bims-librar Biomed News on Biomedical librarianship
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Issue of 2020‒06‒07 │
eighteen papers selected by │
Thomas Krichel (Open Library │
 Society) │
 http://e.biomed.news/librar │
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 1. Identification of the Best Semantic Expansion to Query PubMed Through
     Automatic Performance Assessment of Four Search Strategies on All Medical
     Subject Heading Descriptors: Comparative Study.
 2. Systematic mixed studies reviews: leveraging the literature to answer
     complex questions through the integration of quantitative and qualitative
     evidence.
 3. Citizen Science im Kaiserreich. Die Systemstelle „Wertlose
     Einsendungen aus der Bevölkerung“ im Archiv der Berlin‐Brandenburgischen
     Akademie der Wissenschaften.
 4. Readability of web-based sources about induced abortion: a
     cross-sectional study.
 5. Quality and Readability of Online Health Information for Acral
     Lentiginous Melanoma.
 6. COVID-19-Related Information Sources and the Relationship With
     Confidence in People Coping with COVID-19: Facebook Survey Study in
     Taiwan.
 7. Evaluation of Spanish Language Proficiency and Resources Available in
     Academic Pediatric Orthopaedic Centers.
 8. Use of the Internet by pregnant women to seek information about
     pregnancy and childbirth.
 9. YouTube™ as a source of information for Candida auris infection: a
     systematic review.
10. Googling fibroids: A critical appraisal of information available on
     the internet.
11. Assessment of Online Sites Reliability, Accountability, Readability,
     Accessibility and Translation for Intravitreal Injections.
12. How adolescent patients search for and appraise online health
     information: A pilot study.
13. Use and importance of different information sources among patients
     with rare diseases and their relatives over time: a qualitative study.
14. Developing a Search Engine for Precision Medicine.
15. BRret: Retrieval of Brain Research Related Literature.
16. Chemical Entity Recognition for MEDLINE Indexing.
17. Database combinations to retrieve systematic reviews in overviews of
     reviews: a methodological study.
18. Text Snippets to Corroborate Medical Relations: An Unsupervised
     Approach using a Knowledge Graph and Embeddings.

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                                      JMIR Med Inform. 2020 Jun 04. 8(6): e12799
 1. Identification of the Best Semantic Expansion to Query PubMed Through
     Automatic Performance Assessment of Four Search Strategies on All Medical
     Subject Heading Descriptors: Comparative Study.
   Massonnaud CR, Kerdelhué G, Grosjean J, Lelong R, Griffon N, Darmoni SJ
  BACKGROUND: With the continuous expansion of available biomedical data,
  efficient and effective information retrieval has become of utmost
  importance. Semantic expansion of queries using synonyms may improve
  information retrieval.
   OBJECTIVE: The aim of this study was to automatically construct and evaluate
  expanded PubMed queries of the form "preferred term"[MH] OR "preferred
  term"[TIAB] OR "synonym 1"[TIAB] OR "synonym 2"[TIAB] OR …, for each of the
  28,313 Medical Subject Heading (MeSH) descriptors, by using different
  semantic expansion strategies. We sought to propose an innovative method
  that could automatically evaluate these strategies, based on the three main
  metrics used in information science (precision, recall, and F-measure).
   METHODS: Three semantic expansion strategies were assessed. They differed by
  the synonyms used to build the queries as follows: MeSH synonyms, Unified
  Medical Language System (UMLS) mappings, and custom mappings (Catalogue et
  Index des Sites Médicaux de langue Française [CISMeF]). The precision,
  recall, and F-measure metrics were automatically computed for the three
  strategies and for the standard automatic term mapping (ATM) of PubMed. The
  method to automatically compute the metrics involved computing the number of
  all relevant citations (A), using National Library of Medicine indexing as
  the gold standard ("preferred term"[MH]), the number of citations retrieved
  by the added terms ("synonym 1"[TIAB] OR "synonym 2"[TIAB] OR …) (B), and
  the number of relevant citations retrieved by the added terms (combining the
  previous two queries with an "AND" operator) (C). It was possible to
  programmatically compute the metrics for each strategy using each of the
  28,313 MeSH descriptors as a "preferred term," corresponding to 239,724
  different queries built and sent to the PubMed application program
  interface. The four search strategies were ranked and compared for each
  metric.
   RESULTS: ATM had the worst performance for all three metrics among the four
  strategies. The MeSH strategy had the best mean precision (51%, SD 23%). The
  UMLS strategy had the best recall and F-measure (41%, SD 31% and 36%, SD
  24%, respectively). CISMeF had the second best recall and F-measure (40%, SD
  31% and 35%, SD 24%, respectively). However, considering a cutoff of 5%,
  CISMeF had better precision than UMLS for 1180 descriptors, better recall
  for 793 descriptors, and better F-measure for 678 descriptors.
   CONCLUSIONS: This study highlights the importance of using semantic
  expansion strategies to improve information retrieval. However, the
  performances of a given strategy, relatively to another, varied greatly
  depending on the MeSH descriptor. These results confirm there is no ideal
  search strategy for all descriptors. Different semantic expansions should be
  used depending on the descriptor and the user's objectives. Thus, we
  developed an interface that allows users to input a descriptor and then
  proposes the best semantic expansion to maximize the three main metrics
  (precision, recall, and F-measure).
   Keywords: MEDLINE; Medical Subject Headings; PubMed; bibliographic
    database; information retrieval; literature search; precision; recall;
    search strategy; thesaurus
  DOI: https://doi.org/10.2196/12799
  URL: http://pubmed.ncbi.nlm.nih.gov/32496201

