FerrDb V3: expanding the manually curated resource for regulators and disease associations from ferroptosis to regulated cell death

Nucleic Acids Res. 2025 Oct 31:gkaf1119. doi: 10.1093/nar/gkaf1119. Online ahead of print.

ABSTRACT

Regulated cell death (RCD) is essential to both physiological homeostasis and numerous diseases. FerrDb is a curated database for ferroptosis regulators and ferroptosis-disease associations. Though widely used, FerrDb is limited by its singular focus on ferroptosis. The field of cell death is rapidly expanding, marked by continuous discovery of novel RCD modalities. The need for a high-quality database that encompasses the entire spectrum of RCD is urgent, but none exists. Here, we introduce FerrDb V3, an upgraded version featuring extensive enhancements in content and functionality. Remarkably, it expands from the focus on ferroptosis to 22 RCD modalities. RCD regulators and RCD-disease associations were manually curated from >20 000 articles. Database content was additionally enriched by public resources. A conversational intelligent assistant that enables users to explore the database through natural language queries was created. A suite of web-based analytical utilities tailored for RCD research was developed. The web interface was updated accordingly to offer a seamless user experience. In conclusion, FerrDb V3 has evolved into a comprehensive resource and a valuable research tool for the RCD research community. FerrDb V3 is freely accessible at https://www.zhounan.org/ferrdb/.

PMID:41171133 | DOI:10.1093/nar/gkaf1119