Limits of search filter development.
Ontology highlight
ABSTRACT: Objective
The research attempted to develop search filters for biomedical literature databases that improve retrieval of studies of clinical relevance for the nursing and rehabilitation professions.Methods
Diagnostic testing framework compared machine-culled and practitioner-nominated search terms with a hand-tagged clinical literature database.Results
We were unable to: (1) develop filters for nursing, likely because of the overlapping and expanding scope of practice for nurses in comparison with medical professionals, or (2) develop filters for rehabilitation, because of its broad scope and the profession's multifaceted understanding of "health and ability."Conclusions
We found limitations on search filter development for these health professions: nursing and rehabilitation.
SUBMITTER: Wilczynski NL
PROVIDER: S-EPMC4722641 | biostudies-literature | 2016 Jan
REPOSITORIES: biostudies-literature
Publications
Limits of search filter development.
Wilczynski Nancy L NL Lokker Cynthia C McKibbon Kathleen Ann KA Hobson Nicholas N Haynes R Brian RB
Journal of the Medical Library Association : JMLA 20160101 1
<h4>Objective</h4>The research attempted to develop search filters for biomedical literature databases that improve retrieval of studies of clinical relevance for the nursing and rehabilitation professions.<h4>Methods</h4>Diagnostic testing framework compared machine-culled and practitioner-nominated search terms with a hand-tagged clinical literature database.<h4>Results</h4>We were unable to: (1) develop filters for nursing, likely because of the overlapping and expanding scope of practice for ...[more]
Similar Datasets
Project description:BACKGROUND:Integrated care is an increasingly important principle for organising healthcare. Integrated care models show promise in reducing resource wastage and service fragmentation whilst improving the accessibility, patient-centredness and quality of care for patients. Those needing reliable access to the growing research evidence base for integrated care can be frustrated by search challenges reflective of the topic's complexity. The aim of this study is to report the empirical development and validation of two search filters for rapid and effective retrieval of integrated care evidence in PubMed. One filter is optimised for recall and the other for precision. METHODS:An Expert Advisory Group comprising international integrated care experts guided the study. A gold standard test set of citations was formed from screening Handbook Integrated Care chapter references for relevance. This set was divided into a Term Identification Set (20%) for determining candidate terms using frequency analysis; a Filter Development Set (40%) for testing performance of term combinations; and a Filter Validation Set (40%) reserved for confirming final filter performance. In developing the high recall filter, recall was steadily increased while maintaining precision at ?50%. Similarly, the high precision filter sought to maximise precision while keeping recall ?50%. For each term combination tested, an approximation of precision was obtained by reviewing the first 100 citations retrieved in Medline for relevance. RESULTS:The gold standard set comprised 534 citations. The search filter optimised for recall ('Broad Integrated Care Search') achieved 86.0-88.3% recall with corresponding low precision (47-53%). The search filter optimised for precise searching ('Narrow Integrated Care Search') demonstrated precision of 73-95% with recall reduced to between 55.9 and 59.8%. These filters are now available as one-click URL hyperlinks in the website of International Foundation for Integrated Care. CONCLUSIONS:The Broad and Narrow Integrated Care Search filters provide potential users, such as policy makers and researchers, seamless, reliable and ongoing access to integrated care evidence for decision making. These filters were developed according to a rigorous and transparent methodology designed to circumvent the challenges of information retrieval posed by this complex, multifaceted topic.