                                               Int J Public Health. 2020 Jun 03.
 2. Systematic mixed studies reviews: leveraging the literature to answer
     complex questions through the integration of quantitative and qualitative
     evidence.
   Cerigo H, Quesnel-Vallée A
  DOI: https://doi.org/10.1007/s00038-020-01386-3
  URL: http://pubmed.ncbi.nlm.nih.gov/32494870

                                               Ber Wiss. 2018 Dec;41(4): 383-386
 3. Citizen Science im Kaiserreich. Die Systemstelle „Wertlose
     Einsendungen aus der Bevölkerung“ im Archiv der Berlin‐Brandenburgischen
     Akademie der Wissenschaften.
   Krajewski M
   Keywords: Archiv; Archivpraktiken; Citizen Science; Einstein; Fermat'sche
    Vermutung; Fermats Last Theorem; Gutachten; Populärwissenschaft; archival
    practices; archives; review; scientific ecognition; vernacular science;
    wissenschaftliche Anerkennung
  DOI: https://doi.org/10.1002/bewi.201801917
  URL: http://pubmed.ncbi.nlm.nih.gov/32495428

                               BMC Med Inform Decis Mak. 2020 Jun 05. 20(1): 102
 4. Readability of web-based sources about induced abortion: a
     cross-sectional study.
   Georgsson S, Carlsson T
  BACKGROUND: High-quality information is essential if clients who request an
  abortion are to reach informed decisions and feel prepared for the
  procedure, but little is known concerning the readability of web-based
  sources containing such material. The aim was to investigate the readability
  of web-based information about induced abortion.
   METHODS: The search engine Google was used to identify web pages about
  induced abortion, written in the English language. A total of 240 hits were
  screened and 236 web pages fulfilled the inclusion criteria. After
  correcting for duplicate hits, 185 web pages were included. The readability
  of the text-based content of each web page was determined with Flesch
  Kincaid Grade Level, Gunning Fog Index, Coleman-Liau Index, Simple Measure
  of Gobbledygook, and Flesch Reading Ease. Data were analyzed with
  descriptive statistics, Pearson's correlation coefficient and Kruskal-Wallis
  with Dunn's test as post hoc analysis.
   RESULTS: Across all grade level measures, a small minority of the web pages
  had a readability corresponding to elementary school (n < 3, 1%), while the
  majority had readability corresponding to senior high school or above
  (n > 153, 65%). The means of the grade level measures ranged between 10.5
  and 13.1, and the mean Flesch Reading Ease score was 45.3 (SD 13.6). Only
  weak correlations (rho < 0.2) were found between the readability measures
  and search rank in the hit lists. Consistently, web pages affiliated with
  health care had the least difficult readability and those affiliated with
  scientific sources had the most difficult readability.
   CONCLUSIONS: Overall, web-based information about induced abortions has
  difficult readability. Incentives are needed to improve the readability of
  these texts and ensure that clients encounter understandable information so
  that they may reach informed decisions and feel adequately prepared when
  requesting an abortion.
   Keywords: Consumer health information; Induced abortion; Quality;
    Readability; World wide web
  DOI: https://doi.org/10.1186/s12911-020-01132-y
  URL: http://pubmed.ncbi.nlm.nih.gov/32503524

