bims-librar Biomed News
on Biomedical librarianship
Issue of 2019–12–15
fiveteen papers selected by
Thomas Krichel, Open Library Society
  1. Performance evaluation of three semantic expansions to query PubMed.
  2. Partnering With Librarians.
  3. GenoSurf: metadata driven semantic search system for integrated genomic datasets.
  4. Medical library services in Switzerland: catching up with EBM.
  5. Semantic persistence of ambiguous biomedical names in the citation network.
  6. Impact of Automatic Query Generation and Quality Recognition Using Deep Learning to Curate Evidence From Biomedical Literature: Empirical Study.
  7. An open invitation to join HILJ [Journal] Club.
  8. Mesophotic.org: a repository for scientific information on mesophotic ecosystems.
  9. Web browsing habits of healthcare professions students in gross anatomy laboratory.
  10. Perspective on Systematic Literature Reviews and Meta-Analyses.
  11. Recommendations to conduct and report systematic reviews in medical literature: a scoping review.
  12. Searching the Internet for Infertility Information: A Survey of Patient Needs and Preferences.
  13. Improving cancer survivors' e-health literacy via online health communities (OHCs): a social support perspective.
  14. Health information on social media. Perceptions, attitudes, and practices of patients and their companions.
  15. Is internet a missed opportunity? Evaluating radon websites from a stakeholder engagement perspective.
  1. Health Info Libr J. 2019 Dec 14.
    Performance evaluation of three semantic expansions to query PubMed.
    Clément Massonnaud, Romain Lelong, Gaétan Kerdelhué, Emeline Lejeune, Julien Grosjean, Nicolas Griffon, Stefan J Darmoni.
       BACKGROUND: PubMed is one of the most important basic tools to access medical literature. Semantic query expansion using synonyms can improve retrieval efficacy.
    OBJECTIVE: The objective was to evaluate the performance of three semantic query expansion strategies.
    METHODS: Queries were built for forty MeSH descriptors using three semantic expansion strategies (MeSH synonyms, UMLS mappings, and mappings created by the CISMeF team), then sent to PubMed. To evaluate expansion performances for each query, the first twenty citations were selected, and their relevance were judged by three independent evaluators based on the title and abstract.
    RESULTS: Queries built with the UMLS expansion provided new citations with a slightly higher mean precision (74.19%) than with the CISMeF expansion (70.28%), although the difference was not significant. Inter-rater agreement was 0.28. Results varied greatly depending on the descriptor selected.
    DISCUSSION: The number of citations retrieved by the three strategies and their precision varied greatly according to the descriptor. This heterogeneity could be explained by the quality of the synonyms. Optimal use of these different expansions would be through various combinations of UMLS and CISMeF intersections or unions.
    CONCLUSION: Information retrieval tools should propose different semantic expansions depending on the descriptor and the search objectives.
    Keywords:  MEDLINE; PubMed; bibliographic databases; information retrieval; literature searching; medical subject headings (MeSH); precision; recall; search strategies; thesaurus
    DOI:  https://doi.org/10.1111/hir.12291
  2. J Pediatr Health Care. 2020 Jan - Feb;34(1):pii: S0891-5245(19)30513-9. [Epub ahead of print]34(1): 1
    Partnering With Librarians.
    Janene Batten.
      
    DOI:  https://doi.org/10.1016/j.pedhc.2019.09.011
  3. Database (Oxford). 2019 Jan 01. pii: baz132. [Epub ahead of print]2019
    GenoSurf: metadata driven semantic search system for integrated genomic datasets.
    Arif Canakoglu, Anna Bernasconi, Andrea Colombo, Marco Masseroli, Stefano Ceri.
      Many valuable resources developed by world-wide research institutions and consortia describe genomic datasets that are both open and available for secondary research, but their metadata search interfaces are heterogeneous, not interoperable and sometimes with very limited capabilities. We implemented GenoSurf, a multi-ontology semantic search system providing access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of 10 attributes are semantically enriched by making use of the most suited available ontologies. The user of GenoSurf provides as input the search terms, sets the desired level of ontological enrichment and obtains as output the identity of matching data files at the various sources. Search is facilitated by drop-down lists of matching values; aggregate counts describing resulting files are updated in real time while the search terms are progressively added. In addition to the consolidated attributes, users can perform keyword-based searches on the original (raw) metadata, which are also imported; GenoSurf supports the interplay of attribute-based and keyword-based search through well-defined interfaces. Currently, GenoSurf integrates about 40 million metadata of several major valuable data sources, including three providers of clinical and experimental data (TCGA, ENCODE and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq); it can be used as a standalone resource for targeting the genomic datasets at their original sources (identified with their accession IDs and URLs), or as part of an integrated query answering system for performing complex queries over genomic regions and metadata.
