Dataset Information

MiRetrieve-an R package and web application for miRNA text mining.

ABSTRACT: microRNAs (miRNAs) regulate gene expression and thereby influence biological processes in health and disease. As a consequence, miRNAs are intensely studied and literature on miRNAs has been constantly growing. While this growing body of literature reflects the interest in miRNAs, it generates a challenge to maintain an overview, and the comparison of miRNAs that may function across diverse disease fields is complex due to this large number of relevant publications. To address these challenges, we designed miRetrieve, an R package and web application that provides an overview on miRNAs. By text mining, miRetrieve can characterize and compare miRNAs within specific disease fields and across disease areas. This overview provides focus and facilitates the generation of new hypotheses. Here, we explain how miRetrieve works and how it is used. Furthermore, we demonstrate its applicability in an exemplary case study and discuss its advantages and disadvantages.

SUBMITTER: Friedrich J

PROVIDER: S-EPMC8696973 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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miRetrieve-an R package and web application for miRNA text mining.

Friedrich Julian J Hammes Hans-Peter HP Krenning Guido G

NAR genomics and bioinformatics 20211223 4

microRNAs (miRNAs) regulate gene expression and thereby influence biological processes in health and disease. As a consequence, miRNAs are intensely studied and literature on miRNAs has been constantly growing. While this growing body of literature reflects the interest in miRNAs, it generates a challenge to maintain an overview, and the comparison of miRNAs that may function across diverse disease fields is complex due to this large number of relevant publications. To address these challenges, ...[more]

PMID: 34988440

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Project description:BackgroundContextual variables that capture the characteristics of delimited geographic or jurisdictional areas are vital for health and social research. However, obtaining data sets with contextual-level data can be challenging in the absence of monitoring systems or public census data.ObjectiveWe describe and implement an 8-step method that combines web scraping, text mining, and spatial overlay analysis (WeTMS) to transform extensive text data from government websites into analyzable data sets containing contextual data for jurisdictional areas.MethodsThis tutorial describes the method and provides resources for its application by health and social researchers. We used this method to create data sets of health assets aimed at enhancing older adults' social connections (eg, activities and resources such as walking groups and senior clubs) across the 374 health jurisdictions in Catalonia from 2015 to 2022. These assets are registered on a web-based government platform by local stakeholders from various health and nonhealth organizations as part of a national public health program. Steps 1 to 3 involved defining the variables of interest, identifying data sources, and using Python to extract information from 50,000 websites linked to the platform. Steps 4 to 6 comprised preprocessing the scraped text, defining new variables to classify health assets based on social connection constructs, analyzing word frequencies in titles and descriptions of the assets, creating topic-specific dictionaries, implementing a rule-based classifier in R, and verifying the results. Steps 7 and 8 integrate the spatial overlay analysis to determine the geographic location of each asset. We conducted a descriptive analysis of the data sets to report the characteristics of the assets identified and the patterns of asset registrations across areas.ResultsWe identified and extracted data from 17,305 websites describing health assets. The titles and descriptions of the activities and resources contained 12,560 and 7301 unique words, respectively. After applying our classifier and spatial analysis algorithm, we generated 2 data sets containing 9546 health assets (5022 activities and 4524 resources) with the potential to enhance social connections among older adults. Stakeholders from 318 health jurisdictions registered identified assets on the platform between July 2015 and December 2022. The agreement rate between the classification algorithm and verified data sets ranged from 62.02% to 99.47% across variables. Leisure and skill development activities were the most prevalent (1844/5022, 36.72%). Leisure and cultural associations, such as social clubs for older adults, were the most common resources (878/4524, 19.41%). Health asset registration varied across areas, ranging between 0 and 263 activities and 0 and 265 resources.ConclusionsThe sequential use of WeTMS offers a robust method for generating data sets containing contextual-level variables from internet text data. This study can guide health and social researchers in efficiently generating ready-to-analyze data sets containing contextual variables.

Dataset Information

MiRetrieve-an R package and web application for miRNA text mining.

Publications

miRetrieve-an R package and web application for miRNA text mining.

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