bims-librar Biomed News
on Biomedical librarianship
Issue of 2021‒08‒15
eighteen papers selected by
Thomas Krichel
Open Library Society

  1. BMC Med Inform Decis Mak. 2021 Aug 09. 21(1): 240
      BACKGROUND: A clinical librarian is a member of the medical team in many countries. To strengthen this new job, librarians need to acquire professional skills in order to provide information services to medical staff. In this study, we aimed to explor the skills required for the presence of a clinical librarian in the treatment team.METHODS: In this study, we sonducted a qualitative study in which 15 experienced librarians were interviewed in connection with information services. Also, a treatment team was involved in this study using purposive-convenience and snowball sampling methods. The data collection tool was a semi-structured interview that continued until the data was saturated; finally the data analysis was performed using thematic analysis.
    RESULTS: Out of the total interviews, 158 primary codes and, 107 main codes were extracted in 25 subclasses. After careful evaluation and integration of subclasses and classes, they were finally classified into 13 categories and four main themes, namely clinical librarian's role, professional and specialized skills, communication skills, and training programs.
    CONCLUSION: The results showed that specialized skills and training programs for the clinical librarian are defined based on his/her duties in the treatment team. We also defined the most important key skills for the clinical librarian in two categories of professional and communication skills such as specialized information search, content production, resource management, familiarity with various sources related to evidence-based medicine, teamwork, and effective communication. To acquire these skills, officials and policy-makers should develop and implement related educational programs at medical universities and colleges.
    Keywords:  Clinical Librarian—specialized skills; Clinical librarianship; Professional skills
  2. Res Synth Methods. 2021 Aug 10.
      Academic research has changed in recent years. It has entered the age of abundant scholarly information. New scientometric data shows impressive increases in both the quantity and quality of information researchers produce. Since 2007 about the same number of publications have become accessible on databases as more than the hundred years prior. At the same time, evidence synthesis has become key in making this wealth of information understandable and useful. Researchers need to be increasingly proficient in identifying relevant information - to be able to build on an increasingly comprehensive research base and to adhere to rising standards in evidence synthesis. Both these requirements make a 'true partnership between librarians and researchers' in demand like never before. This article is protected by copyright. All rights reserved.
    Keywords:  Abundance of scholarly information; Conduct and reporting guidance; Evidence synthesis; Librarians; Search literacy; Systematic reviews and meta-analyses
  3. Curr Protoc. 2021 Aug;1(8): e217
      PubChem ( is a public chemical database that serves scientific communities as well as the general public. This database collects chemical information from hundreds of data sources and organizes them into multiple data collections, including Substance, Compound, BioAssay, Protein, Gene, Pathway, and Patent. These collections are interlinked with each other, allowing users to discover related records in the various collections (e.g., drugs targeting a protein or genes modulated by a chemical). PubChem can be searched by keyword (e.g., a chemical, protein, or gene name) as well as by chemical structure. The input structure can be provided using popular line notations or drawn with the PubChem Sketcher. PubChem supports various types of structure searches, including identity search, 2-D and 3-D similarity searches, and substructure and superstructure searches. Results from multiple searches can be combined using Boolean operators (i.e., AND, OR, and NOT) to formulate complex queries. PubChem allows the user to quickly retrieve a list of records annotated with a particular classification or ontological term. This paper provides step-by-step instructions on how to explore PubChem data with examples of commonly requested tasks. © 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Finding genes and proteins that interact with a given compound Basic Protocol 2: Finding drug-like compounds similar to a query compound through a two-dimensional (2-D) similarity search Basic Protocol 3: Finding compounds similar to a query compound through a three-dimensional (3-D) similarity search Support Protocol: Computing similarity scores between compounds Basic Protocol 4: Getting the bioactivity data for the hit compounds from substructure search Basic Protocol 5: Finding drugs that target a particular gene Basic Protocol 6: Getting bioactivity data of all chemicals tested against a protein. Basic Protocol 7: Finding compounds annotated with classifications or ontological terms Basic Protocol 8: Finding stereoisomers and isotopomers of a compound through identity search.