    DOI:  https://doi.org/10.1093/database/baz132
  4. Health Info Libr J. 2019 Dec;36(4): 372-377
    Medical library services in Switzerland: catching up with EBM.
    Gerhard Bissels, Sabine D Klein, Isabelle de Kaenel.
      The feature is a part of the series about medical library services in various countries. It gives an overview of medical library services to support research, education and clinical practice in Switzerland. Data were collected by means of an online survey and set in the wider context of the Swiss healthcare system. Key findings are that library services, including support by academic librarians, are provided to health care staff in hospitals - both university and others, while there is no information service infrastructure to serve the large number of GPs and specialists who mostly run their own practice. The authors recommend that - if the health authorities take EBM seriously - information services should be introduced for these small practices. J.M.
    Keywords:  Europe, central; evidence-based medicine (EBM); libraries, medical; surveys
    DOI:  https://doi.org/10.1111/hir.12284
  5. Bioinformatics. 2019 Dec 12. pii: btz923. [Epub ahead of print]
    Semantic persistence of ambiguous biomedical names in the citation network.
    Raul Rodriguez-Esteban.
       MOTIVATION: Name ambiguity has long been a central problem in biomedical text mining. To tackle it, it has been usually assumed that names present only one meaning within a given text. It is not known whether this assumption applies beyond the scope of single documents.
    RESULTS: Using a new method that leverages large numbers of biomedical annotations and normalized citations, this study shows that ambiguous biomedical names mentioned in scientific articles tend to present the same meaning in articles that cite them or that they cite, and, to a lesser extent, two steps away in the citation network. Citations, therefore, can be regarded as semantic connections between articles and the citation network should be considered for tasks such as automatic name disambiguation, entity linking and biomedical database annotation. A simple experiment shows the applicability of these findings to name disambiguation.
    AVAILABILITY: The code used for this analysis is available at: https://github.com/raroes/one-sense-per-citation-network.
    DOI:  https://doi.org/10.1093/bioinformatics/btz923
  6. JMIR Med Inform. 2019 Dec 09. 7(4): e13430
    Impact of Automatic Query Generation and Quality Recognition Using Deep Learning to Curate Evidence From Biomedical Literature: Empirical Study.
    Muhammad Afzal, Maqbool Hussain, Khalid Mahmood Malik, Sungyoung Lee.
       BACKGROUND: The quality of health care is continuously improving and is expected to improve further because of the advancement of machine learning and knowledge-based techniques along with innovation and availability of wearable sensors. With these advancements, health care professionals are now becoming more interested and involved in seeking scientific research evidence from external sources for decision making relevant to medical diagnosis, treatments, and prognosis. Not much work has been done to develop methods for unobtrusive and seamless curation of data from the biomedical literature.
    OBJECTIVE: This study aimed to design a framework that can enable bringing quality publications intelligently to the users' desk to assist medical practitioners in answering clinical questions and fulfilling their informational needs.
    METHODS: The proposed framework consists of methods for efficient biomedical literature curation, including the automatic construction of a well-built question, the recognition of evidence quality by proposing extended quality recognition model (E-QRM), and the ranking and summarization of the extracted evidence.
    RESULTS: Unlike previous works, the proposed framework systematically integrates the echelons of biomedical literature curation by including methods for searching queries, content quality assessments, and ranking and summarization. Using an ensemble approach, our high-impact classifier E-QRM obtained significantly improved accuracy than the existing quality recognition model (1723/1894, 90.97% vs 1462/1894, 77.21%).
    CONCLUSIONS: Our proposed methods and evaluation demonstrate the validity and rigorousness of the results, which can be used in different applications, including evidence-based medicine, precision medicine, and medical education.
    Keywords:  biomedical research; clinical decision support systems; data curation; deep learning; evidence-based medicine; machine learning; precision medicine
    DOI:  https://doi.org/10.2196/13430
  7. Health Info Libr J. 2019 Dec;36(4): 295-298
    An open invitation to join HILJ [Journal] Club.
    Alan Fricker, Tom Roper.
      Journal clubs are an effective means to increase skills in handling evidence and support the continuing professional development of library and knowledge services workers. This editorial examines the progression of HILJ Club, an online journal club, from an idea to the launch of a dedicated platform. One article is selected per issue of the Health Information and Libraries Journal with an open discussion invited following a brief summary and reflections by a host. Participation in HILJ Club is growing. Future success is reliant on wider engagement, and an invitation is extended to join in the discussions or even host an edition.
