TY - JOUR
T1 - GORetriever : Reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation
AU - Yan, Huiying
AU - Wang, Shaojun
AU - Liu, Hancheng
AU - Mamitsuka, Hiroshi
AU - Zhu, Shanfeng
N1 - Publisher Copyright: © 2024 The Author(s).
PY - 2024/9/1
Y1 - 2024/9/1
N2 - Summary: The vast majority of proteins still lack experimentally validated functional annotations, which highlights the importance of developing high-performance automated protein function prediction/annotation (AFP) methods. While existing approaches focus on protein sequences, networks, and structural data, textual information related to proteins has been overlooked. However, roughly 82% of SwissProt proteins already possess literature information that experts have annotated. To efficiently and effectively use literature information, we present GORetriever, a two-stage deep information retrieval-based method for AFP. Given a target protein, in the first stage, candidate Gene Ontology (GO) terms are retrieved by using annotated proteins with similar descriptions. In the second stage, the GO terms are reranked based on semantic matching between the GO definitions and textual information (literature and protein description) of the target protein. Extensive experiments over benchmark datasets demonstrate the remarkable effectiveness of GORetriever in enhancing the AFP performance. Note that GORetriever is the key component of GOCurator, which has achieved first place in the latest critical assessment of protein function annotation (CAFA5: over 1600 teams participated), held in 2023-2024.
AB - Summary: The vast majority of proteins still lack experimentally validated functional annotations, which highlights the importance of developing high-performance automated protein function prediction/annotation (AFP) methods. While existing approaches focus on protein sequences, networks, and structural data, textual information related to proteins has been overlooked. However, roughly 82% of SwissProt proteins already possess literature information that experts have annotated. To efficiently and effectively use literature information, we present GORetriever, a two-stage deep information retrieval-based method for AFP. Given a target protein, in the first stage, candidate Gene Ontology (GO) terms are retrieved by using annotated proteins with similar descriptions. In the second stage, the GO terms are reranked based on semantic matching between the GO definitions and textual information (literature and protein description) of the target protein. Extensive experiments over benchmark datasets demonstrate the remarkable effectiveness of GORetriever in enhancing the AFP performance. Note that GORetriever is the key component of GOCurator, which has achieved first place in the latest critical assessment of protein function annotation (CAFA5: over 1600 teams participated), held in 2023-2024.
UR - http://www.scopus.com/inward/record.url?scp=85203191862&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btae401
DO - 10.1093/bioinformatics/btae401
M3 - Article
AN - SCOPUS:85203191862
SN - 1367-4803
VL - 40
SP - ii53-ii61
JO - Bioinformatics
JF - Bioinformatics
ER -