scholarly journals Two Similarity Metrics for Medical Subject Headings (MeSH): An Aid to Biomedical Text Mining and Author Name Disambiguation

2016 ◽  
Author(s):  
Neil R Smalheiser ◽  
Gary Bonifield
Keyword(s):  
Scientific Discovery ◽  
Semantic Relatedness ◽  
Mesh Term ◽  
The Body ◽  
Similarity Metrics ◽  
Name Disambiguation ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Author Name Disambiguation ◽  
Subject Headings

In the present paper, we have created and characterized several similarity metrics for relating any two Medical Subject Headings (MeSH terms) to each other. The article-based metric measures the tendency of two MeSH terms to appear in the MEDLINE record of the same article. The author-based metric measures the tendency of two MeSH terms to appear in the body of articles written by the same individual (using the 2009 Author-ity author name disambiguation dataset as a gold standard). The two metrics are only modestly correlated with each other (r = 0.50), indicating that they capture different aspects of term usage. The article-based metric provides a measure of semantic relatedness, and MeSH term pairs that co-occur more often than expected by chance may reflect relations between the two terms. In contrast, the author metric is indicative of how individuals practice science, and may have value for author name disambiguation and studies of scientific discovery. We have calculated article metrics for all MeSH terms appearing in at least 25 articles in MEDLINE (as of 2014) and author metrics for MeSH terms published as of 2009. The dataset is freely available for download and can be queried at http://arrowsmith.psych.uic.edu/arrowsmith_uic/mesh_pair_metrics.html.

scholarly journals Using MeSH (Medical Subject Headings) to Enhance PubMed Search Strategies for Evidence-Based Practice in Physical Therapy

2012 ◽  
Vol 92 (1) ◽  
pp. 124-132 ◽  
Author(s):  
Randy R. Richter ◽  
Tricia M. Austin
Keyword(s):  
Search Strategy ◽  
Evidence Based Practice ◽  
Physical Therapists ◽  
Mesh Term ◽  
Evidence Based ◽  
Medical Subject Headings ◽  
Search Terms ◽  
Mesh Terms ◽  
Subject Headings ◽  
Pubmed Search

Background Evidence-based practice (EBP) is an important paradigm in health care. Physical therapists report lack of knowledge and time constraints as barriers to EBP. Objective The purpose of this technical report is to illustrate how Medical Subject Headings (MeSH), a controlled vocabulary thesaurus of indexing terms, is used to efficiently search MEDLINE, the largest component of PubMed. Using clinical questions, this report illustrates how search terms common to physical therapist practice do or do not map to appropriate MeSH terms. A PubMed search strategy that takes advantage of text words and MeSH terms is provided. Results A search of 139 terms and 13 acronyms was conducted to determine whether they appropriately mapped to a MeSH term. The search results were categorized into 1 of 5 outcomes. Nearly half (66/139) of the search terms mapped to an appropriate MeSH term (outcome 1). When a search term did not appropriately map to a MeSH term, it was entered into the MeSH database to search for an appropriate MeSH term. Twenty-one appropriate MeSH terms were found (outcomes 2 and 4), and there were 52 search terms for which an appropriate MeSH term was not found (outcomes 3 and 5). Nearly half of the acronyms did not map to an appropriate MeSH term, and an appropriate MeSH term was not found in the database. Limitations The results are based on a limited number of search terms and acronyms. Conclusions Understanding how search terms map to MeSH terms and using the PubMed search strategy can enable physical therapists to take full advantage of available MeSH terms and should result in more-efficient and better-informed searches.

scholarly journals Mapping the biomedical sciences using Medical Subject Headings: a comparison between MeSH co-assignments and MeSH citation pairs

2021 ◽  
Vol 109 (3) ◽  
Author(s):  
Fei Shu ◽  
Junping Qiu ◽  
Vincent Larivière
Keyword(s):  
Web Of Science ◽  
Mesh Term ◽  
Biomedical Science ◽  
Journal Articles ◽  
Biomedical Sciences ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Subject Headings ◽  
Direct Citation ◽  
The Relationship