                                                     Dermatol Surg. 2020 May 29.
 5. Quality and Readability of Online Health Information for Acral
     Lentiginous Melanoma.
   Yu Z, Dee EC, Nambudiri VE, Ogbechie-Godec OA, Jakus J, Siegel DM
  DOI: https://doi.org/10.1097/DSS.0000000000002457
  URL: http://pubmed.ncbi.nlm.nih.gov/32483094

                                  J Med Internet Res. 2020 Jun 05. 22(6): e20021
 6. COVID-19-Related Information Sources and the Relationship With
     Confidence in People Coping with COVID-19: Facebook Survey Study in
     Taiwan.
   Wang PW, Lu WH, Ko NY, Chen YL, Li DJ, Chang YP, Yen CF
  BACKGROUND: People obtain information on the coronavirus disease (COVID-19)
  from the internet and other sources. Understanding the factors related to
  such information sources aids health professionals in educating individuals.
   OBJECTIVE: This study used data collected from the online survey study on
  COVID-19 in Taiwan to examine what major COVID-19 information sources are
  available and which sources are significantly related to the self-confidence
  of people in coping with COVID-19 in Taiwan.
   METHODS: A total of 1904 participants (1270 non-health-care workers and 634
  health care workers) were recruited from the Facebook advertisement. Their
  major sources of information about COVID-19, the relationships between the
  sources and demographic factors, and the relationships between the sources
  and the self-confidence in coping with COVID-19 were surveyed.
   RESULTS: Most Taiwanese people relied on the internet for COVID-19
  information. Many respondents also used a variety of sources of information
  on COVID-19; such variety was associated with sex, age, and the level of
  worry toward COVID-19, as well as if one was a health care worker. For
  health care workers, the use of formal lessons as an information source was
  significantly associated with better self-confidence in coping with
  COVID-19. The significant association between receiving information from
  more sources and greater self-confidence was found only in health care
  workers but not in non-health-care workers.
   CONCLUSIONS: Medical professionals should consider subgroups of the
  population when establishing various means to deliver information on
  COVID-19.
   Keywords: COVID-19; Facebook; confidence; coping; information; internet;
    mental health; online health information; social media; survey
  DOI: https://doi.org/10.2196/20021
  URL: http://pubmed.ncbi.nlm.nih.gov/32490839

