Evaluating Protein Functional Annotation at IBMCP, Universitat Politècnica de València
From May 4 to May 29, 2026, Fabian Jetzinger, LongTREC Doctoral Candidate at BioBam Bioinformatics, had the opportunity to carry out a research secondment at IBMCP, Universitat Politècnica de València, supervised by Aureliano Bombarely. This secondment offered valuable growth, both in scientific expertise and personal development.
My goal? Evaluating functional annotations produced by FANTASIA, which the Bombarely group applies to plant proteomes, against my own work-in-progress tool for predicting protein functional annotations, and expanding my evaluation suite with term-centric performance measurements.
Fabian reflects on his experience:
What I Learned 🎓
I learned to use FANTASIA and evaluated it on my set of test proteins and their GO annotations using standard CAFA metrics such as the protein-centric Fmax, allowing a direct comparison to my tool.
Takeaways 🌱
I expanded my evaluation suite with a term-centric overview of metrics such as AUC and term-centric F1 and F0.5. I also measured the distance between predicted and ground-truth annotations, enabling the recreation of plots used in FANTASIA’s publication.
Impact 🌟
Comparison on the Arabidopsis thaliana proteome was not completed due to time constraints. The evaluation can now be expanded from my test set to proteomes of specific species such as Arabidopsis thaliana.
Overall, this secondment produced a direct benchmark against FANTASIA and a more complete evaluation framework for my tool.
