A Survey of Bioinformatics Database and Software Usage through Mining the Literature

Area of Science:

• Bioinformatics
• Computational Biology
• Biomedical Informatics

Background:

• Computer-based resources are essential for modern biological and medical research.
• The availability and usage of bioinformatics databases and software are not well-evaluated.
• Understanding resource trends is crucial for research efficiency and collaboration.

Purpose of the Study:

• To audit and compare the usage of bioinformatics databases and software mentioned in scientific literature.
• To analyze trends in resource usage across bioinformatics, biology, and medicine sub-disciplines.
• To investigate the reuse and sharing of bioinformatics tools and practices.

Main Methods:

• Text mining of the PubMed Central full-text corpus.
• Identification and extraction of mentions of databases and software.
• Quantitative analysis of resource usage over time and across research domains.

Main Results:

• Bioinformatics literature focuses on novel resource development, while biology and medicine show stable usage patterns.
• Many resources are domain-specific, with limited cross-disciplinary adoption.
• A significant imbalance in resource usage exists, with a few resources dominating and many being mentioned only once.
• Some established resources show declining usage, while newer ones like Gene Ontology (GO) and R are rapidly growing.

Conclusions:

• Bioinformatics research is dynamic but raises concerns about software reuse and knowledge sharing.
• The limited reuse of many bioinformatics resources warrants further investigation into adoption barriers.
• This study provides a foundation for automated extraction of scientific methods and resource usage from literature.