bims-librar Biomed News
on Biomedical librarianship
Issue of 2021‒05‒30
fifteen papers selected by
Thomas Krichel
Open Library Society

  1. Stud Health Technol Inform. 2021 May 27. 281 78-82
      During the current COVID-19 pandemic, the rapid availability of profound information is crucial in order to derive information about diagnosis, disease trajectory, treatment or to adapt the rules of conduct in public. The increased importance of preprints for COVID-19 research initiated the design of the preprint search engine preVIEW. Conceptually, it is a lightweight semantic search engine focusing on easy inclusion of specialized COVID-19 textual collections and provides a user friendly web interface for semantic information retrieval. In order to support semantic search functionality, we integrated a text mining workflow for indexing with relevant terminologies. Currently, diseases, human genes and SARS-CoV-2 proteins are annotated, and more will be added in future. The system integrates collections from several different preprint servers that are used in the biomedical domain to publish non-peer-reviewed work, thereby enabling one central access point for the users. In addition, our service offers facet searching, export functionality and an API access. COVID-19 preVIEW is publicly available at
    Keywords:  Biomedical Text Mining; COVID-19; Information Retrieval
  2. Int J Technol Assess Health Care. 2021 May 24. 37(1): e64
      INTRODUCTION: Peer review of searches is a process whereby both the search strategies and the search process description are reviewed, ideally using an evidence-based checklist.RATIONALE: As the search strategy underpins any well-conducted evidence synthesis, its quality could affect the final result. Evidence shows, however, that search strategies are prone to error.
    FINDINGS: There is increasing awareness and use of the PRESS Evidence-Based Checklist and peer review of search strategies, at the outset of evidence syntheses, prior to the searches being run, and this is now recommended by a number of evidence synthesis organizations.
    RECOMMENDATIONS AND CONCLUSIONS: Searches for evidence syntheses should be peer reviewed by a suitably qualified and experienced librarian or information specialist after being designed, ideally, by another suitably qualified and experienced librarian or information specialist. Peer review of searches should take place at two important stages in the evidence synthesis process; at the outset of the project prior to the searches being run and at the prepublication stage. There is little empirical evidence, however, to support the effectiveness of peer review of searches. Further research is required to assess this. Those wishing to stay up to date with the latest developments in information retrieval, including peer review of searches, should consult the SuRe Info resource (, which seeks to help information specialists and others by providing easy access to the findings from current information retrieval methods research and thus support more research-based information retrieval practice.
    Keywords:  Databases as topic; Information storage and retrieval; Peer review; Systematic reviews as topic; Technology assessment, biomedical
  3. Nucleic Acids Res. 2021 May 28. pii: gkab417. [Epub ahead of print]
      The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal ( was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.
  4. F1000Res. 2020 ;9 1095
      Cohort studies collect, generate and distribute data over long periods of time - often over the lifecourse of their participants. It is common for these studies to host a list of publications (which can number many thousands) on their website to demonstrate the impact of the study and facilitate the search of existing research to which the study data has contributed. The ability to search and explore these publication lists varies greatly between studies. We believe a lack of rich search and exploration functionality is a barrier to entry for new or prospective users of a study's data, since it may be difficult to find and evaluate previous work in a given area. These lists of publications are also typically manually curated, resulting in a lack of rich metadata to analyse, making bibliometric analysis difficult. We present here a software pipeline that aggregates metadata from a variety of third-party providers to power a web based search and exploration tool for lists of publications. Alongside core publication metadata (i.e. author lists, keywords etc.), we include geocoding of first authors and citations in our pipeline. This allows a characterisation of a study as a whole based on common locations of authors, frequency of keywords, citation profile etc. This enriched publications metadata can be useful for generating project impact metrics and web-based graphics useful for public dissemination. In addition, the pipeline produces a research data set for bibliometric analysis or social studies of science.
    Keywords:  ALSPAC; Bibliography; Bibliometrics; Longitudinal birth cohort
  5. J Appl Toxicol. 2021 May 29.
      Systematic reviews of the scientific literature can be an important source of information supporting the daily work of the regulators in their decision making, particularly in areas of innovative technologies where the regulatory experience is still limited. Significant research activities in the field of nanotechnology resulted in a huge number of publications in the last decades. However, even if the published data can provide relevant information, scientific articles are often of diverse quality, and it is nearly impossible to manually process and evaluate such amount of data in a systematic manner. In this feasibility study, we investigated to what extent open-access automation tools can support a systematic review of toxic effects of nanomaterials for health applications reported in the scientific literature. In this study, we used a battery of available tools to perform the initial steps of a systematic review such as targeted searches, data curation and abstract screening. This work was complemented with an in-house developed tool that allowed us to extract specific sections of the articles such as the materials and methods part or the results section where we could perform subsequent text analysis. We ranked the articles according to quality criteria based on the reported nanomaterial characterisation and extracted most frequently described toxic effects induced by different types of nanomaterials. Even if further demonstration of the reliability and applicability of automation tools is necessary, this study demonstrated the potential to leverage information from the scientific literature by using automation systems in a tiered strategy.
