Acknowledgments

FANTASIA is the result of a collaborative effort between Ana Roja’s Lab (Andalusian Center for Developmental Biology, CSIC) and Rosa Fernández’s Lab (Metazoa Phylogenomics Lab, Institute of Evolutionary Biology, CSIC-UPF). This project demonstrates the synergy between research teams with diverse expertise.

This version of FANTASIA builds upon previous work from:

• Metazoa Phylogenomics Lab’s FANTASIA The original implementation of FANTASIA for functional annotation.

• bio_embeddings A state-of-the-art framework for generating protein sequence embeddings.

• GoPredSim A similarity-based approach for Gene Ontology annotation.

• protein-information-system Serves as the reference biological information system, providing a robust data model and curated datasets for protein structural and functional analysis.

We also extend our gratitude to LifeHUB-CSIC for inspiring this initiative and fostering innovation in computational biology.