bims-librar Biomed News
on Biomedical librarianship
Issue of 2020‒12‒27
fifteen papers selected by
Thomas Krichel
Open Library Society


  1. BMC Bioinformatics. 2020 Dec 21. 21(Suppl 19): 572
    Rybinski M, Karimi S, Nguyen V, Paris C.
      BACKGROUND: Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published literature, given a query. However, they are limited in how users can control the processing of queries and articles-or as we call them documents-by the search engine. To give this control to both biomedical researchers and computer scientists working in biomedical information retrieval, we introduce a public online tool for searching over biomedical literature. Our setup is guided by the NIST setup of the relevant TREC evaluation tasks in genomics, clinical decision support, and precision medicine.RESULTS: To provide benchmark results for some of the most common biomedical information retrieval strategies, such as querying MeSH subject headings with a specific weight or querying over the title of the articles only, we present our evaluations on public datasets. Our experiments report well-known information retrieval metrics such as precision at a cutoff of ranked documents.
    CONCLUSIONS: We introduce the A2A search and benchmarking tool which is publicly available for the researchers who want to explore different search strategies over published biomedical literature. We outline several query formulation strategies and present their evaluations with known human judgements for a large pool of topics, from genomics to precision medicine.
    Keywords:  Biomedical search; Clinical decision support; Evaluation; Genomics; Information retrieval; Precision medicine; Software platform
    DOI:  https://doi.org/10.1186/s12859-020-03894-8
  2. Heart Lung. 2020 Dec 16. pii: S0147-9563(20)30347-2. [Epub ahead of print]50(2): 220-222
    Batten J, Brackett A.
      The third column, in this seven part series, highlights: Systematic reviews must include published sources as well as consider including unpublished sources for data collection. Systematic reviews require rigorous search strategies, that are transparent and reproducible. Systematic reviews require adequate reporting of search methods.
    Keywords:  Grey literature; Librarian; Meta-analysis; PICO; PRISMA; Peer review; Searching; Systematic review
    DOI:  https://doi.org/10.1016/j.hrtlng.2020.08.005
  3. J Ayurveda Integr Med. 2020 Dec 17. pii: S0975-9476(20)30100-5. [Epub ahead of print]
    Rastogi S, Sharma KG, Varma S, Verma S.
      Libraries have always been the integral components of the academic institutions world over. Earlier known for housing the spectrum of books permitting their ready access to knowledge seekers, libraries of current age are no more confined spaces with limited functions. With the advancing information technology, the conventional definition of a library is changing to accommodate newer roles and challenges. Twenty-first century academic libraries are extending beyond the walls of their individual institutions and are evolving as open access information spaces, dealing with intelligent sharing through social communication and networking technologies. Despite such massive changes in the information storage and retrieval patterns across the globe, libraries at Ayurveda institutions in India seem by and large unbothered and unaffected. Poor educational and research standards in Ayurveda seem to have direct links with libraries contributing minimally to academic exchange and progress. An SCONUL survey conducted for the first time in any ayurvedic library setting in the country came as an eye opener stating clearly that Ayurveda institutional libraries require a major reform first to bring them at par with other academic libraries and subsequently to evolve them as the nucleus of knowledge fostering. These setups direly need a hand of help to become eligible for contributing what they are really meant to.
    Keywords:  Ayurveda; Educational reforms; Medical library; SCONUL survey
    DOI:  https://doi.org/10.1016/j.jaim.2020.10.009
  4. Health Info Libr J. 2020 Dec 21.
    Atiogbe P, Fricker A, Reid L.
      Over the course of her life, Shane influenced the careers of many people working in health library and knowledge services. This article brings together three personal perspectives exploring aspects of this influence. By considering the activities prompted by contact with Shane, we look to how librarians might build on the example she provided of living a full professional life.
    Keywords:  librarianship International; librarianship health science; professional associations
    DOI:  https://doi.org/10.1111/hir.12349
  5. Health Info Libr J. 2020 Dec 21.
    Gorring H.
      This paper from CILIP's Health Libraries Group (HLG) committee is written by the previous International Officer who worked in partnership with Shane Godbolt. It outlines Shane's contribution to the Health Libraries Group over several decades and focuses on the collaborative work on international visits.
    Keywords:  International; collaboration; health science; librarianship; professional associations; professional development
    DOI:  https://doi.org/10.1111/hir.12346
  6. Health Info Libr J. 2020 Dec 22.
    Phillips R, Twomey C.