| S-EPMC6971984 | biostudies-literature
Project description:BackgroundDegenerative cervical myelopathy (DCM) is a common condition with many unmet clinical needs. Pooled analysis of studies is an important tool for advancing medical understanding. This process starts with a systematic search of the literature. Identification of studies in DCM is challenged by a number of factors, including non-specific terminology and index terms. Search filters or HEDGEs, are search strings developed and validated to optimise medical literature searches. We aimed to develop a search filter for DCM for the MEDLINE database.MethodsThe diagnostic test assessment framework of a "development dataset" and seperate "validation dataset" was used. The development dataset was formed by hand searching four leading spinal journals (Spine, Journal of Neurosurgery Spine, Spinal Cord and Journal of Spinal Disorders and Techniques) in 2005 and 2010. The search filter was initially developed focusing on sensitivity and subsequently refined using NOT functions to improve specificity. One validation dataset was formed from DCM narrative and systematic review articles and the second, articles published in April of 1989, 1993, 1997, 2001, 2005, 2009, 2013 and 2017 retrieved via the search MeSH term 'Spine'. Metrics of sensitivity, specificity, precision and accuracy were used to test performance.ResultsHand searching identified 77/1094 relevant articles for 2005 and 55/1199 for 2010. We developed a search hedge with 100% sensitivity and a precision of 30 and 29% for the 2005 and 2010 development datasets respectively. For the selected time periods, EXP Spine returned 2113 publications and 30 were considered relevant. The search filter identified all 30 relevant articles, with a specificity of 94% and precision of 20%. Of the 255 references listed in the narrative index reviews, 225 were indexed in MEDLINE and 165 (73%) were relevant articles. All relevant articles were identified and accuracy ranged from 67 to 97% over the three reviews. Of the 42 articles returned from 3 recent systematic reviews, all were identified by the filter.ConclusionsWe have developed a highly sensitive hedge for the research of DCM. Whilst precision is similarly low as other hedges, this search filter can be used as an adjunct for DCM search strategies.
| S-EPMC6034255 | biostudies-literature
Project description:OBJECTIVES: For the measurement of patient-reported outcomes, such as (health-related) quality of life, often many measurement instruments exist that intend to measure the same construct. To facilitate instrument selection, our aim was to develop a highly sensitive search filter for finding studies on measurement properties of measurement instruments in PubMed and a more precise search filter that needs less abstracts to be screened, but at a higher risk of missing relevant studies. METHODS: A random sample of 10,000 PubMed records (01-01-1990 to 31-12-2006) was used as a gold standard. Studies on measurement properties were identified using an exclusion filter and hand searching. Search terms were selected from the relevant records in the gold standard as well as from 100 systematic reviews of measurement properties and combined based on sensitivity and precision. The performance of the filters was tested in the gold standard as well as in two validation sets, by calculating sensitivity, precision, specificity, and number needed to read. RESULTS: We identified 116 studies on measurement properties in the gold standard. The sensitive search filter was able to retrieve 113 of these 116 studies (sensitivity 97.4%, precision 4.4%). The precise search filter had a sensitivity of 93.1% and a precision of 9.4%. Both filters performed very well in the validation sets. CONCLUSION: The use of these search filters will contribute to evidence-based selection of measurement instruments in all medical fields.
| S-EPMC2744791 | biostudies-other
Project description:The research sought to establish validated search filters for retrieval of studies on patients' knowledge and values.Two nonprofit organizations in the Netherlands were studied for guideline development.An existing filter was adapted to three bibliographic interfaces. After defining the scope, a reference database was built for the development of the new filters. The performance of the new filters was validated in different disease categories.Sensitivity, specificity, precision, negative predictive value, and accuracy were (%): 90.5/98/77/99.2/97 (MEDLINE-Ovid), 90.1/98.8/79.3/99.5/98.3 (PubMed), and 93.1/98.4/81.8/99.6/98.7 (Embase).The filters provide pragmatic tools for searching for patients' issues. Further optimization and validation is recommended.