                                       J Pediatr Orthop. 2020 Jul;40(6): 310-313
 7. Evaluation of Spanish Language Proficiency and Resources Available in
     Academic Pediatric Orthopaedic Centers.
   Sobel AD, Ramirez JM, Walsh DF, Defroda SF, Cruz AI
  INTRODUCTION: Given the rapidly increasing population of Spanish-speaking
  patients in the United States, medical providers must have the capability to
  effectively communicate both with pediatric patients and their caregivers.
  The purpose of this study was to query the Spanish language proficiency of
  pediatric orthopaedic surgeons, assess the educational resources available
  to Spanish-speaking patients and their families, and identify the barriers
  to care at academic pediatric orthopaedic centers.
   METHODS: The Web sites of medical centers within the United States that have
  pediatric orthopaedic surgery fellowships recognized by the Pediatric
  Orthopaedic Society of North America (POSNA) were accessed. Web sites were
  investigated for a health library as well as the availability of interpreter
  services. Profiles of attending surgeons within each Pediatric Orthopaedic
  Department were evaluated for evidence of Spanish proficiency as well as
  educational qualifications. Centers were contacted by phone to determine if
  the resources and physicians who could converse in Spanish were different
  than what was readily available online and if automated instructions in
  Spanish or a person who could converse in Spanish were available.
   RESULTS: Forty-six centers with 44 fellowship programs were identified. The
  profiles of 12 of 334 (3.6%) surgeons who completed pediatric orthopaedic
  fellowships indicated Spanish proficiency. Seventeen physicians (5.1%) were
  identified as proficient in Spanish after phone calls. Thirty-eight
  pediatric orthopaedic centers (82.6%) noted interpreter service availability
  online, although services varied from around-the-clock availability of live
  interpreters to interpreter phones. When contacted by phone, 45 of 46
  centers (97.8%) confirmed the availability of any interpreter service for
  both inpatient and outpatient settings. Sixteen centers (34.8%) had online
  information on orthopaedic conditions or surgical care translated into
  Spanish. Twenty centers (43.5%) did not have automated phone messages in
  Spanish or live operators that spoke Spanish.
   CONCLUSIONS: There is a scarcity of surgical providers in pediatric
  orthopaedic centers proficient in Spanish, demonstrating a large discrepancy
  with the growing Hispanic population. Interpreter services are widely
  available, although there is variability in the services provided.
  Considerable barriers exist to Spanish-speaking patients who attempt to
  access care by phone or online.
  DOI: https://doi.org/10.1097/BPO.0000000000001466
  URL: http://pubmed.ncbi.nlm.nih.gov/32501928

                                       Inform Health Soc Care. 2020 Jun 02. 1-11
 8. Use of the Internet by pregnant women to seek information about
     pregnancy and childbirth.
   Ahmadian L, Khajouei R, Kamali S, Mirzaee M
  Pregnant women get information about pregnancy andchild-birth from many
  sources, including the Internet. There is alack of evidence about the extent
  to which pregnant women usethis source. This study aimed to investigate the
  use of the Internetby pregnant women to search for information about
  pregnancyand childbirth. This study was conducted in Kerman, Iran.
  Threehundred eighty-five pregnant women waiting for their appointmentswith
  obstetricians/gynecologists participated in the survey byfilling out a
  questionnaire. The most common searched topicswere nutrition in pregnancy
  (81%), fetal development (67%), andcomplications of pregnancy (49%). The
  most popular sources ofinformation were physicians (61%), the Internet
  (51%), and printedsources (41%), respectively. More than half of the
  participantsdid not share the retrieved information from the Internet with
  theirhealth professionals. After being examined by a physician, 43% ofthe
  participants searched the Internet about the discussed topic.Beside
  physicians, the Internet is the second common source ofpregnancy and
  childbirth information for Iranian pregnant women.Future studies are needed
  to analyze the quality and accuracy ofonline pregnancy and childbirth
  information.
   Keywords: Pregnancy; childbirth; information; internet; online; pregnant
    woman; world Wide Web
  DOI: https://doi.org/10.1080/17538157.2020.1769106
  URL: http://pubmed.ncbi.nlm.nih.gov/32484715

                                      BMC Public Health. 2020 Jun 01. 20(1): 832
 9. YouTube™ as a source of information for Candida auris infection: a
     systematic review.
   Huang J, Zhang S, Xiao Q, Cao Y, Li B
  BACKGROUND: Candida auris is a novel Candida species, and has emerged
  globally as a multidrug-resistant health care-associated fungal pathogen.
  YouTube™ (http://www.youtube.com) as the largest free video-sharing website
  is increasingly used to search health information. Thus, the aim of this
  study was to evaluate the content, reliability and quality of YouTube™
  videos regarding Candida auris infection, and to identify whether it is a
  useful resource for people.
   METHODS: The YouTube™ was used to search systematically for videos using the
  keywords: "Candida auris infection" and "Candida auris". Strict inclusion
  and exclusion criteria were used to select the videos. The videos were
  reviewed and scored by two independent reviewers and recorded the "title",
  "length", "views", "comments", "dislike", "like", "posted days" and
  "category of videos". The videos were categorized as "poor", "good" and
  "excellent" by the score. The DISCERN tool was used to assess the
  reliability of the YouTube™ videos.
   RESULTS: Seventy-six videos were included in final analysis in our study.
  Most videos (59.2%, 55/76) had better quality. There were no statistically
  significant differences between groups in respect of the number of likes,
  dislikes, views, comments, percentage positivity, likebility, view rate and
  viewers' interaction. Length and posted days were significantly associated
  with the classification. The videos were categorized as "educational video",
  "new report", "personal experience and blog entertainment" and "interview".
  Significant differences were found in the source of videos and the
  characteristics of the individuals appearing in a video between the groups.
   CONCLUSION: YouTube™ has striking potential to be an effective user-friendly
  learning interface for people to obtain information of Candida auris
  infection.
   Keywords: Candida auris; Infection; Internet; Reliability; YouTube™
  DOI: https://doi.org/10.1186/s12889-020-08731-4
  URL: http://pubmed.ncbi.nlm.nih.gov/32487232