      Partnerships in Health Information (Phi) was a UK charity which worked with African health librarians, and other information professionals, to improve access to high-quality information for health professionals and the public in Africa from 1992 to 2016. This research was initiated by Shane Godbolt and aims to explore the experiences of African librarians and information professionals who visited the UK and who otherwise worked in partnership with Phi, following up on a previous Phi report that had shown significant mutual learning and development benefits for the UK hosts of such visitors. Also, to derive lessons on how visits and partnerships may be improved. In March 2020, a total of 21 people who had participated in partnership activities with Phi were invited to take part in an online survey. Thirteen people completed the survey. The results from the survey indicate it was hugely beneficial to visiting information professionals from Africa, for themselves and their services, through capacity building, networking, professional and personal development and learning tangible skills. Respondents provided several ideas on how partnerships could be improved in the future, including more opportunities for networking, longer-term evaluation, enlarged programmes and increased funding. We conclude that partnerships based on Phi's long-term, flexible approach can be of great benefit and provide insights and recommendations that could help any organisation seeking to emulate the Phi model of partnership working, based on co-development between UK health libraries and those in low- to middle-income countries.
    Keywords:  Africa; East; Godbolt; Shane; South; United Kingdom (UK); West; collaboration; health science; libraries; professional development
    DOI:  https://doi.org/10.1111/hir.12336
  7. Brief Bioinform. 2020 Dec 21. pii: bbaa344. [Epub ahead of print]
    Zheng S, Rao J, Song Y, Zhang J, Xiao X, Fang EF, Yang Y, Niu Z.
      Biomedical knowledge graphs (KGs), which can help with the understanding of complex biological systems and pathologies, have begun to play a critical role in medical practice and research. However, challenges remain in their embedding and use due to their complex nature and the specific demands of their construction. Existing studies often suffer from problems such as sparse and noisy datasets, insufficient modeling methods and non-uniform evaluation metrics. In this work, we established a comprehensive KG system for the biomedical field in an attempt to bridge the gap. Here, we introduced PharmKG, a multi-relational, attributed biomedical KG, composed of more than 500 000 individual interconnections between genes, drugs and diseases, with 29 relation types over a vocabulary of ~8000 disambiguated entities. Each entity in PharmKG is attached with heterogeneous, domain-specific information obtained from multi-omics data, i.e. gene expression, chemical structure and disease word embedding, while preserving the semantic and biomedical features. For baselines, we offered nine state-of-the-art KG embedding (KGE) approaches and a new biological, intuitive, graph neural network-based KGE method that uses a combination of both global network structure and heterogeneous domain features. Based on the proposed benchmark, we conducted extensive experiments to assess these KGE models using multiple evaluation metrics. Finally, we discussed our observations across various downstream biological tasks and provide insights and guidelines for how to use a KG in biomedicine. We hope that the unprecedented quality and diversity of PharmKG will lead to advances in biomedical KG construction, embedding and application.
    Keywords:  Alzheimer’s disease; computational prediction model; drug repositioning; knowledge graph; knowledge graph embedding
    DOI:  https://doi.org/10.1093/bib/bbaa344
  8. Iran J Nurs Midwifery Res. 2020 Sep-Oct;25(5):25(5): 393-400
    Goudarzi F, Abedi H, Zarea K.
      Background: Providing care for patients in Persistent Vegetative State (PVS) by family caregivers without enough training and knowledge may be problematic both for the patients and for the caregivers. Therefore, the present study tries to explain the experiences of family caregivers of patients with PVS of seeking information needed to provide adequate care.Materials and Methods: Twenty two participants, including 17 family caregivers and 5 professional caregivers were enrolled by purposive sampling into this qualitative content analysis study, carried out between 2013 and 2015. Unstructured interviews and field notes were used to gather the data. Data collection was stopped when data saturation was achieved. Data analysis was performed by content analysis based on Graneheim and Lundman's approach.
    Results: As a result of the analysis of the collected data a main theme emerged labeled as "Seeking constructive education" with three categories including "Neglected requisite education," "Greedy search for useful education" and "Dynamic independence in care."
    Conclusions: In this study, information seeking by family caregivers of patients with PVS was constructive. Family caregivers insistently sought needed information from various sources. Ultimately, they found these insistent efforts beneficial and fruitful, because their efforts made them independent in providing care for their patients.
    Keywords:  Caregivers; family; home nursing; information seeking behavior; nursing; persistent vegetative state
    DOI:  https://doi.org/10.4103/ijnmr.IJNMR_187_18
  9. Int J Environ Res Public Health. 2020 Dec 17. pii: E9467. [Epub ahead of print]17(24):
    Kim M, Chae K, Lee S, Jang HJ, Kim S.