    Keywords:  PubChem; chemical structure search; cheminformatics; drug discovery; molecular similarity; public database
  4. J Med Internet Res. 2021 Aug 05.
      BACKGROUND: The coronavirus disease (COVID-19) global health crisis has led to an exponential surge in the published scientific literature. In the attempt to tackle the pandemic, extremely large COVID-19-related corpora are being created, sometimes with inaccurate information, which is no longer at scale of human analyses.OBJECTIVE: In the context of searching for scientific evidence in the deluge of COVID-19-related literature, we present an information retrieval methodology for effective identification of relevant sources to answer biomedical queries posed using natural language.
    METHODS: Our multi-stage retrieval methodology combines probabilistic weighting models and re-ranking algorithms based on deep neural architectures to boost the ranking of relevant documents. Similarity of COVID-19 queries are compared to documents and a series of post-processing methods are applied to the initial ranking list to improve the match between the query and the biomedical information source and boost the position of relevant documents.
    RESULTS: The methodology was evaluated in the context of the TREC-COVID challenge, achieving competitive results with the top-ranking teams participating in the competition. Particularly, the combination of bag-of-words and deep neural language models significantly outperformed a BM25-based baseline, retrieving on average 83% of relevant documents in the top 20.
    CONCLUSIONS: These results indicate that multi-stage retrieval supported by deep learning could enhance identification of literature for COVID-19-related questions posed using natural language.
  5. Health Commun. 2021 Aug 11. 1-11
      This study tested the utility of the Risk Information Seeking and Processing (RISP) model in understanding why people seek or avoid online information about COVID-19. Data collected at three different time points (i.e., February, April, and May 2020) showed the measured RISP model constructs explained between 70-78.8% of the variance for information seeking, and between 36.9-62.5% of the variance for information avoiding. Specifically, fear, information insufficiency, and relevant channel beliefs consistently predicted information seeking. Further, information insufficiency and relevant channel beliefs consistently predicted information avoidance. However, fear had no association with information avoidance. Longitudinally, the study found that within individuals, there were larger increases in most RISP model constructs between Time 1 and Time 2, and smaller changes occurred from Time 2 to Time 3. However, there was no significant change in information seeking over time.
  6. Wellcome Open Res. 2021 ;6 88
      Pharmacokinetic (PK) predictions of new chemical entities are aided by prior knowledge from other compounds. The development of robust algorithms that improve preclinical and clinical phases of drug development remains constrained by the need to search, curate and standardise PK information across the constantly-growing scientific literature. The lack of centralised, up-to-date and comprehensive repositories of PK data represents a significant limitation in the drug development pipeline.In this work, we propose a machine learning approach to automatically identify and characterise scientific publications reporting PK parameters from in vivo data, providing a centralised repository of PK literature. A dataset of 4,792 PubMed publications was labelled by field experts depending on whether in vivo PK parameters were estimated in the study. Different classification pipelines were compared using a bootstrap approach and the best-performing architecture was used to develop a comprehensive and automatically-updated repository of PK publications. The best-performing architecture encoded documents using unigram features and mean pooling of BioBERT embeddings obtaining an F1 score of 83.8% on the test set. The pipeline retrieved over 121K PubMed publications in which in vivo PK parameters were estimated and it was scheduled to perform weekly updates on newly published articles. All the relevant documents were released through a publicly available web interface ( and characterised by the drugs, species and conditions mentioned in the abstract, to facilitate the subsequent search of relevant PK data. This automated, open-access repository can be used to accelerate the search and comparison of PK results, curate ADME datasets, and facilitate subsequent text mining tasks in the PK domain.
    Keywords:  Bioinformatics; Information extraction; Machine Learning; Natural Language Processing; Pharmacokinetics; Pharmacometrics; Text mining
  7. Hum Vaccin Immunother. 2021 Aug 10. 1-6
      Our objective was to analyze the sources, characteristics, tone, and content of the most viewed YouTube videos in Spanish about Covid-19 vaccines. In February 2021, a search was carried out on YouTube using the terms "Vacuna Covid," "Vacuna coronavirus," and "Vacuna Covid19." Associations between tone, source, and others variables (e.g. number of views or dislikes) were studied with a Mann-Whitney U-test and a chi-square test. A total of 118 videos were analyzed; 63.6% were originated from Mexico and the USA; media created 57.6% of the videos. Positive tone was observed in 53.4%. The most discussed topics were target groups for vaccination (38.9%) and safety (43.2%). The 68 videos produced by media accumulated 31,565,295 views (55.0% of views), and the 19 videos created by health professionals obtained 10,742,825 views (18.7% of views). A significantly smaller number of likes was obtained in videos of media compared to those created by health professionals (p = .004). Videos made by health professionals, compared to those of media, showed a greater positive tone (OR = 3.09). Hoaxes/conspiracy theories were identified in 1.7% of the videos. Monitoring that the information on YouTube about Covid-19 vaccines is reliable should be a central part of Covid-19 vaccination campaigns.
