Consistency and Accuracy of the Medical Subject Headings® Thesaurus for Electronic Indexing and Retrieval of Chronobiologic References

Evaluation of Medical Subject Headings assignment in simulated patient articles

OBJECTIVES

To evaluate human-based Medical Subject Headings (MeSH) allocation in articles about 'patient simulation'-a technique that mimics real-life patient scenarios with controlled patient responses.

METHODS

A validation set of articles indexed before the Medical Text Indexer-Auto implementation (in 2019) was created with 150 combinations potentially referring to 'patient simulation'. Articles were classified into four categories of simulation studies. Allocation of seven MeSH terms (Simulation Training, Patient Simulation, High Fidelity Simulation Training, Computer Simulation, Patient-Specific Modelling, Virtual Reality, and Virtual Reality Exposure Therapy) was investigated. Accuracy metrics (sensitivity, precision, or positive predictive value) were calculated for each category of studies.

KEY FINDINGS

A set of 7213 articles was obtained from 53 different word combinations, with 2634 excluded as irrelevant. 'Simulated patient' and 'standardized/standardized patient' were the most used terms. The 4579 included articles, published in 1044 different journals, were classified into: 'Machine/Automation' (8.6%), 'Education' (75.9%) and 'Practice audit' (11.4%); 4.1% were 'Unclear'. Articles were indexed with a median of 10 MeSH (IQR 8-13); however, 45.5% were not indexed with any of the seven MeSH terms. Patient Simulation was the most prevalent MeSH (24.0%). Automation articles were more associated with Computer Simulation MeSH (sensitivity = 54.5%; precision = 25.1%), while Education articles were associated with Patient Simulation MeSH (sensitivity = 40.2%; precision = 80.9%). Practice audit articles were also polarized to Patient Simulation MeSH (sensitivity = 34.6%; precision = 10.5%).

CONCLUSIONS

Inconsistent use of free-text words related to patient simulation was observed, as well as inaccuracies in human-based MeSH assignments. These limitations can compromise relevant literature retrieval to support evidence synthesis exercises.

Influence of automated indexing in Medical Subject Headings (MeSH) selection for pharmacy practice journals

BACKGROUND

The Medical Subject Headings (MeSH) thesaurus is the controlled vocabulary used to index articles in MEDLINE. MeSH were mainly manually selected until June 2022 when an automated algorithm, the Medical Text Indexer (MTI) automated was fully implemented. A selection of automated indexed articles is then reviewed (curated) by human indexers to ensure the quality of the process.

OBJECTIVE

To describe the association of MEDLINE indexing methods (i.e., manual, automated, and automated + curated) on the MeSH assignment in pharmacy practice journals compared with medical journals.

METHODS

Original research articles published between 2016 and 2023 in two groups of journals (i.e., the Big-five general medicine and three pharmacy practice journals) were selected from PubMed using journal-specific search strategies. Metadata of the articles, including MeSH terms and indexing method, was extracted. A list of pharmacy-specific MeSH terms had been compiled from previously published studies, and their presence in pharmacy practice journal records was investigated. Using bivariate and multivariate analyses, as well as effect size measures, the number of MeSH per article was compared between journal groups, geographic origin of the journal, and indexing method.

RESULTS

A total of 8479 original research articles was retrieved: 6254 from the medical journals and 2225 from pharmacy practice journals. The number of articles indexed by the various methods was disproportionate; 77.8 % of medical and 50.5 % of pharmacy manually indexed. Among those indexed using the automated system, 51.1 % medical and 10.9 % pharmacy practice articles were then curated to ensure the indexing quality. Number of MeSH per article varied among the three indexing methods for medical and pharmacy journals, with 15.5 vs. 13.0 in manually indexed, 9.4 vs. 7.4 in automated indexed, and 12.1 vs. 7.8 in automated and then curated, respectively. Multivariate analysis showed significant effect of indexing method and journal group in the number of MeSH attributed, but not the geographical origin of the journal.

CONCLUSIONS

Articles indexed using automated MTI have less MeSH than manually indexed articles. Articles published in pharmacy practice journals were indexed with fewer number of MeSH compared with general medical journal articles regardless of the indexing method used.

Use of 'Pharmaceutical services' Medical Subject Headings (MeSH) in articles assessing pharmacists' interventions

Background

Medical Subject Headings (MeSH) thesaurus contribute towards efficient searching of biomedical information. However, insufficient coverage of specific fields and inaccuracies in the indexing of articles can lead to bias during literature retrieval.