| S-EPMC5079497 | biostudies-literature
Project description:BACKGROUND:Health inequalities, worse health associated with social and economic disadvantage, are reported by a minority of research articles. Locating these studies when conducting an equity-focused systematic review is challenging due to a deficit in standardised terminology, indexing, and lack of validated search filters. Current reporting guidelines recommend not applying filters, meaning that increased resources are needed at the screening stage. METHODS:We aimed to design and test search filters to locate studies that reported outcomes by a social determinant of health. We developed and expanded a 'specific terms strategy' using keywords and subject headings compiled from recent systematic reviews that applied an equity filter. A 'non-specific strategy' was compiled from phrases used to describe equity analyses that were reported in titles and abstracts, and related subject headings. Gold standard evaluation and validation sets were compiled. The filters were developed in MEDLINE, adapted for Embase and tested in both. We set a target of 0.90 sensitivity (95% CI; 0.84, 0.94) in retrieving 150 gold standard validation papers. We noted the reduction in the number needed to screen in a proposed equity-focused systematic review and the proportion of equity-focused reviews we assessed in the project that applied an equity filter to their search strategy. RESULTS:The specific terms strategy filtered out 93-95% of all records, and retrieved a validation set of articles with a sensitivity of 0.84 in MEDLINE (0.77, 0.89), and 0.87 (0.81, 0.92) in Embase. When combined (Boolean 'OR') with the non-specific strategy sensitivity was 0.92 (0.86, 0.96) in MEDLINE (Embase 0.94; 0.89, 0.97). The number needed to screen was reduced by 77% by applying the specific terms strategy, and by 59.7% (MEDLINE) and 63.5% (Embase) by applying the combined strategy. Eighty-one per cent of systematic reviews filtered studies by equity. CONCLUSIONS:A combined approach of using specific and non-specific terms is recommended if systematic reviewers wish to filter studies for reporting outcomes by social determinants. Future research should concentrate on the indexing standardisation for equity studies and further development and testing of both specific and non-specific terms for accurate study retrieval.
| S-EPMC6186133 | biostudies-literature
Project description:BackgroundHealth-evidence.ca is an online registry of systematic reviews evaluating the effectiveness of public health interventions. Extensive searching of bibliographic databases is required to keep the registry up to date. However, search filters have been developed to assist in searching the extensive amount of published literature indexed. Search filters can be designed to find literature related to a certain subject (i.e. content-specific filter) or particular study designs (i.e. methodological filter). The objective of this paper is to describe the development and validation of the health-evidence.ca Systematic Review search filter and to compare its performance to other available systematic review filters.MethodsThis analysis of search filters was conducted in MEDLINE, EMBASE, and CINAHL. The performance of thirty-one search filters in total was assessed. A validation data set of 219 articles indexed between January 2004 and December 2005 was used to evaluate performance on sensitivity, specificity, precision and the number needed to read for each filter.ResultsNineteen of 31 search filters were effective in retrieving a high level of relevant articles (sensitivity scores greater than 85%). The majority achieved a high degree of sensitivity at the expense of precision and yielded large result sets. The main advantage of the health-evidence.ca Systematic Review search filter in comparison to the other filters was that it maintained the same level of sensitivity while reducing the number of articles that needed to be screened.ConclusionsThe health-evidence.ca Systematic Review search filter is a useful tool for identifying published systematic reviews, with further screening to identify those evaluating the effectiveness of public health interventions. The filter that narrows the focus saves considerable time and resources during updates of this online resource, without sacrificing sensitivity.
| S-EPMC3515398 | biostudies-literature
Project description:Tail-anchored (TA) proteins play essential roles in mammalian cells, and their accurate localization is critical for proteostasis. Biophysical similarities lead to mistargeting of mitochondrial TA proteins to the ER, where they are delivered to the insertase, the ER membrane protein complex (EMC). Leveraging an improved structural model of the human EMC, we used mutagenesis and site-specific crosslinking to map the path of a TA protein from its cytosolic capture by methionine-rich loops to its membrane insertion through a hydrophilic vestibule. Positively charged residues at the entrance to the vestibule function as a selectivity filter that uses charge-repulsion to reject mitochondrial TA proteins. Similarly, this selectivity filter retains the positively charged soluble domains of multipass substrates in the cytosol, thereby ensuring they adopt the correct topology and enforcing the "positive-inside" rule. Substrate discrimination by the EMC provides a biochemical explanation for one role of charge in TA protein sorting and protects compartment integrity by limiting protein misinsertion.
