Assessing resource use: a case study with the Human Disease Ontology

Area of Science:

• Genomic resource management
• Bioinformatics
• Scholarly communication

Background:

• Assessing the utilization of genomic resources is vital for demonstrating sustainability.
• Manual tracking of resource usage in published literature is challenging and time-consuming.
• The Human Disease Ontology (DO) project sought to improve its methods for identifying publication uses.

Purpose of the Study:

• To develop and implement a flexible, semi-automated workflow for identifying uses of the Human Disease Ontology (DO) in published literature.
• To create a sustainable method for tracking resource utilization and demonstrating scientific impact.
• To provide a transferable workflow applicable to other scientific resources.

Main Methods:

• Development of the R package DO.utils with key functions for literature analysis.
• Integration of DO.utils with Google Sheets for workflow management.
• Application of the semi-automated workflow to identify publications citing the DO.
• Analysis of identified publications to gain usage insights.

Main Results:

• A 3-fold increase in the number of identified publications utilizing the DO.
• Novel insights into the diverse use cases and applications of the DO.
• Clearer understanding of the DO's scientific impact and reach.
• Demonstration of the workflow's effectiveness in enhancing resource assessment.

Conclusions:

• The developed workflow and DO.utils R package provide an efficient method for tracking ontology usage.
• This semi-automated approach significantly enhances the identification of publications and provides valuable usage insights.
• The workflow is adaptable and beneficial for other genomic resources, databases, and web tools seeking to assess their impact.