Changing trends in clinical research literature on PubMed database from 1991 to 2020.

BACKGROUND: Clinical research publications have become the dominant source and basis of clinical evidence-based decision-making. Exploring the type and quantity of clinical research publications in the PubMed database is useful for clarifying the changing trends of clinical research development in recent years. Therefore, a longitudinal analysis of the type and quantity of clinical research publications in the PubMed database over three decades was conducted. METHODS: The PubMed database was searched to retrieve clinical research according to the type and year of publication from January 1, 1991 to December 31, 2020. The research types were classified as primary and secondary literature. RESULTS: A total of 1,078,404 primary literatures were retrieved and the constituent proportions were ranked from high to low as case report/series (27.54%), randomized clinical trials (RCTs) (23.62%), cohort studies (21.05%), cross-sectional studies (17.49%), case control studies (9.15%), non-RCTs (1.01%), and pragmatic clinical trials (PCTs) (0.15%). Correspondingly, 1,302,173 secondary literatures were retrieved and ranked as narrative review (70.88%), systematic review (15.02%), systematic review and meta-analyses (13.89%), traditional meta-analyses (4.48%), expert consensus (2.31%), guidelines (1.49%), scoping reviews (0.68%), net meta-analyses (0.40%), and umbrella reviews (0.04%). The average annual growth rate for the primary literature was 10.28%, and ranked from high to low as PCTs (83.68%), cohort studies (17.74%), cross-sectional studies (17.61%), non-RCTs (12.11%), case control studies (8.86%), RCTs (7.68%), case report/series (7.51%); while that for the secondary literature was 10.57%, and ranked from high to low as net meta-analyses (48.97%), umbrella reviews (47.09%), scoping reviews (41.92%), systematic reviews and meta-analyses (33.44%), systematic reviews (33.05%), traditional meta-analyses (12.49%), expert consensuses (9.22%), narrative review (8.72%), and guidelines (2.82%). CONCLUSION: Both the composition and number of clinical studies changed significantly from 1991 to 2020. Based on the trend, the case report/series, case control study, and narrative review are on the decline, while cohort study, cross-sectional study, systematic reviews, and systematic review and meta-analysis literature have increased. To improve the quality of clinical evidence, we recommend RCT and cohort study give priority to access to allocated research resources in future.

REDIRECT: Mapping Drug Prescriptions and Evidence from Biomedical Literature.

To enhance their practice, healthcare professionals need to cross-link various usage recommendations provided by heterogeneous vocabularies that must be retrieved and integrated conjointly. This is the aim of the Knowledge Warehouse / K-Ware platform. It enables establishing relevant bridges between different knowledge sources (structured vocabularies, thesaurus, ontologies) expressed in the semantic web standard languages (i.e. SKOS, OWL, RDF). This poster presents the strategy applied in K-Ware to hide the different aspects of linking literals with medical entities encoded in these knowledge sources to fetch some publications abstracts from Pubmed.

Who is blocking access to PubMed? Educational 'Escape Room' for medical residents.

Teaching students how to conduct bibliographic searches in health sciences' databases is essential training. One of the challenges librarians face is how to motivate students during classroom learning. In this article, two hospital libraries, in Spain, used Escape rooms as a method of bringing creativity, teamwork, communication and critical thinking into bibliographic search instruction. Escape rooms are a series of puzzles that must be solved to exit the game. This article explores the methods used for integrating escape rooms into training programmes and evaluates the results. Escape Rooms are a useful tool that can be integrated into residents' training to support their instruction on bibliographic searches. This kind of learning stablishes competences like logical thinking and deductive approaching. These aspects aid participants to make their own decision and to develop social and intellectual skills.

Anne O'Tate: Value-added PubMed search engine for analysis and text mining.

Over a decade ago, we introduced Anne O'Tate, a free, public web-based tool http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi to support user-driven summarization, drill-down and mining of search results from PubMed, the leading search engine for biomedical literature. A set of hotlinked buttons allows the user to sort and rank retrieved articles according to important words in titles and abstracts; topics; author names; affiliations; journal names; publication year; and clustered by topic. Any result can be further mined by choosing any other button, and small search results can be expanded to include related articles. It has been deployed continuously, serving a wide range of biomedical users and needs, and over time has also served as a platform to support the creation of new tools that address additional needs. Here we describe the current, greatly expanded implementation of Anne O'Tate, which has added additional buttons to provide new functionalities: We now allow users to sort and rank search results by important phrases contained in titles and abstracts; the number of authors listed on the article; and pairs of topics that co-occur significantly more than chance. We also display articles according to NLM-indexed publication types, as well as according to 50 different publication types and study designs as predicted by a novel machine learning-based model. Furthermore, users can import search results into two new tools: e) Mine the Gap!, which identifies pairs of topics that are under-represented within set of the search results, and f) Citation Cloud, which for any given article, allows users to visualize the set of articles that cite it; that are cited by it; that are co-cited with it; and that are bibliographically coupled to it. We invite the scientific community to explore how Anne O'Tate can assist in analyzing biomedical literature, in a variety of use cases.