    Keywords:  Covid-19 vaccines; Spanish; YouTube; evaluation; information
  8. Health Commun. 2021 Aug 11. 1-9
      The present study tests and extends the RISP model (a) by applying the model in the context of COVID-19 in South Korea and (b) by examining the impacts of information seeking and processing on misinformation exposure and acceptance. Based on a survey of 346 Korean adults, this study showed that information avoidance, but not information seeking, was a positive predictor of misinformation exposure. In addition, heuristic processing, but not systematic processing, moderated the relationship between misinformation exposure and misinformation acceptance, such that the relationship between misinformation exposure and misinformation acceptance was stronger among those who showed greater tendency for heuristic processing. In addition, information insufficiency was a negative predictor of both information avoidance and heuristic processing. Theoretical and practical implications are discussed.
  9. J Am Med Inform Assoc. 2021 Aug 12. pii: ocab150. [Epub ahead of print]
      OBJECTIVE: The purpose of this study is to describe online health information seeking among a sample of transgender and gender diverse (TGD) people compared with cisgender sexual minority people to explore associations with human papillomavirus (HPV) vaccination, and whether general health literacy and eHealth literacy moderate this relationship.MATERIALS AND METHODS: We performed a cross-sectional online survey of TGD and cisgender sexual minority participants from The PRIDE Study, a longitudinal, U.S.-based, national health study of sexual and gender minority people. We employed multivariable logistic regression to model the association of online health information seeking and HPV vaccination.
    RESULTS: The online survey yielded 3258 responses. Compared with cisgender sexual minority participants, TGD had increased odds of reporting HPV vaccination (aOR, 1.5; 95% CI, 1.1-2.2) but decreased odds when they had looked for information about vaccines online (aOR, 0.7; 95% CI, 0.5-0.9). TGD participants had over twice the odds of reporting HPV vaccination if they visited a social networking site like Facebook (aOR, 2.4; 95% CI, 1.1-5.6). No moderating effects from general or eHealth literacy were observed.
    DISCUSSION: Decreased reporting of HPV vaccination among TGD people after searching for vaccine information online suggests vaccine hesitancy, which may potentially be related to the quality of online content. Increased reporting of vaccination after using social media may be related to peer validation.
    CONCLUSIONS: Future studies should investigate potential deterrents to HPV vaccination in online health information to enhance its effectiveness and further explore which aspects of social media might increase vaccine uptake among TGD people.
    Keywords:  health literacy; information seeking behavior; papillomavirus vaccines; sexual and gender minorities; transgender persons
  10. Int Arch Otorhinolaryngol. 2021 Jul;25(3): e446-e452
      Introduction  The quality of information on websites about tonsillectomy regarding the knowledge level may be low. Tonsillectomy is a surgical procedure to hypertrophy of the palatine and pharyngeal tonsils. So, it is an invasive procedure with possible complications, which creates insecurity in parents. Significantly, Internet searches have been increased to address possible health concerns, questioning the quality of websites about tonsillectomy. Objective  To evaluate the readability, reliability, and comprehensiveness of the Italian websites dedicated to parental guidance regarding the indications for tonsillectomy in children. Methods  The search engine was used to search the websites. The Gulpease index, which is a widely used readability formula ranging from 0 (difficult) to 100 (easy readability), was employed to evaluate these websites. The Health on the Net Code of Conduct (HONcode) was used to assess the quality of information, by taking ethical principles into account, with values ranging from 0 to 13. The content comprehensiveness of the web pages was assessed by assigning points ranging from 1 (very insufficient) to 5 (very satisfying) to each page. A final comparison with previous studies on tonsillectomy published on websites from other countries was performed. Results  Fourteen Italian websites were selected, and the Gulpease index showed a mean average of 40.77 ± 8.45. The mean of the HONcode analysis was 6.00 ± 1.92, in which the principles with the poorest scores were Attribution and Update . As far as the comprehensiveness of the websites is concerned, the resulting mean was 2.57 ± 0.77, in which Indications was the topic with the highest mean, whereas Benefits was the one with the lowest. Conclusion  The Italian websites were characterized by a lower readability level, a middle position regarding ethical principles, and the same (insufficient) comprehensiveness of tonsillectomy when compared with websites from different countries.