    Keywords:  Evidence Based Library and Information Practice; continuing professional development; library and information professionals
    DOI:  https://doi.org/10.1111/hir.12288
  8. Database (Oxford). 2019 Jan 01. pii: baz140. [Epub ahead of print]2019
    Mesophotic.org: a repository for scientific information on mesophotic ecosystems.
    Pim Bongaerts, Gonzalo Perez-Rosales, Veronica Z Radice, Gal Eyal, Andrea Gori, Erika Gress, Nicholas M Hammerman, Alejandra Hernandez-Agreda, Jack Laverick, Paul Muir, Hudson Pinheiro, Richard L Pyle, Luiz Rocha, Joseph A Turner, Ryan Booker.
      Mesophotic coral ecosystems (MCEs) and temperate mesophotic ecosystems (TMEs) occur at depths of roughly 30-150 m depth and are characterized by the presence of photosynthetic organisms despite reduced light availability. Exploration of these ecosystems dates back several decades, but our knowledge remained extremely limited until about a decade ago, when a renewed interest resulted in the establishment of a rapidly growing research community. Here, we present the 'mesophotic.org' database, a comprehensive and curated repository of scientific literature on mesophotic ecosystems. Through both manually curated and automatically extracted metadata, the repository facilitates rapid retrieval of available information about particular topics (e.g. taxa or geographic regions), exploration of spatial/temporal trends in research and identification of knowledge gaps. The repository can be queried to comprehensively obtain available data to address large-scale questions and guide future research directions. Overall, the 'mesophotic.org' repository provides an independent and open-source platform for the ever-growing research community working on MCEs and TMEs to collate and expedite our understanding of the occurrence, composition and functioning of these ecosystems. Database URL: http://mesophotic.org/.
    DOI:  https://doi.org/10.1093/database/baz140
  9. Anat Sci Educ. 2019 Dec 12.
    Web browsing habits of healthcare professions students in gross anatomy laboratory.
    Michael A Pascoe.
      Personal computer use for educational purposes by healthcare professions students has become ubiquitous. Although the effect of computer-based dissection instructions has been studied, there is a paucity of information regarding student browsing habits of information available on the internet. Although current students have favorable attitudes toward accessing anatomical information online, web browsing habits have not yet been investigated specifically in the dissection laboratory setting. The purpose of this study was to describe the browsing habits of healthcare professions students in the gross anatomy setting using a retrospective analysis. Files containing web browser history were retrieved from desktop computers in gross anatomy laboratory and custom code was written to parse them into comma separated value files. Each web address was categorized and descriptive statistics calculated. Browser history for 24 computers was analyzed from June 2013 to January 2015. During this period, students accumulated 100,857 webpage visits. Most often, students performed a Google search for anatomy (22.0% of all visits) and non-anatomy related (20.6% of all visits) information. Students also used the web browser to access various entertainment (16.4% of all visits) and productivity related services (15.9% of all visits). This analysis revealed a large volume of webpage visits by healthcare professions students in gross anatomy laboratory. A wide diversity of anatomy and non-anatomy related webpages were visited. Future analyses could be directed at examination of when in relation to class time students accessed the information, how browsing habits change over time, and what anatomical structures were most commonly searched for.
    Keywords:  anatomical structures; anatomy laboratory; gross anatomy education; healthcare professions education; information seeking; web browser
    DOI:  https://doi.org/10.1002/ase.1934
  10. Am J Ophthalmol. 2019 Dec 04. pii: S0002-9394(19)30592-6. [Epub ahead of print]
    Perspective on Systematic Literature Reviews and Meta-Analyses.
    Jay S Pepose, Gary N Foulks, J Daniel Nelson, Susan Erickson, Michael A Lemp.
       PURPOSE: To identify factors contributing to the inadequacies of systematic reviews and meta-analyses (SRMAs) published in the ophthalmology literature.
    DESIGN: Perspective METHODS: Review and synthesis of selective literature, with interpretation and perspective.
    RESULTS: While recommendations for the design, conduct, and assessment of quality and risk of bias of systematic reviews have been widely available, some recent publications illustrate a serious potential failing in this domain: inclusion of refuted science, lack of citation of post publication correspondence and failure to utilize ≥1 alternative search strategy.
    CONCLUSIONS: Examples of inadequacies of peer review in medical literature and their perpetuation of erroneous science by unfiltered inclusion in subsequent systematic reviews have been identified and the problem can be traced to authors, peer reviewers, and editors of journals. This perspective identifies and analyzes several possible causes of the problem and recommends some specific corrective actions to improve the quality and accuracy of such reviews.