Performance evaluation of three semantic expansions to query PubMed.

BACKGROUND: PubMed is one of the most important basic tools to access medical literature. Semantic query expansion using synonyms can improve retrieval efficacy. OBJECTIVE: The objective was to evaluate the performance of three semantic query expansion strategies. METHODS: Queries were built for forty MeSH descriptors using three semantic expansion strategies (MeSH synonyms, UMLS mappings, and mappings created by the CISMeF team), then sent to PubMed. To evaluate expansion performances for each query, the first twenty citations were selected, and their relevance were judged by three independent evaluators based on the title and abstract. RESULTS: Queries built with the UMLS expansion provided new citations with a slightly higher mean precision (74.19%) than with the CISMeF expansion (70.28%), although the difference was not significant. Inter-rater agreement was 0.28. Results varied greatly depending on the descriptor selected. DISCUSSION: The number of citations retrieved by the three strategies and their precision varied greatly according to the descriptor. This heterogeneity could be explained by the quality of the synonyms. Optimal use of these different expansions would be through various combinations of UMLS and CISMeF intersections or unions. CONCLUSION: Information retrieval tools should propose different semantic expansions depending on the descriptor and the search objectives.

The COVID-19 Infodemic: Infodemiology Study Analyzing Stigmatizing Search Terms.

BACKGROUND: In the context of the COVID-19 infodemic, the global profusion of monikers and hashtags for COVID-19 have found their way into daily communication and contributed to a backlash against China and the Chinese people. OBJECTIVE: This study examines public engagement in crisis communication about COVID-19 during the early epidemic stage and the practical strategy of social mobilization to mitigate the infodemic. METHODS: We retrieved the unbiased values of the top-ranked search phrases between December 30, 2019, and July 15, 2020, which normalized the anonymized, categorized, and aggregated samples from Google Search data. This study illustrates the most-searched terms, including the official COVID-19 terms, the stigmatized terms, and other controls, to measure the collective behavioral propensities to stigmatized terms and to explore the global reaction to the COVID-19 epidemic in the real world. We calculated the ratio of the cumulative number of COVID-19 cases to the regional population as the cumulative rate (R) of a specific country or territory and calculated the Gini coefficient (G) to measure the collective heterogeneity of crowd behavior. RESULTS: People around the world are using stigmatizing terms on Google Search, and these terms were used earlier than the official names. Many stigmatized monikers against China (eg, "Wuhan pneumonia," G=0.73; "Wuhan coronavirus," G=0.60; "China pneumonia," G=0.59; "China coronavirus," G=0.52; "Chinese coronavirus," G=0.50) had high collective heterogeneity of crowd behavior between December 30, 2019, and July 15, 2020, while the official terms "COVID-19" (G=0.44) and "SARS-CoV-2" (G=0.42) have not become de facto standard usages. Moreover, the pattern of high consistent usage was observed in 13 territories with low cumulative rates (R) between January 16 and July 15, 2020, out of 58 countries and territories that have reported confirmed cases of COVID-19. In the scientific literature, multifarious naming practices may have provoked unintended negative impacts by stigmatizing Chinese people. The World Health Organization; the United Nations Educational, Scientific and Cultural Organization; and the media initiated campaigns for fighting back against the COVID-19 infodemic with the same mission but in diverse voices. CONCLUSIONS: Infodemiological analysis can articulate the collective propensities to stigmatized monikers across search behaviors, which may reflect the collective sentiment of backlash against China and Chinese people in the real world. The full-fledged official terms are expected to fight back against the resilience of negative perceptual bias amid the COVID-19 epidemic. Such official naming efforts against the infodemic should be met with a fair share of identification in scientific conventions and sociocultural paradigms. As an integral component of preparedness, appropriate nomenclatures should be duly assigned to the newly identified coronavirus, and social mobilization in a uniform voice is a priority for combating the next infodemic.

Global Dental Publications in PubMed Databases between 2009 and 2019-A Bibliometric Analysis.

The objective of this study was to evaluate the publications in the field of dentistry on the PubMed database over a span of 10 years, from 2009 to 2019. Articles published between January 2009 to December 2019 were searched for in the MEDLINE database via PubMed. Data analysis was done using R-base packages, including the specialized R-packages Bibliometrix and String. For descriptive statistics and sequence charting, SPSS version 23.0 was used. A total of 104,975 articles were extracted, with a total of 153,530 authors in the given time frame. The proportion of articles steadily increased from 2009, plateauing at its peak from 2010 to 2016, and then seeing a decline from 2017 to 2019. Journal articles (60.58%), comparative studies (16.05%) and case reports (10.8%) were recorded as the most reported type of publication globally, accounting for 81.43% of the total documents extracted. All the articles came from 81 countries, with the USA reporting the greatest number of published articles (45,911). Dentistry proves to be a multi-faceted arena and many researchers and authors around the globe are contributing to the burgeoning literature over time.

Towards PubMed 2.0.

Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs.

Science and Facebook: The same popularity law!