    Keywords:  automation tools; knowledge management; nanomedicines; quality evaluation; systematic review automation; toxicity of nanomaterials
  6. Database (Oxford). 2021 May 28. pii: baab031. [Epub ahead of print]2021
      microRNAs (miRNAs) are essential gene regulators, and their dysregulation often leads to diseases. Easy access to miRNA information is crucial for interpreting generated experimental data, connecting facts across publications and developing new hypotheses built on previous knowledge. Here, we present extracting miRNA Information from Text (emiRIT), a text-miningbased resource, which presents miRNA information mined from the literature through a user-friendly interface. We collected 149 ,233 miRNA -PubMed ID pairs from Medline between January 1997 and May 2020. emiRIT currently contains 'miRNA -gene regulation' (69 ,152 relations), 'miRNA disease (cancer)' (12 ,300 relations), 'miRNA -biological process and pathways' (23, 390 relations) and circulatory 'miRNAs in extracellular locations' (3782 relations). Biological entities and their relation to miRNAs were extracted from Medline abstracts using publicly available and in-house developed text-mining tools, and the entities were normalized to facilitate querying and integration. We built a database and an interface to store and access the integrated data, respectively. We provide an up-to-date and user-friendly resource to facilitate access to comprehensive miRNA information from the literature on a large scale, enabling users to navigate through different roles of miRNA and examine them in a context specific to their information needs. To assess our resource's information coverage, we have conducted two case studies focusing on the target and differential expression information of miRNAs in the context of cancer and a third case study to assess the usage of emiRIT in the curation of miRNA information. Database URL:
  7. J Cheminform. 2021 May 24. 13(1): 40
      The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and integration of large chemical databases. InChI version 1.05 was released in January 2017 and version 1.06 in December 2020. In this paper, we report on the current state of the InChI Software, the details of the improvements in the v1.06 release, and the results of a test of the InChI run on PubChem, a database of more than a hundred million molecules. The upgrade introduces significant new features, including support for pseudo-element atoms and an improved description of polymers. We expect that few, if any, applications using the standard InChI will need to change as a result of the changes in version 1.06. Numerical instability was discovered for 0.002% of this database, and a small number of other molecules were discovered for which the algorithm did not run smoothly. On the basis of PubChem data, we can demonstrate that InChI version 1.05 was 99.996% accurate, and InChI version 1.06 represents a step closer to perfection. Finally, we look forward to future releases and extensions for the InChI Chemical identifier.
    Keywords:  InChI; InChIKey; PubChem; RInChI
  8. Epilepsy Behav. 2021 May 20. pii: S1525-5050(21)00267-5. [Epub ahead of print]121(Pt A): 108033
      INTRODUCTION: People with epilepsy can have cognitive deficits, including difficulty with reading tasks. This can potentially impact on how written information is understood. Websites increasingly provide information about different medical interventions including epilepsy surgery. Our aim was to assess the readability of a sample of one hundred patient-oriented educational English language websites related to epilepsy surgery.METHODS: A Google search was carried out using the terms epilepsy and surgery, and a sample of forty-nine websites from both the UK and the US were chosen. These websites were uploaded to a freely available online readability scoring tool ( and seven measures of readability generated were examined. Other data including use of figures/diagrams, patient narratives, and mention of the risks/benefits of surgery were noted.
    RESULTS: The majority of the websites analyzed in this study were found to be 'difficult' to read for the average reading level of the population (n = 1-impossible, 10-very difficult, 23-difficult, 14 fairly difficult). Only 1 website was considered suitable for average reading level. The use of infographics was variable - some webpages used them extensively to reiterate the textual information and other websites did not.
    DISCUSSION AND CONCLUSION: The available online patient information literature is likely to be too difficult for the average reader to understand. It is important that websites are accessible, reliable, and aid understanding related to epilepsy surgery, taking potential cognitive deficits into consideration.