     Eur J Obstet Gynecol Reprod Biol. 2020 Apr 18. pii: S0301-2115(20)30172-X.
10. Googling fibroids: A critical appraisal of information available on
     the internet.
   Hirsch M, Wojtaszewska A, Saridogan E, Mavrelos D, Barker C, Duffy JMN
  OBJECTIVE: We aim to evaluate the accuracy, quality, and readability of
  online patient information concerning fibroids.
   STUDY DESIGN: We searched the most popular Internet search engine:
  Google.com. We developed a search strategy in consultation with patients
  with fibroids, to identify relevant websites. Two independent authors
  screened the search results. Websites were evaluated using validated
  instruments across three domains, including assessments of: [1] quality
  (DISCERN instrument; range 0-85); [2] readability (Flesch-Kincaid
  instrument; range 0-100); and [3] accuracy. Accuracy was assessed using
  evidence-based statements. We summarised this data narratively including the
  use of figures and tables.
   RESULTS: We identified 750 websites, of which 48 were included. Over a third
  of websites did not attribute authorship and almost half the included
  websites did not report the sources of information or academic references.
  No website provided written patient information in line with recommendations
  from the American Medical Association. A minority (18%) of websites were
  assessed as high quality. Twelve webpages provided only accurate statements.
  Available information was, in general, skewed towards the surgical
  management of fibroids. No website scored highly across all three domains.
   CONCLUSION: In the unlikely event that a website reports high quality and
  accurate health information, it is typically challenging for a lay audience
  to comprehend. Healthcare professionals and the wider community, should
  inform women with fibroids of the risk of outdated, inaccurate, or even
  dangerous information online. The implementation of an Information Standard
  certification will incentivise providers of online information to establish
  and adhere to codes of conduct. VIDEO ABSTRACT.
   Keywords: Accuracy; Fibroids; Online information; Patients; Quality;
    Readability
  DOI: https://doi.org/10.1016/j.ejogrb.2020.04.004
  URL: http://pubmed.ncbi.nlm.nih.gov/32473505

                    Ophthalmol Retina. 2020 Jun 01. pii: S2468-6530(20)30215-3.
11. Assessment of Online Sites Reliability, Accountability, Readability,
     Accessibility and Translation for Intravitreal Injections.
   Rayess N, Li AS, Do DV, Rahimy E
  PURPOSE: Patients increasingly use the internet to access health-related
  information to further understand their treatments and conditions. This
  study compares the quality, accountability, readability, accessibility and
  presence of translation between private and academic online source material
  available to the public regarding intravitreal injections.
   DESIGN: Cross-sectional analysis PARTICIPANTS: Top 20 websites on a Google
  search for the terms 'eye injections', 'intravitreal injections' and
  'anti-VEGF injections'.
   METHODS: Websites were classified as private or academic. Quality and
  accountability were assessed using the internationally recognized DISCERN
  criteria and the Health on the Net (HONcode). All 20 sites were
  independently graded by 2 retinal physicians and differences were
  adjudicated by a third experienced retinal physician. Readability was
  evaluated using an online tool that provides a consensus readability grade
  level. The presence of and languages available for translation were
  recorded. The top 5 ranked websites' content quality, accountability and
  readability was also compared with the other 15 websites.
   MAIN OUTCOME MEASURES: Primary outcome measure is comparing the DISCERN and
  HONcode quality and accountability scores between academic and private
  websites. Secondary outcome measures include evaluating readability,
  accessibility and presence of translation (in particular, Spanish).
   RESULTS: Eleven academic and 9 private websites were included. The overall
  mean score using DISCERN criteria for the academic websites (3.11±0.46) was
  significantly higher than that of private websites (2.23±0.61; p<0.007).
  Similarly, out of a possible total 14 points for the HONcode, the average
  quality score for academic websites (10.91±2.66) was higher compared to
  private websites (6.44±3.36; p<0.009). The mean consensus reading grade
  level was similar between academic (11.73±1.68) and private websites
  (11.78±1.48; p=0.94). Spanish translation was offered by only 7 of the 20
  websites (5 academic and 2 private websites).
   CONCLUSION: The overall quality and accountability of online content for
  academic sites was significantly higher compared to private websites.
  Translation was rarely provided and the readability grade level was
  significantly higher for both groups than recommended. Improving the
  quality, accountability, readability, accessibility and incorporating
  translation in websites can help improve patients' health literacy regarding
  intravitreal injections, potentially leading to increased adherence to
  therapy plans and improved treatment outcomes.
  DOI: https://doi.org/10.1016/j.oret.2020.05.019
  URL: http://pubmed.ncbi.nlm.nih.gov/32497854

