TY - JOUR
T1 - The Gene Ontology knowledgebase in 2023
AU - Gene Ontology Consortium
AU - Aleksander, Suzi A
AU - Balhoff, James
AU - Carbon, Seth
AU - Cherry, J Michael
AU - Drabkin, Harold J
AU - Ebert, Dustin
AU - Feuermann, Marc
AU - Gaudet, Pascale
AU - Harris, Nomi L
AU - Hill, David P
AU - Lee, Raymond
AU - Mi, Huaiyu
AU - Moxon, Sierra
AU - Mungall, Christopher J
AU - Muruganugan, Anushya
AU - Mushayahama, Tremayne
AU - Sternberg, Paul W
AU - Van Auken, Kimberly
AU - Ramsey, Jolene
AU - Siegele, Deborah A
AU - Chisholm, Rex L
AU - Fey, Petra
AU - Aspromonte, Maria Cristina
AU - Nugnes, Maria Victoria
AU - Quaglia, Federica
AU - Tosatto, Silvio
AU - Giglio, Michelle
AU - Nadendla, Suvarna
AU - Antonazzo, Giulia
AU - Attrill, Helen
AU - Dos Santos, Gil
AU - Marygold, Steven
AU - Strelets, Victor
AU - Tabone, Christopher J
AU - Thurmond, Jim
AU - Zhou, Pinglei
AU - Ahmed, Saadullah H
AU - Asanitthong, Praoparn
AU - Luna Buitrago, Diana
AU - Erdol, Meltem N
AU - Gage, Matthew C
AU - Ali Kadhum, Mohamed
AU - Li, Kan Yan Chloe
AU - Long, Miao
AU - Michalak, Aleksandra
AU - Pesala, Angeline
AU - Pritazahra, Armalya
AU - Saverimuttu, Shirin C C
AU - Su, Renzhi
AU - Oliferenko, Snezhana
N1 - © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.
PY - 2023/5/4
Y1 - 2023/5/4
N2 - The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
AB - The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
KW - Gene Ontology
KW - Proteins/genetics
KW - Molecular Sequence Annotation
KW - Databases, Genetic
KW - Computational Biology
U2 - 10.1093/genetics/iyad031
DO - 10.1093/genetics/iyad031
M3 - Review article
C2 - 36866529
SN - 0016-6731
VL - 224
JO - Genetics
JF - Genetics
IS - 1
ER -