAn online survey was constructed using evidence-based methodologies. A systematic sample of staff and physicians requesting literature searches at London Health Sciences Centre were invited to participate in the study over a one-year period. Data analyses included descriptive statistics of closed-ended questions and coding of open-ended questions.ResultsA range of staff including clinicians, researchers, educators, leaders, and analysts submitted a total of 137 surveys, representing a response rate of 71%. Staff requested literature searches for the following "primary" purposes: research or publication (34%), teaching or training (20%), informing a policy or standard practice (16%), patient care (15%), and "other" purposes (15%). While the majority of staff (76%) submitted search requests using methods of written communication, including email and search request forms, staff using methods of verbal communication, including face-to-face and telephone conversations, were significantly more likely to be extremely satisfied with the librarian's interpretation of the search request (p=0.004) and to rate the perceived quality of the search results as excellent (p=0.005). In most cases, librarians followed up with staff to clarify the details of their search requests (72%), and these staff were significantly more likely to be extremely satisfied with the librarian's interpretation of the search request (p=0.002).ConclusionsOur results demonstrate the limitations of written communication in the context of librarian-mediated literature searching and suggest a multifaceted approach to quality improvement efforts.
| S-EPMC5370602 | biostudies-literature
Project description:BackgroundLiterature searches underlie the foundations of systematic reviews and related review types. Yet, the literature searching component of systematic reviews and related review types is often poorly reported. Guidance for literature search reporting has been diverse, and, in many cases, does not offer enough detail to authors who need more specific information about reporting search methods and information sources in a clear, reproducible way. This document presents the PRISMA-S (Preferred Reporting Items for Systematic reviews and Meta-Analyses literature search extension) checklist, and explanation and elaboration.MethodsThe checklist was developed using a 3-stage Delphi survey process, followed by a consensus conference and public review process.ResultsThe final checklist includes 16 reporting items, each of which is detailed with exemplar reporting and rationale.ConclusionsThe intent of PRISMA-S is to complement the PRISMA Statement and its extensions by providing a checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of a search is completely reported and therefore reproducible.
| S-EPMC7839230 | biostudies-literature
Project description:BackgroundLiterature searches underlie the foundations of systematic reviews and related review types. Yet, the literature searching component of systematic reviews and related review types is often poorly reported. Guidance for literature search reporting has been diverse and, in many cases, does not offer enough detail to authors who need more specific information about reporting search methods and information sources in a clear, reproducible way. This document presents the PRISMA-S (Preferred Reporting Items for Systematic reviews and Meta-Analyses literature search extension) checklist, and explanation and elaboration.MethodsThe checklist was developed using a three-stage Delphi survey process, followed by a consensus conference and public review process.ResultsThe final checklist includes sixteen reporting items, each of which is detailed with exemplar reporting and rationale.ConclusionsThe intent of PRISMA-S is to complement the PRISMA Statement and its extensions by providing a checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of a search is completely reported and, therefore, reproducible.
| S-EPMC8270366 | biostudies-literature
Project description:BACKGROUND:The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. METHODS:The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. RESULTS:GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. CONCLUSIONS:Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert.
| S-EPMC3882110 | biostudies-literature
Project description:Creating search strategies for systematic reviews, finding the best balance between sensitivity and specificity, and translating search strategies between databases is challenging. Several methods describe standards for systematic search strategies, but a consistent approach for creating an exhaustive search strategy has not yet been fully described in enough detail to be fully replicable. The authors have established a method that describes step by step the process of developing a systematic search strategy as needed in the systematic review. This method describes how single-line search strategies can be prepared in a text document by typing search syntax (such as field codes, parentheses, and Boolean operators) before copying and pasting search terms (keywords and free-text synonyms) that are found in the thesaurus. To help ensure term completeness, we developed a novel optimization technique that is mainly based on comparing the results retrieved by thesaurus terms with those retrieved by the free-text search words to identify potentially relevant candidate search terms. Macros in Microsoft Word have been developed to convert syntaxes between databases and interfaces almost automatically. This method helps information specialists in developing librarian-mediated searches for systematic reviews as well as medical and health care practitioners who are searching for evidence to answer clinical questions. The described method can be used to create complex and comprehensive search strategies for different databases and interfaces, such as those that are needed when searching for relevant references for systematic reviews, and will assist both information specialists and practitioners when they are searching the biomedical literature.