| S-EPMC10200711 | biostudies-literature
Project description:ObjectiveHealthcare debates and policy developments are increasingly concerned with a broad range of values-related areas. These include not only ethical, moral, religious, and other types of values 'proper', but also beliefs, preferences, experiences, choices, satisfaction, quality of life, etc. Research on such issues may be difficult to retrieve. This study used word frequency analysis to generate a broad pool of search terms and a brief filter to facilitate relevant searches in bibliographic databases.MethodsWord frequency analysis for 'values terms' was performed on citations on diabetes, obesity, dementia, and schizophrenia (Medline; 2004-2006; 4440 citations; 1,110,291 words). Concordance® and SPSS 14.0 were used. Text words and MeSH terms of high frequency and precision were compiled into a search filter. It was validated on datasets of citations on dentistry and food hypersensitivity.Results144 unique text words and 124 unique MeSH terms of moderate and high frequency (≥ 20) and very high precision (≥ 90%) were identified. Of these, 19 text words and seven MeSH terms were compiled into a 'brief values filter'. In the derivation dataset, it had a sensitivity of 76.8% and precision of 86.8%. In the validation datasets, its sensitivity and precision were, respectively, 70.1% and 63.6% (food hypersensitivity) and 47.1% and 82.6% (dentistry).ConclusionsThis study provided a varied pool of search terms and a simple and highly effective tool for retrieving publications on health-related values. Further work is required to facilitate access to such research and enhance its chances of being translated into practice, policy, and service improvements.
| S-EPMC3341778 | biostudies-literature
Project description:ObjectivesThis paper describes the development, execution, and subsequent failure of an attempt to create an Ovid Embase search filter for locating systematic review methodology articles.MethodsThe authors devised a work plan, based on best practices, for search filter development that has been outlined in the literature. Three reference samples were gathered by identifying the OVID Embase records for specific articles that were included in the PubMed Systematic Review Methods subset. The first sample was analyzed to develop a set of keywords and subject headings to include in the search filter. The second and third samples would have been used to calibrate the search filter and to calculate filter sensitivity and precision, respectively.ResultsTechnical shortcomings, database indexing practices, and the fuzzy nature of keyword terminology relevant to the topic prevented us from designing the search filter.ConclusionCreating a search filter to identify systematic review methodology articles in Ovid Embase is not possible at this time.
| S-EPMC6466493 | biostudies-literature
Project description:Macrophages define a key component of immune cells present in atherosclerotic lesions and are central regulators of the disease. Since epigenetic processes are important in controlling macrophage function, interfering with epigenetic pathways in macrophages might be a novel approach to combat atherosclerosis. Histone H3K27 trimethylation is a repressive histone mark catalyzed by polycomb repressive complex with EZH2 as the catalytic subunit. EZH2 is described to increase macrophage inflammatory responses by supressing the suppressor of cytokine signaling, Socs3. We previously showed that myeloid deletion of Kdm6b, an enzymes that in contrast to EZH2 removes repressive histone H3K27me3 marks, results in advanced atherosclerosis. Because of its opposing function and importance of EZH2 in macrophage inflammatory responses, we here studied the role of myeloid EZH2 in atherosclerosis. A myeloid-specific Ezh2 deficient mouse strain (Ezh2del) was generated (LysM-cre+ x Ezh2fl/fl) and bone marrow from Ezh2del or Ezh2wt mice was transplanted to Ldlr-/- mice which were fed a high fat diet for 9 weeks to study atherosclerosis. Atherosclerotic lesion size was significantly decreased in Ezh2del transplanted mice compared to control. The percentage of macrophages in the atherosclerotic lesion was similar, however neutrophil numbers were lower in Ezh2del transplanted mice. Correspondingly, the migratory capacity of neutrophils was decreased in Ezh2del mice. Moreover, peritoneal Ezh2del foam cells showed a reduction in the inflammatory response with reduced production of nitric oxide, IL-6 and IL-12. In Conclusion, myeloid Ezh2 deficiency impairs neutrophil migration and reduces macrophage foam cell inflammatory responses, both contributing to reduced atherosclerosis.
| S-EPMC7871783 | biostudies-literature