    Keywords:  Epilepsy surgery; Linguistics; Readability
  9. J Pain Res. 2021 ;14 1353-1357
      Objective: With the advance of the internet, social media platforms have become a major source of medical information. We assessed the reliability, quality, and usefulness of the most-viewed YouTube videos of epidural steroid injection (ESI).Methods: A search was conducted on YouTube on February 13, 2020, using the keywords "epidural injection," "epidural steroid injection," "epidural transforaminal injection," and "epidural transforaminal steroid injection." The top 50 most-viewed videos were assessed with a modified DISCERN scale (mDISCERN) and a Global Quality Scale (GQS). Further, the usefulness of information in each video was evaluated.
    Results: Only 22% of videos contained information with high reliability, and these were produced by hospitals or physicians. None of the videos provided by media organizations and patients were reliable. As for information quality, only 34% were moderate to excellent quality. Even of the videos produced by hospitals or physicians, approximately half were of generally poor or poor quality. Regarding the usefulness of information, although 76% were assessed to contain useful information, 8% had misleading information. Particularly, four of these videos contained misleading information, and three were provided by patients who experienced ESI.
    Conclusion: YouTube is a platform where medical information is actively shared and widespread. Here, we found that the reliability and quality of videos were low even when these were produced by hospitals or physicians. Further, the quality tended to be much lower when it was provided by media organizations or patients. Future efforts by physicians and professional societies to improve the reliability and quality of medical content are necessary.
    Keywords:  back pain; epidural steroid injection; online media; quality; sciatica; social media
  10. J Hand Surg Am. 2021 May 19. pii: S0363-5023(21)00202-1. [Epub ahead of print]
      PURPOSE: Online patient educational materials have historically been written at a higher-than-recommended sixth grade reading level. The objectives of this study were to assess the readability of online hand surgery patient educational materials from the official online patient resource website of the American Society for Surgery of the Hand (ASSH) and to compare changes in the readability of the current ASSH online patient educational materials with those in 2008 and 2015.METHODS: An internet-based study of all 88 English language patient educational materials on, the official online patient resource website of the ASSH, was performed. The readability of each article was assessed using the Flesch reading ease formula, Flesch-Kincaid grade level, Coleman-Liau index, Gunning-Fog index, and Simple Measure of Gobbledygook grade level. To evaluate the trend in the readability of ASSH online hand surgery patient educational materials, the Flesch-Kincaid grade levels of articles published in 2020 were compared with those of data published in 2008 and 2015.
    RESULTS: The average Flesch reading ease score of the patient educational materials was 57.6, which is at the high-school reading level. The average reading grade level of patient educational materials ranged from 9.0 to 12.3 depending on the readability metric used. The average Flesch-Kincaid grade level of all the ASSH patient educational materials was 9.8 in 2020, which is significantly better than 10.4 in 2008 but significantly worse than 8.5 in 2015.
    CONCLUSIONS: Online hand surgery patient educational materials continue to be written for the general public at a higher-than-recommended reading grade level. There has been no substantial improvement in the readability of online hand surgery patient educational materials since 2008.
    CLINICAL RELEVANCE: Improvements are needed in the readability of online patient educational materials to ensure that patients with all health literacy levels are able to comprehend and benefit from health information.
    Keywords:  Health literacy; internet; online; patient education; readability
  11. Foot Ankle Surg. 2021 May 18. pii: S1268-7731(21)00099-0. [Epub ahead of print]
      BACKGROUND: Previous studies have determined the videos on YouTube® have misleading information in medicine, however the assessment of the information for hallux valgus surgery is lacking.METHODS: YouTube® was analyzed using two keywords as 'hallux valgus surgery' and 'bunion surgery'. Once redundancies were eliminated, each video was evaluated for the characteristic as following: duration, number of views, likes and dislikes, days since upload, view and like ratios and video power index (VPI). The quality of the information was evaluated using DISCERN, JAMA and hallux valgus score (HVS).
    RESULTS: A total of 49 videos included. Fair or poor results for DISCERN and HVS (90% and 69% of videos, respectively) were found. No difference was found between video source and quality scores. Number of likes and VPI negatively correlated with all scores (p < 0.001).
    CONCLUSIONS: YouTube® had poor quality of information for hallux valgus surgery.
    Keywords:  Hallux valgus surgery; Information; Internet; YouTube
  12. Otol Neurotol. 2021 May 21.
      HYPOTHESIS: Vestibular rehabilitation (VR) education videos on YouTube are poor-quality and unreliable.BACKGROUND: YouTube has become a health information source. Recent studies have determined that videos on YouTube contain misleading and inappropriate information for different medical conditions. The aim of the present study was to assess the quality and reliability of VR education videos.
