The Gene Ontology resource: enriching a GOld mine
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 notabl...
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| Veröffentlicht in: | Nucleic acids research Jg. 49; H. D1; S. D325 - D334 |
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| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
England
Oxford University Press
08.01.2021
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| ISSN: | 0305-1048, 1362-4962, 1362-4962 |
| Online-Zugang: | Volltext |
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| Abstract | 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. |
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| AbstractList | 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. 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.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. 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. |
| Author | Vedi, Mahima Goodman, Joshua L Unni, Deepak R Aleksander, Suzi A Kuiper, Martin Mitchell, Alexander Lawson Chibucos, Marcus Ishtiaq, Rizwan Christie, Karen R Dolan, Mary E Harris, Nomi L Ebert, Dustin Engel, Stacia R Thurmond, Jim Giglio, Michelle Zhou, Pinglei Finn, Robert Daniel Garapati, Phani Meldal, Birgit H M Richardson, Lorna Cherry, J Michael Hartline, Eric Antonazzo, Giulia Lægreid, Astrid Carbon, Seth Hill, David P Sitnikov, Dmitry M Logie, Colin Harris, Midori A Mi, Huaiyu Hayles, Jaqueline Rodríguez-López, Milagros Mushayahama, Tremayne Sangrador-Vegas, Amaia Douglass, Eric Matthews, Lisa Jackson, Rebecca Brown, Nick H Chang, Hsin-Yu Bolton, Elizabeth R Munro, James Kwitek, Anne E Kesling, Michael J Kaldunski, Mary L Strelets, Victor B Gunn, Heather Plasterer, Cody Balhoff, James P Siegele, Deborah A Rawlings, Neil David De Pons, Jeffery L Fey, Petra Garmiri, Penelope Albou, Laurent-Philippe LaBonte, Sandra A Dodson, Robert J Drabkin, Harold J Chisholm, Rex L Tabone, Christopher Ni, Li Nadendla, Suvarna Basu, Siddartha Thomas, Paul D d |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33290552$$D View this record in MEDLINE/PubMed https://www.osti.gov/servlets/purl/1828339$$D View this record in Osti.gov |
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| ContentType | Journal Article |
| Contributor | Vedi, Mahima Goodman, Joshua L Unni, Deepak R Aleksander, Suzi A Kuiper, Martin Mitchell, Alexander Lawson Chibucos, Marcus Ishtiaq, Rizwan Christie, Karen R Dolan, Mary E Harris, Nomi L Ebert, Dustin Engel, Stacia R Thurmond, Jim D'Eustachio, Peter Giglio, Michelle Zhou, Pinglei Finn, Robert Daniel Garapati, Phani Meldal, Birgit H M Richardson, Lorna Cherry, J Michael Hartline, Eric Antonazzo, Giulia Lægreid, Astrid Carbon, Seth Hill, David P Sitnikov, Dmitry M Logie, Colin Harris, Midori A Mi, Huaiyu Hayles, Jaqueline Rodríguez-López, Milagros Mushayahama, Tremayne Sangrador-Vegas, Amaia Douglass, Eric Matthews, Lisa Jackson, Rebecca Brown, Nick H Chang, Hsin-Yu Bolton, Elizabeth R Dos Santos, Gil Munro, James Kwitek, Anne E Kesling, Michael J Kaldunski, Mary L Strelets, Victor B Gunn, Heather Plasterer, Cody Balhoff, James P Siegele, Deborah A Rawlings, Neil David De Pons, Jeffery L Fey, Petra Garmiri, Penelope Albou, Laurent-Philippe LaBonte, Sandra A Dodson, Robert J Drabkin, Harold J Chisholm, Rex L Tabone, Christopher Ni, Li Nadendla, Suva |
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| Copyright | The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021 The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. |
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| References | Giglio (2021010313123930900_B1) 2019; 47 Diehl (2021010313123930900_B21) 2016; 7 Thomas (2021010313123930900_B2) 2019; 51 Mi (2021010313123930900_B3) 2019; 47 Huntley (2021010313123930900_B17) 2017; 1446 Consortium, T.A. of G.R. (2021010313123930900_B8) 2020; 48 Hasnain (2021010313123930900_B22) 2017; 8 Gaudet (2021010313123930900_B16) 2011; 12 Hastings (2021010313123930900_B13) 2016; 44 Carbon (2021010313123930900_B4) 2009; 25 Morgat (2021010313123930900_B15) 2020; 36 Dillen (2021010313123930900_B23) 2019; 3 Koopmans (2021010313123930900_B12) 2019; 103 Gaudet (2021010313123930900_B6) 2017; 1446 Haendel (2021010313123930900_B20) 2014; 5 Wood (2021010313123930900_B18) 2020; 10 Gene Ontology Consortium (2021010313123930900_B5) 2015; 43 The Gene Ontology Consortium (2021010313123930900_B7) 2019; 47 James-Zorn (2021010313123930900_B9) 2018; 1757 Lombardot (2021010313123930900_B14) 2019; 47 Deegan (née Clark) (2021010313123930900_B19) 2010; 11 Harris (2021010313123930900_B10) 2020; 48 Wilkinson (2021010313123930900_B24) 2016; 3 Bult (2021010313123930900_B11) 2019; 47 |
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The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of... The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and... |
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| SubjectTerms | Animals Arabidopsis - genetics Arabidopsis - metabolism Caenorhabditis elegans - genetics Caenorhabditis elegans - metabolism Database Issue Dictyostelium - genetics Dictyostelium - metabolism Drosophila melanogaster - genetics Drosophila melanogaster - metabolism Escherichia coli - genetics Escherichia coli - metabolism Gene Ontology Humans Internet Mice Molecular Sequence Annotation - statistics & numerical data Rats Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Schizosaccharomyces - genetics Schizosaccharomyces - metabolism User-Computer Interface Zebrafish - genetics Zebrafish - metabolism |
| Title | The Gene Ontology resource: enriching a GOld mine |
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