    Keywords:  internet; patient information; patient portals; readability; tonsillectomy
  11. J Cancer Educ. 2021 Aug 08.
      The internet is a common source of health information for patients with cancer. Despite research surrounding the quality of online resources for individual types of cancer, these results may not necessarily be easily extrapolated to cancer resources as a whole. Thus, we aim to use a standardized tool to produce generalizable results by analyzing the quality of online resources for the most common cancers. Educational websites pertaining to breast, lung, prostate, and colorectal cancers were searched using multiple search engines. After screening against pre-specified inclusion criteria, the most visible 100 websites for each cancer were extracted for analysis. A validated tool was then used to assess their quality. Pooled results were evaluated using descriptive and inferential statistics. Of the 400 analyzed websites, 43% were commercially affiliated, and these were significantly associated with greater use of biased language. Thirty percent of websites disclosed authorship, 47% cited at least one reliable source, and 43% were updated within the last 2 years. The average Flesch-Kincaid readability was determined to be at a grade 10.9 level, which is significantly more difficult than the recommended grade 6 level. Risk factors, symptoms, and detection were the most accurately covered topics. However, most websites did not cover prognosis. This study comprehensively examines the quality of online cancer resources for the four most common cancers. Our results could help guide the development of future resources, support patient education endeavors, and raise awareness among healthcare providers about the limitations of online cancer resources.
    Keywords:  Breast cancer; Colorectal cancer; Lung cancer; Online health information; Patient education; Prostate cancer; Quality assessment
  12. Otolaryngol Head Neck Surg. 2021 Aug 10. 1945998211033254
      OBJECTIVE: Patient education materials across 3 national English otolaryngology-head and neck surgery (OHNS) societies: the American Academy of Otolaryngology-Head and Neck Surgery (AAO-HNS), the Canadian Society of Otolaryngology-Head and Neck Surgery (CSOHNS), and Ear, Nose, and Throat United Kingdom (ENT UK) were examined to determine whether they are written at a level suitable for patient comprehension.STUDY DESIGN: Cross-sectional study.
    SETTING: Online patient materials presented through OHNS national societies.
    METHODS: Readability was calculated using the Flesch-Kincaid Grade Level, Flesch-Kincaid Reading Ease Score, and Simple Measure of Gobbledygook Index. All public patient education materials available through the CSOHNS, AAO-HNS, and ENT UK websites were assessed. Patient education materials were grouped into categories by subspecialty.
    RESULTS: In total, 128 patient materials from the 3 societies were included in the study. All 3 societies required a minimum grade 9 reading comprehension level to understand their online materials. According to Flesch-Kincaid Grade Level, the CSOHNS required a significantly higher reading grade level to comprehend the materials presented when compared to AAO-HNS (11.3 vs 9.9; 95% CI, 0.5-2.4; P < .01) and ENT UK (11.3 vs 9.4; 95% CI, 0.9-2.9; P < .01). Patient education materials related to rhinology were the least readable among all 3 societies.
    CONCLUSION: This study suggests that the reading level of the current patient materials presented through 3 national OHNS societies are written at a level that exceeds current recommendations. Promisingly, it highlights an improvement for the readability of patient materials presented through the AAO-HNS.
    Keywords:  health literacy; otolaryngology; patient education; readability
  13. Eur J Obstet Gynecol Reprod Biol. 2021 Jul 31. pii: S0301-2115(21)00399-7. [Epub ahead of print]264 330-335
      OBJECTIVE: The objective of this study was to evaluate the quality of information on the internet about vaginal meshes available to the general population.STUDY DESIGN: The terms "vaginal sling," "sling vagina," "vaginal mesh," "mesh vagina," "vaginal tape," and "tape vagina" were used every time on three major search engines, and the first 10 websites retrieved by each search engine were selected and evaluated using the DISCERN questionnaire. The websites were divided into four categories based on the type of agency that created the website. These included websites created by private health institutions, non-private health institutions, and non-health institutions and websites for encyclopedias, libraries, articles and scientific papers. They were compared in terms of the reliability, information quality, and total DISCERN score.