                                           J Paediatr Child Health. 2020 Jun 01.
12. How adolescent patients search for and appraise online health
     information: A pilot study.
   McKinnon KA, H Y Caldwell P, Scott KM
  AIM: Adolescents increasingly use smartphones to look up online health
  information. This pilot study aimed to explore the search and assessment
  strategies of adolescents looking for online health information.
   METHODS: We performed an observed, practical task on mobile devices,
  followed by a semi-structured interview with adolescent patients at The
  Children's Hospital at Westmead, Sydney. Observational data were analysed
  using an observation rubric, and interviews were transcribed verbatim. Data
  were analysed through inductive thematic analysis using line-by-line coding
  and the constant comparative process.
   RESULTS: The research was undertaken with 10 participants. Three themes were
  identified: (i) participants' searching strategies to find online health
  information; (ii) techniques for assessing relevance; and (iii) techniques
  for assessing credibility. These themes demonstrated that most participants
  accessed online health information due to its ease and accessibility but
  failed to assess credibility. Most prioritised relevance of information over
  credibility, determined by their personal knowledge and experience. Our
  results indicate that there was a large discrepancy between adolescents'
  ability to search for and assess online health information and their
  perceived ability. This demonstrates a discrepancy between perceived and
  performance-based eHealth literacy and highlights poor critical
  self-awareness, which can prevent adolescents from seeking help. This may
  underlie the biggest challenge in adolescents' access of online health
  information and highlights the need for education.
   CONCLUSIONS: Many adolescents' search and appraisal ability is negatively
  impacted by low eHealth literacy. These adolescents' inability to recognise
  their need for assistance in improving their search and assessment
  strategies highlights the need for multi-stage education.
   Keywords: adolescent; digital health literacy; eHealth literacy; health
    promotion; information seeking behaviour
  DOI: https://doi.org/10.1111/jpc.14918
  URL: http://pubmed.ncbi.nlm.nih.gov/32479676

