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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