The distribution of scientific citations for publications selected with different rules (author, topic, institution, country, journal, etc…) collapse on a single curve if one plots the citations relative to their mean value. We find that the distribution of "shares" for the Facebook posts rescale in the same manner to the very same curve with scientific citations. This finding suggests that citations are subjected to the same growth mechanism with Facebook popularity measures, being influenced by a statistically similar social environment and selection mechanism. In a simple master-equation approach the exponential growth of the number of publications and a preferential selection mechanism leads to a Tsallis-Pareto distribution offering an excellent description for the observed statistics. Based on our model and on the data derived from PubMed we predict that according to the present trend the average citations per scientific publications exponentially relaxes to about 4.

Publication trends in cachexia and sarcopenia in elderly heart failure patients.

The loss of skeletal mass - sarcopenia and cachexia - is considered to be a major contributor to morbidity and mortality in chronic heart failure (CHF). Unfortunately, sarcopenia is generally considered to be a geriatric syndrome, but not necessarily seen as a comorbidity in CHF, even though it has a wide range of adverse health outcomes. While there were 15,574 publication with the title word "heart failure" in PubMed in the 5­year period from 1 June 2011 to 31 May 2016, only 22 or 71 publications were found with the search combination "sarcopenia" or "cachexia" (title word) and "heart failure" (all fields), respectively. This shows very clearly that loss of muscle quality and function due to heart failure is still an underappreciated problem in the medical field.

A guide for building biological pathways along with two case studies: hair and breast development.

Genomic information is being underlined in the format of biological pathways. Building these biological pathways is an ongoing demand and benefits from methods for extracting information from biomedical literature with the aid of text-mining tools. Here we hopefully guide you in the attempt of building a customized pathway or chart representation of a system. Our manual is based on a group of software designed to look at biointeractions in a set of abstracts retrieved from PubMed. However, they aim to support the work of someone with biological background, who does not need to be an expert on the subject and will play the role of manual curator while designing the representation of the system, the pathway. We therefore illustrate with two challenging case studies: hair and breast development. They were chosen for focusing on recent acquisitions of human evolution. We produced sub-pathways for each study, representing different phases of development. Differently from most charts present in current databases, we present detailed descriptions, which will additionally guide PESCADOR users along the process. The implementation as a web interface makes PESCADOR a unique tool for guiding the user along the biointeractions, which will constitute a novel pathway.

Scientific publications and research groups on alcohol consumption and related problems worldwide: authorship analysis of papers indexed in PubMed and Scopus databases (2005 to 2009).

BACKGROUND: The research of alcohol consumption-related problems is a multidisciplinary field. The aim of this study is to analyze the worldwide scientific production in the area of alcohol-drinking and alcohol-related problems from 2005 to 2009. METHODS: A MEDLINE and Scopus search on alcohol (alcohol-drinking and alcohol-related problems) published from 2005 to 2009 was carried out. Using bibliometric indicators, the distribution of the publications was determined within the journals that publish said articles, specialty of the journal (broad subject terms), article type, language of the publication, and country where the journal is published. Also, authorship characteristics were assessed (collaboration index and number of authors who have published more than 9 documents). The existing research groups were also determined. RESULTS: About 24,100 documents on alcohol, published in 3,862 journals, and authored by 69,640 authors were retrieved from MEDLINE and Scopus between the years 2005 and 2009. The collaboration index of the articles was 4.83 ± 3.7. The number of consolidated research groups in the field was identified as 383, with 1,933 authors. Documents on alcohol were published mainly in journals covering the field of "Substance-Related Disorders," 23.18%, followed by "Medicine," 8.7%, "Psychiatry," 6.17%, and "Gastroenterology," 5.25%. CONCLUSIONS: Research on alcohol is a consolidated field, with an average of 4,820 documents published each year between 2005 and 2009 in MEDLINE and Scopus. Alcohol-related publications have a marked multidisciplinary nature. Collaboration was common among alcohol researchers. There is an underrepresentation of alcohol-related publications in languages other than English and from developing countries, in MEDLINE and Scopus databases.

PubMed in progress: latest changes in MeSH and MyNCBI.

PubMed interface re-engineering has moved further steps with the latest changes in the MeSH - Medical Subject Headings database and in the MyNCBI homepage. Aim of this contribution is to present the most relevant added feature in order to improve your query efficiency.

Medical literature search dot com.

The Internet provides a quick access to a plethora of the medical literature, in the form of journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualized, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Commercial web resources (Medscape, MedConnect, MedicineNet) add to the list of resource databases providing some of their content for open access. Several web-libraries (Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. Availability of specific dermatology-related websites (DermIs, DermNet, and Genamics Jornalseek) is useful addition to the ever growing list of web-based resources. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature and levels of detail available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine.

PubMed reloaded: new interface, enhanced discovery.

The aim of this contribution was to present the redesigned version of the worldwide known PubMed interface. The changes relate to a simplified visualization, in order to require less efforts to find resources; they do not concern the functionalities or the search processing. This brief article will focus on the main differences between the old and the new version.