                                      BMC Public Health. 2020 Jun 05. 20(1): 860
13. Use and importance of different information sources among patients
     with rare diseases and their relatives over time: a qualitative study.
   Litzkendorf S, Frank M, Babac A, Rosenfeldt D, Schauer F, Hartz T, Graf von
   der Schulenburg JM
  BACKGROUND: Finding reliable information on one of more than 7000 rare
  diseases is a major challenge for those affected. Since rare diseases are
  defined only by the prevalence criterion, a multitude of heterogeneous
  diseases are included. Common to all, however, are difficulties regarding
  information access. Even though various quantitative studies have analyzed
  the use of different information sources for specific rare diseases, little
  is known about the use of information sources for different rare diseases,
  how users rate these information sources based on their experiences, and how
  the use and importance of these information sources change over time.
   METHODS: Fifty-five patients with a variety of rare diseases and 13 close
  relatives participated in qualitative interviews. For these interviews, a
  semi-structured guideline was developed, piloted, and revised. Data analysis
  involved a qualitative content analysis developed by Philipp Mayring.
   RESULTS: The participants considered internet as the most important and
  widespread information source, especially for early information. Although
  patients have difficulty dealing with information obtained online, they
  consider online searching a quick and practical option to gather
  information. During the course of the disease, personal contact partners,
  especially self-help associations and specialized doctors, become more
  important. This is also because information provided online is sometimes
  insufficiently detailed to answer their information needs, which can be
  complemented by information from doctors and self-help.
   CONCLUSIONS: People rarely use just one type of source, but rather refer to
  different sources and informants. The source used depends on the type of
  information sought as well as other person-related factors such as
  preexisting knowledge and the disease stage. To improve people's information
  searching and connect them with medical specialists in rare diseases, a
  central information portal on rare diseases might be a suitable access point
  to provide free and quality assured information for patients, caregivers,
  and physicians. This would allow not only patients but also doctors to find
  quality assured information on symptoms and therapies as well as patient
  associations and specialized doctors.
   Keywords: Content analysis; Health information seeking; Informants;
    Information sources; Online information; Qualitative research; Rare
    diseases; Self-help; Written information
  DOI: https://doi.org/10.1186/s12889-020-08926-9
  URL: http://pubmed.ncbi.nlm.nih.gov/32503483

                             AMIA Jt Summits Transl Sci Proc. 2020 ;2020 579-588
14. Developing a Search Engine for Precision Medicine.
   Shenoi SJ, Ly V, Soni S, Roberts K
  Precision medicine focuses on developing new treatments based on an
  individual's genetic, environmental, and lifestyle profile. While this
  data-driven approach has led to significant advances, retrieving information
  specific to a patient's condition has proved challenging for oncologists due
  to the large volume of data. In this paper, we propose the PRecIsion
  Medicine Robust Oncology Search Engine (PRIMROSE) for cancer patients that
  retrieves scientific articles and clinical trials based on a patient's
  condition, genetic profile, age, and gender. Our search engine utilizes
  Elasticsearch indexes for information storage and retrieval, and we
  developed a knowledge graph for query expansion in order to improve recall.
  Additionally, we experimented with machine learning and learning-to-rank
  components to the search engine and compared the results of the two
  approaches. Finally, we developed a front-facing ReactJS website and a REST
  API for connecting with our search engine. The development of this
  front-facing website allows for easy access to our system by healthcare
  providers.
  URL: http://pubmed.ncbi.nlm.nih.gov/32477680

                               AMIA Jt Summits Transl Sci Proc. 2020 ;2020 53-62
15. BRret: Retrieval of Brain Research Related Literature.
   Anani M, Kuntz M, Kahanda I
  Research Domain Criteria (RDoC), which is a recently introduced framework
  for mental illness, utilizes various units of analysis from genetics, neural
  circuits, etc., for accurate multi-dimensional classification of mental
  illnesses. Due to the large amount of relevant biomedical research
  available, automating the process of extracting evidence from the literature
  to assist with the curation of the RDoC matrix is essential for processing
  the full breadth of data in an accurate and cost-effective manner. In this
  work, we formulate the task of information retrieval of brain research
  literature from general PubMed abstracts. We develop BRret (Brain Research
  retriever), a novel algorithm for brain research related article retrieval.
  We use a large dataset of PubMed abstracts annotated with RDoC concepts to
  demonstrate the effectiveness of BRret. To the best of our knowledge, this
  is the first study aimed at automated retrieval of brain research related
  literature.
  URL: http://pubmed.ncbi.nlm.nih.gov/32477623

                             AMIA Jt Summits Transl Sci Proc. 2020 ;2020 561-568
16. Chemical Entity Recognition for MEDLINE Indexing.
   Savery ME, Rogers WJ, Pillai M, Mork JG, Demner-Fushman D
  Chemical entity recognition is essential for indexing scientific literature
  in the MEDLINE database at the National Library of Medicine. However, the
  tool currently used to suggest terms for indexing, the Medical Text Indexer,
  was not originally conceived as a chemical recognition tool. It has instead
  been adapted to the task via its use of MetaMap and the addition of in-house
  patterns and rules. In order to develop a tool more suitable for chemical
  recognition, we have created a collection of 200 MEDLINE titles and
  abstracts annotated with genes, proteins, inorganic and organic chemicals,
  as well as other biological molecules. We use this collection to evaluate
  eleven chemical entity recognition systems, where we seek to identify a tool
  that effectively recognizes chemical entities for indexing and also performs
  well on chemical recognition beyond the indexing task. We observe the
  highest performance with a SciBERT ensemble.
  URL: http://pubmed.ncbi.nlm.nih.gov/32477678