      Collecting valid information from electronic sources to detect the potential outbreak of infectious disease is time-consuming and labor-intensive. The automated identification of relevant information using machine learning is necessary to respond to a potential disease outbreak. A total of 2864 documents were collected from various websites and subsequently manually categorized and labeled by two reviewers. Accurate labels for the training and test data were provided based on a reviewer consensus. Two machine learning algorithms-ConvNet and bidirectional long short-term memory (BiLSTM)-and two classification methods-DocClass and SenClass-were used for classifying the documents. The precision, recall, F1, accuracy, and area under the curve were measured to evaluate the performance of each model. ConvNet yielded higher average, min, and max accuracies (87.6%, 85.2%, and 91.1%, respectively) than BiLSTM with DocClass, while BiLSTM performed better than ConvNet with SenClass with average, min, and max accuracies of 92.8%, 92.6%, and 93.3%, respectively. The performance of BiLSTM with SenClass yielded an overall accuracy of 92.9% in classifying infectious disease occurrences. Machine learning had a compatible performance with a human expert given a particular text extraction system. This study suggests that analyzing information from the website using machine learning can achieve significant accuracies in the presence of abundant articles/documents.
    Keywords:  classification; infectious disease; machine learning; online document; public health surveillance
    DOI:  https://doi.org/10.3390/ijerph17249467
  10. J Laparoendosc Adv Surg Tech A. 2020 Dec 21.
    Citgez B, Aygün N, Yigit B, Uludag M.
      Background: The internet is a broadly preferred source of information both by patients and medical professionals. YouTube™ is a significant information source that may be a useful tool to inform the public, medical students, and residents, and may improve the learning experience if used adequately. In this study, we aimed to estimate the quality and accuracy of videos regarding Transoral Endoscopic Thyroidectomy Vestibular Approach (TOETVA) aired on YouTube, which is the most popular video platform of the online world. Materials and Methods: We evaluated the first 50 videos, returned by the YouTube research engine, in reply to the "TOETVA" keyword. The popularity of the videos was assessed using the video power index (VPI). The educational quality, accuracy, and transparency of the content regarding TOETVA were estimated by using the DISCERN questionnaire score (DISCERNqs), Journal of American Medical Association benchmark criteria (JAMABC), and global quality score (GQSc). The technical quality was ranked through TOETVA Scoring System (TOETVA-SS) by a TOETVA practicioning endocrine surgeon. Results: The content of the videos were about surgical technique with a rate of 68%. According to sources, videos uploaded by physicians had significantly higher DISCERNqs, JAMABC, GQSc, and TOETVA-SS scores. Unlike, videos uploaded by physicians had a lower VPI than videos uploaded by nonmedical sources. The videos of surgical technique had significantly higher DISCERNqs, JAMABC, GQSc, and TOETVA-SS scores. Surgical technique videos also had higher VPI scores than "information about disease or surgery" videos. Also, negative correlations were found between the VPI (popularity index) and educational value (GQSc), transparency (JAMABC), and technical quality (TOETVA-SS) scores. Conclusions: The data acquired from YouTube videos regarding TOETVA is of below expected quality and reliability. Nevertheless, the educative potential of the online video platform, YouTube, cannot be underestimated.
    Keywords:  TOETVA; YouTube; online; thyroid surgery
    DOI:  https://doi.org/10.1089/lap.2020.0849
  11. Ann Plast Surg. 2020 Dec 15. Publish Ahead of Print
    Nnamani Silva ON, Ammanuel SG, Segobiano BM, Edwards CS, Hoffman WY.
      BACKGROUND: The Internet has a plethora of online patient education resources for many symptoms and diseases. National medical governing bodies recommend that patient education materials are written at or below the eighth-grade level, and the literature suggests that health literacy has been linked to increased adherence to treatment regimens and improved outcomes. The primary aim of the study is to assess the readability of online patient materials relating to gynecomastia and ascertain the availability of patient materials in non-English languages.METHODS: The readability of patient education materials relating to gynecomastia for academic-based websites and nonacademic websites was assessed using the Flesch Reading Ease (FRE), Flesch-Kincaid Grade Level (FKGL), and Simple Measure of Gobbledygook (SMOG). The prevalence of non-English patient education materials was assessed for both academic-based and nonacademic websites.
    RESULTS: Fifty-eight documents were collected across academic websites. Overall median values were 10.7 for the FKGL, 47.0 for the FRE, and 11.4 for the SMOG. For the 10 nonacademic institutions, the overall median values were 10.6 for the FKGL, 45.2 for the FRE, and 10.8 for the SMOG. No appreciable differences were observed for readability when stratified by region or source. The prevalence of non-English patient materials was 19.1% across institutions. None of the noninstitutional materials had information in non-English languages.