    DOI:  https://doi.org/10.1016/j.ajo.2019.11.028
  11. BMC Med Res Methodol. 2019 Dec 11. 19(1): 234
    Recommendations to conduct and report systematic reviews in medical literature: a scoping review.
    Ana Penedones, Carlos Alves, Francisco Batel-Marques.
       BACKGROUND: This scoping review aims to identify, review and characterize the published recommendations to conduct and/or to report a systematic review in medical interventions area.
    METHODS: A search was carried out in PubMed, EMBASE and Cochrane Library databases, using systematic reviews search filters. The search comprises all recommendations to conduct and/or report a systematic review. Data on methods were extracted from each recommendation. A descriptive analysis was performed.
    RESULTS: Eighty-three recommendations were identified. Approximately 60% of retrieved references were published in the last 6 years. Recommendations to both conduct and report a systematic review were issued in 47% studies. The guidance presented in each recommendation to conduct and/ or report a systematic review varied. Almost 96% of the recommendations offer guidance on systematic review methods section. The need and time for updating was only recommended in 29% of recommendations. Forty percent of recommendations endorsed their methods to any subject related to medical interventions. Half of the studies did not specify the design of studies to be included in a systematic review.
    CONCLUSIONS: Several recommendations to conduct and/or report a systematic review were published and offered different guidance. Further research on the impact of such heterogeneity can improve systematic reviews quality.
    Keywords:  Epidemiology; Evidence-based medicine; Review literature as topic
    DOI:  https://doi.org/10.1186/s12874-019-0870-1
  12. J Med Internet Res. 2019 Dec 12. 21(12): e15132
    Searching the Internet for Infertility Information: A Survey of Patient Needs and Preferences.
    Felicia Brochu, Stephanie Robins, Skye A Miner, Paul H Grunberg, Peter Chan, Kirk Lo, Hananel E G Holzer, Neal Mahutte, Sophia Ouhilal, Togas Tulandi, Phyllis Zelkowitz.
       BACKGROUND: Given the complexity of infertility diagnoses and treatments and the convenience of the internet for finding health-related information, people undergoing infertility treatments often use Web-based resources to obtain infertility information and support. However, little is known about the types of information and support resources infertility patients search for on the internet and whether these resources meet their needs.
    OBJECTIVE: The aims of this study were to (1) examine what individual factors, namely, demographic characteristics and distress, are associated with searching the internet for different types of infertility-related information and support resources and (2) determine whether Web-based resources meet the needs of patients.
    METHODS: Men and women seeking infertility care responded to a survey assessing use of Web-based resources for accessing infertility-related information and support. The survey further assessed satisfaction with Web-based resources as well as perceived stress and depressive symptomatology.
    RESULTS: A total of 567 participants, including 254 men and 313 women, completed the survey. Most participants (490/558, 87.8%) had searched the internet for infertility information and support. Searchers were more likely to be women (P<.001), highly educated (P=.04), long-term patients (P=.03), and more distressed (P=.04). Causes of infertility, treatment options, and scientific literature about infertility were the three most frequently searched topics, whereas ways to discuss treatment with family and friends as well as surrogacy and ways to find peer support were the three least searched topics. Of those who searched the internet, 70.9% (346/488) indicated that their needs were met by Web-based information, whereas 29.1% (142/488) said that their needs were not met. Having unmet needs was related to greater levels of perceived stress (P=.005) and depressive symptomatology (P=.03).
    CONCLUSIONS: This study provides evidence for the important role of the internet in accessing infertility information and support and for the ability of Web-based resources to meet patients' needs. However, although distressed patients reported particularly high rates of searching, their needs were not always met, suggesting that they may benefit from alternative sources of information and support or guidance from health care providers when searching the internet.
    Keywords:  consumer health information; infertility; internet; patient satisfaction; stress, psychological
    DOI:  https://doi.org/10.2196/15132
  13. J Cancer Surviv. 2019 Dec 09.
    Improving cancer survivors' e-health literacy via online health communities (OHCs): a social support perspective.
    Junjie Zhou, Changyu Wang.
       PURPOSE: Cancer survivors should have adequate e-health literacy to help them better use online health information. Online health communities (OHCs) can offer cancer survivors different types of social support that can represent another resource to improve health outcomes. However, there is little knowledge of how these OHC are directly related to a cancer survivors' e-health literacy. This study explores how different types of social support in OHCs are associated with cancer survivors' e-health literacy.
