The Gene Ontology knowledgebase in 2023

Published: 2023-03-03
Venue: Genetics, vol. 224, no. 1
Cited by: 2,687
Open access: Yes, hybrid
DOI: 10.1093/genetics/iyad031
PubMed: 36866529

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.

@article{aleksander2023gene, title = {{The Gene Ontology knowledgebase in 2023}}, author = {Suzi Aleksander and James P. Balhoff and Seth J Carbon and J. Michael Cherry and Harold Drabkin and Dustin Ebert and Marc Feuermann and Pascale Gaudet and Nomi L. Harris and David P. Hill and Raymond Lee and Huaiyu Mi and Sierra A. Taylor Moxon and Chris Mungall and Anushya Muruganugan and Tremayne Mushayahama and Paul W. Sternberg and Paul D. Thomas and Kimberly M. Van Auken and Jolene Ramsey and Deborah A. Siegele and Rex L. Chisholm and Petra Fey and Maria Cristina Aspromonte and María Victoria Nugnes and Federica Quaglia and Silvio C. E. Tosatto and Michelle Gwinn Giglio and Suvarna Nadendla and Giulia Antonazzo and Helen L. Attrill and Gil dos Santos and Steven J Marygold and Victor B. Strelets and Christopher J. Tabone and Jim Thurmond and Pinglei Zhou and Saadullah H. Ahmed and Praoparn Asanitthong and Diana Luna Buitrago and Meltem N Erdol and Matthew Gage and Mohamed Ali Kadhum and Kan Yan Chloe Li and Miao Long and Aleksandra Michalak and Angeline Pesala and Armalya Pritazahra and Shirin C C Saverimuttu and Renzhi Su and Kate E. Thurlow and Ruth C. Lovering and Colin Logie and Snezhana Oliferenko and Judith A. Blake and Karen Renee Christie and Lori E Corbani and Mary Eileen Dolan and Harold Drabkin and David P. Hill and Li Ni and Dmitry M. Sitnikov and Cynthia L. Smith and Alayne Cuzick and James W. Seager and Laurel Cooper and Justin L. Elser and Pankaj Jaiswal and Parul Gupta and Pankaj Jaiswal and Sushma Naithani and Manuel Lera-Ramírez and Kim Rutherford and Valerie Wood and Jeff De Pons and Melinda R. Dwinell and G. Thomas Hayman and Mary L. Kaldunski and Anne E. Kwitek and Stanley J. F. Laulederkind and Marek Tutaj and Mahima Vedi and Shur‐Jen Wang and Peter D’Eustachio and Lucila Aimo and Kristian B. Axelsen and Alan James Bridge and Nevila Hyka‐Nouspikel and Anne Morgat and Suzi Aleksander and J. Michael Cherry and Stacia R. Engel and Kalpana Karra and Stuart R. Miyasato and Robert S Nash and Marek S. Skrzypek and Shuai Weng and Edith D. Wong and Erika Bakker and Tanya Berardini and Leonore Reiser and Andrea H Auchincloss and Kristian B. Axelsen and Ghislaine Argoud‐Puy and Marie-Claude Blatter and Emmanuel Boutet and Lionel Breuza and Alan James Bridge and Cristina Casals‐Casas and Elisabeth Coudert and Anne Estreicher and Maria Livia Famiglietti and Marc Feuermann and Arnaud Gos and Nadine Gruaz-Gumowski and Chantal Hulo and Nevila Hyka‐Nouspikel and Florence Jungo and Philippe Le Mercier and Damien Lieberherr and Patrick Masson and Anne Morgat and Ivo Pedruzzi and Lucille Pourcel and Sylvain Poux and Catherine Rivoire and Shyamala Sundaram and Alex G. Bateman and Emily Bowler-Barnett and Hema Bye‐A‐Jee and Paul Denny and Alexandr Ignatchenko and Rizwan Ishtiaq and Antonia Lock and Yvonne Lussi and Michele Magrane and Maria Jesus Martin and Sandra E. Orchard and Pedro Raposo and Elena Speretta and Nidhi Tyagi and Kate Warner and Rossana Zaru and Alexander D. Diehl and Raymond Lee and Juancarlos Chan and Stavros Diamantakis and Daniela Raciti and Magdalena Zarowiecki and Malcolm E Fisher and Christina James‐Zorn and Virgilio G. Ponferrada