Abstract
Adjutant is an open-source, interactive and R-based application to support mining PubMed for literature reviews. Given a PubMed-compatible search query, Adjutant downloads the relevant articles and allows the user to perform an unsupervised clustering analysis to identify data-driven topic clusters. Following clustering, users can also sample documents using different strategies to obtain a more manageable dataset for further analysis. Adjutant makes explicit trade-offs between speed and accuracy, which are modifiable by the user, such that a complete analysis of several thousand documents can take a few minutes. All analytic datasets generated by Adjutant are saved, allowing users to easily conduct other downstream analyses that Adjutant does not explicitly support. Adjutant is implemented in R, using Shiny, and is available at https://github.com/amcrisan/Adjutant. Supplementary data are available at Bioinformatics online.
Highlights
Literature reviews, whether systematic or not [7], are often the first step a researcher takes when entering on a new area of inquiry
We developed Adjutant, an R-based tool supporting quick, visual assessments of topics within a document corpus
Given a PubMed-compatible search query, Adjutant uses the RISmed package [5] to obtain a summary of articles, including PubMed ID, Journal, Article Title, Authors, Abstract, Public Date, and MeSH terms
Summary
Literature reviews, whether systematic or not [7] , are often the first step a researcher takes when entering on a new area of inquiry. These reviews can involve hundreds or thousands of documents, which can become overwhelming, leading to significant culling of a document dataset to facilitate analysis [8]. This culling is antithetical to the purpose of the systematic review, yet few tools exist to help manage and explore these document datasets during the review process [10]. To address this issue, we developed Adjutant, an R-based tool supporting quick, visual assessments of topics within a document corpus. Like the military rank from which it draws its name, Adjutant’s purpose is to support an individual in their analysis process not supplement their domain knowledge
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