The Gene Ontology knowledgebase in 2023

Abstract 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 knowl...

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Vydané v:Genetics (Austin) Ročník 224; číslo 1
Hlavní autori: Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Harris, Nomi L, Moxon, Sierra, Mungall, Christopher J, Sternberg, Paul W, Thomas, Paul D, Quaglia, Federica, Giglio, Michelle, Antonazzo, Giulia, Attrill, Helen, dos Santos, Gil, Tabone, Christopher J, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, Li, Kan Yan Chloe, Michalak, Aleksandra, Pritazahra, Armalya, Saverimuttu, Shirin C C, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Corbani, Lori, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Seager, James, Cooper, Laurel, Jaiswal, Pankaj, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kwitek, Anne E, Laulederkind, Stanley J F, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Axelsen, Kristian, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Berardini, Tanya Z, Reiser, Leonore, Auchincloss, Andrea, Argoud-Puy, Ghislaine, Blatter, Marie-Claude, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bowler-Barnett, Emily, Denny, Paul, Ignatchenko, Alexandr, Lock, Antonia, Magrane, Michele, Martin, Maria J, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Lee, Raymond, Chan, Juancarlos, Zarowiecki, Magdalena, Fisher, Malcolm, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: US Oxford University Press 04.05.2023
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ISSN:1943-2631, 1943-2631
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Abstract Abstract 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.
AbstractList 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.
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.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.
Abstract 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.
Author Vedi, Mahima
Hulo, Chantal
Elser, Justin
Aleksander, Suzi A
Ahmed, Saadullah H
Luna Buitrago, Diana
Ignatchenko, Alexandr
Ishtiaq, Rizwan
Rivoire, Catherine
Warner, Kate
Fisher, Malcolm
Axelsen, Kristian
Dolan, Mary E
Ebert, Dustin
Harris, Nomi L
Ponferrada, Virgilio
Poux, Sylvain
Lera-Ramirez, Manuel
Long, Miao
Engel, Stacia R
Lock, Antonia
Diamantakis, Stavros
Thurmond, Jim
Lussi, Yvonne
Giglio, Michelle
Zhou, Pinglei
Moxon, Sierra
Magrane, Michele
Cherry, J Michael
Martin, Maria J
Antonazzo, Giulia
Argoud-Puy, Ghislaine
Masson, Patrick
Carbon, Seth
Hill, David P
Logie, Colin
Mi, Huaiyu
Nash, Robert S
Auchincloss, Andrea
Tosatto, Silvio
Berardini, Tanya Z
Mushayahama, Tremayne
Smith, Cynthia
Zorn, Aaron
Aimo, Lucila
Speretta, Elena
Corbani, Lori
Pourcel, Lucille
Tabone, Christopher J
Kwitek, Anne E
Bowler-Barnett, Emily
Kaldunski, Mary L
Wong, Edith D
Ali Kadhum, Mohamed
Weng, Shuai
Bateman, Alex
Gruaz-Gumowski, Nadine
Naithani, Sushma
Pesala, Angeline
Lieberherr, Damien
Lee, Raymond
Siegele, Deborah A
Cooper, Laurel
Tyagi, Nidhi
Cuzick, Alayne
By
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  orcidid: 0000-0003-3217-3590
  surname: Zorn
  fullname: Zorn, Aaron
– sequence: 146
  givenname: Sridhar
  orcidid: 0000-0002-2246-3722
  surname: Ramachandran
  fullname: Ramachandran, Sridhar
– sequence: 147
  givenname: Leyla
  orcidid: 0000-0002-1009-339X
  surname: Ruzicka
  fullname: Ruzicka, Leyla
BackLink https://www.ncbi.nlm.nih.gov/pubmed/36866529$$D View this record in MEDLINE/PubMed
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Contributor Ramsey, Jolene
Pritazahra, Armalya
Vedi, Mahima
Elser, Justin
Fey, Petra
Oliferenko, Snezhana
Aleksander, Suzi A
Ahmed, Saadullah H
Luna Buitrago, Diana
Drabkin, Harold J
Chisholm, Rex L
Strelets, Victor
Axelsen, Kristian
Dolan, Mary E
Ni, Li
Ebert, Dustin
Harris, Nomi L
Nadendla, Suvarna
Blake, Judith
Jaiswal, Pankaj
Lera-Ramirez, Manuel
Thomas, Paul D
Hyka-Nouspikel, Nevila
Long, Miao
Engel, Stacia R
Wood, Valerie
Thurmond, Jim
D'Eustachio, Peter
Giglio, Michelle
Zhou, Pinglei
Moxon, Sierra
Skrzypek, Marek S
Seager, James
Cherry, J Michael
Aspromonte, Maria Cristina
Antonazzo, Giulia
Saverimuttu, Shirin C C
Attrill, Helen
Carbon, Seth
Hill, David P
Christie, Karen
Logie, Colin
Feuermann, Marc
Mi, Huaiyu
Nash, Robert S
Tosatto, Silvio
Berardini, Tanya Z
Mushayahama, Tremayne
Smith, Cynthia
Miyasato, Stuart R
Aimo, Lucila
Laulederkind, Stanley J F
Corbani, Lori
Quaglia, Federica
Balhoff, James
Morgat, Anne
Marygold, Steven
Su, Renzhi
Michalak, Aleksandra
Asanitthong, Praoparn
Wang, Shur-Jen
Muruganugan, Anushya
Sternberg, Paul W
Tabone, Christophe
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Copyright The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. 2023
The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.
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Issue 1
Keywords gene function
gene annotation
knowledge graphs
knowledgebase
Gene Ontology
Language English
License This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.
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Snippet Abstract The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products...
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and...
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SubjectTerms Computational Biology
Databases, Genetic
Gene Ontology
Molecular Sequence Annotation
Proteins - genetics
Title The Gene Ontology knowledgebase in 2023
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