    METHODS: A search was performed using the keywords vertigo, vertigo treatment, vertigo exercise, and vestibular rehabilitation, on YouTube. The first 50 videos for each keyword were analyzed. Videos were divided into four groups according to the video source: Group 1: universities/occupational organizations, Group 2: medical ad/profit-oriented companies, Group 3: independent users, and Group 4: others (news/media/state institution). The quality and reliability of videos were evaluated regarding the modified DISCERN criteria, the modified Journal of the American Medical Association (JAMA) benchmark criteria, and global quality scores (GQS).
    RESULTS: Among the 200 videos analyzed, 103 were included. The main video source was medical ad/profit-oriented companies (60.2%). The mean modified DISCERN criteria score, the mean modified JAMA benchmark criteria score, and the mean GQS value of the videos were found as low (2.46 ± 1.37, 2.09 ± 1.23, and 2.67 ± 1.38, respectively). Videos uploaded by universities/occupational organizations (25.2%) had statistically significant higher modified DISCERN criteria scores, modified JAMA benchmark criteria scores, and GQS values compared with the other groups (p < 0.001).
    CONCLUSION: Online information about VR education on YouTube was of poor quality and unreliable. Expert vestibular providers should be aware of these inappropriate sources and educate patients regarding the poor-quality of videos and also aim to provide more quality and reliable sources of information.
  13. Health Info Libr J. 2021 May 29.
      BACKGROUND: Facebook is a frequently used social media platform and is often used for human health information, yet little research has been conducted on how pet owners use Facebook pet groups to obtain and share pet health information.METHOD: This study was designed to assess how pet owners use dog and cat Facebook groups to provide and receive pet health advice and their perception of these groups' trustworthiness. Two comparable questionnaires (dog and cat owners) were developed and distributed through an online survey platform.
    RESULTS: Results suggest that Facebook groups are a common source of pet health information, with 56.2% of dog owners and 51.8% of cat owners reporting receiving health information through Facebook groups. Similar numbers report giving health information through Facebook groups: 55.0% of dog owners and 57.9% of cat owners. Dog health information most commonly exchanged related to dermatology, gastroenterology and orthopaedics and the most common cat health information focused on gastroenterology, renal and urinary-related issues. While the majority of Facebook users report feeling that Facebook groups are not a trustworthy source of pet health information, a substantial minority of users do appear to be influenced by these groups.
    CONCLUSION: Approximately 50% of cat and dog owning respondents either give or receive pet health advice through Facebook groups. These results suggest that many owners deem Facebook groups as useful, but not entirely trustworthy, sources of information.
    Keywords:  information-seeking behaviour; social media; surveys
  14. J Med Internet Res. 2021 May 26.
      BACKGROUND: Over recent years, medical journals have emphasized the increasingly critical role that social media plays in the dissemination of public health information and disease prevention guidelines. However, platforms such as Facebook and Twitter continue to pose unique challenges for clinical healthcare providers and public health officials alike. In order to effectively communicate during public health emergencies such as Covid-19, it's increasingly critical for healthcare providers and public health officials to understand how patients gather - and adjudicate the merits of - health-related information online.OBJECTIVE: With that goal in mind, we conducted a survey of 1,003 U.S.-based adults to better understand how health consumers have utilized social media to learn and stay informed about the Covid-19 pandemic, including the extent to which they've relied on credible scientific information sources and how they've gone about "fact-checking" pandemic related information.
    METHODS: A web-based survey was conducted via sample purchased through an industry leading market research provider. Results are reported with a 95% confidence level and a margin of error of +/- 3. Participants included 1,003 U.S.-based adults (18 or older). Participants were selected via a stratified quota sampling approach to ensure a representative sample of the U.S. population. Balanced quotas were determined (by region of the country) for gender, age, race, ethnicity.
    RESULTS: The results show a heavy reliance on social media during the Covid-19 pandemic, with more than three quarters of respondents (76%) saying that they have relied on social media a least "a little", and nearly 60% of respondents indicating that they read information about Covid-19 on social media at least once a week. According to the findings, most social media users are unlikely to "fact-check" what they see online with a health professional, despite reporting high levels of mistrust in the accuracy of Covid-related information on social media. We also find a greater likelihood of vaccination among those "following" more credible, scientific sources on social media during the pandemic (X2 = 50.790; φ = 0.258; P < 0.001).
    CONCLUSIONS: The findings suggest that health professionals will need to be both strategic and proactive when engaging with health consumers on social media if they hope to counteract the deleterious effects of erroneous misinformation (as well as malicious disinformation). Effective training, institutional support, and proactive collaboration can help health professionals adapt to evolving patterns of health information seeking.