and Aaron M. Zorn and Sridhar Ramachandran and Leyla Ruzicka and Monte Westerfield and Suzi Aleksander and James P. Balhoff and Seth J Carbon and J. Michael Cherry and Harold Drabkin and Dustin Ebert and Marc Feuermann and Pascale Gaudet and Nomi L. Harris and David P. Hill and Raymond Lee and Huaiyu Mi and Sierra A. Taylor Moxon and Chris Mungall and Anushya Muruganugan and Tremayne Mushayahama and Paul W. Sternberg and Paul D. Thomas and Kimberly M. Van Auken and Jolene Ramsey and Deborah A. Siegele and Rex L. Chisholm and Petra Fey and Maria Cristina Aspromonte and María Victoria Nugnes and Federica Quaglia and Silvio C. E. Tosatto and Michelle Gwinn Giglio and Suvarna Nadendla and Giulia Antonazzo and Helen L. Attrill and Gil dos Santos and Steven J Marygold and Victor B. Strelets and Christopher J. Tabone and Jim Thurmond and Pinglei Zhou and Saadullah H. Ahmed and Praoparn Asanitthong and Diana Luna Buitrago and Meltem N Erdol and Matthew Gage and Mohamed Ali Kadhum and Kan Yan Chloe Li and Miao Long and Aleksandra Michalak and Angeline Pesala and Armalya Pritazahra and Shirin C C Saverimuttu and Renzhi Su and Kate E. Thurlow and Ruth C. Lovering and Colin Logie and Snezhana Oliferenko and Judith A. Blake and Karen Renee Christie and Lori E Corbani and Mary Eileen Dolan and Harold Drabkin and David P. Hill and Li Ni and Dmitry M. Sitnikov and Cynthia L. Smith and Alayne Cuzick and James W. Seager and Laurel Cooper and Justin L. Elser and Pankaj Jaiswal and Parul Gupta and Pankaj Jaiswal and Sushma Naithani and Manuel Lera-Ramírez and Kim Rutherford and Valerie Wood and Jeff De Pons and Melinda R. Dwinell and G. Thomas Hayman and Mary L. Kaldunski and Anne E. Kwitek and Stanley J. F. Laulederkind and Marek Tutaj and Mahima Vedi and Shur‐Jen Wang and Peter D’Eustachio and Lucila Aimo and Kristian B. Axelsen and Alan James Bridge and Nevila Hyka‐Nouspikel and Anne Morgat and Suzi Aleksander and J. Michael Cherry and Stacia R. Engel and Kalpana Karra and Stuart R. Miyasato and Robert S Nash and Marek S. Skrzypek and Shuai Weng and Edith D. Wong and Erika Bakker and Tanya Berardini and Leonore Reiser and Andrea H Auchincloss and Kristian B. Axelsen and Ghislaine Argoud‐Puy and Marie-Claude Blatter and Emmanuel Boutet and Lionel Breuza and Alan James Bridge and Cristina Casals‐Casas and Elisabeth Coudert and Anne Estreicher and Maria Livia Famiglietti and Marc Feuermann and Arnaud Gos and Nadine Gruaz-Gumowski and Chantal Hulo and Nevila Hyka‐Nouspikel and Florence Jungo and Philippe Le Mercier and Damien Lieberherr and Patrick Masson and Anne Morgat and Ivo Pedruzzi and Lucille Pourcel and Sylvain Poux and Catherine Rivoire and Shyamala Sundaram and Alex G. Bateman and Emily Bowler-Barnett and Hema Bye‐A‐Jee and Paul Denny and Alexandr Ignatchenko and Rizwan Ishtiaq and Antonia Lock and Yvonne Lussi and Michele Magrane and Maria Jesus Martin and Sandra E. Orchard and Pedro Raposo and Elena Speretta and Nidhi Tyagi and Kate Warner and Rossana Zaru and Alexander D. Diehl and Raymond Lee and Juancarlos Chan and Stavros Diamantakis and Daniela Raciti and Magdalena Zarowiecki and Malcolm E Fisher and Christina James‐Zorn and Virgilio G. Ponferrada and Aaron M. Zorn and Sridhar Ramachandran and Leyla Ruzicka and Monte Westerfield}, journal = {Genetics}, year = {2023}, volume = {224}, number = {1}, doi = {10.1093/genetics/iyad031}, url = {https://doi.org/10.1093/genetics/iyad031} }