Objective: This study compares two maps of biomedical sciences using Medical Subject Headings (MeSH) term co-assignments versus MeSH terms of citing/cited articles and reveals similarities and differences between the two approaches. Methods: MeSH terms assigned to 397,475 journal articles published in 2015, as well as their 4,632,992 cited references, were retrieved from Web of Science and MEDLINE databases, respectively, which formed over 7 million MeSH co-assignments and nearly 18 million direct citation pairs. We generated six network visualizations of biomedical science at three levels using Gephi software based on these MeSH co-assignments and citation pairs.Results: The MeSH co-assignment map contained more nodes and edges, as MeSH co-assignments cover all medical topics discussed in articles. By contrast, the MeSH citation map contained fewer but larger nodes and wider edges, as citation links indicate connections to two similar medical topics. Conclusion: These two types of maps emphasize different aspects of biomedical sciences, with MeSH co-assignment maps focusing on the relationship between topics in different categories and MeSH direct citation maps providing insights into relationships between topics in the same or similar category.

The Most Cited Mesh Terms and Authors who Published Papers in Pubmed Central on the Topic of Medicine and Health Using Bibliometric Analyses

2019 ◽  
pp. 1-9
Author(s):  
Tsair-Wei Chien ◽  
Hing-Man Wu ◽  
Hsien-Yi Wang ◽  
Willy Chou
Keyword(s):  
Mesh Term ◽  
Deep Insight ◽  
Medical Subject Headings ◽  
Microsoft Excel ◽  
Pubmed Central ◽  
Current State ◽  
Mesh Terms ◽  
Control Gain ◽  
State Of Research ◽  
Insight Into

Aims: We visualized the current state of research on publication outputs and citations in the field of medicine and health to uncover topic burst and citations among medical subject headings (MeSH) clusters. Study Design: A bibliometric analysis. Place and duration of Study: Using Pubmed indexed articles to inspect the characteristics of topics on medicine and health since 1969. Methodology: Selecting 156 abstracts, author names, countries, and MeSH terms on January 10, 2019, from Pubmed Central (PMC) based on the terms of medicine and health in the title since 1969, we applied the x-index and impact factor to evaluate author individual research achievements and compute MeSH bibliometric performances. The bootstrapping method was used to estimate the median and its 95% confidence intervals and make differences in metrics among MeSH clusters. The dominant nations were selected using the x-index to display on a dashboard. We programmed Microsoft Excel VBA routines to extract data. Google Maps and Pajek software were used for displaying graphical representations. Results: We found that (1)the dominant countries/areas are the Unlited States, Taiwan, and Australia; (2) the author Grajales, Francisco Jose 3rd form Canada has the most cited metrics such as author IF=39.46 and x-index=6.28; (3)the MeSH terms of organization & administration, standards, and prevention & control gain the top three degree centralities among MeSH clusters; (4) No any differences in metrics were found among MeSH clusters; (5) the article(PMID= 24518354) with three MeSH term of delivery of health care, social media, and software and published in 2014 was cited most at least 62 times. Conclusion: Social network analysis provides wide and deep insight into the relationships among MeSH terms. The MeSH weighted scheme and x-index were recommended to academics for computing MeSH citations in the future.

scholarly journals Cited references and Medical Subject Headings (MeSH) as two different knowledge representations: clustering and mappings at the paper level

2016 ◽  
Vol 109 (3) ◽  
pp. 2077-2091 ◽  
Author(s):  
Loet Leydesdorff ◽  
Jordan A. Comins ◽  
Aaron A. Sorensen ◽  
Lutz Bornmann ◽  
Iina Hellsten
Keyword(s):  
Web Of Science ◽  
Research Front ◽  
Biomedical Sciences ◽  
Medical Subject Headings ◽  
Knowledge Representations ◽  
Mesh Terms ◽  
Subject Categories ◽  
Subject Headings ◽  
The Matrix ◽  
Amyloid Cascade

AbstractFor the biomedical sciences, the Medical Subject Headings (MeSH) make available a rich feature which cannot currently be merged properly with widely used citing/cited data. Here, we provide methods and routines that make MeSH terms amenable to broader usage in the study of science indicators: using Web-of-Science (WoS) data, one can generate the matrix of citing versus cited documents; using PubMed/MEDLINE data, a matrix of the citing documents versus MeSH terms can be generated analogously. The two matrices can also be reorganized into a 2-mode matrix of MeSH terms versus cited references. Using the abbreviated journal names in the references, one can, for example, address the question whether MeSH terms can be used as an alternative to WoS Subject Categories for the purpose of normalizing citation data. We explore the applicability of the routines in the case of a research program about the amyloid cascade hypothesis in Alzheimer’s disease. One conclusion is that referenced journals provide archival structures, whereas MeSH terms indicate mainly variation (including novelty) at the research front. Furthermore, we explore the option of using the citing/cited matrix for main-path analysis as a by-product of the software.