Objectives

This meta-research study aimed to assess the use of 'Pharmaceutical Services' MeSH terms in studies evaluating the effect of pharmacists' interventions.

Methods

An updated systematic search (Jan-2022) to gather meta-analyses comparing pharmacists' interventions vs. other forms of care was performed. All MeSH terms allocated to the MEDLINE record of each primary study included in the selected meta-analyses were systematically extracted. Terms from the 'Pharmaceutical Services' branch, including its descendants, as well as other 26 pharmacy-specific MeSH terms were identified. The assignment of these terms as a 'Major MeSH' was also evaluated. Descriptive statistics and social network analyses to evaluate the co-occurrence of the MeSH terms in the articles were conducted. Sensitivity analyses including only meta-analyses with declared objectives mentioning the words 'pharmacist' or 'pharmacy' were performed (SPSS v.24.0).

Results

Overall, 138 meta-analyses including 2012 primary articles were evaluated. A median of 15 [IQR 12-18] MeSH terms were assigned per article with a slight positive time-trend (Spearman rho = 0.193; p < 0.001). Only 36.6% (n = 736/2012) and 58.1% (n = 338/1099) of studies were indexed with one MeSH term from the 'Pharmaceutical Services' branch in the overall and sensitivity analyses, respectively. In <20% of cases, these terms were a 'Major MeSH'. The pharmacy-specific term 'Pharmacists' was the most frequently used, yet in only 27.8% and 47.7% of articles in the original and sensitivity analyses, respectively. Social networks showed a weak association between pharmacy-specific and 'Pharmaceutical services' branch MeSH terms.

Conclusions

The availability of a 'Pharmaceutical services' branch hierarchic tree and further pharmacy-specific MeSH terms incorporated to the MeSH thesaurus in the past years is not related with accurate indexing of articles.

Laboratory animals search filter for different literature databases: PubMed, Embase, Web of Science and PsycINFO

Systematic reviews are important tools in animal research, but the ever-increasing number of studies makes retrieval of all relevant publications challenging. Search filters aid in retrieving as many animal studies as possible. In this paper we provide updated and expanded versions of the SYRCLE animal filters for PubMed and Embase. We provide the Embase filter for both Embase.com and via Ovid. Furthermore, we provide new animal search filters for Web of Science (WoS) and APA PsycINFO via psycnet.apa.org and via Ovid. Compared with previous versions, the new filters retrieved 0.5-47.1% (19 references for PubMed, 837 for WoS) more references in a real-life example. All filters retrieved additional references, comprising multiple relevant reviews. A random sample from WoS found at least one potentially relevant primary study. These animal search filters facilitate identifying as many animal studies as possible while minimising the number of non-animal studies.

Trends in prenatal diagnosis: An analysis of 40 years of Medical Subject Heading (MeSH) terms in publications

OBJECTIVE

To understand the evolution of the field of prenatal diagnosis over the past four decades.

METHOD

We analyzed the publications in the journal Prenatal Diagnosis from its inception in 1980 to 2019 using Medical Subject Headings (MeSH) to examine the major research topics and trends. The results were analyzed by 10-year intervals.

RESULTS

Publications on prenatal cytogenetics, congenital anomalies and fetal imaging predominated during the first three decades, with a steady increase in molecular genetics over time. Publications on NIPT did not appear until the most recent decade and are likely under-counted because there was no MeSH term for NIPT until 2020.

CONCLUSION

The topics covered in Prenatal Diagnosis articles have evolved considerably over the past four decades and reflect a response to advances in technology and widespread incorporation of prenatal screening and diagnosis into standard obstetric care. The strengths of this analysis are its objective nature, its use of the standard MeSH terms used for coding, and application of a novel cluster analysis to visualize trends. The analysis also pointed out the fact that MeSH terms in this sub-specialty area are often inconsistent due to manually coding based on individual subject matter expertise.

Assessment of indexing trends with specific and general terms for herbal medicine

BACKGROUND

Concepts for medicinal plants are represented by a variety of associated general terms with specific indexing patterns in databases, which may not consistently reflect growth of records.

OBJECTIVES

The objectives of this study are to assess the development in databases by identifying general terms that describe herbal medicine with optimal retrieval recall and to identify possible special trends in co-occurrence of specific and general concepts.

METHODS

Different search strategies are tested in cab abstracts, medline and web of science. Specific terms (Origanum and Salvia) are employed. Relevant general terms (e.g. 'Plants, Medicinal', Phytotherapy, Herbal drugs) are identified, along with indexing trends and co-occurrences.