TY - JOUR AU - Aleksander, Suzi AU - Balhoff, James P. AU - Carbon, Seth J AU - Cherry, J. Michael AU - Drabkin, Harold 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 A. Taylor AU - Mungall, Chris AU - Muruganugan, Anushya AU - Mushayahama, Tremayne AU - Sternberg, Paul W. AU - Thomas, Paul D. AU - Auken, Kimberly M. Van AU - Ramsey, Jolene AU - Siegele, Deborah A. AU - Chisholm, Rex L. AU - Fey, Petra AU - Aspromonte, Maria Cristina AU - Nugnes, María Victoria AU - Quaglia, Federica AU - Tosatto, Silvio C. E. AU - Giglio, Michelle Gwinn AU - Nadendla, Suvarna AU - Antonazzo, Giulia AU - Attrill, Helen L. AU - Santos, Gil dos AU - Marygold, Steven J AU - Strelets, Victor B. AU - Tabone, Christopher J. AU - Thurmond, Jim AU - Zhou, Pinglei AU - Ahmed, Saadullah H. AU - Asanitthong, Praoparn AU - Buitrago, Diana Luna AU - Erdol, Meltem N AU - Gage, Matthew AU - Kadhum, Mohamed Ali 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 - Thurlow, Kate E. AU - Lovering, Ruth C. AU - Logie, Colin AU - Oliferenko, Snezhana AU - Blake, Judith A. AU - Christie, Karen Renee AU - Corbani, Lori E AU - Dolan, Mary Eileen AU - Drabkin, Harold AU - Hill, David P. AU - Ni, Li AU - Sitnikov, Dmitry M. AU - Smith, Cynthia L. AU - Cuzick, Alayne AU - Seager, James W. AU - Cooper, Laurel AU - Elser, Justin L. AU - Jaiswal, Pankaj AU - Gupta, Parul AU - Jaiswal, Pankaj AU - Naithani, Sushma AU - Lera-Ramírez, Manuel AU - Rutherford, Kim AU - Wood, Valerie AU - Pons, Jeff De AU - Dwinell, Melinda R. AU - Hayman, G. Thomas AU - Kaldunski, Mary L. AU - Kwitek, Anne E. AU - Laulederkind, Stanley J. F. AU - Tutaj, Marek AU - Vedi, Mahima AU - Wang, Shur‐Jen AU - D’Eustachio, Peter AU - Aimo, Lucila AU - Axelsen, Kristian B. AU - Bridge, Alan James AU - Hyka‐Nouspikel, Nevila AU - Morgat, Anne AU - Aleksander, Suzi AU - Cherry, J. Michael AU - Engel, Stacia R. AU - Karra, Kalpana AU - Miyasato, Stuart R. AU - Nash, Robert S AU - Skrzypek, Marek S. AU - Weng, Shuai AU - Wong, Edith D. AU - Bakker, Erika AU - Berardini, Tanya AU - Reiser, Leonore AU - Auchincloss, Andrea H AU - Axelsen, Kristian B. AU - Argoud‐Puy, Ghislaine AU - Blatter, Marie-Claude AU - Boutet, Emmanuel AU - Breuza, Lionel AU - Bridge, Alan James AU - Casals‐Casas, Cristina AU - Coudert, Elisabeth AU - Estreicher, Anne AU - Famiglietti, Maria Livia AU - Feuermann, Marc AU - Gos, Arnaud AU - Gruaz-Gumowski, Nadine AU - Hulo, Chantal AU - Hyka‐Nouspikel, Nevila AU - Jungo, Florence AU - Mercier, Philippe Le AU - Lieberherr, Damien AU - Masson, Patrick AU - Morgat, Anne AU - Pedruzzi, Ivo AU - Pourcel, Lucille AU - Poux, Sylvain AU - Rivoire, Catherine AU - Sundaram, Shyamala AU - Bateman, Alex G. AU - Bowler-Barnett, Emily AU - Bye‐A‐Jee, Hema AU - Denny, Paul AU - Ignatchenko, Alexandr AU - Ishtiaq, Rizwan AU - Lock, Antonia AU - Lussi, Yvonne AU - Magrane, Michele AU - Martin, Maria Jesus AU - Orchard, Sandra E. AU - Raposo, Pedro AU - Speretta, Elena AU - Tyagi, Nidhi AU - Warner, Kate AU - Zaru, Rossana AU - Diehl, Alexander D. AU - Lee, Raymond AU - Chan, Juancarlos AU - Diamantakis, Stavros AU - Raciti, Daniela AU - Zarowiecki, Magdalena AU - Fisher, Malcolm E AU - James‐Zorn, Christina AU - Ponferrada, Virgilio G. AU - Zorn, Aaron M. AU - Ramachandran, Sridhar AU - Ruzicka, Leyla AU - Westerfield, Monte AU - Aleksander, Suzi AU - Balhoff, James P. AU - Carbon, Seth J AU - Cherry, J. Michael AU - Drabkin, Harold 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 A. Taylor AU - Mungall, Chris AU - Muruganugan, Anushya AU - Mushayahama, Tremayne AU - Sternberg, Paul W. AU - Thomas, Paul D. AU - Auken, Kimberly M. Van AU - Ramsey, Jolene AU - Siegele, Deborah A. AU - Chisholm, Rex L. AU - Fey, Petra AU - Aspromonte, Maria Cristina AU - Nugnes, María Victoria AU - Quaglia, Federica AU - Tosatto, Silvio C. E. AU - Giglio, Michelle Gwinn AU - Nadendla, Suvarna AU - Antonazzo, Giulia AU - Attrill, Helen L. AU - Santos, Gil dos AU - Marygold, Steven J AU - Strelets, Victor B. AU - Tabone, Christopher J. AU - Thurmond, Jim AU - Zhou, Pinglei AU - Ahmed, Saadullah H. AU - Asanitthong, Praoparn AU - Buitrago, Diana Luna AU - Erdol, Meltem N AU - Gage, Matthew AU - Kadhum, Mohamed Ali 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 - Thurlow, Kate E. AU - Lovering, Ruth C. AU - Logie, Colin AU - Oliferenko, Snezhana AU - Blake, Judith A. AU - Christie, Karen Renee AU - Corbani, Lori E AU - Dolan, Mary Eileen AU - Drabkin, Harold AU - Hill, David P. AU - Ni, Li AU - Sitnikov, Dmitry M. AU - Smith, Cynthia L. AU - Cuzick, Alayne AU - Seager, James W. AU - Cooper, Laurel AU - Elser, Justin L. AU - Jaiswal, Pankaj AU - Gupta, Parul AU - Jaiswal, Pankaj AU - Naithani, Sushma AU - Lera-Ramírez, Manuel AU - Rutherford, Kim AU - Wood, Valerie AU - Pons, Jeff De AU - Dwinell, Melinda R. AU - Hayman, G. Thomas AU - Kaldunski, Mary L. AU - Kwitek, Anne E. AU - Laulederkind, Stanley J. F. AU - Tutaj, Marek AU - Vedi, Mahima AU - Wang, Shur‐Jen AU - D’Eustachio, Peter AU - Aimo, Lucila AU - Axelsen, Kristian B. AU - Bridge, Alan James AU - Hyka‐Nouspikel, Nevila AU - Morgat, Anne AU - Aleksander, Suzi AU - Cherry, J. Michael AU - Engel, Stacia R. AU - Karra, Kalpana AU - Miyasato, Stuart R. AU - Nash, Robert S AU - Skrzypek, Marek S. AU - Weng, Shuai AU - Wong, Edith D. AU - Bakker, Erika AU - Berardini, Tanya AU - Reiser, Leonore AU - Auchincloss, Andrea H AU - Axelsen, Kristian B. AU - Argoud‐Puy, Ghislaine AU - Blatter, Marie-Claude AU - Boutet, Emmanuel AU - Breuza, Lionel AU - Bridge, Alan James AU - Casals‐Casas, Cristina AU - Coudert, Elisabeth AU - Estreicher, Anne AU - Famiglietti, Maria Livia AU - Feuermann, Marc AU - Gos, Arnaud AU - Gruaz-Gumowski, Nadine AU - Hulo, Chantal AU - Hyka‐Nouspikel, Nevila AU - Jungo, Florence AU - Mercier, Philippe Le AU - Lieberherr, Damien AU - Masson, Patrick AU - Morgat, Anne AU - Pedruzzi, Ivo AU - Pourcel, Lucille AU - Poux, Sylvain AU - Rivoire, Catherine AU - Sundaram, Shyamala AU - Bateman, Alex G. AU - Bowler-Barnett, Emily AU - Bye‐A‐Jee, Hema AU - Denny, Paul AU - Ignatchenko, Alexandr AU - Ishtiaq, Rizwan AU - Lock, Antonia AU - Lussi, Yvonne AU - Magrane, Michele AU - Martin, Maria Jesus AU - Orchard, Sandra E. AU - Raposo, Pedro AU - Speretta, Elena AU - Tyagi, Nidhi AU - Warner, Kate AU - Zaru, Rossana AU - Diehl, Alexander D. AU - Lee, Raymond AU - Chan, Juancarlos AU - Diamantakis, Stavros AU - Raciti, Daniela AU - Zarowiecki, Magdalena AU - Fisher, Malcolm E AU - James‐Zorn, Christina AU - Ponferrada, Virgilio G. AU - Zorn, Aaron M. AU - Ramachandran, Sridhar AU - Ruzicka, Leyla AU - Westerfield, Monte TI - The Gene Ontology knowledgebase in 2023 JO - Genetics VL - 224 IS - 1 PY - 2023 DA - 2023/03/03 DO - 10.1093/genetics/iyad031 UR - https://doi.org/10.1093/genetics/iyad031 ER -

The Gene Ontology knowledgebase in 2023

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The Gene Ontology knowledgebase in 2023

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