scholarly journals Human Breathomics Database

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Tien-Chueh Kuo ◽  
Cheng-En Tan ◽  
San-Yuan Wang ◽  
Olivia A Lin ◽  
Bo-Han Su ◽  
...  
Keyword(s):  
Text Mining ◽  
Exhaled Breath Condensate ◽  
Mesh Term ◽  
Exhaled Breath ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Disease Information ◽  
Volatile Organic ◽  
Breath Condensate ◽  
Automatic Pipeline

Abstract Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how breath molecules are related to diseases, mechanisms and pathways identified from experimental analytical measurements is challenging due to the lack of an organized resource describing breath molecules, related references and biomedical information embedded in the literature. To provide breath VOCs, related references and biomedical information, we aim to organize a database composed of manually curated information and automatically extracted biomedical information. First, VOCs-related disease information was manually organized from 207 literature linked to 99 VOCs and known Medical Subject Headings (MeSH) terms. Then an automated text mining algorithm was used to extract biomedical information from this literature. In the end, the manually curated information and auto-extracted biomedical information was combined to form a breath molecule database—the Human Breathomics Database (HBDB). We first manually curated and organized disease information including MeSH term from 207 literatures associated with 99 VOCs. Then, an automatic pipeline of text mining approach was used to collect 2766 literatures and extract biomedical information from breath researches. We combined curated information with automatically extracted biomedical information to assemble a breath molecule database, the HBDB. The HBDB is a database that includes references, VOCs and diseases associated with human breathomics. Most of these VOCs were detected in human breath samples or exhaled breath condensate samples. So far, the database contains a total of 913 VOCs in relation to human exhaled breath researches reported in 2766 publications. The HBDB is the most comprehensive HBDB of VOCs in human exhaled breath to date. It is a useful and organized resource for researchers and clinicians to identify and further investigate potential biomarkers from the breath of patients. Database URL: https://hbdb.cmdm.tw

Tratamientos endodónticos regenerativos en dientes permanentes jóvenes con necrosis pulpar: revisión bibliográfica

2021 ◽  
Vol 4 (1) ◽  
pp. 63-74
Author(s):  
Tania Lissette Ayala-Galdámez ◽  
Walter Vladimir Roque Esquivel ◽  
Ruth Elizabeth Fuentes de Sermeño
Keyword(s):  
Medical Subject Headings ◽  
Mesh Terms ◽  
Palabras Clave ◽  
Subject Headings

Objetivo. El objetivo de esta revisión bibliográfica es analizar la evidencia científica existente, sobre los diferentes tratamientos regenerativos pulpares, en dientes permanentes jóvenes con necrosis pulpar, para conocer las diversas alternativas de materiales y técnicas utilizadas. Materiales y métodos Se realizó una búsqueda electrónica biomédica avanzada en base de datos PubMed, utilizando palabras clave MeSh Terms (Medical Subject Headings), para identificar la cantidad de artículos científicos disponibles, en la que se encontraron estudios sobre tratamientos de regeneración pulpar en dientes permanentes jóvenes inmaduros, con el fin de identificar los diferentes tratamientos, materiales, técnicas, y resultados obtenidos con dichas maniobras clínicas. Resultados Se encontraron 30 artículos, en los que se identificaron los diversos tratamientos en regeneración pulpar de dientes permanentes jóvenes inmaduros, investigaciones de ensayos clínicos aleatorios, utilizando 11 artículos. Conclusiones En las diversas investigaciones se encuentran diferentes tratamientos, materiales y técnicas a utilizar de para la regeneración pulpar, encontrando variaciones en soluciones irrigadoras, medicaciones intraconductos, número de citas y material de sellado coronal, sin embargo el Trióxido Mineral Agregado MTA es el utilizado con mayor frecuencia; se necesitan más investigaciones que puedan destacar un protocolo de atención.