| S-EPMC6148622 | biostudies-literature
Project description:ObjectivesTo determine whether librarian or information specialist authorship is associated with better reproducibility of the search, at least three databases searched, and better reporting quality in dental systematic reviews (SRs).MethodsSRs from the top ten dental research journals (as determined by Journal Citation Reports and Scimago) were reviewed for search quality and reproducibility by independent reviewers using two Qualtrics survey instruments. Data was reviewed for all SRs based on reproducibility and librarian participation and further reviewed for search quality of reproducible searches.ResultsLibrarians were co-authors in only 2.5% of the 913 included SRs and librarians were mentioned or acknowledged in only 9% of included SRs. Librarian coauthors were associated with more reproducible searches, higher search quality, and at least three databases searched. Although the results indicate librarians are associated with improved SR quality, due to the small number of SRs that included a librarian, results were not statistically significant.ConclusionDespite guidance from organizations that produce SR guidelines recommending the inclusion of a librarian or information specialist on the review team, and despite evidence showing that librarians improve the reproducibility of searches and the reporting of methodology in SRs, librarians are not being included in SRs in the field of dental medicine. The authors of this review recommend the inclusion of a librarian on SR teams in dental medicine and other fields.
| S-EPMC8409615 | biostudies-literature
Project description:A novel molecular structure prediction method, the Z Method, is described. It provides a versatile platform for the development and use of systematic, grid-based conformational search protocols, in which statistical information (i.e., rotamers) can also be included. The Z Method generates trial structures by applying many changes of the same type to a single starting structure, thereby sampling the conformation space in an unbiased way. The method, implemented in the CHARMM program as the Z Module, is applied here to an illustrative model problem in which rigid, systematic searches are performed in a 36-dimensional conformational space that describes the relative positions of the 10 secondary structural elements of the protein CheY. A polar hydrogen representation with an implicit solvation term (EEF1) is used to evaluate successively larger fragments of the protein generated in a hierarchical build-up procedure. After a final refinement stage, and a total computational time of about two-and-a-half CPU days on AMD Opteron processors, the prediction is within 1.56 Å of the native structure. The errors in the predicted backbone dihedral angles are found to approximately cancel. Monte Carlo and simulated annealing trials on the same or smaller versions of the problem, using the same atomic model and energy terms, are shown to result in less accurate predictions. Although the problem solved here is a limited one, the findings illustrate the utility of systematic searches with atom-based models for macromolecular structure prediction and the importance of unbiased sampling in structure prediction methods.
| S-EPMC3298744 | biostudies-literature
Project description:PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a given protein. The scope of these publications varies a lot: they include studies focused on biochemical functions of individual proteins, but also reports from genome sequencing projects that introduce tens of thousands of proteins. Collecting and analyzing publications related to sets of homologous proteins help in functional annotation of novel protein families and in improving annotations of well-studied protein families or individual genes. However, performing such collection and analysis manually is a tedious and time-consuming process. PubServer automatically collects identifiers of homologous proteins using PSI-Blast, retrieves literature references from corresponding database entries and filters out publications unlikely to contain useful information about individual proteins. It also prepares simple vocabulary statistics from titles, abstracts and MeSH terms to identify the most frequently occurring keywords, which may help to quickly identify common themes in these publications. The filtering criteria applied to collected publications are user-adjustable. The results of the server are presented as an interactive page that allows re-filtering and different presentations of the output.
| S-EPMC4086066 | biostudies-literature
Project description:BACKGROUND:Research turnover in the HIV field is rapid, and as a result, maintaining high-quality, up-to-date, and relevant systematic reviews is a challenge. One approach is to frequently update published reviews. METHODS:We evaluated the methods and relevance of all HIV systematic reviews and protocols published in the Cochrane Library over a 16-year period (2000-2016) to determine the need to update published reviews or complete of reviews in progress. RESULTS:Of 148 published reviews and protocols, 129 (87%) were identified as not for updating or progression to publication, mostly due to research questions which were either entirely outdated or addressed questions in an outdated manner (N?=?89; 60%); this was anticipated for older reviews, but was found also to be the case for recent publications. Some research questions were also inadequately conceptualized, particularly when complex pragmatic trials or behavioral interventions were included. CONCLUSIONS:We suggest that authors clearly characterize interventions and synthesis approaches in their review protocols. In research fields, such as HIV, where questions change frequently, systematic reviews and protocols should be regularly re-evaluated to ensure relevance to current questions. This process of re-evaluation should be incorporated into the methods of living systematic reviews.
| S-EPMC6366015 | biostudies-literature