                                   BMC Med Res Methodol. 2020 Jun 01. 20(1): 138
17. Database combinations to retrieve systematic reviews in overviews of
     reviews: a methodological study.
   Goossen K, Hess S, Lunny C, Pieper D
  BACKGROUND: When conducting an Overviews of Reviews on health-related
  topics, it is unclear which combination of bibliographic databases authors
  should use for searching for SRs. Our goal was to determine which databases
  included the most systematic reviews and identify an optimal database
  combination for searching systematic reviews.
   METHODS: A set of 86 Overviews of Reviews with 1219 included systematic
  reviews was extracted from a previous study. Inclusion of the systematic
  reviews was assessed in MEDLINE, CINAHL, Embase, Epistemonikos, PsycINFO,
  and TRIP. The mean inclusion rate (% of included systematic reviews) and
  corresponding 95% confidence interval were calculated for each database
  individually, as well as for combinations of MEDLINE with each other
  database and reference checking.
   RESULTS: Inclusion of systematic reviews was higher in MEDLINE than in any
  other single database (mean inclusion rate 89.7%; 95% confidence interval
  [89.0-90.3%]). Combined with reference checking, this value increased to
  93.7% [93.2-94.2%]. The best combination of two databases plus reference
  checking consisted of MEDLINE and Epistemonikos (99.2% [99.0-99.3%]).
  Stratification by Health Technology Assessment reports (97.7% [96.5-98.9%])
  vs. Cochrane Overviews (100.0%) vs. non-Cochrane Overviews (99.3%
  [99.1-99.4%]) showed that inclusion was only slightly lower for Health
  Technology Assessment reports. However, MEDLINE, Epistemonikos, and
  reference checking remained the best combination. Among the 10/1219
  systematic reviews not identified by this combination, five were published
  as websites rather than journals, two were included in CINAHL and Embase,
  and one was included in the database ERIC.
   CONCLUSIONS: MEDLINE and Epistemonikos, complemented by reference checking
  of included studies, is the best database combination to identify systematic
  reviews on health-related topics.
   Keywords: Databases; Overview of reviews; Review methods; Search strategy;
    Systematic reviews; Umbrella review
  DOI: https://doi.org/10.1186/s12874-020-00983-3
  URL: http://pubmed.ncbi.nlm.nih.gov/32487023

                             AMIA Jt Summits Transl Sci Proc. 2020 ;2020 288-297
18. Text Snippets to Corroborate Medical Relations: An Unsupervised
     Approach using a Knowledge Graph and Embeddings.
   Kamdar MR, Stanley CE, Carroll M, Wogulis L, Dowling W, Deus HF,
   Samarasinghe M
  Knowledge graphs have been shown to significantly improve search results.
  Usually populated by subject matter experts, relations therein need to keep
  up to date with medical literature in order for search to remain relevant.
  Dynamically identifying text snippets in literature that confirm or deny
  knowledge graph triples is increasingly becoming the differentiator between
  trusted and untrusted medical decision support systems. This work describes
  our approach to mapping triples to medical text. A medical knowledge graph
  is used as a source of triples that are used to find matching sentences in
  reference text. Our unsupervised approach uses phrase embeddings and cosine
  similarity measures, and boosts candidate text snippets when certain key
  concepts exist. Using this approach, we can accurately map semantic
  relations within the medical knowledge graph to text snippets with a
  precision of 61.4% and recall of 86.3%. This method will be used to develop
  a novel application in the future to retrieve medical relations and
  corroborating snippets from medical text given a user query.
  URL: http://pubmed.ncbi.nlm.nih.gov/32477648

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