    RESULTS: The survey yielded 98 different websites; after applying the exclusion criteria, 62 sites were selected. Websites for articles, magazines, libraries, and encyclopedias and those by non-private health services had significantly high scores for the reliability dimension of the DISCERN tool as compared to the other two website categories (p < 0.05). Regarding the quality of information, websites for non-specific health services and those for articles, magazines, libraries, and encyclopedias presented significantly lower scores as compared to the other two website categories. Websites for non-specific health services had significantly lower average total DISCERN points when compared to other website categories. The websites for private health services and those for articles, magazines, libraries, and encyclopedias had significantly lower DISCERN scores than the websites for non-private health services did.
    CONCLUSION: Our findings showed that the quality of information regarding vaginal meshes on the first 10 websites on major search engines was moderate.
    Keywords:  Evaluation; Internet; Quality of information; Vaginal mesh
  14. Perit Dial Int. 2021 Aug 09. 8968608211035947
      BACKGROUND: One of the main barriers to choosing peritoneal dialysis (PD) is the lack of awareness and PD knowledge. There is an increasing trend in the use of the internet as a search tool for health-related information. This study aims to determine how useful YouTube videos are to get information about PD.METHODS: YouTube videos were evaluated independently by two nephrologists. The videos' quality was assessed with DISCERN scoring system, global quality score (GQS) and the Journal of the American Medical Association (JAMA) scoring system. We determined the quartile (Q) of the videos as follows: most reliable top 25% videos Q1 and others Q2-4.
    RESULTS: A total of 295 videos were evaluated. University or society-sourced videos made up 15% (n = 43) of all videos, and healthcare providers were the primary target audience compared to patients (p < 0.001). JAMA, GQS and DISCERN scores were significantly higher for the videos that were targeted healthcare providers compared to the patients (p < 0.001, for all). A total of 34% of the videos in Q1 were obtained from the university or society. Nevertheless, only 17% of the videos prepared for the patients were among the Q1. A small number of videos mentioned that PD maintains the residual kidney function (RKF) longer compared to haemodialysis.
    CONCLUSIONS: Universities and societies should upload videos to provide easy-to-understand information on PD. Also, the important benefits of PD, like the preservation of RKF, should be further highlighted in these videos. It may increase the PD penetrance by increasing patients' awareness.
    Keywords:  Awareness; YouTube; internet; knowledge; peritoneal dialysis; video
  15. Cureus. 2021 Jul;13(7): e16203
      INTRODUCTION: To examine English language YouTube videos that covered both COVID-19 and peripheral artery disease (PAD).METHODS: The research was planned from October 1 to 5, 2020. Two cardiologists (CB and ES) executed online searches in which the term COVID-19/coronavirus was paired with common keywords about PAD, including 'peripheral artery disease + COVID-19,' 'leg pain + coronavirus,' 'leg vascular disease + COVID-19,' 'atherosclerosis + COVID-19,' and 'claudication + coronavirus.' For each video, a record was made of the number of days on YouTube, length, number of views and comments, and the number of 'likes' and 'dislikes'. Videos were also categorized according to content as informative videos (with accurate content about the frequency of disease, symptoms, transmission, prevention techniques, and proven treatment methods), patient experience videos (with patient testimonies), or news update videos (i.e., those uploaded by professional news channels). Moreover, DISCERN and Medical Information and Content Index (MICI) were evaluated.
    RESULTS: Totally, 91 YouTube videos met study inclusion criteria. News update videos were the most-watched when compared with informative and patient experience videos (63,910 views vs 43,725 views vs19,778 views, p=0.032). The DISCERN score was significantly higher in the informative group: 2.8 for informative videos, 1.7 for patients' experience videos, and 1.8 for news update videos (p= 0.001). The most common theme was clinical symptoms in the informative videos (82.4%). The mean MICI score was calculated as 3.7±1.4 points for informative videos.
    CONCLUSION: YouTube videos about COVID-19 and PAD are widely-viewed information sources for patients. Our study has demonstrated that YouTube videos about COVID-19 and PAD generally had poor quality content.
    Keywords:  covid-19; discern score; mici; peripheral artery disease; youtube