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1. The Gene Ontology knowledgebase in 2023

Author

Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, and Berardini, Tanya Z

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Gene Ontology, Proteins, Molecular Sequence Annotation, Databases, Genetic, Computational Biology, gene annotation, gene function, knowledgebase, knowledge graphs, Gene Ontology Consortium, Developmental Biology, Biochemistry and cell biology
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.

Published
2023

2. Harmonizing model organism data in the Alliance of Genome Resources

Author

Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A, Alexander, Micheal, Anagnostopoulos, Anna V, Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M, Blake, Judith A, Blodgett, Olin, Bradford, Yvonne M, Bult, Carol J, Cain, Scott, Calvi, Brian R, Carbon, Seth, Chan, Juancarlos, Chen, Wen J, Cherry, J Michael, Cho, Jaehyoung, Christie, Karen R, Crosby, Madeline A, Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L, D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E, dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R, Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C, Gondwe, Felix, Goodman, Josh, Gramates, L Sian, Grove, Christian A, Hale, Paul, Harris, Todd, Hayman, G Thomas, Hill, David P, Howe, Douglas G, Howe, Kevin L, Hu, Yanhui, Jha, Sagar, Kadin, James A, Kaufman, Thomas C, Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E, Laulederkind, Stanley JF, Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A, Martin, Ryan, Marygold, Steven J, Matthews, Beverley, McAndrews, Monica S, Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Muller, Hans-Michael, Mungall, Christopher J, Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S, Nash, Robert S, Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E, Gelbart, Susan Russo, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R, Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M, and Smith, Cynthia L

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.5 Resources and infrastructure (underpinning), Alleles, Animals, Caenorhabditis elegans, Databases, Genetic, Drosophila, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomycetales, Zebrafish, Alliance of Genome Resources Consortium, biocuration, data mining, gene expression, gene function, gene interaction, genome, knowledgebase, phenotype, variants, Developmental Biology, Biochemistry and cell biology
Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Published
2022

3. The Gene Ontology resource: enriching a GOld mine

Author

Carbon, Seth, Douglass, Eric, Good, Benjamin M, Unni, Deepak R, Harris, Nomi L, Mungall, Christopher J, Basu, Siddartha, Chisholm, Rex L, Dodson, Robert J, Hartline, Eric, Fey, Petra, Thomas, Paul D, Albou, Laurent-Philippe, Ebert, Dustin, Kesling, Michael J, Mi, Huaiyu, Muruganujan, Anushya, Huang, Xiaosong, Mushayahama, Tremayne, LaBonte, Sandra A, Siegele, Deborah A, Antonazzo, Giulia, Attrill, Helen, Brown, Nick H, Garapati, Phani, Marygold, Steven J, Trovisco, Vitor, dos Santos, Gil, Falls, Kathleen, Tabone, Christopher, Zhou, Pinglei, Goodman, Joshua L, Strelets, Victor B, Thurmond, Jim, Garmiri, Penelope, Ishtiaq, Rizwan, Rodríguez-López, Milagros, Acencio, Marcio L, Kuiper, Martin, Lægreid, Astrid, Logie, Colin, Lovering, Ruth C, Kramarz, Barbara, Saverimuttu, Shirin CC, Pinheiro, Sandra M, Gunn, Heather, Su, Renzhi, Thurlow, Katherine E, Chibucos, Marcus, Giglio, Michelle, Nadendla, Suvarna, Munro, James, Jackson, Rebecca, Duesbury, Margaret J, Del-Toro, Noemi, Meldal, Birgit HM, Paneerselvam, Kalpana, Perfetto, Livia, Porras, Pablo, Orchard, Sandra, Shrivastava, Anjali, Chang, Hsin-Yu, Finn, Robert Daniel, Mitchell, Alexander Lawson, Rawlings, Neil David, Richardson, Lorna, Sangrador-Vegas, Amaia, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry M, Harris, Midori A, Oliver, Stephen G, Rutherford, Kim, Wood, Valerie, Hayles, Jaqueline, Bähler, Jürg, Bolton, Elizabeth R, De Pons, Jeffery L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Plasterer, Cody, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Matthews, Lisa, Balhoff, James P, Aleksander, Suzi A, Alexander, Michael J, Cherry, J Michael, Engel, Stacia R, Gondwe, Felix, and Karra, Kalpana

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Genetics, 1.5 Resources and infrastructure (underpinning), 2.6 Resources and infrastructure (aetiology), Animals, Arabidopsis, Caenorhabditis elegans, Dictyostelium, Drosophila melanogaster, Escherichia coli, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomyces cerevisiae, Schizosaccharomyces, User-Computer Interface, Zebrafish, Gene Ontology Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Published
2021

4. RNAcentral: a hub of information for non-coding RNA sequences

Author

Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley JF, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, and Williams, Kelly P

Subjects
Biological Sciences, Environmental Sciences, Chemical Sciences, The RNAcentral Consortium, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Published
2019

5. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Author

Köhler, Sebastian, Carmody, Leigh, Vasilevsky, Nicole, Jacobsen, Julius OB, Danis, Daniel, Gourdine, Jean-Philippe, Gargano, Michael, Harris, Nomi L, Matentzoglu, Nicolas, McMurry, Julie A, Osumi-Sutherland, David, Cipriani, Valentina, Balhoff, James P, Conlin, Tom, Blau, Hannah, Baynam, Gareth, Palmer, Richard, Gratian, Dylan, Dawkins, Hugh, Segal, Michael, Jansen, Anna C, Muaz, Ahmed, Chang, Willie H, Bergerson, Jenna, Laulederkind, Stanley JF, Yüksel, Zafer, Beltran, Sergi, Freeman, Alexandra F, Sergouniotis, Panagiotis I, Durkin, Daniel, Storm, Andrea L, Hanauer, Marc, Brudno, Michael, Bello, Susan M, Sincan, Murat, Rageth, Kayli, Wheeler, Matthew T, Oegema, Renske, Lourghi, Halima, Della Rocca, Maria G, Thompson, Rachel, Castellanos, Francisco, Priest, James, Cunningham-Rundles, Charlotte, Hegde, Ayushi, Lovering, Ruth C, Hajek, Catherine, Olry, Annie, Notarangelo, Luigi, Similuk, Morgan, Zhang, Xingmin A, Gómez-Andrés, David, Lochmüller, Hanns, Dollfus, Hélène, Rosenzweig, Sergio, Marwaha, Shruti, Rath, Ana, Sullivan, Kathleen, Smith, Cynthia, Milner, Joshua D, Leroux, Dorothée, Boerkoel, Cornelius F, Klion, Amy, Carter, Melody C, Groza, Tudor, Smedley, Damian, Haendel, Melissa A, Mungall, Chris, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Networking and Information Technology R&D (NITRD), Rare Diseases, Generic health relevance, Good Health and Well Being, Biological Ontologies, Computational Biology, Congenital Abnormalities, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Humans, Internet, Knowledge Bases, Phenotype, Whole Genome Sequencing, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.

Published
2019

6. The Human Phenotype Ontology in 2017

Author

Köhler, Sebastian, Vasilevsky, Nicole A, Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M, Boerkoel, Cornelius F, Boycott, Kym M, Brudno, Michael, Buske, Orion J, Chinnery, Patrick F, Cipriani, Valentina, Connell, Laureen E, Dawkins, Hugh JS, DeMare, Laura E, Devereau, Andrew D, de Vries, Bert BA, Firth, Helen V, Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A, James, Roger, Krause, Roland, Laulederkind, Stanley JF, Lochmüller, Hanns, Lyon, Gholson J, Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H, Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H, Segal, Michael, Sergouniotis, Panagiotis I, Sever, Richard, Smith, Cynthia L, Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke WM, Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius OB, Groza, Tudor, Smedley, Damian, Mungall, Christopher J, Haendel, Melissa, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Networking and Information Technology R&D (NITRD), Human Genome, 2.6 Resources and infrastructure (aetiology), 4.5 Resources and infrastructure (detection), Generic health relevance, Good Health and Well Being, Algorithms, Biological Ontologies, Computational Biology, Genetic Association Studies, Genomics, Humans, Phenotype, Precision Medicine, Rare Diseases, Software, Translational Research, Biomedical, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Published
2017

7. The Gene Ontology knowledgebase in 2023.

Author

Gene Ontology Consortium, Baryshnikova, A1, Gene Ontology Consortium, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Gene Ontology Consortium, Baryshnikova, A1, Gene Ontology Consortium, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, and Bakker, Erika

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.

Published
2023

8. The Gene Ontology knowledgebase in 2023

Author

Consortium, Gene Ontology, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek 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, Coudert, Elisabeth, Estreicher, Anne, Famiglietti, Maria Livia, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bateman, Alex, Bowler-Barnett, Emily, Bye-A-Jee, Hema, Denny, Paul, Ignatchenko, Alexandr, Ishtiaq, Rizwan, Lock, Antonia, Lussi, Yvonne, Magrane, Michele, Martin, Maria J, Orchard, Sandra, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Chan, Juancarlos, Diamantakis, Stavros, Raciti, Daniela, Zarowiecki, Magdalena, Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla, and Westerfield, Monte

Subjects
Ecology,Evolution & Ethology, Cell Cycle & Chromosomes, Cell Biology
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.

Published
2023
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9. Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease

Author

Petri, Victoria, primary, Hayman, G Thomas, additional, Tutaj, Marek, additional, Smith, Jennifer R, additional, Laulederkind, Stanley JF, additional, Wang, Shur-Jen, additional, Nigam, Rajni, additional, De Pons, Jeff, additional, Shimoyama, Mary, additional, Dwinell, Melinda R, additional, Worthey, Elizabeth A, additional, and Jacob, Howard J, additional

Published
2014
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10. The pathway ontology – updates and applications

Author

Petri, Victoria, primary, Jayaraman, Pushkala, additional, Tutaj, Marek, additional, Hayman, G, additional, Smith, Jennifer R, additional, De Pons, Jeff, additional, Laulederkind, Stanley JF, additional, Lowry, Timothy F, additional, Nigam, Rajni, additional, Wang, Shur-Jen, additional, Shimoyama, Mary, additional, Dwinell, Melinda R, additional, Munzenmaier, Diane H, additional, Worthey, Elizabeth A, additional, and Jacob, Howard J, additional

Published
2014
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11. The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications

Author

Smith, Jennifer R, primary, Park, Carissa A, additional, Nigam, Rajni, additional, Laulederkind, Stanley JF, additional, Hayman, G Thomas, additional, Wang, Shur-Jen, additional, Lowry, Timothy F, additional, Petri, Victoria, additional, Pons, Jeff De, additional, Tutaj, Marek, additional, Liu, Weisong, additional, Worthey, Elizabeth A, additional, Shimoyama, Mary, additional, and Dwinell, Melinda R, additional

Published
2013
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