    CONCLUSIONS: The readability of patient education materials related to gynecomastia is at higher levels than recommended by national organizations. There are limited non-English patient education materials. Future efforts should focus on improving the readability and accessibility of patient materials.
    DOI:  https://doi.org/10.1097/SAP.0000000000002620
  12. J Plast Reconstr Aesthet Surg. 2020 Dec 10. pii: S1748-6815(20)30671-9. [Epub ahead of print]
    Sinha V, Malik M, Borrelli MR, Sinha A, Cavale N.
      BACKGROUND: The rapid growth of non-surgical aesthetics has led to a scarcity of regulation that raises concerns for serious consequences to public health. Services are advertised primarily through websites which are not necessarily centrally monitored or maintained to a set gold standard. We quantitatively assess the quality of online information regarding non-surgical procedures in order to promote patient safety and informed decision making.METHODS: Google and Bing, search engines that represent 95.27of global searches, were queried with the expanded search terms "facial filler" and "Botox". The top 100 results were sampled and two validated tools were used to assess the quality of healthcare information retrieved; the DISCERN instrument and the JAMA benchmark criteria.
    RESULTS: Once duplicates were removed, a total of 77 unique websites were retrieved by the search. The majority of websites were published by private marketing firms. The median score for website quality across all included websites was 'fair' (42) when assessed according to the DISCERN instrument, and 'poor' (1) when assessed against the JAMA criteria. Private websites had the lowest quality of information online and institutional websites had the highest.
    CONCLUSION: Non-surgical aesthetics are becoming increasingly popular with patients and clinicians due to their convenience, scope of treatment, and novel and strategic marketing. Online information available to patients, however, is often of poor quality, dominated by private clinics and commercial entities, and thus presents a significant risk of misinforming patients desiring to undertake these procedures. Significant reform and regulation of information is required in order to make this industry safer for patients.
    Keywords:  Aesthetic procedures; Botulinum toxin; Cosmetic procedures; Dermal filler; Plastic surgery
    DOI:  https://doi.org/10.1016/j.bjps.2020.12.006
  13. J Vasc Surg Venous Lymphat Disord. 2020 Dec 16. pii: S2213-333X(20)30727-7. [Epub ahead of print]
    Yan Q, Langley AR, Jensen KJ, Goei C, Jiang Z, Davies MG.
      OBJECTIVE: Patients increasingly seek information on their medical conditions from the internet. This study aims to evaluate the quality and readability of readily available online patient resources for varicose veins.METHODS: An internet search for "varicose veins" was conducted on the meta-search engines Yippy and Dogpile and the general search engines Google, Yahoo, and Bing with a cleared-cache web browser in July 2019. Two separate trained raters scored websites on the dimensions of accessibility, accountability, interactivity, structure, and content. Discrepancies were discussed and consensus was reached. Readability was calculated using four readability metric systems. Rater consistency was evaluated using Kappa, weighted Kappa, and interrater correlation coefficient as indicated.
    RESULTS: A total of 189 websites met inclusion criteria. Total median quality score was 15.6 (IQR 13.1-20.5, range 7.4-31.3) out of 38. Websites scored median 4 (IQR 1-8) out of 15 for accountability, 2 (2-2) out of 5 for interactivity, 4 (2-4) out of 4 for organization, and 6.4 (3.9-7.9) out of 4 for weighted contents. Most websites (81.5%) were accessible. Overall readability was poor. Median Flesch-Kincaid Reading Ease score was 55.1 (49.4-6.7) indicating that the text was fairly difficult to read. The median grade level was 10th grade using both Flesch-Kincaid Grade Level and simple measure of Gobbledygook index and 11-12th grade using new Dale-Chall. Government websites were the most accountable, featured the best content, and were the most readable. Website traffic had a positive, nonlinear correlation with total score and a negative, nonlinear correlation with website rank (or position on search result page). Website rank was negatively correlated with total score, although the correlation was weak.
    CONCLUSIONS: Quality of online patient resources on varicose veins is highly variable and readability for most sites is poor. Government sponsored websites have the highest quality while remaining the most readable. Physicians are advised to consider providing a list of appropriate websites to their patients to better inform them, to avoid confusion, and to ensure appropriate delivery of accurate and readable information.
    Keywords:  internet web resources; patient information; varicose veins
    DOI:  https://doi.org/10.1016/j.jvsv.2020.12.072