Two decades of Gene Ontology evolution from expansion to consolidation
Abstract
The Gene Ontology (GO) is a long-standing knowledge resource that underpins the functional annotation of gene products across numerous biological databases. Released regularly, GO and its associated annotations form a large, continuously evolving dataset whose temporal dynamics have direct consequences for data reuse, versioning, and reproducibility. Because analytical results derived from GO are inherently tied to specific ontology and annotation releases, a systematic understanding of how GO changes over time is essential for transparent interpretation and long-term reuse of GO-based analyses. Here, we present a comprehensive temporal characterization of the Gene Ontology and its annotations spanning 21 years of publicly available releases. Treating successive ontology and annotation versions as longitudinal research data, we quantify changes in ontology structure, term composition, relationships, and annotation content across time and across three representative annotation resources. Our analysis reveals sustained growth of GO over its lifetime, accompanied by marked structural reorganization, particularly affecting high-level, general ontology terms. Notably, across multiple structural metrics, we identify a transition toward increased stability beginning around 2017, consistent with a maturation phase of the resource. This work provides a reference framework for researchers who rely on GO releases for data integration, benchmarking, and reproducible functional analysis.
Related
- Letters and biological process: linguistic structure encodes hierarchical depth in the gene ontology
- LitGene: an interpretable transformer model integrating text and ontology for gene representation learning
- Adventures through wonderland: the wild world of histone gene organization, evolution, and regulation in over 250 species
- mRNA Decay Mediates Evolution and Biological Functions in Plant Gene Expression.
- SnoRNA Evolution, Genomic Context, and Mobility: The Role of Function and Host Gene Association
BibTeX
@article{pitarch2026decades,
title = {{Two decades of Gene Ontology evolution from expansion to consolidation}},
author = {Borja Pitarch and Florencio Pazos and Monica Chagoyen},
journal = {Scientific Reports},
year = {2026},
month = oct,
doi = {10.1038/s41598-026-74506-3},
url = {https://www.nature.com/articles/s41598-026-74506-3},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Two decades of Gene Ontology evolution from expansion to consolidation
AU - Borja Pitarch
AU - Florencio Pazos
AU - Monica Chagoyen
PY - 2026
DA - 2026/10/09
JO - Scientific Reports
DO - 10.1038/s41598-026-74506-3
UR - https://www.nature.com/articles/s41598-026-74506-3
AB - The Gene Ontology (GO) is a long-standing knowledge resource that underpins the functional annotation of gene products across numerous biological databases. Released regularly, GO and its associated annotations form a large, continuously evolving dataset whose temporal dynamics have direct consequences for data reuse, versioning, and reproducibility. Because analytical results derived from GO are inherently tied to specific ontology and annotation releases, a systematic understanding of how GO changes over time is essential for transparent interpretation and long-term reuse of GO-based analyses. Here, we present a comprehensive temporal characterization of the Gene Ontology and its annotations spanning 21 years of publicly available releases. Treating successive ontology and annotation versions as longitudinal research data, we quantify changes in ontology structure, term composition, relationships, and annotation content across time and across three representative annotation resources. Our analysis reveals sustained growth of GO over its lifetime, accompanied by marked structural reorganization, particularly affecting high-level, general ontology terms. Notably, across multiple structural metrics, we identify a transition toward increased stability beginning around 2017, consistent with a maturation phase of the resource. This work provides a reference framework for researchers who rely on GO releases for data integration, benchmarking, and reproducible functional analysis.
SN - 2045-2322
ER -