A guide to performing systematic literature reviews in bioinformatics

TL;DR

This paper introduces BiSLR, a comprehensive guideline tailored for conducting systematic literature reviews in bioinformatics, aiming to improve data quality and reproducibility in bioinformatics research.

Contribution

It provides a step-by-step protocol adapted from traditional SLR methods specifically for bioinformatics, including a case study demonstrating its application.

Findings

Successfully applied BiSLR to identify relevant bioinformatics papers

Reduced bias through independent evaluation by four researchers

Produced a reproducible review process for bioinformatics data

Abstract

Bioinformatics research depends on high-quality databases to provide accurate results. In silico experiments, correctly performed, may prospect novel discoveries and elucidates pathways for biological experiments through data analysis in large scale. However, most biological databases have presented mistakes, such as data incorrectly classified or incomplete information. Also, sometimes, data mining algorithms cannot treat these errors, leading to serious problems for the in silico analysis. Manual curation of data extracted from literature is a possible solution for this problem. Systematic Literature Review (SLR), or Systematic Review, is a method to identify, evaluate and summarize the state-of-the-art of a specific theme. Moreover, SLR allows the collection from databases restrictively, which allows an analysis with lower bias than traditional reviews. The SRL approaches have been widely used for decision-making in medical and environmental studies. However, other research areas, such as bioinformatics, do not have a specific step-by-step to guide researchers undertaking the procedures of an SLR. In this study, we propose a guideline, called BiSRL, to perform SLR in bioinformatics. Our procedures cover the most traditional guides to produce SLRs adapted to bioinformatics. To evaluate our method, we propose a case study to detect and summarize SLRs developed for bioinformatics data. We used two databases: PubMed and ScienceDirect. A total of 207 papers were screened in four steps: title, abstract, diagonal and full-text reading. Four evaluators performed the SLR independently to reduce bias risk. A total of 8 papers was included in the SLR case study. The case study demonstrates how to implement the methods of BiSLR to procedure SLR for bioinformatics. BiSLR may guide bioinformaticians to perform systematic reviews reproducible to collect accurate data for higher quality analysis.