RESULTS

Growth trends, in specific (narrower) terms, are similar among databases. General terms, however, exhibit dissimilar trends, sometimes almost opposing one another. Co-occurrence of specific and general terms is changing over time.

CONCLUSIONS

General terms may not denote definite development of trends as the use of terms differs amongst databases, making it difficult to correctly assess possible numbers of relevant records. Perceived increase can, sometimes, be attributed to an increased occurrence of a more general term alongside the specific one. Thesaurus-controlled databases may yield more hits, because of 'up-posted' (broader) terms. Use of broader terms is helpful as it enhances retrieval of relevant documents.

Consistency and accuracy of indexing systematic review articles and meta-analyses in medline

BACKGROUND

Systematic review articles support the advance of science and translation of research evidence into healthcare practice. Inaccurate retrieval from medline could limit access to reviews.

OBJECTIVE

To determine the quality of indexing systematic reviews and meta-analyses in medline.

METHODS

The Clinical Hedges Database, containing the results of a hand search of 161 journals, was used to test medline indexing terms for their ability to retrieve systematic reviews that met predefined methodologic criteria (labelled as 'pass' review articles) and reviews that reported a meta-analysis.

RESULTS

The Clinical Hedges Database contained 49 028 articles; 753 were 'pass' review articles (552 with a meta-analysis). In total 758 review articles (independent of whether they passed) reported a meta-analysis. The search strategy that retrieved the highest number of 'pass' systematic reviews achieved a sensitivity of 97.1%. The publication type 'meta analysis' had a false positive rate of 5.6% (95% CI 3.9 to 7.6), and false negative rate of 0.31% (95% CI 0.26 to 0.36) for retrieving systematic reviews that reported a meta-analysis.

CONCLUSIONS

Inaccuracies in indexing systematic reviews and meta-analyses in medline can be partly overcome by a 5-term search strategy. Introducing a publication type for systematic reviews of the literature could improve retrieval performance.

Do restless legs syndrome (RLS) and periodic limb movements of sleep (PLMS) play a role in nocturnal hypertension and increased cardiovascular risk of renally impaired patients?

Hypertension can cause or promote renal failure and is related to cardiovascular mortality, the major cause of death in patients with renal impairment. Changes in the circadian BP pattern, particularly the blunting or reversal of the nocturnal decline in BP, are common in chronic renal failure. These changes in turn are among the major determinants of left ventricular hypertrophy. Using a chronobiological approach, it is possible to obtain better insight into the reciprocal relationship between hypertension, renal disease, and increased cardiovascular risk of renal patients. Disruption of the normal circadian rhythm of rest/activity may be hypothesized to underlie the high cardiovascular morbidity and mortality of such patients. Epidemiological studies reveal that hemodialysis patients experience poor subjective sleep quality and insomnia and, in comparison to healthy persons, are more likely to show shorter sleep duration and lower sleep efficiency. Sleep apnea may be present and is usually investigated in these patients; however, the prevalence of restless legs syndrome (RLS), which is high in dialysis patients and which has been associated with increased risk for cardiovascular disease in the general population, could also play a role in the pathogenesis of sleep-time hypertension in renal patients. Careful assessment of sleep quality, in particular, diagnostic screening for RLS and periodic limb movements (PLM) in renal patients, is highly recommended. In renal failure, attention to sleep quality and related perturbations of the sleep/wake cycle may help prevent the occurrence and progression of cardiovascular disease.

Filtering Medline for a clinical discipline: diagnostic test assessment framework

OBJECTIVE

To develop and test a Medline filter that allows clinicians to search for articles within a clinical discipline, rather than searching the entire Medline database.

DESIGN

Diagnostic test assessment framework with development and validation phases.

SETTING

Sample of 4657 articles published in 2006 from 40 journals. Reviews Each article was manually reviewed, and 19.8% contained information relevant to the discipline of nephrology. The performance of 1 155 087 unique renal filters was compared with the manual review.

MAIN OUTCOME MEASURES

Sensitivity, specificity, precision, and accuracy of each filter.

RESULTS

The best renal filters combined two to 14 terms or phrases and included the terms "kidney" with multiple endings (that is, truncation), "renal replacement therapy", "renal dialysis", "kidney function tests", "renal", "nephr" truncated, "glomerul" truncated, and "proteinuria". These filters achieved peak sensitivities of 97.8% and specificities of 98.5%. Performance of filters remained excellent in the validation phase.

CONCLUSIONS

Medline can be filtered for the discipline of nephrology in a reliable manner. Storing these high performance renal filters in PubMed could help clinicians with their everyday searching. Filters can also be developed for other clinical disciplines by using similar methods.