The Role of Technology and Informatics in Disaster Planning and Response

2012 ◽  
Vol 30 (1) ◽  
pp. 149-168 ◽  
Author(s):  
Elizabeth Weiner ◽  
Lynn A. Slepski
Keyword(s):  
Disaster Planning ◽  
Mesh Term ◽  
Disaster Medicine ◽  
Medical Subject Headings ◽  
Humanitarian Response ◽  
Mesh Terms ◽  
Pubmed Search ◽  
Impact Of Technology ◽  
The Impact

It is clear that technology and informatics are becoming increasingly important in disasters and humanitarian response. Technology is a critical tool to recording, analyzing, and predicting trends in data that could not be achieved prior to its implementation. Informatics is the translation of this data into information, knowledge, and wisdom. Combining technology and informatics applications with response efforts has resulted in various enhanced biosurveillance efforts, advanced communications, and information management during disasters. Although these efforts have been well described in the literature, research on the impact of technology and informatics during these efforts has been limited. As a result, this chapter will provide an overview of these technology and informatics solutions and present suggestions for further research in an era when disaster and humanitarian response efforts continue to increase as well. A literature search was performed using PubMed search tools with the National Library of Medicine Medical Subject Headings (MeSH) terms of “disasters,” “disaster planning,” “disaster medicine,” “technology,” “informatics,” and “research.” Search limitations were set for 5 years and in English. Because of the limited number of research articles in this field, the MeSH term research was deleted.

scholarly journals Using Kano diagrams to display the most cited article types, affiliated countries, authors and MeSH terms on spinal surgery in recent 12 years

2021 ◽  
Vol 26 (1) ◽  
Author(s):  
Po-Hsin Chou ◽  
Yu-Tsen Yeh ◽  
Wei-Chih Kan ◽  
Tsair-Wei Chien ◽  
Shu-Chun Kuo
Keyword(s):  
Impact Factor ◽  
Spinal Surgery ◽  
Scientific Productivity ◽  
The United States ◽  
Mesh Term ◽  
Medical Subject Headings ◽  
Productive Author ◽  
Mesh Terms ◽  
The Us ◽  
European Spine Journal

Abstract Background Citation analysis has been increasingly applied to assess the quantity and quality of scientific research in various fields worldwide. However, these analyses on spinal surgery do not provide visualization of results. This study aims (1) to evaluate the worldwide research citations and publications on spinal surgery and (2) to provide visual representations using Kano diagrams onto the research analysis for spinal surgeons and researchers. Methods Article abstracts published between 2007 and 2018 were downloaded from PubMed Central (PMC) in 5 journals, including Spine, European Spine Journal, The Spine Journal, Journal of Neurosurgery: Spine, and Journal of Spinal Disorders and Techniques. The article types, affiliated countries, authors, and Medical subject headings (MeSH terms) were analyzed by the number of article citations using x-index. Choropleth maps and Kano diagrams were applied to present these results. The trends of MeSH terms over the years were plotted and analyzed. Results A total of 18,808 publications were extracted from the PMC database, and 17,245 were affiliated to countries/areas. The 12-year impact factor for the five spine journals is 5.758. We observed that (1) the largest number of articles on spinal surgery was from North America (6417, 37.21%). Spine earns the highest x-index (= 82.96). Comparative Study has the highest x-index (= 66.74) among all article types. (2) The United States performed exceptionally in x-indexes (= 56.86 and 44.5) on both analyses done on the total 18,808 and the top 100 most cited articles, respectively. The most influential author whose x-index reaches 15.11 was Simon Dagenais from the US. (3) The most cited MeSH term with an x-index of 23.05 was surgery based on the top 100 most cited articles. The most cited article (PMID = 18164449) was written by Dagenais and his colleagues in 2008. The most productive author was Michael G. Fehlings, whose x-index and the author's impact factor are 13.57(= √(13.16*14)) and 9.86(= 331.57/33.64), respectively. Conclusions There was a rapidly increasing scientific productivity in the field of spinal surgery in the past 12 years. The US has extraordinary contributions to the publications. Furthermore, China and Japan have increasing numbers of publications on spinal surgery. This study with Kano diagrams provides an insight into the research for spinal surgeons and researchers.

Sign in / Sign up

Export Citation Format

Share Document