    METHODS: A questionnaire was developed to collect data from two Chinese OHCs used by cancer survivors. The questionnaire is composed of two parts: six sociodemographic variables (i.e., gender, age, city, education, tenure, and prior Internet experience), two scales for informational support behaviors (i.e., health knowledge seeking and provision of health knowledge), a measure of emotional support within such a setting, and a measure of e-health literacy. Based on 162 complete samples, we determined the measurement properties of the scales used, provided descriptive statistics on major sociodemographic variables and conducted bivariate and multivariable hierarchical regression.
    RESULTS: For cancer survivors, females demonstrate higher levels of e-health literacy. Higher education level was related to higher e-health literacy. Health knowledge seeking, contributing to health knowledge, and emotional support were all positively associated with e-health literacy. The interaction effect between health knowledge and emotional support is positively associated with e-health literacy.
    CONCLUSIONS: Informational support and emotional support, as two major subtypes of social support within resources available in OHCs, are positively associated with e-health literacy among cancer survivors.
    IMPLICATIONS FOR CANCER SURVIVORS: Cancer survivors might benefit from an active strategy for improving personal e-health literacy that includes more active informational involvement and emotional support rather than a passive lurking through e-health information and seeking and reading postings in OHCs.
    Keywords:  E-health literacy; Emotional support; Health knowledge contribution; Health knowledge seeking; Online health community
    DOI:  https://doi.org/10.1007/s11764-019-00833-2
  14. Saudi Med J. 2019 Dec;40(12): 1294-1298
    Health information on social media. Perceptions, attitudes, and practices of patients and their companions.
    Marar D Sumayyia, May M Al-Madaney, Fatimah H Almousawi.
       OBJECTIVES: To assess social media and search engines used to find health information in Saudi patients and their companions and to describe their perceptions, attitudes, and practices. Methods: A cross-sectional study was carried out on 374 patients and their companions at a tertiary care hospital in Riyadh, Saudi Arabia. The data were collected between January and March 2018 using a self-administrated questionnaire adopted from the literature and developed in Arabic. The questionnaire was validated and modified by the researchers to fulfill the purpose of this study. The questionnaire contains 4 sections (25 questions), divided into a demographic section and the 3 sections assessing perceptions, attitudes, and practices. Results: Eighty-five percent sought health information using social media; of whom 293 (78.3%) used WhatsApp, 237 (63.4%) used YouTube, and 46 (12.3%) used Facebook. Furthermore, 72% searched information for themselves and 52% for a family member. Approximately 28% of participants had used social media for medical consultations. The reliability of health information on social media was met for 51% of participants, and 81.4% claimed that the health information obtained was knowledgeable. However, only 29% share their personal health experience with the public on social media. Conclusion: Our findings suggest that the majority of the participants used social media platforms to find information related to their health conditions, while approximately one third received direct medical consultations online. Public awareness to use reputable sources for health information is needed.
    DOI:  https://doi.org/10.15537/smj.2019.12.24682
  15. J Environ Radioact. 2019 Dec 09. pii: S0265-931X(19)30430-8. [Epub ahead of print]212 106123
    Is internet a missed opportunity? Evaluating radon websites from a stakeholder engagement perspective.
    Tanja Perko, Catrinel Turcanu.
      Exposure to indoor radon, a naturally occurring radioactive gas, is one of the main causes of lung cancer worldwide. Although radon tests are easily accessible in most countries, and protective actions are effective and relatively easy to apply, the levels of radon testing and subsequent home remediation remain lower than aimed for. Public engagement, particularly through internet, may contribute to addressing this value-action gap. Given their role as common interaction points between citizens and public services, this research analyzed radon websites from a stakeholder engagement perspective. The rich database assembled, of websites in eight European countries with highly radon prone areas, provides for the empirical novelty of the study. The website evaluation relied on internet communication metrics adapted for radon risk mitigation. This included availability of radon information, accessibility, stakeholder interaction, dialogue, responsiveness, content and design, and transparency and openness. Unexpectedly, results show that availability of radon information on the internet in radon prone areas is often limited and poor, as for instance only three internet pages dedicated to radon have been found. Radon websites should be improved with consistent information supported by engaging stories, provide for personalized features, support stakeholder feedback and dialogue, and include the use of social media. We conclude by consolidating the analysis into a list of recommendations for health communication practitioners, which should support radon risk mitigation, and contribute to improving public health, particularly decreasing the numbers of lung cancers. The effect of radon information available on internet pages on changing protective behaviors is suggested for future research.
    Keywords:  Cancer; Internet; Radon; Risk communication; Stakeholder engagement; Value-action gap
    DOI:  https://doi.org/10.1016/j.jenvrad.2019.106123
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:18.